cola Report for GDS3929

Date: 2019-12-25 21:05:23 CET, cola version: 1.3.2

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Summary

All available functions which can be applied to this res_list object:

res_list
#> A 'ConsensusPartitionList' object with 24 methods.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows are extracted by 'SD, CV, MAD, ATC' methods.
#>   Subgroups are detected by 'hclust, kmeans, skmeans, pam, mclust, NMF' method.
#>   Number of partitions are tried for k = 2, 3, 4, 5, 6.
#>   Performed in total 30000 partitions by row resampling.
#> 
#> Following methods can be applied to this 'ConsensusPartitionList' object:
#>  [1] "cola_report"           "collect_classes"       "collect_plots"         "collect_stats"        
#>  [5] "colnames"              "functional_enrichment" "get_anno_col"          "get_anno"             
#>  [9] "get_classes"           "get_matrix"            "get_membership"        "get_stats"            
#> [13] "is_best_k"             "is_stable_k"           "ncol"                  "nrow"                 
#> [17] "rownames"              "show"                  "suggest_best_k"        "test_to_known_factors"
#> [21] "top_rows_heatmap"      "top_rows_overlap"     
#> 
#> You can get result for a single method by, e.g. object["SD", "hclust"] or object["SD:hclust"]
#> or a subset of methods by object[c("SD", "CV")], c("hclust", "kmeans")]

The call of run_all_consensus_partition_methods() was:

#> run_all_consensus_partition_methods(data = mat, mc.cores = 4, anno = anno)

Dimension of the input matrix:

mat = get_matrix(res_list)
dim(mat)
#> [1] 23299   183

Density distribution

The density distribution for each sample is visualized as in one column in the following heatmap. The clustering is based on the distance which is the Kolmogorov-Smirnov statistic between two distributions.

library(ComplexHeatmap)
densityHeatmap(mat, top_annotation = HeatmapAnnotation(df = get_anno(res_list), 
    col = get_anno_col(res_list)), ylab = "value", cluster_columns = TRUE, show_column_names = FALSE,
    mc.cores = 4)

plot of chunk density-heatmap

Suggest the best k

Folowing table shows the best k (number of partitions) for each combination of top-value methods and partition methods. Clicking on the method name in the table goes to the section for a single combination of methods.

The cola vignette explains the definition of the metrics used for determining the best number of partitions.

suggest_best_k(res_list)
The best k 1-PAC Mean silhouette Concordance Optional k
SD:kmeans 2 1.000 1.000 1.000 **
SD:skmeans 3 1.000 1.000 1.000 ** 2
SD:pam 4 1.000 0.978 0.981 ** 2,3
SD:NMF 3 1.000 0.991 0.995 ** 2
CV:kmeans 2 1.000 1.000 1.000 **
CV:skmeans 3 1.000 1.000 1.000 ** 2
CV:pam 3 1.000 0.998 0.999 ** 2
MAD:kmeans 2 1.000 1.000 1.000 **
ATC:kmeans 2 1.000 1.000 1.000 **
ATC:pam 3 1.000 0.997 0.999 ** 2
ATC:NMF 2 1.000 1.000 1.000 **
CV:hclust 4 0.976 0.908 0.961 ** 2
MAD:hclust 4 0.948 0.887 0.951 * 2,3
MAD:skmeans 5 0.939 0.928 0.954 * 2,3,4
CV:mclust 5 0.933 0.717 0.873 * 2,3,4
CV:NMF 4 0.927 0.902 0.937 * 2,3
MAD:NMF 4 0.925 0.873 0.937 * 2,3
MAD:mclust 6 0.924 0.905 0.939 * 2,3,4
ATC:skmeans 5 0.921 0.823 0.903 * 2,3,4
MAD:pam 6 0.918 0.862 0.936 * 2,3,4
ATC:mclust 5 0.915 0.869 0.938 * 2,3,4
SD:hclust 5 0.905 0.807 0.915 * 2,3,4
ATC:hclust 4 0.902 0.888 0.950 * 2,3
SD:mclust 5 0.900 0.893 0.926 * 2,3,4

**: 1-PAC > 0.95, *: 1-PAC > 0.9

CDF of consensus matrices

Cumulative distribution function curves of consensus matrix for all methods.

collect_plots(res_list, fun = plot_ecdf)

plot of chunk collect-plots

Consensus heatmap

Consensus heatmaps for all methods. (What is a consensus heatmap?)

collect_plots(res_list, k = 2, fun = consensus_heatmap, mc.cores = 4)

plot of chunk tab-collect-consensus-heatmap-1

collect_plots(res_list, k = 3, fun = consensus_heatmap, mc.cores = 4)

plot of chunk tab-collect-consensus-heatmap-2

collect_plots(res_list, k = 4, fun = consensus_heatmap, mc.cores = 4)

plot of chunk tab-collect-consensus-heatmap-3

collect_plots(res_list, k = 5, fun = consensus_heatmap, mc.cores = 4)

plot of chunk tab-collect-consensus-heatmap-4

collect_plots(res_list, k = 6, fun = consensus_heatmap, mc.cores = 4)

plot of chunk tab-collect-consensus-heatmap-5

Membership heatmap

Membership heatmaps for all methods. (What is a membership heatmap?)

collect_plots(res_list, k = 2, fun = membership_heatmap, mc.cores = 4)

plot of chunk tab-collect-membership-heatmap-1

collect_plots(res_list, k = 3, fun = membership_heatmap, mc.cores = 4)

plot of chunk tab-collect-membership-heatmap-2

collect_plots(res_list, k = 4, fun = membership_heatmap, mc.cores = 4)

plot of chunk tab-collect-membership-heatmap-3

collect_plots(res_list, k = 5, fun = membership_heatmap, mc.cores = 4)

plot of chunk tab-collect-membership-heatmap-4

collect_plots(res_list, k = 6, fun = membership_heatmap, mc.cores = 4)

plot of chunk tab-collect-membership-heatmap-5

Signature heatmap

Signature heatmaps for all methods. (What is a signature heatmap?)

Note in following heatmaps, rows are scaled.

collect_plots(res_list, k = 2, fun = get_signatures, mc.cores = 4)

plot of chunk tab-collect-get-signatures-1

collect_plots(res_list, k = 3, fun = get_signatures, mc.cores = 4)

plot of chunk tab-collect-get-signatures-2

collect_plots(res_list, k = 4, fun = get_signatures, mc.cores = 4)

plot of chunk tab-collect-get-signatures-3

collect_plots(res_list, k = 5, fun = get_signatures, mc.cores = 4)

plot of chunk tab-collect-get-signatures-4

collect_plots(res_list, k = 6, fun = get_signatures, mc.cores = 4)

plot of chunk tab-collect-get-signatures-5

Statistics table

The statistics used for measuring the stability of consensus partitioning. (How are they defined?)

get_stats(res_list, k = 2)
#>             k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> SD:NMF      2     1               1           1          0.419 0.582   0.582
#> CV:NMF      2     1               1           1          0.419 0.582   0.582
#> MAD:NMF     2     1               1           1          0.419 0.582   0.582
#> ATC:NMF     2     1               1           1          0.419 0.582   0.582
#> SD:skmeans  2     1               1           1          0.419 0.582   0.582
#> CV:skmeans  2     1               1           1          0.419 0.582   0.582
#> MAD:skmeans 2     1               1           1          0.419 0.582   0.582
#> ATC:skmeans 2     1               1           1          0.419 0.582   0.582
#> SD:mclust   2     1               1           1          0.419 0.582   0.582
#> CV:mclust   2     1               1           1          0.419 0.582   0.582
#> MAD:mclust  2     1               1           1          0.419 0.582   0.582
#> ATC:mclust  2     1               1           1          0.419 0.582   0.582
#> SD:kmeans   2     1               1           1          0.419 0.582   0.582
#> CV:kmeans   2     1               1           1          0.419 0.582   0.582
#> MAD:kmeans  2     1               1           1          0.419 0.582   0.582
#> ATC:kmeans  2     1               1           1          0.419 0.582   0.582
#> SD:pam      2     1               1           1          0.419 0.582   0.582
#> CV:pam      2     1               1           1          0.419 0.582   0.582
#> MAD:pam     2     1               1           1          0.419 0.582   0.582
#> ATC:pam     2     1               1           1          0.419 0.582   0.582
#> SD:hclust   2     1               1           1          0.419 0.582   0.582
#> CV:hclust   2     1               1           1          0.419 0.582   0.582
#> MAD:hclust  2     1               1           1          0.419 0.582   0.582
#> ATC:hclust  2     1               1           1          0.419 0.582   0.582
get_stats(res_list, k = 3)
#>             k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> SD:NMF      3 1.000           0.991       0.995          0.594 0.750   0.571
#> CV:NMF      3 1.000           0.999       0.991          0.582 0.750   0.571
#> MAD:NMF     3 1.000           0.999       1.000          0.596 0.750   0.571
#> ATC:NMF     3 0.696           0.748       0.878          0.378 0.792   0.643
#> SD:skmeans  3 1.000           1.000       1.000          0.596 0.750   0.571
#> CV:skmeans  3 1.000           1.000       1.000          0.596 0.750   0.571
#> MAD:skmeans 3 1.000           1.000       1.000          0.596 0.750   0.571
#> ATC:skmeans 3 1.000           0.996       0.998          0.596 0.750   0.571
#> SD:mclust   3 1.000           1.000       1.000          0.596 0.750   0.571
#> CV:mclust   3 1.000           1.000       1.000          0.596 0.750   0.571
#> MAD:mclust  3 1.000           1.000       1.000          0.596 0.750   0.571
#> ATC:mclust  3 1.000           0.986       0.994          0.596 0.750   0.571
#> SD:kmeans   3 0.702           0.982       0.898          0.483 0.750   0.571
#> CV:kmeans   3 0.703           0.973       0.868          0.460 0.750   0.571
#> MAD:kmeans  3 0.709           0.979       0.904          0.492 0.750   0.571
#> ATC:kmeans  3 0.709           0.980       0.902          0.488 0.750   0.571
#> SD:pam      3 1.000           0.997       0.999          0.596 0.750   0.571
#> CV:pam      3 1.000           0.998       0.999          0.596 0.750   0.571
#> MAD:pam     3 1.000           0.994       0.997          0.596 0.750   0.571
#> ATC:pam     3 1.000           0.997       0.999          0.595 0.750   0.571
#> SD:hclust   3 1.000           1.000       1.000          0.596 0.750   0.571
#> CV:hclust   3 0.706           0.976       0.874          0.463 0.750   0.571
#> MAD:hclust  3 1.000           0.997       0.998          0.595 0.750   0.571
#> ATC:hclust  3 1.000           0.976       0.989          0.594 0.751   0.571
get_stats(res_list, k = 4)
#>             k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> SD:NMF      4 0.928           0.948       0.948         0.0289 1.000   1.000
#> CV:NMF      4 0.927           0.902       0.937         0.0569 0.968   0.904
#> MAD:NMF     4 0.925           0.873       0.937         0.0542 0.974   0.922
#> ATC:NMF     4 0.813           0.915       0.923         0.1438 0.839   0.629
#> SD:skmeans  4 0.890           0.932       0.928         0.0905 0.939   0.815
#> CV:skmeans  4 0.870           0.908       0.909         0.0895 0.939   0.815
#> MAD:skmeans 4 0.998           0.953       0.960         0.0904 0.939   0.815
#> ATC:skmeans 4 1.000           0.992       0.994         0.0961 0.935   0.804
#> SD:mclust   4 0.970           0.970       0.967         0.0534 0.957   0.870
#> CV:mclust   4 0.957           0.913       0.952         0.0543 0.958   0.875
#> MAD:mclust  4 0.965           0.921       0.956         0.0490 0.979   0.937
#> ATC:mclust  4 0.915           0.937       0.917         0.0584 0.949   0.848
#> SD:kmeans   4 0.815           0.874       0.823         0.1285 1.000   1.000
#> CV:kmeans   4 0.806           0.876       0.821         0.1466 1.000   1.000
#> MAD:kmeans  4 0.818           0.868       0.826         0.1176 1.000   1.000
#> ATC:kmeans  4 0.819           0.851       0.826         0.1420 0.992   0.977
#> SD:pam      4 1.000           0.978       0.981         0.0645 0.956   0.869
#> CV:pam      4 0.893           0.959       0.930         0.0711 0.957   0.870
#> MAD:pam     4 0.969           0.909       0.950         0.0932 0.933   0.799
#> ATC:pam     4 0.862           0.859       0.879         0.0945 0.923   0.772
#> SD:hclust   4 0.966           0.912       0.943         0.0504 0.956   0.869
#> CV:hclust   4 0.976           0.908       0.961         0.1548 0.956   0.869
#> MAD:hclust  4 0.948           0.887       0.951         0.0633 0.967   0.900
#> ATC:hclust  4 0.902           0.888       0.950         0.0431 0.974   0.920
get_stats(res_list, k = 5)
#>             k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> SD:NMF      5 0.816           0.731       0.870         0.0586 0.958   0.875
#> CV:NMF      5 0.863           0.844       0.903         0.0471 0.959   0.865
#> MAD:NMF     5 0.867           0.873       0.919         0.0232 0.980   0.935
#> ATC:NMF     5 0.732           0.704       0.855         0.0744 0.959   0.878
#> SD:skmeans  5 0.858           0.848       0.871         0.0731 0.937   0.769
#> CV:skmeans  5 0.805           0.821       0.842         0.0742 0.933   0.753
#> MAD:skmeans 5 0.939           0.928       0.954         0.0681 0.949   0.812
#> ATC:skmeans 5 0.921           0.823       0.903         0.0343 0.985   0.944
#> SD:mclust   5 0.900           0.893       0.926         0.0368 0.982   0.939
#> CV:mclust   5 0.933           0.717       0.873         0.0258 0.961   0.872
#> MAD:mclust  5 0.855           0.800       0.873         0.0544 0.978   0.930
#> ATC:mclust  5 0.915           0.869       0.938         0.0596 0.964   0.875
#> SD:kmeans   5 0.766           0.766       0.724         0.0732 0.941   0.822
#> CV:kmeans   5 0.753           0.547       0.648         0.0821 0.896   0.687
#> MAD:kmeans  5 0.770           0.787       0.743         0.0778 1.000   1.000
#> ATC:kmeans  5 0.798           0.740       0.732         0.0656 0.879   0.635
#> SD:pam      5 0.894           0.842       0.898         0.0732 0.939   0.789
#> CV:pam      5 0.897           0.866       0.909         0.0717 0.939   0.789
#> MAD:pam     5 0.856           0.810       0.856         0.0705 0.937   0.771
#> ATC:pam     5 0.900           0.875       0.938         0.0676 0.937   0.770
#> SD:hclust   5 0.905           0.807       0.915         0.0477 0.948   0.830
#> CV:hclust   5 0.883           0.831       0.883         0.0460 1.000   1.000
#> MAD:hclust  5 0.799           0.774       0.869         0.0728 0.940   0.799
#> ATC:hclust  5 0.836           0.823       0.913         0.0365 0.988   0.962
get_stats(res_list, k = 6)
#>             k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> SD:NMF      6 0.762           0.785       0.848         0.0410 0.964   0.879
#> CV:NMF      6 0.805           0.816       0.884         0.0349 0.993   0.973
#> MAD:NMF     6 0.793           0.796       0.864         0.0354 1.000   1.000
#> ATC:NMF     6 0.653           0.704       0.795         0.0386 0.957   0.861
#> SD:skmeans  6 0.816           0.773       0.831         0.0384 0.996   0.982
#> CV:skmeans  6 0.793           0.780       0.830         0.0467 0.937   0.712
#> MAD:skmeans 6 0.854           0.794       0.882         0.0315 0.998   0.991
#> ATC:skmeans 6 0.847           0.856       0.907         0.0346 0.954   0.826
#> SD:mclust   6 0.830           0.846       0.893         0.0290 0.986   0.948
#> CV:mclust   6 0.825           0.784       0.869         0.0425 0.942   0.809
#> MAD:mclust  6 0.924           0.905       0.939         0.0375 0.950   0.828
#> ATC:mclust  6 0.787           0.751       0.860         0.0320 0.982   0.930
#> SD:kmeans   6 0.728           0.638       0.659         0.0473 0.873   0.557
#> CV:kmeans   6 0.719           0.581       0.657         0.0389 0.905   0.619
#> MAD:kmeans  6 0.739           0.633       0.693         0.0465 0.843   0.527
#> ATC:kmeans  6 0.747           0.786       0.782         0.0506 0.915   0.638
#> SD:pam      6 0.802           0.752       0.841         0.0649 0.940   0.740
#> CV:pam      6 0.787           0.714       0.837         0.0699 0.937   0.728
#> MAD:pam     6 0.918           0.862       0.936         0.0625 0.938   0.722
#> ATC:pam     6 0.840           0.842       0.902         0.0647 0.916   0.643
#> SD:hclust   6 0.785           0.615       0.826         0.0559 0.948   0.808
#> CV:hclust   6 0.816           0.696       0.831         0.0315 0.941   0.808
#> MAD:hclust  6 0.794           0.680       0.843         0.0298 0.985   0.940
#> ATC:hclust  6 0.820           0.769       0.881         0.0276 0.983   0.942

Following heatmap plots the partition for each combination of methods and the lightness correspond to the silhouette scores for samples in each method. On top the consensus subgroup is inferred from all methods by taking the mean silhouette scores as weight.

collect_stats(res_list, k = 2)

plot of chunk tab-collect-stats-from-consensus-partition-list-1

collect_stats(res_list, k = 3)

plot of chunk tab-collect-stats-from-consensus-partition-list-2

collect_stats(res_list, k = 4)

plot of chunk tab-collect-stats-from-consensus-partition-list-3

collect_stats(res_list, k = 5)

plot of chunk tab-collect-stats-from-consensus-partition-list-4

collect_stats(res_list, k = 6)

plot of chunk tab-collect-stats-from-consensus-partition-list-5

Partition from all methods

Collect partitions from all methods:

collect_classes(res_list, k = 2)
#> Error in valid.viewport(x, y, width, height, just, gp, clip, xscale, yscale, : invalid 'xscale' in viewport

plot of chunk tab-collect-classes-from-consensus-partition-list-1

collect_classes(res_list, k = 3)

plot of chunk tab-collect-classes-from-consensus-partition-list-2

collect_classes(res_list, k = 4)

plot of chunk tab-collect-classes-from-consensus-partition-list-3

collect_classes(res_list, k = 5)

plot of chunk tab-collect-classes-from-consensus-partition-list-4

collect_classes(res_list, k = 6)

plot of chunk tab-collect-classes-from-consensus-partition-list-5

Top rows overlap

Overlap of top rows from different top-row methods:

top_rows_overlap(res_list, top_n = 1000, method = "euler")

plot of chunk tab-top-rows-overlap-by-euler-1

top_rows_overlap(res_list, top_n = 2000, method = "euler")

plot of chunk tab-top-rows-overlap-by-euler-2

top_rows_overlap(res_list, top_n = 3000, method = "euler")

plot of chunk tab-top-rows-overlap-by-euler-3

top_rows_overlap(res_list, top_n = 4000, method = "euler")

plot of chunk tab-top-rows-overlap-by-euler-4

top_rows_overlap(res_list, top_n = 5000, method = "euler")

plot of chunk tab-top-rows-overlap-by-euler-5

Also visualize the correspondance of rankings between different top-row methods:

top_rows_overlap(res_list, top_n = 1000, method = "correspondance")

plot of chunk tab-top-rows-overlap-by-correspondance-1

top_rows_overlap(res_list, top_n = 2000, method = "correspondance")

plot of chunk tab-top-rows-overlap-by-correspondance-2

top_rows_overlap(res_list, top_n = 3000, method = "correspondance")

plot of chunk tab-top-rows-overlap-by-correspondance-3

top_rows_overlap(res_list, top_n = 4000, method = "correspondance")

plot of chunk tab-top-rows-overlap-by-correspondance-4

top_rows_overlap(res_list, top_n = 5000, method = "correspondance")

plot of chunk tab-top-rows-overlap-by-correspondance-5

Heatmaps of the top rows:

top_rows_heatmap(res_list, top_n = 1000)

plot of chunk tab-top-rows-heatmap-1

top_rows_heatmap(res_list, top_n = 2000)

plot of chunk tab-top-rows-heatmap-2

top_rows_heatmap(res_list, top_n = 3000)

plot of chunk tab-top-rows-heatmap-3

top_rows_heatmap(res_list, top_n = 4000)

plot of chunk tab-top-rows-heatmap-4

top_rows_heatmap(res_list, top_n = 5000)

plot of chunk tab-top-rows-heatmap-5

Test to known annotations

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res_list, k = 2)
#>               n disease.state(p) specimen(p) k
#> SD:NMF      183            0.924    1.83e-40 2
#> CV:NMF      183            0.924    1.83e-40 2
#> MAD:NMF     183            0.924    1.83e-40 2
#> ATC:NMF     183            0.924    1.83e-40 2
#> SD:skmeans  183            0.924    1.83e-40 2
#> CV:skmeans  183            0.924    1.83e-40 2
#> MAD:skmeans 183            0.924    1.83e-40 2
#> ATC:skmeans 183            0.924    1.83e-40 2
#> SD:mclust   183            0.924    1.83e-40 2
#> CV:mclust   183            0.924    1.83e-40 2
#> MAD:mclust  183            0.924    1.83e-40 2
#> ATC:mclust  183            0.924    1.83e-40 2
#> SD:kmeans   183            0.924    1.83e-40 2
#> CV:kmeans   183            0.924    1.83e-40 2
#> MAD:kmeans  183            0.924    1.83e-40 2
#> ATC:kmeans  183            0.924    1.83e-40 2
#> SD:pam      183            0.924    1.83e-40 2
#> CV:pam      183            0.924    1.83e-40 2
#> MAD:pam     183            0.924    1.83e-40 2
#> ATC:pam     183            0.924    1.83e-40 2
#> SD:hclust   183            0.924    1.83e-40 2
#> CV:hclust   183            0.924    1.83e-40 2
#> MAD:hclust  183            0.924    1.83e-40 2
#> ATC:hclust  183            0.924    1.83e-40 2
test_to_known_factors(res_list, k = 3)
#>               n disease.state(p) specimen(p) k
#> SD:NMF      183            0.962    6.15e-78 3
#> CV:NMF      183            0.962    6.15e-78 3
#> MAD:NMF     183            0.962    6.15e-78 3
#> ATC:NMF     163            0.964    6.65e-61 3
#> SD:skmeans  183            0.962    6.15e-78 3
#> CV:skmeans  183            0.962    6.15e-78 3
#> MAD:skmeans 183            0.962    6.15e-78 3
#> ATC:skmeans 183            0.942    1.46e-75 3
#> SD:mclust   183            0.962    6.15e-78 3
#> CV:mclust   183            0.962    6.15e-78 3
#> MAD:mclust  183            0.962    6.15e-78 3
#> ATC:mclust  182            0.936    4.00e-75 3
#> SD:kmeans   183            0.962    6.15e-78 3
#> CV:kmeans   183            0.962    6.15e-78 3
#> MAD:kmeans  183            0.962    6.15e-78 3
#> ATC:kmeans  183            0.942    1.46e-75 3
#> SD:pam      183            0.962    6.15e-78 3
#> CV:pam      183            0.962    6.15e-78 3
#> MAD:pam     183            0.962    6.15e-78 3
#> ATC:pam     183            0.942    1.46e-75 3
#> SD:hclust   183            0.962    6.15e-78 3
#> CV:hclust   183            0.962    6.15e-78 3
#> MAD:hclust  183            0.962    6.15e-78 3
#> ATC:hclust  181            0.974    1.51e-73 3
test_to_known_factors(res_list, k = 4)
#>               n disease.state(p) specimen(p) k
#> SD:NMF      183           0.9620    6.15e-78 4
#> CV:NMF      178           0.0924    7.95e-74 4
#> MAD:NMF     174           0.8687    4.15e-72 4
#> ATC:NMF     180           0.9425    7.30e-72 4
#> SD:skmeans  182           0.9709    1.52e-75 4
#> CV:skmeans  180           0.9935    1.10e-74 4
#> MAD:skmeans 179           0.9731    2.96e-74 4
#> ATC:skmeans 183           0.8335    1.12e-73 4
#> SD:mclust   183           0.8443    5.66e-76 4
#> CV:mclust   177           0.5875    2.14e-73 4
#> MAD:mclust  179           0.8884    2.96e-74 4
#> ATC:mclust  182           0.7706    3.41e-73 4
#> SD:kmeans   183           0.9620    6.15e-78 4
#> CV:kmeans   183           0.9620    6.15e-78 4
#> MAD:kmeans  183           0.9620    6.15e-78 4
#> ATC:kmeans  181           0.9511    7.33e-76 4
#> SD:pam      182           0.8644    1.52e-75 4
#> CV:pam      183           0.8443    5.66e-76 4
#> MAD:pam     173           0.8810    1.11e-71 4
#> ATC:pam     172           0.9009    6.69e-69 4
#> SD:hclust   173           0.2857    1.11e-71 4
#> CV:hclust   172           0.4172    3.00e-71 4
#> MAD:hclust  174           0.9930    4.15e-72 4
#> ATC:hclust  172           0.3591    6.39e-68 4
test_to_known_factors(res_list, k = 5)
#>               n disease.state(p) specimen(p) k
#> SD:NMF      161            0.229    1.57e-66 5
#> CV:NMF      168            0.371    1.56e-69 5
#> MAD:NMF     173            0.747    8.43e-70 5
#> ATC:NMF     149            0.791    5.61e-60 5
#> SD:skmeans  171            0.997    4.61e-69 5
#> CV:skmeans  175            1.000    9.06e-71 5
#> MAD:skmeans 178            0.930    4.74e-72 5
#> ATC:skmeans 170            0.799    2.16e-70 5
#> SD:mclust   181            0.552    2.48e-73 5
#> CV:mclust   150            0.548    8.18e-62 5
#> MAD:mclust  177            0.891    1.27e-71 5
#> ATC:mclust  171            0.533    4.42e-68 5
#> SD:kmeans   176            0.995    5.74e-73 5
#> CV:kmeans   149            0.914    1.10e-59 5
#> MAD:kmeans  183            0.962    6.15e-78 5
#> ATC:kmeans  165            0.871    2.86e-65 5
#> SD:pam      170            0.809    1.23e-68 5
#> CV:pam      175            0.905    9.06e-71 5
#> MAD:pam     173            0.980    6.47e-70 5
#> ATC:pam     172            0.896    3.86e-66 5
#> SD:hclust   161            0.415    8.49e-65 5
#> CV:hclust   171            0.307    8.05e-71 5
#> MAD:hclust  168            0.974    8.79e-68 5
#> ATC:hclust  172            0.520    3.46e-66 5
test_to_known_factors(res_list, k = 6)
#>               n disease.state(p) specimen(p) k
#> SD:NMF      170           0.8332    1.23e-68 6
#> CV:NMF      172           0.5025    1.73e-69 6
#> MAD:NMF     171           0.8820    1.15e-68 6
#> ATC:NMF     153           0.7607    1.80e-60 6
#> SD:skmeans  171           0.9921    4.61e-69 6
#> CV:skmeans  167           0.9645    9.86e-66 6
#> MAD:skmeans 167           0.9014    2.35e-67 6
#> ATC:skmeans 175           0.8230    3.98e-69 6
#> SD:mclust   177           0.2805    5.64e-70 6
#> CV:mclust   172           0.0333    7.47e-68 6
#> MAD:mclust  180           0.7773    3.00e-71 6
#> ATC:mclust  168           0.8744    1.08e-66 6
#> SD:kmeans   157           0.6876    1.70e-61 6
#> CV:kmeans   153           0.9862    8.37e-60 6
#> MAD:kmeans  155           0.6333    1.19e-60 6
#> ATC:kmeans  167           0.7330    1.43e-64 6
#> SD:pam      165           0.8857    6.95e-65 6
#> CV:pam      164           0.9109    1.84e-64 6
#> MAD:pam     172           0.9396    7.47e-68 6
#> ATC:pam     172           0.9831    1.10e-66 6
#> SD:hclust   148           0.5780    1.09e-57 6
#> CV:hclust   158           0.3578    6.41e-62 6
#> MAD:hclust  157           0.6682    1.70e-61 6
#> ATC:hclust  164           0.4129    7.79e-63 6

Results for each method


SD:hclust*

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["SD", "hclust"]
# you can also extract it by
# res = res_list["SD:hclust"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#>   Subgroups are detected by 'hclust' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 5.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk SD-hclust-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk SD-hclust-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 1.000           1.000       1.000         0.5958 0.750   0.571
#> 4 4 0.966           0.912       0.943         0.0504 0.956   0.869
#> 5 5 0.905           0.807       0.915         0.0477 0.948   0.830
#> 6 6 0.785           0.615       0.826         0.0559 0.948   0.808

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3 4

There is also optional best \(k\) = 2 3 4 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette p1 p2 p3
#> GSM674344     3       0          1  0  0  1
#> GSM674346     3       0          1  0  0  1
#> GSM674347     3       0          1  0  0  1
#> GSM674348     3       0          1  0  0  1
#> GSM674349     3       0          1  0  0  1
#> GSM674350     3       0          1  0  0  1
#> GSM674353     3       0          1  0  0  1
#> GSM674354     3       0          1  0  0  1
#> GSM674355     3       0          1  0  0  1
#> GSM674356     3       0          1  0  0  1
#> GSM674357     3       0          1  0  0  1
#> GSM674358     3       0          1  0  0  1
#> GSM674361     3       0          1  0  0  1
#> GSM674363     3       0          1  0  0  1
#> GSM674364     3       0          1  0  0  1
#> GSM674365     3       0          1  0  0  1
#> GSM674366     3       0          1  0  0  1
#> GSM674367     3       0          1  0  0  1
#> GSM674368     3       0          1  0  0  1
#> GSM674370     3       0          1  0  0  1
#> GSM674371     3       0          1  0  0  1
#> GSM674373     3       0          1  0  0  1
#> GSM674375     3       0          1  0  0  1
#> GSM674379     3       0          1  0  0  1
#> GSM674380     3       0          1  0  0  1
#> GSM674381     3       0          1  0  0  1
#> GSM674382     3       0          1  0  0  1
#> GSM674384     3       0          1  0  0  1
#> GSM674385     3       0          1  0  0  1
#> GSM674388     3       0          1  0  0  1
#> GSM674389     3       0          1  0  0  1
#> GSM674390     3       0          1  0  0  1
#> GSM674391     3       0          1  0  0  1
#> GSM674393     3       0          1  0  0  1
#> GSM674394     3       0          1  0  0  1
#> GSM674395     3       0          1  0  0  1
#> GSM674397     3       0          1  0  0  1
#> GSM674398     3       0          1  0  0  1
#> GSM674400     3       0          1  0  0  1
#> GSM674401     3       0          1  0  0  1
#> GSM674402     3       0          1  0  0  1
#> GSM674403     3       0          1  0  0  1
#> GSM674405     3       0          1  0  0  1
#> GSM674406     3       0          1  0  0  1
#> GSM674407     3       0          1  0  0  1
#> GSM674181     2       0          1  0  1  0
#> GSM674183     2       0          1  0  1  0
#> GSM674184     2       0          1  0  1  0
#> GSM674185     2       0          1  0  1  0
#> GSM674186     2       0          1  0  1  0
#> GSM674187     2       0          1  0  1  0
#> GSM674190     2       0          1  0  1  0
#> GSM674191     2       0          1  0  1  0
#> GSM674192     2       0          1  0  1  0
#> GSM674193     2       0          1  0  1  0
#> GSM674194     2       0          1  0  1  0
#> GSM674195     2       0          1  0  1  0
#> GSM674198     2       0          1  0  1  0
#> GSM674200     2       0          1  0  1  0
#> GSM674201     2       0          1  0  1  0
#> GSM674202     2       0          1  0  1  0
#> GSM674203     2       0          1  0  1  0
#> GSM674204     2       0          1  0  1  0
#> GSM674205     2       0          1  0  1  0
#> GSM674206     2       0          1  0  1  0
#> GSM674208     2       0          1  0  1  0
#> GSM674209     2       0          1  0  1  0
#> GSM674210     2       0          1  0  1  0
#> GSM674212     2       0          1  0  1  0
#> GSM674214     2       0          1  0  1  0
#> GSM674218     2       0          1  0  1  0
#> GSM674219     2       0          1  0  1  0
#> GSM674220     2       0          1  0  1  0
#> GSM674221     2       0          1  0  1  0
#> GSM674223     2       0          1  0  1  0
#> GSM674225     2       0          1  0  1  0
#> GSM674226     2       0          1  0  1  0
#> GSM674229     2       0          1  0  1  0
#> GSM674230     2       0          1  0  1  0
#> GSM674231     2       0          1  0  1  0
#> GSM674232     2       0          1  0  1  0
#> GSM674234     2       0          1  0  1  0
#> GSM674235     2       0          1  0  1  0
#> GSM674236     2       0          1  0  1  0
#> GSM674237     2       0          1  0  1  0
#> GSM674239     2       0          1  0  1  0
#> GSM674240     2       0          1  0  1  0
#> GSM674242     2       0          1  0  1  0
#> GSM674243     2       0          1  0  1  0
#> GSM674244     2       0          1  0  1  0
#> GSM674245     2       0          1  0  1  0
#> GSM674282     1       0          1  1  0  0
#> GSM674284     1       0          1  1  0  0
#> GSM674285     1       0          1  1  0  0
#> GSM674287     1       0          1  1  0  0
#> GSM674288     1       0          1  1  0  0
#> GSM674289     1       0          1  1  0  0
#> GSM674290     1       0          1  1  0  0
#> GSM674291     1       0          1  1  0  0
#> GSM674292     1       0          1  1  0  0
#> GSM674295     1       0          1  1  0  0
#> GSM674297     1       0          1  1  0  0
#> GSM674298     1       0          1  1  0  0
#> GSM674299     1       0          1  1  0  0
#> GSM674300     1       0          1  1  0  0
#> GSM674301     1       0          1  1  0  0
#> GSM674302     1       0          1  1  0  0
#> GSM674304     1       0          1  1  0  0
#> GSM674305     1       0          1  1  0  0
#> GSM674306     1       0          1  1  0  0
#> GSM674308     1       0          1  1  0  0
#> GSM674309     1       0          1  1  0  0
#> GSM674313     1       0          1  1  0  0
#> GSM674314     1       0          1  1  0  0
#> GSM674315     1       0          1  1  0  0
#> GSM674316     1       0          1  1  0  0
#> GSM674318     1       0          1  1  0  0
#> GSM674320     1       0          1  1  0  0
#> GSM674323     1       0          1  1  0  0
#> GSM674324     1       0          1  1  0  0
#> GSM674325     1       0          1  1  0  0
#> GSM674327     1       0          1  1  0  0
#> GSM674328     1       0          1  1  0  0
#> GSM674330     1       0          1  1  0  0
#> GSM674331     1       0          1  1  0  0
#> GSM674332     1       0          1  1  0  0
#> GSM674334     1       0          1  1  0  0
#> GSM674335     1       0          1  1  0  0
#> GSM674345     3       0          1  0  0  1
#> GSM674351     3       0          1  0  0  1
#> GSM674352     3       0          1  0  0  1
#> GSM674359     3       0          1  0  0  1
#> GSM674360     3       0          1  0  0  1
#> GSM674362     3       0          1  0  0  1
#> GSM674369     3       0          1  0  0  1
#> GSM674372     3       0          1  0  0  1
#> GSM674374     3       0          1  0  0  1
#> GSM674376     3       0          1  0  0  1
#> GSM674377     3       0          1  0  0  1
#> GSM674378     3       0          1  0  0  1
#> GSM674383     3       0          1  0  0  1
#> GSM674386     3       0          1  0  0  1
#> GSM674387     3       0          1  0  0  1
#> GSM674392     3       0          1  0  0  1
#> GSM674396     3       0          1  0  0  1
#> GSM674399     3       0          1  0  0  1
#> GSM674404     3       0          1  0  0  1
#> GSM674182     2       0          1  0  1  0
#> GSM674188     2       0          1  0  1  0
#> GSM674189     2       0          1  0  1  0
#> GSM674196     2       0          1  0  1  0
#> GSM674197     2       0          1  0  1  0
#> GSM674199     2       0          1  0  1  0
#> GSM674207     2       0          1  0  1  0
#> GSM674211     2       0          1  0  1  0
#> GSM674213     2       0          1  0  1  0
#> GSM674215     2       0          1  0  1  0
#> GSM674216     2       0          1  0  1  0
#> GSM674217     2       0          1  0  1  0
#> GSM674222     2       0          1  0  1  0
#> GSM674224     2       0          1  0  1  0
#> GSM674227     2       0          1  0  1  0
#> GSM674228     2       0          1  0  1  0
#> GSM674233     2       0          1  0  1  0
#> GSM674238     2       0          1  0  1  0
#> GSM674241     2       0          1  0  1  0
#> GSM674283     1       0          1  1  0  0
#> GSM674286     1       0          1  1  0  0
#> GSM674293     1       0          1  1  0  0
#> GSM674294     1       0          1  1  0  0
#> GSM674296     1       0          1  1  0  0
#> GSM674303     1       0          1  1  0  0
#> GSM674307     1       0          1  1  0  0
#> GSM674310     1       0          1  1  0  0
#> GSM674311     1       0          1  1  0  0
#> GSM674312     1       0          1  1  0  0
#> GSM674317     1       0          1  1  0  0
#> GSM674319     1       0          1  1  0  0
#> GSM674321     1       0          1  1  0  0
#> GSM674322     1       0          1  1  0  0
#> GSM674326     1       0          1  1  0  0
#> GSM674329     1       0          1  1  0  0
#> GSM674333     1       0          1  1  0  0

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1 p2 p3    p4
#> GSM674344     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674346     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674347     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674348     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674349     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674350     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674353     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674354     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674355     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674356     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674357     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674358     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674361     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674363     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674364     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674365     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674366     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674367     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674368     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674370     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674371     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674373     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674375     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674379     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674380     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674381     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674382     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674384     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674385     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674388     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674389     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674390     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674391     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674393     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674394     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674395     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674397     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674398     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674400     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674401     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674402     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674403     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674405     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674406     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674407     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674181     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674183     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674184     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674185     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674186     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674187     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674190     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674191     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674192     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674193     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674194     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674195     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674198     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674200     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674201     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674202     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674203     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674204     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674205     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674206     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674208     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674209     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674210     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674212     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674214     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674218     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674219     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674220     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674221     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674223     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674225     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674226     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674229     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674230     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674231     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674232     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674234     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674235     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674236     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674237     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674239     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674240     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674242     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674243     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674244     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674245     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674282     1  0.3649      0.924 0.796  0  0 0.204
#> GSM674284     1  0.3764      0.916 0.784  0  0 0.216
#> GSM674285     1  0.3649      0.924 0.796  0  0 0.204
#> GSM674287     1  0.3764      0.916 0.784  0  0 0.216
#> GSM674288     4  0.4406      0.481 0.300  0  0 0.700
#> GSM674289     1  0.3649      0.924 0.796  0  0 0.204
#> GSM674290     1  0.3649      0.924 0.796  0  0 0.204
#> GSM674291     1  0.3649      0.924 0.796  0  0 0.204
#> GSM674292     1  0.3649      0.924 0.796  0  0 0.204
#> GSM674295     4  0.1716      0.703 0.064  0  0 0.936
#> GSM674297     1  0.3764      0.916 0.784  0  0 0.216
#> GSM674298     1  0.3764      0.916 0.784  0  0 0.216
#> GSM674299     1  0.4477      0.768 0.688  0  0 0.312
#> GSM674300     1  0.2011      0.608 0.920  0  0 0.080
#> GSM674301     1  0.3649      0.924 0.796  0  0 0.204
#> GSM674302     1  0.3649      0.924 0.796  0  0 0.204
#> GSM674304     1  0.3649      0.924 0.796  0  0 0.204
#> GSM674305     1  0.3649      0.924 0.796  0  0 0.204
#> GSM674306     1  0.1022      0.646 0.968  0  0 0.032
#> GSM674308     1  0.3649      0.924 0.796  0  0 0.204
#> GSM674309     4  0.4967      0.196 0.452  0  0 0.548
#> GSM674313     4  0.3649      0.529 0.204  0  0 0.796
#> GSM674314     4  0.4961      0.197 0.448  0  0 0.552
#> GSM674315     1  0.1022      0.646 0.968  0  0 0.032
#> GSM674316     4  0.1389      0.712 0.048  0  0 0.952
#> GSM674318     4  0.0188      0.711 0.004  0  0 0.996
#> GSM674320     4  0.0000      0.709 0.000  0  0 1.000
#> GSM674323     4  0.1557      0.710 0.056  0  0 0.944
#> GSM674324     4  0.4967      0.196 0.452  0  0 0.548
#> GSM674325     4  0.1389      0.712 0.048  0  0 0.952
#> GSM674327     1  0.2081      0.602 0.916  0  0 0.084
#> GSM674328     1  0.3837      0.909 0.776  0  0 0.224
#> GSM674330     4  0.4967      0.196 0.452  0  0 0.548
#> GSM674331     4  0.4967      0.196 0.452  0  0 0.548
#> GSM674332     4  0.4972      0.180 0.456  0  0 0.544
#> GSM674334     4  0.4972      0.180 0.456  0  0 0.544
#> GSM674335     4  0.4967      0.194 0.452  0  0 0.548
#> GSM674345     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674351     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674352     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674359     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674360     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674362     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674369     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674372     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674374     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674376     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674377     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674378     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674383     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674386     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674387     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674392     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674396     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674399     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674404     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674182     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674188     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674189     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674196     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674197     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674199     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674207     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674211     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674213     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674215     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674216     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674217     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674222     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674224     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674227     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674228     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674233     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674238     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674241     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674283     1  0.3649      0.924 0.796  0  0 0.204
#> GSM674286     1  0.3649      0.924 0.796  0  0 0.204
#> GSM674293     1  0.3172      0.866 0.840  0  0 0.160
#> GSM674294     1  0.3649      0.924 0.796  0  0 0.204
#> GSM674296     1  0.3649      0.924 0.796  0  0 0.204
#> GSM674303     1  0.4103      0.855 0.744  0  0 0.256
#> GSM674307     1  0.3649      0.924 0.796  0  0 0.204
#> GSM674310     4  0.0188      0.711 0.004  0  0 0.996
#> GSM674311     4  0.4967      0.196 0.452  0  0 0.548
#> GSM674312     4  0.0188      0.711 0.004  0  0 0.996
#> GSM674317     1  0.3837      0.909 0.776  0  0 0.224
#> GSM674319     4  0.1792      0.703 0.068  0  0 0.932
#> GSM674321     4  0.1637      0.709 0.060  0  0 0.940
#> GSM674322     4  0.0188      0.711 0.004  0  0 0.996
#> GSM674326     4  0.0188      0.711 0.004  0  0 0.996
#> GSM674329     4  0.0000      0.709 0.000  0  0 1.000
#> GSM674333     4  0.0336      0.712 0.008  0  0 0.992

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2 p3    p4    p5
#> GSM674344     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674346     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674347     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674348     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674349     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674350     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674353     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674354     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674355     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674356     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674357     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674358     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674361     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674363     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674364     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674365     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674366     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674367     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674368     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674370     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674371     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674373     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674375     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674379     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674380     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674381     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674382     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674384     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674385     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674388     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674389     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674390     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674391     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674393     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674394     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674395     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674397     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674398     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674400     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674401     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674402     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674403     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674405     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674406     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674407     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674181     2  0.4242    -0.5278 0.000 0.572  0 0.000 0.428
#> GSM674183     5  0.4192     0.9167 0.000 0.404  0 0.000 0.596
#> GSM674184     5  0.4249     0.9171 0.000 0.432  0 0.000 0.568
#> GSM674185     5  0.4201     0.9294 0.000 0.408  0 0.000 0.592
#> GSM674186     2  0.2516     0.6650 0.000 0.860  0 0.000 0.140
#> GSM674187     2  0.1608     0.7780 0.000 0.928  0 0.000 0.072
#> GSM674190     2  0.2690     0.6370 0.000 0.844  0 0.000 0.156
#> GSM674191     2  0.2690     0.6370 0.000 0.844  0 0.000 0.156
#> GSM674192     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674193     2  0.0162     0.8381 0.000 0.996  0 0.000 0.004
#> GSM674194     2  0.3612     0.3150 0.000 0.732  0 0.000 0.268
#> GSM674195     5  0.4192     0.9329 0.000 0.404  0 0.000 0.596
#> GSM674198     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674200     5  0.4101     0.9074 0.000 0.372  0 0.000 0.628
#> GSM674201     2  0.4227    -0.4942 0.000 0.580  0 0.000 0.420
#> GSM674202     2  0.0880     0.8213 0.000 0.968  0 0.000 0.032
#> GSM674203     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674204     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674205     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674206     2  0.3895     0.0651 0.000 0.680  0 0.000 0.320
#> GSM674208     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674209     2  0.0162     0.8381 0.000 0.996  0 0.000 0.004
#> GSM674210     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674212     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674214     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674218     5  0.4273     0.8947 0.000 0.448  0 0.000 0.552
#> GSM674219     2  0.3395     0.4230 0.000 0.764  0 0.000 0.236
#> GSM674220     2  0.4210    -0.4840 0.000 0.588  0 0.000 0.412
#> GSM674221     2  0.3336     0.4483 0.000 0.772  0 0.000 0.228
#> GSM674223     2  0.0290     0.8369 0.000 0.992  0 0.000 0.008
#> GSM674225     2  0.2074     0.7056 0.000 0.896  0 0.000 0.104
#> GSM674226     2  0.0404     0.8350 0.000 0.988  0 0.000 0.012
#> GSM674229     2  0.0162     0.8381 0.000 0.996  0 0.000 0.004
#> GSM674230     2  0.0609     0.8321 0.000 0.980  0 0.000 0.020
#> GSM674231     2  0.0290     0.8377 0.000 0.992  0 0.000 0.008
#> GSM674232     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674234     2  0.0162     0.8381 0.000 0.996  0 0.000 0.004
#> GSM674235     2  0.0880     0.8213 0.000 0.968  0 0.000 0.032
#> GSM674236     2  0.0880     0.8213 0.000 0.968  0 0.000 0.032
#> GSM674237     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674239     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674240     2  0.3774     0.1710 0.000 0.704  0 0.000 0.296
#> GSM674242     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674243     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674244     2  0.2127     0.6979 0.000 0.892  0 0.000 0.108
#> GSM674245     2  0.0404     0.8350 0.000 0.988  0 0.000 0.012
#> GSM674282     1  0.0000     0.8428 1.000 0.000  0 0.000 0.000
#> GSM674284     1  0.0671     0.8391 0.980 0.000  0 0.016 0.004
#> GSM674285     1  0.0000     0.8428 1.000 0.000  0 0.000 0.000
#> GSM674287     1  0.0671     0.8391 0.980 0.000  0 0.016 0.004
#> GSM674288     4  0.4367     0.2229 0.416 0.000  0 0.580 0.004
#> GSM674289     1  0.0000     0.8428 1.000 0.000  0 0.000 0.000
#> GSM674290     1  0.0000     0.8428 1.000 0.000  0 0.000 0.000
#> GSM674291     1  0.0000     0.8428 1.000 0.000  0 0.000 0.000
#> GSM674292     1  0.0000     0.8428 1.000 0.000  0 0.000 0.000
#> GSM674295     4  0.3911     0.8276 0.144 0.000  0 0.796 0.060
#> GSM674297     1  0.0671     0.8391 0.980 0.000  0 0.016 0.004
#> GSM674298     1  0.0671     0.8391 0.980 0.000  0 0.016 0.004
#> GSM674299     1  0.2389     0.7740 0.880 0.000  0 0.116 0.004
#> GSM674300     1  0.4810     0.6466 0.712 0.000  0 0.084 0.204
#> GSM674301     1  0.0000     0.8428 1.000 0.000  0 0.000 0.000
#> GSM674302     1  0.0000     0.8428 1.000 0.000  0 0.000 0.000
#> GSM674304     1  0.0000     0.8428 1.000 0.000  0 0.000 0.000
#> GSM674305     1  0.0000     0.8428 1.000 0.000  0 0.000 0.000
#> GSM674306     1  0.4054     0.6710 0.760 0.000  0 0.036 0.204
#> GSM674308     1  0.0000     0.8428 1.000 0.000  0 0.000 0.000
#> GSM674309     1  0.4276     0.4324 0.616 0.000  0 0.380 0.004
#> GSM674313     4  0.3932     0.6872 0.000 0.000  0 0.672 0.328
#> GSM674314     1  0.4528     0.2672 0.548 0.000  0 0.444 0.008
#> GSM674315     1  0.4054     0.6710 0.760 0.000  0 0.036 0.204
#> GSM674316     4  0.1792     0.8747 0.084 0.000  0 0.916 0.000
#> GSM674318     4  0.0963     0.8842 0.036 0.000  0 0.964 0.000
#> GSM674320     4  0.2514     0.8720 0.044 0.000  0 0.896 0.060
#> GSM674323     4  0.1908     0.8707 0.092 0.000  0 0.908 0.000
#> GSM674324     1  0.4276     0.4324 0.616 0.000  0 0.380 0.004
#> GSM674325     4  0.3109     0.7712 0.200 0.000  0 0.800 0.000
#> GSM674327     1  0.4602     0.6449 0.708 0.000  0 0.052 0.240
#> GSM674328     1  0.0771     0.8382 0.976 0.000  0 0.020 0.004
#> GSM674330     1  0.4276     0.4324 0.616 0.000  0 0.380 0.004
#> GSM674331     1  0.4276     0.4324 0.616 0.000  0 0.380 0.004
#> GSM674332     1  0.4276     0.4299 0.616 0.000  0 0.380 0.004
#> GSM674334     1  0.4264     0.4399 0.620 0.000  0 0.376 0.004
#> GSM674335     1  0.4299     0.4114 0.608 0.000  0 0.388 0.004
#> GSM674345     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674351     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674352     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674359     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674360     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674362     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674369     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674372     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674374     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674376     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674377     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674378     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674383     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674386     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674387     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674392     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674396     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674399     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674404     3  0.0000     1.0000 0.000 0.000  1 0.000 0.000
#> GSM674182     2  0.4235    -0.5112 0.000 0.576  0 0.000 0.424
#> GSM674188     2  0.1608     0.7780 0.000 0.928  0 0.000 0.072
#> GSM674189     5  0.4291     0.8617 0.000 0.464  0 0.000 0.536
#> GSM674196     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674197     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674199     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674207     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674211     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674213     2  0.0290     0.8365 0.000 0.992  0 0.000 0.008
#> GSM674215     2  0.4307    -0.7656 0.000 0.504  0 0.000 0.496
#> GSM674216     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674217     2  0.3336     0.4483 0.000 0.772  0 0.000 0.228
#> GSM674222     2  0.0703     0.8221 0.000 0.976  0 0.000 0.024
#> GSM674224     2  0.0290     0.8371 0.000 0.992  0 0.000 0.008
#> GSM674227     2  0.0880     0.8213 0.000 0.968  0 0.000 0.032
#> GSM674228     2  0.0404     0.8359 0.000 0.988  0 0.000 0.012
#> GSM674233     2  0.3366     0.4352 0.000 0.768  0 0.000 0.232
#> GSM674238     5  0.4126     0.9188 0.000 0.380  0 0.000 0.620
#> GSM674241     2  0.0000     0.8393 0.000 1.000  0 0.000 0.000
#> GSM674283     1  0.0162     0.8423 0.996 0.000  0 0.004 0.000
#> GSM674286     1  0.0000     0.8428 1.000 0.000  0 0.000 0.000
#> GSM674293     1  0.1341     0.8097 0.944 0.000  0 0.000 0.056
#> GSM674294     1  0.0000     0.8428 1.000 0.000  0 0.000 0.000
#> GSM674296     1  0.0000     0.8428 1.000 0.000  0 0.000 0.000
#> GSM674303     1  0.1502     0.8169 0.940 0.000  0 0.056 0.004
#> GSM674307     1  0.0000     0.8428 1.000 0.000  0 0.000 0.000
#> GSM674310     4  0.0963     0.8842 0.036 0.000  0 0.964 0.000
#> GSM674311     1  0.4276     0.4324 0.616 0.000  0 0.380 0.004
#> GSM674312     4  0.2359     0.8683 0.036 0.000  0 0.904 0.060
#> GSM674317     1  0.0771     0.8382 0.976 0.000  0 0.020 0.004
#> GSM674319     4  0.4496     0.7480 0.216 0.000  0 0.728 0.056
#> GSM674321     4  0.1908     0.8703 0.092 0.000  0 0.908 0.000
#> GSM674322     4  0.0963     0.8842 0.036 0.000  0 0.964 0.000
#> GSM674326     4  0.0963     0.8842 0.036 0.000  0 0.964 0.000
#> GSM674329     4  0.3110     0.8672 0.080 0.000  0 0.860 0.060
#> GSM674333     4  0.1124     0.8840 0.036 0.000  0 0.960 0.004

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4    p5    p6
#> GSM674344     3  0.1196     0.6040 0.000 0.000 0.952 0.040 0.000 0.008
#> GSM674346     3  0.0632     0.6237 0.000 0.000 0.976 0.024 0.000 0.000
#> GSM674347     3  0.3862    -0.7245 0.000 0.000 0.524 0.476 0.000 0.000
#> GSM674348     3  0.1204     0.6351 0.000 0.000 0.944 0.056 0.000 0.000
#> GSM674349     3  0.1007     0.6334 0.000 0.000 0.956 0.044 0.000 0.000
#> GSM674350     3  0.1610     0.6283 0.000 0.000 0.916 0.084 0.000 0.000
#> GSM674353     3  0.1501     0.6311 0.000 0.000 0.924 0.076 0.000 0.000
#> GSM674354     3  0.0891     0.6245 0.000 0.000 0.968 0.024 0.000 0.008
#> GSM674355     3  0.1444     0.6323 0.000 0.000 0.928 0.072 0.000 0.000
#> GSM674356     3  0.0260     0.6353 0.000 0.000 0.992 0.008 0.000 0.000
#> GSM674357     3  0.0260     0.6353 0.000 0.000 0.992 0.008 0.000 0.000
#> GSM674358     3  0.1141     0.6369 0.000 0.000 0.948 0.052 0.000 0.000
#> GSM674361     3  0.1387     0.6341 0.000 0.000 0.932 0.068 0.000 0.000
#> GSM674363     3  0.1444     0.6324 0.000 0.000 0.928 0.072 0.000 0.000
#> GSM674364     3  0.0547     0.6266 0.000 0.000 0.980 0.020 0.000 0.000
#> GSM674365     3  0.1501     0.6245 0.000 0.000 0.924 0.076 0.000 0.000
#> GSM674366     3  0.1957     0.5903 0.000 0.000 0.888 0.112 0.000 0.000
#> GSM674367     3  0.3737    -0.3559 0.000 0.000 0.608 0.392 0.000 0.000
#> GSM674368     3  0.1141     0.6345 0.000 0.000 0.948 0.052 0.000 0.000
#> GSM674370     3  0.3672    -0.2715 0.000 0.000 0.632 0.368 0.000 0.000
#> GSM674371     3  0.1863     0.6061 0.000 0.000 0.896 0.104 0.000 0.000
#> GSM674373     3  0.3695    -0.2644 0.000 0.000 0.624 0.376 0.000 0.000
#> GSM674375     3  0.3789    -0.4688 0.000 0.000 0.584 0.416 0.000 0.000
#> GSM674379     4  0.3868     0.8182 0.000 0.000 0.492 0.508 0.000 0.000
#> GSM674380     4  0.4083     0.8461 0.000 0.000 0.460 0.532 0.000 0.008
#> GSM674381     3  0.3076     0.3343 0.000 0.000 0.760 0.240 0.000 0.000
#> GSM674382     4  0.3851     0.8920 0.000 0.000 0.460 0.540 0.000 0.000
#> GSM674384     3  0.3737    -0.3309 0.000 0.000 0.608 0.392 0.000 0.000
#> GSM674385     3  0.1714     0.6166 0.000 0.000 0.908 0.092 0.000 0.000
#> GSM674388     3  0.0937     0.6318 0.000 0.000 0.960 0.040 0.000 0.000
#> GSM674389     3  0.3828    -0.5825 0.000 0.000 0.560 0.440 0.000 0.000
#> GSM674390     3  0.3756    -0.4096 0.000 0.000 0.600 0.400 0.000 0.000
#> GSM674391     4  0.3838     0.8994 0.000 0.000 0.448 0.552 0.000 0.000
#> GSM674393     3  0.3860    -0.7222 0.000 0.000 0.528 0.472 0.000 0.000
#> GSM674394     3  0.3482     0.0717 0.000 0.000 0.684 0.316 0.000 0.000
#> GSM674395     3  0.3592    -0.0790 0.000 0.000 0.656 0.344 0.000 0.000
#> GSM674397     3  0.3288     0.1843 0.000 0.000 0.724 0.276 0.000 0.000
#> GSM674398     4  0.3843     0.8983 0.000 0.000 0.452 0.548 0.000 0.000
#> GSM674400     4  0.3756     0.7886 0.000 0.000 0.400 0.600 0.000 0.000
#> GSM674401     4  0.3756     0.7886 0.000 0.000 0.400 0.600 0.000 0.000
#> GSM674402     3  0.1333     0.5961 0.000 0.000 0.944 0.048 0.000 0.008
#> GSM674403     4  0.3765     0.7898 0.000 0.000 0.404 0.596 0.000 0.000
#> GSM674405     4  0.3828     0.8982 0.000 0.000 0.440 0.560 0.000 0.000
#> GSM674406     3  0.3823    -0.5855 0.000 0.000 0.564 0.436 0.000 0.000
#> GSM674407     3  0.3868    -0.7821 0.000 0.000 0.508 0.492 0.000 0.000
#> GSM674181     2  0.3854    -0.3305 0.000 0.536 0.000 0.000 0.000 0.464
#> GSM674183     6  0.2597     0.7681 0.000 0.176 0.000 0.000 0.000 0.824
#> GSM674184     6  0.3428     0.8243 0.000 0.304 0.000 0.000 0.000 0.696
#> GSM674185     6  0.3266     0.8359 0.000 0.272 0.000 0.000 0.000 0.728
#> GSM674186     2  0.2378     0.7273 0.000 0.848 0.000 0.000 0.000 0.152
#> GSM674187     2  0.1814     0.8055 0.000 0.900 0.000 0.000 0.000 0.100
#> GSM674190     2  0.2491     0.7078 0.000 0.836 0.000 0.000 0.000 0.164
#> GSM674191     2  0.2491     0.7078 0.000 0.836 0.000 0.000 0.000 0.164
#> GSM674192     2  0.0000     0.8714 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674193     2  0.0146     0.8704 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674194     2  0.3266     0.4841 0.000 0.728 0.000 0.000 0.000 0.272
#> GSM674195     6  0.3221     0.8356 0.000 0.264 0.000 0.000 0.000 0.736
#> GSM674198     2  0.0000     0.8714 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674200     6  0.2300     0.7412 0.000 0.144 0.000 0.000 0.000 0.856
#> GSM674201     2  0.3828    -0.2245 0.000 0.560 0.000 0.000 0.000 0.440
#> GSM674202     2  0.1267     0.8382 0.000 0.940 0.000 0.000 0.000 0.060
#> GSM674203     2  0.0000     0.8714 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674204     2  0.0146     0.8703 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674205     2  0.0000     0.8714 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674206     2  0.3592     0.2617 0.000 0.656 0.000 0.000 0.000 0.344
#> GSM674208     2  0.0000     0.8714 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674209     2  0.0260     0.8700 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674210     2  0.0000     0.8714 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674212     2  0.0000     0.8714 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674214     2  0.0000     0.8714 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674218     6  0.3756     0.7065 0.000 0.400 0.000 0.000 0.000 0.600
#> GSM674219     2  0.3198     0.5185 0.000 0.740 0.000 0.000 0.000 0.260
#> GSM674220     6  0.3843     0.6112 0.000 0.452 0.000 0.000 0.000 0.548
#> GSM674221     2  0.3151     0.5354 0.000 0.748 0.000 0.000 0.000 0.252
#> GSM674223     2  0.0363     0.8689 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM674225     2  0.2048     0.7429 0.000 0.880 0.000 0.000 0.000 0.120
#> GSM674226     2  0.0363     0.8688 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM674229     2  0.0260     0.8699 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674230     2  0.0790     0.8610 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM674231     2  0.0363     0.8690 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM674232     2  0.0000     0.8714 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674234     2  0.0146     0.8704 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674235     2  0.1204     0.8429 0.000 0.944 0.000 0.000 0.000 0.056
#> GSM674236     2  0.1267     0.8382 0.000 0.940 0.000 0.000 0.000 0.060
#> GSM674237     2  0.0000     0.8714 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674239     2  0.0000     0.8714 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674240     2  0.3499     0.3359 0.000 0.680 0.000 0.000 0.000 0.320
#> GSM674242     2  0.0000     0.8714 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674243     2  0.0146     0.8703 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674244     2  0.2135     0.7323 0.000 0.872 0.000 0.000 0.000 0.128
#> GSM674245     2  0.0363     0.8688 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM674282     1  0.0000     0.8355 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674284     1  0.0603     0.8319 0.980 0.000 0.000 0.004 0.016 0.000
#> GSM674285     1  0.0000     0.8355 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674287     1  0.0603     0.8319 0.980 0.000 0.000 0.004 0.016 0.000
#> GSM674288     5  0.4084     0.2394 0.400 0.000 0.000 0.012 0.588 0.000
#> GSM674289     1  0.0000     0.8355 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0000     0.8355 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674291     1  0.0000     0.8355 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674292     1  0.0000     0.8355 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674295     5  0.3645     0.8261 0.128 0.000 0.000 0.056 0.804 0.012
#> GSM674297     1  0.0603     0.8319 0.980 0.000 0.000 0.004 0.016 0.000
#> GSM674298     1  0.0603     0.8319 0.980 0.000 0.000 0.004 0.016 0.000
#> GSM674299     1  0.2212     0.7691 0.880 0.000 0.000 0.008 0.112 0.000
#> GSM674300     1  0.5291     0.5921 0.652 0.000 0.000 0.232 0.056 0.060
#> GSM674301     1  0.0000     0.8355 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674302     1  0.0000     0.8355 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0000     0.8355 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674305     1  0.0000     0.8355 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674306     1  0.4443     0.6233 0.700 0.000 0.000 0.232 0.008 0.060
#> GSM674308     1  0.0000     0.8355 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674309     1  0.3862     0.4324 0.608 0.000 0.000 0.004 0.388 0.000
#> GSM674313     5  0.4831     0.6710 0.000 0.000 0.000 0.268 0.636 0.096
#> GSM674314     1  0.4114     0.2469 0.532 0.000 0.000 0.004 0.460 0.004
#> GSM674315     1  0.4443     0.6233 0.700 0.000 0.000 0.232 0.008 0.060
#> GSM674316     5  0.1387     0.8732 0.068 0.000 0.000 0.000 0.932 0.000
#> GSM674318     5  0.0547     0.8828 0.020 0.000 0.000 0.000 0.980 0.000
#> GSM674320     5  0.2231     0.8704 0.028 0.000 0.000 0.048 0.908 0.016
#> GSM674323     5  0.1501     0.8694 0.076 0.000 0.000 0.000 0.924 0.000
#> GSM674324     1  0.3862     0.4324 0.608 0.000 0.000 0.004 0.388 0.000
#> GSM674325     5  0.2730     0.7606 0.192 0.000 0.000 0.000 0.808 0.000
#> GSM674327     1  0.5590     0.5905 0.648 0.000 0.000 0.188 0.064 0.100
#> GSM674328     1  0.0692     0.8311 0.976 0.000 0.000 0.004 0.020 0.000
#> GSM674330     1  0.3862     0.4324 0.608 0.000 0.000 0.004 0.388 0.000
#> GSM674331     1  0.3862     0.4324 0.608 0.000 0.000 0.004 0.388 0.000
#> GSM674332     1  0.3862     0.4298 0.608 0.000 0.000 0.004 0.388 0.000
#> GSM674334     1  0.3852     0.4397 0.612 0.000 0.000 0.004 0.384 0.000
#> GSM674335     1  0.3984     0.4030 0.596 0.000 0.000 0.008 0.396 0.000
#> GSM674345     3  0.0547     0.6253 0.000 0.000 0.980 0.020 0.000 0.000
#> GSM674351     3  0.1501     0.6311 0.000 0.000 0.924 0.076 0.000 0.000
#> GSM674352     3  0.1610     0.6283 0.000 0.000 0.916 0.084 0.000 0.000
#> GSM674359     3  0.0547     0.6253 0.000 0.000 0.980 0.020 0.000 0.000
#> GSM674360     3  0.1204     0.6333 0.000 0.000 0.944 0.056 0.000 0.000
#> GSM674362     3  0.1082     0.6080 0.000 0.000 0.956 0.040 0.000 0.004
#> GSM674369     3  0.1501     0.6181 0.000 0.000 0.924 0.076 0.000 0.000
#> GSM674372     3  0.3765    -0.3773 0.000 0.000 0.596 0.404 0.000 0.000
#> GSM674374     3  0.3634    -0.2293 0.000 0.000 0.644 0.356 0.000 0.000
#> GSM674376     3  0.3869    -0.8147 0.000 0.000 0.500 0.500 0.000 0.000
#> GSM674377     4  0.3862     0.8708 0.000 0.000 0.476 0.524 0.000 0.000
#> GSM674378     3  0.3695    -0.2912 0.000 0.000 0.624 0.376 0.000 0.000
#> GSM674383     3  0.2048     0.5904 0.000 0.000 0.880 0.120 0.000 0.000
#> GSM674386     4  0.3847     0.8970 0.000 0.000 0.456 0.544 0.000 0.000
#> GSM674387     4  0.3869     0.7965 0.000 0.000 0.500 0.500 0.000 0.000
#> GSM674392     3  0.2340     0.5568 0.000 0.000 0.852 0.148 0.000 0.000
#> GSM674396     4  0.3838     0.9004 0.000 0.000 0.448 0.552 0.000 0.000
#> GSM674399     4  0.3828     0.8990 0.000 0.000 0.440 0.560 0.000 0.000
#> GSM674404     4  0.3828     0.8982 0.000 0.000 0.440 0.560 0.000 0.000
#> GSM674182     2  0.3843    -0.2753 0.000 0.548 0.000 0.000 0.000 0.452
#> GSM674188     2  0.1814     0.8055 0.000 0.900 0.000 0.000 0.000 0.100
#> GSM674189     6  0.3817     0.6408 0.000 0.432 0.000 0.000 0.000 0.568
#> GSM674196     2  0.0146     0.8703 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674197     2  0.0000     0.8714 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674199     2  0.0000     0.8714 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674207     2  0.0000     0.8714 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674211     2  0.0000     0.8714 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674213     2  0.0363     0.8692 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM674215     6  0.3672     0.7692 0.000 0.368 0.000 0.000 0.000 0.632
#> GSM674216     2  0.0000     0.8714 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674217     2  0.3126     0.5428 0.000 0.752 0.000 0.000 0.000 0.248
#> GSM674222     2  0.0790     0.8529 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM674224     2  0.0363     0.8690 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM674227     2  0.0865     0.8557 0.000 0.964 0.000 0.000 0.000 0.036
#> GSM674228     2  0.0790     0.8597 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM674233     2  0.3175     0.5279 0.000 0.744 0.000 0.000 0.000 0.256
#> GSM674238     6  0.3076     0.8280 0.000 0.240 0.000 0.000 0.000 0.760
#> GSM674241     2  0.0000     0.8714 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674283     1  0.0146     0.8350 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM674286     1  0.0000     0.8355 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674293     1  0.2605     0.7768 0.884 0.000 0.000 0.064 0.012 0.040
#> GSM674294     1  0.0000     0.8355 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674296     1  0.0000     0.8355 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674303     1  0.1411     0.8094 0.936 0.000 0.000 0.004 0.060 0.000
#> GSM674307     1  0.0000     0.8355 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674310     5  0.0547     0.8828 0.020 0.000 0.000 0.000 0.980 0.000
#> GSM674311     1  0.3862     0.4324 0.608 0.000 0.000 0.004 0.388 0.000
#> GSM674312     5  0.2103     0.8653 0.020 0.000 0.000 0.056 0.912 0.012
#> GSM674317     1  0.0692     0.8311 0.976 0.000 0.000 0.004 0.020 0.000
#> GSM674319     5  0.4201     0.7426 0.204 0.000 0.000 0.056 0.732 0.008
#> GSM674321     5  0.1501     0.8690 0.076 0.000 0.000 0.000 0.924 0.000
#> GSM674322     5  0.0547     0.8828 0.020 0.000 0.000 0.000 0.980 0.000
#> GSM674326     5  0.0547     0.8828 0.020 0.000 0.000 0.000 0.980 0.000
#> GSM674329     5  0.2831     0.8658 0.064 0.000 0.000 0.048 0.872 0.016
#> GSM674333     5  0.0806     0.8827 0.020 0.000 0.000 0.008 0.972 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-SD-hclust-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-SD-hclust-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-SD-hclust-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-SD-hclust-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-SD-hclust-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-SD-hclust-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-SD-hclust-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-SD-hclust-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-SD-hclust-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-SD-hclust-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-SD-hclust-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-SD-hclust-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-SD-hclust-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-SD-hclust-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-SD-hclust-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-SD-hclust-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-SD-hclust-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-SD-hclust-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-SD-hclust-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-SD-hclust-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk SD-hclust-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-SD-hclust-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-SD-hclust-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-SD-hclust-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-SD-hclust-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-SD-hclust-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk SD-hclust-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>             n disease.state(p) specimen(p) k
#> SD:hclust 183            0.924    1.83e-40 2
#> SD:hclust 183            0.962    6.15e-78 3
#> SD:hclust 173            0.286    1.11e-71 4
#> SD:hclust 161            0.415    8.49e-65 5
#> SD:hclust 148            0.578    1.09e-57 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


SD:kmeans**

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["SD", "kmeans"]
# you can also extract it by
# res = res_list["SD:kmeans"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#>   Subgroups are detected by 'kmeans' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 2.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk SD-kmeans-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk SD-kmeans-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 0.702           0.982       0.898         0.4830 0.750   0.571
#> 4 4 0.815           0.874       0.823         0.1285 1.000   1.000
#> 5 5 0.766           0.766       0.724         0.0732 0.941   0.822
#> 6 6 0.728           0.638       0.659         0.0473 0.873   0.557

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 2

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette    p1    p2    p3
#> GSM674344     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674346     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674347     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674348     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674349     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674350     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674353     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674354     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674355     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674356     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674357     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674358     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674361     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674363     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674364     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674365     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674366     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674367     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674368     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674370     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674371     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674373     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674375     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674379     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674380     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674381     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674382     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674384     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674385     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674388     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674389     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674390     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674391     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674393     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674394     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674395     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674397     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674398     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674400     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674401     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674402     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674403     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674405     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674406     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674407     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674181     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674183     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674184     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674185     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674186     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674187     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674190     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674191     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674192     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674193     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674194     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674195     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674198     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674200     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674201     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674202     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674203     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674204     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674205     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674206     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674208     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674209     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674210     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674212     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674214     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674218     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674219     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674220     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674221     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674223     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674225     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674226     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674229     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674230     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674231     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674232     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674234     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674235     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674236     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674237     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674239     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674240     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674242     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674243     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674244     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674245     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674282     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674284     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674285     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674287     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674288     1  0.4062      0.930 0.836 0.164 0.000
#> GSM674289     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674290     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674291     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674292     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674295     1  0.4605      0.920 0.796 0.204 0.000
#> GSM674297     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674298     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674299     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674300     1  0.2711      0.938 0.912 0.088 0.000
#> GSM674301     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674302     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674304     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674305     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674306     1  0.2711      0.938 0.912 0.088 0.000
#> GSM674308     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674309     1  0.1529      0.948 0.960 0.040 0.000
#> GSM674313     1  0.4842      0.913 0.776 0.224 0.000
#> GSM674314     1  0.4504      0.922 0.804 0.196 0.000
#> GSM674315     1  0.2711      0.938 0.912 0.088 0.000
#> GSM674316     1  0.4062      0.930 0.836 0.164 0.000
#> GSM674318     1  0.4504      0.922 0.804 0.196 0.000
#> GSM674320     1  0.4605      0.920 0.796 0.204 0.000
#> GSM674323     1  0.4504      0.922 0.804 0.196 0.000
#> GSM674324     1  0.0747      0.948 0.984 0.016 0.000
#> GSM674325     1  0.4062      0.930 0.836 0.164 0.000
#> GSM674327     1  0.4842      0.913 0.776 0.224 0.000
#> GSM674328     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674330     1  0.4062      0.930 0.836 0.164 0.000
#> GSM674331     1  0.1289      0.948 0.968 0.032 0.000
#> GSM674332     1  0.1529      0.948 0.960 0.040 0.000
#> GSM674334     1  0.4062      0.930 0.836 0.164 0.000
#> GSM674335     1  0.4062      0.930 0.836 0.164 0.000
#> GSM674345     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674351     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674352     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674359     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674360     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674362     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674369     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674372     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674374     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674376     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674377     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674378     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674383     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674386     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674387     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674392     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674396     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674399     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674404     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674182     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674188     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674189     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674196     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674197     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674199     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674207     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674211     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674213     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674215     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674216     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674217     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674222     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674224     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674227     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674228     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674233     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674238     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674241     2  0.4842      1.000 0.000 0.776 0.224
#> GSM674283     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674286     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674293     1  0.2066      0.936 0.940 0.060 0.000
#> GSM674294     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674296     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674303     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674307     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674310     1  0.4504      0.922 0.804 0.196 0.000
#> GSM674311     1  0.1529      0.948 0.960 0.040 0.000
#> GSM674312     1  0.4235      0.927 0.824 0.176 0.000
#> GSM674317     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674319     1  0.4062      0.930 0.836 0.164 0.000
#> GSM674321     1  0.4504      0.922 0.804 0.196 0.000
#> GSM674322     1  0.4062      0.930 0.836 0.164 0.000
#> GSM674326     1  0.4605      0.920 0.796 0.204 0.000
#> GSM674329     1  0.4504      0.922 0.804 0.196 0.000
#> GSM674333     1  0.4062      0.930 0.836 0.164 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1    p2    p3    p4
#> GSM674344     3  0.3975      0.899 0.000 0.000 0.760 0.240
#> GSM674346     3  0.3975      0.899 0.000 0.000 0.760 0.240
#> GSM674347     3  0.1637      0.910 0.000 0.000 0.940 0.060
#> GSM674348     3  0.3873      0.901 0.000 0.000 0.772 0.228
#> GSM674349     3  0.3764      0.903 0.000 0.000 0.784 0.216
#> GSM674350     3  0.3649      0.905 0.000 0.000 0.796 0.204
#> GSM674353     3  0.3688      0.904 0.000 0.000 0.792 0.208
#> GSM674354     3  0.3975      0.899 0.000 0.000 0.760 0.240
#> GSM674355     3  0.3801      0.903 0.000 0.000 0.780 0.220
#> GSM674356     3  0.3907      0.901 0.000 0.000 0.768 0.232
#> GSM674357     3  0.3975      0.899 0.000 0.000 0.760 0.240
#> GSM674358     3  0.3649      0.905 0.000 0.000 0.796 0.204
#> GSM674361     3  0.3688      0.904 0.000 0.000 0.792 0.208
#> GSM674363     3  0.3907      0.901 0.000 0.000 0.768 0.232
#> GSM674364     3  0.3975      0.899 0.000 0.000 0.760 0.240
#> GSM674365     3  0.3942      0.899 0.000 0.000 0.764 0.236
#> GSM674366     3  0.2530      0.911 0.000 0.000 0.888 0.112
#> GSM674367     3  0.0000      0.902 0.000 0.000 1.000 0.000
#> GSM674368     3  0.3975      0.899 0.000 0.000 0.760 0.240
#> GSM674370     3  0.2814      0.911 0.000 0.000 0.868 0.132
#> GSM674371     3  0.3726      0.904 0.000 0.000 0.788 0.212
#> GSM674373     3  0.2149      0.910 0.000 0.000 0.912 0.088
#> GSM674375     3  0.0000      0.902 0.000 0.000 1.000 0.000
#> GSM674379     3  0.0000      0.902 0.000 0.000 1.000 0.000
#> GSM674380     3  0.1118      0.904 0.000 0.000 0.964 0.036
#> GSM674381     3  0.1118      0.904 0.000 0.000 0.964 0.036
#> GSM674382     3  0.0000      0.902 0.000 0.000 1.000 0.000
#> GSM674384     3  0.0336      0.903 0.000 0.000 0.992 0.008
#> GSM674385     3  0.3907      0.900 0.000 0.000 0.768 0.232
#> GSM674388     3  0.3942      0.899 0.000 0.000 0.764 0.236
#> GSM674389     3  0.0000      0.902 0.000 0.000 1.000 0.000
#> GSM674390     3  0.0000      0.902 0.000 0.000 1.000 0.000
#> GSM674391     3  0.0000      0.902 0.000 0.000 1.000 0.000
#> GSM674393     3  0.0000      0.902 0.000 0.000 1.000 0.000
#> GSM674394     3  0.2345      0.912 0.000 0.000 0.900 0.100
#> GSM674395     3  0.1022      0.904 0.000 0.000 0.968 0.032
#> GSM674397     3  0.2469      0.912 0.000 0.000 0.892 0.108
#> GSM674398     3  0.0000      0.902 0.000 0.000 1.000 0.000
#> GSM674400     3  0.0188      0.901 0.000 0.000 0.996 0.004
#> GSM674401     3  0.0188      0.901 0.000 0.000 0.996 0.004
#> GSM674402     3  0.4008      0.898 0.000 0.000 0.756 0.244
#> GSM674403     3  0.3942      0.900 0.000 0.000 0.764 0.236
#> GSM674405     3  0.0000      0.902 0.000 0.000 1.000 0.000
#> GSM674406     3  0.0336      0.903 0.000 0.000 0.992 0.008
#> GSM674407     3  0.0336      0.903 0.000 0.000 0.992 0.008
#> GSM674181     2  0.2334      0.843 0.000 0.908 0.088 0.004
#> GSM674183     2  0.2843      0.840 0.000 0.892 0.088 0.020
#> GSM674184     2  0.3421      0.842 0.000 0.868 0.088 0.044
#> GSM674185     2  0.2843      0.839 0.000 0.892 0.088 0.020
#> GSM674186     2  0.3894      0.852 0.000 0.844 0.088 0.068
#> GSM674187     2  0.3745      0.851 0.000 0.852 0.088 0.060
#> GSM674190     2  0.2843      0.850 0.000 0.892 0.088 0.020
#> GSM674191     2  0.2334      0.843 0.000 0.908 0.088 0.004
#> GSM674192     2  0.6617      0.828 0.000 0.532 0.088 0.380
#> GSM674193     2  0.6635      0.827 0.000 0.524 0.088 0.388
#> GSM674194     2  0.3745      0.846 0.000 0.852 0.088 0.060
#> GSM674195     2  0.3333      0.840 0.000 0.872 0.088 0.040
#> GSM674198     2  0.6607      0.828 0.000 0.536 0.088 0.376
#> GSM674200     2  0.2949      0.839 0.000 0.888 0.088 0.024
#> GSM674201     2  0.2610      0.842 0.000 0.900 0.088 0.012
#> GSM674202     2  0.3894      0.849 0.000 0.844 0.088 0.068
#> GSM674203     2  0.6562      0.828 0.000 0.552 0.088 0.360
#> GSM674204     2  0.6536      0.829 0.000 0.560 0.088 0.352
#> GSM674205     2  0.6607      0.828 0.000 0.536 0.088 0.376
#> GSM674206     2  0.2480      0.842 0.000 0.904 0.088 0.008
#> GSM674208     2  0.6607      0.828 0.000 0.536 0.088 0.376
#> GSM674209     2  0.6508      0.838 0.000 0.568 0.088 0.344
#> GSM674210     2  0.6617      0.828 0.000 0.532 0.088 0.380
#> GSM674212     2  0.6523      0.829 0.000 0.564 0.088 0.348
#> GSM674214     2  0.6617      0.828 0.000 0.532 0.088 0.380
#> GSM674218     2  0.3243      0.841 0.000 0.876 0.088 0.036
#> GSM674219     2  0.2334      0.843 0.000 0.908 0.088 0.004
#> GSM674220     2  0.2843      0.839 0.000 0.892 0.088 0.020
#> GSM674221     2  0.2730      0.849 0.000 0.896 0.088 0.016
#> GSM674223     2  0.6523      0.829 0.000 0.564 0.088 0.348
#> GSM674225     2  0.4236      0.851 0.000 0.824 0.088 0.088
#> GSM674226     2  0.6375      0.839 0.000 0.600 0.088 0.312
#> GSM674229     2  0.6536      0.829 0.000 0.560 0.088 0.352
#> GSM674230     2  0.3333      0.852 0.000 0.872 0.088 0.040
#> GSM674231     2  0.6523      0.837 0.000 0.564 0.088 0.348
#> GSM674232     2  0.6607      0.828 0.000 0.536 0.088 0.376
#> GSM674234     2  0.6607      0.828 0.000 0.536 0.088 0.376
#> GSM674235     2  0.3333      0.852 0.000 0.872 0.088 0.040
#> GSM674236     2  0.4236      0.852 0.000 0.824 0.088 0.088
#> GSM674237     2  0.6617      0.828 0.000 0.532 0.088 0.380
#> GSM674239     2  0.6523      0.829 0.000 0.564 0.088 0.348
#> GSM674240     2  0.2480      0.846 0.000 0.904 0.088 0.008
#> GSM674242     2  0.6562      0.828 0.000 0.552 0.088 0.360
#> GSM674243     2  0.6523      0.829 0.000 0.564 0.088 0.348
#> GSM674244     2  0.4036      0.848 0.000 0.836 0.088 0.076
#> GSM674245     2  0.6336      0.841 0.000 0.608 0.088 0.304
#> GSM674282     1  0.0188      0.899 0.996 0.004 0.000 0.000
#> GSM674284     1  0.0592      0.900 0.984 0.016 0.000 0.000
#> GSM674285     1  0.0188      0.899 0.996 0.004 0.000 0.000
#> GSM674287     1  0.0188      0.899 0.996 0.004 0.000 0.000
#> GSM674288     1  0.5085      0.865 0.708 0.032 0.000 0.260
#> GSM674289     1  0.0188      0.899 0.996 0.004 0.000 0.000
#> GSM674290     1  0.0188      0.899 0.996 0.004 0.000 0.000
#> GSM674291     1  0.0188      0.899 0.996 0.004 0.000 0.000
#> GSM674292     1  0.0188      0.899 0.996 0.004 0.000 0.000
#> GSM674295     1  0.5277      0.853 0.668 0.028 0.000 0.304
#> GSM674297     1  0.0592      0.899 0.984 0.016 0.000 0.000
#> GSM674298     1  0.0592      0.899 0.984 0.016 0.000 0.000
#> GSM674299     1  0.0707      0.900 0.980 0.020 0.000 0.000
#> GSM674300     1  0.3858      0.885 0.844 0.056 0.000 0.100
#> GSM674301     1  0.0188      0.899 0.996 0.004 0.000 0.000
#> GSM674302     1  0.0188      0.899 0.996 0.004 0.000 0.000
#> GSM674304     1  0.0188      0.899 0.996 0.004 0.000 0.000
#> GSM674305     1  0.0188      0.899 0.996 0.004 0.000 0.000
#> GSM674306     1  0.3778      0.885 0.848 0.052 0.000 0.100
#> GSM674308     1  0.0188      0.899 0.996 0.004 0.000 0.000
#> GSM674309     1  0.2915      0.898 0.892 0.028 0.000 0.080
#> GSM674313     1  0.5814      0.842 0.644 0.056 0.000 0.300
#> GSM674314     1  0.5321      0.858 0.672 0.032 0.000 0.296
#> GSM674315     1  0.3778      0.885 0.848 0.052 0.000 0.100
#> GSM674316     1  0.4535      0.863 0.704 0.004 0.000 0.292
#> GSM674318     1  0.4585      0.852 0.668 0.000 0.000 0.332
#> GSM674320     1  0.5152      0.850 0.664 0.020 0.000 0.316
#> GSM674323     1  0.4585      0.852 0.668 0.000 0.000 0.332
#> GSM674324     1  0.1837      0.900 0.944 0.028 0.000 0.028
#> GSM674325     1  0.4382      0.862 0.704 0.000 0.000 0.296
#> GSM674327     1  0.5764      0.846 0.644 0.052 0.000 0.304
#> GSM674328     1  0.0707      0.899 0.980 0.020 0.000 0.000
#> GSM674330     1  0.5022      0.866 0.708 0.028 0.000 0.264
#> GSM674331     1  0.2214      0.900 0.928 0.028 0.000 0.044
#> GSM674332     1  0.2915      0.898 0.892 0.028 0.000 0.080
#> GSM674334     1  0.4993      0.867 0.712 0.028 0.000 0.260
#> GSM674335     1  0.5143      0.865 0.708 0.036 0.000 0.256
#> GSM674345     3  0.3801      0.903 0.000 0.000 0.780 0.220
#> GSM674351     3  0.3726      0.904 0.000 0.000 0.788 0.212
#> GSM674352     3  0.3649      0.905 0.000 0.000 0.796 0.204
#> GSM674359     3  0.3975      0.899 0.000 0.000 0.760 0.240
#> GSM674360     3  0.3942      0.899 0.000 0.000 0.764 0.236
#> GSM674362     3  0.3975      0.899 0.000 0.000 0.760 0.240
#> GSM674369     3  0.3942      0.899 0.000 0.000 0.764 0.236
#> GSM674372     3  0.0336      0.903 0.000 0.000 0.992 0.008
#> GSM674374     3  0.1792      0.910 0.000 0.000 0.932 0.068
#> GSM674376     3  0.0000      0.902 0.000 0.000 1.000 0.000
#> GSM674377     3  0.0336      0.903 0.000 0.000 0.992 0.008
#> GSM674378     3  0.0336      0.903 0.000 0.000 0.992 0.008
#> GSM674383     3  0.3942      0.899 0.000 0.000 0.764 0.236
#> GSM674386     3  0.0000      0.902 0.000 0.000 1.000 0.000
#> GSM674387     3  0.0000      0.902 0.000 0.000 1.000 0.000
#> GSM674392     3  0.2760      0.911 0.000 0.000 0.872 0.128
#> GSM674396     3  0.0000      0.902 0.000 0.000 1.000 0.000
#> GSM674399     3  0.0000      0.902 0.000 0.000 1.000 0.000
#> GSM674404     3  0.0188      0.902 0.000 0.000 0.996 0.004
#> GSM674182     2  0.2334      0.843 0.000 0.908 0.088 0.004
#> GSM674188     2  0.3894      0.850 0.000 0.844 0.088 0.068
#> GSM674189     2  0.3667      0.843 0.000 0.856 0.088 0.056
#> GSM674196     2  0.6574      0.829 0.000 0.548 0.088 0.364
#> GSM674197     2  0.6562      0.828 0.000 0.552 0.088 0.360
#> GSM674199     2  0.6607      0.828 0.000 0.536 0.088 0.376
#> GSM674207     2  0.6607      0.828 0.000 0.536 0.088 0.376
#> GSM674211     2  0.6607      0.828 0.000 0.536 0.088 0.376
#> GSM674213     2  0.2480      0.846 0.000 0.904 0.088 0.008
#> GSM674215     2  0.2843      0.839 0.000 0.892 0.088 0.020
#> GSM674216     2  0.6635      0.827 0.000 0.524 0.088 0.388
#> GSM674217     2  0.2334      0.846 0.000 0.908 0.088 0.004
#> GSM674222     2  0.4236      0.851 0.000 0.824 0.088 0.088
#> GSM674224     2  0.6494      0.838 0.000 0.572 0.088 0.340
#> GSM674227     2  0.5681      0.849 0.000 0.704 0.088 0.208
#> GSM674228     2  0.3667      0.853 0.000 0.856 0.088 0.056
#> GSM674233     2  0.2480      0.846 0.000 0.904 0.088 0.008
#> GSM674238     2  0.3333      0.840 0.000 0.872 0.088 0.040
#> GSM674241     2  0.6607      0.828 0.000 0.536 0.088 0.376
#> GSM674283     1  0.0188      0.899 0.996 0.004 0.000 0.000
#> GSM674286     1  0.0188      0.899 0.996 0.004 0.000 0.000
#> GSM674293     1  0.2546      0.885 0.912 0.028 0.000 0.060
#> GSM674294     1  0.0188      0.899 0.996 0.004 0.000 0.000
#> GSM674296     1  0.0188      0.899 0.996 0.004 0.000 0.000
#> GSM674303     1  0.0921      0.899 0.972 0.028 0.000 0.000
#> GSM674307     1  0.0188      0.899 0.996 0.004 0.000 0.000
#> GSM674310     1  0.4585      0.852 0.668 0.000 0.000 0.332
#> GSM674311     1  0.2915      0.898 0.892 0.028 0.000 0.080
#> GSM674312     1  0.4988      0.860 0.692 0.020 0.000 0.288
#> GSM674317     1  0.0592      0.900 0.984 0.016 0.000 0.000
#> GSM674319     1  0.5050      0.863 0.704 0.028 0.000 0.268
#> GSM674321     1  0.4585      0.852 0.668 0.000 0.000 0.332
#> GSM674322     1  0.4382      0.862 0.704 0.000 0.000 0.296
#> GSM674326     1  0.4605      0.851 0.664 0.000 0.000 0.336
#> GSM674329     1  0.5130      0.852 0.668 0.020 0.000 0.312
#> GSM674333     1  0.4382      0.862 0.704 0.000 0.000 0.296

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3 p4    p5
#> GSM674344     3  0.1579      0.808 0.000 0.032 0.944 NA 0.024
#> GSM674346     3  0.1668      0.808 0.000 0.032 0.940 NA 0.028
#> GSM674347     3  0.5600      0.827 0.000 0.032 0.636 NA 0.048
#> GSM674348     3  0.3089      0.810 0.000 0.032 0.880 NA 0.040
#> GSM674349     3  0.2515      0.813 0.000 0.032 0.908 NA 0.040
#> GSM674350     3  0.2829      0.815 0.000 0.032 0.892 NA 0.024
#> GSM674353     3  0.2269      0.814 0.000 0.032 0.920 NA 0.028
#> GSM674354     3  0.1753      0.809 0.000 0.032 0.936 NA 0.032
#> GSM674355     3  0.2082      0.814 0.000 0.032 0.928 NA 0.024
#> GSM674356     3  0.1168      0.811 0.000 0.032 0.960 NA 0.008
#> GSM674357     3  0.1579      0.810 0.000 0.032 0.944 NA 0.024
#> GSM674358     3  0.2450      0.816 0.000 0.032 0.912 NA 0.028
#> GSM674361     3  0.2269      0.814 0.000 0.032 0.920 NA 0.028
#> GSM674363     3  0.1739      0.811 0.000 0.032 0.940 NA 0.024
#> GSM674364     3  0.2278      0.809 0.000 0.032 0.908 NA 0.060
#> GSM674365     3  0.3219      0.807 0.000 0.032 0.872 NA 0.060
#> GSM674366     3  0.5182      0.829 0.000 0.032 0.704 NA 0.048
#> GSM674367     3  0.5361      0.812 0.000 0.032 0.532 NA 0.012
#> GSM674368     3  0.2278      0.808 0.000 0.032 0.908 NA 0.060
#> GSM674370     3  0.4959      0.834 0.000 0.032 0.704 NA 0.028
#> GSM674371     3  0.3236      0.811 0.000 0.032 0.872 NA 0.044
#> GSM674373     3  0.5081      0.830 0.000 0.032 0.664 NA 0.020
#> GSM674375     3  0.5390      0.806 0.000 0.032 0.504 NA 0.012
#> GSM674379     3  0.5272      0.808 0.000 0.032 0.528 NA 0.008
#> GSM674380     3  0.5439      0.822 0.000 0.032 0.596 NA 0.024
#> GSM674381     3  0.6021      0.820 0.000 0.032 0.548 NA 0.056
#> GSM674382     3  0.5433      0.810 0.000 0.032 0.540 NA 0.016
#> GSM674384     3  0.5479      0.819 0.000 0.032 0.556 NA 0.020
#> GSM674385     3  0.3445      0.811 0.000 0.032 0.860 NA 0.060
#> GSM674388     3  0.2875      0.810 0.000 0.032 0.888 NA 0.060
#> GSM674389     3  0.5631      0.806 0.000 0.032 0.504 NA 0.024
#> GSM674390     3  0.5295      0.806 0.000 0.032 0.504 NA 0.008
#> GSM674391     3  0.5451      0.809 0.000 0.032 0.528 NA 0.016
#> GSM674393     3  0.5881      0.810 0.000 0.032 0.512 NA 0.040
#> GSM674394     3  0.5166      0.834 0.000 0.032 0.680 NA 0.032
#> GSM674395     3  0.5012      0.821 0.000 0.032 0.600 NA 0.004
#> GSM674397     3  0.4849      0.834 0.000 0.032 0.712 NA 0.024
#> GSM674398     3  0.5631      0.805 0.000 0.032 0.504 NA 0.024
#> GSM674400     3  0.6058      0.812 0.000 0.032 0.532 NA 0.056
#> GSM674401     3  0.6058      0.812 0.000 0.032 0.532 NA 0.056
#> GSM674402     3  0.2515      0.809 0.000 0.032 0.908 NA 0.040
#> GSM674403     3  0.3016      0.816 0.000 0.032 0.884 NA 0.044
#> GSM674405     3  0.5603      0.808 0.000 0.032 0.528 NA 0.024
#> GSM674406     3  0.5088      0.815 0.000 0.032 0.572 NA 0.004
#> GSM674407     3  0.5106      0.814 0.000 0.032 0.564 NA 0.004
#> GSM674181     2  0.1549      0.738 0.000 0.944 0.000 NA 0.016
#> GSM674183     2  0.1121      0.735 0.000 0.956 0.000 NA 0.000
#> GSM674184     2  0.2208      0.736 0.000 0.908 0.000 NA 0.020
#> GSM674185     2  0.1121      0.735 0.000 0.956 0.000 NA 0.000
#> GSM674186     2  0.3912      0.696 0.000 0.804 0.000 NA 0.088
#> GSM674187     2  0.3946      0.669 0.000 0.800 0.000 NA 0.120
#> GSM674190     2  0.2726      0.733 0.000 0.884 0.000 NA 0.052
#> GSM674191     2  0.1469      0.744 0.000 0.948 0.000 NA 0.016
#> GSM674192     5  0.4767      0.938 0.000 0.420 0.000 NA 0.560
#> GSM674193     2  0.5968     -0.714 0.000 0.448 0.000 NA 0.444
#> GSM674194     2  0.3307      0.717 0.000 0.844 0.000 NA 0.052
#> GSM674195     2  0.2046      0.737 0.000 0.916 0.000 NA 0.016
#> GSM674198     5  0.4227      0.951 0.000 0.420 0.000 NA 0.580
#> GSM674200     2  0.1121      0.735 0.000 0.956 0.000 NA 0.000
#> GSM674201     2  0.1195      0.740 0.000 0.960 0.000 NA 0.012
#> GSM674202     2  0.4020      0.670 0.000 0.796 0.000 NA 0.096
#> GSM674203     5  0.4256      0.948 0.000 0.436 0.000 NA 0.564
#> GSM674204     5  0.4287      0.921 0.000 0.460 0.000 NA 0.540
#> GSM674205     5  0.4235      0.952 0.000 0.424 0.000 NA 0.576
#> GSM674206     2  0.1012      0.743 0.000 0.968 0.000 NA 0.012
#> GSM674208     5  0.4235      0.952 0.000 0.424 0.000 NA 0.576
#> GSM674209     2  0.5913     -0.435 0.000 0.524 0.000 NA 0.364
#> GSM674210     5  0.4227      0.951 0.000 0.420 0.000 NA 0.580
#> GSM674212     5  0.4291      0.914 0.000 0.464 0.000 NA 0.536
#> GSM674214     5  0.4227      0.951 0.000 0.420 0.000 NA 0.580
#> GSM674218     2  0.2208      0.736 0.000 0.908 0.000 NA 0.020
#> GSM674219     2  0.0566      0.746 0.000 0.984 0.000 NA 0.012
#> GSM674220     2  0.1043      0.742 0.000 0.960 0.000 NA 0.000
#> GSM674221     2  0.1764      0.730 0.000 0.928 0.000 NA 0.064
#> GSM674223     5  0.4827      0.887 0.000 0.476 0.000 NA 0.504
#> GSM674225     2  0.3888      0.687 0.000 0.804 0.000 NA 0.076
#> GSM674226     2  0.5700     -0.548 0.000 0.532 0.000 NA 0.380
#> GSM674229     5  0.4653      0.898 0.000 0.472 0.000 NA 0.516
#> GSM674230     2  0.3301      0.700 0.000 0.848 0.000 NA 0.072
#> GSM674231     2  0.5968     -0.482 0.000 0.512 0.000 NA 0.372
#> GSM674232     5  0.4696      0.936 0.000 0.428 0.000 NA 0.556
#> GSM674234     5  0.5003      0.919 0.000 0.424 0.000 NA 0.544
#> GSM674235     2  0.3242      0.700 0.000 0.852 0.000 NA 0.076
#> GSM674236     2  0.4172      0.654 0.000 0.784 0.000 NA 0.108
#> GSM674237     5  0.4227      0.951 0.000 0.420 0.000 NA 0.580
#> GSM674239     5  0.4287      0.921 0.000 0.460 0.000 NA 0.540
#> GSM674240     2  0.1403      0.742 0.000 0.952 0.000 NA 0.024
#> GSM674242     5  0.4256      0.948 0.000 0.436 0.000 NA 0.564
#> GSM674243     5  0.4821      0.906 0.000 0.464 0.000 NA 0.516
#> GSM674244     2  0.3719      0.695 0.000 0.816 0.000 NA 0.068
#> GSM674245     2  0.5645     -0.500 0.000 0.540 0.000 NA 0.376
#> GSM674282     1  0.0162      0.840 0.996 0.000 0.004 NA 0.000
#> GSM674284     1  0.1410      0.841 0.940 0.000 0.000 NA 0.060
#> GSM674285     1  0.0162      0.840 0.996 0.000 0.004 NA 0.000
#> GSM674287     1  0.1043      0.841 0.960 0.000 0.000 NA 0.040
#> GSM674288     1  0.6220      0.794 0.564 0.000 0.004 NA 0.180
#> GSM674289     1  0.0162      0.840 0.996 0.000 0.004 NA 0.000
#> GSM674290     1  0.0162      0.840 0.996 0.000 0.004 NA 0.000
#> GSM674291     1  0.0162      0.840 0.996 0.000 0.004 NA 0.000
#> GSM674292     1  0.0162      0.840 0.996 0.000 0.004 NA 0.000
#> GSM674295     1  0.6406      0.783 0.536 0.000 0.008 NA 0.168
#> GSM674297     1  0.0963      0.841 0.964 0.000 0.000 NA 0.036
#> GSM674298     1  0.0963      0.841 0.964 0.000 0.000 NA 0.036
#> GSM674299     1  0.1410      0.841 0.940 0.000 0.000 NA 0.060
#> GSM674300     1  0.5077      0.819 0.728 0.000 0.020 NA 0.168
#> GSM674301     1  0.0162      0.840 0.996 0.000 0.004 NA 0.000
#> GSM674302     1  0.0162      0.840 0.996 0.000 0.004 NA 0.000
#> GSM674304     1  0.0162      0.840 0.996 0.000 0.004 NA 0.000
#> GSM674305     1  0.0162      0.840 0.996 0.000 0.004 NA 0.000
#> GSM674306     1  0.4870      0.820 0.748 0.000 0.020 NA 0.152
#> GSM674308     1  0.0162      0.840 0.996 0.000 0.004 NA 0.000
#> GSM674309     1  0.4094      0.837 0.788 0.000 0.000 NA 0.128
#> GSM674313     1  0.6861      0.762 0.508 0.000 0.024 NA 0.188
#> GSM674314     1  0.6255      0.789 0.540 0.000 0.000 NA 0.208
#> GSM674315     1  0.4870      0.820 0.748 0.000 0.020 NA 0.152
#> GSM674316     1  0.5796      0.790 0.572 0.000 0.000 NA 0.116
#> GSM674318     1  0.5873      0.777 0.540 0.000 0.000 NA 0.112
#> GSM674320     1  0.6175      0.775 0.536 0.000 0.008 NA 0.120
#> GSM674323     1  0.5873      0.777 0.540 0.000 0.000 NA 0.112
#> GSM674324     1  0.2813      0.841 0.868 0.000 0.000 NA 0.108
#> GSM674325     1  0.5744      0.786 0.564 0.000 0.000 NA 0.104
#> GSM674327     1  0.6858      0.768 0.508 0.000 0.020 NA 0.236
#> GSM674328     1  0.1478      0.841 0.936 0.000 0.000 NA 0.064
#> GSM674330     1  0.6053      0.797 0.576 0.000 0.000 NA 0.196
#> GSM674331     1  0.3427      0.840 0.836 0.000 0.000 NA 0.108
#> GSM674332     1  0.4049      0.838 0.792 0.000 0.000 NA 0.124
#> GSM674334     1  0.5981      0.800 0.588 0.000 0.000 NA 0.196
#> GSM674335     1  0.6212      0.797 0.580 0.000 0.008 NA 0.172
#> GSM674345     3  0.1682      0.814 0.000 0.032 0.944 NA 0.012
#> GSM674351     3  0.2269      0.814 0.000 0.032 0.920 NA 0.028
#> GSM674352     3  0.2899      0.815 0.000 0.032 0.888 NA 0.024
#> GSM674359     3  0.1485      0.809 0.000 0.032 0.948 NA 0.020
#> GSM674360     3  0.3219      0.807 0.000 0.032 0.872 NA 0.060
#> GSM674362     3  0.2829      0.805 0.000 0.032 0.892 NA 0.052
#> GSM674369     3  0.2778      0.808 0.000 0.032 0.892 NA 0.060
#> GSM674372     3  0.5741      0.819 0.000 0.032 0.556 NA 0.036
#> GSM674374     3  0.5142      0.831 0.000 0.032 0.652 NA 0.020
#> GSM674376     3  0.5295      0.806 0.000 0.032 0.504 NA 0.008
#> GSM674377     3  0.5821      0.812 0.000 0.032 0.512 NA 0.036
#> GSM674378     3  0.5068      0.817 0.000 0.032 0.580 NA 0.004
#> GSM674383     3  0.3165      0.810 0.000 0.032 0.876 NA 0.048
#> GSM674386     3  0.5701      0.805 0.000 0.032 0.504 NA 0.028
#> GSM674387     3  0.5166      0.808 0.000 0.032 0.528 NA 0.004
#> GSM674392     3  0.4636      0.832 0.000 0.032 0.752 NA 0.032
#> GSM674396     3  0.5631      0.805 0.000 0.032 0.504 NA 0.024
#> GSM674399     3  0.5672      0.808 0.000 0.032 0.528 NA 0.028
#> GSM674404     3  0.5643      0.811 0.000 0.032 0.544 NA 0.028
#> GSM674182     2  0.1300      0.742 0.000 0.956 0.000 NA 0.016
#> GSM674188     2  0.3916      0.676 0.000 0.804 0.000 NA 0.104
#> GSM674189     2  0.3365      0.719 0.000 0.836 0.000 NA 0.044
#> GSM674196     5  0.4262      0.945 0.000 0.440 0.000 NA 0.560
#> GSM674197     5  0.4256      0.948 0.000 0.436 0.000 NA 0.564
#> GSM674199     5  0.4227      0.951 0.000 0.420 0.000 NA 0.580
#> GSM674207     5  0.4227      0.951 0.000 0.420 0.000 NA 0.580
#> GSM674211     5  0.4227      0.951 0.000 0.420 0.000 NA 0.580
#> GSM674213     2  0.1484      0.741 0.000 0.944 0.000 NA 0.048
#> GSM674215     2  0.1121      0.743 0.000 0.956 0.000 NA 0.000
#> GSM674216     5  0.5677      0.820 0.000 0.424 0.000 NA 0.496
#> GSM674217     2  0.1043      0.742 0.000 0.960 0.000 NA 0.040
#> GSM674222     2  0.4123      0.659 0.000 0.788 0.000 NA 0.104
#> GSM674224     2  0.5861     -0.467 0.000 0.520 0.000 NA 0.376
#> GSM674227     2  0.5116      0.437 0.000 0.692 0.000 NA 0.188
#> GSM674228     2  0.3532      0.677 0.000 0.832 0.000 NA 0.092
#> GSM674233     2  0.1408      0.741 0.000 0.948 0.000 NA 0.044
#> GSM674238     2  0.1597      0.737 0.000 0.940 0.000 NA 0.012
#> GSM674241     5  0.4227      0.951 0.000 0.420 0.000 NA 0.580
#> GSM674283     1  0.0000      0.840 1.000 0.000 0.000 NA 0.000
#> GSM674286     1  0.0162      0.840 0.996 0.000 0.004 NA 0.000
#> GSM674293     1  0.2419      0.823 0.904 0.000 0.004 NA 0.064
#> GSM674294     1  0.0162      0.840 0.996 0.000 0.004 NA 0.000
#> GSM674296     1  0.0162      0.840 0.996 0.000 0.004 NA 0.000
#> GSM674303     1  0.1851      0.840 0.912 0.000 0.000 NA 0.088
#> GSM674307     1  0.0000      0.840 1.000 0.000 0.000 NA 0.000
#> GSM674310     1  0.5873      0.777 0.540 0.000 0.000 NA 0.112
#> GSM674311     1  0.4094      0.837 0.788 0.000 0.000 NA 0.128
#> GSM674312     1  0.6046      0.782 0.552 0.000 0.008 NA 0.108
#> GSM674317     1  0.1197      0.841 0.952 0.000 0.000 NA 0.048
#> GSM674319     1  0.6164      0.794 0.576 0.000 0.008 NA 0.148
#> GSM674321     1  0.5873      0.777 0.540 0.000 0.000 NA 0.112
#> GSM674322     1  0.5684      0.785 0.564 0.000 0.000 NA 0.096
#> GSM674326     1  0.5912      0.775 0.536 0.000 0.000 NA 0.116
#> GSM674329     1  0.6175      0.775 0.536 0.000 0.008 NA 0.120
#> GSM674333     1  0.5744      0.786 0.564 0.000 0.000 NA 0.104

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4    p5    p6
#> GSM674344     3  0.0508     0.7325 0.000 0.000 0.984 0.000 0.004 0.012
#> GSM674346     3  0.0508     0.7325 0.000 0.000 0.984 0.000 0.004 0.012
#> GSM674347     3  0.5813    -0.4210 0.000 0.000 0.544 0.332 0.068 0.056
#> GSM674348     3  0.2427     0.7231 0.000 0.000 0.900 0.032 0.032 0.036
#> GSM674349     3  0.2563     0.7197 0.000 0.000 0.892 0.028 0.044 0.036
#> GSM674350     3  0.3135     0.6865 0.000 0.000 0.856 0.068 0.028 0.048
#> GSM674353     3  0.2415     0.6994 0.000 0.000 0.900 0.040 0.024 0.036
#> GSM674354     3  0.1176     0.7261 0.000 0.000 0.956 0.000 0.024 0.020
#> GSM674355     3  0.2351     0.7028 0.000 0.000 0.904 0.032 0.028 0.036
#> GSM674356     3  0.1078     0.7336 0.000 0.000 0.964 0.008 0.016 0.012
#> GSM674357     3  0.1138     0.7278 0.000 0.000 0.960 0.004 0.024 0.012
#> GSM674358     3  0.2484     0.6982 0.000 0.000 0.896 0.044 0.024 0.036
#> GSM674361     3  0.2415     0.6994 0.000 0.000 0.900 0.040 0.024 0.036
#> GSM674363     3  0.1851     0.7148 0.000 0.000 0.928 0.012 0.024 0.036
#> GSM674364     3  0.1341     0.7329 0.000 0.000 0.948 0.000 0.024 0.028
#> GSM674365     3  0.3242     0.6989 0.000 0.000 0.848 0.024 0.060 0.068
#> GSM674366     3  0.5448     0.1673 0.000 0.000 0.640 0.232 0.060 0.068
#> GSM674367     4  0.5133     0.8683 0.000 0.000 0.412 0.524 0.044 0.020
#> GSM674368     3  0.2209     0.7231 0.000 0.000 0.904 0.004 0.040 0.052
#> GSM674370     3  0.5425    -0.0225 0.000 0.000 0.612 0.280 0.052 0.056
#> GSM674371     3  0.3351     0.7003 0.000 0.000 0.844 0.036 0.060 0.060
#> GSM674373     3  0.4876    -0.3773 0.000 0.000 0.596 0.348 0.036 0.020
#> GSM674375     4  0.4778     0.8815 0.000 0.000 0.400 0.556 0.012 0.032
#> GSM674379     4  0.4554     0.8864 0.000 0.000 0.400 0.568 0.024 0.008
#> GSM674380     3  0.5008    -0.7981 0.000 0.000 0.480 0.468 0.024 0.028
#> GSM674381     3  0.5668    -0.6513 0.000 0.000 0.480 0.420 0.044 0.056
#> GSM674382     4  0.4652     0.8862 0.000 0.000 0.404 0.560 0.024 0.012
#> GSM674384     4  0.5109     0.8440 0.000 0.000 0.424 0.516 0.028 0.032
#> GSM674385     3  0.2979     0.7077 0.000 0.000 0.868 0.036 0.044 0.052
#> GSM674388     3  0.2579     0.7151 0.000 0.000 0.884 0.008 0.048 0.060
#> GSM674389     4  0.5309     0.8774 0.000 0.000 0.392 0.532 0.036 0.040
#> GSM674390     4  0.4638     0.8819 0.000 0.000 0.392 0.572 0.016 0.020
#> GSM674391     4  0.4644     0.8859 0.000 0.000 0.400 0.564 0.024 0.012
#> GSM674393     4  0.5706     0.8459 0.000 0.000 0.404 0.492 0.048 0.056
#> GSM674394     3  0.5141    -0.0115 0.000 0.000 0.628 0.284 0.032 0.056
#> GSM674395     4  0.4652     0.8232 0.000 0.000 0.472 0.496 0.012 0.020
#> GSM674397     3  0.4735    -0.1652 0.000 0.000 0.632 0.312 0.040 0.016
#> GSM674398     4  0.4845     0.8838 0.000 0.000 0.392 0.560 0.032 0.016
#> GSM674400     4  0.5902     0.8083 0.000 0.000 0.408 0.472 0.064 0.056
#> GSM674401     4  0.5902     0.8083 0.000 0.000 0.408 0.472 0.064 0.056
#> GSM674402     3  0.2259     0.7264 0.000 0.000 0.908 0.020 0.032 0.040
#> GSM674403     3  0.3116     0.7045 0.000 0.000 0.860 0.044 0.052 0.044
#> GSM674405     4  0.4713     0.8872 0.000 0.000 0.400 0.560 0.028 0.012
#> GSM674406     4  0.4380     0.8666 0.000 0.000 0.436 0.544 0.012 0.008
#> GSM674407     4  0.4274     0.8700 0.000 0.000 0.432 0.552 0.012 0.004
#> GSM674181     6  0.4818     0.7866 0.000 0.296 0.016 0.016 0.024 0.648
#> GSM674183     6  0.5901     0.7691 0.000 0.272 0.016 0.048 0.068 0.596
#> GSM674184     6  0.6668     0.7522 0.000 0.292 0.016 0.088 0.088 0.516
#> GSM674185     6  0.6078     0.7661 0.000 0.268 0.016 0.052 0.080 0.584
#> GSM674186     6  0.6100     0.6640 0.000 0.388 0.016 0.084 0.028 0.484
#> GSM674187     6  0.6238     0.6621 0.000 0.388 0.016 0.080 0.040 0.476
#> GSM674190     6  0.5276     0.7457 0.000 0.344 0.016 0.036 0.020 0.584
#> GSM674191     6  0.4490     0.7906 0.000 0.296 0.016 0.012 0.012 0.664
#> GSM674192     2  0.2170     0.7834 0.000 0.912 0.016 0.056 0.008 0.008
#> GSM674193     2  0.5142     0.5997 0.000 0.716 0.016 0.136 0.036 0.096
#> GSM674194     6  0.6275     0.7217 0.000 0.328 0.016 0.084 0.048 0.524
#> GSM674195     6  0.6587     0.7591 0.000 0.280 0.016 0.084 0.088 0.532
#> GSM674198     2  0.0458     0.8014 0.000 0.984 0.016 0.000 0.000 0.000
#> GSM674200     6  0.6078     0.7661 0.000 0.268 0.016 0.052 0.080 0.584
#> GSM674201     6  0.4992     0.7878 0.000 0.284 0.016 0.028 0.024 0.648
#> GSM674202     6  0.7253     0.6194 0.000 0.356 0.016 0.092 0.144 0.392
#> GSM674203     2  0.0964     0.8010 0.000 0.968 0.016 0.000 0.004 0.012
#> GSM674204     2  0.1534     0.7883 0.000 0.944 0.016 0.004 0.004 0.032
#> GSM674205     2  0.0603     0.8019 0.000 0.980 0.016 0.000 0.000 0.004
#> GSM674206     6  0.4002     0.7949 0.000 0.284 0.016 0.008 0.000 0.692
#> GSM674208     2  0.0603     0.8005 0.000 0.980 0.016 0.000 0.000 0.004
#> GSM674209     2  0.5774     0.4891 0.000 0.656 0.016 0.140 0.044 0.144
#> GSM674210     2  0.0603     0.8015 0.000 0.980 0.016 0.004 0.000 0.000
#> GSM674212     2  0.2107     0.7761 0.000 0.916 0.016 0.008 0.008 0.052
#> GSM674214     2  0.0603     0.8015 0.000 0.980 0.016 0.004 0.000 0.000
#> GSM674218     6  0.6668     0.7522 0.000 0.292 0.016 0.088 0.088 0.516
#> GSM674219     6  0.4576     0.7897 0.000 0.296 0.016 0.012 0.016 0.660
#> GSM674220     6  0.6473     0.7573 0.000 0.264 0.016 0.040 0.144 0.536
#> GSM674221     6  0.4785     0.7725 0.000 0.328 0.016 0.012 0.020 0.624
#> GSM674223     2  0.4460     0.6541 0.000 0.756 0.016 0.072 0.012 0.144
#> GSM674225     6  0.7434     0.6076 0.000 0.356 0.016 0.108 0.156 0.364
#> GSM674226     2  0.5502     0.5367 0.000 0.680 0.016 0.104 0.040 0.160
#> GSM674229     2  0.2711     0.7633 0.000 0.884 0.016 0.036 0.004 0.060
#> GSM674230     6  0.6421     0.6681 0.000 0.360 0.016 0.048 0.092 0.484
#> GSM674231     2  0.5692     0.5174 0.000 0.668 0.016 0.140 0.048 0.128
#> GSM674232     2  0.1007     0.8007 0.000 0.968 0.016 0.004 0.008 0.004
#> GSM674234     2  0.3059     0.7556 0.000 0.868 0.016 0.068 0.016 0.032
#> GSM674235     6  0.6371     0.6786 0.000 0.360 0.016 0.032 0.112 0.480
#> GSM674236     2  0.7180    -0.5921 0.000 0.388 0.016 0.088 0.136 0.372
#> GSM674237     2  0.0748     0.8010 0.000 0.976 0.016 0.004 0.000 0.004
#> GSM674239     2  0.1534     0.7883 0.000 0.944 0.016 0.004 0.004 0.032
#> GSM674240     6  0.4594     0.7869 0.000 0.300 0.016 0.016 0.012 0.656
#> GSM674242     2  0.0964     0.8010 0.000 0.968 0.016 0.000 0.004 0.012
#> GSM674243     2  0.3647     0.7364 0.000 0.828 0.016 0.064 0.012 0.080
#> GSM674244     6  0.7430     0.6272 0.000 0.344 0.016 0.108 0.156 0.376
#> GSM674245     2  0.5628     0.5104 0.000 0.680 0.016 0.064 0.096 0.144
#> GSM674282     1  0.0000     0.7610 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674284     1  0.1644     0.7407 0.932 0.000 0.000 0.028 0.000 0.040
#> GSM674285     1  0.0363     0.7604 0.988 0.000 0.000 0.012 0.000 0.000
#> GSM674287     1  0.1074     0.7532 0.960 0.000 0.000 0.012 0.000 0.028
#> GSM674288     1  0.6120    -0.7714 0.440 0.012 0.000 0.044 0.436 0.068
#> GSM674289     1  0.0000     0.7610 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0508     0.7601 0.984 0.004 0.000 0.012 0.000 0.000
#> GSM674291     1  0.0508     0.7601 0.984 0.004 0.000 0.012 0.000 0.000
#> GSM674292     1  0.0405     0.7607 0.988 0.004 0.000 0.008 0.000 0.000
#> GSM674295     5  0.5564     0.8595 0.372 0.012 0.000 0.024 0.540 0.052
#> GSM674297     1  0.0993     0.7545 0.964 0.000 0.000 0.012 0.000 0.024
#> GSM674298     1  0.0993     0.7545 0.964 0.000 0.000 0.012 0.000 0.024
#> GSM674299     1  0.1788     0.7388 0.928 0.004 0.000 0.028 0.000 0.040
#> GSM674300     1  0.5849     0.2501 0.620 0.000 0.000 0.124 0.192 0.064
#> GSM674301     1  0.0508     0.7601 0.984 0.004 0.000 0.012 0.000 0.000
#> GSM674302     1  0.0508     0.7601 0.984 0.004 0.000 0.012 0.000 0.000
#> GSM674304     1  0.0363     0.7604 0.988 0.000 0.000 0.012 0.000 0.000
#> GSM674305     1  0.0363     0.7604 0.988 0.000 0.000 0.012 0.000 0.000
#> GSM674306     1  0.5839     0.2872 0.624 0.000 0.000 0.132 0.180 0.064
#> GSM674308     1  0.0508     0.7601 0.984 0.004 0.000 0.012 0.000 0.000
#> GSM674309     1  0.5211     0.3073 0.680 0.000 0.000 0.056 0.188 0.076
#> GSM674313     5  0.6181     0.7548 0.352 0.008 0.000 0.076 0.508 0.056
#> GSM674314     5  0.5958     0.7958 0.380 0.000 0.000 0.056 0.492 0.072
#> GSM674315     1  0.5839     0.2872 0.624 0.000 0.000 0.132 0.180 0.064
#> GSM674316     5  0.4555     0.8288 0.440 0.000 0.000 0.012 0.532 0.016
#> GSM674318     5  0.3841     0.8858 0.380 0.000 0.000 0.004 0.616 0.000
#> GSM674320     5  0.4744     0.8727 0.372 0.008 0.000 0.012 0.588 0.020
#> GSM674323     5  0.3841     0.8858 0.380 0.000 0.000 0.004 0.616 0.000
#> GSM674324     1  0.4317     0.5565 0.776 0.000 0.000 0.056 0.092 0.076
#> GSM674325     5  0.4093     0.8414 0.440 0.000 0.000 0.004 0.552 0.004
#> GSM674327     5  0.6556     0.6979 0.352 0.000 0.000 0.124 0.452 0.072
#> GSM674328     1  0.1716     0.7410 0.932 0.004 0.000 0.028 0.000 0.036
#> GSM674330     1  0.5957    -0.7239 0.440 0.000 0.000 0.056 0.436 0.068
#> GSM674331     1  0.4667     0.4898 0.744 0.000 0.000 0.056 0.124 0.076
#> GSM674332     1  0.5211     0.3073 0.680 0.000 0.000 0.056 0.188 0.076
#> GSM674334     1  0.5866    -0.6987 0.456 0.000 0.000 0.052 0.428 0.064
#> GSM674335     1  0.6160    -0.7720 0.440 0.012 0.000 0.044 0.432 0.072
#> GSM674345     3  0.2201     0.7275 0.000 0.000 0.912 0.028 0.032 0.028
#> GSM674351     3  0.2415     0.6994 0.000 0.000 0.900 0.040 0.024 0.036
#> GSM674352     3  0.3135     0.6865 0.000 0.000 0.856 0.068 0.028 0.048
#> GSM674359     3  0.1003     0.7334 0.000 0.000 0.964 0.000 0.016 0.020
#> GSM674360     3  0.2638     0.7186 0.000 0.000 0.884 0.016 0.040 0.060
#> GSM674362     3  0.2084     0.7270 0.000 0.000 0.916 0.016 0.024 0.044
#> GSM674369     3  0.2579     0.7151 0.000 0.000 0.884 0.008 0.048 0.060
#> GSM674372     4  0.5676     0.7907 0.000 0.000 0.436 0.464 0.044 0.056
#> GSM674374     3  0.4934    -0.4384 0.000 0.000 0.568 0.376 0.040 0.016
#> GSM674376     4  0.4555     0.8843 0.000 0.000 0.392 0.576 0.012 0.020
#> GSM674377     4  0.5509     0.8062 0.000 0.000 0.416 0.496 0.040 0.048
#> GSM674378     4  0.5004     0.8198 0.000 0.000 0.456 0.492 0.028 0.024
#> GSM674383     3  0.3238     0.6984 0.000 0.000 0.848 0.024 0.056 0.072
#> GSM674386     4  0.4994     0.8823 0.000 0.000 0.392 0.552 0.032 0.024
#> GSM674387     4  0.4168     0.8875 0.000 0.000 0.400 0.584 0.016 0.000
#> GSM674392     3  0.4289     0.3751 0.000 0.000 0.740 0.192 0.028 0.040
#> GSM674396     4  0.4763     0.8858 0.000 0.000 0.392 0.564 0.032 0.012
#> GSM674399     4  0.4860     0.8855 0.000 0.000 0.400 0.552 0.032 0.016
#> GSM674404     4  0.5089     0.8823 0.000 0.000 0.408 0.532 0.028 0.032
#> GSM674182     6  0.4302     0.7895 0.000 0.296 0.016 0.008 0.008 0.672
#> GSM674188     6  0.6577     0.6587 0.000 0.376 0.016 0.096 0.056 0.456
#> GSM674189     6  0.7112     0.7279 0.000 0.304 0.016 0.128 0.096 0.456
#> GSM674196     2  0.1293     0.7957 0.000 0.956 0.016 0.004 0.004 0.020
#> GSM674197     2  0.1232     0.7975 0.000 0.956 0.016 0.004 0.000 0.024
#> GSM674199     2  0.0458     0.8014 0.000 0.984 0.016 0.000 0.000 0.000
#> GSM674207     2  0.0976     0.8019 0.000 0.968 0.016 0.000 0.008 0.008
#> GSM674211     2  0.0748     0.8023 0.000 0.976 0.016 0.000 0.004 0.004
#> GSM674213     6  0.4628     0.7866 0.000 0.308 0.016 0.012 0.016 0.648
#> GSM674215     6  0.6443     0.7575 0.000 0.264 0.016 0.036 0.148 0.536
#> GSM674216     2  0.3783     0.6978 0.000 0.820 0.016 0.060 0.088 0.016
#> GSM674217     6  0.4542     0.7856 0.000 0.308 0.016 0.012 0.012 0.652
#> GSM674222     2  0.7309    -0.6062 0.000 0.372 0.016 0.096 0.148 0.368
#> GSM674224     2  0.5712     0.4926 0.000 0.660 0.016 0.144 0.040 0.140
#> GSM674227     2  0.7017    -0.2345 0.000 0.488 0.016 0.092 0.132 0.272
#> GSM674228     6  0.6289     0.5937 0.000 0.404 0.016 0.056 0.064 0.460
#> GSM674233     6  0.4645     0.7832 0.000 0.312 0.016 0.012 0.016 0.644
#> GSM674238     6  0.6300     0.7645 0.000 0.276 0.016 0.060 0.088 0.560
#> GSM674241     2  0.0603     0.8022 0.000 0.980 0.016 0.000 0.000 0.004
#> GSM674283     1  0.0405     0.7612 0.988 0.000 0.000 0.004 0.000 0.008
#> GSM674286     1  0.0000     0.7610 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674293     1  0.3193     0.6197 0.852 0.004 0.000 0.032 0.088 0.024
#> GSM674294     1  0.0000     0.7610 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674296     1  0.0363     0.7604 0.988 0.000 0.000 0.012 0.000 0.000
#> GSM674303     1  0.2499     0.7005 0.880 0.000 0.000 0.048 0.000 0.072
#> GSM674307     1  0.0405     0.7616 0.988 0.000 0.000 0.008 0.000 0.004
#> GSM674310     5  0.3841     0.8858 0.380 0.000 0.000 0.004 0.616 0.000
#> GSM674311     1  0.5211     0.3073 0.680 0.000 0.000 0.056 0.188 0.076
#> GSM674312     5  0.4916     0.8604 0.424 0.008 0.000 0.012 0.532 0.024
#> GSM674317     1  0.1478     0.7467 0.944 0.004 0.000 0.020 0.000 0.032
#> GSM674319     5  0.5648     0.8031 0.440 0.012 0.000 0.024 0.472 0.052
#> GSM674321     5  0.3841     0.8858 0.380 0.000 0.000 0.004 0.616 0.000
#> GSM674322     5  0.4057     0.8513 0.436 0.000 0.000 0.008 0.556 0.000
#> GSM674326     5  0.3819     0.8802 0.372 0.000 0.000 0.004 0.624 0.000
#> GSM674329     5  0.4817     0.8716 0.372 0.008 0.000 0.012 0.584 0.024
#> GSM674333     5  0.4189     0.8523 0.436 0.000 0.000 0.004 0.552 0.008

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-SD-kmeans-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-SD-kmeans-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-SD-kmeans-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-SD-kmeans-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-SD-kmeans-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-SD-kmeans-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-SD-kmeans-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-SD-kmeans-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-SD-kmeans-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-SD-kmeans-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-SD-kmeans-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-SD-kmeans-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-SD-kmeans-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-SD-kmeans-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-SD-kmeans-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-SD-kmeans-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-SD-kmeans-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-SD-kmeans-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-SD-kmeans-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-SD-kmeans-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk SD-kmeans-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-SD-kmeans-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-SD-kmeans-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-SD-kmeans-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-SD-kmeans-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-SD-kmeans-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk SD-kmeans-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>             n disease.state(p) specimen(p) k
#> SD:kmeans 183            0.924    1.83e-40 2
#> SD:kmeans 183            0.962    6.15e-78 3
#> SD:kmeans 183            0.962    6.15e-78 4
#> SD:kmeans 176            0.995    5.74e-73 5
#> SD:kmeans 157            0.688    1.70e-61 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


SD:skmeans**

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["SD", "skmeans"]
# you can also extract it by
# res = res_list["SD:skmeans"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#>   Subgroups are detected by 'skmeans' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk SD-skmeans-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk SD-skmeans-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 1.000           1.000       1.000         0.5958 0.750   0.571
#> 4 4 0.890           0.932       0.928         0.0905 0.939   0.815
#> 5 5 0.858           0.848       0.871         0.0731 0.937   0.769
#> 6 6 0.816           0.773       0.831         0.0384 0.996   0.982

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2

There is also optional best \(k\) = 2 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette p1 p2 p3
#> GSM674344     3       0          1  0  0  1
#> GSM674346     3       0          1  0  0  1
#> GSM674347     3       0          1  0  0  1
#> GSM674348     3       0          1  0  0  1
#> GSM674349     3       0          1  0  0  1
#> GSM674350     3       0          1  0  0  1
#> GSM674353     3       0          1  0  0  1
#> GSM674354     3       0          1  0  0  1
#> GSM674355     3       0          1  0  0  1
#> GSM674356     3       0          1  0  0  1
#> GSM674357     3       0          1  0  0  1
#> GSM674358     3       0          1  0  0  1
#> GSM674361     3       0          1  0  0  1
#> GSM674363     3       0          1  0  0  1
#> GSM674364     3       0          1  0  0  1
#> GSM674365     3       0          1  0  0  1
#> GSM674366     3       0          1  0  0  1
#> GSM674367     3       0          1  0  0  1
#> GSM674368     3       0          1  0  0  1
#> GSM674370     3       0          1  0  0  1
#> GSM674371     3       0          1  0  0  1
#> GSM674373     3       0          1  0  0  1
#> GSM674375     3       0          1  0  0  1
#> GSM674379     3       0          1  0  0  1
#> GSM674380     3       0          1  0  0  1
#> GSM674381     3       0          1  0  0  1
#> GSM674382     3       0          1  0  0  1
#> GSM674384     3       0          1  0  0  1
#> GSM674385     3       0          1  0  0  1
#> GSM674388     3       0          1  0  0  1
#> GSM674389     3       0          1  0  0  1
#> GSM674390     3       0          1  0  0  1
#> GSM674391     3       0          1  0  0  1
#> GSM674393     3       0          1  0  0  1
#> GSM674394     3       0          1  0  0  1
#> GSM674395     3       0          1  0  0  1
#> GSM674397     3       0          1  0  0  1
#> GSM674398     3       0          1  0  0  1
#> GSM674400     3       0          1  0  0  1
#> GSM674401     3       0          1  0  0  1
#> GSM674402     3       0          1  0  0  1
#> GSM674403     3       0          1  0  0  1
#> GSM674405     3       0          1  0  0  1
#> GSM674406     3       0          1  0  0  1
#> GSM674407     3       0          1  0  0  1
#> GSM674181     2       0          1  0  1  0
#> GSM674183     2       0          1  0  1  0
#> GSM674184     2       0          1  0  1  0
#> GSM674185     2       0          1  0  1  0
#> GSM674186     2       0          1  0  1  0
#> GSM674187     2       0          1  0  1  0
#> GSM674190     2       0          1  0  1  0
#> GSM674191     2       0          1  0  1  0
#> GSM674192     2       0          1  0  1  0
#> GSM674193     2       0          1  0  1  0
#> GSM674194     2       0          1  0  1  0
#> GSM674195     2       0          1  0  1  0
#> GSM674198     2       0          1  0  1  0
#> GSM674200     2       0          1  0  1  0
#> GSM674201     2       0          1  0  1  0
#> GSM674202     2       0          1  0  1  0
#> GSM674203     2       0          1  0  1  0
#> GSM674204     2       0          1  0  1  0
#> GSM674205     2       0          1  0  1  0
#> GSM674206     2       0          1  0  1  0
#> GSM674208     2       0          1  0  1  0
#> GSM674209     2       0          1  0  1  0
#> GSM674210     2       0          1  0  1  0
#> GSM674212     2       0          1  0  1  0
#> GSM674214     2       0          1  0  1  0
#> GSM674218     2       0          1  0  1  0
#> GSM674219     2       0          1  0  1  0
#> GSM674220     2       0          1  0  1  0
#> GSM674221     2       0          1  0  1  0
#> GSM674223     2       0          1  0  1  0
#> GSM674225     2       0          1  0  1  0
#> GSM674226     2       0          1  0  1  0
#> GSM674229     2       0          1  0  1  0
#> GSM674230     2       0          1  0  1  0
#> GSM674231     2       0          1  0  1  0
#> GSM674232     2       0          1  0  1  0
#> GSM674234     2       0          1  0  1  0
#> GSM674235     2       0          1  0  1  0
#> GSM674236     2       0          1  0  1  0
#> GSM674237     2       0          1  0  1  0
#> GSM674239     2       0          1  0  1  0
#> GSM674240     2       0          1  0  1  0
#> GSM674242     2       0          1  0  1  0
#> GSM674243     2       0          1  0  1  0
#> GSM674244     2       0          1  0  1  0
#> GSM674245     2       0          1  0  1  0
#> GSM674282     1       0          1  1  0  0
#> GSM674284     1       0          1  1  0  0
#> GSM674285     1       0          1  1  0  0
#> GSM674287     1       0          1  1  0  0
#> GSM674288     1       0          1  1  0  0
#> GSM674289     1       0          1  1  0  0
#> GSM674290     1       0          1  1  0  0
#> GSM674291     1       0          1  1  0  0
#> GSM674292     1       0          1  1  0  0
#> GSM674295     1       0          1  1  0  0
#> GSM674297     1       0          1  1  0  0
#> GSM674298     1       0          1  1  0  0
#> GSM674299     1       0          1  1  0  0
#> GSM674300     1       0          1  1  0  0
#> GSM674301     1       0          1  1  0  0
#> GSM674302     1       0          1  1  0  0
#> GSM674304     1       0          1  1  0  0
#> GSM674305     1       0          1  1  0  0
#> GSM674306     1       0          1  1  0  0
#> GSM674308     1       0          1  1  0  0
#> GSM674309     1       0          1  1  0  0
#> GSM674313     1       0          1  1  0  0
#> GSM674314     1       0          1  1  0  0
#> GSM674315     1       0          1  1  0  0
#> GSM674316     1       0          1  1  0  0
#> GSM674318     1       0          1  1  0  0
#> GSM674320     1       0          1  1  0  0
#> GSM674323     1       0          1  1  0  0
#> GSM674324     1       0          1  1  0  0
#> GSM674325     1       0          1  1  0  0
#> GSM674327     1       0          1  1  0  0
#> GSM674328     1       0          1  1  0  0
#> GSM674330     1       0          1  1  0  0
#> GSM674331     1       0          1  1  0  0
#> GSM674332     1       0          1  1  0  0
#> GSM674334     1       0          1  1  0  0
#> GSM674335     1       0          1  1  0  0
#> GSM674345     3       0          1  0  0  1
#> GSM674351     3       0          1  0  0  1
#> GSM674352     3       0          1  0  0  1
#> GSM674359     3       0          1  0  0  1
#> GSM674360     3       0          1  0  0  1
#> GSM674362     3       0          1  0  0  1
#> GSM674369     3       0          1  0  0  1
#> GSM674372     3       0          1  0  0  1
#> GSM674374     3       0          1  0  0  1
#> GSM674376     3       0          1  0  0  1
#> GSM674377     3       0          1  0  0  1
#> GSM674378     3       0          1  0  0  1
#> GSM674383     3       0          1  0  0  1
#> GSM674386     3       0          1  0  0  1
#> GSM674387     3       0          1  0  0  1
#> GSM674392     3       0          1  0  0  1
#> GSM674396     3       0          1  0  0  1
#> GSM674399     3       0          1  0  0  1
#> GSM674404     3       0          1  0  0  1
#> GSM674182     2       0          1  0  1  0
#> GSM674188     2       0          1  0  1  0
#> GSM674189     2       0          1  0  1  0
#> GSM674196     2       0          1  0  1  0
#> GSM674197     2       0          1  0  1  0
#> GSM674199     2       0          1  0  1  0
#> GSM674207     2       0          1  0  1  0
#> GSM674211     2       0          1  0  1  0
#> GSM674213     2       0          1  0  1  0
#> GSM674215     2       0          1  0  1  0
#> GSM674216     2       0          1  0  1  0
#> GSM674217     2       0          1  0  1  0
#> GSM674222     2       0          1  0  1  0
#> GSM674224     2       0          1  0  1  0
#> GSM674227     2       0          1  0  1  0
#> GSM674228     2       0          1  0  1  0
#> GSM674233     2       0          1  0  1  0
#> GSM674238     2       0          1  0  1  0
#> GSM674241     2       0          1  0  1  0
#> GSM674283     1       0          1  1  0  0
#> GSM674286     1       0          1  1  0  0
#> GSM674293     1       0          1  1  0  0
#> GSM674294     1       0          1  1  0  0
#> GSM674296     1       0          1  1  0  0
#> GSM674303     1       0          1  1  0  0
#> GSM674307     1       0          1  1  0  0
#> GSM674310     1       0          1  1  0  0
#> GSM674311     1       0          1  1  0  0
#> GSM674312     1       0          1  1  0  0
#> GSM674317     1       0          1  1  0  0
#> GSM674319     1       0          1  1  0  0
#> GSM674321     1       0          1  1  0  0
#> GSM674322     1       0          1  1  0  0
#> GSM674326     1       0          1  1  0  0
#> GSM674329     1       0          1  1  0  0
#> GSM674333     1       0          1  1  0  0

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette p1    p2    p3    p4
#> GSM674344     4  0.0000      0.915  0 0.000 0.000 1.000
#> GSM674346     4  0.0000      0.915  0 0.000 0.000 1.000
#> GSM674347     3  0.4643      0.749  0 0.000 0.656 0.344
#> GSM674348     4  0.1637      0.897  0 0.000 0.060 0.940
#> GSM674349     4  0.1302      0.911  0 0.000 0.044 0.956
#> GSM674350     4  0.2921      0.874  0 0.000 0.140 0.860
#> GSM674353     4  0.2081      0.885  0 0.000 0.084 0.916
#> GSM674354     4  0.0000      0.915  0 0.000 0.000 1.000
#> GSM674355     4  0.1867      0.896  0 0.000 0.072 0.928
#> GSM674356     4  0.1211      0.911  0 0.000 0.040 0.960
#> GSM674357     4  0.1118      0.912  0 0.000 0.036 0.964
#> GSM674358     4  0.2149      0.884  0 0.000 0.088 0.912
#> GSM674361     4  0.2081      0.885  0 0.000 0.084 0.916
#> GSM674363     4  0.1474      0.907  0 0.000 0.052 0.948
#> GSM674364     4  0.0000      0.915  0 0.000 0.000 1.000
#> GSM674365     4  0.1637      0.897  0 0.000 0.060 0.940
#> GSM674366     4  0.5000     -0.331  0 0.000 0.500 0.500
#> GSM674367     3  0.3610      0.906  0 0.000 0.800 0.200
#> GSM674368     4  0.0000      0.915  0 0.000 0.000 1.000
#> GSM674370     3  0.4941      0.535  0 0.000 0.564 0.436
#> GSM674371     4  0.1716      0.898  0 0.000 0.064 0.936
#> GSM674373     3  0.4746      0.781  0 0.000 0.632 0.368
#> GSM674375     3  0.2973      0.899  0 0.000 0.856 0.144
#> GSM674379     3  0.3569      0.908  0 0.000 0.804 0.196
#> GSM674380     3  0.4356      0.864  0 0.000 0.708 0.292
#> GSM674381     3  0.4040      0.837  0 0.000 0.752 0.248
#> GSM674382     3  0.3569      0.908  0 0.000 0.804 0.196
#> GSM674384     3  0.3356      0.894  0 0.000 0.824 0.176
#> GSM674385     4  0.2081      0.886  0 0.000 0.084 0.916
#> GSM674388     4  0.0188      0.915  0 0.000 0.004 0.996
#> GSM674389     3  0.2973      0.899  0 0.000 0.856 0.144
#> GSM674390     3  0.2973      0.899  0 0.000 0.856 0.144
#> GSM674391     3  0.3569      0.908  0 0.000 0.804 0.196
#> GSM674393     3  0.2973      0.899  0 0.000 0.856 0.144
#> GSM674394     3  0.4643      0.724  0 0.000 0.656 0.344
#> GSM674395     3  0.4008      0.891  0 0.000 0.756 0.244
#> GSM674397     3  0.4746      0.765  0 0.000 0.632 0.368
#> GSM674398     3  0.2973      0.899  0 0.000 0.856 0.144
#> GSM674400     3  0.3569      0.908  0 0.000 0.804 0.196
#> GSM674401     3  0.3569      0.908  0 0.000 0.804 0.196
#> GSM674402     4  0.1474      0.899  0 0.000 0.052 0.948
#> GSM674403     4  0.1637      0.906  0 0.000 0.060 0.940
#> GSM674405     3  0.3569      0.908  0 0.000 0.804 0.196
#> GSM674406     3  0.3688      0.905  0 0.000 0.792 0.208
#> GSM674407     3  0.3649      0.906  0 0.000 0.796 0.204
#> GSM674181     2  0.2973      0.935  0 0.856 0.144 0.000
#> GSM674183     2  0.2973      0.935  0 0.856 0.144 0.000
#> GSM674184     2  0.2814      0.938  0 0.868 0.132 0.000
#> GSM674185     2  0.2973      0.935  0 0.856 0.144 0.000
#> GSM674186     2  0.2345      0.945  0 0.900 0.100 0.000
#> GSM674187     2  0.1792      0.952  0 0.932 0.068 0.000
#> GSM674190     2  0.2814      0.939  0 0.868 0.132 0.000
#> GSM674191     2  0.2973      0.935  0 0.856 0.144 0.000
#> GSM674192     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674193     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674194     2  0.2469      0.942  0 0.892 0.108 0.000
#> GSM674195     2  0.2973      0.935  0 0.856 0.144 0.000
#> GSM674198     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674200     2  0.2973      0.935  0 0.856 0.144 0.000
#> GSM674201     2  0.2973      0.935  0 0.856 0.144 0.000
#> GSM674202     2  0.1211      0.955  0 0.960 0.040 0.000
#> GSM674203     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674204     2  0.0921      0.954  0 0.972 0.028 0.000
#> GSM674205     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674206     2  0.2973      0.935  0 0.856 0.144 0.000
#> GSM674208     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674209     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674210     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674212     2  0.0921      0.954  0 0.972 0.028 0.000
#> GSM674214     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674218     2  0.2814      0.938  0 0.868 0.132 0.000
#> GSM674219     2  0.2973      0.935  0 0.856 0.144 0.000
#> GSM674220     2  0.2973      0.935  0 0.856 0.144 0.000
#> GSM674221     2  0.2408      0.947  0 0.896 0.104 0.000
#> GSM674223     2  0.1022      0.954  0 0.968 0.032 0.000
#> GSM674225     2  0.1211      0.955  0 0.960 0.040 0.000
#> GSM674226     2  0.0188      0.954  0 0.996 0.004 0.000
#> GSM674229     2  0.1022      0.954  0 0.968 0.032 0.000
#> GSM674230     2  0.1792      0.953  0 0.932 0.068 0.000
#> GSM674231     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674232     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674234     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674235     2  0.1792      0.953  0 0.932 0.068 0.000
#> GSM674236     2  0.1118      0.955  0 0.964 0.036 0.000
#> GSM674237     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674239     2  0.0817      0.954  0 0.976 0.024 0.000
#> GSM674240     2  0.2973      0.935  0 0.856 0.144 0.000
#> GSM674242     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674243     2  0.0921      0.954  0 0.972 0.028 0.000
#> GSM674244     2  0.1389      0.955  0 0.952 0.048 0.000
#> GSM674245     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674282     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674284     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674285     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674287     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674288     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674289     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674290     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674291     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674292     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674295     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674297     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674298     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674299     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674300     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674301     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674302     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674304     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674305     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674306     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674308     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674309     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674313     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674314     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674315     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674316     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674318     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674320     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674323     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674324     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674325     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674327     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674328     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674330     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674331     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674332     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674334     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674335     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674345     4  0.1637      0.905  0 0.000 0.060 0.940
#> GSM674351     4  0.2081      0.885  0 0.000 0.084 0.916
#> GSM674352     4  0.2921      0.874  0 0.000 0.140 0.860
#> GSM674359     4  0.0000      0.915  0 0.000 0.000 1.000
#> GSM674360     4  0.1557      0.897  0 0.000 0.056 0.944
#> GSM674362     4  0.1474      0.899  0 0.000 0.052 0.948
#> GSM674369     4  0.0188      0.915  0 0.000 0.004 0.996
#> GSM674372     3  0.3024      0.899  0 0.000 0.852 0.148
#> GSM674374     3  0.4624      0.802  0 0.000 0.660 0.340
#> GSM674376     3  0.2973      0.899  0 0.000 0.856 0.144
#> GSM674377     3  0.3688      0.863  0 0.000 0.792 0.208
#> GSM674378     3  0.3764      0.902  0 0.000 0.784 0.216
#> GSM674383     4  0.1637      0.897  0 0.000 0.060 0.940
#> GSM674386     3  0.2973      0.899  0 0.000 0.856 0.144
#> GSM674387     3  0.3569      0.908  0 0.000 0.804 0.196
#> GSM674392     3  0.4981      0.505  0 0.000 0.536 0.464
#> GSM674396     3  0.2973      0.899  0 0.000 0.856 0.144
#> GSM674399     3  0.3569      0.908  0 0.000 0.804 0.196
#> GSM674404     3  0.3610      0.906  0 0.000 0.800 0.200
#> GSM674182     2  0.2973      0.935  0 0.856 0.144 0.000
#> GSM674188     2  0.1792      0.952  0 0.932 0.068 0.000
#> GSM674189     2  0.2530      0.941  0 0.888 0.112 0.000
#> GSM674196     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674197     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674199     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674207     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674211     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674213     2  0.2589      0.944  0 0.884 0.116 0.000
#> GSM674215     2  0.2973      0.935  0 0.856 0.144 0.000
#> GSM674216     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674217     2  0.2704      0.942  0 0.876 0.124 0.000
#> GSM674222     2  0.1118      0.955  0 0.964 0.036 0.000
#> GSM674224     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674227     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674228     2  0.1557      0.954  0 0.944 0.056 0.000
#> GSM674233     2  0.2589      0.944  0 0.884 0.116 0.000
#> GSM674238     2  0.2973      0.935  0 0.856 0.144 0.000
#> GSM674241     2  0.0000      0.954  0 1.000 0.000 0.000
#> GSM674283     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674286     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674293     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674294     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674296     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674303     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674307     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674310     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674311     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674312     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674317     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674319     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674321     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674322     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674326     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674329     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674333     1  0.0000      1.000  1 0.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4    p5
#> GSM674344     5  0.0671     0.9195 0.000 0.000 0.016 0.004 0.980
#> GSM674346     5  0.0798     0.9196 0.000 0.000 0.016 0.008 0.976
#> GSM674347     3  0.4065     0.6890 0.000 0.000 0.720 0.016 0.264
#> GSM674348     5  0.2927     0.8988 0.000 0.000 0.092 0.040 0.868
#> GSM674349     5  0.2464     0.9123 0.000 0.000 0.096 0.016 0.888
#> GSM674350     5  0.3326     0.8858 0.000 0.000 0.152 0.024 0.824
#> GSM674353     5  0.2305     0.9025 0.000 0.000 0.092 0.012 0.896
#> GSM674354     5  0.0912     0.9191 0.000 0.000 0.016 0.012 0.972
#> GSM674355     5  0.2305     0.9038 0.000 0.000 0.092 0.012 0.896
#> GSM674356     5  0.1544     0.9157 0.000 0.000 0.068 0.000 0.932
#> GSM674357     5  0.1740     0.9168 0.000 0.000 0.056 0.012 0.932
#> GSM674358     5  0.2470     0.8994 0.000 0.000 0.104 0.012 0.884
#> GSM674361     5  0.2305     0.9025 0.000 0.000 0.092 0.012 0.896
#> GSM674363     5  0.2069     0.9105 0.000 0.000 0.076 0.012 0.912
#> GSM674364     5  0.1549     0.9161 0.000 0.000 0.016 0.040 0.944
#> GSM674365     5  0.3297     0.8913 0.000 0.000 0.084 0.068 0.848
#> GSM674366     3  0.5368     0.4213 0.000 0.000 0.596 0.072 0.332
#> GSM674367     3  0.1408     0.8922 0.000 0.000 0.948 0.008 0.044
#> GSM674368     5  0.1914     0.9131 0.000 0.000 0.016 0.060 0.924
#> GSM674370     3  0.4989     0.5952 0.000 0.000 0.648 0.056 0.296
#> GSM674371     5  0.3569     0.8886 0.000 0.000 0.104 0.068 0.828
#> GSM674373     3  0.4141     0.7858 0.000 0.000 0.736 0.028 0.236
#> GSM674375     3  0.0404     0.8863 0.000 0.000 0.988 0.012 0.000
#> GSM674379     3  0.1282     0.8920 0.000 0.000 0.952 0.004 0.044
#> GSM674380     3  0.3565     0.8436 0.000 0.000 0.800 0.024 0.176
#> GSM674381     3  0.3471     0.8201 0.000 0.000 0.836 0.072 0.092
#> GSM674382     3  0.1484     0.8924 0.000 0.000 0.944 0.008 0.048
#> GSM674384     3  0.2067     0.8790 0.000 0.000 0.920 0.032 0.048
#> GSM674385     5  0.3825     0.8593 0.000 0.000 0.136 0.060 0.804
#> GSM674388     5  0.2193     0.9118 0.000 0.000 0.028 0.060 0.912
#> GSM674389     3  0.0404     0.8863 0.000 0.000 0.988 0.012 0.000
#> GSM674390     3  0.0404     0.8863 0.000 0.000 0.988 0.012 0.000
#> GSM674391     3  0.1408     0.8924 0.000 0.000 0.948 0.008 0.044
#> GSM674393     3  0.0609     0.8856 0.000 0.000 0.980 0.020 0.000
#> GSM674394     3  0.4240     0.7207 0.000 0.000 0.736 0.036 0.228
#> GSM674395     3  0.2389     0.8747 0.000 0.000 0.880 0.004 0.116
#> GSM674397     3  0.4223     0.7542 0.000 0.000 0.724 0.028 0.248
#> GSM674398     3  0.0404     0.8863 0.000 0.000 0.988 0.012 0.000
#> GSM674400     3  0.1981     0.8899 0.000 0.000 0.924 0.028 0.048
#> GSM674401     3  0.2054     0.8891 0.000 0.000 0.920 0.028 0.052
#> GSM674402     5  0.2344     0.9093 0.000 0.000 0.064 0.032 0.904
#> GSM674403     5  0.2983     0.9075 0.000 0.000 0.096 0.040 0.864
#> GSM674405     3  0.1282     0.8920 0.000 0.000 0.952 0.004 0.044
#> GSM674406     3  0.1952     0.8841 0.000 0.000 0.912 0.004 0.084
#> GSM674407     3  0.1831     0.8864 0.000 0.000 0.920 0.004 0.076
#> GSM674181     4  0.3210     0.8851 0.000 0.212 0.000 0.788 0.000
#> GSM674183     4  0.3177     0.8846 0.000 0.208 0.000 0.792 0.000
#> GSM674184     4  0.3835     0.8472 0.000 0.244 0.000 0.744 0.012
#> GSM674185     4  0.3109     0.8844 0.000 0.200 0.000 0.800 0.000
#> GSM674186     4  0.4622     0.5792 0.000 0.440 0.000 0.548 0.012
#> GSM674187     2  0.4574    -0.1187 0.000 0.576 0.000 0.412 0.012
#> GSM674190     4  0.3932     0.7952 0.000 0.328 0.000 0.672 0.000
#> GSM674191     4  0.3336     0.8835 0.000 0.228 0.000 0.772 0.000
#> GSM674192     2  0.0290     0.8417 0.000 0.992 0.000 0.008 0.000
#> GSM674193     2  0.0771     0.8324 0.000 0.976 0.000 0.020 0.004
#> GSM674194     4  0.4494     0.6865 0.000 0.380 0.000 0.608 0.012
#> GSM674195     4  0.3487     0.8688 0.000 0.212 0.000 0.780 0.008
#> GSM674198     2  0.0162     0.8409 0.000 0.996 0.000 0.004 0.000
#> GSM674200     4  0.3109     0.8844 0.000 0.200 0.000 0.800 0.000
#> GSM674201     4  0.3177     0.8846 0.000 0.208 0.000 0.792 0.000
#> GSM674202     2  0.4306     0.2965 0.000 0.660 0.000 0.328 0.012
#> GSM674203     2  0.0510     0.8399 0.000 0.984 0.000 0.016 0.000
#> GSM674204     2  0.1908     0.7872 0.000 0.908 0.000 0.092 0.000
#> GSM674205     2  0.0290     0.8416 0.000 0.992 0.000 0.008 0.000
#> GSM674206     4  0.3177     0.8846 0.000 0.208 0.000 0.792 0.000
#> GSM674208     2  0.0290     0.8416 0.000 0.992 0.000 0.008 0.000
#> GSM674209     2  0.1195     0.8276 0.000 0.960 0.000 0.028 0.012
#> GSM674210     2  0.0000     0.8416 0.000 1.000 0.000 0.000 0.000
#> GSM674212     2  0.2074     0.7776 0.000 0.896 0.000 0.104 0.000
#> GSM674214     2  0.0000     0.8416 0.000 1.000 0.000 0.000 0.000
#> GSM674218     4  0.3779     0.8536 0.000 0.236 0.000 0.752 0.012
#> GSM674219     4  0.3661     0.8526 0.000 0.276 0.000 0.724 0.000
#> GSM674220     4  0.3109     0.8844 0.000 0.200 0.000 0.800 0.000
#> GSM674221     4  0.4283     0.4847 0.000 0.456 0.000 0.544 0.000
#> GSM674223     2  0.2179     0.7690 0.000 0.888 0.000 0.112 0.000
#> GSM674225     2  0.4016     0.4734 0.000 0.716 0.000 0.272 0.012
#> GSM674226     2  0.1043     0.8290 0.000 0.960 0.000 0.040 0.000
#> GSM674229     2  0.2179     0.7690 0.000 0.888 0.000 0.112 0.000
#> GSM674230     2  0.4210     0.0614 0.000 0.588 0.000 0.412 0.000
#> GSM674231     2  0.1106     0.8287 0.000 0.964 0.000 0.024 0.012
#> GSM674232     2  0.0404     0.8409 0.000 0.988 0.000 0.012 0.000
#> GSM674234     2  0.0510     0.8356 0.000 0.984 0.000 0.016 0.000
#> GSM674235     2  0.4138     0.1898 0.000 0.616 0.000 0.384 0.000
#> GSM674236     2  0.4173     0.3872 0.000 0.688 0.000 0.300 0.012
#> GSM674237     2  0.0162     0.8408 0.000 0.996 0.000 0.004 0.000
#> GSM674239     2  0.1792     0.7945 0.000 0.916 0.000 0.084 0.000
#> GSM674240     4  0.3424     0.8781 0.000 0.240 0.000 0.760 0.000
#> GSM674242     2  0.0510     0.8399 0.000 0.984 0.000 0.016 0.000
#> GSM674243     2  0.1851     0.7910 0.000 0.912 0.000 0.088 0.000
#> GSM674244     2  0.4339     0.2746 0.000 0.652 0.000 0.336 0.012
#> GSM674245     2  0.0510     0.8410 0.000 0.984 0.000 0.016 0.000
#> GSM674282     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674284     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674285     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674287     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674288     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674289     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674291     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674292     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674295     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674297     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674298     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674299     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674300     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674301     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674302     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674305     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674306     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674308     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674309     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674313     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674314     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674315     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674316     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674318     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674320     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674323     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674324     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674325     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674327     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674328     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674330     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674331     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674332     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674334     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674335     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674345     5  0.2068     0.9132 0.000 0.000 0.092 0.004 0.904
#> GSM674351     5  0.2305     0.9025 0.000 0.000 0.092 0.012 0.896
#> GSM674352     5  0.3409     0.8822 0.000 0.000 0.160 0.024 0.816
#> GSM674359     5  0.0671     0.9199 0.000 0.000 0.016 0.004 0.980
#> GSM674360     5  0.2974     0.8973 0.000 0.000 0.080 0.052 0.868
#> GSM674362     5  0.2514     0.9016 0.000 0.000 0.060 0.044 0.896
#> GSM674369     5  0.2193     0.9118 0.000 0.000 0.028 0.060 0.912
#> GSM674372     3  0.1310     0.8845 0.000 0.000 0.956 0.024 0.020
#> GSM674374     3  0.3574     0.8262 0.000 0.000 0.804 0.028 0.168
#> GSM674376     3  0.0404     0.8863 0.000 0.000 0.988 0.012 0.000
#> GSM674377     3  0.2659     0.8460 0.000 0.000 0.888 0.052 0.060
#> GSM674378     3  0.2124     0.8802 0.000 0.000 0.900 0.004 0.096
#> GSM674383     5  0.3359     0.8905 0.000 0.000 0.084 0.072 0.844
#> GSM674386     3  0.0510     0.8858 0.000 0.000 0.984 0.016 0.000
#> GSM674387     3  0.1282     0.8920 0.000 0.000 0.952 0.004 0.044
#> GSM674392     3  0.4517     0.4820 0.000 0.000 0.600 0.012 0.388
#> GSM674396     3  0.0404     0.8863 0.000 0.000 0.988 0.012 0.000
#> GSM674399     3  0.1282     0.8920 0.000 0.000 0.952 0.004 0.044
#> GSM674404     3  0.1430     0.8912 0.000 0.000 0.944 0.004 0.052
#> GSM674182     4  0.3242     0.8851 0.000 0.216 0.000 0.784 0.000
#> GSM674188     2  0.4582    -0.1155 0.000 0.572 0.000 0.416 0.012
#> GSM674189     4  0.4173     0.7867 0.000 0.300 0.000 0.688 0.012
#> GSM674196     2  0.0609     0.8386 0.000 0.980 0.000 0.020 0.000
#> GSM674197     2  0.0609     0.8385 0.000 0.980 0.000 0.020 0.000
#> GSM674199     2  0.0404     0.8373 0.000 0.988 0.000 0.012 0.000
#> GSM674207     2  0.0162     0.8409 0.000 0.996 0.000 0.004 0.000
#> GSM674211     2  0.0162     0.8417 0.000 0.996 0.000 0.004 0.000
#> GSM674213     4  0.3949     0.7858 0.000 0.332 0.000 0.668 0.000
#> GSM674215     4  0.3109     0.8844 0.000 0.200 0.000 0.800 0.000
#> GSM674216     2  0.0771     0.8324 0.000 0.976 0.000 0.020 0.004
#> GSM674217     4  0.3895     0.8036 0.000 0.320 0.000 0.680 0.000
#> GSM674222     2  0.3942     0.4942 0.000 0.728 0.000 0.260 0.012
#> GSM674224     2  0.0807     0.8390 0.000 0.976 0.000 0.012 0.012
#> GSM674227     2  0.1195     0.8276 0.000 0.960 0.000 0.028 0.012
#> GSM674228     2  0.3336     0.6203 0.000 0.772 0.000 0.228 0.000
#> GSM674233     4  0.3966     0.7800 0.000 0.336 0.000 0.664 0.000
#> GSM674238     4  0.3421     0.8712 0.000 0.204 0.000 0.788 0.008
#> GSM674241     2  0.0162     0.8409 0.000 0.996 0.000 0.004 0.000
#> GSM674283     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674286     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674293     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674294     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674296     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674303     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674307     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674310     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674311     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674312     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674317     1  0.0000     0.9703 1.000 0.000 0.000 0.000 0.000
#> GSM674319     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674321     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674322     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674326     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674329     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004
#> GSM674333     1  0.1952     0.9527 0.912 0.000 0.000 0.084 0.004

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4 p5    p6
#> GSM674344     3  0.0692     0.8449 0.000 0.000 0.976 0.000 NA 0.004
#> GSM674346     3  0.0260     0.8441 0.000 0.000 0.992 0.000 NA 0.000
#> GSM674347     4  0.4843     0.5113 0.000 0.000 0.300 0.616 NA 0.000
#> GSM674348     3  0.3422     0.8245 0.000 0.000 0.788 0.036 NA 0.000
#> GSM674349     3  0.4100     0.8185 0.000 0.000 0.752 0.064 NA 0.008
#> GSM674350     3  0.3221     0.8058 0.000 0.000 0.828 0.076 NA 0.000
#> GSM674353     3  0.2499     0.8157 0.000 0.000 0.880 0.072 NA 0.000
#> GSM674354     3  0.0713     0.8402 0.000 0.000 0.972 0.000 NA 0.000
#> GSM674355     3  0.2488     0.8172 0.000 0.000 0.880 0.076 NA 0.000
#> GSM674356     3  0.2078     0.8415 0.000 0.000 0.912 0.044 NA 0.004
#> GSM674357     3  0.1408     0.8366 0.000 0.000 0.944 0.036 NA 0.000
#> GSM674358     3  0.2712     0.8120 0.000 0.000 0.864 0.088 NA 0.000
#> GSM674361     3  0.2499     0.8156 0.000 0.000 0.880 0.072 NA 0.000
#> GSM674363     3  0.2136     0.8252 0.000 0.000 0.904 0.048 NA 0.000
#> GSM674364     3  0.2389     0.8350 0.000 0.000 0.864 0.000 NA 0.008
#> GSM674365     3  0.4274     0.7802 0.000 0.000 0.676 0.024 NA 0.012
#> GSM674366     4  0.6383     0.0160 0.000 0.000 0.308 0.384 NA 0.012
#> GSM674367     4  0.1788     0.8560 0.000 0.000 0.028 0.928 NA 0.004
#> GSM674368     3  0.3394     0.8034 0.000 0.000 0.752 0.000 NA 0.012
#> GSM674370     4  0.5567     0.5820 0.000 0.000 0.232 0.584 NA 0.008
#> GSM674371     3  0.4608     0.7764 0.000 0.000 0.656 0.044 NA 0.012
#> GSM674373     4  0.4543     0.7216 0.000 0.000 0.216 0.704 NA 0.012
#> GSM674375     4  0.1387     0.8542 0.000 0.000 0.000 0.932 NA 0.000
#> GSM674379     4  0.0692     0.8574 0.000 0.000 0.020 0.976 NA 0.000
#> GSM674380     4  0.2982     0.8145 0.000 0.000 0.164 0.820 NA 0.004
#> GSM674381     4  0.4361     0.7325 0.000 0.000 0.076 0.716 NA 0.004
#> GSM674382     4  0.0692     0.8574 0.000 0.000 0.020 0.976 NA 0.000
#> GSM674384     4  0.3068     0.8348 0.000 0.000 0.072 0.840 NA 0.000
#> GSM674385     3  0.4761     0.7706 0.000 0.000 0.688 0.088 NA 0.012
#> GSM674388     3  0.3445     0.8001 0.000 0.000 0.744 0.000 NA 0.012
#> GSM674389     4  0.1501     0.8538 0.000 0.000 0.000 0.924 NA 0.000
#> GSM674390     4  0.1075     0.8543 0.000 0.000 0.000 0.952 NA 0.000
#> GSM674391     4  0.0692     0.8574 0.000 0.000 0.020 0.976 NA 0.000
#> GSM674393     4  0.2003     0.8474 0.000 0.000 0.000 0.884 NA 0.000
#> GSM674394     4  0.5183     0.5986 0.000 0.000 0.272 0.608 NA 0.004
#> GSM674395     4  0.2623     0.8304 0.000 0.000 0.132 0.852 NA 0.000
#> GSM674397     4  0.4998     0.6326 0.000 0.000 0.252 0.648 NA 0.012
#> GSM674398     4  0.1327     0.8540 0.000 0.000 0.000 0.936 NA 0.000
#> GSM674400     4  0.3994     0.7613 0.000 0.000 0.040 0.752 NA 0.012
#> GSM674401     4  0.4120     0.7556 0.000 0.000 0.048 0.744 NA 0.012
#> GSM674402     3  0.2237     0.8349 0.000 0.000 0.896 0.020 NA 0.004
#> GSM674403     3  0.5030     0.7548 0.000 0.000 0.660 0.084 NA 0.020
#> GSM674405     4  0.1003     0.8569 0.000 0.000 0.020 0.964 NA 0.000
#> GSM674406     4  0.1387     0.8516 0.000 0.000 0.068 0.932 NA 0.000
#> GSM674407     4  0.1267     0.8534 0.000 0.000 0.060 0.940 NA 0.000
#> GSM674181     6  0.1918     0.8352 0.000 0.088 0.000 0.000 NA 0.904
#> GSM674183     6  0.1930     0.8322 0.000 0.048 0.000 0.000 NA 0.916
#> GSM674184     6  0.3092     0.7953 0.000 0.060 0.000 0.000 NA 0.836
#> GSM674185     6  0.2001     0.8311 0.000 0.048 0.000 0.000 NA 0.912
#> GSM674186     6  0.5174     0.4065 0.000 0.368 0.000 0.000 NA 0.536
#> GSM674187     2  0.5233     0.0446 0.000 0.500 0.000 0.000 NA 0.404
#> GSM674190     6  0.3528     0.6350 0.000 0.296 0.000 0.000 NA 0.700
#> GSM674191     6  0.2092     0.8250 0.000 0.124 0.000 0.000 NA 0.876
#> GSM674192     2  0.0146     0.8309 0.000 0.996 0.000 0.000 NA 0.004
#> GSM674193     2  0.2586     0.7874 0.000 0.868 0.000 0.000 NA 0.032
#> GSM674194     6  0.4809     0.6069 0.000 0.240 0.000 0.000 NA 0.652
#> GSM674195     6  0.2747     0.8063 0.000 0.044 0.000 0.000 NA 0.860
#> GSM674198     2  0.0146     0.8300 0.000 0.996 0.000 0.000 NA 0.000
#> GSM674200     6  0.1930     0.8322 0.000 0.048 0.000 0.000 NA 0.916
#> GSM674201     6  0.1204     0.8364 0.000 0.056 0.000 0.000 NA 0.944
#> GSM674202     2  0.5440     0.3339 0.000 0.536 0.000 0.000 NA 0.324
#> GSM674203     2  0.0603     0.8298 0.000 0.980 0.000 0.000 NA 0.016
#> GSM674204     2  0.1387     0.8066 0.000 0.932 0.000 0.000 NA 0.068
#> GSM674205     2  0.0363     0.8302 0.000 0.988 0.000 0.000 NA 0.012
#> GSM674206     6  0.1327     0.8369 0.000 0.064 0.000 0.000 NA 0.936
#> GSM674208     2  0.0508     0.8304 0.000 0.984 0.000 0.000 NA 0.012
#> GSM674209     2  0.3227     0.7651 0.000 0.824 0.000 0.000 NA 0.060
#> GSM674210     2  0.0000     0.8303 0.000 1.000 0.000 0.000 NA 0.000
#> GSM674212     2  0.1610     0.7989 0.000 0.916 0.000 0.000 NA 0.084
#> GSM674214     2  0.0146     0.8300 0.000 0.996 0.000 0.000 NA 0.000
#> GSM674218     6  0.2971     0.7994 0.000 0.052 0.000 0.000 NA 0.844
#> GSM674219     6  0.2416     0.8064 0.000 0.156 0.000 0.000 NA 0.844
#> GSM674220     6  0.2201     0.8342 0.000 0.048 0.000 0.000 NA 0.900
#> GSM674221     6  0.3727     0.4011 0.000 0.388 0.000 0.000 NA 0.612
#> GSM674223     2  0.2003     0.7820 0.000 0.884 0.000 0.000 NA 0.116
#> GSM674225     2  0.5283     0.4828 0.000 0.588 0.000 0.000 NA 0.264
#> GSM674226     2  0.2412     0.8023 0.000 0.880 0.000 0.000 NA 0.092
#> GSM674229     2  0.1814     0.7907 0.000 0.900 0.000 0.000 NA 0.100
#> GSM674230     2  0.4778     0.2127 0.000 0.524 0.000 0.000 NA 0.424
#> GSM674231     2  0.2843     0.7761 0.000 0.848 0.000 0.000 NA 0.036
#> GSM674232     2  0.0725     0.8309 0.000 0.976 0.000 0.000 NA 0.012
#> GSM674234     2  0.1088     0.8206 0.000 0.960 0.000 0.000 NA 0.016
#> GSM674235     2  0.4806     0.3478 0.000 0.560 0.000 0.000 NA 0.380
#> GSM674236     2  0.5183     0.4894 0.000 0.604 0.000 0.000 NA 0.256
#> GSM674237     2  0.0146     0.8300 0.000 0.996 0.000 0.000 NA 0.000
#> GSM674239     2  0.1141     0.8149 0.000 0.948 0.000 0.000 NA 0.052
#> GSM674240     6  0.2340     0.8118 0.000 0.148 0.000 0.000 NA 0.852
#> GSM674242     2  0.0603     0.8298 0.000 0.980 0.000 0.000 NA 0.016
#> GSM674243     2  0.1327     0.8092 0.000 0.936 0.000 0.000 NA 0.064
#> GSM674244     2  0.5578     0.2290 0.000 0.492 0.000 0.000 NA 0.360
#> GSM674245     2  0.1572     0.8268 0.000 0.936 0.000 0.000 NA 0.036
#> GSM674282     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674284     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674285     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674287     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674288     1  0.3634     0.7862 0.644 0.000 0.000 0.000 NA 0.000
#> GSM674289     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674290     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674291     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674292     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674295     1  0.3634     0.7862 0.644 0.000 0.000 0.000 NA 0.000
#> GSM674297     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674298     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674299     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674300     1  0.1075     0.8589 0.952 0.000 0.000 0.000 NA 0.000
#> GSM674301     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674302     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674304     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674305     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674306     1  0.0458     0.8573 0.984 0.000 0.000 0.000 NA 0.000
#> GSM674308     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674309     1  0.1141     0.8590 0.948 0.000 0.000 0.000 NA 0.000
#> GSM674313     1  0.3684     0.7767 0.628 0.000 0.000 0.000 NA 0.000
#> GSM674314     1  0.3634     0.7862 0.644 0.000 0.000 0.000 NA 0.000
#> GSM674315     1  0.0547     0.8584 0.980 0.000 0.000 0.000 NA 0.000
#> GSM674316     1  0.3634     0.7862 0.644 0.000 0.000 0.000 NA 0.000
#> GSM674318     1  0.3634     0.7862 0.644 0.000 0.000 0.000 NA 0.000
#> GSM674320     1  0.3634     0.7862 0.644 0.000 0.000 0.000 NA 0.000
#> GSM674323     1  0.3634     0.7862 0.644 0.000 0.000 0.000 NA 0.000
#> GSM674324     1  0.0363     0.8640 0.988 0.000 0.000 0.000 NA 0.000
#> GSM674325     1  0.3634     0.7862 0.644 0.000 0.000 0.000 NA 0.000
#> GSM674327     1  0.3647     0.7832 0.640 0.000 0.000 0.000 NA 0.000
#> GSM674328     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674330     1  0.3634     0.7862 0.644 0.000 0.000 0.000 NA 0.000
#> GSM674331     1  0.0937     0.8608 0.960 0.000 0.000 0.000 NA 0.000
#> GSM674332     1  0.0937     0.8608 0.960 0.000 0.000 0.000 NA 0.000
#> GSM674334     1  0.3634     0.7862 0.644 0.000 0.000 0.000 NA 0.000
#> GSM674335     1  0.3634     0.7862 0.644 0.000 0.000 0.000 NA 0.000
#> GSM674345     3  0.3068     0.8337 0.000 0.000 0.840 0.072 NA 0.000
#> GSM674351     3  0.2499     0.8156 0.000 0.000 0.880 0.072 NA 0.000
#> GSM674352     3  0.3424     0.8014 0.000 0.000 0.812 0.092 NA 0.000
#> GSM674359     3  0.1493     0.8461 0.000 0.000 0.936 0.004 NA 0.004
#> GSM674360     3  0.3855     0.8072 0.000 0.000 0.748 0.024 NA 0.012
#> GSM674362     3  0.3294     0.8246 0.000 0.000 0.812 0.020 NA 0.012
#> GSM674369     3  0.3445     0.8001 0.000 0.000 0.744 0.000 NA 0.012
#> GSM674372     4  0.3252     0.8239 0.000 0.000 0.068 0.824 NA 0.000
#> GSM674374     4  0.4202     0.7563 0.000 0.000 0.152 0.756 NA 0.012
#> GSM674376     4  0.1075     0.8543 0.000 0.000 0.000 0.952 NA 0.000
#> GSM674377     4  0.2973     0.8148 0.000 0.000 0.024 0.836 NA 0.004
#> GSM674378     4  0.2126     0.8481 0.000 0.000 0.072 0.904 NA 0.004
#> GSM674383     3  0.4293     0.7793 0.000 0.000 0.672 0.024 NA 0.012
#> GSM674386     4  0.1327     0.8540 0.000 0.000 0.000 0.936 NA 0.000
#> GSM674387     4  0.0547     0.8575 0.000 0.000 0.020 0.980 NA 0.000
#> GSM674392     3  0.4855    -0.1670 0.000 0.000 0.484 0.460 NA 0.000
#> GSM674396     4  0.1327     0.8540 0.000 0.000 0.000 0.936 NA 0.000
#> GSM674399     4  0.1003     0.8569 0.000 0.000 0.020 0.964 NA 0.000
#> GSM674404     4  0.1418     0.8567 0.000 0.000 0.024 0.944 NA 0.000
#> GSM674182     6  0.1765     0.8329 0.000 0.096 0.000 0.000 NA 0.904
#> GSM674188     2  0.5357    -0.0168 0.000 0.464 0.000 0.000 NA 0.428
#> GSM674189     6  0.4121     0.7295 0.000 0.116 0.000 0.000 NA 0.748
#> GSM674196     2  0.0547     0.8284 0.000 0.980 0.000 0.000 NA 0.020
#> GSM674197     2  0.0458     0.8293 0.000 0.984 0.000 0.000 NA 0.016
#> GSM674199     2  0.0291     0.8289 0.000 0.992 0.000 0.000 NA 0.004
#> GSM674207     2  0.0146     0.8309 0.000 0.996 0.000 0.000 NA 0.004
#> GSM674211     2  0.0260     0.8307 0.000 0.992 0.000 0.000 NA 0.008
#> GSM674213     6  0.3445     0.6977 0.000 0.260 0.000 0.000 NA 0.732
#> GSM674215     6  0.2136     0.8350 0.000 0.048 0.000 0.000 NA 0.904
#> GSM674216     2  0.2432     0.7909 0.000 0.876 0.000 0.000 NA 0.024
#> GSM674217     6  0.3050     0.7285 0.000 0.236 0.000 0.000 NA 0.764
#> GSM674222     2  0.5092     0.5357 0.000 0.624 0.000 0.000 NA 0.232
#> GSM674224     2  0.2728     0.7875 0.000 0.860 0.000 0.000 NA 0.040
#> GSM674227     2  0.3356     0.7564 0.000 0.808 0.000 0.000 NA 0.052
#> GSM674228     2  0.3717     0.6100 0.000 0.708 0.000 0.000 NA 0.276
#> GSM674233     6  0.3221     0.6878 0.000 0.264 0.000 0.000 NA 0.736
#> GSM674238     6  0.2190     0.8190 0.000 0.040 0.000 0.000 NA 0.900
#> GSM674241     2  0.0146     0.8309 0.000 0.996 0.000 0.000 NA 0.004
#> GSM674283     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674286     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674293     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674294     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674296     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674303     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674307     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674310     1  0.3634     0.7862 0.644 0.000 0.000 0.000 NA 0.000
#> GSM674311     1  0.1204     0.8583 0.944 0.000 0.000 0.000 NA 0.000
#> GSM674312     1  0.3634     0.7862 0.644 0.000 0.000 0.000 NA 0.000
#> GSM674317     1  0.0000     0.8647 1.000 0.000 0.000 0.000 NA 0.000
#> GSM674319     1  0.3634     0.7862 0.644 0.000 0.000 0.000 NA 0.000
#> GSM674321     1  0.3634     0.7862 0.644 0.000 0.000 0.000 NA 0.000
#> GSM674322     1  0.3634     0.7862 0.644 0.000 0.000 0.000 NA 0.000
#> GSM674326     1  0.3634     0.7862 0.644 0.000 0.000 0.000 NA 0.000
#> GSM674329     1  0.3634     0.7862 0.644 0.000 0.000 0.000 NA 0.000
#> GSM674333     1  0.3634     0.7862 0.644 0.000 0.000 0.000 NA 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-SD-skmeans-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-SD-skmeans-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-SD-skmeans-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-SD-skmeans-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-SD-skmeans-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-SD-skmeans-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-SD-skmeans-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-SD-skmeans-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-SD-skmeans-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-SD-skmeans-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-SD-skmeans-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-SD-skmeans-get-signatures-2

get_signatures(res, k = 4)
#> Error in mat[ceiling(1:nr/h_ratio), ceiling(1:nc/w_ratio), drop = FALSE]: subscript out of bounds

plot of chunk tab-SD-skmeans-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-SD-skmeans-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-SD-skmeans-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-SD-skmeans-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-SD-skmeans-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-SD-skmeans-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-SD-skmeans-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-SD-skmeans-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk SD-skmeans-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-SD-skmeans-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-SD-skmeans-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-SD-skmeans-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-SD-skmeans-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-SD-skmeans-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk SD-skmeans-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>              n disease.state(p) specimen(p) k
#> SD:skmeans 183            0.924    1.83e-40 2
#> SD:skmeans 183            0.962    6.15e-78 3
#> SD:skmeans 182            0.971    1.52e-75 4
#> SD:skmeans 171            0.997    4.61e-69 5
#> SD:skmeans 171            0.992    4.61e-69 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


SD:pam**

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["SD", "pam"]
# you can also extract it by
# res = res_list["SD:pam"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#>   Subgroups are detected by 'pam' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 4.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk SD-pam-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk SD-pam-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 1.000           0.997       0.999         0.5957 0.750   0.571
#> 4 4 1.000           0.978       0.981         0.0645 0.956   0.869
#> 5 5 0.894           0.842       0.898         0.0732 0.939   0.789
#> 6 6 0.802           0.752       0.841         0.0649 0.940   0.740

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3

There is also optional best \(k\) = 2 3 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette p1    p2    p3
#> GSM674344     3  0.0237      0.993  0 0.004 0.996
#> GSM674346     3  0.0000      0.997  0 0.000 1.000
#> GSM674347     3  0.0000      0.997  0 0.000 1.000
#> GSM674348     3  0.0000      0.997  0 0.000 1.000
#> GSM674349     3  0.0000      0.997  0 0.000 1.000
#> GSM674350     3  0.0000      0.997  0 0.000 1.000
#> GSM674353     3  0.0000      0.997  0 0.000 1.000
#> GSM674354     3  0.0000      0.997  0 0.000 1.000
#> GSM674355     3  0.0000      0.997  0 0.000 1.000
#> GSM674356     3  0.0000      0.997  0 0.000 1.000
#> GSM674357     3  0.0000      0.997  0 0.000 1.000
#> GSM674358     3  0.0000      0.997  0 0.000 1.000
#> GSM674361     3  0.0000      0.997  0 0.000 1.000
#> GSM674363     3  0.0000      0.997  0 0.000 1.000
#> GSM674364     3  0.0000      0.997  0 0.000 1.000
#> GSM674365     3  0.0000      0.997  0 0.000 1.000
#> GSM674366     3  0.0000      0.997  0 0.000 1.000
#> GSM674367     3  0.0000      0.997  0 0.000 1.000
#> GSM674368     3  0.0000      0.997  0 0.000 1.000
#> GSM674370     3  0.0000      0.997  0 0.000 1.000
#> GSM674371     3  0.0000      0.997  0 0.000 1.000
#> GSM674373     3  0.0000      0.997  0 0.000 1.000
#> GSM674375     3  0.0000      0.997  0 0.000 1.000
#> GSM674379     3  0.0000      0.997  0 0.000 1.000
#> GSM674380     3  0.0000      0.997  0 0.000 1.000
#> GSM674381     3  0.0000      0.997  0 0.000 1.000
#> GSM674382     3  0.0000      0.997  0 0.000 1.000
#> GSM674384     3  0.0000      0.997  0 0.000 1.000
#> GSM674385     3  0.0000      0.997  0 0.000 1.000
#> GSM674388     3  0.0000      0.997  0 0.000 1.000
#> GSM674389     3  0.0000      0.997  0 0.000 1.000
#> GSM674390     3  0.0000      0.997  0 0.000 1.000
#> GSM674391     3  0.0000      0.997  0 0.000 1.000
#> GSM674393     3  0.0000      0.997  0 0.000 1.000
#> GSM674394     3  0.0000      0.997  0 0.000 1.000
#> GSM674395     3  0.0000      0.997  0 0.000 1.000
#> GSM674397     3  0.0000      0.997  0 0.000 1.000
#> GSM674398     3  0.0000      0.997  0 0.000 1.000
#> GSM674400     3  0.0000      0.997  0 0.000 1.000
#> GSM674401     3  0.0000      0.997  0 0.000 1.000
#> GSM674402     3  0.0000      0.997  0 0.000 1.000
#> GSM674403     3  0.0000      0.997  0 0.000 1.000
#> GSM674405     3  0.0000      0.997  0 0.000 1.000
#> GSM674406     3  0.0000      0.997  0 0.000 1.000
#> GSM674407     3  0.0000      0.997  0 0.000 1.000
#> GSM674181     2  0.0000      1.000  0 1.000 0.000
#> GSM674183     2  0.0000      1.000  0 1.000 0.000
#> GSM674184     2  0.0000      1.000  0 1.000 0.000
#> GSM674185     2  0.0000      1.000  0 1.000 0.000
#> GSM674186     2  0.0000      1.000  0 1.000 0.000
#> GSM674187     2  0.0000      1.000  0 1.000 0.000
#> GSM674190     2  0.0000      1.000  0 1.000 0.000
#> GSM674191     2  0.0000      1.000  0 1.000 0.000
#> GSM674192     2  0.0000      1.000  0 1.000 0.000
#> GSM674193     2  0.0000      1.000  0 1.000 0.000
#> GSM674194     2  0.0000      1.000  0 1.000 0.000
#> GSM674195     2  0.0000      1.000  0 1.000 0.000
#> GSM674198     2  0.0000      1.000  0 1.000 0.000
#> GSM674200     2  0.0000      1.000  0 1.000 0.000
#> GSM674201     2  0.0000      1.000  0 1.000 0.000
#> GSM674202     2  0.0000      1.000  0 1.000 0.000
#> GSM674203     2  0.0000      1.000  0 1.000 0.000
#> GSM674204     2  0.0000      1.000  0 1.000 0.000
#> GSM674205     2  0.0000      1.000  0 1.000 0.000
#> GSM674206     2  0.0000      1.000  0 1.000 0.000
#> GSM674208     2  0.0000      1.000  0 1.000 0.000
#> GSM674209     2  0.0000      1.000  0 1.000 0.000
#> GSM674210     2  0.0000      1.000  0 1.000 0.000
#> GSM674212     2  0.0000      1.000  0 1.000 0.000
#> GSM674214     2  0.0000      1.000  0 1.000 0.000
#> GSM674218     2  0.0000      1.000  0 1.000 0.000
#> GSM674219     2  0.0000      1.000  0 1.000 0.000
#> GSM674220     2  0.0000      1.000  0 1.000 0.000
#> GSM674221     2  0.0000      1.000  0 1.000 0.000
#> GSM674223     2  0.0000      1.000  0 1.000 0.000
#> GSM674225     2  0.0000      1.000  0 1.000 0.000
#> GSM674226     2  0.0000      1.000  0 1.000 0.000
#> GSM674229     2  0.0000      1.000  0 1.000 0.000
#> GSM674230     2  0.0000      1.000  0 1.000 0.000
#> GSM674231     2  0.0000      1.000  0 1.000 0.000
#> GSM674232     2  0.0000      1.000  0 1.000 0.000
#> GSM674234     2  0.0000      1.000  0 1.000 0.000
#> GSM674235     2  0.0000      1.000  0 1.000 0.000
#> GSM674236     2  0.0000      1.000  0 1.000 0.000
#> GSM674237     2  0.0000      1.000  0 1.000 0.000
#> GSM674239     2  0.0000      1.000  0 1.000 0.000
#> GSM674240     2  0.0000      1.000  0 1.000 0.000
#> GSM674242     2  0.0000      1.000  0 1.000 0.000
#> GSM674243     2  0.0000      1.000  0 1.000 0.000
#> GSM674244     2  0.0000      1.000  0 1.000 0.000
#> GSM674245     2  0.0000      1.000  0 1.000 0.000
#> GSM674282     1  0.0000      1.000  1 0.000 0.000
#> GSM674284     1  0.0000      1.000  1 0.000 0.000
#> GSM674285     1  0.0000      1.000  1 0.000 0.000
#> GSM674287     1  0.0000      1.000  1 0.000 0.000
#> GSM674288     1  0.0000      1.000  1 0.000 0.000
#> GSM674289     1  0.0000      1.000  1 0.000 0.000
#> GSM674290     1  0.0000      1.000  1 0.000 0.000
#> GSM674291     1  0.0000      1.000  1 0.000 0.000
#> GSM674292     1  0.0000      1.000  1 0.000 0.000
#> GSM674295     1  0.0000      1.000  1 0.000 0.000
#> GSM674297     1  0.0000      1.000  1 0.000 0.000
#> GSM674298     1  0.0000      1.000  1 0.000 0.000
#> GSM674299     1  0.0000      1.000  1 0.000 0.000
#> GSM674300     1  0.0000      1.000  1 0.000 0.000
#> GSM674301     1  0.0000      1.000  1 0.000 0.000
#> GSM674302     1  0.0000      1.000  1 0.000 0.000
#> GSM674304     1  0.0000      1.000  1 0.000 0.000
#> GSM674305     1  0.0000      1.000  1 0.000 0.000
#> GSM674306     1  0.0000      1.000  1 0.000 0.000
#> GSM674308     1  0.0000      1.000  1 0.000 0.000
#> GSM674309     1  0.0000      1.000  1 0.000 0.000
#> GSM674313     1  0.0000      1.000  1 0.000 0.000
#> GSM674314     1  0.0000      1.000  1 0.000 0.000
#> GSM674315     1  0.0000      1.000  1 0.000 0.000
#> GSM674316     1  0.0000      1.000  1 0.000 0.000
#> GSM674318     1  0.0000      1.000  1 0.000 0.000
#> GSM674320     1  0.0000      1.000  1 0.000 0.000
#> GSM674323     1  0.0000      1.000  1 0.000 0.000
#> GSM674324     1  0.0000      1.000  1 0.000 0.000
#> GSM674325     1  0.0000      1.000  1 0.000 0.000
#> GSM674327     1  0.0000      1.000  1 0.000 0.000
#> GSM674328     1  0.0000      1.000  1 0.000 0.000
#> GSM674330     1  0.0000      1.000  1 0.000 0.000
#> GSM674331     1  0.0000      1.000  1 0.000 0.000
#> GSM674332     1  0.0000      1.000  1 0.000 0.000
#> GSM674334     1  0.0000      1.000  1 0.000 0.000
#> GSM674335     1  0.0000      1.000  1 0.000 0.000
#> GSM674345     3  0.0000      0.997  0 0.000 1.000
#> GSM674351     3  0.0000      0.997  0 0.000 1.000
#> GSM674352     3  0.0000      0.997  0 0.000 1.000
#> GSM674359     3  0.0000      0.997  0 0.000 1.000
#> GSM674360     3  0.0000      0.997  0 0.000 1.000
#> GSM674362     3  0.4555      0.750  0 0.200 0.800
#> GSM674369     3  0.0000      0.997  0 0.000 1.000
#> GSM674372     3  0.0000      0.997  0 0.000 1.000
#> GSM674374     3  0.0000      0.997  0 0.000 1.000
#> GSM674376     3  0.0000      0.997  0 0.000 1.000
#> GSM674377     3  0.0000      0.997  0 0.000 1.000
#> GSM674378     3  0.0000      0.997  0 0.000 1.000
#> GSM674383     3  0.0000      0.997  0 0.000 1.000
#> GSM674386     3  0.0000      0.997  0 0.000 1.000
#> GSM674387     3  0.0000      0.997  0 0.000 1.000
#> GSM674392     3  0.0000      0.997  0 0.000 1.000
#> GSM674396     3  0.0000      0.997  0 0.000 1.000
#> GSM674399     3  0.0000      0.997  0 0.000 1.000
#> GSM674404     3  0.0000      0.997  0 0.000 1.000
#> GSM674182     2  0.0000      1.000  0 1.000 0.000
#> GSM674188     2  0.0000      1.000  0 1.000 0.000
#> GSM674189     2  0.0000      1.000  0 1.000 0.000
#> GSM674196     2  0.0000      1.000  0 1.000 0.000
#> GSM674197     2  0.0000      1.000  0 1.000 0.000
#> GSM674199     2  0.0000      1.000  0 1.000 0.000
#> GSM674207     2  0.0000      1.000  0 1.000 0.000
#> GSM674211     2  0.0000      1.000  0 1.000 0.000
#> GSM674213     2  0.0000      1.000  0 1.000 0.000
#> GSM674215     2  0.0000      1.000  0 1.000 0.000
#> GSM674216     2  0.0000      1.000  0 1.000 0.000
#> GSM674217     2  0.0000      1.000  0 1.000 0.000
#> GSM674222     2  0.0000      1.000  0 1.000 0.000
#> GSM674224     2  0.0000      1.000  0 1.000 0.000
#> GSM674227     2  0.0000      1.000  0 1.000 0.000
#> GSM674228     2  0.0000      1.000  0 1.000 0.000
#> GSM674233     2  0.0000      1.000  0 1.000 0.000
#> GSM674238     2  0.0000      1.000  0 1.000 0.000
#> GSM674241     2  0.0000      1.000  0 1.000 0.000
#> GSM674283     1  0.0000      1.000  1 0.000 0.000
#> GSM674286     1  0.0000      1.000  1 0.000 0.000
#> GSM674293     1  0.0000      1.000  1 0.000 0.000
#> GSM674294     1  0.0000      1.000  1 0.000 0.000
#> GSM674296     1  0.0000      1.000  1 0.000 0.000
#> GSM674303     1  0.0000      1.000  1 0.000 0.000
#> GSM674307     1  0.0000      1.000  1 0.000 0.000
#> GSM674310     1  0.0000      1.000  1 0.000 0.000
#> GSM674311     1  0.0000      1.000  1 0.000 0.000
#> GSM674312     1  0.0000      1.000  1 0.000 0.000
#> GSM674317     1  0.0000      1.000  1 0.000 0.000
#> GSM674319     1  0.0000      1.000  1 0.000 0.000
#> GSM674321     1  0.0000      1.000  1 0.000 0.000
#> GSM674322     1  0.0000      1.000  1 0.000 0.000
#> GSM674326     1  0.0000      1.000  1 0.000 0.000
#> GSM674329     1  0.0000      1.000  1 0.000 0.000
#> GSM674333     1  0.0000      1.000  1 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1    p2    p3    p4
#> GSM674344     3  0.0779      0.982 0.000 0.004 0.980 0.016
#> GSM674346     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674347     3  0.0000      0.986 0.000 0.000 1.000 0.000
#> GSM674348     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674349     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674350     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674353     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674354     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674355     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674356     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674357     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674358     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674361     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674363     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674364     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674365     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674366     3  0.0188      0.986 0.000 0.000 0.996 0.004
#> GSM674367     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674368     3  0.0188      0.986 0.000 0.000 0.996 0.004
#> GSM674370     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674371     3  0.0000      0.986 0.000 0.000 1.000 0.000
#> GSM674373     3  0.0592      0.986 0.000 0.000 0.984 0.016
#> GSM674375     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674379     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674380     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674381     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674382     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674384     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674385     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674388     3  0.0188      0.986 0.000 0.000 0.996 0.004
#> GSM674389     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674390     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674391     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674393     3  0.0000      0.986 0.000 0.000 1.000 0.000
#> GSM674394     3  0.0817      0.985 0.000 0.000 0.976 0.024
#> GSM674395     3  0.0817      0.985 0.000 0.000 0.976 0.024
#> GSM674397     3  0.0000      0.986 0.000 0.000 1.000 0.000
#> GSM674398     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674400     3  0.0000      0.986 0.000 0.000 1.000 0.000
#> GSM674401     3  0.0000      0.986 0.000 0.000 1.000 0.000
#> GSM674402     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674403     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674405     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674406     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674407     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674181     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674183     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674184     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674185     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674186     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674187     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674190     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674191     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674192     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674193     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674194     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674195     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674198     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674200     2  0.0592      0.983 0.000 0.984 0.000 0.016
#> GSM674201     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674202     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674203     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674204     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674205     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674206     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674208     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674209     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674210     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674212     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674214     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674218     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674219     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674220     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674221     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674223     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674225     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674226     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674229     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674230     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674231     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674232     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674234     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674235     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674236     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674237     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674239     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674240     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674242     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674243     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674244     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674245     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674282     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674284     1  0.0188      0.988 0.996 0.000 0.000 0.004
#> GSM674285     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674287     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674288     1  0.0336      0.985 0.992 0.000 0.000 0.008
#> GSM674289     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674290     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674291     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674292     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674295     4  0.3726      0.819 0.212 0.000 0.000 0.788
#> GSM674297     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674298     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674299     1  0.0188      0.988 0.996 0.000 0.000 0.004
#> GSM674300     1  0.1637      0.940 0.940 0.000 0.000 0.060
#> GSM674301     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674302     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674304     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674305     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674306     1  0.2011      0.925 0.920 0.000 0.000 0.080
#> GSM674308     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674309     4  0.2011      0.945 0.080 0.000 0.000 0.920
#> GSM674313     4  0.0921      0.937 0.028 0.000 0.000 0.972
#> GSM674314     4  0.1867      0.946 0.072 0.000 0.000 0.928
#> GSM674315     1  0.2011      0.925 0.920 0.000 0.000 0.080
#> GSM674316     4  0.1867      0.946 0.072 0.000 0.000 0.928
#> GSM674318     4  0.1022      0.939 0.032 0.000 0.000 0.968
#> GSM674320     4  0.1022      0.939 0.032 0.000 0.000 0.968
#> GSM674323     4  0.1022      0.939 0.032 0.000 0.000 0.968
#> GSM674324     4  0.3975      0.777 0.240 0.000 0.000 0.760
#> GSM674325     4  0.1867      0.946 0.072 0.000 0.000 0.928
#> GSM674327     4  0.1792      0.923 0.068 0.000 0.000 0.932
#> GSM674328     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674330     4  0.1867      0.946 0.072 0.000 0.000 0.928
#> GSM674331     4  0.2149      0.941 0.088 0.000 0.000 0.912
#> GSM674332     4  0.4977      0.312 0.460 0.000 0.000 0.540
#> GSM674334     4  0.2011      0.945 0.080 0.000 0.000 0.920
#> GSM674335     4  0.2281      0.935 0.096 0.000 0.000 0.904
#> GSM674345     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674351     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674352     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674359     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674360     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674362     3  0.4175      0.716 0.000 0.200 0.784 0.016
#> GSM674369     3  0.0188      0.986 0.000 0.000 0.996 0.004
#> GSM674372     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674374     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674376     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674377     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674378     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674383     3  0.0000      0.986 0.000 0.000 1.000 0.000
#> GSM674386     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674387     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674392     3  0.0592      0.984 0.000 0.000 0.984 0.016
#> GSM674396     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674399     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674404     3  0.0469      0.985 0.000 0.000 0.988 0.012
#> GSM674182     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674188     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674189     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674196     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674197     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674199     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674207     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674211     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674213     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674215     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674216     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674217     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674222     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674224     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674227     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674228     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674233     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674238     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674241     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> GSM674283     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674286     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674293     1  0.0592      0.979 0.984 0.000 0.000 0.016
#> GSM674294     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674296     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674303     1  0.0188      0.988 0.996 0.000 0.000 0.004
#> GSM674307     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674310     4  0.1022      0.939 0.032 0.000 0.000 0.968
#> GSM674311     4  0.2011      0.945 0.080 0.000 0.000 0.920
#> GSM674312     4  0.1867      0.946 0.072 0.000 0.000 0.928
#> GSM674317     1  0.0000      0.991 1.000 0.000 0.000 0.000
#> GSM674319     4  0.2011      0.945 0.080 0.000 0.000 0.920
#> GSM674321     4  0.1022      0.939 0.032 0.000 0.000 0.968
#> GSM674322     4  0.1211      0.942 0.040 0.000 0.000 0.960
#> GSM674326     4  0.0921      0.937 0.028 0.000 0.000 0.972
#> GSM674329     4  0.1022      0.939 0.032 0.000 0.000 0.968
#> GSM674333     4  0.2011      0.945 0.080 0.000 0.000 0.920

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4    p5
#> GSM674344     4  0.3730     0.7599 0.000 0.000 0.288 0.712 0.000
#> GSM674346     4  0.2852     0.7876 0.000 0.000 0.172 0.828 0.000
#> GSM674347     4  0.4307     0.1826 0.000 0.000 0.496 0.504 0.000
#> GSM674348     4  0.4074     0.7151 0.000 0.000 0.364 0.636 0.000
#> GSM674349     4  0.3876     0.7611 0.000 0.000 0.316 0.684 0.000
#> GSM674350     4  0.3730     0.7405 0.000 0.000 0.288 0.712 0.000
#> GSM674353     4  0.3336     0.7855 0.000 0.000 0.228 0.772 0.000
#> GSM674354     4  0.3305     0.7875 0.000 0.000 0.224 0.776 0.000
#> GSM674355     4  0.3424     0.7836 0.000 0.000 0.240 0.760 0.000
#> GSM674356     4  0.3395     0.7855 0.000 0.000 0.236 0.764 0.000
#> GSM674357     4  0.3837     0.7866 0.000 0.000 0.308 0.692 0.000
#> GSM674358     4  0.3424     0.7836 0.000 0.000 0.240 0.760 0.000
#> GSM674361     4  0.3395     0.7844 0.000 0.000 0.236 0.764 0.000
#> GSM674363     4  0.3395     0.7845 0.000 0.000 0.236 0.764 0.000
#> GSM674364     4  0.2966     0.7895 0.000 0.000 0.184 0.816 0.000
#> GSM674365     4  0.3876     0.7481 0.000 0.000 0.316 0.684 0.000
#> GSM674366     3  0.4088     0.0449 0.000 0.000 0.632 0.368 0.000
#> GSM674367     3  0.1544     0.7474 0.000 0.000 0.932 0.068 0.000
#> GSM674368     4  0.4304     0.4687 0.000 0.000 0.484 0.516 0.000
#> GSM674370     3  0.1544     0.7032 0.000 0.000 0.932 0.068 0.000
#> GSM674371     3  0.4268    -0.2685 0.000 0.000 0.556 0.444 0.000
#> GSM674373     3  0.2605     0.6381 0.000 0.000 0.852 0.148 0.000
#> GSM674375     3  0.0510     0.7375 0.000 0.000 0.984 0.016 0.000
#> GSM674379     3  0.0609     0.7406 0.000 0.000 0.980 0.020 0.000
#> GSM674380     3  0.1043     0.7490 0.000 0.000 0.960 0.040 0.000
#> GSM674381     3  0.1544     0.7014 0.000 0.000 0.932 0.068 0.000
#> GSM674382     3  0.2561     0.7204 0.000 0.000 0.856 0.144 0.000
#> GSM674384     3  0.2471     0.7223 0.000 0.000 0.864 0.136 0.000
#> GSM674385     4  0.4030     0.7268 0.000 0.000 0.352 0.648 0.000
#> GSM674388     4  0.4268     0.5530 0.000 0.000 0.444 0.556 0.000
#> GSM674389     3  0.2471     0.7223 0.000 0.000 0.864 0.136 0.000
#> GSM674390     3  0.0404     0.7389 0.000 0.000 0.988 0.012 0.000
#> GSM674391     3  0.2127     0.7388 0.000 0.000 0.892 0.108 0.000
#> GSM674393     3  0.4283    -0.0799 0.000 0.000 0.544 0.456 0.000
#> GSM674394     3  0.3895     0.4683 0.000 0.000 0.680 0.320 0.000
#> GSM674395     3  0.4045     0.3958 0.000 0.000 0.644 0.356 0.000
#> GSM674397     3  0.4192    -0.2189 0.000 0.000 0.596 0.404 0.000
#> GSM674398     3  0.0703     0.7415 0.000 0.000 0.976 0.024 0.000
#> GSM674400     3  0.4235     0.0830 0.000 0.000 0.576 0.424 0.000
#> GSM674401     3  0.4278    -0.2498 0.000 0.000 0.548 0.452 0.000
#> GSM674402     4  0.3274     0.7740 0.000 0.000 0.220 0.780 0.000
#> GSM674403     4  0.4030     0.7355 0.000 0.000 0.352 0.648 0.000
#> GSM674405     3  0.2471     0.7241 0.000 0.000 0.864 0.136 0.000
#> GSM674406     3  0.2648     0.7185 0.000 0.000 0.848 0.152 0.000
#> GSM674407     3  0.0609     0.7406 0.000 0.000 0.980 0.020 0.000
#> GSM674181     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674183     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674184     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674185     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674186     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674187     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674190     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674191     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674192     2  0.0290     0.9908 0.000 0.992 0.000 0.008 0.000
#> GSM674193     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674194     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674195     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674198     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674200     2  0.2648     0.8220 0.000 0.848 0.000 0.152 0.000
#> GSM674201     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674202     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674203     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674204     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674205     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674206     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674208     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674209     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674210     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674212     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674214     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674218     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674219     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674220     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674221     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674223     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674225     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674226     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674229     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674230     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674231     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674232     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674234     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674235     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674236     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674237     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674239     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674240     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674242     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674243     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674244     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674245     2  0.0162     0.9919 0.000 0.996 0.000 0.004 0.000
#> GSM674282     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674284     1  0.0703     0.9613 0.976 0.000 0.000 0.000 0.024
#> GSM674285     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674287     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674288     1  0.0880     0.9548 0.968 0.000 0.000 0.000 0.032
#> GSM674289     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674291     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674292     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674295     5  0.2852     0.8338 0.172 0.000 0.000 0.000 0.828
#> GSM674297     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674298     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674299     1  0.0290     0.9739 0.992 0.000 0.000 0.000 0.008
#> GSM674300     1  0.3573     0.8402 0.812 0.000 0.000 0.152 0.036
#> GSM674301     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674302     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674305     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674306     1  0.3649     0.8367 0.808 0.000 0.000 0.152 0.040
#> GSM674308     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674309     5  0.0963     0.9472 0.036 0.000 0.000 0.000 0.964
#> GSM674313     5  0.2648     0.8610 0.000 0.000 0.000 0.152 0.848
#> GSM674314     5  0.0880     0.9480 0.032 0.000 0.000 0.000 0.968
#> GSM674315     1  0.3649     0.8367 0.808 0.000 0.000 0.152 0.040
#> GSM674316     5  0.0880     0.9480 0.032 0.000 0.000 0.000 0.968
#> GSM674318     5  0.0162     0.9427 0.004 0.000 0.000 0.000 0.996
#> GSM674320     5  0.0162     0.9427 0.004 0.000 0.000 0.000 0.996
#> GSM674323     5  0.0162     0.9427 0.004 0.000 0.000 0.000 0.996
#> GSM674324     5  0.2732     0.8435 0.160 0.000 0.000 0.000 0.840
#> GSM674325     5  0.0880     0.9480 0.032 0.000 0.000 0.000 0.968
#> GSM674327     5  0.3649     0.8323 0.040 0.000 0.000 0.152 0.808
#> GSM674328     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674330     5  0.0880     0.9480 0.032 0.000 0.000 0.000 0.968
#> GSM674331     5  0.1121     0.9442 0.044 0.000 0.000 0.000 0.956
#> GSM674332     5  0.4201     0.4017 0.408 0.000 0.000 0.000 0.592
#> GSM674334     5  0.1043     0.9458 0.040 0.000 0.000 0.000 0.960
#> GSM674335     5  0.1410     0.9346 0.060 0.000 0.000 0.000 0.940
#> GSM674345     4  0.3895     0.7646 0.000 0.000 0.320 0.680 0.000
#> GSM674351     4  0.3336     0.7855 0.000 0.000 0.228 0.772 0.000
#> GSM674352     4  0.3480     0.7786 0.000 0.000 0.248 0.752 0.000
#> GSM674359     4  0.3876     0.7611 0.000 0.000 0.316 0.684 0.000
#> GSM674360     4  0.3837     0.7512 0.000 0.000 0.308 0.692 0.000
#> GSM674362     4  0.4717     0.5553 0.000 0.144 0.120 0.736 0.000
#> GSM674369     4  0.4307     0.4326 0.000 0.000 0.500 0.500 0.000
#> GSM674372     3  0.2471     0.7223 0.000 0.000 0.864 0.136 0.000
#> GSM674374     3  0.3039     0.5812 0.000 0.000 0.808 0.192 0.000
#> GSM674376     3  0.0963     0.7466 0.000 0.000 0.964 0.036 0.000
#> GSM674377     3  0.1608     0.7003 0.000 0.000 0.928 0.072 0.000
#> GSM674378     3  0.0880     0.7380 0.000 0.000 0.968 0.032 0.000
#> GSM674383     3  0.4262    -0.2413 0.000 0.000 0.560 0.440 0.000
#> GSM674386     3  0.2648     0.7242 0.000 0.000 0.848 0.152 0.000
#> GSM674387     3  0.0703     0.7398 0.000 0.000 0.976 0.024 0.000
#> GSM674392     4  0.3561     0.7679 0.000 0.000 0.260 0.740 0.000
#> GSM674396     3  0.2424     0.7248 0.000 0.000 0.868 0.132 0.000
#> GSM674399     3  0.1792     0.7460 0.000 0.000 0.916 0.084 0.000
#> GSM674404     3  0.2561     0.7204 0.000 0.000 0.856 0.144 0.000
#> GSM674182     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674188     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674189     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674196     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674197     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674199     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674207     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674211     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674213     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674215     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674216     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674217     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674222     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674224     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674227     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674228     2  0.0162     0.9919 0.000 0.996 0.000 0.004 0.000
#> GSM674233     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674238     2  0.0000     0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM674241     2  0.0510     0.9885 0.000 0.984 0.000 0.016 0.000
#> GSM674283     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674286     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674293     1  0.0992     0.9597 0.968 0.000 0.000 0.024 0.008
#> GSM674294     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674296     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674303     1  0.0162     0.9767 0.996 0.000 0.000 0.000 0.004
#> GSM674307     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674310     5  0.0162     0.9427 0.004 0.000 0.000 0.000 0.996
#> GSM674311     5  0.0963     0.9472 0.036 0.000 0.000 0.000 0.964
#> GSM674312     5  0.0880     0.9480 0.032 0.000 0.000 0.000 0.968
#> GSM674317     1  0.0000     0.9791 1.000 0.000 0.000 0.000 0.000
#> GSM674319     5  0.0963     0.9472 0.036 0.000 0.000 0.000 0.964
#> GSM674321     5  0.0162     0.9427 0.004 0.000 0.000 0.000 0.996
#> GSM674322     5  0.0290     0.9438 0.008 0.000 0.000 0.000 0.992
#> GSM674326     5  0.0000     0.9402 0.000 0.000 0.000 0.000 1.000
#> GSM674329     5  0.0162     0.9427 0.004 0.000 0.000 0.000 0.996
#> GSM674333     5  0.0963     0.9472 0.036 0.000 0.000 0.000 0.964

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4    p5    p6
#> GSM674344     3  0.2092     0.7268 0.000 0.000 0.876 0.124 0.000 0.000
#> GSM674346     3  0.0363     0.7431 0.000 0.000 0.988 0.012 0.000 0.000
#> GSM674347     3  0.3797     0.2551 0.000 0.000 0.580 0.420 0.000 0.000
#> GSM674348     3  0.3428     0.6656 0.000 0.000 0.696 0.304 0.000 0.000
#> GSM674349     3  0.3101     0.7382 0.000 0.000 0.756 0.244 0.000 0.000
#> GSM674350     3  0.3151     0.6668 0.000 0.000 0.748 0.252 0.000 0.000
#> GSM674353     3  0.2260     0.7363 0.000 0.000 0.860 0.140 0.000 0.000
#> GSM674354     3  0.1556     0.7458 0.000 0.000 0.920 0.080 0.000 0.000
#> GSM674355     3  0.2491     0.7305 0.000 0.000 0.836 0.164 0.000 0.000
#> GSM674356     3  0.2527     0.7332 0.000 0.000 0.832 0.168 0.000 0.000
#> GSM674357     3  0.3050     0.7462 0.000 0.000 0.764 0.236 0.000 0.000
#> GSM674358     3  0.2562     0.7309 0.000 0.000 0.828 0.172 0.000 0.000
#> GSM674361     3  0.1714     0.7443 0.000 0.000 0.908 0.092 0.000 0.000
#> GSM674363     3  0.1957     0.7417 0.000 0.000 0.888 0.112 0.000 0.000
#> GSM674364     3  0.0937     0.7474 0.000 0.000 0.960 0.040 0.000 0.000
#> GSM674365     3  0.2854     0.6979 0.000 0.000 0.792 0.208 0.000 0.000
#> GSM674366     4  0.3804    -0.0386 0.000 0.000 0.424 0.576 0.000 0.000
#> GSM674367     4  0.2003     0.7413 0.000 0.000 0.116 0.884 0.000 0.000
#> GSM674368     3  0.3607     0.5386 0.000 0.000 0.652 0.348 0.000 0.000
#> GSM674370     4  0.1910     0.6880 0.000 0.000 0.108 0.892 0.000 0.000
#> GSM674371     4  0.3868    -0.3222 0.000 0.000 0.492 0.508 0.000 0.000
#> GSM674373     4  0.3023     0.6033 0.000 0.000 0.232 0.768 0.000 0.000
#> GSM674375     4  0.0865     0.7336 0.000 0.000 0.036 0.964 0.000 0.000
#> GSM674379     4  0.1141     0.7395 0.000 0.000 0.052 0.948 0.000 0.000
#> GSM674380     4  0.2135     0.7347 0.000 0.000 0.128 0.872 0.000 0.000
#> GSM674381     4  0.2178     0.6663 0.000 0.000 0.132 0.868 0.000 0.000
#> GSM674382     4  0.2562     0.7275 0.000 0.000 0.172 0.828 0.000 0.000
#> GSM674384     4  0.2527     0.7215 0.000 0.000 0.168 0.832 0.000 0.000
#> GSM674385     3  0.3101     0.6776 0.000 0.000 0.756 0.244 0.000 0.000
#> GSM674388     3  0.3446     0.5959 0.000 0.000 0.692 0.308 0.000 0.000
#> GSM674389     4  0.2340     0.7282 0.000 0.000 0.148 0.852 0.000 0.000
#> GSM674390     4  0.0713     0.7363 0.000 0.000 0.028 0.972 0.000 0.000
#> GSM674391     4  0.2340     0.7399 0.000 0.000 0.148 0.852 0.000 0.000
#> GSM674393     4  0.3866    -0.0939 0.000 0.000 0.484 0.516 0.000 0.000
#> GSM674394     4  0.3765     0.4272 0.000 0.000 0.404 0.596 0.000 0.000
#> GSM674395     4  0.3851     0.3382 0.000 0.000 0.460 0.540 0.000 0.000
#> GSM674397     4  0.3864    -0.3160 0.000 0.000 0.480 0.520 0.000 0.000
#> GSM674398     4  0.1075     0.7382 0.000 0.000 0.048 0.952 0.000 0.000
#> GSM674400     4  0.3862     0.0385 0.000 0.000 0.476 0.524 0.000 0.000
#> GSM674401     3  0.3867     0.2808 0.000 0.000 0.512 0.488 0.000 0.000
#> GSM674402     3  0.1814     0.7119 0.000 0.000 0.900 0.100 0.000 0.000
#> GSM674403     3  0.3330     0.7132 0.000 0.000 0.716 0.284 0.000 0.000
#> GSM674405     4  0.2454     0.7327 0.000 0.000 0.160 0.840 0.000 0.000
#> GSM674406     4  0.2793     0.7160 0.000 0.000 0.200 0.800 0.000 0.000
#> GSM674407     4  0.1387     0.7384 0.000 0.000 0.068 0.932 0.000 0.000
#> GSM674181     2  0.0000     0.8715 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674183     2  0.0000     0.8715 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674184     2  0.0146     0.8705 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674185     2  0.0146     0.8705 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674186     2  0.0260     0.8699 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674187     2  0.0363     0.8688 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM674190     2  0.0000     0.8715 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674191     2  0.0000     0.8715 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674192     6  0.3867     0.6279 0.000 0.488 0.000 0.000 0.000 0.512
#> GSM674193     2  0.3547     0.1750 0.000 0.668 0.000 0.000 0.000 0.332
#> GSM674194     2  0.0458     0.8674 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM674195     2  0.0146     0.8705 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674198     6  0.3547     0.9547 0.000 0.332 0.000 0.000 0.000 0.668
#> GSM674200     2  0.0000     0.8715 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674201     2  0.0000     0.8715 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674202     2  0.0458     0.8674 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM674203     6  0.3563     0.9563 0.000 0.336 0.000 0.000 0.000 0.664
#> GSM674204     6  0.3592     0.9511 0.000 0.344 0.000 0.000 0.000 0.656
#> GSM674205     6  0.3563     0.9563 0.000 0.336 0.000 0.000 0.000 0.664
#> GSM674206     2  0.0000     0.8715 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674208     6  0.3563     0.9543 0.000 0.336 0.000 0.000 0.000 0.664
#> GSM674209     2  0.2260     0.7251 0.000 0.860 0.000 0.000 0.000 0.140
#> GSM674210     6  0.3563     0.9563 0.000 0.336 0.000 0.000 0.000 0.664
#> GSM674212     2  0.3817    -0.4295 0.000 0.568 0.000 0.000 0.000 0.432
#> GSM674214     6  0.3563     0.9563 0.000 0.336 0.000 0.000 0.000 0.664
#> GSM674218     2  0.0146     0.8705 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674219     2  0.0000     0.8715 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674220     2  0.0000     0.8715 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674221     2  0.0260     0.8685 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674223     2  0.1765     0.7813 0.000 0.904 0.000 0.000 0.000 0.096
#> GSM674225     2  0.0713     0.8603 0.000 0.972 0.000 0.000 0.000 0.028
#> GSM674226     2  0.0937     0.8487 0.000 0.960 0.000 0.000 0.000 0.040
#> GSM674229     6  0.3737     0.8984 0.000 0.392 0.000 0.000 0.000 0.608
#> GSM674230     2  0.0000     0.8715 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674231     2  0.2416     0.6858 0.000 0.844 0.000 0.000 0.000 0.156
#> GSM674232     6  0.3563     0.9563 0.000 0.336 0.000 0.000 0.000 0.664
#> GSM674234     6  0.3620     0.9388 0.000 0.352 0.000 0.000 0.000 0.648
#> GSM674235     2  0.0790     0.8494 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM674236     2  0.2793     0.6044 0.000 0.800 0.000 0.000 0.000 0.200
#> GSM674237     6  0.3547     0.9547 0.000 0.332 0.000 0.000 0.000 0.668
#> GSM674239     6  0.3672     0.9303 0.000 0.368 0.000 0.000 0.000 0.632
#> GSM674240     2  0.0000     0.8715 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674242     6  0.3563     0.9563 0.000 0.336 0.000 0.000 0.000 0.664
#> GSM674243     2  0.3695    -0.1453 0.000 0.624 0.000 0.000 0.000 0.376
#> GSM674244     2  0.0363     0.8686 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM674245     2  0.3266     0.3872 0.000 0.728 0.000 0.000 0.000 0.272
#> GSM674282     1  0.0000     0.9265 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674284     1  0.0632     0.9148 0.976 0.000 0.000 0.000 0.024 0.000
#> GSM674285     1  0.2135     0.9280 0.872 0.000 0.000 0.000 0.000 0.128
#> GSM674287     1  0.0000     0.9265 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674288     1  0.1663     0.8854 0.912 0.000 0.000 0.000 0.088 0.000
#> GSM674289     1  0.0146     0.9273 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM674290     1  0.2135     0.9280 0.872 0.000 0.000 0.000 0.000 0.128
#> GSM674291     1  0.2135     0.9280 0.872 0.000 0.000 0.000 0.000 0.128
#> GSM674292     1  0.2092     0.9284 0.876 0.000 0.000 0.000 0.000 0.124
#> GSM674295     5  0.3330     0.6856 0.284 0.000 0.000 0.000 0.716 0.000
#> GSM674297     1  0.0000     0.9265 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674298     1  0.0000     0.9265 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674299     1  0.0260     0.9235 0.992 0.000 0.000 0.000 0.008 0.000
#> GSM674300     1  0.3104     0.7941 0.788 0.000 0.004 0.000 0.004 0.204
#> GSM674301     1  0.2135     0.9280 0.872 0.000 0.000 0.000 0.000 0.128
#> GSM674302     1  0.2135     0.9280 0.872 0.000 0.000 0.000 0.000 0.128
#> GSM674304     1  0.2135     0.9280 0.872 0.000 0.000 0.000 0.000 0.128
#> GSM674305     1  0.2135     0.9280 0.872 0.000 0.000 0.000 0.000 0.128
#> GSM674306     1  0.3543     0.7959 0.720 0.000 0.004 0.000 0.004 0.272
#> GSM674308     1  0.2135     0.9280 0.872 0.000 0.000 0.000 0.000 0.128
#> GSM674309     5  0.0146     0.9400 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM674313     5  0.2964     0.8183 0.000 0.000 0.004 0.000 0.792 0.204
#> GSM674314     5  0.0146     0.9400 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM674315     1  0.3809     0.7850 0.732 0.000 0.004 0.000 0.024 0.240
#> GSM674316     5  0.0146     0.9400 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM674318     5  0.0000     0.9396 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674320     5  0.0000     0.9396 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674323     5  0.0000     0.9396 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674324     5  0.3076     0.7326 0.240 0.000 0.000 0.000 0.760 0.000
#> GSM674325     5  0.0146     0.9400 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM674327     5  0.3848     0.7840 0.040 0.000 0.004 0.000 0.752 0.204
#> GSM674328     1  0.0000     0.9265 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674330     5  0.0146     0.9400 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM674331     5  0.0363     0.9364 0.012 0.000 0.000 0.000 0.988 0.000
#> GSM674332     5  0.3867     0.2027 0.488 0.000 0.000 0.000 0.512 0.000
#> GSM674334     5  0.0260     0.9386 0.008 0.000 0.000 0.000 0.992 0.000
#> GSM674335     5  0.1327     0.9066 0.064 0.000 0.000 0.000 0.936 0.000
#> GSM674345     3  0.3076     0.7412 0.000 0.000 0.760 0.240 0.000 0.000
#> GSM674351     3  0.1957     0.7445 0.000 0.000 0.888 0.112 0.000 0.000
#> GSM674352     3  0.2823     0.7148 0.000 0.000 0.796 0.204 0.000 0.000
#> GSM674359     3  0.3101     0.7383 0.000 0.000 0.756 0.244 0.000 0.000
#> GSM674360     3  0.2664     0.7055 0.000 0.000 0.816 0.184 0.000 0.000
#> GSM674362     3  0.2462     0.7214 0.000 0.004 0.860 0.132 0.000 0.004
#> GSM674369     3  0.3717     0.5074 0.000 0.000 0.616 0.384 0.000 0.000
#> GSM674372     4  0.2340     0.7282 0.000 0.000 0.148 0.852 0.000 0.000
#> GSM674374     4  0.3023     0.5774 0.000 0.000 0.232 0.768 0.000 0.000
#> GSM674376     4  0.1141     0.7440 0.000 0.000 0.052 0.948 0.000 0.000
#> GSM674377     4  0.1714     0.6923 0.000 0.000 0.092 0.908 0.000 0.000
#> GSM674378     4  0.1556     0.7316 0.000 0.000 0.080 0.920 0.000 0.000
#> GSM674383     3  0.3843     0.3118 0.000 0.000 0.548 0.452 0.000 0.000
#> GSM674386     4  0.2416     0.7333 0.000 0.000 0.156 0.844 0.000 0.000
#> GSM674387     4  0.1387     0.7358 0.000 0.000 0.068 0.932 0.000 0.000
#> GSM674392     3  0.2697     0.7141 0.000 0.000 0.812 0.188 0.000 0.000
#> GSM674396     4  0.2300     0.7304 0.000 0.000 0.144 0.856 0.000 0.000
#> GSM674399     4  0.1957     0.7510 0.000 0.000 0.112 0.888 0.000 0.000
#> GSM674404     4  0.2664     0.7215 0.000 0.000 0.184 0.816 0.000 0.000
#> GSM674182     2  0.0000     0.8715 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674188     2  0.0363     0.8692 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM674189     2  0.0458     0.8674 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM674196     6  0.3563     0.9563 0.000 0.336 0.000 0.000 0.000 0.664
#> GSM674197     6  0.3765     0.8758 0.000 0.404 0.000 0.000 0.000 0.596
#> GSM674199     6  0.3547     0.9547 0.000 0.332 0.000 0.000 0.000 0.668
#> GSM674207     2  0.3838    -0.4819 0.000 0.552 0.000 0.000 0.000 0.448
#> GSM674211     2  0.3851    -0.5030 0.000 0.540 0.000 0.000 0.000 0.460
#> GSM674213     2  0.0260     0.8691 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674215     2  0.0000     0.8715 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674216     6  0.3547     0.9547 0.000 0.332 0.000 0.000 0.000 0.668
#> GSM674217     2  0.0000     0.8715 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674222     2  0.1141     0.8371 0.000 0.948 0.000 0.000 0.000 0.052
#> GSM674224     2  0.1714     0.7858 0.000 0.908 0.000 0.000 0.000 0.092
#> GSM674227     2  0.3101     0.4740 0.000 0.756 0.000 0.000 0.000 0.244
#> GSM674228     2  0.2300     0.6802 0.000 0.856 0.000 0.000 0.000 0.144
#> GSM674233     2  0.0000     0.8715 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674238     2  0.0146     0.8705 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674241     6  0.3774     0.8602 0.000 0.408 0.000 0.000 0.000 0.592
#> GSM674283     1  0.1387     0.9298 0.932 0.000 0.000 0.000 0.000 0.068
#> GSM674286     1  0.1075     0.9308 0.952 0.000 0.000 0.000 0.000 0.048
#> GSM674293     1  0.2520     0.9179 0.844 0.000 0.004 0.000 0.000 0.152
#> GSM674294     1  0.0146     0.9272 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM674296     1  0.2135     0.9280 0.872 0.000 0.000 0.000 0.000 0.128
#> GSM674303     1  0.0146     0.9256 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM674307     1  0.2135     0.9280 0.872 0.000 0.000 0.000 0.000 0.128
#> GSM674310     5  0.0000     0.9396 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674311     5  0.0146     0.9400 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM674312     5  0.0146     0.9400 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM674317     1  0.0000     0.9265 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674319     5  0.0865     0.9243 0.036 0.000 0.000 0.000 0.964 0.000
#> GSM674321     5  0.0000     0.9396 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674322     5  0.0000     0.9396 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674326     5  0.0000     0.9396 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674329     5  0.0000     0.9396 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674333     5  0.0146     0.9400 0.004 0.000 0.000 0.000 0.996 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-SD-pam-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-SD-pam-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-SD-pam-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-SD-pam-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-SD-pam-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-SD-pam-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-SD-pam-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-SD-pam-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-SD-pam-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-SD-pam-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-SD-pam-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-SD-pam-get-signatures-2

get_signatures(res, k = 4)
#> Error in mat[ceiling(1:nr/h_ratio), ceiling(1:nc/w_ratio), drop = FALSE]: subscript out of bounds

plot of chunk tab-SD-pam-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-SD-pam-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-SD-pam-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-SD-pam-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-SD-pam-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-SD-pam-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-SD-pam-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-SD-pam-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk SD-pam-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-SD-pam-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-SD-pam-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-SD-pam-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-SD-pam-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-SD-pam-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk SD-pam-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>          n disease.state(p) specimen(p) k
#> SD:pam 183            0.924    1.83e-40 2
#> SD:pam 183            0.962    6.15e-78 3
#> SD:pam 182            0.864    1.52e-75 4
#> SD:pam 170            0.809    1.23e-68 5
#> SD:pam 165            0.886    6.95e-65 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


SD:mclust*

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["SD", "mclust"]
# you can also extract it by
# res = res_list["SD:mclust"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#>   Subgroups are detected by 'mclust' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 5.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk SD-mclust-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk SD-mclust-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2  1.00           1.000       1.000         0.4189 0.582   0.582
#> 3 3  1.00           1.000       1.000         0.5958 0.750   0.571
#> 4 4  0.97           0.970       0.967         0.0534 0.957   0.870
#> 5 5  0.90           0.893       0.926         0.0368 0.982   0.939
#> 6 6  0.83           0.846       0.893         0.0290 0.986   0.948

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3 4

There is also optional best \(k\) = 2 3 4 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette p1 p2 p3
#> GSM674344     3       0          1  0  0  1
#> GSM674346     3       0          1  0  0  1
#> GSM674347     3       0          1  0  0  1
#> GSM674348     3       0          1  0  0  1
#> GSM674349     3       0          1  0  0  1
#> GSM674350     3       0          1  0  0  1
#> GSM674353     3       0          1  0  0  1
#> GSM674354     3       0          1  0  0  1
#> GSM674355     3       0          1  0  0  1
#> GSM674356     3       0          1  0  0  1
#> GSM674357     3       0          1  0  0  1
#> GSM674358     3       0          1  0  0  1
#> GSM674361     3       0          1  0  0  1
#> GSM674363     3       0          1  0  0  1
#> GSM674364     3       0          1  0  0  1
#> GSM674365     3       0          1  0  0  1
#> GSM674366     3       0          1  0  0  1
#> GSM674367     3       0          1  0  0  1
#> GSM674368     3       0          1  0  0  1
#> GSM674370     3       0          1  0  0  1
#> GSM674371     3       0          1  0  0  1
#> GSM674373     3       0          1  0  0  1
#> GSM674375     3       0          1  0  0  1
#> GSM674379     3       0          1  0  0  1
#> GSM674380     3       0          1  0  0  1
#> GSM674381     3       0          1  0  0  1
#> GSM674382     3       0          1  0  0  1
#> GSM674384     3       0          1  0  0  1
#> GSM674385     3       0          1  0  0  1
#> GSM674388     3       0          1  0  0  1
#> GSM674389     3       0          1  0  0  1
#> GSM674390     3       0          1  0  0  1
#> GSM674391     3       0          1  0  0  1
#> GSM674393     3       0          1  0  0  1
#> GSM674394     3       0          1  0  0  1
#> GSM674395     3       0          1  0  0  1
#> GSM674397     3       0          1  0  0  1
#> GSM674398     3       0          1  0  0  1
#> GSM674400     3       0          1  0  0  1
#> GSM674401     3       0          1  0  0  1
#> GSM674402     3       0          1  0  0  1
#> GSM674403     3       0          1  0  0  1
#> GSM674405     3       0          1  0  0  1
#> GSM674406     3       0          1  0  0  1
#> GSM674407     3       0          1  0  0  1
#> GSM674181     2       0          1  0  1  0
#> GSM674183     2       0          1  0  1  0
#> GSM674184     2       0          1  0  1  0
#> GSM674185     2       0          1  0  1  0
#> GSM674186     2       0          1  0  1  0
#> GSM674187     2       0          1  0  1  0
#> GSM674190     2       0          1  0  1  0
#> GSM674191     2       0          1  0  1  0
#> GSM674192     2       0          1  0  1  0
#> GSM674193     2       0          1  0  1  0
#> GSM674194     2       0          1  0  1  0
#> GSM674195     2       0          1  0  1  0
#> GSM674198     2       0          1  0  1  0
#> GSM674200     2       0          1  0  1  0
#> GSM674201     2       0          1  0  1  0
#> GSM674202     2       0          1  0  1  0
#> GSM674203     2       0          1  0  1  0
#> GSM674204     2       0          1  0  1  0
#> GSM674205     2       0          1  0  1  0
#> GSM674206     2       0          1  0  1  0
#> GSM674208     2       0          1  0  1  0
#> GSM674209     2       0          1  0  1  0
#> GSM674210     2       0          1  0  1  0
#> GSM674212     2       0          1  0  1  0
#> GSM674214     2       0          1  0  1  0
#> GSM674218     2       0          1  0  1  0
#> GSM674219     2       0          1  0  1  0
#> GSM674220     2       0          1  0  1  0
#> GSM674221     2       0          1  0  1  0
#> GSM674223     2       0          1  0  1  0
#> GSM674225     2       0          1  0  1  0
#> GSM674226     2       0          1  0  1  0
#> GSM674229     2       0          1  0  1  0
#> GSM674230     2       0          1  0  1  0
#> GSM674231     2       0          1  0  1  0
#> GSM674232     2       0          1  0  1  0
#> GSM674234     2       0          1  0  1  0
#> GSM674235     2       0          1  0  1  0
#> GSM674236     2       0          1  0  1  0
#> GSM674237     2       0          1  0  1  0
#> GSM674239     2       0          1  0  1  0
#> GSM674240     2       0          1  0  1  0
#> GSM674242     2       0          1  0  1  0
#> GSM674243     2       0          1  0  1  0
#> GSM674244     2       0          1  0  1  0
#> GSM674245     2       0          1  0  1  0
#> GSM674282     1       0          1  1  0  0
#> GSM674284     1       0          1  1  0  0
#> GSM674285     1       0          1  1  0  0
#> GSM674287     1       0          1  1  0  0
#> GSM674288     1       0          1  1  0  0
#> GSM674289     1       0          1  1  0  0
#> GSM674290     1       0          1  1  0  0
#> GSM674291     1       0          1  1  0  0
#> GSM674292     1       0          1  1  0  0
#> GSM674295     1       0          1  1  0  0
#> GSM674297     1       0          1  1  0  0
#> GSM674298     1       0          1  1  0  0
#> GSM674299     1       0          1  1  0  0
#> GSM674300     1       0          1  1  0  0
#> GSM674301     1       0          1  1  0  0
#> GSM674302     1       0          1  1  0  0
#> GSM674304     1       0          1  1  0  0
#> GSM674305     1       0          1  1  0  0
#> GSM674306     1       0          1  1  0  0
#> GSM674308     1       0          1  1  0  0
#> GSM674309     1       0          1  1  0  0
#> GSM674313     1       0          1  1  0  0
#> GSM674314     1       0          1  1  0  0
#> GSM674315     1       0          1  1  0  0
#> GSM674316     1       0          1  1  0  0
#> GSM674318     1       0          1  1  0  0
#> GSM674320     1       0          1  1  0  0
#> GSM674323     1       0          1  1  0  0
#> GSM674324     1       0          1  1  0  0
#> GSM674325     1       0          1  1  0  0
#> GSM674327     1       0          1  1  0  0
#> GSM674328     1       0          1  1  0  0
#> GSM674330     1       0          1  1  0  0
#> GSM674331     1       0          1  1  0  0
#> GSM674332     1       0          1  1  0  0
#> GSM674334     1       0          1  1  0  0
#> GSM674335     1       0          1  1  0  0
#> GSM674345     3       0          1  0  0  1
#> GSM674351     3       0          1  0  0  1
#> GSM674352     3       0          1  0  0  1
#> GSM674359     3       0          1  0  0  1
#> GSM674360     3       0          1  0  0  1
#> GSM674362     3       0          1  0  0  1
#> GSM674369     3       0          1  0  0  1
#> GSM674372     3       0          1  0  0  1
#> GSM674374     3       0          1  0  0  1
#> GSM674376     3       0          1  0  0  1
#> GSM674377     3       0          1  0  0  1
#> GSM674378     3       0          1  0  0  1
#> GSM674383     3       0          1  0  0  1
#> GSM674386     3       0          1  0  0  1
#> GSM674387     3       0          1  0  0  1
#> GSM674392     3       0          1  0  0  1
#> GSM674396     3       0          1  0  0  1
#> GSM674399     3       0          1  0  0  1
#> GSM674404     3       0          1  0  0  1
#> GSM674182     2       0          1  0  1  0
#> GSM674188     2       0          1  0  1  0
#> GSM674189     2       0          1  0  1  0
#> GSM674196     2       0          1  0  1  0
#> GSM674197     2       0          1  0  1  0
#> GSM674199     2       0          1  0  1  0
#> GSM674207     2       0          1  0  1  0
#> GSM674211     2       0          1  0  1  0
#> GSM674213     2       0          1  0  1  0
#> GSM674215     2       0          1  0  1  0
#> GSM674216     2       0          1  0  1  0
#> GSM674217     2       0          1  0  1  0
#> GSM674222     2       0          1  0  1  0
#> GSM674224     2       0          1  0  1  0
#> GSM674227     2       0          1  0  1  0
#> GSM674228     2       0          1  0  1  0
#> GSM674233     2       0          1  0  1  0
#> GSM674238     2       0          1  0  1  0
#> GSM674241     2       0          1  0  1  0
#> GSM674283     1       0          1  1  0  0
#> GSM674286     1       0          1  1  0  0
#> GSM674293     1       0          1  1  0  0
#> GSM674294     1       0          1  1  0  0
#> GSM674296     1       0          1  1  0  0
#> GSM674303     1       0          1  1  0  0
#> GSM674307     1       0          1  1  0  0
#> GSM674310     1       0          1  1  0  0
#> GSM674311     1       0          1  1  0  0
#> GSM674312     1       0          1  1  0  0
#> GSM674317     1       0          1  1  0  0
#> GSM674319     1       0          1  1  0  0
#> GSM674321     1       0          1  1  0  0
#> GSM674322     1       0          1  1  0  0
#> GSM674326     1       0          1  1  0  0
#> GSM674329     1       0          1  1  0  0
#> GSM674333     1       0          1  1  0  0

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1 p2    p3    p4
#> GSM674344     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674346     3  0.0336      0.994 0.000  0 0.992 0.008
#> GSM674347     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674348     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674349     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674350     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674353     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674354     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674355     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674356     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674357     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674358     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674361     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674363     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674364     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674365     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674366     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674367     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674368     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674370     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674371     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674373     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674375     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674379     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674380     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674381     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674382     3  0.0336      0.994 0.000  0 0.992 0.008
#> GSM674384     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674385     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674388     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674389     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674390     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674391     3  0.0336      0.994 0.000  0 0.992 0.008
#> GSM674393     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674394     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674395     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674397     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674398     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674400     3  0.0336      0.994 0.000  0 0.992 0.008
#> GSM674401     3  0.0336      0.994 0.000  0 0.992 0.008
#> GSM674402     3  0.0336      0.994 0.000  0 0.992 0.008
#> GSM674403     3  0.0336      0.994 0.000  0 0.992 0.008
#> GSM674405     3  0.0336      0.994 0.000  0 0.992 0.008
#> GSM674406     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674407     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674181     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674183     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674184     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674185     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674186     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674187     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674190     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674191     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674192     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674193     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674194     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674195     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674198     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674200     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674201     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674202     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674203     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674204     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674205     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674206     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674208     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674209     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674210     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674212     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674214     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674218     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674219     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674220     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674221     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674223     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674225     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674226     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674229     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674230     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674231     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674232     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674234     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674235     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674236     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674237     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674239     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674240     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674242     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674243     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674244     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674245     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674282     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674284     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674285     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674287     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674288     4  0.4277      0.888 0.280  0 0.000 0.720
#> GSM674289     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674290     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674291     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674292     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674295     4  0.4072      0.891 0.252  0 0.000 0.748
#> GSM674297     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674298     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674299     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674300     4  0.0336      0.730 0.008  0 0.000 0.992
#> GSM674301     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674302     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674304     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674305     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674306     4  0.0336      0.730 0.008  0 0.000 0.992
#> GSM674308     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674309     1  0.2011      0.887 0.920  0 0.000 0.080
#> GSM674313     4  0.0336      0.730 0.008  0 0.000 0.992
#> GSM674314     4  0.4250      0.891 0.276  0 0.000 0.724
#> GSM674315     4  0.0336      0.730 0.008  0 0.000 0.992
#> GSM674316     4  0.4697      0.796 0.356  0 0.000 0.644
#> GSM674318     4  0.4103      0.893 0.256  0 0.000 0.744
#> GSM674320     4  0.4134      0.894 0.260  0 0.000 0.740
#> GSM674323     4  0.4222      0.893 0.272  0 0.000 0.728
#> GSM674324     1  0.1118      0.940 0.964  0 0.000 0.036
#> GSM674325     4  0.4454      0.864 0.308  0 0.000 0.692
#> GSM674327     4  0.0592      0.735 0.016  0 0.000 0.984
#> GSM674328     1  0.1022      0.944 0.968  0 0.000 0.032
#> GSM674330     4  0.4477      0.860 0.312  0 0.000 0.688
#> GSM674331     1  0.1302      0.932 0.956  0 0.000 0.044
#> GSM674332     1  0.4134      0.507 0.740  0 0.000 0.260
#> GSM674334     1  0.2530      0.838 0.888  0 0.000 0.112
#> GSM674335     4  0.4543      0.846 0.324  0 0.000 0.676
#> GSM674345     3  0.0188      0.997 0.000  0 0.996 0.004
#> GSM674351     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674352     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674359     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674360     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674362     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674369     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674372     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674374     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674376     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674377     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674378     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674383     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674386     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674387     3  0.0188      0.997 0.000  0 0.996 0.004
#> GSM674392     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674396     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674399     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674404     3  0.0000      0.999 0.000  0 1.000 0.000
#> GSM674182     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674188     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674189     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674196     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674197     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674199     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674207     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674211     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674213     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674215     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674216     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674217     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674222     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674224     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674227     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674228     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674233     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674238     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674241     2  0.0000      1.000 0.000  1 0.000 0.000
#> GSM674283     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674286     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674293     4  0.4040      0.887 0.248  0 0.000 0.752
#> GSM674294     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674296     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674303     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674307     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674310     4  0.4134      0.894 0.260  0 0.000 0.740
#> GSM674311     1  0.1716      0.908 0.936  0 0.000 0.064
#> GSM674312     4  0.4222      0.893 0.272  0 0.000 0.728
#> GSM674317     1  0.0000      0.971 1.000  0 0.000 0.000
#> GSM674319     4  0.4543      0.846 0.324  0 0.000 0.676
#> GSM674321     4  0.4193      0.894 0.268  0 0.000 0.732
#> GSM674322     4  0.4222      0.893 0.272  0 0.000 0.728
#> GSM674326     4  0.4040      0.889 0.248  0 0.000 0.752
#> GSM674329     4  0.4193      0.894 0.268  0 0.000 0.732
#> GSM674333     4  0.4222      0.893 0.272  0 0.000 0.728

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4    p5
#> GSM674344     3  0.2179      0.804 0.000 0.000 0.888 0.000 0.112
#> GSM674346     5  0.4283      0.841 0.000 0.000 0.456 0.000 0.544
#> GSM674347     3  0.1671      0.852 0.000 0.000 0.924 0.000 0.076
#> GSM674348     3  0.0703      0.887 0.000 0.000 0.976 0.000 0.024
#> GSM674349     3  0.1341      0.869 0.000 0.000 0.944 0.000 0.056
#> GSM674350     3  0.0404      0.890 0.000 0.000 0.988 0.000 0.012
#> GSM674353     3  0.1732      0.844 0.000 0.000 0.920 0.000 0.080
#> GSM674354     3  0.1197      0.871 0.000 0.000 0.952 0.000 0.048
#> GSM674355     3  0.1608      0.851 0.000 0.000 0.928 0.000 0.072
#> GSM674356     3  0.1608      0.851 0.000 0.000 0.928 0.000 0.072
#> GSM674357     3  0.1732      0.845 0.000 0.000 0.920 0.000 0.080
#> GSM674358     3  0.1608      0.851 0.000 0.000 0.928 0.000 0.072
#> GSM674361     3  0.1270      0.867 0.000 0.000 0.948 0.000 0.052
#> GSM674363     3  0.1608      0.851 0.000 0.000 0.928 0.000 0.072
#> GSM674364     3  0.0000      0.889 0.000 0.000 1.000 0.000 0.000
#> GSM674365     3  0.1197      0.878 0.000 0.000 0.952 0.000 0.048
#> GSM674366     3  0.0963      0.885 0.000 0.000 0.964 0.000 0.036
#> GSM674367     3  0.0794      0.884 0.000 0.000 0.972 0.000 0.028
#> GSM674368     3  0.0162      0.889 0.000 0.000 0.996 0.000 0.004
#> GSM674370     3  0.0510      0.890 0.000 0.000 0.984 0.000 0.016
#> GSM674371     3  0.0880      0.885 0.000 0.000 0.968 0.000 0.032
#> GSM674373     3  0.0609      0.885 0.000 0.000 0.980 0.000 0.020
#> GSM674375     3  0.1270      0.878 0.000 0.000 0.948 0.000 0.052
#> GSM674379     3  0.1410      0.871 0.000 0.000 0.940 0.000 0.060
#> GSM674380     3  0.1197      0.879 0.000 0.000 0.952 0.000 0.048
#> GSM674381     3  0.1410      0.871 0.000 0.000 0.940 0.000 0.060
#> GSM674382     3  0.2852      0.710 0.000 0.000 0.828 0.000 0.172
#> GSM674384     3  0.1410      0.871 0.000 0.000 0.940 0.000 0.060
#> GSM674385     3  0.0703      0.888 0.000 0.000 0.976 0.000 0.024
#> GSM674388     3  0.0609      0.887 0.000 0.000 0.980 0.000 0.020
#> GSM674389     3  0.1732      0.856 0.000 0.000 0.920 0.000 0.080
#> GSM674390     3  0.1043      0.884 0.000 0.000 0.960 0.000 0.040
#> GSM674391     3  0.2929      0.685 0.000 0.000 0.820 0.000 0.180
#> GSM674393     3  0.0963      0.884 0.000 0.000 0.964 0.000 0.036
#> GSM674394     3  0.0703      0.888 0.000 0.000 0.976 0.000 0.024
#> GSM674395     3  0.1608      0.874 0.000 0.000 0.928 0.000 0.072
#> GSM674397     3  0.0000      0.889 0.000 0.000 1.000 0.000 0.000
#> GSM674398     3  0.1908      0.845 0.000 0.000 0.908 0.000 0.092
#> GSM674400     5  0.4291      0.835 0.000 0.000 0.464 0.000 0.536
#> GSM674401     5  0.4138      0.882 0.000 0.000 0.384 0.000 0.616
#> GSM674402     5  0.3999      0.865 0.000 0.000 0.344 0.000 0.656
#> GSM674403     5  0.4161      0.892 0.000 0.000 0.392 0.000 0.608
#> GSM674405     3  0.4192     -0.381 0.000 0.000 0.596 0.000 0.404
#> GSM674406     3  0.0880      0.884 0.000 0.000 0.968 0.000 0.032
#> GSM674407     3  0.2074      0.852 0.000 0.000 0.896 0.000 0.104
#> GSM674181     2  0.0510      0.986 0.000 0.984 0.000 0.000 0.016
#> GSM674183     2  0.2488      0.886 0.000 0.872 0.000 0.004 0.124
#> GSM674184     2  0.0162      0.991 0.000 0.996 0.000 0.000 0.004
#> GSM674185     2  0.0162      0.991 0.000 0.996 0.000 0.000 0.004
#> GSM674186     2  0.0000      0.991 0.000 1.000 0.000 0.000 0.000
#> GSM674187     2  0.0162      0.991 0.000 0.996 0.000 0.000 0.004
#> GSM674190     2  0.0162      0.990 0.000 0.996 0.000 0.000 0.004
#> GSM674191     2  0.0162      0.990 0.000 0.996 0.000 0.000 0.004
#> GSM674192     2  0.0000      0.991 0.000 1.000 0.000 0.000 0.000
#> GSM674193     2  0.0162      0.991 0.000 0.996 0.000 0.000 0.004
#> GSM674194     2  0.0162      0.991 0.000 0.996 0.000 0.000 0.004
#> GSM674195     2  0.0162      0.991 0.000 0.996 0.000 0.000 0.004
#> GSM674198     2  0.0162      0.990 0.000 0.996 0.000 0.000 0.004
#> GSM674200     2  0.2488      0.886 0.000 0.872 0.000 0.004 0.124
#> GSM674201     2  0.0290      0.989 0.000 0.992 0.000 0.000 0.008
#> GSM674202     2  0.0162      0.991 0.000 0.996 0.000 0.000 0.004
#> GSM674203     2  0.0290      0.990 0.000 0.992 0.000 0.000 0.008
#> GSM674204     2  0.1121      0.964 0.000 0.956 0.000 0.000 0.044
#> GSM674205     2  0.0000      0.991 0.000 1.000 0.000 0.000 0.000
#> GSM674206     2  0.0162      0.990 0.000 0.996 0.000 0.000 0.004
#> GSM674208     2  0.0162      0.990 0.000 0.996 0.000 0.000 0.004
#> GSM674209     2  0.0162      0.991 0.000 0.996 0.000 0.000 0.004
#> GSM674210     2  0.0162      0.990 0.000 0.996 0.000 0.000 0.004
#> GSM674212     2  0.0162      0.990 0.000 0.996 0.000 0.000 0.004
#> GSM674214     2  0.0162      0.990 0.000 0.996 0.000 0.000 0.004
#> GSM674218     2  0.0162      0.991 0.000 0.996 0.000 0.000 0.004
#> GSM674219     2  0.0162      0.990 0.000 0.996 0.000 0.000 0.004
#> GSM674220     2  0.0290      0.990 0.000 0.992 0.000 0.000 0.008
#> GSM674221     2  0.0000      0.991 0.000 1.000 0.000 0.000 0.000
#> GSM674223     2  0.0162      0.990 0.000 0.996 0.000 0.000 0.004
#> GSM674225     2  0.0510      0.985 0.000 0.984 0.000 0.000 0.016
#> GSM674226     2  0.0162      0.990 0.000 0.996 0.000 0.000 0.004
#> GSM674229     2  0.0162      0.990 0.000 0.996 0.000 0.000 0.004
#> GSM674230     2  0.0162      0.990 0.000 0.996 0.000 0.000 0.004
#> GSM674231     2  0.0162      0.991 0.000 0.996 0.000 0.000 0.004
#> GSM674232     2  0.0162      0.990 0.000 0.996 0.000 0.000 0.004
#> GSM674234     2  0.0000      0.991 0.000 1.000 0.000 0.000 0.000
#> GSM674235     2  0.0000      0.991 0.000 1.000 0.000 0.000 0.000
#> GSM674236     2  0.0162      0.991 0.000 0.996 0.000 0.000 0.004
#> GSM674237     2  0.0290      0.990 0.000 0.992 0.000 0.000 0.008
#> GSM674239     2  0.0290      0.990 0.000 0.992 0.000 0.000 0.008
#> GSM674240     2  0.0162      0.990 0.000 0.996 0.000 0.000 0.004
#> GSM674242     2  0.0404      0.990 0.000 0.988 0.000 0.000 0.012
#> GSM674243     2  0.1908      0.920 0.000 0.908 0.000 0.000 0.092
#> GSM674244     2  0.0162      0.991 0.000 0.996 0.000 0.000 0.004
#> GSM674245     2  0.0162      0.990 0.000 0.996 0.000 0.000 0.004
#> GSM674282     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674284     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674285     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674287     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674288     4  0.4339      0.723 0.336 0.000 0.000 0.652 0.012
#> GSM674289     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674291     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674292     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674295     4  0.3355      0.835 0.184 0.000 0.000 0.804 0.012
#> GSM674297     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674298     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674299     1  0.0290      0.979 0.992 0.000 0.000 0.008 0.000
#> GSM674300     4  0.3635      0.644 0.004 0.000 0.000 0.748 0.248
#> GSM674301     1  0.0404      0.973 0.988 0.000 0.000 0.012 0.000
#> GSM674302     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674305     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674306     4  0.3635      0.644 0.004 0.000 0.000 0.748 0.248
#> GSM674308     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674309     1  0.1281      0.949 0.956 0.000 0.000 0.032 0.012
#> GSM674313     4  0.3395      0.646 0.000 0.000 0.000 0.764 0.236
#> GSM674314     4  0.3496      0.829 0.200 0.000 0.000 0.788 0.012
#> GSM674315     4  0.3635      0.644 0.004 0.000 0.000 0.748 0.248
#> GSM674316     4  0.3983      0.718 0.340 0.000 0.000 0.660 0.000
#> GSM674318     4  0.2953      0.833 0.144 0.000 0.000 0.844 0.012
#> GSM674320     4  0.3081      0.836 0.156 0.000 0.000 0.832 0.012
#> GSM674323     4  0.2813      0.838 0.168 0.000 0.000 0.832 0.000
#> GSM674324     1  0.0703      0.966 0.976 0.000 0.000 0.024 0.000
#> GSM674325     4  0.3884      0.773 0.288 0.000 0.000 0.708 0.004
#> GSM674327     4  0.1764      0.720 0.008 0.000 0.000 0.928 0.064
#> GSM674328     1  0.0880      0.960 0.968 0.000 0.000 0.032 0.000
#> GSM674330     4  0.4537      0.644 0.396 0.000 0.000 0.592 0.012
#> GSM674331     1  0.0703      0.966 0.976 0.000 0.000 0.024 0.000
#> GSM674332     1  0.2818      0.800 0.856 0.000 0.000 0.132 0.012
#> GSM674334     1  0.1740      0.918 0.932 0.000 0.000 0.056 0.012
#> GSM674335     4  0.4627      0.551 0.444 0.000 0.000 0.544 0.012
#> GSM674345     3  0.4256     -0.590 0.000 0.000 0.564 0.000 0.436
#> GSM674351     3  0.1732      0.844 0.000 0.000 0.920 0.000 0.080
#> GSM674352     3  0.0609      0.889 0.000 0.000 0.980 0.000 0.020
#> GSM674359     3  0.2127      0.808 0.000 0.000 0.892 0.000 0.108
#> GSM674360     3  0.0703      0.888 0.000 0.000 0.976 0.000 0.024
#> GSM674362     3  0.0609      0.888 0.000 0.000 0.980 0.000 0.020
#> GSM674369     3  0.0000      0.889 0.000 0.000 1.000 0.000 0.000
#> GSM674372     3  0.0794      0.891 0.000 0.000 0.972 0.000 0.028
#> GSM674374     3  0.0290      0.888 0.000 0.000 0.992 0.000 0.008
#> GSM674376     3  0.1908      0.845 0.000 0.000 0.908 0.000 0.092
#> GSM674377     3  0.1410      0.871 0.000 0.000 0.940 0.000 0.060
#> GSM674378     3  0.0703      0.883 0.000 0.000 0.976 0.000 0.024
#> GSM674383     3  0.0880      0.885 0.000 0.000 0.968 0.000 0.032
#> GSM674386     3  0.1478      0.868 0.000 0.000 0.936 0.000 0.064
#> GSM674387     3  0.3074      0.656 0.000 0.000 0.804 0.000 0.196
#> GSM674392     3  0.1544      0.855 0.000 0.000 0.932 0.000 0.068
#> GSM674396     3  0.1792      0.853 0.000 0.000 0.916 0.000 0.084
#> GSM674399     3  0.1732      0.856 0.000 0.000 0.920 0.000 0.080
#> GSM674404     3  0.2377      0.836 0.000 0.000 0.872 0.000 0.128
#> GSM674182     2  0.0162      0.990 0.000 0.996 0.000 0.000 0.004
#> GSM674188     2  0.0162      0.991 0.000 0.996 0.000 0.000 0.004
#> GSM674189     2  0.0162      0.991 0.000 0.996 0.000 0.000 0.004
#> GSM674196     2  0.0290      0.990 0.000 0.992 0.000 0.000 0.008
#> GSM674197     2  0.0000      0.991 0.000 1.000 0.000 0.000 0.000
#> GSM674199     2  0.0000      0.991 0.000 1.000 0.000 0.000 0.000
#> GSM674207     2  0.0162      0.991 0.000 0.996 0.000 0.000 0.004
#> GSM674211     2  0.0000      0.991 0.000 1.000 0.000 0.000 0.000
#> GSM674213     2  0.0000      0.991 0.000 1.000 0.000 0.000 0.000
#> GSM674215     2  0.0162      0.991 0.000 0.996 0.000 0.000 0.004
#> GSM674216     2  0.0290      0.990 0.000 0.992 0.000 0.000 0.008
#> GSM674217     2  0.0000      0.991 0.000 1.000 0.000 0.000 0.000
#> GSM674222     2  0.0162      0.991 0.000 0.996 0.000 0.000 0.004
#> GSM674224     2  0.0162      0.990 0.000 0.996 0.000 0.000 0.004
#> GSM674227     2  0.0162      0.991 0.000 0.996 0.000 0.000 0.004
#> GSM674228     2  0.0000      0.991 0.000 1.000 0.000 0.000 0.000
#> GSM674233     2  0.0290      0.989 0.000 0.992 0.000 0.000 0.008
#> GSM674238     2  0.1341      0.952 0.000 0.944 0.000 0.000 0.056
#> GSM674241     2  0.0000      0.991 0.000 1.000 0.000 0.000 0.000
#> GSM674283     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674286     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674293     4  0.4982      0.604 0.412 0.000 0.000 0.556 0.032
#> GSM674294     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674296     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674303     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674307     1  0.0000      0.983 1.000 0.000 0.000 0.000 0.000
#> GSM674310     4  0.2953      0.833 0.144 0.000 0.000 0.844 0.012
#> GSM674311     1  0.1195      0.954 0.960 0.000 0.000 0.028 0.012
#> GSM674312     4  0.3280      0.837 0.176 0.000 0.000 0.812 0.012
#> GSM674317     1  0.0162      0.981 0.996 0.000 0.000 0.004 0.000
#> GSM674319     4  0.4649      0.633 0.404 0.000 0.000 0.580 0.016
#> GSM674321     4  0.2813      0.838 0.168 0.000 0.000 0.832 0.000
#> GSM674322     4  0.3160      0.835 0.188 0.000 0.000 0.808 0.004
#> GSM674326     4  0.2674      0.833 0.140 0.000 0.000 0.856 0.004
#> GSM674329     4  0.2970      0.837 0.168 0.000 0.000 0.828 0.004
#> GSM674333     4  0.3196      0.834 0.192 0.000 0.000 0.804 0.004

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4    p5    p6
#> GSM674344     3  0.3050      0.816 0.000 0.000 0.764 0.236 0.000 0.000
#> GSM674346     4  0.2793      0.843 0.000 0.000 0.200 0.800 0.000 0.000
#> GSM674347     3  0.1663      0.829 0.000 0.000 0.912 0.088 0.000 0.000
#> GSM674348     3  0.2562      0.839 0.000 0.000 0.828 0.172 0.000 0.000
#> GSM674349     3  0.1714      0.860 0.000 0.000 0.908 0.092 0.000 0.000
#> GSM674350     3  0.0865      0.854 0.000 0.000 0.964 0.036 0.000 0.000
#> GSM674353     3  0.1663      0.827 0.000 0.000 0.912 0.088 0.000 0.000
#> GSM674354     3  0.2854      0.833 0.000 0.000 0.792 0.208 0.000 0.000
#> GSM674355     3  0.1556      0.832 0.000 0.000 0.920 0.080 0.000 0.000
#> GSM674356     3  0.2730      0.838 0.000 0.000 0.808 0.192 0.000 0.000
#> GSM674357     3  0.2178      0.841 0.000 0.000 0.868 0.132 0.000 0.000
#> GSM674358     3  0.1610      0.830 0.000 0.000 0.916 0.084 0.000 0.000
#> GSM674361     3  0.1610      0.842 0.000 0.000 0.916 0.084 0.000 0.000
#> GSM674363     3  0.2378      0.842 0.000 0.000 0.848 0.152 0.000 0.000
#> GSM674364     3  0.2340      0.843 0.000 0.000 0.852 0.148 0.000 0.000
#> GSM674365     3  0.2562      0.839 0.000 0.000 0.828 0.172 0.000 0.000
#> GSM674366     3  0.2416      0.848 0.000 0.000 0.844 0.156 0.000 0.000
#> GSM674367     3  0.0865      0.854 0.000 0.000 0.964 0.036 0.000 0.000
#> GSM674368     3  0.2340      0.843 0.000 0.000 0.852 0.148 0.000 0.000
#> GSM674370     3  0.1327      0.864 0.000 0.000 0.936 0.064 0.000 0.000
#> GSM674371     3  0.2491      0.843 0.000 0.000 0.836 0.164 0.000 0.000
#> GSM674373     3  0.2454      0.843 0.000 0.000 0.840 0.160 0.000 0.000
#> GSM674375     3  0.0713      0.855 0.000 0.000 0.972 0.028 0.000 0.000
#> GSM674379     3  0.0790      0.854 0.000 0.000 0.968 0.032 0.000 0.000
#> GSM674380     3  0.2562      0.839 0.000 0.000 0.828 0.172 0.000 0.000
#> GSM674381     3  0.2491      0.844 0.000 0.000 0.836 0.164 0.000 0.000
#> GSM674382     3  0.2260      0.791 0.000 0.000 0.860 0.140 0.000 0.000
#> GSM674384     3  0.2416      0.848 0.000 0.000 0.844 0.156 0.000 0.000
#> GSM674385     3  0.2562      0.839 0.000 0.000 0.828 0.172 0.000 0.000
#> GSM674388     3  0.2003      0.861 0.000 0.000 0.884 0.116 0.000 0.000
#> GSM674389     3  0.1267      0.842 0.000 0.000 0.940 0.060 0.000 0.000
#> GSM674390     3  0.1075      0.861 0.000 0.000 0.952 0.048 0.000 0.000
#> GSM674391     3  0.2003      0.793 0.000 0.000 0.884 0.116 0.000 0.000
#> GSM674393     3  0.0713      0.855 0.000 0.000 0.972 0.028 0.000 0.000
#> GSM674394     3  0.2416      0.848 0.000 0.000 0.844 0.156 0.000 0.000
#> GSM674395     3  0.1204      0.846 0.000 0.000 0.944 0.056 0.000 0.000
#> GSM674397     3  0.2340      0.843 0.000 0.000 0.852 0.148 0.000 0.000
#> GSM674398     3  0.1556      0.829 0.000 0.000 0.920 0.080 0.000 0.000
#> GSM674400     4  0.3023      0.872 0.000 0.000 0.232 0.768 0.000 0.000
#> GSM674401     4  0.2912      0.858 0.000 0.000 0.216 0.784 0.000 0.000
#> GSM674402     4  0.2092      0.808 0.000 0.000 0.124 0.876 0.000 0.000
#> GSM674403     4  0.2912      0.865 0.000 0.000 0.216 0.784 0.000 0.000
#> GSM674405     3  0.3857     -0.368 0.000 0.000 0.532 0.468 0.000 0.000
#> GSM674406     3  0.1141      0.848 0.000 0.000 0.948 0.052 0.000 0.000
#> GSM674407     3  0.1663      0.831 0.000 0.000 0.912 0.088 0.000 0.000
#> GSM674181     2  0.1262      0.940 0.000 0.956 0.000 0.008 0.020 0.016
#> GSM674183     2  0.5269      0.654 0.000 0.664 0.000 0.044 0.084 0.208
#> GSM674184     2  0.2135      0.883 0.000 0.872 0.000 0.000 0.000 0.128
#> GSM674185     2  0.0000      0.958 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674186     2  0.0937      0.944 0.000 0.960 0.000 0.000 0.000 0.040
#> GSM674187     2  0.2178      0.878 0.000 0.868 0.000 0.000 0.000 0.132
#> GSM674190     2  0.0260      0.958 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674191     2  0.0405      0.957 0.000 0.988 0.000 0.004 0.000 0.008
#> GSM674192     2  0.0291      0.958 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM674193     2  0.0146      0.958 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674194     2  0.1957      0.895 0.000 0.888 0.000 0.000 0.000 0.112
#> GSM674195     2  0.2664      0.835 0.000 0.816 0.000 0.000 0.000 0.184
#> GSM674198     2  0.0291      0.958 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM674200     2  0.5269      0.654 0.000 0.664 0.000 0.044 0.084 0.208
#> GSM674201     2  0.2209      0.913 0.000 0.900 0.000 0.004 0.024 0.072
#> GSM674202     2  0.0000      0.958 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674203     2  0.0436      0.957 0.000 0.988 0.000 0.004 0.004 0.004
#> GSM674204     2  0.2738      0.844 0.000 0.820 0.000 0.004 0.000 0.176
#> GSM674205     2  0.0146      0.958 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674206     2  0.0260      0.958 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674208     2  0.0291      0.958 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM674209     2  0.2454      0.856 0.000 0.840 0.000 0.000 0.000 0.160
#> GSM674210     2  0.0146      0.958 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674212     2  0.0291      0.958 0.000 0.992 0.000 0.004 0.000 0.004
#> GSM674214     2  0.0291      0.958 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM674218     2  0.2597      0.842 0.000 0.824 0.000 0.000 0.000 0.176
#> GSM674219     2  0.0603      0.956 0.000 0.980 0.000 0.004 0.000 0.016
#> GSM674220     2  0.0260      0.958 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674221     2  0.0146      0.958 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674223     2  0.1814      0.908 0.000 0.900 0.000 0.000 0.000 0.100
#> GSM674225     2  0.0291      0.958 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM674226     2  0.0291      0.958 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM674229     2  0.0291      0.958 0.000 0.992 0.000 0.004 0.000 0.004
#> GSM674230     2  0.0405      0.957 0.000 0.988 0.000 0.004 0.000 0.008
#> GSM674231     2  0.0146      0.958 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674232     2  0.0146      0.958 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674234     2  0.0260      0.958 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674235     2  0.0000      0.958 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674236     2  0.0000      0.958 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674237     2  0.0146      0.958 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM674239     2  0.0436      0.957 0.000 0.988 0.000 0.004 0.004 0.004
#> GSM674240     2  0.0363      0.958 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM674242     2  0.0291      0.958 0.000 0.992 0.000 0.004 0.004 0.000
#> GSM674243     2  0.3078      0.821 0.000 0.796 0.000 0.012 0.000 0.192
#> GSM674244     2  0.0146      0.958 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM674245     2  0.0291      0.958 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM674282     1  0.0146      0.946 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM674284     1  0.0146      0.946 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM674285     1  0.0146      0.946 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM674287     1  0.0508      0.944 0.984 0.000 0.000 0.000 0.012 0.004
#> GSM674288     5  0.3171      0.691 0.204 0.000 0.000 0.000 0.784 0.012
#> GSM674289     1  0.0405      0.945 0.988 0.000 0.000 0.004 0.008 0.000
#> GSM674290     1  0.0146      0.946 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM674291     1  0.0146      0.946 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM674292     1  0.0291      0.946 0.992 0.000 0.000 0.004 0.000 0.004
#> GSM674295     5  0.2257      0.707 0.116 0.000 0.000 0.000 0.876 0.008
#> GSM674297     1  0.0146      0.946 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM674298     1  0.0260      0.946 0.992 0.000 0.000 0.000 0.008 0.000
#> GSM674299     1  0.0692      0.940 0.976 0.000 0.000 0.000 0.020 0.004
#> GSM674300     6  0.3647      0.875 0.000 0.000 0.000 0.000 0.360 0.640
#> GSM674301     1  0.0935      0.919 0.964 0.000 0.000 0.004 0.032 0.000
#> GSM674302     1  0.0146      0.946 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM674304     1  0.0291      0.945 0.992 0.000 0.000 0.004 0.004 0.000
#> GSM674305     1  0.0260      0.946 0.992 0.000 0.000 0.000 0.008 0.000
#> GSM674306     6  0.3647      0.875 0.000 0.000 0.000 0.000 0.360 0.640
#> GSM674308     1  0.0146      0.946 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM674309     1  0.1124      0.927 0.956 0.000 0.000 0.000 0.036 0.008
#> GSM674313     6  0.3851      0.541 0.000 0.000 0.000 0.000 0.460 0.540
#> GSM674314     5  0.3717      0.609 0.276 0.000 0.000 0.000 0.708 0.016
#> GSM674315     6  0.3647      0.875 0.000 0.000 0.000 0.000 0.360 0.640
#> GSM674316     1  0.4076     -0.195 0.540 0.000 0.000 0.000 0.452 0.008
#> GSM674318     5  0.3307      0.670 0.108 0.000 0.000 0.000 0.820 0.072
#> GSM674320     5  0.3878      0.647 0.116 0.000 0.000 0.000 0.772 0.112
#> GSM674323     5  0.2191      0.711 0.120 0.000 0.000 0.000 0.876 0.004
#> GSM674324     1  0.0363      0.945 0.988 0.000 0.000 0.000 0.012 0.000
#> GSM674325     5  0.3965      0.516 0.388 0.000 0.000 0.000 0.604 0.008
#> GSM674327     5  0.2823      0.152 0.000 0.000 0.000 0.000 0.796 0.204
#> GSM674328     1  0.0777      0.938 0.972 0.000 0.000 0.000 0.024 0.004
#> GSM674330     5  0.4242      0.437 0.448 0.000 0.000 0.000 0.536 0.016
#> GSM674331     1  0.0363      0.945 0.988 0.000 0.000 0.000 0.012 0.000
#> GSM674332     1  0.2553      0.782 0.848 0.000 0.000 0.000 0.144 0.008
#> GSM674334     1  0.1049      0.922 0.960 0.000 0.000 0.000 0.032 0.008
#> GSM674335     1  0.4099      0.130 0.612 0.000 0.000 0.000 0.372 0.016
#> GSM674345     4  0.3672      0.725 0.000 0.000 0.368 0.632 0.000 0.000
#> GSM674351     3  0.1663      0.827 0.000 0.000 0.912 0.088 0.000 0.000
#> GSM674352     3  0.0865      0.855 0.000 0.000 0.964 0.036 0.000 0.000
#> GSM674359     3  0.3023      0.818 0.000 0.000 0.768 0.232 0.000 0.000
#> GSM674360     3  0.2527      0.840 0.000 0.000 0.832 0.168 0.000 0.000
#> GSM674362     3  0.2527      0.840 0.000 0.000 0.832 0.168 0.000 0.000
#> GSM674369     3  0.2340      0.843 0.000 0.000 0.852 0.148 0.000 0.000
#> GSM674372     3  0.0632      0.857 0.000 0.000 0.976 0.024 0.000 0.000
#> GSM674374     3  0.2378      0.843 0.000 0.000 0.848 0.152 0.000 0.000
#> GSM674376     3  0.1387      0.838 0.000 0.000 0.932 0.068 0.000 0.000
#> GSM674377     3  0.2562      0.839 0.000 0.000 0.828 0.172 0.000 0.000
#> GSM674378     3  0.0713      0.856 0.000 0.000 0.972 0.028 0.000 0.000
#> GSM674383     3  0.2562      0.839 0.000 0.000 0.828 0.172 0.000 0.000
#> GSM674386     3  0.0865      0.853 0.000 0.000 0.964 0.036 0.000 0.000
#> GSM674387     3  0.2527      0.759 0.000 0.000 0.832 0.168 0.000 0.000
#> GSM674392     3  0.1556      0.832 0.000 0.000 0.920 0.080 0.000 0.000
#> GSM674396     3  0.1267      0.842 0.000 0.000 0.940 0.060 0.000 0.000
#> GSM674399     3  0.1267      0.842 0.000 0.000 0.940 0.060 0.000 0.000
#> GSM674404     3  0.1863      0.824 0.000 0.000 0.896 0.104 0.000 0.000
#> GSM674182     2  0.0405      0.957 0.000 0.988 0.000 0.004 0.000 0.008
#> GSM674188     2  0.0146      0.958 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674189     2  0.2664      0.835 0.000 0.816 0.000 0.000 0.000 0.184
#> GSM674196     2  0.1082      0.943 0.000 0.956 0.000 0.004 0.000 0.040
#> GSM674197     2  0.0260      0.958 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674199     2  0.0291      0.958 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM674207     2  0.0000      0.958 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674211     2  0.0260      0.958 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674213     2  0.0260      0.958 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674215     2  0.0000      0.958 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674216     2  0.0146      0.958 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM674217     2  0.0363      0.957 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM674222     2  0.0146      0.958 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM674224     2  0.0291      0.958 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM674227     2  0.0146      0.958 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674228     2  0.0146      0.958 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674233     2  0.0508      0.956 0.000 0.984 0.000 0.004 0.000 0.012
#> GSM674238     2  0.2730      0.828 0.000 0.808 0.000 0.000 0.000 0.192
#> GSM674241     2  0.0260      0.958 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674283     1  0.0000      0.946 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674286     1  0.0146      0.946 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM674293     5  0.5861      0.177 0.308 0.000 0.000 0.000 0.472 0.220
#> GSM674294     1  0.0363      0.945 0.988 0.000 0.000 0.000 0.012 0.000
#> GSM674296     1  0.0405      0.945 0.988 0.000 0.000 0.004 0.008 0.000
#> GSM674303     1  0.0260      0.946 0.992 0.000 0.000 0.000 0.008 0.000
#> GSM674307     1  0.0458      0.944 0.984 0.000 0.000 0.000 0.016 0.000
#> GSM674310     5  0.3514      0.658 0.108 0.000 0.000 0.000 0.804 0.088
#> GSM674311     1  0.0603      0.942 0.980 0.000 0.000 0.000 0.016 0.004
#> GSM674312     5  0.3958      0.661 0.128 0.000 0.000 0.000 0.764 0.108
#> GSM674317     1  0.0508      0.944 0.984 0.000 0.000 0.000 0.012 0.004
#> GSM674319     5  0.3934      0.509 0.376 0.000 0.000 0.000 0.616 0.008
#> GSM674321     5  0.2191      0.711 0.120 0.000 0.000 0.000 0.876 0.004
#> GSM674322     5  0.2597      0.711 0.176 0.000 0.000 0.000 0.824 0.000
#> GSM674326     5  0.2165      0.691 0.108 0.000 0.000 0.000 0.884 0.008
#> GSM674329     5  0.2146      0.709 0.116 0.000 0.000 0.000 0.880 0.004
#> GSM674333     5  0.2631      0.710 0.180 0.000 0.000 0.000 0.820 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-SD-mclust-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-SD-mclust-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-SD-mclust-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-SD-mclust-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-SD-mclust-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-SD-mclust-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-SD-mclust-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-SD-mclust-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-SD-mclust-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-SD-mclust-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-SD-mclust-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-SD-mclust-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-SD-mclust-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-SD-mclust-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-SD-mclust-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-SD-mclust-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-SD-mclust-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-SD-mclust-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-SD-mclust-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-SD-mclust-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk SD-mclust-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-SD-mclust-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-SD-mclust-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-SD-mclust-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-SD-mclust-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-SD-mclust-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk SD-mclust-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>             n disease.state(p) specimen(p) k
#> SD:mclust 183            0.924    1.83e-40 2
#> SD:mclust 183            0.962    6.15e-78 3
#> SD:mclust 183            0.844    5.66e-76 4
#> SD:mclust 181            0.552    2.48e-73 5
#> SD:mclust 177            0.280    5.64e-70 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


SD:NMF**

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["SD", "NMF"]
# you can also extract it by
# res = res_list["SD:NMF"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#>   Subgroups are detected by 'NMF' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk SD-NMF-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk SD-NMF-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 1.000           0.991       0.995         0.5940 0.750   0.571
#> 4 4 0.928           0.948       0.948         0.0289 1.000   1.000
#> 5 5 0.816           0.731       0.870         0.0586 0.958   0.875
#> 6 6 0.762           0.785       0.848         0.0410 0.964   0.879

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2

There is also optional best \(k\) = 2 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette p1    p2    p3
#> GSM674344     3  0.3267      0.884  0 0.116 0.884
#> GSM674346     3  0.0237      0.985  0 0.004 0.996
#> GSM674347     3  0.0000      0.984  0 0.000 1.000
#> GSM674348     3  0.0592      0.981  0 0.012 0.988
#> GSM674349     3  0.0237      0.985  0 0.004 0.996
#> GSM674350     3  0.0237      0.985  0 0.004 0.996
#> GSM674353     3  0.0237      0.985  0 0.004 0.996
#> GSM674354     3  0.0747      0.979  0 0.016 0.984
#> GSM674355     3  0.0237      0.985  0 0.004 0.996
#> GSM674356     3  0.0237      0.985  0 0.004 0.996
#> GSM674357     3  0.0237      0.985  0 0.004 0.996
#> GSM674358     3  0.0000      0.984  0 0.000 1.000
#> GSM674361     3  0.0237      0.985  0 0.004 0.996
#> GSM674363     3  0.0237      0.985  0 0.004 0.996
#> GSM674364     3  0.0592      0.981  0 0.012 0.988
#> GSM674365     3  0.1163      0.970  0 0.028 0.972
#> GSM674366     3  0.0237      0.985  0 0.004 0.996
#> GSM674367     3  0.0000      0.984  0 0.000 1.000
#> GSM674368     3  0.3038      0.897  0 0.104 0.896
#> GSM674370     3  0.0237      0.985  0 0.004 0.996
#> GSM674371     3  0.0237      0.985  0 0.004 0.996
#> GSM674373     3  0.0424      0.984  0 0.008 0.992
#> GSM674375     3  0.0000      0.984  0 0.000 1.000
#> GSM674379     3  0.0000      0.984  0 0.000 1.000
#> GSM674380     3  0.1753      0.953  0 0.048 0.952
#> GSM674381     3  0.0237      0.985  0 0.004 0.996
#> GSM674382     3  0.0000      0.984  0 0.000 1.000
#> GSM674384     3  0.0424      0.984  0 0.008 0.992
#> GSM674385     3  0.2261      0.935  0 0.068 0.932
#> GSM674388     3  0.0237      0.985  0 0.004 0.996
#> GSM674389     3  0.0000      0.984  0 0.000 1.000
#> GSM674390     3  0.0237      0.985  0 0.004 0.996
#> GSM674391     3  0.0000      0.984  0 0.000 1.000
#> GSM674393     3  0.0000      0.984  0 0.000 1.000
#> GSM674394     3  0.0237      0.985  0 0.004 0.996
#> GSM674395     3  0.0000      0.984  0 0.000 1.000
#> GSM674397     3  0.0424      0.984  0 0.008 0.992
#> GSM674398     3  0.0000      0.984  0 0.000 1.000
#> GSM674400     3  0.0000      0.984  0 0.000 1.000
#> GSM674401     3  0.0000      0.984  0 0.000 1.000
#> GSM674402     3  0.1289      0.967  0 0.032 0.968
#> GSM674403     3  0.0000      0.984  0 0.000 1.000
#> GSM674405     3  0.0000      0.984  0 0.000 1.000
#> GSM674406     3  0.0237      0.985  0 0.004 0.996
#> GSM674407     3  0.0000      0.984  0 0.000 1.000
#> GSM674181     2  0.0000      1.000  0 1.000 0.000
#> GSM674183     2  0.0000      1.000  0 1.000 0.000
#> GSM674184     2  0.0000      1.000  0 1.000 0.000
#> GSM674185     2  0.0000      1.000  0 1.000 0.000
#> GSM674186     2  0.0000      1.000  0 1.000 0.000
#> GSM674187     2  0.0000      1.000  0 1.000 0.000
#> GSM674190     2  0.0000      1.000  0 1.000 0.000
#> GSM674191     2  0.0000      1.000  0 1.000 0.000
#> GSM674192     2  0.0000      1.000  0 1.000 0.000
#> GSM674193     2  0.0000      1.000  0 1.000 0.000
#> GSM674194     2  0.0000      1.000  0 1.000 0.000
#> GSM674195     2  0.0000      1.000  0 1.000 0.000
#> GSM674198     2  0.0000      1.000  0 1.000 0.000
#> GSM674200     2  0.0000      1.000  0 1.000 0.000
#> GSM674201     2  0.0000      1.000  0 1.000 0.000
#> GSM674202     2  0.0000      1.000  0 1.000 0.000
#> GSM674203     2  0.0000      1.000  0 1.000 0.000
#> GSM674204     2  0.0000      1.000  0 1.000 0.000
#> GSM674205     2  0.0000      1.000  0 1.000 0.000
#> GSM674206     2  0.0000      1.000  0 1.000 0.000
#> GSM674208     2  0.0000      1.000  0 1.000 0.000
#> GSM674209     2  0.0000      1.000  0 1.000 0.000
#> GSM674210     2  0.0000      1.000  0 1.000 0.000
#> GSM674212     2  0.0000      1.000  0 1.000 0.000
#> GSM674214     2  0.0000      1.000  0 1.000 0.000
#> GSM674218     2  0.0000      1.000  0 1.000 0.000
#> GSM674219     2  0.0000      1.000  0 1.000 0.000
#> GSM674220     2  0.0000      1.000  0 1.000 0.000
#> GSM674221     2  0.0000      1.000  0 1.000 0.000
#> GSM674223     2  0.0000      1.000  0 1.000 0.000
#> GSM674225     2  0.0000      1.000  0 1.000 0.000
#> GSM674226     2  0.0000      1.000  0 1.000 0.000
#> GSM674229     2  0.0000      1.000  0 1.000 0.000
#> GSM674230     2  0.0000      1.000  0 1.000 0.000
#> GSM674231     2  0.0000      1.000  0 1.000 0.000
#> GSM674232     2  0.0000      1.000  0 1.000 0.000
#> GSM674234     2  0.0000      1.000  0 1.000 0.000
#> GSM674235     2  0.0000      1.000  0 1.000 0.000
#> GSM674236     2  0.0000      1.000  0 1.000 0.000
#> GSM674237     2  0.0000      1.000  0 1.000 0.000
#> GSM674239     2  0.0000      1.000  0 1.000 0.000
#> GSM674240     2  0.0000      1.000  0 1.000 0.000
#> GSM674242     2  0.0000      1.000  0 1.000 0.000
#> GSM674243     2  0.0000      1.000  0 1.000 0.000
#> GSM674244     2  0.0000      1.000  0 1.000 0.000
#> GSM674245     2  0.0000      1.000  0 1.000 0.000
#> GSM674282     1  0.0000      1.000  1 0.000 0.000
#> GSM674284     1  0.0000      1.000  1 0.000 0.000
#> GSM674285     1  0.0000      1.000  1 0.000 0.000
#> GSM674287     1  0.0000      1.000  1 0.000 0.000
#> GSM674288     1  0.0000      1.000  1 0.000 0.000
#> GSM674289     1  0.0000      1.000  1 0.000 0.000
#> GSM674290     1  0.0000      1.000  1 0.000 0.000
#> GSM674291     1  0.0000      1.000  1 0.000 0.000
#> GSM674292     1  0.0000      1.000  1 0.000 0.000
#> GSM674295     1  0.0000      1.000  1 0.000 0.000
#> GSM674297     1  0.0000      1.000  1 0.000 0.000
#> GSM674298     1  0.0000      1.000  1 0.000 0.000
#> GSM674299     1  0.0000      1.000  1 0.000 0.000
#> GSM674300     1  0.0000      1.000  1 0.000 0.000
#> GSM674301     1  0.0000      1.000  1 0.000 0.000
#> GSM674302     1  0.0000      1.000  1 0.000 0.000
#> GSM674304     1  0.0000      1.000  1 0.000 0.000
#> GSM674305     1  0.0000      1.000  1 0.000 0.000
#> GSM674306     1  0.0000      1.000  1 0.000 0.000
#> GSM674308     1  0.0000      1.000  1 0.000 0.000
#> GSM674309     1  0.0000      1.000  1 0.000 0.000
#> GSM674313     1  0.0000      1.000  1 0.000 0.000
#> GSM674314     1  0.0000      1.000  1 0.000 0.000
#> GSM674315     1  0.0000      1.000  1 0.000 0.000
#> GSM674316     1  0.0000      1.000  1 0.000 0.000
#> GSM674318     1  0.0000      1.000  1 0.000 0.000
#> GSM674320     1  0.0000      1.000  1 0.000 0.000
#> GSM674323     1  0.0000      1.000  1 0.000 0.000
#> GSM674324     1  0.0000      1.000  1 0.000 0.000
#> GSM674325     1  0.0000      1.000  1 0.000 0.000
#> GSM674327     1  0.0000      1.000  1 0.000 0.000
#> GSM674328     1  0.0000      1.000  1 0.000 0.000
#> GSM674330     1  0.0000      1.000  1 0.000 0.000
#> GSM674331     1  0.0000      1.000  1 0.000 0.000
#> GSM674332     1  0.0000      1.000  1 0.000 0.000
#> GSM674334     1  0.0000      1.000  1 0.000 0.000
#> GSM674335     1  0.0000      1.000  1 0.000 0.000
#> GSM674345     3  0.0237      0.985  0 0.004 0.996
#> GSM674351     3  0.0237      0.985  0 0.004 0.996
#> GSM674352     3  0.0237      0.985  0 0.004 0.996
#> GSM674359     3  0.0424      0.984  0 0.008 0.992
#> GSM674360     3  0.3116      0.893  0 0.108 0.892
#> GSM674362     3  0.4974      0.715  0 0.236 0.764
#> GSM674369     3  0.1289      0.967  0 0.032 0.968
#> GSM674372     3  0.0000      0.984  0 0.000 1.000
#> GSM674374     3  0.0237      0.985  0 0.004 0.996
#> GSM674376     3  0.0000      0.984  0 0.000 1.000
#> GSM674377     3  0.1163      0.970  0 0.028 0.972
#> GSM674378     3  0.0237      0.985  0 0.004 0.996
#> GSM674383     3  0.0592      0.981  0 0.012 0.988
#> GSM674386     3  0.0237      0.985  0 0.004 0.996
#> GSM674387     3  0.0000      0.984  0 0.000 1.000
#> GSM674392     3  0.0000      0.984  0 0.000 1.000
#> GSM674396     3  0.0000      0.984  0 0.000 1.000
#> GSM674399     3  0.0000      0.984  0 0.000 1.000
#> GSM674404     3  0.0000      0.984  0 0.000 1.000
#> GSM674182     2  0.0000      1.000  0 1.000 0.000
#> GSM674188     2  0.0000      1.000  0 1.000 0.000
#> GSM674189     2  0.0000      1.000  0 1.000 0.000
#> GSM674196     2  0.0000      1.000  0 1.000 0.000
#> GSM674197     2  0.0000      1.000  0 1.000 0.000
#> GSM674199     2  0.0000      1.000  0 1.000 0.000
#> GSM674207     2  0.0000      1.000  0 1.000 0.000
#> GSM674211     2  0.0000      1.000  0 1.000 0.000
#> GSM674213     2  0.0000      1.000  0 1.000 0.000
#> GSM674215     2  0.0000      1.000  0 1.000 0.000
#> GSM674216     2  0.0000      1.000  0 1.000 0.000
#> GSM674217     2  0.0000      1.000  0 1.000 0.000
#> GSM674222     2  0.0000      1.000  0 1.000 0.000
#> GSM674224     2  0.0000      1.000  0 1.000 0.000
#> GSM674227     2  0.0000      1.000  0 1.000 0.000
#> GSM674228     2  0.0000      1.000  0 1.000 0.000
#> GSM674233     2  0.0000      1.000  0 1.000 0.000
#> GSM674238     2  0.0000      1.000  0 1.000 0.000
#> GSM674241     2  0.0000      1.000  0 1.000 0.000
#> GSM674283     1  0.0000      1.000  1 0.000 0.000
#> GSM674286     1  0.0000      1.000  1 0.000 0.000
#> GSM674293     1  0.0000      1.000  1 0.000 0.000
#> GSM674294     1  0.0000      1.000  1 0.000 0.000
#> GSM674296     1  0.0000      1.000  1 0.000 0.000
#> GSM674303     1  0.0000      1.000  1 0.000 0.000
#> GSM674307     1  0.0000      1.000  1 0.000 0.000
#> GSM674310     1  0.0000      1.000  1 0.000 0.000
#> GSM674311     1  0.0000      1.000  1 0.000 0.000
#> GSM674312     1  0.0000      1.000  1 0.000 0.000
#> GSM674317     1  0.0000      1.000  1 0.000 0.000
#> GSM674319     1  0.0000      1.000  1 0.000 0.000
#> GSM674321     1  0.0000      1.000  1 0.000 0.000
#> GSM674322     1  0.0000      1.000  1 0.000 0.000
#> GSM674326     1  0.0000      1.000  1 0.000 0.000
#> GSM674329     1  0.0000      1.000  1 0.000 0.000
#> GSM674333     1  0.0000      1.000  1 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1    p2    p3    p4
#> GSM674344     3  0.5226      0.824 0.000 0.116 0.756 0.128
#> GSM674346     3  0.3160      0.924 0.000 0.020 0.872 0.108
#> GSM674347     3  0.0469      0.961 0.000 0.000 0.988 0.012
#> GSM674348     3  0.2521      0.943 0.000 0.024 0.912 0.064
#> GSM674349     3  0.1305      0.958 0.000 0.004 0.960 0.036
#> GSM674350     3  0.0921      0.959 0.000 0.000 0.972 0.028
#> GSM674353     3  0.1389      0.954 0.000 0.000 0.952 0.048
#> GSM674354     3  0.3308      0.924 0.000 0.036 0.872 0.092
#> GSM674355     3  0.0592      0.961 0.000 0.000 0.984 0.016
#> GSM674356     3  0.1978      0.948 0.000 0.004 0.928 0.068
#> GSM674357     3  0.2480      0.939 0.000 0.008 0.904 0.088
#> GSM674358     3  0.0817      0.960 0.000 0.000 0.976 0.024
#> GSM674361     3  0.0188      0.961 0.000 0.000 0.996 0.004
#> GSM674363     3  0.1854      0.954 0.000 0.012 0.940 0.048
#> GSM674364     3  0.1913      0.949 0.000 0.040 0.940 0.020
#> GSM674365     3  0.2483      0.938 0.000 0.052 0.916 0.032
#> GSM674366     3  0.0672      0.962 0.000 0.008 0.984 0.008
#> GSM674367     3  0.0188      0.961 0.000 0.000 0.996 0.004
#> GSM674368     3  0.4130      0.875 0.000 0.108 0.828 0.064
#> GSM674370     3  0.0779      0.961 0.000 0.004 0.980 0.016
#> GSM674371     3  0.1256      0.959 0.000 0.008 0.964 0.028
#> GSM674373     3  0.1297      0.959 0.000 0.020 0.964 0.016
#> GSM674375     3  0.0188      0.961 0.000 0.000 0.996 0.004
#> GSM674379     3  0.0592      0.960 0.000 0.000 0.984 0.016
#> GSM674380     3  0.2635      0.921 0.000 0.076 0.904 0.020
#> GSM674381     3  0.0779      0.961 0.000 0.016 0.980 0.004
#> GSM674382     3  0.0817      0.958 0.000 0.000 0.976 0.024
#> GSM674384     3  0.0927      0.961 0.000 0.016 0.976 0.008
#> GSM674385     3  0.2805      0.902 0.000 0.100 0.888 0.012
#> GSM674388     3  0.1059      0.960 0.000 0.012 0.972 0.016
#> GSM674389     3  0.0469      0.961 0.000 0.000 0.988 0.012
#> GSM674390     3  0.0336      0.961 0.000 0.000 0.992 0.008
#> GSM674391     3  0.1118      0.955 0.000 0.000 0.964 0.036
#> GSM674393     3  0.0188      0.961 0.000 0.000 0.996 0.004
#> GSM674394     3  0.0336      0.962 0.000 0.008 0.992 0.000
#> GSM674395     3  0.0336      0.962 0.000 0.000 0.992 0.008
#> GSM674397     3  0.0895      0.960 0.000 0.020 0.976 0.004
#> GSM674398     3  0.0469      0.961 0.000 0.000 0.988 0.012
#> GSM674400     3  0.0707      0.959 0.000 0.000 0.980 0.020
#> GSM674401     3  0.0817      0.959 0.000 0.000 0.976 0.024
#> GSM674402     3  0.3081      0.929 0.000 0.048 0.888 0.064
#> GSM674403     3  0.0817      0.960 0.000 0.000 0.976 0.024
#> GSM674405     3  0.0817      0.958 0.000 0.000 0.976 0.024
#> GSM674406     3  0.0188      0.961 0.000 0.000 0.996 0.004
#> GSM674407     3  0.0592      0.961 0.000 0.000 0.984 0.016
#> GSM674181     2  0.1118      0.976 0.000 0.964 0.000 0.036
#> GSM674183     2  0.1584      0.966 0.000 0.952 0.012 0.036
#> GSM674184     2  0.0469      0.992 0.000 0.988 0.000 0.012
#> GSM674185     2  0.0469      0.992 0.000 0.988 0.000 0.012
#> GSM674186     2  0.0469      0.992 0.000 0.988 0.000 0.012
#> GSM674187     2  0.0469      0.992 0.000 0.988 0.000 0.012
#> GSM674190     2  0.0188      0.993 0.000 0.996 0.000 0.004
#> GSM674191     2  0.0469      0.992 0.000 0.988 0.000 0.012
#> GSM674192     2  0.0188      0.993 0.000 0.996 0.000 0.004
#> GSM674193     2  0.0000      0.993 0.000 1.000 0.000 0.000
#> GSM674194     2  0.0188      0.993 0.000 0.996 0.000 0.004
#> GSM674195     2  0.1356      0.973 0.000 0.960 0.008 0.032
#> GSM674198     2  0.0000      0.993 0.000 1.000 0.000 0.000
#> GSM674200     2  0.2611      0.923 0.000 0.896 0.008 0.096
#> GSM674201     2  0.0336      0.992 0.000 0.992 0.000 0.008
#> GSM674202     2  0.0000      0.993 0.000 1.000 0.000 0.000
#> GSM674203     2  0.0336      0.990 0.000 0.992 0.000 0.008
#> GSM674204     2  0.0000      0.993 0.000 1.000 0.000 0.000
#> GSM674205     2  0.0000      0.993 0.000 1.000 0.000 0.000
#> GSM674206     2  0.0188      0.993 0.000 0.996 0.000 0.004
#> GSM674208     2  0.0188      0.992 0.000 0.996 0.000 0.004
#> GSM674209     2  0.0188      0.993 0.000 0.996 0.000 0.004
#> GSM674210     2  0.0000      0.993 0.000 1.000 0.000 0.000
#> GSM674212     2  0.0336      0.992 0.000 0.992 0.000 0.008
#> GSM674214     2  0.0188      0.993 0.000 0.996 0.000 0.004
#> GSM674218     2  0.0469      0.992 0.000 0.988 0.000 0.012
#> GSM674219     2  0.0469      0.992 0.000 0.988 0.000 0.012
#> GSM674220     2  0.0336      0.992 0.000 0.992 0.000 0.008
#> GSM674221     2  0.0469      0.992 0.000 0.988 0.000 0.012
#> GSM674223     2  0.0336      0.992 0.000 0.992 0.000 0.008
#> GSM674225     2  0.0469      0.990 0.000 0.988 0.000 0.012
#> GSM674226     2  0.0336      0.991 0.000 0.992 0.000 0.008
#> GSM674229     2  0.0188      0.993 0.000 0.996 0.000 0.004
#> GSM674230     2  0.0592      0.989 0.000 0.984 0.000 0.016
#> GSM674231     2  0.0188      0.993 0.000 0.996 0.000 0.004
#> GSM674232     2  0.0188      0.993 0.000 0.996 0.000 0.004
#> GSM674234     2  0.0000      0.993 0.000 1.000 0.000 0.000
#> GSM674235     2  0.0336      0.992 0.000 0.992 0.000 0.008
#> GSM674236     2  0.0188      0.993 0.000 0.996 0.000 0.004
#> GSM674237     2  0.0336      0.990 0.000 0.992 0.000 0.008
#> GSM674239     2  0.0000      0.993 0.000 1.000 0.000 0.000
#> GSM674240     2  0.0336      0.992 0.000 0.992 0.000 0.008
#> GSM674242     2  0.0592      0.987 0.000 0.984 0.000 0.016
#> GSM674243     2  0.0000      0.993 0.000 1.000 0.000 0.000
#> GSM674244     2  0.0336      0.993 0.000 0.992 0.000 0.008
#> GSM674245     2  0.0188      0.993 0.000 0.996 0.000 0.004
#> GSM674282     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674284     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674285     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674287     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674288     1  0.2921      0.902 0.860 0.000 0.000 0.140
#> GSM674289     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674290     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674291     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674292     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674295     1  0.3569      0.887 0.804 0.000 0.000 0.196
#> GSM674297     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674298     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674299     1  0.0188      0.929 0.996 0.000 0.000 0.004
#> GSM674300     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674301     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674302     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674304     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674305     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674306     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674308     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674309     1  0.0469      0.928 0.988 0.000 0.000 0.012
#> GSM674313     1  0.4746      0.809 0.632 0.000 0.000 0.368
#> GSM674314     1  0.3400      0.891 0.820 0.000 0.000 0.180
#> GSM674315     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674316     1  0.3649      0.884 0.796 0.000 0.000 0.204
#> GSM674318     1  0.4804      0.800 0.616 0.000 0.000 0.384
#> GSM674320     1  0.4855      0.790 0.600 0.000 0.000 0.400
#> GSM674323     1  0.4008      0.870 0.756 0.000 0.000 0.244
#> GSM674324     1  0.0188      0.929 0.996 0.000 0.000 0.004
#> GSM674325     1  0.4040      0.868 0.752 0.000 0.000 0.248
#> GSM674327     1  0.2216      0.912 0.908 0.000 0.000 0.092
#> GSM674328     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674330     1  0.3444      0.890 0.816 0.000 0.000 0.184
#> GSM674331     1  0.0469      0.928 0.988 0.000 0.000 0.012
#> GSM674332     1  0.0188      0.929 0.996 0.000 0.000 0.004
#> GSM674334     1  0.3356      0.892 0.824 0.000 0.000 0.176
#> GSM674335     1  0.3528      0.888 0.808 0.000 0.000 0.192
#> GSM674345     3  0.1940      0.945 0.000 0.000 0.924 0.076
#> GSM674351     3  0.1557      0.953 0.000 0.000 0.944 0.056
#> GSM674352     3  0.1211      0.957 0.000 0.000 0.960 0.040
#> GSM674359     3  0.3749      0.904 0.000 0.032 0.840 0.128
#> GSM674360     3  0.4130      0.876 0.000 0.108 0.828 0.064
#> GSM674362     3  0.5952      0.738 0.000 0.184 0.692 0.124
#> GSM674369     3  0.2722      0.930 0.000 0.064 0.904 0.032
#> GSM674372     3  0.0188      0.961 0.000 0.000 0.996 0.004
#> GSM674374     3  0.0524      0.962 0.000 0.004 0.988 0.008
#> GSM674376     3  0.0592      0.960 0.000 0.000 0.984 0.016
#> GSM674377     3  0.1938      0.944 0.000 0.052 0.936 0.012
#> GSM674378     3  0.0000      0.961 0.000 0.000 1.000 0.000
#> GSM674383     3  0.1510      0.955 0.000 0.028 0.956 0.016
#> GSM674386     3  0.0817      0.958 0.000 0.000 0.976 0.024
#> GSM674387     3  0.0469      0.961 0.000 0.000 0.988 0.012
#> GSM674392     3  0.0188      0.961 0.000 0.000 0.996 0.004
#> GSM674396     3  0.0817      0.958 0.000 0.000 0.976 0.024
#> GSM674399     3  0.0817      0.958 0.000 0.000 0.976 0.024
#> GSM674404     3  0.0592      0.960 0.000 0.000 0.984 0.016
#> GSM674182     2  0.0469      0.992 0.000 0.988 0.000 0.012
#> GSM674188     2  0.0188      0.993 0.000 0.996 0.000 0.004
#> GSM674189     2  0.0336      0.992 0.000 0.992 0.000 0.008
#> GSM674196     2  0.0000      0.993 0.000 1.000 0.000 0.000
#> GSM674197     2  0.0336      0.991 0.000 0.992 0.000 0.008
#> GSM674199     2  0.0000      0.993 0.000 1.000 0.000 0.000
#> GSM674207     2  0.0188      0.993 0.000 0.996 0.000 0.004
#> GSM674211     2  0.0000      0.993 0.000 1.000 0.000 0.000
#> GSM674213     2  0.0469      0.992 0.000 0.988 0.000 0.012
#> GSM674215     2  0.0592      0.990 0.000 0.984 0.000 0.016
#> GSM674216     2  0.0592      0.988 0.000 0.984 0.000 0.016
#> GSM674217     2  0.0336      0.992 0.000 0.992 0.000 0.008
#> GSM674222     2  0.0707      0.988 0.000 0.980 0.000 0.020
#> GSM674224     2  0.0000      0.993 0.000 1.000 0.000 0.000
#> GSM674227     2  0.0188      0.993 0.000 0.996 0.000 0.004
#> GSM674228     2  0.0336      0.992 0.000 0.992 0.000 0.008
#> GSM674233     2  0.0336      0.992 0.000 0.992 0.000 0.008
#> GSM674238     2  0.1004      0.981 0.000 0.972 0.004 0.024
#> GSM674241     2  0.0000      0.993 0.000 1.000 0.000 0.000
#> GSM674283     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674286     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674293     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674294     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674296     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674303     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674307     1  0.0000      0.929 1.000 0.000 0.000 0.000
#> GSM674310     1  0.4855      0.790 0.600 0.000 0.000 0.400
#> GSM674311     1  0.1118      0.924 0.964 0.000 0.000 0.036
#> GSM674312     1  0.4855      0.790 0.600 0.000 0.000 0.400
#> GSM674317     1  0.0188      0.929 0.996 0.000 0.000 0.004
#> GSM674319     1  0.3975      0.871 0.760 0.000 0.000 0.240
#> GSM674321     1  0.4008      0.870 0.756 0.000 0.000 0.244
#> GSM674322     1  0.4713      0.814 0.640 0.000 0.000 0.360
#> GSM674326     1  0.4072      0.866 0.748 0.000 0.000 0.252
#> GSM674329     1  0.4730      0.812 0.636 0.000 0.000 0.364
#> GSM674333     1  0.4605      0.827 0.664 0.000 0.000 0.336

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4    p5
#> GSM674344     5  0.5594     0.2669 0.000 0.064 0.400 0.004 0.532
#> GSM674346     3  0.4708     0.1177 0.000 0.016 0.548 0.000 0.436
#> GSM674347     3  0.1608     0.8175 0.000 0.000 0.928 0.000 0.072
#> GSM674348     3  0.3724     0.7005 0.000 0.020 0.776 0.000 0.204
#> GSM674349     3  0.2843     0.7678 0.000 0.008 0.848 0.000 0.144
#> GSM674350     3  0.2605     0.7688 0.000 0.000 0.852 0.000 0.148
#> GSM674353     3  0.3398     0.6968 0.000 0.004 0.780 0.000 0.216
#> GSM674354     3  0.4909     0.2750 0.000 0.032 0.588 0.000 0.380
#> GSM674355     3  0.1478     0.8162 0.000 0.000 0.936 0.000 0.064
#> GSM674356     3  0.3246     0.7358 0.000 0.008 0.808 0.000 0.184
#> GSM674357     3  0.4482     0.3439 0.000 0.012 0.612 0.000 0.376
#> GSM674358     3  0.2020     0.8001 0.000 0.000 0.900 0.000 0.100
#> GSM674361     3  0.1205     0.8243 0.000 0.004 0.956 0.000 0.040
#> GSM674363     3  0.3628     0.6888 0.000 0.012 0.772 0.000 0.216
#> GSM674364     3  0.2554     0.7959 0.000 0.036 0.892 0.000 0.072
#> GSM674365     3  0.3452     0.7446 0.000 0.032 0.820 0.000 0.148
#> GSM674366     3  0.0693     0.8234 0.000 0.012 0.980 0.000 0.008
#> GSM674367     3  0.1270     0.8170 0.000 0.000 0.948 0.000 0.052
#> GSM674368     3  0.4100     0.6754 0.000 0.044 0.764 0.000 0.192
#> GSM674370     3  0.1628     0.8188 0.000 0.008 0.936 0.000 0.056
#> GSM674371     3  0.1106     0.8238 0.000 0.012 0.964 0.000 0.024
#> GSM674373     3  0.1800     0.8206 0.000 0.020 0.932 0.000 0.048
#> GSM674375     3  0.0404     0.8235 0.000 0.000 0.988 0.000 0.012
#> GSM674379     3  0.2439     0.7853 0.000 0.000 0.876 0.004 0.120
#> GSM674380     3  0.4308     0.6841 0.000 0.060 0.768 0.004 0.168
#> GSM674381     3  0.1809     0.8168 0.000 0.012 0.928 0.000 0.060
#> GSM674382     3  0.2516     0.7739 0.000 0.000 0.860 0.000 0.140
#> GSM674384     3  0.2054     0.8140 0.000 0.028 0.920 0.000 0.052
#> GSM674385     3  0.2983     0.7795 0.000 0.040 0.864 0.000 0.096
#> GSM674388     3  0.2873     0.7787 0.000 0.020 0.860 0.000 0.120
#> GSM674389     3  0.1341     0.8144 0.000 0.000 0.944 0.000 0.056
#> GSM674390     3  0.2127     0.7951 0.000 0.000 0.892 0.000 0.108
#> GSM674391     3  0.3366     0.7021 0.000 0.000 0.784 0.004 0.212
#> GSM674393     3  0.0963     0.8201 0.000 0.000 0.964 0.000 0.036
#> GSM674394     3  0.1522     0.8202 0.000 0.012 0.944 0.000 0.044
#> GSM674395     3  0.0880     0.8251 0.000 0.000 0.968 0.000 0.032
#> GSM674397     3  0.1830     0.8158 0.000 0.028 0.932 0.000 0.040
#> GSM674398     3  0.2179     0.7903 0.000 0.000 0.888 0.000 0.112
#> GSM674400     3  0.1671     0.8095 0.000 0.000 0.924 0.000 0.076
#> GSM674401     3  0.2127     0.7973 0.000 0.000 0.892 0.000 0.108
#> GSM674402     3  0.4980     0.2376 0.000 0.036 0.584 0.000 0.380
#> GSM674403     3  0.2280     0.7869 0.000 0.000 0.880 0.000 0.120
#> GSM674405     3  0.2719     0.7690 0.000 0.000 0.852 0.004 0.144
#> GSM674406     3  0.1197     0.8182 0.000 0.000 0.952 0.000 0.048
#> GSM674407     3  0.2124     0.8009 0.000 0.000 0.900 0.004 0.096
#> GSM674181     2  0.4801     0.2598 0.000 0.604 0.020 0.004 0.372
#> GSM674183     5  0.5734     0.2586 0.000 0.444 0.084 0.000 0.472
#> GSM674184     2  0.2824     0.8452 0.000 0.864 0.020 0.000 0.116
#> GSM674185     2  0.2474     0.8827 0.000 0.896 0.012 0.008 0.084
#> GSM674186     2  0.1197     0.9214 0.000 0.952 0.000 0.000 0.048
#> GSM674187     2  0.0963     0.9252 0.000 0.964 0.000 0.000 0.036
#> GSM674190     2  0.1197     0.9176 0.000 0.952 0.000 0.000 0.048
#> GSM674191     2  0.1991     0.8977 0.000 0.916 0.004 0.004 0.076
#> GSM674192     2  0.0609     0.9305 0.000 0.980 0.000 0.000 0.020
#> GSM674193     2  0.0609     0.9310 0.000 0.980 0.000 0.000 0.020
#> GSM674194     2  0.1357     0.9163 0.000 0.948 0.004 0.000 0.048
#> GSM674195     2  0.5302    -0.0724 0.000 0.536 0.052 0.000 0.412
#> GSM674198     2  0.0609     0.9280 0.000 0.980 0.000 0.000 0.020
#> GSM674200     5  0.5883     0.4513 0.000 0.368 0.108 0.000 0.524
#> GSM674201     2  0.3098     0.8099 0.000 0.836 0.016 0.000 0.148
#> GSM674202     2  0.0566     0.9312 0.000 0.984 0.004 0.000 0.012
#> GSM674203     2  0.0609     0.9279 0.000 0.980 0.000 0.000 0.020
#> GSM674204     2  0.0290     0.9315 0.000 0.992 0.000 0.000 0.008
#> GSM674205     2  0.0510     0.9294 0.000 0.984 0.000 0.000 0.016
#> GSM674206     2  0.1502     0.9129 0.000 0.940 0.004 0.000 0.056
#> GSM674208     2  0.0510     0.9286 0.000 0.984 0.000 0.000 0.016
#> GSM674209     2  0.0807     0.9293 0.000 0.976 0.012 0.000 0.012
#> GSM674210     2  0.0510     0.9286 0.000 0.984 0.000 0.000 0.016
#> GSM674212     2  0.0404     0.9311 0.000 0.988 0.000 0.000 0.012
#> GSM674214     2  0.0510     0.9294 0.000 0.984 0.000 0.000 0.016
#> GSM674218     2  0.3067     0.8215 0.000 0.844 0.012 0.004 0.140
#> GSM674219     2  0.2166     0.8951 0.000 0.912 0.012 0.004 0.072
#> GSM674220     2  0.2228     0.8980 0.000 0.912 0.012 0.008 0.068
#> GSM674221     2  0.1205     0.9213 0.000 0.956 0.000 0.004 0.040
#> GSM674223     2  0.1195     0.9229 0.000 0.960 0.012 0.000 0.028
#> GSM674225     2  0.2054     0.8850 0.000 0.916 0.008 0.004 0.072
#> GSM674226     2  0.0510     0.9302 0.000 0.984 0.000 0.000 0.016
#> GSM674229     2  0.0404     0.9309 0.000 0.988 0.000 0.000 0.012
#> GSM674230     2  0.0510     0.9313 0.000 0.984 0.000 0.000 0.016
#> GSM674231     2  0.0510     0.9307 0.000 0.984 0.000 0.000 0.016
#> GSM674232     2  0.0404     0.9295 0.000 0.988 0.000 0.000 0.012
#> GSM674234     2  0.0290     0.9304 0.000 0.992 0.000 0.000 0.008
#> GSM674235     2  0.0510     0.9308 0.000 0.984 0.000 0.000 0.016
#> GSM674236     2  0.0609     0.9292 0.000 0.980 0.000 0.000 0.020
#> GSM674237     2  0.0609     0.9276 0.000 0.980 0.000 0.000 0.020
#> GSM674239     2  0.0510     0.9286 0.000 0.984 0.000 0.000 0.016
#> GSM674240     2  0.2077     0.8909 0.000 0.908 0.008 0.000 0.084
#> GSM674242     2  0.0794     0.9249 0.000 0.972 0.000 0.000 0.028
#> GSM674243     2  0.0609     0.9310 0.000 0.980 0.000 0.000 0.020
#> GSM674244     2  0.1788     0.9085 0.000 0.932 0.008 0.004 0.056
#> GSM674245     2  0.0510     0.9302 0.000 0.984 0.000 0.000 0.016
#> GSM674282     1  0.0162     0.8167 0.996 0.000 0.000 0.000 0.004
#> GSM674284     1  0.0162     0.8167 0.996 0.000 0.000 0.004 0.000
#> GSM674285     1  0.0000     0.8170 1.000 0.000 0.000 0.000 0.000
#> GSM674287     1  0.0162     0.8167 0.996 0.000 0.000 0.000 0.004
#> GSM674288     1  0.3884     0.1998 0.708 0.000 0.000 0.288 0.004
#> GSM674289     1  0.0000     0.8170 1.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0162     0.8147 0.996 0.000 0.000 0.004 0.000
#> GSM674291     1  0.0162     0.8167 0.996 0.000 0.000 0.000 0.004
#> GSM674292     1  0.0162     0.8167 0.996 0.000 0.000 0.000 0.004
#> GSM674295     1  0.4166    -0.1050 0.648 0.000 0.000 0.348 0.004
#> GSM674297     1  0.0162     0.8167 0.996 0.000 0.000 0.004 0.000
#> GSM674298     1  0.0000     0.8170 1.000 0.000 0.000 0.000 0.000
#> GSM674299     1  0.0671     0.8100 0.980 0.000 0.000 0.016 0.004
#> GSM674300     1  0.0451     0.8140 0.988 0.000 0.000 0.008 0.004
#> GSM674301     1  0.0162     0.8147 0.996 0.000 0.000 0.004 0.000
#> GSM674302     1  0.0000     0.8170 1.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0000     0.8170 1.000 0.000 0.000 0.000 0.000
#> GSM674305     1  0.0000     0.8170 1.000 0.000 0.000 0.000 0.000
#> GSM674306     1  0.0162     0.8162 0.996 0.000 0.000 0.004 0.000
#> GSM674308     1  0.0000     0.8170 1.000 0.000 0.000 0.000 0.000
#> GSM674309     1  0.1121     0.7815 0.956 0.000 0.000 0.044 0.000
#> GSM674313     4  0.4383     0.8319 0.424 0.000 0.000 0.572 0.004
#> GSM674314     1  0.3983    -0.0641 0.660 0.000 0.000 0.340 0.000
#> GSM674315     1  0.0162     0.8162 0.996 0.000 0.000 0.004 0.000
#> GSM674316     1  0.4227    -0.4391 0.580 0.000 0.000 0.420 0.000
#> GSM674318     4  0.4235     0.8517 0.336 0.000 0.000 0.656 0.008
#> GSM674320     4  0.3857     0.8360 0.312 0.000 0.000 0.688 0.000
#> GSM674323     1  0.4449    -0.6745 0.512 0.000 0.000 0.484 0.004
#> GSM674324     1  0.0510     0.8099 0.984 0.000 0.000 0.016 0.000
#> GSM674325     4  0.4451     0.6997 0.492 0.000 0.000 0.504 0.004
#> GSM674327     1  0.2852     0.5567 0.828 0.000 0.000 0.172 0.000
#> GSM674328     1  0.0451     0.8146 0.988 0.000 0.000 0.008 0.004
#> GSM674330     1  0.4101    -0.2242 0.628 0.000 0.000 0.372 0.000
#> GSM674331     1  0.1043     0.7861 0.960 0.000 0.000 0.040 0.000
#> GSM674332     1  0.0609     0.8068 0.980 0.000 0.000 0.020 0.000
#> GSM674334     1  0.4074    -0.1849 0.636 0.000 0.000 0.364 0.000
#> GSM674335     1  0.4264    -0.2492 0.620 0.000 0.000 0.376 0.004
#> GSM674345     3  0.3430     0.6923 0.000 0.004 0.776 0.000 0.220
#> GSM674351     3  0.2891     0.7447 0.000 0.000 0.824 0.000 0.176
#> GSM674352     3  0.2930     0.7533 0.000 0.004 0.832 0.000 0.164
#> GSM674359     3  0.4824    -0.0379 0.000 0.020 0.512 0.000 0.468
#> GSM674360     3  0.4777     0.5212 0.000 0.052 0.680 0.000 0.268
#> GSM674362     5  0.5779     0.1314 0.000 0.088 0.456 0.000 0.456
#> GSM674369     3  0.2067     0.8028 0.000 0.048 0.920 0.000 0.032
#> GSM674372     3  0.0794     0.8222 0.000 0.000 0.972 0.000 0.028
#> GSM674374     3  0.1331     0.8216 0.000 0.008 0.952 0.000 0.040
#> GSM674376     3  0.2179     0.7902 0.000 0.000 0.888 0.000 0.112
#> GSM674377     3  0.4147     0.7020 0.000 0.048 0.776 0.004 0.172
#> GSM674378     3  0.0794     0.8239 0.000 0.000 0.972 0.000 0.028
#> GSM674383     3  0.1907     0.8122 0.000 0.028 0.928 0.000 0.044
#> GSM674386     3  0.2970     0.7484 0.000 0.004 0.828 0.000 0.168
#> GSM674387     3  0.2068     0.8017 0.000 0.000 0.904 0.004 0.092
#> GSM674392     3  0.1197     0.8223 0.000 0.000 0.952 0.000 0.048
#> GSM674396     3  0.2629     0.7711 0.000 0.000 0.860 0.004 0.136
#> GSM674399     3  0.3074     0.7196 0.000 0.000 0.804 0.000 0.196
#> GSM674404     3  0.1965     0.8036 0.000 0.000 0.904 0.000 0.096
#> GSM674182     2  0.2124     0.8847 0.000 0.900 0.000 0.004 0.096
#> GSM674188     2  0.0794     0.9274 0.000 0.972 0.000 0.000 0.028
#> GSM674189     2  0.2660     0.8465 0.000 0.864 0.008 0.000 0.128
#> GSM674196     2  0.0290     0.9310 0.000 0.992 0.000 0.000 0.008
#> GSM674197     2  0.0162     0.9307 0.000 0.996 0.000 0.000 0.004
#> GSM674199     2  0.0703     0.9268 0.000 0.976 0.000 0.000 0.024
#> GSM674207     2  0.0162     0.9309 0.000 0.996 0.000 0.000 0.004
#> GSM674211     2  0.0404     0.9299 0.000 0.988 0.000 0.000 0.012
#> GSM674213     2  0.1605     0.9160 0.000 0.944 0.012 0.004 0.040
#> GSM674215     2  0.1756     0.9208 0.000 0.940 0.008 0.016 0.036
#> GSM674216     2  0.1502     0.9024 0.000 0.940 0.004 0.000 0.056
#> GSM674217     2  0.1924     0.9038 0.000 0.924 0.008 0.004 0.064
#> GSM674222     2  0.1357     0.9195 0.000 0.948 0.004 0.000 0.048
#> GSM674224     2  0.0771     0.9310 0.000 0.976 0.004 0.000 0.020
#> GSM674227     2  0.0671     0.9292 0.000 0.980 0.004 0.000 0.016
#> GSM674228     2  0.0451     0.9304 0.000 0.988 0.004 0.000 0.008
#> GSM674233     2  0.2116     0.8948 0.000 0.912 0.008 0.004 0.076
#> GSM674238     2  0.5201    -0.0840 0.000 0.532 0.044 0.000 0.424
#> GSM674241     2  0.0510     0.9286 0.000 0.984 0.000 0.000 0.016
#> GSM674283     1  0.0162     0.8167 0.996 0.000 0.000 0.004 0.000
#> GSM674286     1  0.0000     0.8170 1.000 0.000 0.000 0.000 0.000
#> GSM674293     1  0.0324     0.8149 0.992 0.000 0.000 0.004 0.004
#> GSM674294     1  0.0162     0.8167 0.996 0.000 0.000 0.000 0.004
#> GSM674296     1  0.0000     0.8170 1.000 0.000 0.000 0.000 0.000
#> GSM674303     1  0.0290     0.8150 0.992 0.000 0.000 0.008 0.000
#> GSM674307     1  0.0000     0.8170 1.000 0.000 0.000 0.000 0.000
#> GSM674310     4  0.4108     0.8285 0.308 0.000 0.000 0.684 0.008
#> GSM674311     1  0.1965     0.7095 0.904 0.000 0.000 0.096 0.000
#> GSM674312     4  0.4009     0.8363 0.312 0.000 0.000 0.684 0.004
#> GSM674317     1  0.0671     0.8100 0.980 0.000 0.000 0.016 0.004
#> GSM674319     1  0.4448    -0.6533 0.516 0.000 0.000 0.480 0.004
#> GSM674321     1  0.4449    -0.6745 0.512 0.000 0.000 0.484 0.004
#> GSM674322     4  0.4392     0.8619 0.380 0.000 0.000 0.612 0.008
#> GSM674326     4  0.4451     0.6943 0.492 0.000 0.000 0.504 0.004
#> GSM674329     4  0.4359     0.8469 0.412 0.000 0.000 0.584 0.004
#> GSM674333     4  0.4331     0.8572 0.400 0.000 0.000 0.596 0.004

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3 p4    p5    p6
#> GSM674344     6  0.5829   0.220098 0.000 0.028 0.352 NA 0.000 0.516
#> GSM674346     3  0.4968   0.228499 0.000 0.004 0.508 NA 0.000 0.432
#> GSM674347     3  0.2538   0.824229 0.000 0.000 0.860 NA 0.000 0.016
#> GSM674348     3  0.3296   0.767734 0.000 0.004 0.796 NA 0.000 0.180
#> GSM674349     3  0.2633   0.808412 0.000 0.004 0.864 NA 0.000 0.112
#> GSM674350     3  0.3280   0.771464 0.000 0.004 0.808 NA 0.000 0.160
#> GSM674353     3  0.3841   0.677389 0.000 0.000 0.724 NA 0.000 0.244
#> GSM674354     3  0.4555   0.506415 0.000 0.004 0.616 NA 0.000 0.340
#> GSM674355     3  0.1950   0.828930 0.000 0.000 0.912 NA 0.000 0.064
#> GSM674356     3  0.3168   0.781574 0.000 0.004 0.820 NA 0.000 0.148
#> GSM674357     3  0.4576   0.452353 0.000 0.004 0.592 NA 0.000 0.368
#> GSM674358     3  0.2201   0.820447 0.000 0.000 0.896 NA 0.000 0.076
#> GSM674361     3  0.2591   0.831022 0.000 0.004 0.880 NA 0.000 0.064
#> GSM674363     3  0.3858   0.681368 0.000 0.004 0.724 NA 0.000 0.248
#> GSM674364     3  0.2476   0.820233 0.000 0.004 0.880 NA 0.000 0.092
#> GSM674365     3  0.2544   0.805227 0.000 0.004 0.864 NA 0.000 0.120
#> GSM674366     3  0.2152   0.836508 0.000 0.004 0.904 NA 0.000 0.024
#> GSM674367     3  0.1967   0.831001 0.000 0.000 0.904 NA 0.000 0.012
#> GSM674368     3  0.3464   0.784705 0.000 0.032 0.812 NA 0.000 0.140
#> GSM674370     3  0.2138   0.833553 0.000 0.004 0.908 NA 0.000 0.052
#> GSM674371     3  0.2078   0.833424 0.000 0.004 0.912 NA 0.000 0.044
#> GSM674373     3  0.2078   0.834784 0.000 0.004 0.912 NA 0.000 0.044
#> GSM674375     3  0.1232   0.835159 0.000 0.004 0.956 NA 0.000 0.016
#> GSM674379     3  0.2768   0.781755 0.000 0.000 0.832 NA 0.000 0.012
#> GSM674380     3  0.4325   0.705723 0.000 0.056 0.724 NA 0.000 0.012
#> GSM674381     3  0.1728   0.829159 0.000 0.004 0.924 NA 0.000 0.008
#> GSM674382     3  0.2915   0.783707 0.000 0.000 0.808 NA 0.000 0.008
#> GSM674384     3  0.2745   0.818696 0.000 0.020 0.860 NA 0.000 0.008
#> GSM674385     3  0.4217   0.746651 0.000 0.036 0.772 NA 0.000 0.060
#> GSM674388     3  0.1845   0.824598 0.000 0.004 0.916 NA 0.000 0.072
#> GSM674389     3  0.1644   0.826102 0.000 0.000 0.920 NA 0.000 0.004
#> GSM674390     3  0.2592   0.806986 0.000 0.004 0.864 NA 0.000 0.016
#> GSM674391     3  0.3023   0.738015 0.000 0.000 0.768 NA 0.000 0.000
#> GSM674393     3  0.1364   0.834611 0.000 0.004 0.944 NA 0.000 0.004
#> GSM674394     3  0.2437   0.827383 0.000 0.004 0.888 NA 0.000 0.036
#> GSM674395     3  0.1982   0.834664 0.000 0.004 0.912 NA 0.000 0.016
#> GSM674397     3  0.1624   0.834031 0.000 0.008 0.936 NA 0.000 0.012
#> GSM674398     3  0.2738   0.796657 0.000 0.004 0.820 NA 0.000 0.000
#> GSM674400     3  0.2118   0.825163 0.000 0.000 0.888 NA 0.000 0.008
#> GSM674401     3  0.2704   0.810079 0.000 0.000 0.844 NA 0.000 0.016
#> GSM674402     3  0.5303  -0.000513 0.000 0.012 0.464 NA 0.000 0.456
#> GSM674403     3  0.2775   0.807163 0.000 0.000 0.856 NA 0.000 0.104
#> GSM674405     3  0.2896   0.785522 0.000 0.000 0.824 NA 0.000 0.016
#> GSM674406     3  0.1802   0.832922 0.000 0.000 0.916 NA 0.000 0.012
#> GSM674407     3  0.2389   0.817560 0.000 0.000 0.864 NA 0.000 0.008
#> GSM674181     6  0.5233   0.312285 0.000 0.384 0.012 NA 0.000 0.536
#> GSM674183     6  0.4671   0.675142 0.000 0.172 0.084 NA 0.000 0.720
#> GSM674184     2  0.4392   0.542746 0.000 0.628 0.000 NA 0.000 0.332
#> GSM674185     2  0.5421   0.406538 0.000 0.556 0.004 NA 0.000 0.316
#> GSM674186     2  0.2165   0.854522 0.000 0.884 0.000 NA 0.000 0.108
#> GSM674187     2  0.1866   0.864724 0.000 0.908 0.000 NA 0.000 0.084
#> GSM674190     2  0.1700   0.867509 0.000 0.916 0.000 NA 0.000 0.080
#> GSM674191     2  0.2805   0.804569 0.000 0.812 0.000 NA 0.000 0.184
#> GSM674192     2  0.0405   0.873283 0.000 0.988 0.000 NA 0.000 0.008
#> GSM674193     2  0.0820   0.869667 0.000 0.972 0.000 NA 0.000 0.012
#> GSM674194     2  0.1644   0.868673 0.000 0.920 0.000 NA 0.000 0.076
#> GSM674195     6  0.4425   0.526436 0.000 0.296 0.036 NA 0.000 0.660
#> GSM674198     2  0.0260   0.871838 0.000 0.992 0.000 NA 0.000 0.000
#> GSM674200     6  0.5407   0.670732 0.000 0.112 0.116 NA 0.000 0.684
#> GSM674201     2  0.4022   0.537403 0.000 0.628 0.004 NA 0.000 0.360
#> GSM674202     2  0.1501   0.869020 0.000 0.924 0.000 NA 0.000 0.076
#> GSM674203     2  0.0508   0.870308 0.000 0.984 0.000 NA 0.000 0.004
#> GSM674204     2  0.0858   0.875299 0.000 0.968 0.000 NA 0.000 0.028
#> GSM674205     2  0.0622   0.871934 0.000 0.980 0.000 NA 0.000 0.008
#> GSM674206     2  0.2882   0.808126 0.000 0.812 0.000 NA 0.000 0.180
#> GSM674208     2  0.1194   0.860219 0.000 0.956 0.004 NA 0.000 0.008
#> GSM674209     2  0.1518   0.871640 0.000 0.944 0.008 NA 0.000 0.024
#> GSM674210     2  0.0665   0.870796 0.000 0.980 0.004 NA 0.000 0.008
#> GSM674212     2  0.1219   0.876297 0.000 0.948 0.000 NA 0.000 0.048
#> GSM674214     2  0.0725   0.874368 0.000 0.976 0.000 NA 0.000 0.012
#> GSM674218     2  0.5186   0.366381 0.000 0.556 0.016 NA 0.000 0.368
#> GSM674219     2  0.3582   0.719966 0.000 0.732 0.000 NA 0.000 0.252
#> GSM674220     2  0.6223   0.201262 0.000 0.488 0.024 NA 0.000 0.300
#> GSM674221     2  0.2135   0.844117 0.000 0.872 0.000 NA 0.000 0.128
#> GSM674223     2  0.1578   0.876756 0.000 0.936 0.004 NA 0.000 0.048
#> GSM674225     2  0.4484   0.670199 0.000 0.728 0.012 NA 0.000 0.092
#> GSM674226     2  0.1565   0.871588 0.000 0.940 0.004 NA 0.000 0.028
#> GSM674229     2  0.1049   0.877248 0.000 0.960 0.000 NA 0.000 0.032
#> GSM674230     2  0.1745   0.869528 0.000 0.920 0.000 NA 0.000 0.068
#> GSM674231     2  0.0914   0.875679 0.000 0.968 0.000 NA 0.000 0.016
#> GSM674232     2  0.0508   0.870303 0.000 0.984 0.000 NA 0.000 0.004
#> GSM674234     2  0.0508   0.874227 0.000 0.984 0.000 NA 0.000 0.012
#> GSM674235     2  0.1765   0.862022 0.000 0.904 0.000 NA 0.000 0.096
#> GSM674236     2  0.1594   0.874221 0.000 0.932 0.000 NA 0.000 0.052
#> GSM674237     2  0.0777   0.866287 0.000 0.972 0.000 NA 0.000 0.004
#> GSM674239     2  0.0405   0.870499 0.000 0.988 0.000 NA 0.000 0.004
#> GSM674240     2  0.3221   0.763376 0.000 0.772 0.004 NA 0.000 0.220
#> GSM674242     2  0.0363   0.871356 0.000 0.988 0.000 NA 0.000 0.000
#> GSM674243     2  0.0909   0.874396 0.000 0.968 0.000 NA 0.000 0.020
#> GSM674244     2  0.4847   0.655903 0.000 0.688 0.008 NA 0.000 0.156
#> GSM674245     2  0.1391   0.875074 0.000 0.944 0.000 NA 0.000 0.040
#> GSM674282     1  0.0146   0.942812 0.996 0.000 0.000 NA 0.004 0.000
#> GSM674284     1  0.0458   0.941047 0.984 0.000 0.000 NA 0.016 0.000
#> GSM674285     1  0.0000   0.943259 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674287     1  0.0458   0.941273 0.984 0.000 0.000 NA 0.016 0.000
#> GSM674288     1  0.3797  -0.238440 0.580 0.000 0.000 NA 0.420 0.000
#> GSM674289     1  0.0000   0.943259 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674290     1  0.0000   0.943259 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674291     1  0.0146   0.942812 0.996 0.000 0.000 NA 0.004 0.000
#> GSM674292     1  0.0363   0.938986 0.988 0.000 0.000 NA 0.012 0.000
#> GSM674295     5  0.3862   0.581177 0.476 0.000 0.000 NA 0.524 0.000
#> GSM674297     1  0.0363   0.941796 0.988 0.000 0.000 NA 0.012 0.000
#> GSM674298     1  0.0260   0.943170 0.992 0.000 0.000 NA 0.008 0.000
#> GSM674299     1  0.1007   0.920707 0.956 0.000 0.000 NA 0.044 0.000
#> GSM674300     1  0.0458   0.939023 0.984 0.000 0.000 NA 0.016 0.000
#> GSM674301     1  0.0000   0.943259 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674302     1  0.0000   0.943259 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674304     1  0.0146   0.943751 0.996 0.000 0.000 NA 0.004 0.000
#> GSM674305     1  0.0000   0.943259 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674306     1  0.0000   0.943259 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674308     1  0.0146   0.943751 0.996 0.000 0.000 NA 0.004 0.000
#> GSM674309     1  0.1501   0.875332 0.924 0.000 0.000 NA 0.076 0.000
#> GSM674313     5  0.2941   0.849077 0.220 0.000 0.000 NA 0.780 0.000
#> GSM674314     5  0.3851   0.625018 0.460 0.000 0.000 NA 0.540 0.000
#> GSM674315     1  0.0000   0.943259 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674316     5  0.3578   0.809959 0.340 0.000 0.000 NA 0.660 0.000
#> GSM674318     5  0.2553   0.814762 0.144 0.000 0.000 NA 0.848 0.008
#> GSM674320     5  0.2300   0.816351 0.144 0.000 0.000 NA 0.856 0.000
#> GSM674323     5  0.3371   0.844545 0.292 0.000 0.000 NA 0.708 0.000
#> GSM674324     1  0.0790   0.926861 0.968 0.000 0.000 NA 0.032 0.000
#> GSM674325     5  0.3221   0.851063 0.264 0.000 0.000 NA 0.736 0.000
#> GSM674327     1  0.3351   0.344531 0.712 0.000 0.000 NA 0.288 0.000
#> GSM674328     1  0.0713   0.932568 0.972 0.000 0.000 NA 0.028 0.000
#> GSM674330     5  0.3765   0.737651 0.404 0.000 0.000 NA 0.596 0.000
#> GSM674331     1  0.1444   0.880839 0.928 0.000 0.000 NA 0.072 0.000
#> GSM674332     1  0.1663   0.861208 0.912 0.000 0.000 NA 0.088 0.000
#> GSM674334     5  0.3747   0.743944 0.396 0.000 0.000 NA 0.604 0.000
#> GSM674335     5  0.3765   0.730155 0.404 0.000 0.000 NA 0.596 0.000
#> GSM674345     3  0.3163   0.787022 0.000 0.000 0.820 NA 0.000 0.140
#> GSM674351     3  0.3487   0.713731 0.000 0.000 0.756 NA 0.000 0.224
#> GSM674352     3  0.3377   0.748325 0.000 0.000 0.784 NA 0.000 0.188
#> GSM674359     3  0.5345   0.132291 0.000 0.004 0.480 NA 0.000 0.424
#> GSM674360     3  0.5021   0.540407 0.000 0.040 0.640 NA 0.000 0.280
#> GSM674362     6  0.6144   0.064190 0.000 0.056 0.408 NA 0.000 0.448
#> GSM674369     3  0.2961   0.823990 0.000 0.032 0.868 NA 0.000 0.060
#> GSM674372     3  0.0790   0.835250 0.000 0.000 0.968 NA 0.000 0.000
#> GSM674374     3  0.1562   0.836837 0.000 0.004 0.940 NA 0.000 0.024
#> GSM674376     3  0.2362   0.810772 0.000 0.004 0.860 NA 0.000 0.000
#> GSM674377     3  0.4139   0.709529 0.000 0.060 0.744 NA 0.000 0.008
#> GSM674378     3  0.1138   0.835986 0.000 0.004 0.960 NA 0.000 0.012
#> GSM674383     3  0.1555   0.828467 0.000 0.004 0.932 NA 0.000 0.060
#> GSM674386     3  0.3109   0.781077 0.000 0.016 0.812 NA 0.000 0.004
#> GSM674387     3  0.1858   0.826028 0.000 0.000 0.904 NA 0.000 0.004
#> GSM674392     3  0.1434   0.831151 0.000 0.000 0.940 NA 0.000 0.048
#> GSM674396     3  0.2772   0.785205 0.000 0.004 0.816 NA 0.000 0.000
#> GSM674399     3  0.2871   0.768426 0.000 0.004 0.804 NA 0.000 0.000
#> GSM674404     3  0.2234   0.814474 0.000 0.000 0.872 NA 0.000 0.004
#> GSM674182     2  0.3398   0.725019 0.000 0.740 0.000 NA 0.000 0.252
#> GSM674188     2  0.1387   0.870859 0.000 0.932 0.000 NA 0.000 0.068
#> GSM674189     2  0.3816   0.655628 0.000 0.688 0.000 NA 0.000 0.296
#> GSM674196     2  0.1049   0.874122 0.000 0.960 0.000 NA 0.000 0.032
#> GSM674197     2  0.0632   0.874618 0.000 0.976 0.000 NA 0.000 0.024
#> GSM674199     2  0.0520   0.871226 0.000 0.984 0.000 NA 0.000 0.008
#> GSM674207     2  0.1088   0.875205 0.000 0.960 0.000 NA 0.000 0.024
#> GSM674211     2  0.0820   0.874991 0.000 0.972 0.000 NA 0.000 0.016
#> GSM674213     2  0.3012   0.791272 0.000 0.796 0.000 NA 0.000 0.196
#> GSM674215     2  0.5870   0.446133 0.000 0.576 0.028 NA 0.000 0.236
#> GSM674216     2  0.1296   0.860859 0.000 0.952 0.004 NA 0.000 0.012
#> GSM674217     2  0.2520   0.826459 0.000 0.844 0.000 NA 0.000 0.152
#> GSM674222     2  0.2197   0.860129 0.000 0.900 0.000 NA 0.000 0.056
#> GSM674224     2  0.1434   0.877005 0.000 0.940 0.000 NA 0.000 0.048
#> GSM674227     2  0.1232   0.864383 0.000 0.956 0.004 NA 0.000 0.016
#> GSM674228     2  0.1674   0.871463 0.000 0.924 0.004 NA 0.000 0.068
#> GSM674233     2  0.2980   0.795724 0.000 0.800 0.000 NA 0.000 0.192
#> GSM674238     6  0.5907   0.635073 0.000 0.208 0.076 NA 0.000 0.612
#> GSM674241     2  0.0653   0.869852 0.000 0.980 0.004 NA 0.000 0.004
#> GSM674283     1  0.0260   0.943170 0.992 0.000 0.000 NA 0.008 0.000
#> GSM674286     1  0.0146   0.943751 0.996 0.000 0.000 NA 0.004 0.000
#> GSM674293     1  0.0000   0.943259 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674294     1  0.0146   0.942812 0.996 0.000 0.000 NA 0.004 0.000
#> GSM674296     1  0.0146   0.943751 0.996 0.000 0.000 NA 0.004 0.000
#> GSM674303     1  0.0363   0.941796 0.988 0.000 0.000 NA 0.012 0.000
#> GSM674307     1  0.0146   0.943751 0.996 0.000 0.000 NA 0.004 0.000
#> GSM674310     5  0.2431   0.804177 0.132 0.000 0.000 NA 0.860 0.008
#> GSM674311     1  0.2416   0.737750 0.844 0.000 0.000 NA 0.156 0.000
#> GSM674312     5  0.2178   0.806532 0.132 0.000 0.000 NA 0.868 0.000
#> GSM674317     1  0.0937   0.922911 0.960 0.000 0.000 NA 0.040 0.000
#> GSM674319     5  0.3499   0.825164 0.320 0.000 0.000 NA 0.680 0.000
#> GSM674321     5  0.3371   0.844689 0.292 0.000 0.000 NA 0.708 0.000
#> GSM674322     5  0.2527   0.830949 0.168 0.000 0.000 NA 0.832 0.000
#> GSM674326     5  0.3244   0.850657 0.268 0.000 0.000 NA 0.732 0.000
#> GSM674329     5  0.2912   0.848126 0.216 0.000 0.000 NA 0.784 0.000
#> GSM674333     5  0.2562   0.832906 0.172 0.000 0.000 NA 0.828 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-SD-NMF-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-SD-NMF-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-SD-NMF-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-SD-NMF-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-SD-NMF-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-SD-NMF-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-SD-NMF-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-SD-NMF-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-SD-NMF-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-SD-NMF-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-SD-NMF-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-SD-NMF-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-SD-NMF-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-SD-NMF-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-SD-NMF-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-SD-NMF-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-SD-NMF-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-SD-NMF-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-SD-NMF-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-SD-NMF-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk SD-NMF-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-SD-NMF-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-SD-NMF-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-SD-NMF-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-SD-NMF-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-SD-NMF-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk SD-NMF-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>          n disease.state(p) specimen(p) k
#> SD:NMF 183            0.924    1.83e-40 2
#> SD:NMF 183            0.962    6.15e-78 3
#> SD:NMF 183            0.962    6.15e-78 4
#> SD:NMF 161            0.229    1.57e-66 5
#> SD:NMF 170            0.833    1.23e-68 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


CV:hclust**

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["CV", "hclust"]
# you can also extract it by
# res = res_list["CV:hclust"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#>   Subgroups are detected by 'hclust' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 4.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk CV-hclust-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk CV-hclust-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 0.706           0.976       0.874         0.4631 0.750   0.571
#> 4 4 0.976           0.908       0.961         0.1548 0.956   0.869
#> 5 5 0.883           0.831       0.883         0.0460 1.000   1.000
#> 6 6 0.816           0.696       0.831         0.0315 0.941   0.808

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2

There is also optional best \(k\) = 2 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette    p1    p2    p3
#> GSM674344     3  0.5327      0.991 0.000 0.272 0.728
#> GSM674346     3  0.5291      0.995 0.000 0.268 0.732
#> GSM674347     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674348     3  0.5291      0.995 0.000 0.268 0.732
#> GSM674349     3  0.5291      0.995 0.000 0.268 0.732
#> GSM674350     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674353     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674354     3  0.5327      0.991 0.000 0.272 0.728
#> GSM674355     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674356     3  0.5291      0.995 0.000 0.268 0.732
#> GSM674357     3  0.5291      0.995 0.000 0.268 0.732
#> GSM674358     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674361     3  0.5291      0.995 0.000 0.268 0.732
#> GSM674363     3  0.5291      0.995 0.000 0.268 0.732
#> GSM674364     3  0.5327      0.991 0.000 0.272 0.728
#> GSM674365     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674366     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674367     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674368     3  0.5291      0.995 0.000 0.268 0.732
#> GSM674370     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674371     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674373     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674375     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674379     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674380     3  0.5291      0.995 0.000 0.268 0.732
#> GSM674381     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674382     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674384     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674385     3  0.5291      0.995 0.000 0.268 0.732
#> GSM674388     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674389     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674390     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674391     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674393     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674394     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674395     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674397     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674398     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674400     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674401     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674402     3  0.5327      0.991 0.000 0.272 0.728
#> GSM674403     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674405     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674406     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674407     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674181     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674183     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674184     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674185     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674186     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674187     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674190     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674191     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674192     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674193     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674194     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674195     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674198     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674200     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674201     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674202     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674203     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674204     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674205     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674206     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674208     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674209     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674210     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674212     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674214     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674218     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674219     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674220     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674221     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674223     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674225     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674226     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674229     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674230     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674231     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674232     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674234     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674235     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674236     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674237     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674239     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674240     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674242     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674243     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674244     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674245     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674282     1  0.4555      0.909 0.800 0.000 0.200
#> GSM674284     1  0.1031      0.937 0.976 0.000 0.024
#> GSM674285     1  0.4605      0.908 0.796 0.000 0.204
#> GSM674287     1  0.0747      0.937 0.984 0.000 0.016
#> GSM674288     1  0.0237      0.937 0.996 0.000 0.004
#> GSM674289     1  0.4555      0.909 0.800 0.000 0.200
#> GSM674290     1  0.4605      0.908 0.796 0.000 0.204
#> GSM674291     1  0.4605      0.908 0.796 0.000 0.204
#> GSM674292     1  0.4605      0.908 0.796 0.000 0.204
#> GSM674295     1  0.1964      0.927 0.944 0.000 0.056
#> GSM674297     1  0.1529      0.937 0.960 0.000 0.040
#> GSM674298     1  0.1529      0.937 0.960 0.000 0.040
#> GSM674299     1  0.0747      0.937 0.984 0.000 0.016
#> GSM674300     1  0.1860      0.936 0.948 0.000 0.052
#> GSM674301     1  0.4605      0.908 0.796 0.000 0.204
#> GSM674302     1  0.4605      0.908 0.796 0.000 0.204
#> GSM674304     1  0.4605      0.908 0.796 0.000 0.204
#> GSM674305     1  0.4605      0.908 0.796 0.000 0.204
#> GSM674306     1  0.4605      0.908 0.796 0.000 0.204
#> GSM674308     1  0.4605      0.908 0.796 0.000 0.204
#> GSM674309     1  0.0000      0.937 1.000 0.000 0.000
#> GSM674313     1  0.2066      0.926 0.940 0.000 0.060
#> GSM674314     1  0.0000      0.937 1.000 0.000 0.000
#> GSM674315     1  0.4605      0.908 0.796 0.000 0.204
#> GSM674316     1  0.2066      0.926 0.940 0.000 0.060
#> GSM674318     1  0.2066      0.926 0.940 0.000 0.060
#> GSM674320     1  0.2066      0.926 0.940 0.000 0.060
#> GSM674323     1  0.2066      0.926 0.940 0.000 0.060
#> GSM674324     1  0.0000      0.937 1.000 0.000 0.000
#> GSM674325     1  0.2066      0.926 0.940 0.000 0.060
#> GSM674327     1  0.1163      0.938 0.972 0.000 0.028
#> GSM674328     1  0.1643      0.936 0.956 0.000 0.044
#> GSM674330     1  0.0000      0.937 1.000 0.000 0.000
#> GSM674331     1  0.0000      0.937 1.000 0.000 0.000
#> GSM674332     1  0.0000      0.937 1.000 0.000 0.000
#> GSM674334     1  0.0000      0.937 1.000 0.000 0.000
#> GSM674335     1  0.0424      0.936 0.992 0.000 0.008
#> GSM674345     3  0.5291      0.995 0.000 0.268 0.732
#> GSM674351     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674352     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674359     3  0.5291      0.995 0.000 0.268 0.732
#> GSM674360     3  0.5327      0.991 0.000 0.272 0.728
#> GSM674362     3  0.5327      0.991 0.000 0.272 0.728
#> GSM674369     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674372     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674374     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674376     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674377     3  0.5291      0.995 0.000 0.268 0.732
#> GSM674378     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674383     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674386     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674387     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674392     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674396     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674399     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674404     3  0.5254      0.998 0.000 0.264 0.736
#> GSM674182     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674188     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674189     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674196     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674197     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674199     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674207     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674211     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674213     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674215     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674216     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674217     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674222     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674224     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674227     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674228     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674233     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674238     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674241     2  0.0000      1.000 0.000 1.000 0.000
#> GSM674283     1  0.4605      0.908 0.796 0.000 0.204
#> GSM674286     1  0.4555      0.909 0.800 0.000 0.200
#> GSM674293     1  0.4605      0.908 0.796 0.000 0.204
#> GSM674294     1  0.4605      0.908 0.796 0.000 0.204
#> GSM674296     1  0.4605      0.908 0.796 0.000 0.204
#> GSM674303     1  0.1031      0.937 0.976 0.000 0.024
#> GSM674307     1  0.4605      0.908 0.796 0.000 0.204
#> GSM674310     1  0.2066      0.926 0.940 0.000 0.060
#> GSM674311     1  0.0000      0.937 1.000 0.000 0.000
#> GSM674312     1  0.2066      0.926 0.940 0.000 0.060
#> GSM674317     1  0.1643      0.936 0.956 0.000 0.044
#> GSM674319     1  0.1964      0.927 0.944 0.000 0.056
#> GSM674321     1  0.2066      0.926 0.940 0.000 0.060
#> GSM674322     1  0.2066      0.926 0.940 0.000 0.060
#> GSM674326     1  0.2066      0.926 0.940 0.000 0.060
#> GSM674329     1  0.2066      0.926 0.940 0.000 0.060
#> GSM674333     1  0.2066      0.926 0.940 0.000 0.060

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1    p2    p3    p4
#> GSM674344     3  0.0469     0.9877 0.000 0.012 0.988 0.000
#> GSM674346     3  0.0188     0.9955 0.000 0.004 0.996 0.000
#> GSM674347     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674348     3  0.0188     0.9955 0.000 0.004 0.996 0.000
#> GSM674349     3  0.0188     0.9955 0.000 0.004 0.996 0.000
#> GSM674350     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674353     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674354     3  0.0336     0.9919 0.000 0.008 0.992 0.000
#> GSM674355     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674356     3  0.0188     0.9955 0.000 0.004 0.996 0.000
#> GSM674357     3  0.0188     0.9955 0.000 0.004 0.996 0.000
#> GSM674358     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674361     3  0.0188     0.9955 0.000 0.004 0.996 0.000
#> GSM674363     3  0.0188     0.9955 0.000 0.004 0.996 0.000
#> GSM674364     3  0.0469     0.9877 0.000 0.012 0.988 0.000
#> GSM674365     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674366     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674367     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674368     3  0.0188     0.9953 0.000 0.004 0.996 0.000
#> GSM674370     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674371     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674373     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674375     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674379     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674380     3  0.0188     0.9953 0.000 0.004 0.996 0.000
#> GSM674381     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674382     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674384     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674385     3  0.0188     0.9953 0.000 0.004 0.996 0.000
#> GSM674388     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674389     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674390     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674391     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674393     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674394     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674395     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674397     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674398     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674400     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674401     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674402     3  0.0469     0.9877 0.000 0.012 0.988 0.000
#> GSM674403     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674405     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674406     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674407     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674181     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674183     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674184     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674185     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674186     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674187     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674190     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674191     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674192     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674193     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674194     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674195     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674198     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674200     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674201     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674202     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674203     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674204     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674205     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674206     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674208     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674209     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674210     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674212     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674214     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674218     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674219     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674220     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674221     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674223     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674225     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674226     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674229     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674230     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674231     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674232     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674234     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674235     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674236     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674237     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674239     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674240     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674242     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674243     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674244     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674245     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674282     1  0.0188     0.8524 0.996 0.000 0.000 0.004
#> GSM674284     1  0.4193     0.6198 0.732 0.000 0.000 0.268
#> GSM674285     1  0.0000     0.8538 1.000 0.000 0.000 0.000
#> GSM674287     1  0.4250     0.6061 0.724 0.000 0.000 0.276
#> GSM674288     4  0.4948     0.2964 0.440 0.000 0.000 0.560
#> GSM674289     1  0.0336     0.8503 0.992 0.000 0.000 0.008
#> GSM674290     1  0.0000     0.8538 1.000 0.000 0.000 0.000
#> GSM674291     1  0.0000     0.8538 1.000 0.000 0.000 0.000
#> GSM674292     1  0.0000     0.8538 1.000 0.000 0.000 0.000
#> GSM674295     4  0.1637     0.7539 0.060 0.000 0.000 0.940
#> GSM674297     1  0.4072     0.6425 0.748 0.000 0.000 0.252
#> GSM674298     1  0.4072     0.6425 0.748 0.000 0.000 0.252
#> GSM674299     1  0.4855     0.2930 0.600 0.000 0.000 0.400
#> GSM674300     1  0.4134     0.6233 0.740 0.000 0.000 0.260
#> GSM674301     1  0.0000     0.8538 1.000 0.000 0.000 0.000
#> GSM674302     1  0.0000     0.8538 1.000 0.000 0.000 0.000
#> GSM674304     1  0.0000     0.8538 1.000 0.000 0.000 0.000
#> GSM674305     1  0.0000     0.8538 1.000 0.000 0.000 0.000
#> GSM674306     1  0.0000     0.8538 1.000 0.000 0.000 0.000
#> GSM674308     1  0.0000     0.8538 1.000 0.000 0.000 0.000
#> GSM674309     4  0.4888     0.4190 0.412 0.000 0.000 0.588
#> GSM674313     4  0.0000     0.7779 0.000 0.000 0.000 1.000
#> GSM674314     4  0.4888     0.4190 0.412 0.000 0.000 0.588
#> GSM674315     1  0.0000     0.8538 1.000 0.000 0.000 0.000
#> GSM674316     4  0.0817     0.7703 0.024 0.000 0.000 0.976
#> GSM674318     4  0.0000     0.7779 0.000 0.000 0.000 1.000
#> GSM674320     4  0.0000     0.7779 0.000 0.000 0.000 1.000
#> GSM674323     4  0.0000     0.7779 0.000 0.000 0.000 1.000
#> GSM674324     4  0.4888     0.4190 0.412 0.000 0.000 0.588
#> GSM674325     4  0.0188     0.7771 0.004 0.000 0.000 0.996
#> GSM674327     1  0.4955     0.0762 0.556 0.000 0.000 0.444
#> GSM674328     1  0.4164     0.6259 0.736 0.000 0.000 0.264
#> GSM674330     4  0.4888     0.4190 0.412 0.000 0.000 0.588
#> GSM674331     4  0.4888     0.4190 0.412 0.000 0.000 0.588
#> GSM674332     4  0.4888     0.4190 0.412 0.000 0.000 0.588
#> GSM674334     4  0.4855     0.4382 0.400 0.000 0.000 0.600
#> GSM674335     4  0.4193     0.5972 0.268 0.000 0.000 0.732
#> GSM674345     3  0.0188     0.9955 0.000 0.004 0.996 0.000
#> GSM674351     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674352     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674359     3  0.0188     0.9955 0.000 0.004 0.996 0.000
#> GSM674360     3  0.0336     0.9919 0.000 0.008 0.992 0.000
#> GSM674362     3  0.0469     0.9877 0.000 0.012 0.988 0.000
#> GSM674369     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674372     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674374     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674376     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674377     3  0.0188     0.9953 0.000 0.004 0.996 0.000
#> GSM674378     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674383     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674386     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674387     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674392     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674396     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674399     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674404     3  0.0000     0.9978 0.000 0.000 1.000 0.000
#> GSM674182     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674188     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674189     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674196     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674197     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674199     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674207     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674211     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674213     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674215     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674216     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674217     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674222     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674224     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674227     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674228     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674233     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674238     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674241     2  0.0000     1.0000 0.000 1.000 0.000 0.000
#> GSM674283     1  0.0000     0.8538 1.000 0.000 0.000 0.000
#> GSM674286     1  0.0188     0.8524 0.996 0.000 0.000 0.004
#> GSM674293     1  0.0000     0.8538 1.000 0.000 0.000 0.000
#> GSM674294     1  0.0000     0.8538 1.000 0.000 0.000 0.000
#> GSM674296     1  0.0000     0.8538 1.000 0.000 0.000 0.000
#> GSM674303     1  0.4193     0.6202 0.732 0.000 0.000 0.268
#> GSM674307     1  0.0000     0.8538 1.000 0.000 0.000 0.000
#> GSM674310     4  0.0000     0.7779 0.000 0.000 0.000 1.000
#> GSM674311     4  0.4888     0.4190 0.412 0.000 0.000 0.588
#> GSM674312     4  0.0000     0.7779 0.000 0.000 0.000 1.000
#> GSM674317     1  0.4477     0.5348 0.688 0.000 0.000 0.312
#> GSM674319     4  0.0188     0.7773 0.004 0.000 0.000 0.996
#> GSM674321     4  0.0000     0.7779 0.000 0.000 0.000 1.000
#> GSM674322     4  0.0000     0.7779 0.000 0.000 0.000 1.000
#> GSM674326     4  0.0000     0.7779 0.000 0.000 0.000 1.000
#> GSM674329     4  0.0000     0.7779 0.000 0.000 0.000 1.000
#> GSM674333     4  0.0000     0.7779 0.000 0.000 0.000 1.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4    p5
#> GSM674344     3  0.1121     0.9691 0.000 0.000 0.956 0.000 0.044
#> GSM674346     3  0.0880     0.9751 0.000 0.000 0.968 0.000 0.032
#> GSM674347     3  0.0609     0.9804 0.000 0.000 0.980 0.000 0.020
#> GSM674348     3  0.0703     0.9779 0.000 0.000 0.976 0.000 0.024
#> GSM674349     3  0.0703     0.9779 0.000 0.000 0.976 0.000 0.024
#> GSM674350     3  0.0510     0.9793 0.000 0.000 0.984 0.000 0.016
#> GSM674353     3  0.0510     0.9793 0.000 0.000 0.984 0.000 0.016
#> GSM674354     3  0.1043     0.9714 0.000 0.000 0.960 0.000 0.040
#> GSM674355     3  0.0510     0.9793 0.000 0.000 0.984 0.000 0.016
#> GSM674356     3  0.0703     0.9775 0.000 0.000 0.976 0.000 0.024
#> GSM674357     3  0.0703     0.9775 0.000 0.000 0.976 0.000 0.024
#> GSM674358     3  0.0510     0.9793 0.000 0.000 0.984 0.000 0.016
#> GSM674361     3  0.0609     0.9785 0.000 0.000 0.980 0.000 0.020
#> GSM674363     3  0.0609     0.9785 0.000 0.000 0.980 0.000 0.020
#> GSM674364     3  0.0963     0.9734 0.000 0.000 0.964 0.000 0.036
#> GSM674365     3  0.0162     0.9805 0.000 0.000 0.996 0.000 0.004
#> GSM674366     3  0.0162     0.9805 0.000 0.000 0.996 0.000 0.004
#> GSM674367     3  0.0162     0.9801 0.000 0.000 0.996 0.000 0.004
#> GSM674368     3  0.0703     0.9777 0.000 0.000 0.976 0.000 0.024
#> GSM674370     3  0.0290     0.9804 0.000 0.000 0.992 0.000 0.008
#> GSM674371     3  0.0290     0.9804 0.000 0.000 0.992 0.000 0.008
#> GSM674373     3  0.0162     0.9801 0.000 0.000 0.996 0.000 0.004
#> GSM674375     3  0.0290     0.9803 0.000 0.000 0.992 0.000 0.008
#> GSM674379     3  0.0609     0.9766 0.000 0.000 0.980 0.000 0.020
#> GSM674380     3  0.0794     0.9759 0.000 0.000 0.972 0.000 0.028
#> GSM674381     3  0.0404     0.9787 0.000 0.000 0.988 0.000 0.012
#> GSM674382     3  0.0703     0.9751 0.000 0.000 0.976 0.000 0.024
#> GSM674384     3  0.0404     0.9807 0.000 0.000 0.988 0.000 0.012
#> GSM674385     3  0.0703     0.9784 0.000 0.000 0.976 0.000 0.024
#> GSM674388     3  0.0404     0.9807 0.000 0.000 0.988 0.000 0.012
#> GSM674389     3  0.0609     0.9789 0.000 0.000 0.980 0.000 0.020
#> GSM674390     3  0.0290     0.9804 0.000 0.000 0.992 0.000 0.008
#> GSM674391     3  0.0703     0.9751 0.000 0.000 0.976 0.000 0.024
#> GSM674393     3  0.0609     0.9789 0.000 0.000 0.980 0.000 0.020
#> GSM674394     3  0.0510     0.9805 0.000 0.000 0.984 0.000 0.016
#> GSM674395     3  0.0290     0.9807 0.000 0.000 0.992 0.000 0.008
#> GSM674397     3  0.0290     0.9804 0.000 0.000 0.992 0.000 0.008
#> GSM674398     3  0.0703     0.9751 0.000 0.000 0.976 0.000 0.024
#> GSM674400     3  0.2561     0.8725 0.000 0.000 0.856 0.000 0.144
#> GSM674401     3  0.2929     0.8379 0.000 0.000 0.820 0.000 0.180
#> GSM674402     3  0.1121     0.9691 0.000 0.000 0.956 0.000 0.044
#> GSM674403     3  0.2561     0.8725 0.000 0.000 0.856 0.000 0.144
#> GSM674405     3  0.0794     0.9736 0.000 0.000 0.972 0.000 0.028
#> GSM674406     3  0.0510     0.9778 0.000 0.000 0.984 0.000 0.016
#> GSM674407     3  0.0510     0.9778 0.000 0.000 0.984 0.000 0.016
#> GSM674181     2  0.3876     0.7805 0.000 0.684 0.000 0.000 0.316
#> GSM674183     2  0.4242     0.6998 0.000 0.572 0.000 0.000 0.428
#> GSM674184     2  0.4126     0.7369 0.000 0.620 0.000 0.000 0.380
#> GSM674185     2  0.4256     0.6922 0.000 0.564 0.000 0.000 0.436
#> GSM674186     2  0.3876     0.7841 0.000 0.684 0.000 0.000 0.316
#> GSM674187     2  0.1478     0.8927 0.000 0.936 0.000 0.000 0.064
#> GSM674190     2  0.2648     0.8623 0.000 0.848 0.000 0.000 0.152
#> GSM674191     2  0.2648     0.8623 0.000 0.848 0.000 0.000 0.152
#> GSM674192     2  0.0162     0.8960 0.000 0.996 0.000 0.000 0.004
#> GSM674193     2  0.0794     0.8964 0.000 0.972 0.000 0.000 0.028
#> GSM674194     2  0.3636     0.8106 0.000 0.728 0.000 0.000 0.272
#> GSM674195     2  0.4242     0.6999 0.000 0.572 0.000 0.000 0.428
#> GSM674198     2  0.0000     0.8960 0.000 1.000 0.000 0.000 0.000
#> GSM674200     2  0.4278     0.6793 0.000 0.548 0.000 0.000 0.452
#> GSM674201     2  0.3983     0.7667 0.000 0.660 0.000 0.000 0.340
#> GSM674202     2  0.1270     0.8941 0.000 0.948 0.000 0.000 0.052
#> GSM674203     2  0.0000     0.8960 0.000 1.000 0.000 0.000 0.000
#> GSM674204     2  0.0000     0.8960 0.000 1.000 0.000 0.000 0.000
#> GSM674205     2  0.0162     0.8960 0.000 0.996 0.000 0.000 0.004
#> GSM674206     2  0.4015     0.7668 0.000 0.652 0.000 0.000 0.348
#> GSM674208     2  0.0000     0.8960 0.000 1.000 0.000 0.000 0.000
#> GSM674209     2  0.0290     0.8965 0.000 0.992 0.000 0.000 0.008
#> GSM674210     2  0.0000     0.8960 0.000 1.000 0.000 0.000 0.000
#> GSM674212     2  0.0000     0.8960 0.000 1.000 0.000 0.000 0.000
#> GSM674214     2  0.0000     0.8960 0.000 1.000 0.000 0.000 0.000
#> GSM674218     2  0.4262     0.6906 0.000 0.560 0.000 0.000 0.440
#> GSM674219     2  0.2773     0.8580 0.000 0.836 0.000 0.000 0.164
#> GSM674220     2  0.3774     0.7933 0.000 0.704 0.000 0.000 0.296
#> GSM674221     2  0.2516     0.8663 0.000 0.860 0.000 0.000 0.140
#> GSM674223     2  0.0404     0.8966 0.000 0.988 0.000 0.000 0.012
#> GSM674225     2  0.3395     0.8221 0.000 0.764 0.000 0.000 0.236
#> GSM674226     2  0.0609     0.8972 0.000 0.980 0.000 0.000 0.020
#> GSM674229     2  0.0404     0.8964 0.000 0.988 0.000 0.000 0.012
#> GSM674230     2  0.0703     0.8968 0.000 0.976 0.000 0.000 0.024
#> GSM674231     2  0.0510     0.8965 0.000 0.984 0.000 0.000 0.016
#> GSM674232     2  0.0162     0.8960 0.000 0.996 0.000 0.000 0.004
#> GSM674234     2  0.0162     0.8960 0.000 0.996 0.000 0.000 0.004
#> GSM674235     2  0.1197     0.8946 0.000 0.952 0.000 0.000 0.048
#> GSM674236     2  0.1121     0.8948 0.000 0.956 0.000 0.000 0.044
#> GSM674237     2  0.0162     0.8963 0.000 0.996 0.000 0.000 0.004
#> GSM674239     2  0.0000     0.8960 0.000 1.000 0.000 0.000 0.000
#> GSM674240     2  0.2891     0.8539 0.000 0.824 0.000 0.000 0.176
#> GSM674242     2  0.0000     0.8960 0.000 1.000 0.000 0.000 0.000
#> GSM674243     2  0.0404     0.8966 0.000 0.988 0.000 0.000 0.012
#> GSM674244     2  0.3452     0.8170 0.000 0.756 0.000 0.000 0.244
#> GSM674245     2  0.1270     0.8910 0.000 0.948 0.000 0.000 0.052
#> GSM674282     1  0.1043     0.8331 0.960 0.000 0.000 0.040 0.000
#> GSM674284     1  0.3999     0.6417 0.656 0.000 0.000 0.344 0.000
#> GSM674285     1  0.0510     0.8400 0.984 0.000 0.000 0.016 0.000
#> GSM674287     1  0.4030     0.6328 0.648 0.000 0.000 0.352 0.000
#> GSM674288     4  0.4341     0.0894 0.364 0.000 0.000 0.628 0.008
#> GSM674289     1  0.1121     0.8317 0.956 0.000 0.000 0.044 0.000
#> GSM674290     1  0.0000     0.8410 1.000 0.000 0.000 0.000 0.000
#> GSM674291     1  0.0000     0.8410 1.000 0.000 0.000 0.000 0.000
#> GSM674292     1  0.0000     0.8410 1.000 0.000 0.000 0.000 0.000
#> GSM674295     4  0.5002     0.6855 0.052 0.000 0.000 0.636 0.312
#> GSM674297     1  0.3932     0.6562 0.672 0.000 0.000 0.328 0.000
#> GSM674298     1  0.3932     0.6562 0.672 0.000 0.000 0.328 0.000
#> GSM674299     1  0.4300     0.3990 0.524 0.000 0.000 0.476 0.000
#> GSM674300     1  0.4152     0.6524 0.692 0.000 0.000 0.296 0.012
#> GSM674301     1  0.0000     0.8410 1.000 0.000 0.000 0.000 0.000
#> GSM674302     1  0.0000     0.8410 1.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0000     0.8410 1.000 0.000 0.000 0.000 0.000
#> GSM674305     1  0.0000     0.8410 1.000 0.000 0.000 0.000 0.000
#> GSM674306     1  0.0000     0.8410 1.000 0.000 0.000 0.000 0.000
#> GSM674308     1  0.0000     0.8410 1.000 0.000 0.000 0.000 0.000
#> GSM674309     4  0.3966     0.2181 0.336 0.000 0.000 0.664 0.000
#> GSM674313     4  0.3966     0.6992 0.000 0.000 0.000 0.664 0.336
#> GSM674314     4  0.3966     0.2181 0.336 0.000 0.000 0.664 0.000
#> GSM674315     1  0.0000     0.8410 1.000 0.000 0.000 0.000 0.000
#> GSM674316     4  0.4219     0.6957 0.024 0.000 0.000 0.716 0.260
#> GSM674318     4  0.3895     0.7038 0.000 0.000 0.000 0.680 0.320
#> GSM674320     4  0.3932     0.7014 0.000 0.000 0.000 0.672 0.328
#> GSM674323     4  0.3586     0.7030 0.000 0.000 0.000 0.736 0.264
#> GSM674324     4  0.3966     0.2181 0.336 0.000 0.000 0.664 0.000
#> GSM674325     4  0.3635     0.6994 0.004 0.000 0.000 0.748 0.248
#> GSM674327     1  0.4659     0.2267 0.496 0.000 0.000 0.492 0.012
#> GSM674328     1  0.3966     0.6455 0.664 0.000 0.000 0.336 0.000
#> GSM674330     4  0.3966     0.2181 0.336 0.000 0.000 0.664 0.000
#> GSM674331     4  0.3966     0.2181 0.336 0.000 0.000 0.664 0.000
#> GSM674332     4  0.3966     0.2181 0.336 0.000 0.000 0.664 0.000
#> GSM674334     4  0.4288     0.2490 0.324 0.000 0.000 0.664 0.012
#> GSM674335     4  0.3977     0.4280 0.204 0.000 0.000 0.764 0.032
#> GSM674345     3  0.0794     0.9762 0.000 0.000 0.972 0.000 0.028
#> GSM674351     3  0.0510     0.9793 0.000 0.000 0.984 0.000 0.016
#> GSM674352     3  0.0510     0.9793 0.000 0.000 0.984 0.000 0.016
#> GSM674359     3  0.0794     0.9762 0.000 0.000 0.972 0.000 0.028
#> GSM674360     3  0.0880     0.9745 0.000 0.000 0.968 0.000 0.032
#> GSM674362     3  0.1121     0.9691 0.000 0.000 0.956 0.000 0.044
#> GSM674369     3  0.0510     0.9798 0.000 0.000 0.984 0.000 0.016
#> GSM674372     3  0.0290     0.9803 0.000 0.000 0.992 0.000 0.008
#> GSM674374     3  0.0162     0.9801 0.000 0.000 0.996 0.000 0.004
#> GSM674376     3  0.0609     0.9766 0.000 0.000 0.980 0.000 0.020
#> GSM674377     3  0.0609     0.9782 0.000 0.000 0.980 0.000 0.020
#> GSM674378     3  0.0162     0.9801 0.000 0.000 0.996 0.000 0.004
#> GSM674383     3  0.0290     0.9804 0.000 0.000 0.992 0.000 0.008
#> GSM674386     3  0.0703     0.9751 0.000 0.000 0.976 0.000 0.024
#> GSM674387     3  0.0510     0.9778 0.000 0.000 0.984 0.000 0.016
#> GSM674392     3  0.0404     0.9802 0.000 0.000 0.988 0.000 0.012
#> GSM674396     3  0.0703     0.9751 0.000 0.000 0.976 0.000 0.024
#> GSM674399     3  0.0703     0.9751 0.000 0.000 0.976 0.000 0.024
#> GSM674404     3  0.0794     0.9736 0.000 0.000 0.972 0.000 0.028
#> GSM674182     2  0.3816     0.7883 0.000 0.696 0.000 0.000 0.304
#> GSM674188     2  0.1478     0.8927 0.000 0.936 0.000 0.000 0.064
#> GSM674189     2  0.4060     0.7546 0.000 0.640 0.000 0.000 0.360
#> GSM674196     2  0.0000     0.8960 0.000 1.000 0.000 0.000 0.000
#> GSM674197     2  0.0000     0.8960 0.000 1.000 0.000 0.000 0.000
#> GSM674199     2  0.0000     0.8960 0.000 1.000 0.000 0.000 0.000
#> GSM674207     2  0.0000     0.8960 0.000 1.000 0.000 0.000 0.000
#> GSM674211     2  0.0000     0.8960 0.000 1.000 0.000 0.000 0.000
#> GSM674213     2  0.0162     0.8968 0.000 0.996 0.000 0.000 0.004
#> GSM674215     2  0.3949     0.7724 0.000 0.668 0.000 0.000 0.332
#> GSM674216     2  0.0404     0.8963 0.000 0.988 0.000 0.000 0.012
#> GSM674217     2  0.2516     0.8663 0.000 0.860 0.000 0.000 0.140
#> GSM674222     2  0.2074     0.8750 0.000 0.896 0.000 0.000 0.104
#> GSM674224     2  0.0609     0.8972 0.000 0.980 0.000 0.000 0.020
#> GSM674227     2  0.1341     0.8938 0.000 0.944 0.000 0.000 0.056
#> GSM674228     2  0.0609     0.8969 0.000 0.980 0.000 0.000 0.020
#> GSM674233     2  0.2732     0.8593 0.000 0.840 0.000 0.000 0.160
#> GSM674238     2  0.4278     0.6793 0.000 0.548 0.000 0.000 0.452
#> GSM674241     2  0.0000     0.8960 0.000 1.000 0.000 0.000 0.000
#> GSM674283     1  0.0510     0.8400 0.984 0.000 0.000 0.016 0.000
#> GSM674286     1  0.1043     0.8331 0.960 0.000 0.000 0.040 0.000
#> GSM674293     1  0.0000     0.8410 1.000 0.000 0.000 0.000 0.000
#> GSM674294     1  0.0290     0.8409 0.992 0.000 0.000 0.008 0.000
#> GSM674296     1  0.0000     0.8410 1.000 0.000 0.000 0.000 0.000
#> GSM674303     1  0.3999     0.6407 0.656 0.000 0.000 0.344 0.000
#> GSM674307     1  0.0404     0.8405 0.988 0.000 0.000 0.012 0.000
#> GSM674310     4  0.3895     0.7038 0.000 0.000 0.000 0.680 0.320
#> GSM674311     4  0.3966     0.2181 0.336 0.000 0.000 0.664 0.000
#> GSM674312     4  0.3966     0.6992 0.000 0.000 0.000 0.664 0.336
#> GSM674317     1  0.4138     0.5751 0.616 0.000 0.000 0.384 0.000
#> GSM674319     4  0.3895     0.7022 0.000 0.000 0.000 0.680 0.320
#> GSM674321     4  0.3774     0.7057 0.000 0.000 0.000 0.704 0.296
#> GSM674322     4  0.3895     0.7038 0.000 0.000 0.000 0.680 0.320
#> GSM674326     4  0.3895     0.7038 0.000 0.000 0.000 0.680 0.320
#> GSM674329     4  0.3913     0.7027 0.000 0.000 0.000 0.676 0.324
#> GSM674333     4  0.3586     0.7029 0.000 0.000 0.000 0.736 0.264

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4    p5    p6
#> GSM674344     3  0.2257     0.8164 0.000 0.000 0.876 0.116 0.000 0.008
#> GSM674346     3  0.1858     0.8485 0.000 0.000 0.904 0.092 0.000 0.004
#> GSM674347     3  0.1610     0.8743 0.000 0.000 0.916 0.084 0.000 0.000
#> GSM674348     3  0.1152     0.8839 0.000 0.000 0.952 0.044 0.000 0.004
#> GSM674349     3  0.1152     0.8848 0.000 0.000 0.952 0.044 0.000 0.004
#> GSM674350     3  0.1267     0.8794 0.000 0.000 0.940 0.060 0.000 0.000
#> GSM674353     3  0.1267     0.8794 0.000 0.000 0.940 0.060 0.000 0.000
#> GSM674354     3  0.2146     0.8217 0.000 0.000 0.880 0.116 0.000 0.004
#> GSM674355     3  0.1327     0.8785 0.000 0.000 0.936 0.064 0.000 0.000
#> GSM674356     3  0.1471     0.8688 0.000 0.000 0.932 0.064 0.000 0.004
#> GSM674357     3  0.1471     0.8688 0.000 0.000 0.932 0.064 0.000 0.004
#> GSM674358     3  0.1267     0.8794 0.000 0.000 0.940 0.060 0.000 0.000
#> GSM674361     3  0.1285     0.8765 0.000 0.000 0.944 0.052 0.000 0.004
#> GSM674363     3  0.1285     0.8765 0.000 0.000 0.944 0.052 0.000 0.004
#> GSM674364     3  0.1970     0.8445 0.000 0.000 0.900 0.092 0.000 0.008
#> GSM674365     3  0.0632     0.8907 0.000 0.000 0.976 0.024 0.000 0.000
#> GSM674366     3  0.0713     0.8918 0.000 0.000 0.972 0.028 0.000 0.000
#> GSM674367     3  0.0937     0.8890 0.000 0.000 0.960 0.040 0.000 0.000
#> GSM674368     3  0.1444     0.8748 0.000 0.000 0.928 0.072 0.000 0.000
#> GSM674370     3  0.1204     0.8873 0.000 0.000 0.944 0.056 0.000 0.000
#> GSM674371     3  0.0713     0.8904 0.000 0.000 0.972 0.028 0.000 0.000
#> GSM674373     3  0.1141     0.8862 0.000 0.000 0.948 0.052 0.000 0.000
#> GSM674375     3  0.1267     0.8842 0.000 0.000 0.940 0.060 0.000 0.000
#> GSM674379     3  0.1863     0.8509 0.000 0.000 0.896 0.104 0.000 0.000
#> GSM674380     3  0.2048     0.8473 0.000 0.000 0.880 0.120 0.000 0.000
#> GSM674381     3  0.1610     0.8755 0.000 0.000 0.916 0.084 0.000 0.000
#> GSM674382     3  0.1957     0.8432 0.000 0.000 0.888 0.112 0.000 0.000
#> GSM674384     3  0.1141     0.8907 0.000 0.000 0.948 0.052 0.000 0.000
#> GSM674385     3  0.1765     0.8691 0.000 0.000 0.904 0.096 0.000 0.000
#> GSM674388     3  0.0632     0.8926 0.000 0.000 0.976 0.024 0.000 0.000
#> GSM674389     3  0.1814     0.8579 0.000 0.000 0.900 0.100 0.000 0.000
#> GSM674390     3  0.1204     0.8873 0.000 0.000 0.944 0.056 0.000 0.000
#> GSM674391     3  0.1957     0.8432 0.000 0.000 0.888 0.112 0.000 0.000
#> GSM674393     3  0.1863     0.8541 0.000 0.000 0.896 0.104 0.000 0.000
#> GSM674394     3  0.1387     0.8943 0.000 0.000 0.932 0.068 0.000 0.000
#> GSM674395     3  0.0937     0.8907 0.000 0.000 0.960 0.040 0.000 0.000
#> GSM674397     3  0.0790     0.8925 0.000 0.000 0.968 0.032 0.000 0.000
#> GSM674398     3  0.2048     0.8383 0.000 0.000 0.880 0.120 0.000 0.000
#> GSM674400     4  0.3727     0.9353 0.000 0.000 0.388 0.612 0.000 0.000
#> GSM674401     4  0.3464     0.8844 0.000 0.000 0.312 0.688 0.000 0.000
#> GSM674402     3  0.2257     0.8164 0.000 0.000 0.876 0.116 0.000 0.008
#> GSM674403     4  0.3727     0.9353 0.000 0.000 0.388 0.612 0.000 0.000
#> GSM674405     3  0.2527     0.7724 0.000 0.000 0.832 0.168 0.000 0.000
#> GSM674406     3  0.1814     0.8542 0.000 0.000 0.900 0.100 0.000 0.000
#> GSM674407     3  0.1814     0.8542 0.000 0.000 0.900 0.100 0.000 0.000
#> GSM674181     2  0.3789    -0.4258 0.000 0.584 0.000 0.000 0.000 0.416
#> GSM674183     6  0.3923     0.9514 0.000 0.416 0.000 0.004 0.000 0.580
#> GSM674184     2  0.3999    -0.7611 0.000 0.500 0.000 0.004 0.000 0.496
#> GSM674185     6  0.3944     0.9376 0.000 0.428 0.000 0.004 0.000 0.568
#> GSM674186     2  0.3804    -0.4851 0.000 0.576 0.000 0.000 0.000 0.424
#> GSM674187     2  0.1958     0.7137 0.000 0.896 0.000 0.004 0.000 0.100
#> GSM674190     2  0.2762     0.5267 0.000 0.804 0.000 0.000 0.000 0.196
#> GSM674191     2  0.2762     0.5267 0.000 0.804 0.000 0.000 0.000 0.196
#> GSM674192     2  0.0260     0.7713 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674193     2  0.0937     0.7614 0.000 0.960 0.000 0.000 0.000 0.040
#> GSM674194     2  0.3592    -0.0753 0.000 0.656 0.000 0.000 0.000 0.344
#> GSM674195     6  0.3930     0.9489 0.000 0.420 0.000 0.004 0.000 0.576
#> GSM674198     2  0.0000     0.7716 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674200     6  0.3862     0.9424 0.000 0.388 0.000 0.004 0.000 0.608
#> GSM674201     2  0.3843    -0.5857 0.000 0.548 0.000 0.000 0.000 0.452
#> GSM674202     2  0.2100     0.6982 0.000 0.884 0.000 0.004 0.000 0.112
#> GSM674203     2  0.0000     0.7716 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674204     2  0.0000     0.7716 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674205     2  0.0146     0.7708 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674206     2  0.3823    -0.5160 0.000 0.564 0.000 0.000 0.000 0.436
#> GSM674208     2  0.0000     0.7716 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674209     2  0.0458     0.7700 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM674210     2  0.0000     0.7716 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674212     2  0.0000     0.7716 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674214     2  0.0000     0.7716 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674218     6  0.3797     0.9460 0.000 0.420 0.000 0.000 0.000 0.580
#> GSM674219     2  0.2912     0.4762 0.000 0.784 0.000 0.000 0.000 0.216
#> GSM674220     2  0.4010    -0.3742 0.000 0.584 0.000 0.008 0.000 0.408
#> GSM674221     2  0.2527     0.5799 0.000 0.832 0.000 0.000 0.000 0.168
#> GSM674223     2  0.0547     0.7689 0.000 0.980 0.000 0.000 0.000 0.020
#> GSM674225     2  0.3804    -0.0231 0.000 0.656 0.000 0.008 0.000 0.336
#> GSM674226     2  0.0790     0.7670 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM674229     2  0.0363     0.7705 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM674230     2  0.1082     0.7583 0.000 0.956 0.000 0.004 0.000 0.040
#> GSM674231     2  0.0632     0.7676 0.000 0.976 0.000 0.000 0.000 0.024
#> GSM674232     2  0.0146     0.7708 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674234     2  0.0146     0.7708 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674235     2  0.1908     0.7161 0.000 0.900 0.000 0.004 0.000 0.096
#> GSM674236     2  0.1958     0.7110 0.000 0.896 0.000 0.004 0.000 0.100
#> GSM674237     2  0.0146     0.7711 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674239     2  0.0000     0.7716 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674240     2  0.3050     0.4164 0.000 0.764 0.000 0.000 0.000 0.236
#> GSM674242     2  0.0000     0.7716 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674243     2  0.0547     0.7677 0.000 0.980 0.000 0.000 0.000 0.020
#> GSM674244     2  0.3833    -0.0692 0.000 0.648 0.000 0.008 0.000 0.344
#> GSM674245     2  0.1753     0.7251 0.000 0.912 0.000 0.004 0.000 0.084
#> GSM674282     1  0.3784     0.7211 0.680 0.000 0.000 0.012 0.000 0.308
#> GSM674284     1  0.0000     0.6796 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674285     1  0.3592     0.7198 0.656 0.000 0.000 0.000 0.000 0.344
#> GSM674287     1  0.0291     0.6772 0.992 0.000 0.000 0.000 0.004 0.004
#> GSM674288     1  0.3753     0.4069 0.696 0.000 0.000 0.004 0.292 0.008
#> GSM674289     1  0.3766     0.7213 0.684 0.000 0.000 0.012 0.000 0.304
#> GSM674290     1  0.3647     0.7167 0.640 0.000 0.000 0.000 0.000 0.360
#> GSM674291     1  0.3647     0.7167 0.640 0.000 0.000 0.000 0.000 0.360
#> GSM674292     1  0.3647     0.7167 0.640 0.000 0.000 0.000 0.000 0.360
#> GSM674295     5  0.3356     0.8834 0.072 0.000 0.000 0.064 0.840 0.024
#> GSM674297     1  0.0508     0.6819 0.984 0.000 0.000 0.012 0.000 0.004
#> GSM674298     1  0.0508     0.6819 0.984 0.000 0.000 0.012 0.000 0.004
#> GSM674299     1  0.2278     0.5987 0.868 0.000 0.000 0.000 0.128 0.004
#> GSM674300     1  0.3832     0.6797 0.800 0.000 0.000 0.020 0.072 0.108
#> GSM674301     1  0.3647     0.7167 0.640 0.000 0.000 0.000 0.000 0.360
#> GSM674302     1  0.3647     0.7167 0.640 0.000 0.000 0.000 0.000 0.360
#> GSM674304     1  0.3647     0.7167 0.640 0.000 0.000 0.000 0.000 0.360
#> GSM674305     1  0.3647     0.7167 0.640 0.000 0.000 0.000 0.000 0.360
#> GSM674306     1  0.4999     0.6975 0.632 0.000 0.000 0.128 0.000 0.240
#> GSM674308     1  0.3647     0.7167 0.640 0.000 0.000 0.000 0.000 0.360
#> GSM674309     1  0.3707     0.3782 0.680 0.000 0.000 0.000 0.312 0.008
#> GSM674313     5  0.1594     0.9357 0.000 0.000 0.000 0.052 0.932 0.016
#> GSM674314     1  0.3707     0.3782 0.680 0.000 0.000 0.000 0.312 0.008
#> GSM674315     1  0.4999     0.6975 0.632 0.000 0.000 0.128 0.000 0.240
#> GSM674316     5  0.1765     0.8997 0.096 0.000 0.000 0.000 0.904 0.000
#> GSM674318     5  0.0000     0.9455 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674320     5  0.1594     0.9386 0.000 0.000 0.000 0.052 0.932 0.016
#> GSM674323     5  0.1387     0.9221 0.068 0.000 0.000 0.000 0.932 0.000
#> GSM674324     1  0.3707     0.3782 0.680 0.000 0.000 0.000 0.312 0.008
#> GSM674325     5  0.1663     0.9087 0.088 0.000 0.000 0.000 0.912 0.000
#> GSM674327     1  0.4371     0.5339 0.720 0.000 0.000 0.020 0.216 0.044
#> GSM674328     1  0.1173     0.6783 0.960 0.000 0.000 0.016 0.016 0.008
#> GSM674330     1  0.3707     0.3782 0.680 0.000 0.000 0.000 0.312 0.008
#> GSM674331     1  0.3707     0.3782 0.680 0.000 0.000 0.000 0.312 0.008
#> GSM674332     1  0.3725     0.3749 0.676 0.000 0.000 0.000 0.316 0.008
#> GSM674334     1  0.3819     0.3372 0.652 0.000 0.000 0.000 0.340 0.008
#> GSM674335     1  0.4224    -0.0788 0.512 0.000 0.000 0.004 0.476 0.008
#> GSM674345     3  0.1531     0.8683 0.000 0.000 0.928 0.068 0.000 0.004
#> GSM674351     3  0.1267     0.8794 0.000 0.000 0.940 0.060 0.000 0.000
#> GSM674352     3  0.1267     0.8794 0.000 0.000 0.940 0.060 0.000 0.000
#> GSM674359     3  0.1531     0.8660 0.000 0.000 0.928 0.068 0.000 0.004
#> GSM674360     3  0.1958     0.8476 0.000 0.000 0.896 0.100 0.000 0.004
#> GSM674362     3  0.2257     0.8164 0.000 0.000 0.876 0.116 0.000 0.008
#> GSM674369     3  0.0865     0.8894 0.000 0.000 0.964 0.036 0.000 0.000
#> GSM674372     3  0.1204     0.8853 0.000 0.000 0.944 0.056 0.000 0.000
#> GSM674374     3  0.1141     0.8862 0.000 0.000 0.948 0.052 0.000 0.000
#> GSM674376     3  0.1910     0.8472 0.000 0.000 0.892 0.108 0.000 0.000
#> GSM674377     3  0.1765     0.8678 0.000 0.000 0.904 0.096 0.000 0.000
#> GSM674378     3  0.1141     0.8862 0.000 0.000 0.948 0.052 0.000 0.000
#> GSM674383     3  0.0547     0.8919 0.000 0.000 0.980 0.020 0.000 0.000
#> GSM674386     3  0.2092     0.8353 0.000 0.000 0.876 0.124 0.000 0.000
#> GSM674387     3  0.1814     0.8542 0.000 0.000 0.900 0.100 0.000 0.000
#> GSM674392     3  0.1444     0.8858 0.000 0.000 0.928 0.072 0.000 0.000
#> GSM674396     3  0.2092     0.8353 0.000 0.000 0.876 0.124 0.000 0.000
#> GSM674399     3  0.2178     0.8270 0.000 0.000 0.868 0.132 0.000 0.000
#> GSM674404     3  0.2454     0.7863 0.000 0.000 0.840 0.160 0.000 0.000
#> GSM674182     2  0.3765    -0.3766 0.000 0.596 0.000 0.000 0.000 0.404
#> GSM674188     2  0.1958     0.7137 0.000 0.896 0.000 0.004 0.000 0.100
#> GSM674189     2  0.3860    -0.6562 0.000 0.528 0.000 0.000 0.000 0.472
#> GSM674196     2  0.0000     0.7716 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674197     2  0.0000     0.7716 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674199     2  0.0000     0.7716 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674207     2  0.0000     0.7716 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674211     2  0.0000     0.7716 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674213     2  0.0458     0.7690 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM674215     2  0.4083    -0.6035 0.000 0.532 0.000 0.008 0.000 0.460
#> GSM674216     2  0.0458     0.7679 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM674217     2  0.2527     0.5799 0.000 0.832 0.000 0.000 0.000 0.168
#> GSM674222     2  0.2743     0.5871 0.000 0.828 0.000 0.008 0.000 0.164
#> GSM674224     2  0.0713     0.7680 0.000 0.972 0.000 0.000 0.000 0.028
#> GSM674227     2  0.2006     0.7090 0.000 0.892 0.000 0.004 0.000 0.104
#> GSM674228     2  0.0713     0.7674 0.000 0.972 0.000 0.000 0.000 0.028
#> GSM674233     2  0.2854     0.4926 0.000 0.792 0.000 0.000 0.000 0.208
#> GSM674238     6  0.3862     0.9424 0.000 0.388 0.000 0.004 0.000 0.608
#> GSM674241     2  0.0000     0.7716 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674283     1  0.3592     0.7198 0.656 0.000 0.000 0.000 0.000 0.344
#> GSM674286     1  0.3784     0.7211 0.680 0.000 0.000 0.012 0.000 0.308
#> GSM674293     1  0.3647     0.7167 0.640 0.000 0.000 0.000 0.000 0.360
#> GSM674294     1  0.3833     0.7189 0.648 0.000 0.000 0.008 0.000 0.344
#> GSM674296     1  0.3647     0.7167 0.640 0.000 0.000 0.000 0.000 0.360
#> GSM674303     1  0.0520     0.6801 0.984 0.000 0.000 0.000 0.008 0.008
#> GSM674307     1  0.3607     0.7194 0.652 0.000 0.000 0.000 0.000 0.348
#> GSM674310     5  0.0000     0.9455 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674311     1  0.3707     0.3782 0.680 0.000 0.000 0.000 0.312 0.008
#> GSM674312     5  0.1779     0.9329 0.000 0.000 0.000 0.064 0.920 0.016
#> GSM674317     1  0.2036     0.6542 0.912 0.000 0.000 0.016 0.064 0.008
#> GSM674319     5  0.2224     0.9317 0.012 0.000 0.000 0.064 0.904 0.020
#> GSM674321     5  0.0632     0.9434 0.024 0.000 0.000 0.000 0.976 0.000
#> GSM674322     5  0.0000     0.9455 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674326     5  0.0000     0.9455 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674329     5  0.1738     0.9394 0.004 0.000 0.000 0.052 0.928 0.016
#> GSM674333     5  0.1531     0.9239 0.068 0.000 0.000 0.000 0.928 0.004

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-CV-hclust-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-CV-hclust-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-CV-hclust-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-CV-hclust-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-CV-hclust-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-CV-hclust-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-CV-hclust-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-CV-hclust-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-CV-hclust-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-CV-hclust-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-CV-hclust-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-CV-hclust-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-CV-hclust-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-CV-hclust-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-CV-hclust-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-CV-hclust-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-CV-hclust-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-CV-hclust-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-CV-hclust-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-CV-hclust-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk CV-hclust-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-CV-hclust-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-CV-hclust-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-CV-hclust-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-CV-hclust-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-CV-hclust-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk CV-hclust-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>             n disease.state(p) specimen(p) k
#> CV:hclust 183            0.924    1.83e-40 2
#> CV:hclust 183            0.962    6.15e-78 3
#> CV:hclust 172            0.417    3.00e-71 4
#> CV:hclust 171            0.307    8.05e-71 5
#> CV:hclust 158            0.358    6.41e-62 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


CV:kmeans**

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["CV", "kmeans"]
# you can also extract it by
# res = res_list["CV:kmeans"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#>   Subgroups are detected by 'kmeans' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 2.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk CV-kmeans-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk CV-kmeans-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 0.703           0.973       0.868         0.4596 0.750   0.571
#> 4 4 0.806           0.876       0.821         0.1466 1.000   1.000
#> 5 5 0.753           0.547       0.648         0.0821 0.896   0.687
#> 6 6 0.719           0.581       0.657         0.0389 0.905   0.619

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 2

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette    p1    p2    p3
#> GSM674344     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674346     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674347     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674348     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674349     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674350     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674353     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674354     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674355     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674356     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674357     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674358     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674361     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674363     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674364     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674365     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674366     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674367     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674368     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674370     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674371     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674373     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674375     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674379     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674380     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674381     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674382     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674384     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674385     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674388     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674389     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674390     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674391     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674393     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674394     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674395     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674397     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674398     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674400     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674401     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674402     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674403     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674405     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674406     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674407     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674181     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674183     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674184     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674185     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674186     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674187     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674190     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674191     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674192     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674193     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674194     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674195     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674198     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674200     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674201     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674202     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674203     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674204     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674205     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674206     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674208     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674209     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674210     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674212     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674214     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674218     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674219     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674220     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674221     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674223     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674225     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674226     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674229     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674230     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674231     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674232     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674234     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674235     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674236     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674237     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674239     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674240     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674242     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674243     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674244     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674245     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674282     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674284     1  0.0237      0.918 0.996 0.004 0.000
#> GSM674285     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674287     1  0.0000      0.918 1.000 0.000 0.000
#> GSM674288     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674289     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674290     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674291     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674292     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674295     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674297     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674298     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674299     1  0.0592      0.918 0.988 0.012 0.000
#> GSM674300     1  0.0747      0.918 0.984 0.016 0.000
#> GSM674301     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674302     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674304     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674305     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674306     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674308     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674309     1  0.3879      0.912 0.848 0.152 0.000
#> GSM674313     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674314     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674315     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674316     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674318     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674320     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674323     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674324     1  0.3340      0.914 0.880 0.120 0.000
#> GSM674325     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674327     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674328     1  0.0000      0.918 1.000 0.000 0.000
#> GSM674330     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674331     1  0.3340      0.914 0.880 0.120 0.000
#> GSM674332     1  0.4235      0.909 0.824 0.176 0.000
#> GSM674334     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674335     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674345     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674351     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674352     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674359     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674360     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674362     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674369     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674372     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674374     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674376     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674377     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674378     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674383     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674386     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674387     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674392     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674396     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674399     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674404     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674182     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674188     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674189     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674196     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674197     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674199     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674207     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674211     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674213     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674215     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674216     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674217     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674222     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674224     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674227     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674228     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674233     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674238     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674241     2  0.5363      1.000 0.000 0.724 0.276
#> GSM674283     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674286     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674293     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674294     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674296     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674303     1  0.0000      0.918 1.000 0.000 0.000
#> GSM674307     1  0.1289      0.915 0.968 0.032 0.000
#> GSM674310     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674311     1  0.3619      0.913 0.864 0.136 0.000
#> GSM674312     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674317     1  0.0000      0.918 1.000 0.000 0.000
#> GSM674319     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674321     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674322     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674326     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674329     1  0.5058      0.901 0.756 0.244 0.000
#> GSM674333     1  0.5058      0.901 0.756 0.244 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1    p2    p3    p4
#> GSM674344     3  0.5159      0.904 0.000 0.088 0.756 0.156
#> GSM674346     3  0.5113      0.905 0.000 0.088 0.760 0.152
#> GSM674347     3  0.4599      0.915 0.000 0.088 0.800 0.112
#> GSM674348     3  0.5535      0.901 0.000 0.088 0.720 0.192
#> GSM674349     3  0.5018      0.907 0.000 0.088 0.768 0.144
#> GSM674350     3  0.5417      0.904 0.000 0.088 0.732 0.180
#> GSM674353     3  0.4969      0.907 0.000 0.088 0.772 0.140
#> GSM674354     3  0.5113      0.905 0.000 0.088 0.760 0.152
#> GSM674355     3  0.5018      0.906 0.000 0.088 0.768 0.144
#> GSM674356     3  0.4969      0.907 0.000 0.088 0.772 0.140
#> GSM674357     3  0.5018      0.906 0.000 0.088 0.768 0.144
#> GSM674358     3  0.5018      0.907 0.000 0.088 0.768 0.144
#> GSM674361     3  0.4969      0.907 0.000 0.088 0.772 0.140
#> GSM674363     3  0.4969      0.907 0.000 0.088 0.772 0.140
#> GSM674364     3  0.5113      0.905 0.000 0.088 0.760 0.152
#> GSM674365     3  0.5535      0.901 0.000 0.088 0.720 0.192
#> GSM674366     3  0.4655      0.910 0.000 0.088 0.796 0.116
#> GSM674367     3  0.3820      0.903 0.000 0.088 0.848 0.064
#> GSM674368     3  0.5113      0.905 0.000 0.088 0.760 0.152
#> GSM674370     3  0.4104      0.913 0.000 0.088 0.832 0.080
#> GSM674371     3  0.5457      0.904 0.000 0.088 0.728 0.184
#> GSM674373     3  0.2730      0.915 0.000 0.088 0.896 0.016
#> GSM674375     3  0.4483      0.898 0.000 0.088 0.808 0.104
#> GSM674379     3  0.3820      0.903 0.000 0.088 0.848 0.064
#> GSM674380     3  0.3894      0.905 0.000 0.088 0.844 0.068
#> GSM674381     3  0.4599      0.898 0.000 0.088 0.800 0.112
#> GSM674382     3  0.3820      0.903 0.000 0.088 0.848 0.064
#> GSM674384     3  0.4599      0.901 0.000 0.088 0.800 0.112
#> GSM674385     3  0.5018      0.910 0.000 0.088 0.768 0.144
#> GSM674388     3  0.5113      0.905 0.000 0.088 0.760 0.152
#> GSM674389     3  0.4483      0.898 0.000 0.088 0.808 0.104
#> GSM674390     3  0.4483      0.898 0.000 0.088 0.808 0.104
#> GSM674391     3  0.3820      0.903 0.000 0.088 0.848 0.064
#> GSM674393     3  0.4483      0.898 0.000 0.088 0.808 0.104
#> GSM674394     3  0.4655      0.913 0.000 0.088 0.796 0.116
#> GSM674395     3  0.3587      0.908 0.000 0.088 0.860 0.052
#> GSM674397     3  0.2730      0.915 0.000 0.088 0.896 0.016
#> GSM674398     3  0.4542      0.898 0.000 0.088 0.804 0.108
#> GSM674400     3  0.3820      0.903 0.000 0.088 0.848 0.064
#> GSM674401     3  0.3820      0.903 0.000 0.088 0.848 0.064
#> GSM674402     3  0.5572      0.900 0.000 0.088 0.716 0.196
#> GSM674403     3  0.4969      0.908 0.000 0.088 0.772 0.140
#> GSM674405     3  0.3820      0.903 0.000 0.088 0.848 0.064
#> GSM674406     3  0.3745      0.904 0.000 0.088 0.852 0.060
#> GSM674407     3  0.3745      0.904 0.000 0.088 0.852 0.060
#> GSM674181     2  0.0921      0.867 0.000 0.972 0.000 0.028
#> GSM674183     2  0.1118      0.864 0.000 0.964 0.000 0.036
#> GSM674184     2  0.1022      0.865 0.000 0.968 0.000 0.032
#> GSM674185     2  0.1022      0.865 0.000 0.968 0.000 0.032
#> GSM674186     2  0.0921      0.867 0.000 0.972 0.000 0.028
#> GSM674187     2  0.0188      0.874 0.000 0.996 0.000 0.004
#> GSM674190     2  0.0921      0.867 0.000 0.972 0.000 0.028
#> GSM674191     2  0.0921      0.867 0.000 0.972 0.000 0.028
#> GSM674192     2  0.4277      0.871 0.000 0.720 0.000 0.280
#> GSM674193     2  0.4164      0.873 0.000 0.736 0.000 0.264
#> GSM674194     2  0.1022      0.867 0.000 0.968 0.000 0.032
#> GSM674195     2  0.1118      0.864 0.000 0.964 0.000 0.036
#> GSM674198     2  0.4356      0.868 0.000 0.708 0.000 0.292
#> GSM674200     2  0.1118      0.864 0.000 0.964 0.000 0.036
#> GSM674201     2  0.1022      0.865 0.000 0.968 0.000 0.032
#> GSM674202     2  0.0336      0.873 0.000 0.992 0.000 0.008
#> GSM674203     2  0.4356      0.868 0.000 0.708 0.000 0.292
#> GSM674204     2  0.4331      0.869 0.000 0.712 0.000 0.288
#> GSM674205     2  0.4331      0.869 0.000 0.712 0.000 0.288
#> GSM674206     2  0.1022      0.865 0.000 0.968 0.000 0.032
#> GSM674208     2  0.4331      0.869 0.000 0.712 0.000 0.288
#> GSM674209     2  0.4164      0.873 0.000 0.736 0.000 0.264
#> GSM674210     2  0.4356      0.868 0.000 0.708 0.000 0.292
#> GSM674212     2  0.4304      0.870 0.000 0.716 0.000 0.284
#> GSM674214     2  0.4356      0.868 0.000 0.708 0.000 0.292
#> GSM674218     2  0.1022      0.865 0.000 0.968 0.000 0.032
#> GSM674219     2  0.0817      0.869 0.000 0.976 0.000 0.024
#> GSM674220     2  0.1022      0.865 0.000 0.968 0.000 0.032
#> GSM674221     2  0.0592      0.875 0.000 0.984 0.000 0.016
#> GSM674223     2  0.4277      0.870 0.000 0.720 0.000 0.280
#> GSM674225     2  0.2216      0.881 0.000 0.908 0.000 0.092
#> GSM674226     2  0.3837      0.877 0.000 0.776 0.000 0.224
#> GSM674229     2  0.4331      0.869 0.000 0.712 0.000 0.288
#> GSM674230     2  0.1557      0.881 0.000 0.944 0.000 0.056
#> GSM674231     2  0.4193      0.873 0.000 0.732 0.000 0.268
#> GSM674232     2  0.4356      0.868 0.000 0.708 0.000 0.292
#> GSM674234     2  0.4164      0.873 0.000 0.736 0.000 0.264
#> GSM674235     2  0.1302      0.880 0.000 0.956 0.000 0.044
#> GSM674236     2  0.1637      0.881 0.000 0.940 0.000 0.060
#> GSM674237     2  0.4356      0.868 0.000 0.708 0.000 0.292
#> GSM674239     2  0.4331      0.869 0.000 0.712 0.000 0.288
#> GSM674240     2  0.1302      0.878 0.000 0.956 0.000 0.044
#> GSM674242     2  0.4356      0.868 0.000 0.708 0.000 0.292
#> GSM674243     2  0.4304      0.869 0.000 0.716 0.000 0.284
#> GSM674244     2  0.1716      0.877 0.000 0.936 0.000 0.064
#> GSM674245     2  0.3649      0.879 0.000 0.796 0.000 0.204
#> GSM674282     1  0.5060      0.857 0.584 0.000 0.004 0.412
#> GSM674284     1  0.5861      0.864 0.644 0.000 0.060 0.296
#> GSM674285     1  0.4898      0.856 0.584 0.000 0.000 0.416
#> GSM674287     1  0.5658      0.864 0.632 0.000 0.040 0.328
#> GSM674288     1  0.2048      0.837 0.928 0.000 0.064 0.008
#> GSM674289     1  0.5060      0.857 0.584 0.000 0.004 0.412
#> GSM674290     1  0.4898      0.856 0.584 0.000 0.000 0.416
#> GSM674291     1  0.4898      0.856 0.584 0.000 0.000 0.416
#> GSM674292     1  0.4898      0.856 0.584 0.000 0.000 0.416
#> GSM674295     1  0.0188      0.831 0.996 0.000 0.004 0.000
#> GSM674297     1  0.6156      0.859 0.592 0.000 0.064 0.344
#> GSM674298     1  0.6156      0.859 0.592 0.000 0.064 0.344
#> GSM674299     1  0.5791      0.864 0.656 0.000 0.060 0.284
#> GSM674300     1  0.5839      0.864 0.648 0.000 0.060 0.292
#> GSM674301     1  0.5060      0.857 0.584 0.000 0.004 0.412
#> GSM674302     1  0.5060      0.857 0.584 0.000 0.004 0.412
#> GSM674304     1  0.5060      0.857 0.584 0.000 0.004 0.412
#> GSM674305     1  0.5060      0.857 0.584 0.000 0.004 0.412
#> GSM674306     1  0.5781      0.858 0.584 0.000 0.036 0.380
#> GSM674308     1  0.5060      0.857 0.584 0.000 0.004 0.412
#> GSM674309     1  0.4534      0.857 0.800 0.000 0.068 0.132
#> GSM674313     1  0.0592      0.829 0.984 0.000 0.016 0.000
#> GSM674314     1  0.1792      0.835 0.932 0.000 0.068 0.000
#> GSM674315     1  0.5781      0.858 0.584 0.000 0.036 0.380
#> GSM674316     1  0.0707      0.831 0.980 0.000 0.020 0.000
#> GSM674318     1  0.0469      0.830 0.988 0.000 0.012 0.000
#> GSM674320     1  0.0592      0.829 0.984 0.000 0.016 0.000
#> GSM674323     1  0.0469      0.830 0.988 0.000 0.012 0.000
#> GSM674324     1  0.4875      0.859 0.772 0.000 0.068 0.160
#> GSM674325     1  0.0469      0.830 0.988 0.000 0.012 0.000
#> GSM674327     1  0.1557      0.834 0.944 0.000 0.056 0.000
#> GSM674328     1  0.5993      0.863 0.628 0.000 0.064 0.308
#> GSM674330     1  0.1557      0.834 0.944 0.000 0.056 0.000
#> GSM674331     1  0.4875      0.859 0.772 0.000 0.068 0.160
#> GSM674332     1  0.4374      0.855 0.812 0.000 0.068 0.120
#> GSM674334     1  0.1557      0.834 0.944 0.000 0.056 0.000
#> GSM674335     1  0.0592      0.832 0.984 0.000 0.016 0.000
#> GSM674345     3  0.5018      0.907 0.000 0.088 0.768 0.144
#> GSM674351     3  0.4969      0.907 0.000 0.088 0.772 0.140
#> GSM674352     3  0.5417      0.904 0.000 0.088 0.732 0.180
#> GSM674359     3  0.5066      0.906 0.000 0.088 0.764 0.148
#> GSM674360     3  0.5572      0.900 0.000 0.088 0.716 0.196
#> GSM674362     3  0.5572      0.900 0.000 0.088 0.716 0.196
#> GSM674369     3  0.5066      0.906 0.000 0.088 0.764 0.148
#> GSM674372     3  0.4483      0.898 0.000 0.088 0.808 0.104
#> GSM674374     3  0.2334      0.914 0.000 0.088 0.908 0.004
#> GSM674376     3  0.4483      0.898 0.000 0.088 0.808 0.104
#> GSM674377     3  0.4655      0.897 0.000 0.088 0.796 0.116
#> GSM674378     3  0.2730      0.912 0.000 0.088 0.896 0.016
#> GSM674383     3  0.5496      0.902 0.000 0.088 0.724 0.188
#> GSM674386     3  0.4483      0.898 0.000 0.088 0.808 0.104
#> GSM674387     3  0.3820      0.903 0.000 0.088 0.848 0.064
#> GSM674392     3  0.4542      0.912 0.000 0.088 0.804 0.108
#> GSM674396     3  0.4483      0.898 0.000 0.088 0.808 0.104
#> GSM674399     3  0.3820      0.903 0.000 0.088 0.848 0.064
#> GSM674404     3  0.3820      0.903 0.000 0.088 0.848 0.064
#> GSM674182     2  0.0921      0.867 0.000 0.972 0.000 0.028
#> GSM674188     2  0.0188      0.874 0.000 0.996 0.000 0.004
#> GSM674189     2  0.0921      0.867 0.000 0.972 0.000 0.028
#> GSM674196     2  0.4331      0.869 0.000 0.712 0.000 0.288
#> GSM674197     2  0.4331      0.869 0.000 0.712 0.000 0.288
#> GSM674199     2  0.4356      0.868 0.000 0.708 0.000 0.292
#> GSM674207     2  0.4356      0.868 0.000 0.708 0.000 0.292
#> GSM674211     2  0.4331      0.869 0.000 0.712 0.000 0.288
#> GSM674213     2  0.1474      0.879 0.000 0.948 0.000 0.052
#> GSM674215     2  0.1022      0.865 0.000 0.968 0.000 0.032
#> GSM674216     2  0.4331      0.869 0.000 0.712 0.000 0.288
#> GSM674217     2  0.0592      0.875 0.000 0.984 0.000 0.016
#> GSM674222     2  0.1716      0.881 0.000 0.936 0.000 0.064
#> GSM674224     2  0.4134      0.874 0.000 0.740 0.000 0.260
#> GSM674227     2  0.3400      0.881 0.000 0.820 0.000 0.180
#> GSM674228     2  0.3311      0.881 0.000 0.828 0.000 0.172
#> GSM674233     2  0.1389      0.879 0.000 0.952 0.000 0.048
#> GSM674238     2  0.1118      0.864 0.000 0.964 0.000 0.036
#> GSM674241     2  0.4331      0.869 0.000 0.712 0.000 0.288
#> GSM674283     1  0.5060      0.857 0.584 0.000 0.004 0.412
#> GSM674286     1  0.5060      0.857 0.584 0.000 0.004 0.412
#> GSM674293     1  0.4898      0.856 0.584 0.000 0.000 0.416
#> GSM674294     1  0.4898      0.856 0.584 0.000 0.000 0.416
#> GSM674296     1  0.5290      0.857 0.584 0.000 0.012 0.404
#> GSM674303     1  0.5951      0.863 0.636 0.000 0.064 0.300
#> GSM674307     1  0.5290      0.857 0.584 0.000 0.012 0.404
#> GSM674310     1  0.0469      0.830 0.988 0.000 0.012 0.000
#> GSM674311     1  0.4782      0.859 0.780 0.000 0.068 0.152
#> GSM674312     1  0.0592      0.829 0.984 0.000 0.016 0.000
#> GSM674317     1  0.5947      0.863 0.628 0.000 0.060 0.312
#> GSM674319     1  0.0188      0.831 0.996 0.000 0.004 0.000
#> GSM674321     1  0.0469      0.830 0.988 0.000 0.012 0.000
#> GSM674322     1  0.0469      0.830 0.988 0.000 0.012 0.000
#> GSM674326     1  0.0469      0.830 0.988 0.000 0.012 0.000
#> GSM674329     1  0.0592      0.829 0.984 0.000 0.016 0.000
#> GSM674333     1  0.0592      0.829 0.984 0.000 0.016 0.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4    p5
#> GSM674344     4  0.5029      0.943 0.000 0.024 0.444 0.528 0.004
#> GSM674346     4  0.5029      0.943 0.000 0.024 0.444 0.528 0.004
#> GSM674347     3  0.5474     -0.133 0.000 0.024 0.628 0.304 0.044
#> GSM674348     3  0.5214     -0.641 0.000 0.024 0.540 0.424 0.012
#> GSM674349     4  0.5644      0.906 0.000 0.024 0.468 0.476 0.032
#> GSM674350     3  0.5201     -0.652 0.000 0.024 0.548 0.416 0.012
#> GSM674353     4  0.5249      0.942 0.000 0.024 0.456 0.508 0.012
#> GSM674354     4  0.5140      0.942 0.000 0.024 0.444 0.524 0.008
#> GSM674355     4  0.5144      0.946 0.000 0.024 0.448 0.520 0.008
#> GSM674356     4  0.5251      0.939 0.000 0.024 0.460 0.504 0.012
#> GSM674357     4  0.4886      0.948 0.000 0.024 0.448 0.528 0.000
#> GSM674358     4  0.5251      0.938 0.000 0.024 0.460 0.504 0.012
#> GSM674361     4  0.5151      0.944 0.000 0.024 0.456 0.512 0.008
#> GSM674363     4  0.5036      0.947 0.000 0.024 0.452 0.520 0.004
#> GSM674364     4  0.5140      0.940 0.000 0.024 0.444 0.524 0.008
#> GSM674365     3  0.5525     -0.633 0.000 0.024 0.536 0.412 0.028
#> GSM674366     3  0.3197      0.531 0.000 0.024 0.868 0.080 0.028
#> GSM674367     3  0.3226      0.588 0.000 0.024 0.864 0.088 0.024
#> GSM674368     4  0.5493      0.930 0.000 0.024 0.448 0.504 0.024
#> GSM674370     3  0.4426      0.289 0.000 0.024 0.760 0.188 0.028
#> GSM674371     3  0.5602     -0.617 0.000 0.024 0.560 0.380 0.036
#> GSM674373     3  0.4743      0.330 0.000 0.024 0.712 0.240 0.024
#> GSM674375     3  0.1493      0.598 0.000 0.024 0.948 0.000 0.028
#> GSM674379     3  0.2700      0.592 0.000 0.024 0.884 0.088 0.004
#> GSM674380     3  0.3599      0.567 0.000 0.024 0.828 0.132 0.016
#> GSM674381     3  0.1372      0.594 0.000 0.024 0.956 0.016 0.004
#> GSM674382     3  0.2881      0.591 0.000 0.024 0.876 0.092 0.008
#> GSM674384     3  0.2355      0.585 0.000 0.024 0.916 0.036 0.024
#> GSM674385     3  0.4978     -0.357 0.000 0.024 0.628 0.336 0.012
#> GSM674388     4  0.5637      0.922 0.000 0.024 0.448 0.496 0.032
#> GSM674389     3  0.1493      0.597 0.000 0.024 0.948 0.000 0.028
#> GSM674390     3  0.0992      0.599 0.000 0.024 0.968 0.000 0.008
#> GSM674391     3  0.2824      0.592 0.000 0.024 0.880 0.088 0.008
#> GSM674393     3  0.1818      0.594 0.000 0.024 0.932 0.000 0.044
#> GSM674394     3  0.4985     -0.182 0.000 0.024 0.660 0.296 0.020
#> GSM674395     3  0.3694      0.566 0.000 0.024 0.824 0.132 0.020
#> GSM674397     3  0.4857      0.204 0.000 0.024 0.684 0.272 0.020
#> GSM674398     3  0.1493      0.597 0.000 0.024 0.948 0.000 0.028
#> GSM674400     3  0.3839      0.583 0.000 0.024 0.832 0.088 0.056
#> GSM674401     3  0.3905      0.582 0.000 0.024 0.828 0.088 0.060
#> GSM674402     3  0.5394     -0.646 0.000 0.024 0.528 0.428 0.020
#> GSM674403     3  0.5990     -0.816 0.000 0.024 0.484 0.436 0.056
#> GSM674405     3  0.3313      0.591 0.000 0.024 0.860 0.088 0.028
#> GSM674406     3  0.2936      0.590 0.000 0.024 0.872 0.096 0.008
#> GSM674407     3  0.2972      0.587 0.000 0.024 0.864 0.108 0.004
#> GSM674181     5  0.4798      0.951 0.000 0.440 0.000 0.020 0.540
#> GSM674183     5  0.4517      0.959 0.000 0.436 0.000 0.008 0.556
#> GSM674184     5  0.4517      0.959 0.000 0.436 0.000 0.008 0.556
#> GSM674185     5  0.4517      0.959 0.000 0.436 0.000 0.008 0.556
#> GSM674186     5  0.4632      0.948 0.000 0.448 0.000 0.012 0.540
#> GSM674187     2  0.4980     -0.838 0.000 0.488 0.000 0.028 0.484
#> GSM674190     5  0.4718      0.949 0.000 0.444 0.000 0.016 0.540
#> GSM674191     5  0.4627      0.951 0.000 0.444 0.000 0.012 0.544
#> GSM674192     2  0.0671      0.668 0.000 0.980 0.000 0.016 0.004
#> GSM674193     2  0.2754      0.618 0.000 0.880 0.000 0.080 0.040
#> GSM674194     5  0.5042      0.903 0.000 0.460 0.000 0.032 0.508
#> GSM674195     5  0.4522      0.956 0.000 0.440 0.000 0.008 0.552
#> GSM674198     2  0.0404      0.666 0.000 0.988 0.000 0.012 0.000
#> GSM674200     5  0.4517      0.959 0.000 0.436 0.000 0.008 0.556
#> GSM674201     5  0.4617      0.958 0.000 0.436 0.000 0.012 0.552
#> GSM674202     2  0.5731     -0.731 0.000 0.480 0.000 0.084 0.436
#> GSM674203     2  0.0162      0.667 0.000 0.996 0.000 0.004 0.000
#> GSM674204     2  0.0566      0.667 0.000 0.984 0.000 0.012 0.004
#> GSM674205     2  0.0162      0.667 0.000 0.996 0.000 0.004 0.000
#> GSM674206     5  0.4713      0.953 0.000 0.440 0.000 0.016 0.544
#> GSM674208     2  0.0404      0.667 0.000 0.988 0.000 0.012 0.000
#> GSM674209     2  0.3237      0.600 0.000 0.848 0.000 0.104 0.048
#> GSM674210     2  0.0609      0.667 0.000 0.980 0.000 0.020 0.000
#> GSM674212     2  0.1117      0.661 0.000 0.964 0.000 0.016 0.020
#> GSM674214     2  0.0609      0.666 0.000 0.980 0.000 0.020 0.000
#> GSM674218     5  0.4622      0.955 0.000 0.440 0.000 0.012 0.548
#> GSM674219     5  0.4968      0.917 0.000 0.456 0.000 0.028 0.516
#> GSM674220     5  0.5153      0.930 0.000 0.436 0.000 0.040 0.524
#> GSM674221     2  0.4906     -0.817 0.000 0.496 0.000 0.024 0.480
#> GSM674223     2  0.1997      0.644 0.000 0.924 0.000 0.036 0.040
#> GSM674225     2  0.5717     -0.301 0.000 0.572 0.000 0.104 0.324
#> GSM674226     2  0.4219      0.507 0.000 0.780 0.000 0.104 0.116
#> GSM674229     2  0.0865      0.668 0.000 0.972 0.000 0.024 0.004
#> GSM674230     2  0.5751     -0.382 0.000 0.552 0.000 0.100 0.348
#> GSM674231     2  0.3237      0.600 0.000 0.848 0.000 0.104 0.048
#> GSM674232     2  0.0404      0.668 0.000 0.988 0.000 0.012 0.000
#> GSM674234     2  0.0865      0.660 0.000 0.972 0.000 0.004 0.024
#> GSM674235     2  0.5664     -0.402 0.000 0.560 0.000 0.092 0.348
#> GSM674236     2  0.5626     -0.337 0.000 0.572 0.000 0.092 0.336
#> GSM674237     2  0.0510      0.667 0.000 0.984 0.000 0.016 0.000
#> GSM674239     2  0.0566      0.668 0.000 0.984 0.000 0.012 0.004
#> GSM674240     2  0.5111     -0.788 0.000 0.500 0.000 0.036 0.464
#> GSM674242     2  0.0566      0.668 0.000 0.984 0.000 0.012 0.004
#> GSM674243     2  0.1800      0.655 0.000 0.932 0.000 0.048 0.020
#> GSM674244     2  0.5852     -0.494 0.000 0.524 0.000 0.104 0.372
#> GSM674245     2  0.4686      0.417 0.000 0.736 0.000 0.104 0.160
#> GSM674282     1  0.6487      0.797 0.476 0.000 0.000 0.316 0.208
#> GSM674284     1  0.6155      0.808 0.560 0.000 0.000 0.212 0.228
#> GSM674285     1  0.6487      0.797 0.476 0.000 0.000 0.316 0.208
#> GSM674287     1  0.6201      0.808 0.552 0.000 0.000 0.232 0.216
#> GSM674288     1  0.2408      0.773 0.892 0.000 0.004 0.008 0.096
#> GSM674289     1  0.6487      0.797 0.476 0.000 0.000 0.316 0.208
#> GSM674290     1  0.6487      0.797 0.476 0.000 0.000 0.316 0.208
#> GSM674291     1  0.6487      0.797 0.476 0.000 0.000 0.316 0.208
#> GSM674292     1  0.6487      0.797 0.476 0.000 0.000 0.316 0.208
#> GSM674295     1  0.0880      0.765 0.968 0.000 0.000 0.000 0.032
#> GSM674297     1  0.6510      0.800 0.484 0.000 0.000 0.232 0.284
#> GSM674298     1  0.6510      0.800 0.484 0.000 0.000 0.232 0.284
#> GSM674299     1  0.6059      0.809 0.576 0.000 0.000 0.204 0.220
#> GSM674300     1  0.6300      0.808 0.556 0.000 0.004 0.208 0.232
#> GSM674301     1  0.6497      0.797 0.476 0.000 0.000 0.312 0.212
#> GSM674302     1  0.6497      0.797 0.476 0.000 0.000 0.312 0.212
#> GSM674304     1  0.6497      0.797 0.476 0.000 0.000 0.312 0.212
#> GSM674305     1  0.6497      0.797 0.476 0.000 0.000 0.312 0.212
#> GSM674306     1  0.6675      0.798 0.476 0.000 0.004 0.280 0.240
#> GSM674308     1  0.6497      0.797 0.476 0.000 0.000 0.312 0.212
#> GSM674309     1  0.4557      0.797 0.764 0.000 0.008 0.088 0.140
#> GSM674313     1  0.1364      0.763 0.952 0.000 0.012 0.000 0.036
#> GSM674314     1  0.2017      0.770 0.912 0.000 0.008 0.000 0.080
#> GSM674315     1  0.6675      0.798 0.476 0.000 0.004 0.280 0.240
#> GSM674316     1  0.1041      0.767 0.964 0.000 0.004 0.000 0.032
#> GSM674318     1  0.0693      0.764 0.980 0.000 0.012 0.000 0.008
#> GSM674320     1  0.1364      0.763 0.952 0.000 0.012 0.000 0.036
#> GSM674323     1  0.0290      0.764 0.992 0.000 0.000 0.000 0.008
#> GSM674324     1  0.4852      0.800 0.740 0.000 0.008 0.108 0.144
#> GSM674325     1  0.0290      0.764 0.992 0.000 0.000 0.000 0.008
#> GSM674327     1  0.2130      0.771 0.908 0.000 0.012 0.000 0.080
#> GSM674328     1  0.6199      0.807 0.552 0.000 0.000 0.212 0.236
#> GSM674330     1  0.1956      0.770 0.916 0.000 0.008 0.000 0.076
#> GSM674331     1  0.4852      0.800 0.740 0.000 0.008 0.108 0.144
#> GSM674332     1  0.4303      0.795 0.784 0.000 0.008 0.076 0.132
#> GSM674334     1  0.1956      0.770 0.916 0.000 0.008 0.000 0.076
#> GSM674335     1  0.1043      0.767 0.960 0.000 0.000 0.000 0.040
#> GSM674345     4  0.5644      0.906 0.000 0.024 0.468 0.476 0.032
#> GSM674351     4  0.5249      0.942 0.000 0.024 0.456 0.508 0.012
#> GSM674352     3  0.5194     -0.645 0.000 0.024 0.552 0.412 0.012
#> GSM674359     4  0.5239      0.941 0.000 0.024 0.444 0.520 0.012
#> GSM674360     3  0.5019     -0.643 0.000 0.024 0.536 0.436 0.004
#> GSM674362     3  0.5136     -0.656 0.000 0.024 0.528 0.440 0.008
#> GSM674369     4  0.5569      0.920 0.000 0.024 0.452 0.496 0.028
#> GSM674372     3  0.1978      0.597 0.000 0.024 0.928 0.004 0.044
#> GSM674374     3  0.4573      0.359 0.000 0.024 0.728 0.228 0.020
#> GSM674376     3  0.0992      0.599 0.000 0.024 0.968 0.000 0.008
#> GSM674377     3  0.1372      0.594 0.000 0.024 0.956 0.016 0.004
#> GSM674378     3  0.4160      0.503 0.000 0.024 0.784 0.168 0.024
#> GSM674383     3  0.5518     -0.627 0.000 0.024 0.540 0.408 0.028
#> GSM674386     3  0.1493      0.597 0.000 0.024 0.948 0.000 0.028
#> GSM674387     3  0.2881      0.591 0.000 0.024 0.876 0.092 0.008
#> GSM674392     4  0.5427      0.886 0.000 0.024 0.476 0.480 0.020
#> GSM674396     3  0.1493      0.597 0.000 0.024 0.948 0.000 0.028
#> GSM674399     3  0.3313      0.591 0.000 0.024 0.860 0.088 0.028
#> GSM674404     3  0.3452      0.590 0.000 0.024 0.852 0.092 0.032
#> GSM674182     5  0.4798      0.951 0.000 0.440 0.000 0.020 0.540
#> GSM674188     2  0.5401     -0.787 0.000 0.492 0.000 0.056 0.452
#> GSM674189     5  0.5032      0.923 0.000 0.448 0.000 0.032 0.520
#> GSM674196     2  0.0671      0.666 0.000 0.980 0.000 0.016 0.004
#> GSM674197     2  0.0671      0.666 0.000 0.980 0.000 0.016 0.004
#> GSM674199     2  0.0404      0.666 0.000 0.988 0.000 0.012 0.000
#> GSM674207     2  0.0609      0.666 0.000 0.980 0.000 0.020 0.000
#> GSM674211     2  0.0404      0.667 0.000 0.988 0.000 0.012 0.000
#> GSM674213     2  0.4930     -0.655 0.000 0.548 0.000 0.028 0.424
#> GSM674215     5  0.5276      0.917 0.000 0.436 0.000 0.048 0.516
#> GSM674216     2  0.1270      0.658 0.000 0.948 0.000 0.052 0.000
#> GSM674217     2  0.4906     -0.822 0.000 0.496 0.000 0.024 0.480
#> GSM674222     2  0.5701     -0.323 0.000 0.568 0.000 0.100 0.332
#> GSM674224     2  0.3307      0.591 0.000 0.844 0.000 0.104 0.052
#> GSM674227     2  0.5013      0.312 0.000 0.700 0.000 0.108 0.192
#> GSM674228     2  0.4901      0.327 0.000 0.712 0.000 0.104 0.184
#> GSM674233     2  0.5014     -0.680 0.000 0.536 0.000 0.032 0.432
#> GSM674238     5  0.4517      0.959 0.000 0.436 0.000 0.008 0.556
#> GSM674241     2  0.0609      0.667 0.000 0.980 0.000 0.020 0.000
#> GSM674283     1  0.6487      0.797 0.476 0.000 0.000 0.316 0.208
#> GSM674286     1  0.6487      0.797 0.476 0.000 0.000 0.316 0.208
#> GSM674293     1  0.6487      0.797 0.476 0.000 0.000 0.316 0.208
#> GSM674294     1  0.6487      0.797 0.476 0.000 0.000 0.316 0.208
#> GSM674296     1  0.6506      0.797 0.476 0.000 0.000 0.308 0.216
#> GSM674303     1  0.6359      0.808 0.560 0.000 0.008 0.196 0.236
#> GSM674307     1  0.6506      0.797 0.476 0.000 0.000 0.308 0.216
#> GSM674310     1  0.0693      0.764 0.980 0.000 0.012 0.000 0.008
#> GSM674311     1  0.4754      0.799 0.748 0.000 0.008 0.100 0.144
#> GSM674312     1  0.1364      0.763 0.952 0.000 0.012 0.000 0.036
#> GSM674317     1  0.6199      0.807 0.552 0.000 0.000 0.212 0.236
#> GSM674319     1  0.0794      0.765 0.972 0.000 0.000 0.000 0.028
#> GSM674321     1  0.0290      0.764 0.992 0.000 0.000 0.000 0.008
#> GSM674322     1  0.1195      0.764 0.960 0.000 0.012 0.000 0.028
#> GSM674326     1  0.0693      0.764 0.980 0.000 0.012 0.000 0.008
#> GSM674329     1  0.0963      0.763 0.964 0.000 0.000 0.000 0.036
#> GSM674333     1  0.1082      0.764 0.964 0.000 0.008 0.000 0.028

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4    p5    p6
#> GSM674344     3  0.4002     0.8318 0.000 0.000 0.588 0.404 0.000 0.008
#> GSM674346     3  0.3899     0.8318 0.000 0.000 0.592 0.404 0.000 0.004
#> GSM674347     4  0.5895     0.0195 0.000 0.000 0.236 0.600 0.072 0.092
#> GSM674348     3  0.5271     0.7521 0.000 0.000 0.512 0.408 0.068 0.012
#> GSM674349     4  0.6218    -0.7439 0.000 0.000 0.412 0.432 0.108 0.048
#> GSM674350     3  0.4415     0.7699 0.000 0.000 0.556 0.420 0.004 0.020
#> GSM674353     3  0.4751     0.8181 0.000 0.000 0.536 0.424 0.012 0.028
#> GSM674354     3  0.4093     0.8309 0.000 0.000 0.584 0.404 0.000 0.012
#> GSM674355     3  0.4317     0.8278 0.000 0.000 0.572 0.408 0.004 0.016
#> GSM674356     3  0.4913     0.8209 0.000 0.000 0.524 0.428 0.028 0.020
#> GSM674357     3  0.4010     0.8308 0.000 0.000 0.584 0.408 0.000 0.008
#> GSM674358     3  0.4913     0.8149 0.000 0.000 0.524 0.428 0.020 0.028
#> GSM674361     3  0.4726     0.8211 0.000 0.000 0.536 0.424 0.008 0.032
#> GSM674363     3  0.4402     0.8265 0.000 0.000 0.564 0.412 0.004 0.020
#> GSM674364     3  0.5064     0.8235 0.000 0.000 0.536 0.404 0.040 0.020
#> GSM674365     3  0.5936     0.7024 0.000 0.000 0.456 0.404 0.116 0.024
#> GSM674366     4  0.5035     0.4328 0.000 0.000 0.164 0.688 0.124 0.024
#> GSM674367     4  0.2560     0.6855 0.000 0.000 0.000 0.872 0.092 0.036
#> GSM674368     3  0.5671     0.7715 0.000 0.000 0.472 0.412 0.100 0.016
#> GSM674370     4  0.4992     0.2055 0.000 0.000 0.252 0.652 0.080 0.016
#> GSM674371     3  0.5848     0.6927 0.000 0.000 0.444 0.424 0.112 0.020
#> GSM674373     4  0.4603     0.3660 0.000 0.000 0.200 0.712 0.068 0.020
#> GSM674375     4  0.2847     0.7059 0.000 0.000 0.048 0.876 0.036 0.040
#> GSM674379     4  0.1418     0.7077 0.000 0.000 0.000 0.944 0.032 0.024
#> GSM674380     4  0.2323     0.6797 0.000 0.000 0.084 0.892 0.012 0.012
#> GSM674381     4  0.2883     0.6729 0.000 0.000 0.068 0.864 0.060 0.008
#> GSM674382     4  0.1802     0.7045 0.000 0.000 0.024 0.932 0.024 0.020
#> GSM674384     4  0.2990     0.6805 0.000 0.000 0.084 0.860 0.020 0.036
#> GSM674385     4  0.5517    -0.4695 0.000 0.000 0.396 0.512 0.060 0.032
#> GSM674388     3  0.5944     0.7493 0.000 0.000 0.440 0.420 0.116 0.024
#> GSM674389     4  0.2972     0.6979 0.000 0.000 0.048 0.868 0.032 0.052
#> GSM674390     4  0.1285     0.7020 0.000 0.000 0.052 0.944 0.000 0.004
#> GSM674391     4  0.1478     0.7076 0.000 0.000 0.004 0.944 0.032 0.020
#> GSM674393     4  0.3779     0.6847 0.000 0.000 0.048 0.816 0.064 0.072
#> GSM674394     4  0.5073    -0.3029 0.000 0.000 0.368 0.568 0.028 0.036
#> GSM674395     4  0.2418     0.6821 0.000 0.000 0.092 0.884 0.008 0.016
#> GSM674397     4  0.4709     0.2936 0.000 0.000 0.220 0.696 0.060 0.024
#> GSM674398     4  0.2699     0.7015 0.000 0.000 0.048 0.884 0.028 0.040
#> GSM674400     4  0.3612     0.6702 0.000 0.000 0.000 0.796 0.100 0.104
#> GSM674401     4  0.3658     0.6687 0.000 0.000 0.000 0.792 0.104 0.104
#> GSM674402     3  0.5001     0.7622 0.000 0.000 0.548 0.396 0.032 0.024
#> GSM674403     4  0.6625    -0.6535 0.000 0.000 0.352 0.444 0.128 0.076
#> GSM674405     4  0.2740     0.6982 0.000 0.000 0.000 0.864 0.060 0.076
#> GSM674406     4  0.1585     0.7006 0.000 0.000 0.036 0.940 0.012 0.012
#> GSM674407     4  0.1387     0.6924 0.000 0.000 0.068 0.932 0.000 0.000
#> GSM674181     6  0.4661     0.8797 0.000 0.316 0.012 0.016 0.016 0.640
#> GSM674183     6  0.5087     0.8758 0.000 0.308 0.032 0.016 0.020 0.624
#> GSM674184     6  0.5103     0.8757 0.000 0.312 0.032 0.016 0.020 0.620
#> GSM674185     6  0.5035     0.8774 0.000 0.312 0.028 0.016 0.020 0.624
#> GSM674186     6  0.4678     0.8776 0.000 0.324 0.008 0.016 0.020 0.632
#> GSM674187     6  0.5427     0.8170 0.000 0.364 0.016 0.016 0.048 0.556
#> GSM674190     6  0.4618     0.8780 0.000 0.316 0.004 0.016 0.024 0.640
#> GSM674191     6  0.4241     0.8809 0.000 0.316 0.000 0.016 0.012 0.656
#> GSM674192     2  0.2219     0.7214 0.000 0.916 0.012 0.016 0.020 0.036
#> GSM674193     2  0.4929     0.6324 0.000 0.748 0.076 0.016 0.084 0.076
#> GSM674194     6  0.4931     0.8671 0.000 0.328 0.012 0.016 0.028 0.616
#> GSM674195     6  0.5118     0.8749 0.000 0.316 0.032 0.016 0.020 0.616
#> GSM674198     2  0.1078     0.7239 0.000 0.964 0.008 0.016 0.012 0.000
#> GSM674200     6  0.5087     0.8758 0.000 0.308 0.032 0.016 0.020 0.624
#> GSM674201     6  0.4714     0.8818 0.000 0.308 0.016 0.016 0.016 0.644
#> GSM674202     6  0.6553     0.6954 0.000 0.348 0.044 0.016 0.116 0.476
#> GSM674203     2  0.1109     0.7259 0.000 0.964 0.004 0.016 0.004 0.012
#> GSM674204     2  0.1109     0.7251 0.000 0.964 0.012 0.016 0.004 0.004
#> GSM674205     2  0.1337     0.7263 0.000 0.956 0.008 0.016 0.008 0.012
#> GSM674206     6  0.4871     0.8766 0.000 0.312 0.012 0.016 0.028 0.632
#> GSM674208     2  0.1621     0.7265 0.000 0.944 0.008 0.016 0.020 0.012
#> GSM674209     2  0.5287     0.6127 0.000 0.716 0.088 0.016 0.112 0.068
#> GSM674210     2  0.1542     0.7272 0.000 0.944 0.016 0.016 0.024 0.000
#> GSM674212     2  0.1686     0.7227 0.000 0.940 0.024 0.016 0.004 0.016
#> GSM674214     2  0.1622     0.7196 0.000 0.940 0.028 0.016 0.016 0.000
#> GSM674218     6  0.5110     0.8773 0.000 0.312 0.028 0.016 0.024 0.620
#> GSM674219     6  0.5037     0.8628 0.000 0.332 0.020 0.016 0.024 0.608
#> GSM674220     6  0.5932     0.8537 0.000 0.304 0.052 0.016 0.056 0.572
#> GSM674221     6  0.5230     0.8036 0.000 0.376 0.020 0.016 0.028 0.560
#> GSM674223     2  0.4336     0.6630 0.000 0.792 0.068 0.016 0.052 0.072
#> GSM674225     2  0.7071    -0.3128 0.000 0.432 0.072 0.016 0.148 0.332
#> GSM674226     2  0.6298     0.4449 0.000 0.612 0.088 0.016 0.112 0.172
#> GSM674229     2  0.2315     0.7259 0.000 0.908 0.040 0.016 0.032 0.004
#> GSM674230     2  0.6878    -0.4215 0.000 0.404 0.056 0.016 0.136 0.388
#> GSM674231     2  0.5186     0.6176 0.000 0.724 0.084 0.016 0.112 0.064
#> GSM674232     2  0.1647     0.7268 0.000 0.940 0.004 0.016 0.032 0.008
#> GSM674234     2  0.2518     0.7030 0.000 0.892 0.004 0.016 0.020 0.068
#> GSM674235     2  0.6689    -0.4956 0.000 0.412 0.044 0.016 0.128 0.400
#> GSM674236     2  0.6994    -0.3752 0.000 0.420 0.064 0.016 0.144 0.356
#> GSM674237     2  0.1799     0.7269 0.000 0.936 0.016 0.016 0.024 0.008
#> GSM674239     2  0.1337     0.7269 0.000 0.956 0.008 0.016 0.008 0.012
#> GSM674240     6  0.5517     0.6569 0.000 0.436 0.028 0.016 0.032 0.488
#> GSM674242     2  0.1419     0.7259 0.000 0.952 0.004 0.016 0.012 0.016
#> GSM674243     2  0.3923     0.6878 0.000 0.820 0.068 0.016 0.052 0.044
#> GSM674244     2  0.7164    -0.4347 0.000 0.388 0.076 0.016 0.152 0.368
#> GSM674245     2  0.6509     0.2764 0.000 0.564 0.060 0.016 0.140 0.220
#> GSM674282     1  0.0547     0.6823 0.980 0.000 0.000 0.000 0.000 0.020
#> GSM674284     1  0.3394     0.5607 0.776 0.000 0.000 0.000 0.200 0.024
#> GSM674285     1  0.0260     0.6826 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM674287     1  0.3301     0.5700 0.788 0.000 0.000 0.000 0.188 0.024
#> GSM674288     5  0.5226     0.6994 0.412 0.004 0.028 0.000 0.524 0.032
#> GSM674289     1  0.0547     0.6823 0.980 0.000 0.000 0.000 0.000 0.020
#> GSM674290     1  0.0458     0.6817 0.984 0.000 0.000 0.000 0.000 0.016
#> GSM674291     1  0.0363     0.6822 0.988 0.000 0.000 0.000 0.000 0.012
#> GSM674292     1  0.0458     0.6825 0.984 0.000 0.000 0.000 0.000 0.016
#> GSM674295     5  0.6734     0.8243 0.384 0.004 0.140 0.000 0.408 0.064
#> GSM674297     1  0.3395     0.6224 0.812 0.004 0.000 0.000 0.136 0.048
#> GSM674298     1  0.3355     0.6252 0.816 0.004 0.000 0.000 0.132 0.048
#> GSM674299     1  0.3571     0.5381 0.760 0.004 0.000 0.000 0.216 0.020
#> GSM674300     1  0.3970     0.5445 0.756 0.008 0.004 0.000 0.196 0.036
#> GSM674301     1  0.0790     0.6798 0.968 0.000 0.000 0.000 0.000 0.032
#> GSM674302     1  0.0713     0.6794 0.972 0.000 0.000 0.000 0.000 0.028
#> GSM674304     1  0.0713     0.6800 0.972 0.000 0.000 0.000 0.000 0.028
#> GSM674305     1  0.0713     0.6800 0.972 0.000 0.000 0.000 0.000 0.028
#> GSM674306     1  0.2633     0.6617 0.888 0.012 0.004 0.000 0.044 0.052
#> GSM674308     1  0.0713     0.6794 0.972 0.000 0.000 0.000 0.000 0.028
#> GSM674309     1  0.4587    -0.2554 0.516 0.004 0.004 0.000 0.456 0.020
#> GSM674313     1  0.6868    -0.8248 0.384 0.000 0.160 0.000 0.376 0.080
#> GSM674314     5  0.4409     0.6905 0.388 0.004 0.004 0.000 0.588 0.016
#> GSM674315     1  0.2699     0.6603 0.884 0.012 0.004 0.000 0.048 0.052
#> GSM674316     5  0.6321     0.8512 0.384 0.000 0.124 0.000 0.444 0.048
#> GSM674318     5  0.6427     0.8573 0.384 0.000 0.148 0.000 0.424 0.044
#> GSM674320     1  0.6868    -0.8248 0.384 0.000 0.160 0.000 0.376 0.080
#> GSM674323     5  0.6326     0.8595 0.384 0.000 0.140 0.000 0.436 0.040
#> GSM674324     1  0.4630    -0.1331 0.540 0.004 0.004 0.000 0.428 0.024
#> GSM674325     5  0.6326     0.8595 0.384 0.000 0.140 0.000 0.436 0.040
#> GSM674327     5  0.4520     0.6880 0.392 0.008 0.004 0.000 0.580 0.016
#> GSM674328     1  0.3543     0.5559 0.768 0.000 0.000 0.000 0.200 0.032
#> GSM674330     5  0.4100     0.7000 0.388 0.000 0.004 0.000 0.600 0.008
#> GSM674331     1  0.4630    -0.1331 0.540 0.004 0.004 0.000 0.428 0.024
#> GSM674332     1  0.4313    -0.3228 0.504 0.000 0.004 0.000 0.480 0.012
#> GSM674334     5  0.4090     0.7153 0.384 0.000 0.004 0.000 0.604 0.008
#> GSM674335     5  0.6531     0.8273 0.384 0.004 0.116 0.000 0.436 0.060
#> GSM674345     3  0.5930     0.7660 0.000 0.000 0.444 0.432 0.080 0.044
#> GSM674351     3  0.4751     0.8181 0.000 0.000 0.536 0.424 0.012 0.028
#> GSM674352     3  0.4427     0.7648 0.000 0.000 0.548 0.428 0.004 0.020
#> GSM674359     3  0.4569     0.8248 0.000 0.000 0.560 0.408 0.024 0.008
#> GSM674360     3  0.5163     0.7564 0.000 0.000 0.536 0.396 0.048 0.020
#> GSM674362     3  0.5108     0.7571 0.000 0.000 0.540 0.396 0.044 0.020
#> GSM674369     3  0.5960     0.7577 0.000 0.000 0.440 0.412 0.128 0.020
#> GSM674372     4  0.3338     0.6917 0.000 0.000 0.060 0.844 0.032 0.064
#> GSM674374     4  0.4537     0.3886 0.000 0.000 0.184 0.724 0.072 0.020
#> GSM674376     4  0.1219     0.7042 0.000 0.000 0.048 0.948 0.004 0.000
#> GSM674377     4  0.2434     0.6866 0.000 0.000 0.064 0.892 0.036 0.008
#> GSM674378     4  0.3878     0.5612 0.000 0.000 0.128 0.792 0.060 0.020
#> GSM674383     3  0.5906     0.6769 0.000 0.000 0.440 0.420 0.120 0.020
#> GSM674386     4  0.2688     0.7022 0.000 0.000 0.048 0.884 0.024 0.044
#> GSM674387     4  0.1452     0.7060 0.000 0.000 0.020 0.948 0.020 0.012
#> GSM674392     3  0.4781     0.7811 0.000 0.000 0.504 0.456 0.012 0.028
#> GSM674396     4  0.2972     0.6983 0.000 0.000 0.048 0.868 0.032 0.052
#> GSM674399     4  0.2625     0.7002 0.000 0.000 0.000 0.872 0.056 0.072
#> GSM674404     4  0.2685     0.6998 0.000 0.000 0.000 0.868 0.060 0.072
#> GSM674182     6  0.4482     0.8793 0.000 0.316 0.012 0.016 0.008 0.648
#> GSM674188     6  0.5807     0.7918 0.000 0.356 0.024 0.016 0.068 0.536
#> GSM674189     6  0.5594     0.8733 0.000 0.320 0.040 0.016 0.040 0.584
#> GSM674196     2  0.1325     0.7237 0.000 0.956 0.012 0.016 0.012 0.004
#> GSM674197     2  0.1223     0.7238 0.000 0.960 0.008 0.016 0.012 0.004
#> GSM674199     2  0.1078     0.7239 0.000 0.964 0.008 0.016 0.012 0.000
#> GSM674207     2  0.1542     0.7202 0.000 0.944 0.024 0.016 0.016 0.000
#> GSM674211     2  0.1621     0.7234 0.000 0.944 0.020 0.016 0.008 0.012
#> GSM674213     2  0.5644    -0.6097 0.000 0.464 0.032 0.016 0.036 0.452
#> GSM674215     6  0.5932     0.8537 0.000 0.304 0.052 0.016 0.056 0.572
#> GSM674216     2  0.3417     0.6939 0.000 0.844 0.040 0.016 0.084 0.016
#> GSM674217     6  0.5238     0.8036 0.000 0.380 0.020 0.016 0.028 0.556
#> GSM674222     2  0.7011    -0.3733 0.000 0.420 0.068 0.016 0.140 0.356
#> GSM674224     2  0.5311     0.6053 0.000 0.716 0.088 0.016 0.100 0.080
#> GSM674227     2  0.6470     0.3433 0.000 0.584 0.068 0.016 0.164 0.168
#> GSM674228     2  0.6596     0.2213 0.000 0.556 0.076 0.016 0.120 0.232
#> GSM674233     6  0.5638     0.6226 0.000 0.448 0.028 0.016 0.040 0.468
#> GSM674238     6  0.5103     0.8757 0.000 0.312 0.032 0.016 0.020 0.620
#> GSM674241     2  0.1905     0.7270 0.000 0.932 0.020 0.016 0.020 0.012
#> GSM674283     1  0.0260     0.6826 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM674286     1  0.0632     0.6824 0.976 0.000 0.000 0.000 0.000 0.024
#> GSM674293     1  0.0363     0.6825 0.988 0.000 0.000 0.000 0.000 0.012
#> GSM674294     1  0.0458     0.6831 0.984 0.000 0.000 0.000 0.000 0.016
#> GSM674296     1  0.0865     0.6793 0.964 0.000 0.000 0.000 0.000 0.036
#> GSM674303     1  0.3673     0.5143 0.736 0.000 0.004 0.000 0.244 0.016
#> GSM674307     1  0.0790     0.6796 0.968 0.000 0.000 0.000 0.000 0.032
#> GSM674310     5  0.6427     0.8573 0.384 0.000 0.148 0.000 0.424 0.044
#> GSM674311     1  0.4640    -0.1709 0.532 0.004 0.004 0.000 0.436 0.024
#> GSM674312     1  0.6868    -0.8248 0.384 0.000 0.160 0.000 0.376 0.080
#> GSM674317     1  0.3534     0.5579 0.772 0.004 0.000 0.000 0.200 0.024
#> GSM674319     5  0.6608     0.8294 0.384 0.000 0.140 0.000 0.412 0.064
#> GSM674321     5  0.6351     0.8588 0.384 0.000 0.144 0.000 0.432 0.040
#> GSM674322     5  0.6534     0.8475 0.384 0.000 0.168 0.000 0.404 0.044
#> GSM674326     5  0.6427     0.8573 0.384 0.000 0.148 0.000 0.424 0.044
#> GSM674329     1  0.6849    -0.8290 0.384 0.000 0.156 0.000 0.380 0.080
#> GSM674333     5  0.6629     0.8417 0.384 0.000 0.168 0.000 0.396 0.052

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-CV-kmeans-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-CV-kmeans-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-CV-kmeans-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-CV-kmeans-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-CV-kmeans-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-CV-kmeans-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-CV-kmeans-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-CV-kmeans-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-CV-kmeans-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-CV-kmeans-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-CV-kmeans-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-CV-kmeans-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-CV-kmeans-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-CV-kmeans-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-CV-kmeans-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-CV-kmeans-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-CV-kmeans-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-CV-kmeans-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-CV-kmeans-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-CV-kmeans-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk CV-kmeans-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-CV-kmeans-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-CV-kmeans-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-CV-kmeans-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-CV-kmeans-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-CV-kmeans-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk CV-kmeans-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>             n disease.state(p) specimen(p) k
#> CV:kmeans 183            0.924    1.83e-40 2
#> CV:kmeans 183            0.962    6.15e-78 3
#> CV:kmeans 183            0.962    6.15e-78 4
#> CV:kmeans 149            0.914    1.10e-59 5
#> CV:kmeans 153            0.986    8.37e-60 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


CV:skmeans**

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["CV", "skmeans"]
# you can also extract it by
# res = res_list["CV:skmeans"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#>   Subgroups are detected by 'skmeans' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk CV-skmeans-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk CV-skmeans-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 1.000           1.000       1.000         0.5958 0.750   0.571
#> 4 4 0.870           0.908       0.909         0.0895 0.939   0.815
#> 5 5 0.805           0.821       0.842         0.0742 0.933   0.753
#> 6 6 0.793           0.780       0.830         0.0467 0.937   0.712

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2

There is also optional best \(k\) = 2 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette p1 p2 p3
#> GSM674344     3       0          1  0  0  1
#> GSM674346     3       0          1  0  0  1
#> GSM674347     3       0          1  0  0  1
#> GSM674348     3       0          1  0  0  1
#> GSM674349     3       0          1  0  0  1
#> GSM674350     3       0          1  0  0  1
#> GSM674353     3       0          1  0  0  1
#> GSM674354     3       0          1  0  0  1
#> GSM674355     3       0          1  0  0  1
#> GSM674356     3       0          1  0  0  1
#> GSM674357     3       0          1  0  0  1
#> GSM674358     3       0          1  0  0  1
#> GSM674361     3       0          1  0  0  1
#> GSM674363     3       0          1  0  0  1
#> GSM674364     3       0          1  0  0  1
#> GSM674365     3       0          1  0  0  1
#> GSM674366     3       0          1  0  0  1
#> GSM674367     3       0          1  0  0  1
#> GSM674368     3       0          1  0  0  1
#> GSM674370     3       0          1  0  0  1
#> GSM674371     3       0          1  0  0  1
#> GSM674373     3       0          1  0  0  1
#> GSM674375     3       0          1  0  0  1
#> GSM674379     3       0          1  0  0  1
#> GSM674380     3       0          1  0  0  1
#> GSM674381     3       0          1  0  0  1
#> GSM674382     3       0          1  0  0  1
#> GSM674384     3       0          1  0  0  1
#> GSM674385     3       0          1  0  0  1
#> GSM674388     3       0          1  0  0  1
#> GSM674389     3       0          1  0  0  1
#> GSM674390     3       0          1  0  0  1
#> GSM674391     3       0          1  0  0  1
#> GSM674393     3       0          1  0  0  1
#> GSM674394     3       0          1  0  0  1
#> GSM674395     3       0          1  0  0  1
#> GSM674397     3       0          1  0  0  1
#> GSM674398     3       0          1  0  0  1
#> GSM674400     3       0          1  0  0  1
#> GSM674401     3       0          1  0  0  1
#> GSM674402     3       0          1  0  0  1
#> GSM674403     3       0          1  0  0  1
#> GSM674405     3       0          1  0  0  1
#> GSM674406     3       0          1  0  0  1
#> GSM674407     3       0          1  0  0  1
#> GSM674181     2       0          1  0  1  0
#> GSM674183     2       0          1  0  1  0
#> GSM674184     2       0          1  0  1  0
#> GSM674185     2       0          1  0  1  0
#> GSM674186     2       0          1  0  1  0
#> GSM674187     2       0          1  0  1  0
#> GSM674190     2       0          1  0  1  0
#> GSM674191     2       0          1  0  1  0
#> GSM674192     2       0          1  0  1  0
#> GSM674193     2       0          1  0  1  0
#> GSM674194     2       0          1  0  1  0
#> GSM674195     2       0          1  0  1  0
#> GSM674198     2       0          1  0  1  0
#> GSM674200     2       0          1  0  1  0
#> GSM674201     2       0          1  0  1  0
#> GSM674202     2       0          1  0  1  0
#> GSM674203     2       0          1  0  1  0
#> GSM674204     2       0          1  0  1  0
#> GSM674205     2       0          1  0  1  0
#> GSM674206     2       0          1  0  1  0
#> GSM674208     2       0          1  0  1  0
#> GSM674209     2       0          1  0  1  0
#> GSM674210     2       0          1  0  1  0
#> GSM674212     2       0          1  0  1  0
#> GSM674214     2       0          1  0  1  0
#> GSM674218     2       0          1  0  1  0
#> GSM674219     2       0          1  0  1  0
#> GSM674220     2       0          1  0  1  0
#> GSM674221     2       0          1  0  1  0
#> GSM674223     2       0          1  0  1  0
#> GSM674225     2       0          1  0  1  0
#> GSM674226     2       0          1  0  1  0
#> GSM674229     2       0          1  0  1  0
#> GSM674230     2       0          1  0  1  0
#> GSM674231     2       0          1  0  1  0
#> GSM674232     2       0          1  0  1  0
#> GSM674234     2       0          1  0  1  0
#> GSM674235     2       0          1  0  1  0
#> GSM674236     2       0          1  0  1  0
#> GSM674237     2       0          1  0  1  0
#> GSM674239     2       0          1  0  1  0
#> GSM674240     2       0          1  0  1  0
#> GSM674242     2       0          1  0  1  0
#> GSM674243     2       0          1  0  1  0
#> GSM674244     2       0          1  0  1  0
#> GSM674245     2       0          1  0  1  0
#> GSM674282     1       0          1  1  0  0
#> GSM674284     1       0          1  1  0  0
#> GSM674285     1       0          1  1  0  0
#> GSM674287     1       0          1  1  0  0
#> GSM674288     1       0          1  1  0  0
#> GSM674289     1       0          1  1  0  0
#> GSM674290     1       0          1  1  0  0
#> GSM674291     1       0          1  1  0  0
#> GSM674292     1       0          1  1  0  0
#> GSM674295     1       0          1  1  0  0
#> GSM674297     1       0          1  1  0  0
#> GSM674298     1       0          1  1  0  0
#> GSM674299     1       0          1  1  0  0
#> GSM674300     1       0          1  1  0  0
#> GSM674301     1       0          1  1  0  0
#> GSM674302     1       0          1  1  0  0
#> GSM674304     1       0          1  1  0  0
#> GSM674305     1       0          1  1  0  0
#> GSM674306     1       0          1  1  0  0
#> GSM674308     1       0          1  1  0  0
#> GSM674309     1       0          1  1  0  0
#> GSM674313     1       0          1  1  0  0
#> GSM674314     1       0          1  1  0  0
#> GSM674315     1       0          1  1  0  0
#> GSM674316     1       0          1  1  0  0
#> GSM674318     1       0          1  1  0  0
#> GSM674320     1       0          1  1  0  0
#> GSM674323     1       0          1  1  0  0
#> GSM674324     1       0          1  1  0  0
#> GSM674325     1       0          1  1  0  0
#> GSM674327     1       0          1  1  0  0
#> GSM674328     1       0          1  1  0  0
#> GSM674330     1       0          1  1  0  0
#> GSM674331     1       0          1  1  0  0
#> GSM674332     1       0          1  1  0  0
#> GSM674334     1       0          1  1  0  0
#> GSM674335     1       0          1  1  0  0
#> GSM674345     3       0          1  0  0  1
#> GSM674351     3       0          1  0  0  1
#> GSM674352     3       0          1  0  0  1
#> GSM674359     3       0          1  0  0  1
#> GSM674360     3       0          1  0  0  1
#> GSM674362     3       0          1  0  0  1
#> GSM674369     3       0          1  0  0  1
#> GSM674372     3       0          1  0  0  1
#> GSM674374     3       0          1  0  0  1
#> GSM674376     3       0          1  0  0  1
#> GSM674377     3       0          1  0  0  1
#> GSM674378     3       0          1  0  0  1
#> GSM674383     3       0          1  0  0  1
#> GSM674386     3       0          1  0  0  1
#> GSM674387     3       0          1  0  0  1
#> GSM674392     3       0          1  0  0  1
#> GSM674396     3       0          1  0  0  1
#> GSM674399     3       0          1  0  0  1
#> GSM674404     3       0          1  0  0  1
#> GSM674182     2       0          1  0  1  0
#> GSM674188     2       0          1  0  1  0
#> GSM674189     2       0          1  0  1  0
#> GSM674196     2       0          1  0  1  0
#> GSM674197     2       0          1  0  1  0
#> GSM674199     2       0          1  0  1  0
#> GSM674207     2       0          1  0  1  0
#> GSM674211     2       0          1  0  1  0
#> GSM674213     2       0          1  0  1  0
#> GSM674215     2       0          1  0  1  0
#> GSM674216     2       0          1  0  1  0
#> GSM674217     2       0          1  0  1  0
#> GSM674222     2       0          1  0  1  0
#> GSM674224     2       0          1  0  1  0
#> GSM674227     2       0          1  0  1  0
#> GSM674228     2       0          1  0  1  0
#> GSM674233     2       0          1  0  1  0
#> GSM674238     2       0          1  0  1  0
#> GSM674241     2       0          1  0  1  0
#> GSM674283     1       0          1  1  0  0
#> GSM674286     1       0          1  1  0  0
#> GSM674293     1       0          1  1  0  0
#> GSM674294     1       0          1  1  0  0
#> GSM674296     1       0          1  1  0  0
#> GSM674303     1       0          1  1  0  0
#> GSM674307     1       0          1  1  0  0
#> GSM674310     1       0          1  1  0  0
#> GSM674311     1       0          1  1  0  0
#> GSM674312     1       0          1  1  0  0
#> GSM674317     1       0          1  1  0  0
#> GSM674319     1       0          1  1  0  0
#> GSM674321     1       0          1  1  0  0
#> GSM674322     1       0          1  1  0  0
#> GSM674326     1       0          1  1  0  0
#> GSM674329     1       0          1  1  0  0
#> GSM674333     1       0          1  1  0  0

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1    p2    p3    p4
#> GSM674344     4  0.4585      0.897 0.000 0.000 0.332 0.668
#> GSM674346     4  0.4585      0.897 0.000 0.000 0.332 0.668
#> GSM674347     3  0.4888     -0.398 0.000 0.000 0.588 0.412
#> GSM674348     4  0.3400      0.809 0.000 0.000 0.180 0.820
#> GSM674349     4  0.4624      0.896 0.000 0.000 0.340 0.660
#> GSM674350     4  0.3486      0.809 0.000 0.000 0.188 0.812
#> GSM674353     4  0.4624      0.896 0.000 0.000 0.340 0.660
#> GSM674354     4  0.4585      0.897 0.000 0.000 0.332 0.668
#> GSM674355     4  0.4585      0.897 0.000 0.000 0.332 0.668
#> GSM674356     4  0.4624      0.896 0.000 0.000 0.340 0.660
#> GSM674357     4  0.4605      0.897 0.000 0.000 0.336 0.664
#> GSM674358     4  0.4624      0.896 0.000 0.000 0.340 0.660
#> GSM674361     4  0.4624      0.896 0.000 0.000 0.340 0.660
#> GSM674363     4  0.4624      0.896 0.000 0.000 0.340 0.660
#> GSM674364     4  0.4585      0.897 0.000 0.000 0.332 0.668
#> GSM674365     4  0.3400      0.809 0.000 0.000 0.180 0.820
#> GSM674366     3  0.4008      0.754 0.000 0.000 0.756 0.244
#> GSM674367     3  0.0000      0.844 0.000 0.000 1.000 0.000
#> GSM674368     4  0.4585      0.897 0.000 0.000 0.332 0.668
#> GSM674370     3  0.4072      0.749 0.000 0.000 0.748 0.252
#> GSM674371     4  0.3486      0.809 0.000 0.000 0.188 0.812
#> GSM674373     3  0.1637      0.802 0.000 0.000 0.940 0.060
#> GSM674375     3  0.3074      0.822 0.000 0.000 0.848 0.152
#> GSM674379     3  0.0000      0.844 0.000 0.000 1.000 0.000
#> GSM674380     3  0.0921      0.832 0.000 0.000 0.972 0.028
#> GSM674381     3  0.3172      0.817 0.000 0.000 0.840 0.160
#> GSM674382     3  0.0000      0.844 0.000 0.000 1.000 0.000
#> GSM674384     3  0.3356      0.812 0.000 0.000 0.824 0.176
#> GSM674385     4  0.4790      0.424 0.000 0.000 0.380 0.620
#> GSM674388     4  0.4585      0.897 0.000 0.000 0.332 0.668
#> GSM674389     3  0.3074      0.822 0.000 0.000 0.848 0.152
#> GSM674390     3  0.3074      0.822 0.000 0.000 0.848 0.152
#> GSM674391     3  0.0000      0.844 0.000 0.000 1.000 0.000
#> GSM674393     3  0.3074      0.822 0.000 0.000 0.848 0.152
#> GSM674394     3  0.4972      0.237 0.000 0.000 0.544 0.456
#> GSM674395     3  0.0921      0.832 0.000 0.000 0.972 0.028
#> GSM674397     3  0.2921      0.661 0.000 0.000 0.860 0.140
#> GSM674398     3  0.3074      0.822 0.000 0.000 0.848 0.152
#> GSM674400     3  0.0000      0.844 0.000 0.000 1.000 0.000
#> GSM674401     3  0.0000      0.844 0.000 0.000 1.000 0.000
#> GSM674402     4  0.3400      0.809 0.000 0.000 0.180 0.820
#> GSM674403     4  0.4776      0.862 0.000 0.000 0.376 0.624
#> GSM674405     3  0.0000      0.844 0.000 0.000 1.000 0.000
#> GSM674406     3  0.0000      0.844 0.000 0.000 1.000 0.000
#> GSM674407     3  0.0000      0.844 0.000 0.000 1.000 0.000
#> GSM674181     2  0.2921      0.937 0.000 0.860 0.000 0.140
#> GSM674183     2  0.2921      0.937 0.000 0.860 0.000 0.140
#> GSM674184     2  0.2921      0.937 0.000 0.860 0.000 0.140
#> GSM674185     2  0.2921      0.937 0.000 0.860 0.000 0.140
#> GSM674186     2  0.2921      0.937 0.000 0.860 0.000 0.140
#> GSM674187     2  0.2589      0.943 0.000 0.884 0.000 0.116
#> GSM674190     2  0.2868      0.938 0.000 0.864 0.000 0.136
#> GSM674191     2  0.2921      0.937 0.000 0.860 0.000 0.140
#> GSM674192     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674193     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674194     2  0.2921      0.937 0.000 0.860 0.000 0.140
#> GSM674195     2  0.2921      0.937 0.000 0.860 0.000 0.140
#> GSM674198     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674200     2  0.2921      0.937 0.000 0.860 0.000 0.140
#> GSM674201     2  0.2921      0.937 0.000 0.860 0.000 0.140
#> GSM674202     2  0.2408      0.945 0.000 0.896 0.000 0.104
#> GSM674203     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674204     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674205     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674206     2  0.2921      0.937 0.000 0.860 0.000 0.140
#> GSM674208     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674209     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674210     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674212     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674214     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674218     2  0.2921      0.937 0.000 0.860 0.000 0.140
#> GSM674219     2  0.2760      0.940 0.000 0.872 0.000 0.128
#> GSM674220     2  0.2921      0.937 0.000 0.860 0.000 0.140
#> GSM674221     2  0.2589      0.943 0.000 0.884 0.000 0.116
#> GSM674223     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674225     2  0.1716      0.949 0.000 0.936 0.000 0.064
#> GSM674226     2  0.0188      0.949 0.000 0.996 0.000 0.004
#> GSM674229     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674230     2  0.1940      0.948 0.000 0.924 0.000 0.076
#> GSM674231     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674232     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674234     2  0.0188      0.949 0.000 0.996 0.000 0.004
#> GSM674235     2  0.1940      0.948 0.000 0.924 0.000 0.076
#> GSM674236     2  0.1940      0.948 0.000 0.924 0.000 0.076
#> GSM674237     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674239     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674240     2  0.2704      0.941 0.000 0.876 0.000 0.124
#> GSM674242     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674243     2  0.0188      0.949 0.000 0.996 0.000 0.004
#> GSM674244     2  0.1940      0.948 0.000 0.924 0.000 0.076
#> GSM674245     2  0.0188      0.949 0.000 0.996 0.000 0.004
#> GSM674282     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674284     1  0.0000      0.987 1.000 0.000 0.000 0.000
#> GSM674285     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674287     1  0.0000      0.987 1.000 0.000 0.000 0.000
#> GSM674288     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674289     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674290     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674291     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674292     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674295     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674297     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674298     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674299     1  0.0000      0.987 1.000 0.000 0.000 0.000
#> GSM674300     1  0.0000      0.987 1.000 0.000 0.000 0.000
#> GSM674301     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674302     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674304     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674305     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674306     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674308     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674309     1  0.0000      0.987 1.000 0.000 0.000 0.000
#> GSM674313     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674314     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674315     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674316     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674318     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674320     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674323     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674324     1  0.0000      0.987 1.000 0.000 0.000 0.000
#> GSM674325     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674327     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674328     1  0.0000      0.987 1.000 0.000 0.000 0.000
#> GSM674330     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674331     1  0.0000      0.987 1.000 0.000 0.000 0.000
#> GSM674332     1  0.0000      0.987 1.000 0.000 0.000 0.000
#> GSM674334     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674335     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674345     4  0.4624      0.896 0.000 0.000 0.340 0.660
#> GSM674351     4  0.4624      0.896 0.000 0.000 0.340 0.660
#> GSM674352     4  0.3486      0.809 0.000 0.000 0.188 0.812
#> GSM674359     4  0.4585      0.897 0.000 0.000 0.332 0.668
#> GSM674360     4  0.3400      0.809 0.000 0.000 0.180 0.820
#> GSM674362     4  0.3400      0.809 0.000 0.000 0.180 0.820
#> GSM674369     4  0.4605      0.897 0.000 0.000 0.336 0.664
#> GSM674372     3  0.3074      0.822 0.000 0.000 0.848 0.152
#> GSM674374     3  0.1389      0.809 0.000 0.000 0.952 0.048
#> GSM674376     3  0.3074      0.822 0.000 0.000 0.848 0.152
#> GSM674377     3  0.3123      0.819 0.000 0.000 0.844 0.156
#> GSM674378     3  0.0921      0.828 0.000 0.000 0.972 0.028
#> GSM674383     4  0.3569      0.798 0.000 0.000 0.196 0.804
#> GSM674386     3  0.3074      0.822 0.000 0.000 0.848 0.152
#> GSM674387     3  0.0000      0.844 0.000 0.000 1.000 0.000
#> GSM674392     4  0.4933      0.774 0.000 0.000 0.432 0.568
#> GSM674396     3  0.3074      0.822 0.000 0.000 0.848 0.152
#> GSM674399     3  0.0000      0.844 0.000 0.000 1.000 0.000
#> GSM674404     3  0.0000      0.844 0.000 0.000 1.000 0.000
#> GSM674182     2  0.2921      0.937 0.000 0.860 0.000 0.140
#> GSM674188     2  0.2589      0.943 0.000 0.884 0.000 0.116
#> GSM674189     2  0.2921      0.937 0.000 0.860 0.000 0.140
#> GSM674196     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674197     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674199     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674207     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674211     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674213     2  0.2589      0.943 0.000 0.884 0.000 0.116
#> GSM674215     2  0.2921      0.937 0.000 0.860 0.000 0.140
#> GSM674216     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674217     2  0.2704      0.941 0.000 0.876 0.000 0.124
#> GSM674222     2  0.1940      0.948 0.000 0.924 0.000 0.076
#> GSM674224     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674227     2  0.0188      0.950 0.000 0.996 0.000 0.004
#> GSM674228     2  0.0336      0.950 0.000 0.992 0.000 0.008
#> GSM674233     2  0.2589      0.943 0.000 0.884 0.000 0.116
#> GSM674238     2  0.2921      0.937 0.000 0.860 0.000 0.140
#> GSM674241     2  0.0000      0.949 0.000 1.000 0.000 0.000
#> GSM674283     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674286     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674293     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674294     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674296     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674303     1  0.0000      0.987 1.000 0.000 0.000 0.000
#> GSM674307     1  0.1118      0.981 0.964 0.000 0.000 0.036
#> GSM674310     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674311     1  0.0000      0.987 1.000 0.000 0.000 0.000
#> GSM674312     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674317     1  0.0000      0.987 1.000 0.000 0.000 0.000
#> GSM674319     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674321     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674322     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674326     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674329     1  0.0188      0.987 0.996 0.000 0.000 0.004
#> GSM674333     1  0.0188      0.987 0.996 0.000 0.000 0.004

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4    p5
#> GSM674344     4  0.0162     0.8795 0.000 0.000 0.000 0.996 0.004
#> GSM674346     4  0.0162     0.8795 0.000 0.000 0.000 0.996 0.004
#> GSM674347     4  0.4108     0.3783 0.000 0.000 0.308 0.684 0.008
#> GSM674348     4  0.3209     0.7946 0.000 0.000 0.180 0.812 0.008
#> GSM674349     4  0.1310     0.8730 0.000 0.000 0.020 0.956 0.024
#> GSM674350     4  0.3231     0.7960 0.000 0.000 0.196 0.800 0.004
#> GSM674353     4  0.0671     0.8774 0.000 0.000 0.016 0.980 0.004
#> GSM674354     4  0.0162     0.8795 0.000 0.000 0.000 0.996 0.004
#> GSM674355     4  0.0324     0.8797 0.000 0.000 0.004 0.992 0.004
#> GSM674356     4  0.0798     0.8771 0.000 0.000 0.016 0.976 0.008
#> GSM674357     4  0.0162     0.8797 0.000 0.000 0.004 0.996 0.000
#> GSM674358     4  0.0671     0.8774 0.000 0.000 0.016 0.980 0.004
#> GSM674361     4  0.0671     0.8774 0.000 0.000 0.016 0.980 0.004
#> GSM674363     4  0.0324     0.8797 0.000 0.000 0.004 0.992 0.004
#> GSM674364     4  0.0290     0.8794 0.000 0.000 0.000 0.992 0.008
#> GSM674365     4  0.3656     0.7957 0.000 0.000 0.168 0.800 0.032
#> GSM674366     3  0.3241     0.7364 0.000 0.000 0.832 0.144 0.024
#> GSM674367     3  0.3724     0.8390 0.000 0.000 0.776 0.204 0.020
#> GSM674368     4  0.0794     0.8768 0.000 0.000 0.000 0.972 0.028
#> GSM674370     3  0.3779     0.6688 0.000 0.000 0.776 0.200 0.024
#> GSM674371     4  0.3779     0.7923 0.000 0.000 0.200 0.776 0.024
#> GSM674373     3  0.4437     0.7470 0.000 0.000 0.664 0.316 0.020
#> GSM674375     3  0.0865     0.8234 0.000 0.000 0.972 0.024 0.004
#> GSM674379     3  0.3300     0.8436 0.000 0.000 0.792 0.204 0.004
#> GSM674380     3  0.3642     0.8343 0.000 0.000 0.760 0.232 0.008
#> GSM674381     3  0.1205     0.8175 0.000 0.000 0.956 0.040 0.004
#> GSM674382     3  0.3143     0.8437 0.000 0.000 0.796 0.204 0.000
#> GSM674384     3  0.1478     0.8103 0.000 0.000 0.936 0.064 0.000
#> GSM674385     4  0.4564     0.5173 0.000 0.000 0.372 0.612 0.016
#> GSM674388     4  0.0703     0.8776 0.000 0.000 0.000 0.976 0.024
#> GSM674389     3  0.0703     0.8235 0.000 0.000 0.976 0.024 0.000
#> GSM674390     3  0.0865     0.8235 0.000 0.000 0.972 0.024 0.004
#> GSM674391     3  0.3300     0.8436 0.000 0.000 0.792 0.204 0.004
#> GSM674393     3  0.0992     0.8228 0.000 0.000 0.968 0.024 0.008
#> GSM674394     3  0.4182     0.2064 0.000 0.000 0.600 0.400 0.000
#> GSM674395     3  0.3395     0.8332 0.000 0.000 0.764 0.236 0.000
#> GSM674397     3  0.4781     0.5213 0.000 0.000 0.552 0.428 0.020
#> GSM674398     3  0.0703     0.8235 0.000 0.000 0.976 0.024 0.000
#> GSM674400     3  0.3421     0.8424 0.000 0.000 0.788 0.204 0.008
#> GSM674401     3  0.3421     0.8424 0.000 0.000 0.788 0.204 0.008
#> GSM674402     4  0.3203     0.7976 0.000 0.000 0.168 0.820 0.012
#> GSM674403     4  0.2300     0.8316 0.000 0.000 0.072 0.904 0.024
#> GSM674405     3  0.3143     0.8437 0.000 0.000 0.796 0.204 0.000
#> GSM674406     3  0.3300     0.8436 0.000 0.000 0.792 0.204 0.004
#> GSM674407     3  0.3300     0.8436 0.000 0.000 0.792 0.204 0.004
#> GSM674181     2  0.0000     0.7860 0.000 1.000 0.000 0.000 0.000
#> GSM674183     2  0.0000     0.7860 0.000 1.000 0.000 0.000 0.000
#> GSM674184     2  0.0000     0.7860 0.000 1.000 0.000 0.000 0.000
#> GSM674185     2  0.0000     0.7860 0.000 1.000 0.000 0.000 0.000
#> GSM674186     2  0.0703     0.7860 0.000 0.976 0.000 0.000 0.024
#> GSM674187     2  0.3242     0.6505 0.000 0.784 0.000 0.000 0.216
#> GSM674190     2  0.1043     0.7813 0.000 0.960 0.000 0.000 0.040
#> GSM674191     2  0.0794     0.7850 0.000 0.972 0.000 0.000 0.028
#> GSM674192     5  0.3612     0.9810 0.000 0.268 0.000 0.000 0.732
#> GSM674193     5  0.3612     0.9811 0.000 0.268 0.000 0.000 0.732
#> GSM674194     2  0.0794     0.7854 0.000 0.972 0.000 0.000 0.028
#> GSM674195     2  0.0000     0.7860 0.000 1.000 0.000 0.000 0.000
#> GSM674198     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674200     2  0.0000     0.7860 0.000 1.000 0.000 0.000 0.000
#> GSM674201     2  0.0162     0.7865 0.000 0.996 0.000 0.000 0.004
#> GSM674202     2  0.3684     0.5250 0.000 0.720 0.000 0.000 0.280
#> GSM674203     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674204     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674205     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674206     2  0.0404     0.7874 0.000 0.988 0.000 0.000 0.012
#> GSM674208     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674209     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674210     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674212     5  0.3661     0.9711 0.000 0.276 0.000 0.000 0.724
#> GSM674214     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674218     2  0.0000     0.7860 0.000 1.000 0.000 0.000 0.000
#> GSM674219     2  0.2471     0.7280 0.000 0.864 0.000 0.000 0.136
#> GSM674220     2  0.0000     0.7860 0.000 1.000 0.000 0.000 0.000
#> GSM674221     2  0.3109     0.6723 0.000 0.800 0.000 0.000 0.200
#> GSM674223     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674225     2  0.4306    -0.3574 0.000 0.508 0.000 0.000 0.492
#> GSM674226     5  0.3876     0.9069 0.000 0.316 0.000 0.000 0.684
#> GSM674229     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674230     2  0.4283    -0.1568 0.000 0.544 0.000 0.000 0.456
#> GSM674231     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674232     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674234     5  0.3774     0.9401 0.000 0.296 0.000 0.000 0.704
#> GSM674235     2  0.4291    -0.1893 0.000 0.536 0.000 0.000 0.464
#> GSM674236     2  0.4287    -0.1681 0.000 0.540 0.000 0.000 0.460
#> GSM674237     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674239     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674240     2  0.3003     0.6912 0.000 0.812 0.000 0.000 0.188
#> GSM674242     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674243     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674244     2  0.4242    -0.0615 0.000 0.572 0.000 0.000 0.428
#> GSM674245     5  0.3876     0.9069 0.000 0.316 0.000 0.000 0.684
#> GSM674282     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674284     1  0.1774     0.9094 0.932 0.000 0.016 0.000 0.052
#> GSM674285     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674287     1  0.1774     0.9094 0.932 0.000 0.016 0.000 0.052
#> GSM674288     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068
#> GSM674289     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674290     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674291     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674292     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674295     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068
#> GSM674297     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674298     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674299     1  0.1701     0.9096 0.936 0.000 0.016 0.000 0.048
#> GSM674300     1  0.1549     0.9099 0.944 0.000 0.016 0.000 0.040
#> GSM674301     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674302     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674304     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674305     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674306     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674308     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674309     1  0.0000     0.9090 1.000 0.000 0.000 0.000 0.000
#> GSM674313     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068
#> GSM674314     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068
#> GSM674315     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674316     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068
#> GSM674318     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068
#> GSM674320     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068
#> GSM674323     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068
#> GSM674324     1  0.0000     0.9090 1.000 0.000 0.000 0.000 0.000
#> GSM674325     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068
#> GSM674327     1  0.1638     0.9008 0.932 0.000 0.004 0.000 0.064
#> GSM674328     1  0.1701     0.9096 0.936 0.000 0.016 0.000 0.048
#> GSM674330     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068
#> GSM674331     1  0.0162     0.9093 0.996 0.000 0.000 0.000 0.004
#> GSM674332     1  0.0290     0.9084 0.992 0.000 0.000 0.000 0.008
#> GSM674334     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068
#> GSM674335     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068
#> GSM674345     4  0.1117     0.8751 0.000 0.000 0.016 0.964 0.020
#> GSM674351     4  0.0671     0.8774 0.000 0.000 0.016 0.980 0.004
#> GSM674352     4  0.3231     0.7960 0.000 0.000 0.196 0.800 0.004
#> GSM674359     4  0.0671     0.8783 0.000 0.000 0.004 0.980 0.016
#> GSM674360     4  0.3304     0.7971 0.000 0.000 0.168 0.816 0.016
#> GSM674362     4  0.3304     0.7971 0.000 0.000 0.168 0.816 0.016
#> GSM674369     4  0.0771     0.8778 0.000 0.000 0.004 0.976 0.020
#> GSM674372     3  0.1205     0.8187 0.000 0.000 0.956 0.040 0.004
#> GSM674374     3  0.4318     0.7674 0.000 0.000 0.688 0.292 0.020
#> GSM674376     3  0.0703     0.8235 0.000 0.000 0.976 0.024 0.000
#> GSM674377     3  0.1041     0.8208 0.000 0.000 0.964 0.032 0.004
#> GSM674378     3  0.4132     0.8004 0.000 0.000 0.720 0.260 0.020
#> GSM674383     4  0.3724     0.7796 0.000 0.000 0.204 0.776 0.020
#> GSM674386     3  0.0703     0.8235 0.000 0.000 0.976 0.024 0.000
#> GSM674387     3  0.3300     0.8436 0.000 0.000 0.792 0.204 0.004
#> GSM674392     4  0.2848     0.7193 0.000 0.000 0.156 0.840 0.004
#> GSM674396     3  0.0703     0.8235 0.000 0.000 0.976 0.024 0.000
#> GSM674399     3  0.3143     0.8437 0.000 0.000 0.796 0.204 0.000
#> GSM674404     3  0.3143     0.8437 0.000 0.000 0.796 0.204 0.000
#> GSM674182     2  0.0404     0.7871 0.000 0.988 0.000 0.000 0.012
#> GSM674188     2  0.3177     0.6625 0.000 0.792 0.000 0.000 0.208
#> GSM674189     2  0.0290     0.7868 0.000 0.992 0.000 0.000 0.008
#> GSM674196     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674197     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674199     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674207     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674211     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674213     2  0.3274     0.6542 0.000 0.780 0.000 0.000 0.220
#> GSM674215     2  0.0000     0.7860 0.000 1.000 0.000 0.000 0.000
#> GSM674216     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674217     2  0.2891     0.6972 0.000 0.824 0.000 0.000 0.176
#> GSM674222     2  0.4291    -0.1977 0.000 0.536 0.000 0.000 0.464
#> GSM674224     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674227     5  0.3661     0.9709 0.000 0.276 0.000 0.000 0.724
#> GSM674228     5  0.4015     0.8413 0.000 0.348 0.000 0.000 0.652
#> GSM674233     2  0.3336     0.6437 0.000 0.772 0.000 0.000 0.228
#> GSM674238     2  0.0000     0.7860 0.000 1.000 0.000 0.000 0.000
#> GSM674241     5  0.3586     0.9854 0.000 0.264 0.000 0.000 0.736
#> GSM674283     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674286     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674293     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674294     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674296     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674303     1  0.1774     0.9094 0.932 0.000 0.016 0.000 0.052
#> GSM674307     1  0.3278     0.8940 0.824 0.000 0.020 0.000 0.156
#> GSM674310     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068
#> GSM674311     1  0.0000     0.9090 1.000 0.000 0.000 0.000 0.000
#> GSM674312     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068
#> GSM674317     1  0.1701     0.9096 0.936 0.000 0.016 0.000 0.048
#> GSM674319     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068
#> GSM674321     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068
#> GSM674322     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068
#> GSM674326     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068
#> GSM674329     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068
#> GSM674333     1  0.1704     0.9001 0.928 0.000 0.004 0.000 0.068

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4    p5    p6
#> GSM674344     3  0.0603     0.8460 0.000 0.000 0.980 0.000 0.016 0.004
#> GSM674346     3  0.0363     0.8454 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM674347     3  0.5065     0.3503 0.000 0.000 0.616 0.304 0.060 0.020
#> GSM674348     3  0.4697     0.7643 0.000 0.000 0.708 0.184 0.092 0.016
#> GSM674349     3  0.3312     0.8191 0.000 0.000 0.828 0.020 0.124 0.028
#> GSM674350     3  0.2730     0.7787 0.000 0.000 0.808 0.192 0.000 0.000
#> GSM674353     3  0.0508     0.8435 0.000 0.000 0.984 0.012 0.000 0.004
#> GSM674354     3  0.0260     0.8446 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM674355     3  0.0405     0.8449 0.000 0.000 0.988 0.004 0.008 0.000
#> GSM674356     3  0.1555     0.8428 0.000 0.000 0.940 0.012 0.040 0.008
#> GSM674357     3  0.0520     0.8447 0.000 0.000 0.984 0.008 0.008 0.000
#> GSM674358     3  0.0653     0.8433 0.000 0.000 0.980 0.012 0.004 0.004
#> GSM674361     3  0.0405     0.8441 0.000 0.000 0.988 0.008 0.000 0.004
#> GSM674363     3  0.0405     0.8445 0.000 0.000 0.988 0.008 0.004 0.000
#> GSM674364     3  0.1434     0.8445 0.000 0.000 0.940 0.000 0.048 0.012
#> GSM674365     3  0.5358     0.7445 0.000 0.000 0.660 0.164 0.144 0.032
#> GSM674366     4  0.5042     0.5582 0.000 0.000 0.144 0.684 0.152 0.020
#> GSM674367     4  0.4241     0.8096 0.000 0.000 0.136 0.760 0.088 0.016
#> GSM674368     3  0.2744     0.8191 0.000 0.000 0.840 0.000 0.144 0.016
#> GSM674370     4  0.4883     0.5285 0.000 0.000 0.192 0.684 0.112 0.012
#> GSM674371     3  0.5205     0.7409 0.000 0.000 0.648 0.196 0.144 0.012
#> GSM674373     4  0.5114     0.6567 0.000 0.000 0.292 0.604 0.100 0.004
#> GSM674375     4  0.0632     0.8072 0.000 0.000 0.000 0.976 0.024 0.000
#> GSM674379     4  0.3455     0.8183 0.000 0.000 0.132 0.816 0.036 0.016
#> GSM674380     4  0.3722     0.8029 0.000 0.000 0.196 0.764 0.036 0.004
#> GSM674381     4  0.2182     0.7801 0.000 0.000 0.008 0.904 0.068 0.020
#> GSM674382     4  0.3246     0.8165 0.000 0.000 0.160 0.812 0.016 0.012
#> GSM674384     4  0.1364     0.7967 0.000 0.000 0.048 0.944 0.004 0.004
#> GSM674385     3  0.5679     0.4283 0.000 0.000 0.508 0.384 0.076 0.032
#> GSM674388     3  0.2963     0.8163 0.000 0.000 0.828 0.004 0.152 0.016
#> GSM674389     4  0.0363     0.8070 0.000 0.000 0.000 0.988 0.012 0.000
#> GSM674390     4  0.0260     0.8079 0.000 0.000 0.000 0.992 0.008 0.000
#> GSM674391     4  0.3313     0.8192 0.000 0.000 0.140 0.820 0.024 0.016
#> GSM674393     4  0.1010     0.8044 0.000 0.000 0.000 0.960 0.036 0.004
#> GSM674394     4  0.4218     0.1625 0.000 0.000 0.400 0.584 0.012 0.004
#> GSM674395     4  0.3432     0.7966 0.000 0.000 0.216 0.764 0.020 0.000
#> GSM674397     4  0.4903     0.5345 0.000 0.000 0.380 0.552 0.068 0.000
#> GSM674398     4  0.0260     0.8072 0.000 0.000 0.000 0.992 0.008 0.000
#> GSM674400     4  0.4387     0.8062 0.000 0.000 0.128 0.752 0.100 0.020
#> GSM674401     4  0.4556     0.8021 0.000 0.000 0.124 0.740 0.112 0.024
#> GSM674402     3  0.3666     0.7769 0.000 0.000 0.792 0.160 0.024 0.024
#> GSM674403     3  0.4540     0.7450 0.000 0.000 0.732 0.076 0.168 0.024
#> GSM674405     4  0.3613     0.8177 0.000 0.000 0.128 0.808 0.048 0.016
#> GSM674406     4  0.3178     0.8129 0.000 0.000 0.176 0.804 0.016 0.004
#> GSM674407     4  0.3071     0.8097 0.000 0.000 0.180 0.804 0.016 0.000
#> GSM674181     6  0.1838     0.8418 0.000 0.068 0.000 0.000 0.016 0.916
#> GSM674183     6  0.1719     0.8403 0.000 0.060 0.000 0.000 0.016 0.924
#> GSM674184     6  0.1719     0.8403 0.000 0.060 0.000 0.000 0.016 0.924
#> GSM674185     6  0.1719     0.8403 0.000 0.060 0.000 0.000 0.016 0.924
#> GSM674186     6  0.2346     0.8356 0.000 0.124 0.000 0.000 0.008 0.868
#> GSM674187     6  0.4189     0.5580 0.000 0.376 0.000 0.000 0.020 0.604
#> GSM674190     6  0.2631     0.8215 0.000 0.152 0.000 0.000 0.008 0.840
#> GSM674191     6  0.2118     0.8402 0.000 0.104 0.000 0.000 0.008 0.888
#> GSM674192     2  0.1003     0.8843 0.000 0.964 0.000 0.000 0.016 0.020
#> GSM674193     2  0.1334     0.8778 0.000 0.948 0.000 0.000 0.020 0.032
#> GSM674194     6  0.2613     0.8306 0.000 0.140 0.000 0.000 0.012 0.848
#> GSM674195     6  0.1779     0.8393 0.000 0.064 0.000 0.000 0.016 0.920
#> GSM674198     2  0.0363     0.8837 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM674200     6  0.1719     0.8403 0.000 0.060 0.000 0.000 0.016 0.924
#> GSM674201     6  0.1411     0.8411 0.000 0.060 0.000 0.000 0.004 0.936
#> GSM674202     6  0.4774     0.3823 0.000 0.420 0.000 0.000 0.052 0.528
#> GSM674203     2  0.0363     0.8843 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM674204     2  0.0622     0.8844 0.000 0.980 0.000 0.000 0.012 0.008
#> GSM674205     2  0.0405     0.8849 0.000 0.988 0.000 0.000 0.008 0.004
#> GSM674206     6  0.2538     0.8338 0.000 0.124 0.000 0.000 0.016 0.860
#> GSM674208     2  0.0547     0.8831 0.000 0.980 0.000 0.000 0.020 0.000
#> GSM674209     2  0.1049     0.8836 0.000 0.960 0.000 0.000 0.032 0.008
#> GSM674210     2  0.0260     0.8839 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM674212     2  0.1549     0.8659 0.000 0.936 0.000 0.000 0.020 0.044
#> GSM674214     2  0.0632     0.8821 0.000 0.976 0.000 0.000 0.024 0.000
#> GSM674218     6  0.1719     0.8403 0.000 0.060 0.000 0.000 0.016 0.924
#> GSM674219     6  0.3619     0.7529 0.000 0.232 0.000 0.000 0.024 0.744
#> GSM674220     6  0.2190     0.8382 0.000 0.060 0.000 0.000 0.040 0.900
#> GSM674221     6  0.4230     0.5811 0.000 0.364 0.000 0.000 0.024 0.612
#> GSM674223     2  0.0909     0.8838 0.000 0.968 0.000 0.000 0.020 0.012
#> GSM674225     2  0.4392     0.5273 0.000 0.680 0.000 0.000 0.064 0.256
#> GSM674226     2  0.2740     0.8009 0.000 0.852 0.000 0.000 0.028 0.120
#> GSM674229     2  0.0820     0.8856 0.000 0.972 0.000 0.000 0.016 0.012
#> GSM674230     2  0.4703     0.1315 0.000 0.544 0.000 0.000 0.048 0.408
#> GSM674231     2  0.1124     0.8834 0.000 0.956 0.000 0.000 0.036 0.008
#> GSM674232     2  0.0632     0.8826 0.000 0.976 0.000 0.000 0.024 0.000
#> GSM674234     2  0.1657     0.8600 0.000 0.928 0.000 0.000 0.016 0.056
#> GSM674235     2  0.4631     0.2903 0.000 0.596 0.000 0.000 0.052 0.352
#> GSM674236     2  0.4707     0.2653 0.000 0.584 0.000 0.000 0.056 0.360
#> GSM674237     2  0.0632     0.8832 0.000 0.976 0.000 0.000 0.024 0.000
#> GSM674239     2  0.0622     0.8854 0.000 0.980 0.000 0.000 0.012 0.008
#> GSM674240     6  0.4117     0.6903 0.000 0.296 0.000 0.000 0.032 0.672
#> GSM674242     2  0.0603     0.8848 0.000 0.980 0.000 0.000 0.016 0.004
#> GSM674243     2  0.1003     0.8845 0.000 0.964 0.000 0.000 0.020 0.016
#> GSM674244     2  0.4806     0.1893 0.000 0.560 0.000 0.000 0.060 0.380
#> GSM674245     2  0.3278     0.7574 0.000 0.808 0.000 0.000 0.040 0.152
#> GSM674282     1  0.0000     0.8650 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674284     1  0.2146     0.7698 0.880 0.000 0.000 0.000 0.116 0.004
#> GSM674285     1  0.0000     0.8650 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674287     1  0.2100     0.7739 0.884 0.000 0.000 0.000 0.112 0.004
#> GSM674288     5  0.3841     0.9226 0.380 0.000 0.000 0.000 0.616 0.004
#> GSM674289     1  0.0000     0.8650 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0000     0.8650 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674291     1  0.0000     0.8650 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674292     1  0.0000     0.8650 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674295     5  0.3592     0.9848 0.344 0.000 0.000 0.000 0.656 0.000
#> GSM674297     1  0.0146     0.8637 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM674298     1  0.0146     0.8637 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM674299     1  0.2234     0.7588 0.872 0.000 0.000 0.000 0.124 0.004
#> GSM674300     1  0.2278     0.7526 0.868 0.000 0.000 0.000 0.128 0.004
#> GSM674301     1  0.0000     0.8650 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674302     1  0.0000     0.8650 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0000     0.8650 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674305     1  0.0000     0.8650 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674306     1  0.0146     0.8637 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM674308     1  0.0000     0.8650 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674309     1  0.3807    -0.0376 0.628 0.000 0.000 0.000 0.368 0.004
#> GSM674313     5  0.3592     0.9848 0.344 0.000 0.000 0.000 0.656 0.000
#> GSM674314     5  0.3769     0.9642 0.356 0.000 0.000 0.000 0.640 0.004
#> GSM674315     1  0.0146     0.8637 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM674316     5  0.3592     0.9848 0.344 0.000 0.000 0.000 0.656 0.000
#> GSM674318     5  0.3592     0.9848 0.344 0.000 0.000 0.000 0.656 0.000
#> GSM674320     5  0.3592     0.9848 0.344 0.000 0.000 0.000 0.656 0.000
#> GSM674323     5  0.3592     0.9848 0.344 0.000 0.000 0.000 0.656 0.000
#> GSM674324     1  0.3684     0.1656 0.664 0.000 0.000 0.000 0.332 0.004
#> GSM674325     5  0.3592     0.9848 0.344 0.000 0.000 0.000 0.656 0.000
#> GSM674327     5  0.3966     0.7748 0.444 0.000 0.000 0.000 0.552 0.004
#> GSM674328     1  0.2146     0.7698 0.880 0.000 0.000 0.000 0.116 0.004
#> GSM674330     5  0.3728     0.9811 0.344 0.000 0.000 0.000 0.652 0.004
#> GSM674331     1  0.3684     0.1656 0.664 0.000 0.000 0.000 0.332 0.004
#> GSM674332     1  0.3915    -0.2808 0.584 0.000 0.000 0.000 0.412 0.004
#> GSM674334     5  0.3728     0.9811 0.344 0.000 0.000 0.000 0.652 0.004
#> GSM674335     5  0.3592     0.9848 0.344 0.000 0.000 0.000 0.656 0.000
#> GSM674345     3  0.2605     0.8303 0.000 0.000 0.876 0.012 0.092 0.020
#> GSM674351     3  0.0405     0.8441 0.000 0.000 0.988 0.008 0.000 0.004
#> GSM674352     3  0.2762     0.7767 0.000 0.000 0.804 0.196 0.000 0.000
#> GSM674359     3  0.1493     0.8427 0.000 0.000 0.936 0.004 0.056 0.004
#> GSM674360     3  0.4495     0.7682 0.000 0.000 0.740 0.164 0.064 0.032
#> GSM674362     3  0.4094     0.7734 0.000 0.000 0.768 0.160 0.044 0.028
#> GSM674369     3  0.2925     0.8177 0.000 0.000 0.832 0.004 0.148 0.016
#> GSM674372     4  0.1367     0.7989 0.000 0.000 0.044 0.944 0.012 0.000
#> GSM674374     4  0.5063     0.6701 0.000 0.000 0.280 0.616 0.100 0.004
#> GSM674376     4  0.0000     0.8076 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674377     4  0.1769     0.7895 0.000 0.000 0.004 0.924 0.060 0.012
#> GSM674378     4  0.4550     0.7376 0.000 0.000 0.240 0.676 0.084 0.000
#> GSM674383     3  0.5413     0.7274 0.000 0.000 0.640 0.196 0.140 0.024
#> GSM674386     4  0.0146     0.8075 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM674387     4  0.3219     0.8143 0.000 0.000 0.168 0.808 0.016 0.008
#> GSM674392     3  0.2402     0.7208 0.000 0.000 0.856 0.140 0.000 0.004
#> GSM674396     4  0.0363     0.8070 0.000 0.000 0.000 0.988 0.012 0.000
#> GSM674399     4  0.3523     0.8180 0.000 0.000 0.132 0.812 0.040 0.016
#> GSM674404     4  0.3613     0.8177 0.000 0.000 0.128 0.808 0.048 0.016
#> GSM674182     6  0.1918     0.8425 0.000 0.088 0.000 0.000 0.008 0.904
#> GSM674188     6  0.4155     0.5860 0.000 0.364 0.000 0.000 0.020 0.616
#> GSM674189     6  0.2301     0.8379 0.000 0.096 0.000 0.000 0.020 0.884
#> GSM674196     2  0.0622     0.8844 0.000 0.980 0.000 0.000 0.012 0.008
#> GSM674197     2  0.0725     0.8840 0.000 0.976 0.000 0.000 0.012 0.012
#> GSM674199     2  0.0363     0.8837 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM674207     2  0.0713     0.8817 0.000 0.972 0.000 0.000 0.028 0.000
#> GSM674211     2  0.0972     0.8821 0.000 0.964 0.000 0.000 0.028 0.008
#> GSM674213     6  0.4504     0.4593 0.000 0.432 0.000 0.000 0.032 0.536
#> GSM674215     6  0.2119     0.8387 0.000 0.060 0.000 0.000 0.036 0.904
#> GSM674216     2  0.0790     0.8796 0.000 0.968 0.000 0.000 0.032 0.000
#> GSM674217     6  0.4094     0.6503 0.000 0.324 0.000 0.000 0.024 0.652
#> GSM674222     2  0.4619     0.2956 0.000 0.600 0.000 0.000 0.052 0.348
#> GSM674224     2  0.0972     0.8833 0.000 0.964 0.000 0.000 0.028 0.008
#> GSM674227     2  0.1807     0.8651 0.000 0.920 0.000 0.000 0.060 0.020
#> GSM674228     2  0.3253     0.7030 0.000 0.788 0.000 0.000 0.020 0.192
#> GSM674233     6  0.4482     0.4829 0.000 0.416 0.000 0.000 0.032 0.552
#> GSM674238     6  0.1719     0.8403 0.000 0.060 0.000 0.000 0.016 0.924
#> GSM674241     2  0.0622     0.8849 0.000 0.980 0.000 0.000 0.012 0.008
#> GSM674283     1  0.0000     0.8650 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674286     1  0.0000     0.8650 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674293     1  0.0000     0.8650 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674294     1  0.0000     0.8650 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674296     1  0.0000     0.8650 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674303     1  0.2146     0.7698 0.880 0.000 0.000 0.000 0.116 0.004
#> GSM674307     1  0.0000     0.8650 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674310     5  0.3592     0.9848 0.344 0.000 0.000 0.000 0.656 0.000
#> GSM674311     1  0.3728     0.1043 0.652 0.000 0.000 0.000 0.344 0.004
#> GSM674312     5  0.3592     0.9848 0.344 0.000 0.000 0.000 0.656 0.000
#> GSM674317     1  0.2146     0.7698 0.880 0.000 0.000 0.000 0.116 0.004
#> GSM674319     5  0.3592     0.9848 0.344 0.000 0.000 0.000 0.656 0.000
#> GSM674321     5  0.3592     0.9848 0.344 0.000 0.000 0.000 0.656 0.000
#> GSM674322     5  0.3592     0.9848 0.344 0.000 0.000 0.000 0.656 0.000
#> GSM674326     5  0.3592     0.9848 0.344 0.000 0.000 0.000 0.656 0.000
#> GSM674329     5  0.3592     0.9848 0.344 0.000 0.000 0.000 0.656 0.000
#> GSM674333     5  0.3592     0.9848 0.344 0.000 0.000 0.000 0.656 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-CV-skmeans-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-CV-skmeans-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-CV-skmeans-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-CV-skmeans-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-CV-skmeans-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-CV-skmeans-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-CV-skmeans-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-CV-skmeans-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-CV-skmeans-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-CV-skmeans-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-CV-skmeans-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-CV-skmeans-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-CV-skmeans-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-CV-skmeans-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-CV-skmeans-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-CV-skmeans-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-CV-skmeans-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-CV-skmeans-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-CV-skmeans-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-CV-skmeans-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk CV-skmeans-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-CV-skmeans-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-CV-skmeans-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-CV-skmeans-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-CV-skmeans-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-CV-skmeans-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk CV-skmeans-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>              n disease.state(p) specimen(p) k
#> CV:skmeans 183            0.924    1.83e-40 2
#> CV:skmeans 183            0.962    6.15e-78 3
#> CV:skmeans 180            0.993    1.10e-74 4
#> CV:skmeans 175            1.000    9.06e-71 5
#> CV:skmeans 167            0.965    9.86e-66 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


CV:pam**

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["CV", "pam"]
# you can also extract it by
# res = res_list["CV:pam"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#>   Subgroups are detected by 'pam' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk CV-pam-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk CV-pam-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 1.000           0.998       0.999         0.5957 0.750   0.571
#> 4 4 0.893           0.959       0.930         0.0711 0.957   0.870
#> 5 5 0.897           0.866       0.909         0.0717 0.939   0.789
#> 6 6 0.787           0.714       0.837         0.0699 0.937   0.728

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2

There is also optional best \(k\) = 2 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette p1    p2    p3
#> GSM674344     3  0.0000      0.998  0 0.000 1.000
#> GSM674346     3  0.0000      0.998  0 0.000 1.000
#> GSM674347     3  0.0000      0.998  0 0.000 1.000
#> GSM674348     3  0.0000      0.998  0 0.000 1.000
#> GSM674349     3  0.0000      0.998  0 0.000 1.000
#> GSM674350     3  0.0000      0.998  0 0.000 1.000
#> GSM674353     3  0.0000      0.998  0 0.000 1.000
#> GSM674354     3  0.0000      0.998  0 0.000 1.000
#> GSM674355     3  0.0000      0.998  0 0.000 1.000
#> GSM674356     3  0.0000      0.998  0 0.000 1.000
#> GSM674357     3  0.0000      0.998  0 0.000 1.000
#> GSM674358     3  0.0000      0.998  0 0.000 1.000
#> GSM674361     3  0.0000      0.998  0 0.000 1.000
#> GSM674363     3  0.0000      0.998  0 0.000 1.000
#> GSM674364     3  0.0000      0.998  0 0.000 1.000
#> GSM674365     3  0.0000      0.998  0 0.000 1.000
#> GSM674366     3  0.0000      0.998  0 0.000 1.000
#> GSM674367     3  0.0000      0.998  0 0.000 1.000
#> GSM674368     3  0.0000      0.998  0 0.000 1.000
#> GSM674370     3  0.0000      0.998  0 0.000 1.000
#> GSM674371     3  0.0000      0.998  0 0.000 1.000
#> GSM674373     3  0.0000      0.998  0 0.000 1.000
#> GSM674375     3  0.0000      0.998  0 0.000 1.000
#> GSM674379     3  0.0000      0.998  0 0.000 1.000
#> GSM674380     3  0.0000      0.998  0 0.000 1.000
#> GSM674381     3  0.0000      0.998  0 0.000 1.000
#> GSM674382     3  0.0000      0.998  0 0.000 1.000
#> GSM674384     3  0.0000      0.998  0 0.000 1.000
#> GSM674385     3  0.0892      0.979  0 0.020 0.980
#> GSM674388     3  0.0000      0.998  0 0.000 1.000
#> GSM674389     3  0.0000      0.998  0 0.000 1.000
#> GSM674390     3  0.0000      0.998  0 0.000 1.000
#> GSM674391     3  0.0000      0.998  0 0.000 1.000
#> GSM674393     3  0.0000      0.998  0 0.000 1.000
#> GSM674394     3  0.0000      0.998  0 0.000 1.000
#> GSM674395     3  0.0000      0.998  0 0.000 1.000
#> GSM674397     3  0.0000      0.998  0 0.000 1.000
#> GSM674398     3  0.0000      0.998  0 0.000 1.000
#> GSM674400     3  0.0000      0.998  0 0.000 1.000
#> GSM674401     3  0.0000      0.998  0 0.000 1.000
#> GSM674402     3  0.0892      0.979  0 0.020 0.980
#> GSM674403     3  0.0000      0.998  0 0.000 1.000
#> GSM674405     3  0.0000      0.998  0 0.000 1.000
#> GSM674406     3  0.0000      0.998  0 0.000 1.000
#> GSM674407     3  0.0000      0.998  0 0.000 1.000
#> GSM674181     2  0.0000      0.999  0 1.000 0.000
#> GSM674183     2  0.0000      0.999  0 1.000 0.000
#> GSM674184     2  0.0000      0.999  0 1.000 0.000
#> GSM674185     2  0.0000      0.999  0 1.000 0.000
#> GSM674186     2  0.0000      0.999  0 1.000 0.000
#> GSM674187     2  0.0000      0.999  0 1.000 0.000
#> GSM674190     2  0.0000      0.999  0 1.000 0.000
#> GSM674191     2  0.0000      0.999  0 1.000 0.000
#> GSM674192     2  0.0000      0.999  0 1.000 0.000
#> GSM674193     2  0.0000      0.999  0 1.000 0.000
#> GSM674194     2  0.0000      0.999  0 1.000 0.000
#> GSM674195     2  0.0000      0.999  0 1.000 0.000
#> GSM674198     2  0.0000      0.999  0 1.000 0.000
#> GSM674200     2  0.1529      0.957  0 0.960 0.040
#> GSM674201     2  0.0000      0.999  0 1.000 0.000
#> GSM674202     2  0.0000      0.999  0 1.000 0.000
#> GSM674203     2  0.0000      0.999  0 1.000 0.000
#> GSM674204     2  0.0000      0.999  0 1.000 0.000
#> GSM674205     2  0.0000      0.999  0 1.000 0.000
#> GSM674206     2  0.0000      0.999  0 1.000 0.000
#> GSM674208     2  0.0000      0.999  0 1.000 0.000
#> GSM674209     2  0.0000      0.999  0 1.000 0.000
#> GSM674210     2  0.0000      0.999  0 1.000 0.000
#> GSM674212     2  0.0000      0.999  0 1.000 0.000
#> GSM674214     2  0.0000      0.999  0 1.000 0.000
#> GSM674218     2  0.0000      0.999  0 1.000 0.000
#> GSM674219     2  0.0000      0.999  0 1.000 0.000
#> GSM674220     2  0.0000      0.999  0 1.000 0.000
#> GSM674221     2  0.0000      0.999  0 1.000 0.000
#> GSM674223     2  0.0000      0.999  0 1.000 0.000
#> GSM674225     2  0.0000      0.999  0 1.000 0.000
#> GSM674226     2  0.0000      0.999  0 1.000 0.000
#> GSM674229     2  0.0000      0.999  0 1.000 0.000
#> GSM674230     2  0.0000      0.999  0 1.000 0.000
#> GSM674231     2  0.0000      0.999  0 1.000 0.000
#> GSM674232     2  0.0000      0.999  0 1.000 0.000
#> GSM674234     2  0.0000      0.999  0 1.000 0.000
#> GSM674235     2  0.0000      0.999  0 1.000 0.000
#> GSM674236     2  0.0000      0.999  0 1.000 0.000
#> GSM674237     2  0.0000      0.999  0 1.000 0.000
#> GSM674239     2  0.0000      0.999  0 1.000 0.000
#> GSM674240     2  0.0000      0.999  0 1.000 0.000
#> GSM674242     2  0.0000      0.999  0 1.000 0.000
#> GSM674243     2  0.0000      0.999  0 1.000 0.000
#> GSM674244     2  0.0000      0.999  0 1.000 0.000
#> GSM674245     2  0.0000      0.999  0 1.000 0.000
#> GSM674282     1  0.0000      1.000  1 0.000 0.000
#> GSM674284     1  0.0000      1.000  1 0.000 0.000
#> GSM674285     1  0.0000      1.000  1 0.000 0.000
#> GSM674287     1  0.0000      1.000  1 0.000 0.000
#> GSM674288     1  0.0000      1.000  1 0.000 0.000
#> GSM674289     1  0.0000      1.000  1 0.000 0.000
#> GSM674290     1  0.0000      1.000  1 0.000 0.000
#> GSM674291     1  0.0000      1.000  1 0.000 0.000
#> GSM674292     1  0.0000      1.000  1 0.000 0.000
#> GSM674295     1  0.0000      1.000  1 0.000 0.000
#> GSM674297     1  0.0000      1.000  1 0.000 0.000
#> GSM674298     1  0.0000      1.000  1 0.000 0.000
#> GSM674299     1  0.0000      1.000  1 0.000 0.000
#> GSM674300     1  0.0000      1.000  1 0.000 0.000
#> GSM674301     1  0.0000      1.000  1 0.000 0.000
#> GSM674302     1  0.0000      1.000  1 0.000 0.000
#> GSM674304     1  0.0000      1.000  1 0.000 0.000
#> GSM674305     1  0.0000      1.000  1 0.000 0.000
#> GSM674306     1  0.0000      1.000  1 0.000 0.000
#> GSM674308     1  0.0000      1.000  1 0.000 0.000
#> GSM674309     1  0.0000      1.000  1 0.000 0.000
#> GSM674313     1  0.0000      1.000  1 0.000 0.000
#> GSM674314     1  0.0000      1.000  1 0.000 0.000
#> GSM674315     1  0.0000      1.000  1 0.000 0.000
#> GSM674316     1  0.0000      1.000  1 0.000 0.000
#> GSM674318     1  0.0000      1.000  1 0.000 0.000
#> GSM674320     1  0.0000      1.000  1 0.000 0.000
#> GSM674323     1  0.0000      1.000  1 0.000 0.000
#> GSM674324     1  0.0000      1.000  1 0.000 0.000
#> GSM674325     1  0.0000      1.000  1 0.000 0.000
#> GSM674327     1  0.0000      1.000  1 0.000 0.000
#> GSM674328     1  0.0000      1.000  1 0.000 0.000
#> GSM674330     1  0.0000      1.000  1 0.000 0.000
#> GSM674331     1  0.0000      1.000  1 0.000 0.000
#> GSM674332     1  0.0000      1.000  1 0.000 0.000
#> GSM674334     1  0.0000      1.000  1 0.000 0.000
#> GSM674335     1  0.0000      1.000  1 0.000 0.000
#> GSM674345     3  0.0000      0.998  0 0.000 1.000
#> GSM674351     3  0.0000      0.998  0 0.000 1.000
#> GSM674352     3  0.0000      0.998  0 0.000 1.000
#> GSM674359     3  0.0000      0.998  0 0.000 1.000
#> GSM674360     3  0.0424      0.990  0 0.008 0.992
#> GSM674362     3  0.2796      0.900  0 0.092 0.908
#> GSM674369     3  0.0000      0.998  0 0.000 1.000
#> GSM674372     3  0.0000      0.998  0 0.000 1.000
#> GSM674374     3  0.0000      0.998  0 0.000 1.000
#> GSM674376     3  0.0000      0.998  0 0.000 1.000
#> GSM674377     3  0.0000      0.998  0 0.000 1.000
#> GSM674378     3  0.0000      0.998  0 0.000 1.000
#> GSM674383     3  0.0000      0.998  0 0.000 1.000
#> GSM674386     3  0.0000      0.998  0 0.000 1.000
#> GSM674387     3  0.0000      0.998  0 0.000 1.000
#> GSM674392     3  0.0000      0.998  0 0.000 1.000
#> GSM674396     3  0.0000      0.998  0 0.000 1.000
#> GSM674399     3  0.0000      0.998  0 0.000 1.000
#> GSM674404     3  0.0000      0.998  0 0.000 1.000
#> GSM674182     2  0.0000      0.999  0 1.000 0.000
#> GSM674188     2  0.0000      0.999  0 1.000 0.000
#> GSM674189     2  0.0000      0.999  0 1.000 0.000
#> GSM674196     2  0.0000      0.999  0 1.000 0.000
#> GSM674197     2  0.0000      0.999  0 1.000 0.000
#> GSM674199     2  0.0000      0.999  0 1.000 0.000
#> GSM674207     2  0.0000      0.999  0 1.000 0.000
#> GSM674211     2  0.0000      0.999  0 1.000 0.000
#> GSM674213     2  0.0000      0.999  0 1.000 0.000
#> GSM674215     2  0.0000      0.999  0 1.000 0.000
#> GSM674216     2  0.0000      0.999  0 1.000 0.000
#> GSM674217     2  0.0000      0.999  0 1.000 0.000
#> GSM674222     2  0.0000      0.999  0 1.000 0.000
#> GSM674224     2  0.0000      0.999  0 1.000 0.000
#> GSM674227     2  0.0000      0.999  0 1.000 0.000
#> GSM674228     2  0.0000      0.999  0 1.000 0.000
#> GSM674233     2  0.0000      0.999  0 1.000 0.000
#> GSM674238     2  0.0000      0.999  0 1.000 0.000
#> GSM674241     2  0.0000      0.999  0 1.000 0.000
#> GSM674283     1  0.0000      1.000  1 0.000 0.000
#> GSM674286     1  0.0000      1.000  1 0.000 0.000
#> GSM674293     1  0.0000      1.000  1 0.000 0.000
#> GSM674294     1  0.0000      1.000  1 0.000 0.000
#> GSM674296     1  0.0000      1.000  1 0.000 0.000
#> GSM674303     1  0.0000      1.000  1 0.000 0.000
#> GSM674307     1  0.0000      1.000  1 0.000 0.000
#> GSM674310     1  0.0000      1.000  1 0.000 0.000
#> GSM674311     1  0.0000      1.000  1 0.000 0.000
#> GSM674312     1  0.0000      1.000  1 0.000 0.000
#> GSM674317     1  0.0000      1.000  1 0.000 0.000
#> GSM674319     1  0.0000      1.000  1 0.000 0.000
#> GSM674321     1  0.0000      1.000  1 0.000 0.000
#> GSM674322     1  0.0000      1.000  1 0.000 0.000
#> GSM674326     1  0.0000      1.000  1 0.000 0.000
#> GSM674329     1  0.0000      1.000  1 0.000 0.000
#> GSM674333     1  0.0000      1.000  1 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1    p2    p3    p4
#> GSM674344     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674346     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674347     3  0.2469      0.902 0.108 0.000 0.892 0.000
#> GSM674348     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674349     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674350     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674353     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674354     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674355     3  0.0336      0.902 0.008 0.000 0.992 0.000
#> GSM674356     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674357     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674358     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674361     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674363     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674364     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674365     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674366     3  0.3688      0.895 0.208 0.000 0.792 0.000
#> GSM674367     3  0.3837      0.893 0.224 0.000 0.776 0.000
#> GSM674368     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674370     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674371     3  0.1389      0.904 0.048 0.000 0.952 0.000
#> GSM674373     3  0.3837      0.893 0.224 0.000 0.776 0.000
#> GSM674375     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674379     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674380     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674381     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674382     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674384     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674385     3  0.1042      0.891 0.008 0.020 0.972 0.000
#> GSM674388     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674389     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674390     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674391     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674393     3  0.1211      0.904 0.040 0.000 0.960 0.000
#> GSM674394     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674395     3  0.2589      0.902 0.116 0.000 0.884 0.000
#> GSM674397     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674398     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674400     3  0.3688      0.895 0.208 0.000 0.792 0.000
#> GSM674401     3  0.3486      0.896 0.188 0.000 0.812 0.000
#> GSM674402     3  0.0707      0.889 0.000 0.020 0.980 0.000
#> GSM674403     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674405     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674406     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674407     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674181     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674183     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674184     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674185     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674186     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674187     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674190     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674191     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674192     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674193     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674194     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674195     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674198     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674200     2  0.3311      0.799 0.000 0.828 0.172 0.000
#> GSM674201     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674202     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674203     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674204     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674205     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674206     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674208     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674209     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674210     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674212     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674214     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674218     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674219     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674220     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674221     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674223     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674225     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674226     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674229     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674230     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674231     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674232     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674234     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674235     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674236     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674237     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674239     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674240     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674242     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674243     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674244     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674245     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674282     1  0.3907      0.991 0.768 0.000 0.000 0.232
#> GSM674284     1  0.4072      0.969 0.748 0.000 0.000 0.252
#> GSM674285     1  0.3873      0.991 0.772 0.000 0.000 0.228
#> GSM674287     1  0.3907      0.991 0.768 0.000 0.000 0.232
#> GSM674288     1  0.3942      0.988 0.764 0.000 0.000 0.236
#> GSM674289     1  0.3907      0.991 0.768 0.000 0.000 0.232
#> GSM674290     1  0.3873      0.991 0.772 0.000 0.000 0.228
#> GSM674291     1  0.3873      0.991 0.772 0.000 0.000 0.228
#> GSM674292     1  0.3873      0.991 0.772 0.000 0.000 0.228
#> GSM674295     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674297     1  0.3907      0.991 0.768 0.000 0.000 0.232
#> GSM674298     1  0.3907      0.991 0.768 0.000 0.000 0.232
#> GSM674299     1  0.3907      0.991 0.768 0.000 0.000 0.232
#> GSM674300     1  0.3942      0.988 0.764 0.000 0.000 0.236
#> GSM674301     1  0.3873      0.991 0.772 0.000 0.000 0.228
#> GSM674302     1  0.3873      0.991 0.772 0.000 0.000 0.228
#> GSM674304     1  0.3907      0.991 0.768 0.000 0.000 0.232
#> GSM674305     1  0.3873      0.991 0.772 0.000 0.000 0.228
#> GSM674306     1  0.3873      0.991 0.772 0.000 0.000 0.228
#> GSM674308     1  0.3873      0.991 0.772 0.000 0.000 0.228
#> GSM674309     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674313     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674314     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674315     1  0.3907      0.991 0.768 0.000 0.000 0.232
#> GSM674316     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674318     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674320     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674323     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674324     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674325     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674327     1  0.4643      0.831 0.656 0.000 0.000 0.344
#> GSM674328     1  0.3907      0.991 0.768 0.000 0.000 0.232
#> GSM674330     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674331     4  0.0336      0.989 0.008 0.000 0.000 0.992
#> GSM674332     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674334     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674335     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674345     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674351     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674352     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674359     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674360     3  0.0336      0.897 0.000 0.008 0.992 0.000
#> GSM674362     3  0.2216      0.819 0.000 0.092 0.908 0.000
#> GSM674369     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674372     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674374     3  0.1557      0.903 0.056 0.000 0.944 0.000
#> GSM674376     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674377     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674378     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674383     3  0.0817      0.903 0.024 0.000 0.976 0.000
#> GSM674386     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674387     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674392     3  0.0000      0.901 0.000 0.000 1.000 0.000
#> GSM674396     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674399     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674404     3  0.3873      0.892 0.228 0.000 0.772 0.000
#> GSM674182     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674188     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674189     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674196     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674197     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674199     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674207     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674211     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674213     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674215     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674216     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674217     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674222     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674224     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674227     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674228     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674233     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674238     2  0.0188      0.993 0.000 0.996 0.004 0.000
#> GSM674241     2  0.0000      0.997 0.000 1.000 0.000 0.000
#> GSM674283     1  0.3907      0.991 0.768 0.000 0.000 0.232
#> GSM674286     1  0.3907      0.991 0.768 0.000 0.000 0.232
#> GSM674293     1  0.3873      0.991 0.772 0.000 0.000 0.228
#> GSM674294     1  0.3907      0.991 0.768 0.000 0.000 0.232
#> GSM674296     1  0.3873      0.991 0.772 0.000 0.000 0.228
#> GSM674303     1  0.3942      0.988 0.764 0.000 0.000 0.236
#> GSM674307     1  0.3873      0.991 0.772 0.000 0.000 0.228
#> GSM674310     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674311     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674312     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674317     1  0.3907      0.991 0.768 0.000 0.000 0.232
#> GSM674319     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674321     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674322     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674326     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674329     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> GSM674333     4  0.0000      1.000 0.000 0.000 0.000 1.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4    p5
#> GSM674344     3  0.1792      0.744 0.000 0.000 0.916 0.084 0.000
#> GSM674346     3  0.0000      0.746 0.000 0.000 1.000 0.000 0.000
#> GSM674347     3  0.3534      0.332 0.000 0.000 0.744 0.256 0.000
#> GSM674348     3  0.3966      0.617 0.000 0.000 0.664 0.336 0.000
#> GSM674349     3  0.3534      0.663 0.000 0.000 0.744 0.256 0.000
#> GSM674350     3  0.1965      0.695 0.000 0.000 0.904 0.096 0.000
#> GSM674353     3  0.0510      0.744 0.000 0.000 0.984 0.016 0.000
#> GSM674354     3  0.0290      0.746 0.000 0.000 0.992 0.008 0.000
#> GSM674355     3  0.1043      0.728 0.000 0.000 0.960 0.040 0.000
#> GSM674356     3  0.0703      0.750 0.000 0.000 0.976 0.024 0.000
#> GSM674357     3  0.0963      0.751 0.000 0.000 0.964 0.036 0.000
#> GSM674358     3  0.0290      0.746 0.000 0.000 0.992 0.008 0.000
#> GSM674361     3  0.0290      0.746 0.000 0.000 0.992 0.008 0.000
#> GSM674363     3  0.0290      0.746 0.000 0.000 0.992 0.008 0.000
#> GSM674364     3  0.0162      0.746 0.000 0.000 0.996 0.004 0.000
#> GSM674365     3  0.4045      0.595 0.000 0.000 0.644 0.356 0.000
#> GSM674366     4  0.3366      0.689 0.000 0.000 0.232 0.768 0.000
#> GSM674367     4  0.3508      0.724 0.000 0.000 0.252 0.748 0.000
#> GSM674368     3  0.3636      0.649 0.000 0.000 0.728 0.272 0.000
#> GSM674370     4  0.2732      0.752 0.000 0.000 0.160 0.840 0.000
#> GSM674371     3  0.4256      0.401 0.000 0.000 0.564 0.436 0.000
#> GSM674373     4  0.3816      0.646 0.000 0.000 0.304 0.696 0.000
#> GSM674375     4  0.2280      0.763 0.000 0.000 0.120 0.880 0.000
#> GSM674379     4  0.2852      0.763 0.000 0.000 0.172 0.828 0.000
#> GSM674380     4  0.3508      0.758 0.000 0.000 0.252 0.748 0.000
#> GSM674381     4  0.2377      0.759 0.000 0.000 0.128 0.872 0.000
#> GSM674382     4  0.4227      0.666 0.000 0.000 0.420 0.580 0.000
#> GSM674384     4  0.4045      0.686 0.000 0.000 0.356 0.644 0.000
#> GSM674385     3  0.4147      0.621 0.000 0.008 0.676 0.316 0.000
#> GSM674388     3  0.3816      0.619 0.000 0.000 0.696 0.304 0.000
#> GSM674389     4  0.3999      0.698 0.000 0.000 0.344 0.656 0.000
#> GSM674390     4  0.2280      0.763 0.000 0.000 0.120 0.880 0.000
#> GSM674391     4  0.2605      0.766 0.000 0.000 0.148 0.852 0.000
#> GSM674393     3  0.3857      0.491 0.000 0.000 0.688 0.312 0.000
#> GSM674394     4  0.4171      0.646 0.000 0.000 0.396 0.604 0.000
#> GSM674395     4  0.4297      0.213 0.000 0.000 0.472 0.528 0.000
#> GSM674397     3  0.3684      0.653 0.000 0.000 0.720 0.280 0.000
#> GSM674398     4  0.3561      0.758 0.000 0.000 0.260 0.740 0.000
#> GSM674400     3  0.4235     -0.273 0.000 0.000 0.576 0.424 0.000
#> GSM674401     4  0.4262      0.374 0.000 0.000 0.440 0.560 0.000
#> GSM674402     3  0.0992      0.741 0.000 0.008 0.968 0.024 0.000
#> GSM674403     3  0.3395      0.683 0.000 0.000 0.764 0.236 0.000
#> GSM674405     4  0.3796      0.745 0.000 0.000 0.300 0.700 0.000
#> GSM674406     4  0.4150      0.698 0.000 0.000 0.388 0.612 0.000
#> GSM674407     4  0.3143      0.749 0.000 0.000 0.204 0.796 0.000
#> GSM674181     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674183     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674184     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674185     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674186     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674187     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674190     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674191     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674192     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674193     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674194     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674195     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674198     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674200     2  0.3395      0.680 0.000 0.764 0.236 0.000 0.000
#> GSM674201     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674202     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674203     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674204     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674205     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674206     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674208     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674209     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674210     2  0.0162      0.993 0.000 0.996 0.000 0.004 0.000
#> GSM674212     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674214     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674218     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674219     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674220     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674221     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674223     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674225     2  0.0162      0.991 0.000 0.996 0.000 0.004 0.000
#> GSM674226     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674229     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674230     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674231     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674232     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674234     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674235     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674236     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674237     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674239     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674240     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674242     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674243     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674244     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674245     2  0.0162      0.993 0.000 0.996 0.000 0.004 0.000
#> GSM674282     1  0.0162      0.957 0.996 0.000 0.000 0.000 0.004
#> GSM674284     1  0.0404      0.953 0.988 0.000 0.000 0.000 0.012
#> GSM674285     1  0.2179      0.945 0.888 0.000 0.000 0.112 0.000
#> GSM674287     1  0.0162      0.957 0.996 0.000 0.000 0.000 0.004
#> GSM674288     1  0.0290      0.956 0.992 0.000 0.000 0.000 0.008
#> GSM674289     1  0.0162      0.957 0.996 0.000 0.000 0.000 0.004
#> GSM674290     1  0.2179      0.945 0.888 0.000 0.000 0.112 0.000
#> GSM674291     1  0.2179      0.945 0.888 0.000 0.000 0.112 0.000
#> GSM674292     1  0.2179      0.945 0.888 0.000 0.000 0.112 0.000
#> GSM674295     5  0.1792      0.922 0.084 0.000 0.000 0.000 0.916
#> GSM674297     1  0.0162      0.957 0.996 0.000 0.000 0.000 0.004
#> GSM674298     1  0.0162      0.957 0.996 0.000 0.000 0.000 0.004
#> GSM674299     1  0.0162      0.957 0.996 0.000 0.000 0.000 0.004
#> GSM674300     1  0.0290      0.956 0.992 0.000 0.000 0.000 0.008
#> GSM674301     1  0.2179      0.945 0.888 0.000 0.000 0.112 0.000
#> GSM674302     1  0.2179      0.945 0.888 0.000 0.000 0.112 0.000
#> GSM674304     1  0.2011      0.949 0.908 0.000 0.000 0.088 0.004
#> GSM674305     1  0.2179      0.945 0.888 0.000 0.000 0.112 0.000
#> GSM674306     1  0.2179      0.945 0.888 0.000 0.000 0.112 0.000
#> GSM674308     1  0.2179      0.945 0.888 0.000 0.000 0.112 0.000
#> GSM674309     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674313     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674314     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674315     1  0.0324      0.957 0.992 0.000 0.000 0.004 0.004
#> GSM674316     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674318     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674320     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674323     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674324     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674325     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674327     1  0.1410      0.918 0.940 0.000 0.000 0.000 0.060
#> GSM674328     1  0.0162      0.957 0.996 0.000 0.000 0.000 0.004
#> GSM674330     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674331     5  0.0404      0.981 0.012 0.000 0.000 0.000 0.988
#> GSM674332     5  0.2074      0.903 0.104 0.000 0.000 0.000 0.896
#> GSM674334     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674335     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674345     3  0.2929      0.710 0.000 0.000 0.820 0.180 0.000
#> GSM674351     3  0.0290      0.746 0.000 0.000 0.992 0.008 0.000
#> GSM674352     3  0.1965      0.695 0.000 0.000 0.904 0.096 0.000
#> GSM674359     3  0.3177      0.692 0.000 0.000 0.792 0.208 0.000
#> GSM674360     3  0.3814      0.666 0.000 0.004 0.720 0.276 0.000
#> GSM674362     3  0.2067      0.696 0.000 0.048 0.920 0.032 0.000
#> GSM674369     3  0.3730      0.638 0.000 0.000 0.712 0.288 0.000
#> GSM674372     4  0.4192      0.634 0.000 0.000 0.404 0.596 0.000
#> GSM674374     3  0.4294      0.185 0.000 0.000 0.532 0.468 0.000
#> GSM674376     4  0.2377      0.767 0.000 0.000 0.128 0.872 0.000
#> GSM674377     4  0.2377      0.759 0.000 0.000 0.128 0.872 0.000
#> GSM674378     4  0.3274      0.741 0.000 0.000 0.220 0.780 0.000
#> GSM674383     3  0.4235      0.447 0.000 0.000 0.576 0.424 0.000
#> GSM674386     4  0.3983      0.711 0.000 0.000 0.340 0.660 0.000
#> GSM674387     4  0.3177      0.746 0.000 0.000 0.208 0.792 0.000
#> GSM674392     3  0.0404      0.745 0.000 0.000 0.988 0.012 0.000
#> GSM674396     4  0.3707      0.747 0.000 0.000 0.284 0.716 0.000
#> GSM674399     4  0.3796      0.749 0.000 0.000 0.300 0.700 0.000
#> GSM674404     4  0.4182      0.685 0.000 0.000 0.400 0.600 0.000
#> GSM674182     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674188     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674189     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674196     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674197     2  0.0162      0.993 0.000 0.996 0.000 0.004 0.000
#> GSM674199     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674207     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674211     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674213     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674215     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674216     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674217     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674222     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674224     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674227     2  0.0290      0.992 0.000 0.992 0.000 0.008 0.000
#> GSM674228     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674233     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> GSM674238     2  0.0162      0.991 0.000 0.996 0.004 0.000 0.000
#> GSM674241     2  0.0162      0.993 0.000 0.996 0.000 0.004 0.000
#> GSM674283     1  0.0162      0.957 0.996 0.000 0.000 0.000 0.004
#> GSM674286     1  0.0162      0.957 0.996 0.000 0.000 0.000 0.004
#> GSM674293     1  0.2179      0.945 0.888 0.000 0.000 0.112 0.000
#> GSM674294     1  0.0324      0.957 0.992 0.000 0.000 0.004 0.004
#> GSM674296     1  0.2179      0.945 0.888 0.000 0.000 0.112 0.000
#> GSM674303     1  0.0290      0.956 0.992 0.000 0.000 0.000 0.008
#> GSM674307     1  0.2179      0.945 0.888 0.000 0.000 0.112 0.000
#> GSM674310     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674311     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674312     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674317     1  0.0162      0.957 0.996 0.000 0.000 0.000 0.004
#> GSM674319     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674321     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674322     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674326     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674329     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000
#> GSM674333     5  0.0000      0.992 0.000 0.000 0.000 0.000 1.000

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4    p5    p6
#> GSM674344     3  0.1714     0.7363 0.000 0.000 0.908 0.092 0.000 0.000
#> GSM674346     3  0.0260     0.7457 0.000 0.000 0.992 0.008 0.000 0.000
#> GSM674347     3  0.3371     0.2974 0.000 0.000 0.708 0.292 0.000 0.000
#> GSM674348     3  0.3833     0.4617 0.000 0.000 0.556 0.444 0.000 0.000
#> GSM674349     3  0.3221     0.6474 0.000 0.000 0.736 0.264 0.000 0.000
#> GSM674350     3  0.2793     0.5821 0.000 0.000 0.800 0.200 0.000 0.000
#> GSM674353     3  0.0632     0.7408 0.000 0.000 0.976 0.024 0.000 0.000
#> GSM674354     3  0.0363     0.7433 0.000 0.000 0.988 0.012 0.000 0.000
#> GSM674355     3  0.0790     0.7329 0.000 0.000 0.968 0.032 0.000 0.000
#> GSM674356     3  0.0713     0.7475 0.000 0.000 0.972 0.028 0.000 0.000
#> GSM674357     3  0.1007     0.7473 0.000 0.000 0.956 0.044 0.000 0.000
#> GSM674358     3  0.0260     0.7428 0.000 0.000 0.992 0.008 0.000 0.000
#> GSM674361     3  0.0458     0.7425 0.000 0.000 0.984 0.016 0.000 0.000
#> GSM674363     3  0.0458     0.7425 0.000 0.000 0.984 0.016 0.000 0.000
#> GSM674364     3  0.0146     0.7438 0.000 0.000 0.996 0.004 0.000 0.000
#> GSM674365     3  0.3854     0.4373 0.000 0.000 0.536 0.464 0.000 0.000
#> GSM674366     4  0.1863     0.6759 0.000 0.000 0.104 0.896 0.000 0.000
#> GSM674367     4  0.2941     0.6258 0.000 0.000 0.220 0.780 0.000 0.000
#> GSM674368     3  0.3330     0.6310 0.000 0.000 0.716 0.284 0.000 0.000
#> GSM674370     4  0.0937     0.7010 0.000 0.000 0.040 0.960 0.000 0.000
#> GSM674371     4  0.3817    -0.1461 0.000 0.000 0.432 0.568 0.000 0.000
#> GSM674373     4  0.3482     0.4780 0.000 0.000 0.316 0.684 0.000 0.000
#> GSM674375     4  0.0000     0.7078 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674379     4  0.1387     0.7081 0.000 0.000 0.068 0.932 0.000 0.000
#> GSM674380     4  0.3126     0.6369 0.000 0.000 0.248 0.752 0.000 0.000
#> GSM674381     4  0.0260     0.7050 0.000 0.000 0.008 0.992 0.000 0.000
#> GSM674382     4  0.3765     0.5477 0.000 0.000 0.404 0.596 0.000 0.000
#> GSM674384     4  0.3126     0.6447 0.000 0.000 0.248 0.752 0.000 0.000
#> GSM674385     3  0.3563     0.6046 0.000 0.000 0.664 0.336 0.000 0.000
#> GSM674388     3  0.3515     0.5897 0.000 0.000 0.676 0.324 0.000 0.000
#> GSM674389     4  0.2996     0.6561 0.000 0.000 0.228 0.772 0.000 0.000
#> GSM674390     4  0.0000     0.7078 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674391     4  0.1075     0.7109 0.000 0.000 0.048 0.952 0.000 0.000
#> GSM674393     3  0.3843     0.2204 0.000 0.000 0.548 0.452 0.000 0.000
#> GSM674394     4  0.3464     0.5917 0.000 0.000 0.312 0.688 0.000 0.000
#> GSM674395     4  0.3864     0.0191 0.000 0.000 0.480 0.520 0.000 0.000
#> GSM674397     3  0.3371     0.6352 0.000 0.000 0.708 0.292 0.000 0.000
#> GSM674398     4  0.2340     0.7022 0.000 0.000 0.148 0.852 0.000 0.000
#> GSM674400     3  0.3847    -0.2122 0.000 0.000 0.544 0.456 0.000 0.000
#> GSM674401     4  0.3563     0.4616 0.000 0.000 0.336 0.664 0.000 0.000
#> GSM674402     3  0.0937     0.7373 0.000 0.000 0.960 0.040 0.000 0.000
#> GSM674403     3  0.3198     0.6563 0.000 0.000 0.740 0.260 0.000 0.000
#> GSM674405     4  0.2762     0.6983 0.000 0.000 0.196 0.804 0.000 0.000
#> GSM674406     4  0.3695     0.5741 0.000 0.000 0.376 0.624 0.000 0.000
#> GSM674407     4  0.2664     0.6437 0.000 0.000 0.184 0.816 0.000 0.000
#> GSM674181     2  0.0146     0.7515 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674183     2  0.0260     0.7524 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674184     2  0.0146     0.7505 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674185     2  0.0146     0.7505 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674186     2  0.0260     0.7517 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674187     2  0.1556     0.7478 0.000 0.920 0.000 0.000 0.000 0.080
#> GSM674190     2  0.0790     0.7514 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM674191     2  0.0458     0.7525 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM674192     2  0.3244     0.3801 0.000 0.732 0.000 0.000 0.000 0.268
#> GSM674193     2  0.3126     0.4416 0.000 0.752 0.000 0.000 0.000 0.248
#> GSM674194     2  0.0146     0.7505 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674195     2  0.0000     0.7505 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674198     6  0.3101     0.8278 0.000 0.244 0.000 0.000 0.000 0.756
#> GSM674200     2  0.3134     0.5780 0.000 0.808 0.168 0.000 0.000 0.024
#> GSM674201     2  0.0146     0.7505 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674202     2  0.3126     0.6221 0.000 0.752 0.000 0.000 0.000 0.248
#> GSM674203     6  0.3023     0.8276 0.000 0.232 0.000 0.000 0.000 0.768
#> GSM674204     6  0.3023     0.8276 0.000 0.232 0.000 0.000 0.000 0.768
#> GSM674205     6  0.3446     0.8025 0.000 0.308 0.000 0.000 0.000 0.692
#> GSM674206     2  0.0000     0.7505 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674208     6  0.3737     0.6968 0.000 0.392 0.000 0.000 0.000 0.608
#> GSM674209     6  0.3860     0.5208 0.000 0.472 0.000 0.000 0.000 0.528
#> GSM674210     6  0.3330     0.8223 0.000 0.284 0.000 0.000 0.000 0.716
#> GSM674212     6  0.3747     0.6087 0.000 0.396 0.000 0.000 0.000 0.604
#> GSM674214     6  0.3050     0.8259 0.000 0.236 0.000 0.000 0.000 0.764
#> GSM674218     2  0.0000     0.7505 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674219     2  0.3126     0.6162 0.000 0.752 0.000 0.000 0.000 0.248
#> GSM674220     2  0.2300     0.7150 0.000 0.856 0.000 0.000 0.000 0.144
#> GSM674221     2  0.3351     0.5752 0.000 0.712 0.000 0.000 0.000 0.288
#> GSM674223     2  0.1444     0.7365 0.000 0.928 0.000 0.000 0.000 0.072
#> GSM674225     2  0.1387     0.7429 0.000 0.932 0.000 0.000 0.000 0.068
#> GSM674226     2  0.2912     0.5277 0.000 0.784 0.000 0.000 0.000 0.216
#> GSM674229     6  0.3547     0.7822 0.000 0.332 0.000 0.000 0.000 0.668
#> GSM674230     2  0.1444     0.7471 0.000 0.928 0.000 0.000 0.000 0.072
#> GSM674231     2  0.3634     0.1253 0.000 0.644 0.000 0.000 0.000 0.356
#> GSM674232     6  0.3050     0.8278 0.000 0.236 0.000 0.000 0.000 0.764
#> GSM674234     6  0.3684     0.7119 0.000 0.372 0.000 0.000 0.000 0.628
#> GSM674235     2  0.3371     0.5690 0.000 0.708 0.000 0.000 0.000 0.292
#> GSM674236     2  0.3823     0.0927 0.000 0.564 0.000 0.000 0.000 0.436
#> GSM674237     6  0.3747     0.6913 0.000 0.396 0.000 0.000 0.000 0.604
#> GSM674239     6  0.3851     0.6016 0.000 0.460 0.000 0.000 0.000 0.540
#> GSM674240     2  0.2883     0.6492 0.000 0.788 0.000 0.000 0.000 0.212
#> GSM674242     6  0.3695     0.7159 0.000 0.376 0.000 0.000 0.000 0.624
#> GSM674243     2  0.2340     0.6707 0.000 0.852 0.000 0.000 0.000 0.148
#> GSM674244     2  0.2941     0.6578 0.000 0.780 0.000 0.000 0.000 0.220
#> GSM674245     2  0.2762     0.5895 0.000 0.804 0.000 0.000 0.000 0.196
#> GSM674282     1  0.0000     0.9166 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674284     1  0.0000     0.9166 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674285     1  0.2912     0.8903 0.784 0.000 0.000 0.000 0.000 0.216
#> GSM674287     1  0.0000     0.9166 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674288     1  0.0000     0.9166 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674289     1  0.0000     0.9166 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.3023     0.8868 0.768 0.000 0.000 0.000 0.000 0.232
#> GSM674291     1  0.3023     0.8868 0.768 0.000 0.000 0.000 0.000 0.232
#> GSM674292     1  0.2941     0.8895 0.780 0.000 0.000 0.000 0.000 0.220
#> GSM674295     5  0.2664     0.8120 0.184 0.000 0.000 0.000 0.816 0.000
#> GSM674297     1  0.0000     0.9166 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674298     1  0.0000     0.9166 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674299     1  0.0000     0.9166 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674300     1  0.0000     0.9166 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674301     1  0.3023     0.8868 0.768 0.000 0.000 0.000 0.000 0.232
#> GSM674302     1  0.3023     0.8868 0.768 0.000 0.000 0.000 0.000 0.232
#> GSM674304     1  0.2631     0.8963 0.820 0.000 0.000 0.000 0.000 0.180
#> GSM674305     1  0.3023     0.8868 0.768 0.000 0.000 0.000 0.000 0.232
#> GSM674306     1  0.2969     0.8887 0.776 0.000 0.000 0.000 0.000 0.224
#> GSM674308     1  0.3023     0.8868 0.768 0.000 0.000 0.000 0.000 0.232
#> GSM674309     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674313     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674314     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674315     1  0.0632     0.9156 0.976 0.000 0.000 0.000 0.000 0.024
#> GSM674316     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674318     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674320     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674323     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674324     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674325     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674327     1  0.0547     0.9104 0.980 0.000 0.000 0.000 0.020 0.000
#> GSM674328     1  0.0000     0.9166 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674330     5  0.0146     0.9806 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM674331     5  0.0363     0.9728 0.012 0.000 0.000 0.000 0.988 0.000
#> GSM674332     5  0.2762     0.7975 0.196 0.000 0.000 0.000 0.804 0.000
#> GSM674334     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674335     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674345     3  0.2730     0.6968 0.000 0.000 0.808 0.192 0.000 0.000
#> GSM674351     3  0.0363     0.7433 0.000 0.000 0.988 0.012 0.000 0.000
#> GSM674352     3  0.2793     0.5821 0.000 0.000 0.800 0.200 0.000 0.000
#> GSM674359     3  0.2883     0.6783 0.000 0.000 0.788 0.212 0.000 0.000
#> GSM674360     3  0.3607     0.5861 0.000 0.000 0.652 0.348 0.000 0.000
#> GSM674362     3  0.1075     0.7342 0.000 0.000 0.952 0.048 0.000 0.000
#> GSM674369     3  0.3482     0.6016 0.000 0.000 0.684 0.316 0.000 0.000
#> GSM674372     4  0.3351     0.6114 0.000 0.000 0.288 0.712 0.000 0.000
#> GSM674374     3  0.3857     0.2641 0.000 0.000 0.532 0.468 0.000 0.000
#> GSM674376     4  0.0458     0.7111 0.000 0.000 0.016 0.984 0.000 0.000
#> GSM674377     4  0.0260     0.7050 0.000 0.000 0.008 0.992 0.000 0.000
#> GSM674378     4  0.2793     0.6315 0.000 0.000 0.200 0.800 0.000 0.000
#> GSM674383     4  0.3828    -0.1903 0.000 0.000 0.440 0.560 0.000 0.000
#> GSM674386     4  0.2941     0.6697 0.000 0.000 0.220 0.780 0.000 0.000
#> GSM674387     4  0.2793     0.6328 0.000 0.000 0.200 0.800 0.000 0.000
#> GSM674392     3  0.0363     0.7425 0.000 0.000 0.988 0.012 0.000 0.000
#> GSM674396     4  0.2491     0.6963 0.000 0.000 0.164 0.836 0.000 0.000
#> GSM674399     4  0.2762     0.7007 0.000 0.000 0.196 0.804 0.000 0.000
#> GSM674404     4  0.3620     0.6066 0.000 0.000 0.352 0.648 0.000 0.000
#> GSM674182     2  0.0713     0.7542 0.000 0.972 0.000 0.000 0.000 0.028
#> GSM674188     2  0.1814     0.7488 0.000 0.900 0.000 0.000 0.000 0.100
#> GSM674189     2  0.0146     0.7505 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674196     6  0.3817     0.6408 0.000 0.432 0.000 0.000 0.000 0.568
#> GSM674197     2  0.3868    -0.5537 0.000 0.504 0.000 0.000 0.000 0.496
#> GSM674199     6  0.3023     0.8276 0.000 0.232 0.000 0.000 0.000 0.768
#> GSM674207     6  0.3351     0.8027 0.000 0.288 0.000 0.000 0.000 0.712
#> GSM674211     6  0.3330     0.8070 0.000 0.284 0.000 0.000 0.000 0.716
#> GSM674213     2  0.3563     0.4670 0.000 0.664 0.000 0.000 0.000 0.336
#> GSM674215     2  0.2135     0.7219 0.000 0.872 0.000 0.000 0.000 0.128
#> GSM674216     6  0.3023     0.8276 0.000 0.232 0.000 0.000 0.000 0.768
#> GSM674217     2  0.3288     0.5939 0.000 0.724 0.000 0.000 0.000 0.276
#> GSM674222     2  0.3390     0.5617 0.000 0.704 0.000 0.000 0.000 0.296
#> GSM674224     2  0.1663     0.7481 0.000 0.912 0.000 0.000 0.000 0.088
#> GSM674227     2  0.3409     0.4207 0.000 0.700 0.000 0.000 0.000 0.300
#> GSM674228     2  0.3634     0.4138 0.000 0.644 0.000 0.000 0.000 0.356
#> GSM674233     2  0.3288     0.5939 0.000 0.724 0.000 0.000 0.000 0.276
#> GSM674238     2  0.2340     0.7069 0.000 0.852 0.000 0.000 0.000 0.148
#> GSM674241     6  0.3659     0.7310 0.000 0.364 0.000 0.000 0.000 0.636
#> GSM674283     1  0.0000     0.9166 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674286     1  0.0000     0.9166 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674293     1  0.3023     0.8868 0.768 0.000 0.000 0.000 0.000 0.232
#> GSM674294     1  0.0363     0.9164 0.988 0.000 0.000 0.000 0.000 0.012
#> GSM674296     1  0.3023     0.8868 0.768 0.000 0.000 0.000 0.000 0.232
#> GSM674303     1  0.0000     0.9166 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674307     1  0.3023     0.8868 0.768 0.000 0.000 0.000 0.000 0.232
#> GSM674310     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674311     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674312     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674317     1  0.0000     0.9166 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674319     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674321     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674322     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674326     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674329     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674333     5  0.0000     0.9834 0.000 0.000 0.000 0.000 1.000 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-CV-pam-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-CV-pam-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-CV-pam-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-CV-pam-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-CV-pam-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-CV-pam-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-CV-pam-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-CV-pam-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-CV-pam-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-CV-pam-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-CV-pam-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-CV-pam-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-CV-pam-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-CV-pam-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-CV-pam-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-CV-pam-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-CV-pam-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-CV-pam-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-CV-pam-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-CV-pam-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk CV-pam-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-CV-pam-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-CV-pam-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-CV-pam-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-CV-pam-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-CV-pam-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk CV-pam-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>          n disease.state(p) specimen(p) k
#> CV:pam 183            0.924    1.83e-40 2
#> CV:pam 183            0.962    6.15e-78 3
#> CV:pam 183            0.844    5.66e-76 4
#> CV:pam 175            0.905    9.06e-71 5
#> CV:pam 164            0.911    1.84e-64 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


CV:mclust*

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["CV", "mclust"]
# you can also extract it by
# res = res_list["CV:mclust"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#>   Subgroups are detected by 'mclust' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 5.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk CV-mclust-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk CV-mclust-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 1.000           1.000       1.000         0.5958 0.750   0.571
#> 4 4 0.957           0.913       0.952         0.0543 0.958   0.875
#> 5 5 0.933           0.717       0.873         0.0258 0.961   0.872
#> 6 6 0.825           0.784       0.869         0.0425 0.942   0.809

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3 4

There is also optional best \(k\) = 2 3 4 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette p1 p2 p3
#> GSM674344     3       0          1  0  0  1
#> GSM674346     3       0          1  0  0  1
#> GSM674347     3       0          1  0  0  1
#> GSM674348     3       0          1  0  0  1
#> GSM674349     3       0          1  0  0  1
#> GSM674350     3       0          1  0  0  1
#> GSM674353     3       0          1  0  0  1
#> GSM674354     3       0          1  0  0  1
#> GSM674355     3       0          1  0  0  1
#> GSM674356     3       0          1  0  0  1
#> GSM674357     3       0          1  0  0  1
#> GSM674358     3       0          1  0  0  1
#> GSM674361     3       0          1  0  0  1
#> GSM674363     3       0          1  0  0  1
#> GSM674364     3       0          1  0  0  1
#> GSM674365     3       0          1  0  0  1
#> GSM674366     3       0          1  0  0  1
#> GSM674367     3       0          1  0  0  1
#> GSM674368     3       0          1  0  0  1
#> GSM674370     3       0          1  0  0  1
#> GSM674371     3       0          1  0  0  1
#> GSM674373     3       0          1  0  0  1
#> GSM674375     3       0          1  0  0  1
#> GSM674379     3       0          1  0  0  1
#> GSM674380     3       0          1  0  0  1
#> GSM674381     3       0          1  0  0  1
#> GSM674382     3       0          1  0  0  1
#> GSM674384     3       0          1  0  0  1
#> GSM674385     3       0          1  0  0  1
#> GSM674388     3       0          1  0  0  1
#> GSM674389     3       0          1  0  0  1
#> GSM674390     3       0          1  0  0  1
#> GSM674391     3       0          1  0  0  1
#> GSM674393     3       0          1  0  0  1
#> GSM674394     3       0          1  0  0  1
#> GSM674395     3       0          1  0  0  1
#> GSM674397     3       0          1  0  0  1
#> GSM674398     3       0          1  0  0  1
#> GSM674400     3       0          1  0  0  1
#> GSM674401     3       0          1  0  0  1
#> GSM674402     3       0          1  0  0  1
#> GSM674403     3       0          1  0  0  1
#> GSM674405     3       0          1  0  0  1
#> GSM674406     3       0          1  0  0  1
#> GSM674407     3       0          1  0  0  1
#> GSM674181     2       0          1  0  1  0
#> GSM674183     2       0          1  0  1  0
#> GSM674184     2       0          1  0  1  0
#> GSM674185     2       0          1  0  1  0
#> GSM674186     2       0          1  0  1  0
#> GSM674187     2       0          1  0  1  0
#> GSM674190     2       0          1  0  1  0
#> GSM674191     2       0          1  0  1  0
#> GSM674192     2       0          1  0  1  0
#> GSM674193     2       0          1  0  1  0
#> GSM674194     2       0          1  0  1  0
#> GSM674195     2       0          1  0  1  0
#> GSM674198     2       0          1  0  1  0
#> GSM674200     2       0          1  0  1  0
#> GSM674201     2       0          1  0  1  0
#> GSM674202     2       0          1  0  1  0
#> GSM674203     2       0          1  0  1  0
#> GSM674204     2       0          1  0  1  0
#> GSM674205     2       0          1  0  1  0
#> GSM674206     2       0          1  0  1  0
#> GSM674208     2       0          1  0  1  0
#> GSM674209     2       0          1  0  1  0
#> GSM674210     2       0          1  0  1  0
#> GSM674212     2       0          1  0  1  0
#> GSM674214     2       0          1  0  1  0
#> GSM674218     2       0          1  0  1  0
#> GSM674219     2       0          1  0  1  0
#> GSM674220     2       0          1  0  1  0
#> GSM674221     2       0          1  0  1  0
#> GSM674223     2       0          1  0  1  0
#> GSM674225     2       0          1  0  1  0
#> GSM674226     2       0          1  0  1  0
#> GSM674229     2       0          1  0  1  0
#> GSM674230     2       0          1  0  1  0
#> GSM674231     2       0          1  0  1  0
#> GSM674232     2       0          1  0  1  0
#> GSM674234     2       0          1  0  1  0
#> GSM674235     2       0          1  0  1  0
#> GSM674236     2       0          1  0  1  0
#> GSM674237     2       0          1  0  1  0
#> GSM674239     2       0          1  0  1  0
#> GSM674240     2       0          1  0  1  0
#> GSM674242     2       0          1  0  1  0
#> GSM674243     2       0          1  0  1  0
#> GSM674244     2       0          1  0  1  0
#> GSM674245     2       0          1  0  1  0
#> GSM674282     1       0          1  1  0  0
#> GSM674284     1       0          1  1  0  0
#> GSM674285     1       0          1  1  0  0
#> GSM674287     1       0          1  1  0  0
#> GSM674288     1       0          1  1  0  0
#> GSM674289     1       0          1  1  0  0
#> GSM674290     1       0          1  1  0  0
#> GSM674291     1       0          1  1  0  0
#> GSM674292     1       0          1  1  0  0
#> GSM674295     1       0          1  1  0  0
#> GSM674297     1       0          1  1  0  0
#> GSM674298     1       0          1  1  0  0
#> GSM674299     1       0          1  1  0  0
#> GSM674300     1       0          1  1  0  0
#> GSM674301     1       0          1  1  0  0
#> GSM674302     1       0          1  1  0  0
#> GSM674304     1       0          1  1  0  0
#> GSM674305     1       0          1  1  0  0
#> GSM674306     1       0          1  1  0  0
#> GSM674308     1       0          1  1  0  0
#> GSM674309     1       0          1  1  0  0
#> GSM674313     1       0          1  1  0  0
#> GSM674314     1       0          1  1  0  0
#> GSM674315     1       0          1  1  0  0
#> GSM674316     1       0          1  1  0  0
#> GSM674318     1       0          1  1  0  0
#> GSM674320     1       0          1  1  0  0
#> GSM674323     1       0          1  1  0  0
#> GSM674324     1       0          1  1  0  0
#> GSM674325     1       0          1  1  0  0
#> GSM674327     1       0          1  1  0  0
#> GSM674328     1       0          1  1  0  0
#> GSM674330     1       0          1  1  0  0
#> GSM674331     1       0          1  1  0  0
#> GSM674332     1       0          1  1  0  0
#> GSM674334     1       0          1  1  0  0
#> GSM674335     1       0          1  1  0  0
#> GSM674345     3       0          1  0  0  1
#> GSM674351     3       0          1  0  0  1
#> GSM674352     3       0          1  0  0  1
#> GSM674359     3       0          1  0  0  1
#> GSM674360     3       0          1  0  0  1
#> GSM674362     3       0          1  0  0  1
#> GSM674369     3       0          1  0  0  1
#> GSM674372     3       0          1  0  0  1
#> GSM674374     3       0          1  0  0  1
#> GSM674376     3       0          1  0  0  1
#> GSM674377     3       0          1  0  0  1
#> GSM674378     3       0          1  0  0  1
#> GSM674383     3       0          1  0  0  1
#> GSM674386     3       0          1  0  0  1
#> GSM674387     3       0          1  0  0  1
#> GSM674392     3       0          1  0  0  1
#> GSM674396     3       0          1  0  0  1
#> GSM674399     3       0          1  0  0  1
#> GSM674404     3       0          1  0  0  1
#> GSM674182     2       0          1  0  1  0
#> GSM674188     2       0          1  0  1  0
#> GSM674189     2       0          1  0  1  0
#> GSM674196     2       0          1  0  1  0
#> GSM674197     2       0          1  0  1  0
#> GSM674199     2       0          1  0  1  0
#> GSM674207     2       0          1  0  1  0
#> GSM674211     2       0          1  0  1  0
#> GSM674213     2       0          1  0  1  0
#> GSM674215     2       0          1  0  1  0
#> GSM674216     2       0          1  0  1  0
#> GSM674217     2       0          1  0  1  0
#> GSM674222     2       0          1  0  1  0
#> GSM674224     2       0          1  0  1  0
#> GSM674227     2       0          1  0  1  0
#> GSM674228     2       0          1  0  1  0
#> GSM674233     2       0          1  0  1  0
#> GSM674238     2       0          1  0  1  0
#> GSM674241     2       0          1  0  1  0
#> GSM674283     1       0          1  1  0  0
#> GSM674286     1       0          1  1  0  0
#> GSM674293     1       0          1  1  0  0
#> GSM674294     1       0          1  1  0  0
#> GSM674296     1       0          1  1  0  0
#> GSM674303     1       0          1  1  0  0
#> GSM674307     1       0          1  1  0  0
#> GSM674310     1       0          1  1  0  0
#> GSM674311     1       0          1  1  0  0
#> GSM674312     1       0          1  1  0  0
#> GSM674317     1       0          1  1  0  0
#> GSM674319     1       0          1  1  0  0
#> GSM674321     1       0          1  1  0  0
#> GSM674322     1       0          1  1  0  0
#> GSM674326     1       0          1  1  0  0
#> GSM674329     1       0          1  1  0  0
#> GSM674333     1       0          1  1  0  0

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1 p2 p3    p4
#> GSM674344     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674346     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674347     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674348     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674349     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674350     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674353     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674354     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674355     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674356     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674357     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674358     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674361     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674363     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674364     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674365     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674366     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674367     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674368     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674370     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674371     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674373     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674375     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674379     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674380     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674381     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674382     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674384     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674385     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674388     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674389     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674390     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674391     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674393     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674394     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674395     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674397     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674398     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674400     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674401     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674402     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674403     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674405     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674406     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674407     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674181     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674183     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674184     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674185     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674186     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674187     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674190     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674191     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674192     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674193     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674194     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674195     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674198     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674200     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674201     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674202     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674203     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674204     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674205     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674206     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674208     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674209     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674210     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674212     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674214     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674218     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674219     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674220     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674221     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674223     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674225     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674226     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674229     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674230     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674231     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674232     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674234     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674235     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674236     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674237     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674239     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674240     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674242     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674243     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674244     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674245     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674282     1  0.0000      0.825 1.000  0  0 0.000
#> GSM674284     1  0.3219      0.769 0.836  0  0 0.164
#> GSM674285     1  0.0469      0.821 0.988  0  0 0.012
#> GSM674287     1  0.3486      0.750 0.812  0  0 0.188
#> GSM674288     4  0.4776      0.564 0.376  0  0 0.624
#> GSM674289     1  0.0000      0.825 1.000  0  0 0.000
#> GSM674290     1  0.0469      0.821 0.988  0  0 0.012
#> GSM674291     1  0.0469      0.821 0.988  0  0 0.012
#> GSM674292     1  0.0469      0.821 0.988  0  0 0.012
#> GSM674295     4  0.3356      0.826 0.176  0  0 0.824
#> GSM674297     1  0.2530      0.796 0.888  0  0 0.112
#> GSM674298     1  0.0707      0.823 0.980  0  0 0.020
#> GSM674299     1  0.3486      0.750 0.812  0  0 0.188
#> GSM674300     4  0.3801      0.584 0.220  0  0 0.780
#> GSM674301     1  0.0469      0.821 0.988  0  0 0.012
#> GSM674302     1  0.0469      0.821 0.988  0  0 0.012
#> GSM674304     1  0.0469      0.821 0.988  0  0 0.012
#> GSM674305     1  0.0000      0.825 1.000  0  0 0.000
#> GSM674306     4  0.4746      0.381 0.368  0  0 0.632
#> GSM674308     1  0.0592      0.820 0.984  0  0 0.016
#> GSM674309     1  0.3569      0.741 0.804  0  0 0.196
#> GSM674313     4  0.0000      0.690 0.000  0  0 1.000
#> GSM674314     4  0.5000      0.182 0.500  0  0 0.500
#> GSM674315     4  0.4746      0.381 0.368  0  0 0.632
#> GSM674316     1  0.4877      0.237 0.592  0  0 0.408
#> GSM674318     4  0.3219      0.830 0.164  0  0 0.836
#> GSM674320     4  0.3219      0.830 0.164  0  0 0.836
#> GSM674323     4  0.3311      0.828 0.172  0  0 0.828
#> GSM674324     1  0.3444      0.754 0.816  0  0 0.184
#> GSM674325     4  0.4713      0.574 0.360  0  0 0.640
#> GSM674327     4  0.3266      0.807 0.168  0  0 0.832
#> GSM674328     1  0.3356      0.761 0.824  0  0 0.176
#> GSM674330     1  0.5000     -0.242 0.500  0  0 0.500
#> GSM674331     1  0.3444      0.754 0.816  0  0 0.184
#> GSM674332     1  0.3873      0.691 0.772  0  0 0.228
#> GSM674334     1  0.3569      0.741 0.804  0  0 0.196
#> GSM674335     4  0.4746      0.563 0.368  0  0 0.632
#> GSM674345     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674351     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674352     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674359     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674360     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674362     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674369     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674372     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674374     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674376     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674377     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674378     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674383     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674386     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674387     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674392     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674396     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674399     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674404     3  0.0000      1.000 0.000  0  1 0.000
#> GSM674182     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674188     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674189     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674196     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674197     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674199     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674207     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674211     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674213     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674215     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674216     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674217     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674222     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674224     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674227     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674228     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674233     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674238     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674241     2  0.0000      1.000 0.000  1  0 0.000
#> GSM674283     1  0.0000      0.825 1.000  0  0 0.000
#> GSM674286     1  0.0000      0.825 1.000  0  0 0.000
#> GSM674293     1  0.4996     -0.268 0.516  0  0 0.484
#> GSM674294     1  0.0000      0.825 1.000  0  0 0.000
#> GSM674296     1  0.0469      0.821 0.988  0  0 0.012
#> GSM674303     1  0.2921      0.785 0.860  0  0 0.140
#> GSM674307     1  0.0000      0.825 1.000  0  0 0.000
#> GSM674310     4  0.3219      0.830 0.164  0  0 0.836
#> GSM674311     1  0.3486      0.750 0.812  0  0 0.188
#> GSM674312     4  0.3219      0.830 0.164  0  0 0.836
#> GSM674317     1  0.2921      0.785 0.860  0  0 0.140
#> GSM674319     4  0.3975      0.768 0.240  0  0 0.760
#> GSM674321     4  0.3311      0.828 0.172  0  0 0.828
#> GSM674322     4  0.3219      0.830 0.164  0  0 0.836
#> GSM674326     4  0.3219      0.830 0.164  0  0 0.836
#> GSM674329     4  0.3219      0.830 0.164  0  0 0.836
#> GSM674333     4  0.3219      0.830 0.164  0  0 0.836

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4    p5
#> GSM674344     3  0.0404    0.95043 0.000 0.000 0.988 0.012 0.000
#> GSM674346     3  0.4101    0.57858 0.000 0.000 0.628 0.372 0.000
#> GSM674347     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674348     3  0.0162    0.95632 0.000 0.000 0.996 0.004 0.000
#> GSM674349     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674350     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674353     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674354     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674355     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674356     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674357     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674358     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674361     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674363     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674364     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674365     3  0.0162    0.95632 0.000 0.000 0.996 0.004 0.000
#> GSM674366     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674367     3  0.0404    0.95105 0.000 0.000 0.988 0.012 0.000
#> GSM674368     3  0.0162    0.95632 0.000 0.000 0.996 0.004 0.000
#> GSM674370     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674371     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674373     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674375     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674379     3  0.0162    0.95615 0.000 0.000 0.996 0.004 0.000
#> GSM674380     3  0.0162    0.95632 0.000 0.000 0.996 0.004 0.000
#> GSM674381     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674382     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674384     3  0.0162    0.95632 0.000 0.000 0.996 0.004 0.000
#> GSM674385     3  0.0162    0.95632 0.000 0.000 0.996 0.004 0.000
#> GSM674388     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674389     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674390     3  0.0162    0.95617 0.000 0.000 0.996 0.004 0.000
#> GSM674391     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674393     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674394     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674395     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674397     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674398     3  0.1270    0.91996 0.000 0.000 0.948 0.052 0.000
#> GSM674400     3  0.4126    0.56709 0.000 0.000 0.620 0.380 0.000
#> GSM674401     3  0.4161    0.54951 0.000 0.000 0.608 0.392 0.000
#> GSM674402     3  0.4161    0.55153 0.000 0.000 0.608 0.392 0.000
#> GSM674403     3  0.4150    0.55556 0.000 0.000 0.612 0.388 0.000
#> GSM674405     3  0.4030    0.60468 0.000 0.000 0.648 0.352 0.000
#> GSM674406     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674407     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674181     2  0.0794    0.97527 0.000 0.972 0.000 0.028 0.000
#> GSM674183     2  0.1043    0.96505 0.000 0.960 0.000 0.040 0.000
#> GSM674184     2  0.0290    0.99168 0.000 0.992 0.000 0.008 0.000
#> GSM674185     2  0.0162    0.99417 0.000 0.996 0.000 0.004 0.000
#> GSM674186     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674187     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674190     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674191     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674192     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674193     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674194     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674195     2  0.0703    0.97918 0.000 0.976 0.000 0.024 0.000
#> GSM674198     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674200     2  0.1043    0.96505 0.000 0.960 0.000 0.040 0.000
#> GSM674201     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674202     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674203     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674204     2  0.0162    0.99423 0.000 0.996 0.000 0.004 0.000
#> GSM674205     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674206     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674208     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674209     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674210     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674212     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674214     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674218     2  0.0290    0.99168 0.000 0.992 0.000 0.008 0.000
#> GSM674219     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674220     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674221     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674223     2  0.0162    0.99423 0.000 0.996 0.000 0.004 0.000
#> GSM674225     2  0.0162    0.99400 0.000 0.996 0.000 0.004 0.000
#> GSM674226     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674229     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674230     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674231     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674232     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674234     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674235     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674236     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674237     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674239     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674240     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674242     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674243     2  0.0963    0.96821 0.000 0.964 0.000 0.036 0.000
#> GSM674244     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674245     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674282     5  0.4235    0.55579 0.424 0.000 0.000 0.000 0.576
#> GSM674284     1  0.4114    0.01148 0.624 0.000 0.000 0.000 0.376
#> GSM674285     5  0.4101    0.61736 0.372 0.000 0.000 0.000 0.628
#> GSM674287     1  0.4126   -0.00221 0.620 0.000 0.000 0.000 0.380
#> GSM674288     1  0.3752   -0.29752 0.708 0.000 0.000 0.000 0.292
#> GSM674289     5  0.4249    0.54198 0.432 0.000 0.000 0.000 0.568
#> GSM674290     5  0.3983    0.62835 0.340 0.000 0.000 0.000 0.660
#> GSM674291     5  0.3983    0.62835 0.340 0.000 0.000 0.000 0.660
#> GSM674292     5  0.3983    0.62835 0.340 0.000 0.000 0.000 0.660
#> GSM674295     1  0.4823   -0.44362 0.672 0.000 0.000 0.052 0.276
#> GSM674297     1  0.4171   -0.05538 0.604 0.000 0.000 0.000 0.396
#> GSM674298     1  0.4273   -0.23977 0.552 0.000 0.000 0.000 0.448
#> GSM674299     1  0.4074    0.03235 0.636 0.000 0.000 0.000 0.364
#> GSM674300     5  0.5904   -0.59912 0.360 0.000 0.000 0.112 0.528
#> GSM674301     5  0.3983    0.62835 0.340 0.000 0.000 0.000 0.660
#> GSM674302     5  0.3999    0.62810 0.344 0.000 0.000 0.000 0.656
#> GSM674304     5  0.4060    0.62376 0.360 0.000 0.000 0.000 0.640
#> GSM674305     5  0.4138    0.60719 0.384 0.000 0.000 0.000 0.616
#> GSM674306     5  0.5862   -0.58682 0.344 0.000 0.000 0.112 0.544
#> GSM674308     5  0.3983    0.62281 0.340 0.000 0.000 0.000 0.660
#> GSM674309     1  0.3876    0.10834 0.684 0.000 0.000 0.000 0.316
#> GSM674313     4  0.5905    0.78281 0.144 0.000 0.000 0.580 0.276
#> GSM674314     1  0.2230    0.25269 0.884 0.000 0.000 0.000 0.116
#> GSM674315     5  0.5862   -0.58682 0.344 0.000 0.000 0.112 0.544
#> GSM674316     1  0.5064    0.17798 0.680 0.000 0.000 0.088 0.232
#> GSM674318     4  0.6673    0.91629 0.284 0.000 0.000 0.440 0.276
#> GSM674320     1  0.6779   -0.85226 0.364 0.000 0.000 0.360 0.276
#> GSM674323     1  0.5598   -0.48113 0.612 0.000 0.000 0.112 0.276
#> GSM674324     1  0.4030    0.06064 0.648 0.000 0.000 0.000 0.352
#> GSM674325     1  0.2179    0.30928 0.896 0.000 0.000 0.100 0.004
#> GSM674327     1  0.5118   -0.52191 0.548 0.000 0.000 0.040 0.412
#> GSM674328     1  0.4074    0.04195 0.636 0.000 0.000 0.000 0.364
#> GSM674330     1  0.2280    0.25015 0.880 0.000 0.000 0.000 0.120
#> GSM674331     1  0.4030    0.06064 0.648 0.000 0.000 0.000 0.352
#> GSM674332     1  0.3796    0.05765 0.700 0.000 0.000 0.000 0.300
#> GSM674334     1  0.4437    0.11145 0.664 0.000 0.000 0.020 0.316
#> GSM674335     1  0.1830    0.31468 0.924 0.000 0.000 0.068 0.008
#> GSM674345     3  0.4088    0.58401 0.000 0.000 0.632 0.368 0.000
#> GSM674351     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674352     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674359     3  0.0794    0.93865 0.000 0.000 0.972 0.028 0.000
#> GSM674360     3  0.0162    0.95632 0.000 0.000 0.996 0.004 0.000
#> GSM674362     3  0.0162    0.95632 0.000 0.000 0.996 0.004 0.000
#> GSM674369     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674372     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674374     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674376     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674377     3  0.0162    0.95632 0.000 0.000 0.996 0.004 0.000
#> GSM674378     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674383     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674386     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674387     3  0.0162    0.95617 0.000 0.000 0.996 0.004 0.000
#> GSM674392     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674396     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674399     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674404     3  0.0000    0.95806 0.000 0.000 1.000 0.000 0.000
#> GSM674182     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674188     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674189     2  0.0290    0.99168 0.000 0.992 0.000 0.008 0.000
#> GSM674196     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674197     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674199     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674207     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674211     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674213     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674215     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674216     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674217     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674222     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674224     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674227     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674228     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674233     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674238     2  0.0703    0.97921 0.000 0.976 0.000 0.024 0.000
#> GSM674241     2  0.0000    0.99667 0.000 1.000 0.000 0.000 0.000
#> GSM674283     5  0.4256    0.53336 0.436 0.000 0.000 0.000 0.564
#> GSM674286     5  0.4249    0.54192 0.432 0.000 0.000 0.000 0.568
#> GSM674293     5  0.3565   -0.12656 0.176 0.000 0.000 0.024 0.800
#> GSM674294     5  0.4126    0.61056 0.380 0.000 0.000 0.000 0.620
#> GSM674296     5  0.3966    0.62505 0.336 0.000 0.000 0.000 0.664
#> GSM674303     1  0.4138   -0.01294 0.616 0.000 0.000 0.000 0.384
#> GSM674307     5  0.4256    0.53340 0.436 0.000 0.000 0.000 0.564
#> GSM674310     4  0.6650    0.91550 0.276 0.000 0.000 0.448 0.276
#> GSM674311     1  0.3999    0.07266 0.656 0.000 0.000 0.000 0.344
#> GSM674312     4  0.6728    0.90935 0.308 0.000 0.000 0.416 0.276
#> GSM674317     1  0.4192   -0.12847 0.596 0.000 0.000 0.000 0.404
#> GSM674319     1  0.4701   -0.21941 0.720 0.000 0.000 0.076 0.204
#> GSM674321     1  0.5834   -0.51870 0.588 0.000 0.000 0.136 0.276
#> GSM674322     1  0.6552   -0.68005 0.476 0.000 0.000 0.248 0.276
#> GSM674326     4  0.6770    0.88586 0.340 0.000 0.000 0.384 0.276
#> GSM674329     1  0.6402   -0.61355 0.508 0.000 0.000 0.216 0.276
#> GSM674333     1  0.6518   -0.67512 0.484 0.000 0.000 0.240 0.276

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4    p5    p6
#> GSM674344     3  0.1957      0.764 0.000 0.000 0.888 0.112 0.000 0.000
#> GSM674346     4  0.3860      0.487 0.000 0.000 0.472 0.528 0.000 0.000
#> GSM674347     3  0.1765      0.809 0.000 0.000 0.904 0.096 0.000 0.000
#> GSM674348     3  0.1141      0.824 0.000 0.000 0.948 0.052 0.000 0.000
#> GSM674349     3  0.0547      0.846 0.000 0.000 0.980 0.020 0.000 0.000
#> GSM674350     3  0.0146      0.846 0.000 0.000 0.996 0.004 0.000 0.000
#> GSM674353     3  0.1610      0.818 0.000 0.000 0.916 0.084 0.000 0.000
#> GSM674354     3  0.1075      0.826 0.000 0.000 0.952 0.048 0.000 0.000
#> GSM674355     3  0.1075      0.838 0.000 0.000 0.952 0.048 0.000 0.000
#> GSM674356     3  0.0260      0.847 0.000 0.000 0.992 0.008 0.000 0.000
#> GSM674357     3  0.0146      0.847 0.000 0.000 0.996 0.004 0.000 0.000
#> GSM674358     3  0.1444      0.825 0.000 0.000 0.928 0.072 0.000 0.000
#> GSM674361     3  0.0547      0.846 0.000 0.000 0.980 0.020 0.000 0.000
#> GSM674363     3  0.0000      0.847 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM674364     3  0.0458      0.844 0.000 0.000 0.984 0.016 0.000 0.000
#> GSM674365     3  0.1204      0.821 0.000 0.000 0.944 0.056 0.000 0.000
#> GSM674366     3  0.0260      0.846 0.000 0.000 0.992 0.008 0.000 0.000
#> GSM674367     3  0.0790      0.845 0.000 0.000 0.968 0.032 0.000 0.000
#> GSM674368     3  0.1387      0.811 0.000 0.000 0.932 0.068 0.000 0.000
#> GSM674370     3  0.0547      0.843 0.000 0.000 0.980 0.020 0.000 0.000
#> GSM674371     3  0.0146      0.846 0.000 0.000 0.996 0.004 0.000 0.000
#> GSM674373     3  0.0363      0.845 0.000 0.000 0.988 0.012 0.000 0.000
#> GSM674375     3  0.2664      0.717 0.000 0.000 0.816 0.184 0.000 0.000
#> GSM674379     3  0.2941      0.669 0.000 0.000 0.780 0.220 0.000 0.000
#> GSM674380     3  0.1863      0.773 0.000 0.000 0.896 0.104 0.000 0.000
#> GSM674381     3  0.1204      0.836 0.000 0.000 0.944 0.056 0.000 0.000
#> GSM674382     3  0.3244      0.584 0.000 0.000 0.732 0.268 0.000 0.000
#> GSM674384     3  0.2003      0.800 0.000 0.000 0.884 0.116 0.000 0.000
#> GSM674385     3  0.1910      0.769 0.000 0.000 0.892 0.108 0.000 0.000
#> GSM674388     3  0.0146      0.847 0.000 0.000 0.996 0.004 0.000 0.000
#> GSM674389     3  0.3101      0.630 0.000 0.000 0.756 0.244 0.000 0.000
#> GSM674390     3  0.0260      0.847 0.000 0.000 0.992 0.008 0.000 0.000
#> GSM674391     3  0.3371      0.533 0.000 0.000 0.708 0.292 0.000 0.000
#> GSM674393     3  0.2048      0.788 0.000 0.000 0.880 0.120 0.000 0.000
#> GSM674394     3  0.1387      0.811 0.000 0.000 0.932 0.068 0.000 0.000
#> GSM674395     3  0.1327      0.831 0.000 0.000 0.936 0.064 0.000 0.000
#> GSM674397     3  0.0146      0.846 0.000 0.000 0.996 0.004 0.000 0.000
#> GSM674398     3  0.3620      0.370 0.000 0.000 0.648 0.352 0.000 0.000
#> GSM674400     4  0.3309      0.786 0.000 0.000 0.280 0.720 0.000 0.000
#> GSM674401     4  0.2941      0.762 0.000 0.000 0.220 0.780 0.000 0.000
#> GSM674402     4  0.3198      0.674 0.000 0.000 0.260 0.740 0.000 0.000
#> GSM674403     4  0.3050      0.775 0.000 0.000 0.236 0.764 0.000 0.000
#> GSM674405     4  0.3695      0.657 0.000 0.000 0.376 0.624 0.000 0.000
#> GSM674406     3  0.1267      0.832 0.000 0.000 0.940 0.060 0.000 0.000
#> GSM674407     3  0.2996      0.657 0.000 0.000 0.772 0.228 0.000 0.000
#> GSM674181     2  0.0146      0.949 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674183     2  0.2581      0.893 0.000 0.856 0.000 0.016 0.000 0.128
#> GSM674184     2  0.3108      0.893 0.000 0.828 0.000 0.044 0.000 0.128
#> GSM674185     2  0.1398      0.939 0.000 0.940 0.000 0.052 0.000 0.008
#> GSM674186     2  0.2048      0.909 0.000 0.880 0.000 0.000 0.000 0.120
#> GSM674187     2  0.1814      0.922 0.000 0.900 0.000 0.000 0.000 0.100
#> GSM674190     2  0.1010      0.947 0.000 0.960 0.000 0.004 0.000 0.036
#> GSM674191     2  0.1007      0.945 0.000 0.956 0.000 0.000 0.000 0.044
#> GSM674192     2  0.0935      0.947 0.000 0.964 0.000 0.004 0.000 0.032
#> GSM674193     2  0.0363      0.948 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM674194     2  0.2445      0.915 0.000 0.872 0.000 0.020 0.000 0.108
#> GSM674195     2  0.3270      0.884 0.000 0.820 0.000 0.060 0.000 0.120
#> GSM674198     2  0.0260      0.948 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674200     2  0.2667      0.890 0.000 0.852 0.000 0.020 0.000 0.128
#> GSM674201     2  0.1327      0.939 0.000 0.936 0.000 0.000 0.000 0.064
#> GSM674202     2  0.1225      0.943 0.000 0.952 0.000 0.036 0.000 0.012
#> GSM674203     2  0.0972      0.944 0.000 0.964 0.000 0.008 0.000 0.028
#> GSM674204     2  0.2019      0.922 0.000 0.900 0.000 0.012 0.000 0.088
#> GSM674205     2  0.0713      0.947 0.000 0.972 0.000 0.000 0.000 0.028
#> GSM674206     2  0.0508      0.949 0.000 0.984 0.000 0.004 0.000 0.012
#> GSM674208     2  0.1168      0.943 0.000 0.956 0.000 0.016 0.000 0.028
#> GSM674209     2  0.0820      0.950 0.000 0.972 0.000 0.012 0.000 0.016
#> GSM674210     2  0.0260      0.948 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674212     2  0.0972      0.948 0.000 0.964 0.000 0.008 0.000 0.028
#> GSM674214     2  0.0000      0.948 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674218     2  0.2402      0.905 0.000 0.868 0.000 0.012 0.000 0.120
#> GSM674219     2  0.0000      0.948 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674220     2  0.2106      0.923 0.000 0.904 0.000 0.064 0.000 0.032
#> GSM674221     2  0.1007      0.945 0.000 0.956 0.000 0.000 0.000 0.044
#> GSM674223     2  0.1957      0.911 0.000 0.888 0.000 0.000 0.000 0.112
#> GSM674225     2  0.2237      0.919 0.000 0.896 0.000 0.068 0.000 0.036
#> GSM674226     2  0.1644      0.935 0.000 0.932 0.000 0.040 0.000 0.028
#> GSM674229     2  0.0891      0.945 0.000 0.968 0.000 0.008 0.000 0.024
#> GSM674230     2  0.1845      0.930 0.000 0.920 0.000 0.052 0.000 0.028
#> GSM674231     2  0.0146      0.948 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM674232     2  0.0713      0.945 0.000 0.972 0.000 0.000 0.000 0.028
#> GSM674234     2  0.0937      0.945 0.000 0.960 0.000 0.000 0.000 0.040
#> GSM674235     2  0.0909      0.946 0.000 0.968 0.000 0.012 0.000 0.020
#> GSM674236     2  0.1780      0.932 0.000 0.924 0.000 0.048 0.000 0.028
#> GSM674237     2  0.0972      0.944 0.000 0.964 0.000 0.008 0.000 0.028
#> GSM674239     2  0.0972      0.944 0.000 0.964 0.000 0.008 0.000 0.028
#> GSM674240     2  0.0632      0.949 0.000 0.976 0.000 0.000 0.000 0.024
#> GSM674242     2  0.0972      0.944 0.000 0.964 0.000 0.008 0.000 0.028
#> GSM674243     2  0.2730      0.898 0.000 0.836 0.000 0.012 0.000 0.152
#> GSM674244     2  0.2237      0.919 0.000 0.896 0.000 0.068 0.000 0.036
#> GSM674245     2  0.1713      0.934 0.000 0.928 0.000 0.044 0.000 0.028
#> GSM674282     1  0.0713      0.780 0.972 0.000 0.000 0.000 0.028 0.000
#> GSM674284     1  0.3202      0.779 0.800 0.000 0.000 0.000 0.176 0.024
#> GSM674285     1  0.1194      0.752 0.956 0.000 0.000 0.008 0.004 0.032
#> GSM674287     1  0.3098      0.783 0.812 0.000 0.000 0.000 0.164 0.024
#> GSM674288     5  0.4952     -0.156 0.408 0.000 0.000 0.000 0.524 0.068
#> GSM674289     1  0.0547      0.777 0.980 0.000 0.000 0.000 0.020 0.000
#> GSM674290     1  0.1584      0.728 0.928 0.000 0.000 0.008 0.000 0.064
#> GSM674291     1  0.1643      0.726 0.924 0.000 0.000 0.008 0.000 0.068
#> GSM674292     1  0.1643      0.726 0.924 0.000 0.000 0.008 0.000 0.068
#> GSM674295     5  0.2979      0.474 0.116 0.000 0.000 0.000 0.840 0.044
#> GSM674297     1  0.3098      0.783 0.812 0.000 0.000 0.000 0.164 0.024
#> GSM674298     1  0.2744      0.787 0.840 0.000 0.000 0.000 0.144 0.016
#> GSM674299     1  0.3245      0.779 0.800 0.000 0.000 0.000 0.172 0.028
#> GSM674300     6  0.6234      0.871 0.128 0.000 0.000 0.048 0.316 0.508
#> GSM674301     1  0.1584      0.728 0.928 0.000 0.000 0.008 0.000 0.064
#> GSM674302     1  0.1584      0.728 0.928 0.000 0.000 0.008 0.000 0.064
#> GSM674304     1  0.1398      0.737 0.940 0.000 0.000 0.008 0.000 0.052
#> GSM674305     1  0.0508      0.763 0.984 0.000 0.000 0.004 0.000 0.012
#> GSM674306     6  0.6307      0.876 0.144 0.000 0.000 0.048 0.300 0.508
#> GSM674308     1  0.1866      0.715 0.908 0.000 0.000 0.008 0.000 0.084
#> GSM674309     1  0.3925      0.735 0.724 0.000 0.000 0.000 0.236 0.040
#> GSM674313     5  0.3706      0.414 0.000 0.000 0.000 0.000 0.620 0.380
#> GSM674314     1  0.4786      0.583 0.584 0.000 0.000 0.000 0.352 0.064
#> GSM674315     6  0.6307      0.876 0.144 0.000 0.000 0.048 0.300 0.508
#> GSM674316     1  0.3934      0.603 0.616 0.000 0.000 0.000 0.376 0.008
#> GSM674318     5  0.3938      0.523 0.016 0.000 0.000 0.000 0.660 0.324
#> GSM674320     5  0.3841      0.578 0.028 0.000 0.000 0.000 0.716 0.256
#> GSM674323     5  0.1957      0.519 0.112 0.000 0.000 0.000 0.888 0.000
#> GSM674324     1  0.3450      0.771 0.780 0.000 0.000 0.000 0.188 0.032
#> GSM674325     1  0.3989      0.422 0.528 0.000 0.000 0.000 0.468 0.004
#> GSM674327     6  0.5392      0.602 0.112 0.000 0.000 0.000 0.436 0.452
#> GSM674328     1  0.3377      0.772 0.784 0.000 0.000 0.000 0.188 0.028
#> GSM674330     1  0.4775      0.589 0.588 0.000 0.000 0.000 0.348 0.064
#> GSM674331     1  0.3450      0.771 0.780 0.000 0.000 0.000 0.188 0.032
#> GSM674332     1  0.4107      0.714 0.700 0.000 0.000 0.000 0.256 0.044
#> GSM674334     1  0.3863      0.722 0.712 0.000 0.000 0.000 0.260 0.028
#> GSM674335     1  0.4238      0.472 0.540 0.000 0.000 0.000 0.444 0.016
#> GSM674345     3  0.3727     -0.121 0.000 0.000 0.612 0.388 0.000 0.000
#> GSM674351     3  0.0458      0.846 0.000 0.000 0.984 0.016 0.000 0.000
#> GSM674352     3  0.0146      0.848 0.000 0.000 0.996 0.004 0.000 0.000
#> GSM674359     3  0.0632      0.842 0.000 0.000 0.976 0.024 0.000 0.000
#> GSM674360     3  0.1910      0.769 0.000 0.000 0.892 0.108 0.000 0.000
#> GSM674362     3  0.1910      0.769 0.000 0.000 0.892 0.108 0.000 0.000
#> GSM674369     3  0.0547      0.844 0.000 0.000 0.980 0.020 0.000 0.000
#> GSM674372     3  0.1863      0.802 0.000 0.000 0.896 0.104 0.000 0.000
#> GSM674374     3  0.0000      0.847 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM674376     3  0.3390      0.532 0.000 0.000 0.704 0.296 0.000 0.000
#> GSM674377     3  0.1141      0.824 0.000 0.000 0.948 0.052 0.000 0.000
#> GSM674378     3  0.0937      0.842 0.000 0.000 0.960 0.040 0.000 0.000
#> GSM674383     3  0.0547      0.843 0.000 0.000 0.980 0.020 0.000 0.000
#> GSM674386     3  0.2883      0.689 0.000 0.000 0.788 0.212 0.000 0.000
#> GSM674387     3  0.3446      0.494 0.000 0.000 0.692 0.308 0.000 0.000
#> GSM674392     3  0.1204      0.834 0.000 0.000 0.944 0.056 0.000 0.000
#> GSM674396     3  0.3351      0.542 0.000 0.000 0.712 0.288 0.000 0.000
#> GSM674399     3  0.3351      0.542 0.000 0.000 0.712 0.288 0.000 0.000
#> GSM674404     3  0.3076      0.637 0.000 0.000 0.760 0.240 0.000 0.000
#> GSM674182     2  0.0363      0.948 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM674188     2  0.0935      0.947 0.000 0.964 0.000 0.004 0.000 0.032
#> GSM674189     2  0.2858      0.897 0.000 0.844 0.000 0.032 0.000 0.124
#> GSM674196     2  0.1970      0.921 0.000 0.900 0.000 0.008 0.000 0.092
#> GSM674197     2  0.0692      0.949 0.000 0.976 0.000 0.004 0.000 0.020
#> GSM674199     2  0.0000      0.948 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674207     2  0.1267      0.939 0.000 0.940 0.000 0.000 0.000 0.060
#> GSM674211     2  0.0865      0.946 0.000 0.964 0.000 0.000 0.000 0.036
#> GSM674213     2  0.0363      0.948 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM674215     2  0.1984      0.926 0.000 0.912 0.000 0.056 0.000 0.032
#> GSM674216     2  0.1908      0.928 0.000 0.916 0.000 0.056 0.000 0.028
#> GSM674217     2  0.1267      0.940 0.000 0.940 0.000 0.000 0.000 0.060
#> GSM674222     2  0.1970      0.926 0.000 0.912 0.000 0.060 0.000 0.028
#> GSM674224     2  0.0713      0.945 0.000 0.972 0.000 0.000 0.000 0.028
#> GSM674227     2  0.2046      0.925 0.000 0.908 0.000 0.060 0.000 0.032
#> GSM674228     2  0.0713      0.945 0.000 0.972 0.000 0.000 0.000 0.028
#> GSM674233     2  0.0865      0.946 0.000 0.964 0.000 0.000 0.000 0.036
#> GSM674238     2  0.3384      0.877 0.000 0.812 0.000 0.068 0.000 0.120
#> GSM674241     2  0.0909      0.946 0.000 0.968 0.000 0.012 0.000 0.020
#> GSM674283     1  0.0632      0.778 0.976 0.000 0.000 0.000 0.024 0.000
#> GSM674286     1  0.0632      0.778 0.976 0.000 0.000 0.000 0.024 0.000
#> GSM674293     1  0.6084     -0.550 0.420 0.000 0.000 0.008 0.196 0.376
#> GSM674294     1  0.1036      0.761 0.964 0.000 0.000 0.004 0.008 0.024
#> GSM674296     1  0.1584      0.728 0.928 0.000 0.000 0.008 0.000 0.064
#> GSM674303     1  0.3168      0.780 0.804 0.000 0.000 0.000 0.172 0.024
#> GSM674307     1  0.0790      0.780 0.968 0.000 0.000 0.000 0.032 0.000
#> GSM674310     5  0.3852      0.518 0.012 0.000 0.000 0.000 0.664 0.324
#> GSM674311     1  0.3738      0.756 0.752 0.000 0.000 0.000 0.208 0.040
#> GSM674312     5  0.3993      0.550 0.024 0.000 0.000 0.000 0.676 0.300
#> GSM674317     1  0.2558      0.787 0.868 0.000 0.000 0.000 0.104 0.028
#> GSM674319     5  0.3046      0.412 0.188 0.000 0.000 0.000 0.800 0.012
#> GSM674321     5  0.2100      0.522 0.112 0.000 0.000 0.000 0.884 0.004
#> GSM674322     5  0.3920      0.610 0.088 0.000 0.000 0.000 0.764 0.148
#> GSM674326     5  0.3652      0.538 0.016 0.000 0.000 0.000 0.720 0.264
#> GSM674329     5  0.3616      0.608 0.076 0.000 0.000 0.000 0.792 0.132
#> GSM674333     5  0.3637      0.601 0.084 0.000 0.000 0.000 0.792 0.124

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-CV-mclust-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-CV-mclust-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-CV-mclust-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-CV-mclust-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-CV-mclust-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-CV-mclust-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-CV-mclust-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-CV-mclust-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-CV-mclust-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-CV-mclust-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-CV-mclust-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-CV-mclust-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-CV-mclust-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-CV-mclust-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-CV-mclust-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-CV-mclust-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-CV-mclust-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-CV-mclust-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-CV-mclust-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-CV-mclust-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk CV-mclust-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-CV-mclust-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-CV-mclust-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-CV-mclust-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-CV-mclust-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-CV-mclust-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk CV-mclust-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>             n disease.state(p) specimen(p) k
#> CV:mclust 183           0.9238    1.83e-40 2
#> CV:mclust 183           0.9620    6.15e-78 3
#> CV:mclust 177           0.5875    2.14e-73 4
#> CV:mclust 150           0.5483    8.18e-62 5
#> CV:mclust 172           0.0333    7.47e-68 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


CV:NMF*

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["CV", "NMF"]
# you can also extract it by
# res = res_list["CV:NMF"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#>   Subgroups are detected by 'NMF' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 4.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk CV-NMF-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk CV-NMF-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 1.000           0.999       0.991         0.5819 0.750   0.571
#> 4 4 0.927           0.902       0.937         0.0569 0.968   0.904
#> 5 5 0.863           0.844       0.903         0.0471 0.959   0.865
#> 6 6 0.805           0.816       0.884         0.0349 0.993   0.973

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3

There is also optional best \(k\) = 2 3 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette p1    p2    p3
#> GSM674344     3   0.153      0.984  0 0.040 0.960
#> GSM674346     3   0.103      0.998  0 0.024 0.976
#> GSM674347     3   0.103      0.998  0 0.024 0.976
#> GSM674348     3   0.103      0.998  0 0.024 0.976
#> GSM674349     3   0.103      0.998  0 0.024 0.976
#> GSM674350     3   0.103      0.998  0 0.024 0.976
#> GSM674353     3   0.103      0.998  0 0.024 0.976
#> GSM674354     3   0.103      0.998  0 0.024 0.976
#> GSM674355     3   0.103      0.998  0 0.024 0.976
#> GSM674356     3   0.103      0.998  0 0.024 0.976
#> GSM674357     3   0.103      0.998  0 0.024 0.976
#> GSM674358     3   0.103      0.998  0 0.024 0.976
#> GSM674361     3   0.103      0.998  0 0.024 0.976
#> GSM674363     3   0.103      0.998  0 0.024 0.976
#> GSM674364     3   0.103      0.998  0 0.024 0.976
#> GSM674365     3   0.103      0.998  0 0.024 0.976
#> GSM674366     3   0.103      0.998  0 0.024 0.976
#> GSM674367     3   0.103      0.998  0 0.024 0.976
#> GSM674368     3   0.116      0.994  0 0.028 0.972
#> GSM674370     3   0.103      0.998  0 0.024 0.976
#> GSM674371     3   0.103      0.998  0 0.024 0.976
#> GSM674373     3   0.103      0.998  0 0.024 0.976
#> GSM674375     3   0.103      0.998  0 0.024 0.976
#> GSM674379     3   0.103      0.998  0 0.024 0.976
#> GSM674380     3   0.141      0.987  0 0.036 0.964
#> GSM674381     3   0.103      0.998  0 0.024 0.976
#> GSM674382     3   0.103      0.998  0 0.024 0.976
#> GSM674384     3   0.103      0.998  0 0.024 0.976
#> GSM674385     3   0.164      0.980  0 0.044 0.956
#> GSM674388     3   0.103      0.998  0 0.024 0.976
#> GSM674389     3   0.103      0.998  0 0.024 0.976
#> GSM674390     3   0.103      0.998  0 0.024 0.976
#> GSM674391     3   0.103      0.998  0 0.024 0.976
#> GSM674393     3   0.103      0.998  0 0.024 0.976
#> GSM674394     3   0.103      0.998  0 0.024 0.976
#> GSM674395     3   0.103      0.998  0 0.024 0.976
#> GSM674397     3   0.103      0.998  0 0.024 0.976
#> GSM674398     3   0.103      0.998  0 0.024 0.976
#> GSM674400     3   0.103      0.998  0 0.024 0.976
#> GSM674401     3   0.103      0.998  0 0.024 0.976
#> GSM674402     3   0.103      0.998  0 0.024 0.976
#> GSM674403     3   0.103      0.998  0 0.024 0.976
#> GSM674405     3   0.103      0.998  0 0.024 0.976
#> GSM674406     3   0.103      0.998  0 0.024 0.976
#> GSM674407     3   0.103      0.998  0 0.024 0.976
#> GSM674181     2   0.000      1.000  0 1.000 0.000
#> GSM674183     2   0.000      1.000  0 1.000 0.000
#> GSM674184     2   0.000      1.000  0 1.000 0.000
#> GSM674185     2   0.000      1.000  0 1.000 0.000
#> GSM674186     2   0.000      1.000  0 1.000 0.000
#> GSM674187     2   0.000      1.000  0 1.000 0.000
#> GSM674190     2   0.000      1.000  0 1.000 0.000
#> GSM674191     2   0.000      1.000  0 1.000 0.000
#> GSM674192     2   0.000      1.000  0 1.000 0.000
#> GSM674193     2   0.000      1.000  0 1.000 0.000
#> GSM674194     2   0.000      1.000  0 1.000 0.000
#> GSM674195     2   0.000      1.000  0 1.000 0.000
#> GSM674198     2   0.000      1.000  0 1.000 0.000
#> GSM674200     2   0.000      1.000  0 1.000 0.000
#> GSM674201     2   0.000      1.000  0 1.000 0.000
#> GSM674202     2   0.000      1.000  0 1.000 0.000
#> GSM674203     2   0.000      1.000  0 1.000 0.000
#> GSM674204     2   0.000      1.000  0 1.000 0.000
#> GSM674205     2   0.000      1.000  0 1.000 0.000
#> GSM674206     2   0.000      1.000  0 1.000 0.000
#> GSM674208     2   0.000      1.000  0 1.000 0.000
#> GSM674209     2   0.000      1.000  0 1.000 0.000
#> GSM674210     2   0.000      1.000  0 1.000 0.000
#> GSM674212     2   0.000      1.000  0 1.000 0.000
#> GSM674214     2   0.000      1.000  0 1.000 0.000
#> GSM674218     2   0.000      1.000  0 1.000 0.000
#> GSM674219     2   0.000      1.000  0 1.000 0.000
#> GSM674220     2   0.000      1.000  0 1.000 0.000
#> GSM674221     2   0.000      1.000  0 1.000 0.000
#> GSM674223     2   0.000      1.000  0 1.000 0.000
#> GSM674225     2   0.000      1.000  0 1.000 0.000
#> GSM674226     2   0.000      1.000  0 1.000 0.000
#> GSM674229     2   0.000      1.000  0 1.000 0.000
#> GSM674230     2   0.000      1.000  0 1.000 0.000
#> GSM674231     2   0.000      1.000  0 1.000 0.000
#> GSM674232     2   0.000      1.000  0 1.000 0.000
#> GSM674234     2   0.000      1.000  0 1.000 0.000
#> GSM674235     2   0.000      1.000  0 1.000 0.000
#> GSM674236     2   0.000      1.000  0 1.000 0.000
#> GSM674237     2   0.000      1.000  0 1.000 0.000
#> GSM674239     2   0.000      1.000  0 1.000 0.000
#> GSM674240     2   0.000      1.000  0 1.000 0.000
#> GSM674242     2   0.000      1.000  0 1.000 0.000
#> GSM674243     2   0.000      1.000  0 1.000 0.000
#> GSM674244     2   0.000      1.000  0 1.000 0.000
#> GSM674245     2   0.000      1.000  0 1.000 0.000
#> GSM674282     1   0.000      1.000  1 0.000 0.000
#> GSM674284     1   0.000      1.000  1 0.000 0.000
#> GSM674285     1   0.000      1.000  1 0.000 0.000
#> GSM674287     1   0.000      1.000  1 0.000 0.000
#> GSM674288     1   0.000      1.000  1 0.000 0.000
#> GSM674289     1   0.000      1.000  1 0.000 0.000
#> GSM674290     1   0.000      1.000  1 0.000 0.000
#> GSM674291     1   0.000      1.000  1 0.000 0.000
#> GSM674292     1   0.000      1.000  1 0.000 0.000
#> GSM674295     1   0.000      1.000  1 0.000 0.000
#> GSM674297     1   0.000      1.000  1 0.000 0.000
#> GSM674298     1   0.000      1.000  1 0.000 0.000
#> GSM674299     1   0.000      1.000  1 0.000 0.000
#> GSM674300     1   0.000      1.000  1 0.000 0.000
#> GSM674301     1   0.000      1.000  1 0.000 0.000
#> GSM674302     1   0.000      1.000  1 0.000 0.000
#> GSM674304     1   0.000      1.000  1 0.000 0.000
#> GSM674305     1   0.000      1.000  1 0.000 0.000
#> GSM674306     1   0.000      1.000  1 0.000 0.000
#> GSM674308     1   0.000      1.000  1 0.000 0.000
#> GSM674309     1   0.000      1.000  1 0.000 0.000
#> GSM674313     1   0.000      1.000  1 0.000 0.000
#> GSM674314     1   0.000      1.000  1 0.000 0.000
#> GSM674315     1   0.000      1.000  1 0.000 0.000
#> GSM674316     1   0.000      1.000  1 0.000 0.000
#> GSM674318     1   0.000      1.000  1 0.000 0.000
#> GSM674320     1   0.000      1.000  1 0.000 0.000
#> GSM674323     1   0.000      1.000  1 0.000 0.000
#> GSM674324     1   0.000      1.000  1 0.000 0.000
#> GSM674325     1   0.000      1.000  1 0.000 0.000
#> GSM674327     1   0.000      1.000  1 0.000 0.000
#> GSM674328     1   0.000      1.000  1 0.000 0.000
#> GSM674330     1   0.000      1.000  1 0.000 0.000
#> GSM674331     1   0.000      1.000  1 0.000 0.000
#> GSM674332     1   0.000      1.000  1 0.000 0.000
#> GSM674334     1   0.000      1.000  1 0.000 0.000
#> GSM674335     1   0.000      1.000  1 0.000 0.000
#> GSM674345     3   0.103      0.998  0 0.024 0.976
#> GSM674351     3   0.103      0.998  0 0.024 0.976
#> GSM674352     3   0.103      0.998  0 0.024 0.976
#> GSM674359     3   0.103      0.998  0 0.024 0.976
#> GSM674360     3   0.175      0.976  0 0.048 0.952
#> GSM674362     3   0.236      0.950  0 0.072 0.928
#> GSM674369     3   0.103      0.998  0 0.024 0.976
#> GSM674372     3   0.103      0.998  0 0.024 0.976
#> GSM674374     3   0.103      0.998  0 0.024 0.976
#> GSM674376     3   0.103      0.998  0 0.024 0.976
#> GSM674377     3   0.103      0.998  0 0.024 0.976
#> GSM674378     3   0.103      0.998  0 0.024 0.976
#> GSM674383     3   0.103      0.998  0 0.024 0.976
#> GSM674386     3   0.103      0.998  0 0.024 0.976
#> GSM674387     3   0.103      0.998  0 0.024 0.976
#> GSM674392     3   0.103      0.998  0 0.024 0.976
#> GSM674396     3   0.103      0.998  0 0.024 0.976
#> GSM674399     3   0.103      0.998  0 0.024 0.976
#> GSM674404     3   0.103      0.998  0 0.024 0.976
#> GSM674182     2   0.000      1.000  0 1.000 0.000
#> GSM674188     2   0.000      1.000  0 1.000 0.000
#> GSM674189     2   0.000      1.000  0 1.000 0.000
#> GSM674196     2   0.000      1.000  0 1.000 0.000
#> GSM674197     2   0.000      1.000  0 1.000 0.000
#> GSM674199     2   0.000      1.000  0 1.000 0.000
#> GSM674207     2   0.000      1.000  0 1.000 0.000
#> GSM674211     2   0.000      1.000  0 1.000 0.000
#> GSM674213     2   0.000      1.000  0 1.000 0.000
#> GSM674215     2   0.000      1.000  0 1.000 0.000
#> GSM674216     2   0.000      1.000  0 1.000 0.000
#> GSM674217     2   0.000      1.000  0 1.000 0.000
#> GSM674222     2   0.000      1.000  0 1.000 0.000
#> GSM674224     2   0.000      1.000  0 1.000 0.000
#> GSM674227     2   0.000      1.000  0 1.000 0.000
#> GSM674228     2   0.000      1.000  0 1.000 0.000
#> GSM674233     2   0.000      1.000  0 1.000 0.000
#> GSM674238     2   0.000      1.000  0 1.000 0.000
#> GSM674241     2   0.000      1.000  0 1.000 0.000
#> GSM674283     1   0.000      1.000  1 0.000 0.000
#> GSM674286     1   0.000      1.000  1 0.000 0.000
#> GSM674293     1   0.000      1.000  1 0.000 0.000
#> GSM674294     1   0.000      1.000  1 0.000 0.000
#> GSM674296     1   0.000      1.000  1 0.000 0.000
#> GSM674303     1   0.000      1.000  1 0.000 0.000
#> GSM674307     1   0.000      1.000  1 0.000 0.000
#> GSM674310     1   0.000      1.000  1 0.000 0.000
#> GSM674311     1   0.000      1.000  1 0.000 0.000
#> GSM674312     1   0.000      1.000  1 0.000 0.000
#> GSM674317     1   0.000      1.000  1 0.000 0.000
#> GSM674319     1   0.000      1.000  1 0.000 0.000
#> GSM674321     1   0.000      1.000  1 0.000 0.000
#> GSM674322     1   0.000      1.000  1 0.000 0.000
#> GSM674326     1   0.000      1.000  1 0.000 0.000
#> GSM674329     1   0.000      1.000  1 0.000 0.000
#> GSM674333     1   0.000      1.000  1 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1    p2    p3    p4
#> GSM674344     3  0.4164      0.761 0.000 0.000 0.736 0.264
#> GSM674346     3  0.3356      0.853 0.000 0.000 0.824 0.176
#> GSM674347     3  0.0000      0.977 0.000 0.000 1.000 0.000
#> GSM674348     3  0.1716      0.946 0.000 0.000 0.936 0.064
#> GSM674349     3  0.0707      0.971 0.000 0.000 0.980 0.020
#> GSM674350     3  0.0592      0.973 0.000 0.000 0.984 0.016
#> GSM674353     3  0.1022      0.965 0.000 0.000 0.968 0.032
#> GSM674354     3  0.2704      0.899 0.000 0.000 0.876 0.124
#> GSM674355     3  0.0188      0.976 0.000 0.000 0.996 0.004
#> GSM674356     3  0.1792      0.943 0.000 0.000 0.932 0.068
#> GSM674357     3  0.2760      0.897 0.000 0.000 0.872 0.128
#> GSM674358     3  0.0469      0.974 0.000 0.000 0.988 0.012
#> GSM674361     3  0.0000      0.977 0.000 0.000 1.000 0.000
#> GSM674363     3  0.0707      0.971 0.000 0.000 0.980 0.020
#> GSM674364     3  0.0000      0.977 0.000 0.000 1.000 0.000
#> GSM674365     3  0.0188      0.976 0.000 0.000 0.996 0.004
#> GSM674366     3  0.0000      0.977 0.000 0.000 1.000 0.000
#> GSM674367     3  0.0000      0.977 0.000 0.000 1.000 0.000
#> GSM674368     3  0.1474      0.954 0.000 0.000 0.948 0.052
#> GSM674370     3  0.0000      0.977 0.000 0.000 1.000 0.000
#> GSM674371     3  0.0592      0.972 0.000 0.000 0.984 0.016
#> GSM674373     3  0.0000      0.977 0.000 0.000 1.000 0.000
#> GSM674375     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674379     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674380     3  0.0707      0.970 0.000 0.000 0.980 0.020
#> GSM674381     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674382     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674384     3  0.0336      0.976 0.000 0.000 0.992 0.008
#> GSM674385     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674388     3  0.0000      0.977 0.000 0.000 1.000 0.000
#> GSM674389     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674390     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674391     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674393     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674394     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674395     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674397     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674398     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674400     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674401     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674402     3  0.0336      0.976 0.000 0.000 0.992 0.008
#> GSM674403     3  0.0000      0.977 0.000 0.000 1.000 0.000
#> GSM674405     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674406     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674407     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674181     2  0.3444      0.830 0.000 0.816 0.000 0.184
#> GSM674183     2  0.3764      0.796 0.000 0.784 0.000 0.216
#> GSM674184     2  0.0707      0.976 0.000 0.980 0.000 0.020
#> GSM674185     2  0.0592      0.978 0.000 0.984 0.000 0.016
#> GSM674186     2  0.0188      0.983 0.000 0.996 0.000 0.004
#> GSM674187     2  0.0188      0.983 0.000 0.996 0.000 0.004
#> GSM674190     2  0.0188      0.983 0.000 0.996 0.000 0.004
#> GSM674191     2  0.0188      0.983 0.000 0.996 0.000 0.004
#> GSM674192     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674193     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674194     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674195     2  0.3219      0.850 0.000 0.836 0.000 0.164
#> GSM674198     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674200     2  0.3942      0.773 0.000 0.764 0.000 0.236
#> GSM674201     2  0.0336      0.982 0.000 0.992 0.000 0.008
#> GSM674202     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674203     2  0.0188      0.983 0.000 0.996 0.000 0.004
#> GSM674204     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674205     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674206     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674208     2  0.0469      0.980 0.000 0.988 0.000 0.012
#> GSM674209     2  0.0469      0.980 0.000 0.988 0.000 0.012
#> GSM674210     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674212     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674214     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674218     2  0.0188      0.983 0.000 0.996 0.000 0.004
#> GSM674219     2  0.0188      0.983 0.000 0.996 0.000 0.004
#> GSM674220     2  0.0336      0.983 0.000 0.992 0.000 0.008
#> GSM674221     2  0.0188      0.983 0.000 0.996 0.000 0.004
#> GSM674223     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674225     2  0.1022      0.968 0.000 0.968 0.000 0.032
#> GSM674226     2  0.0469      0.980 0.000 0.988 0.000 0.012
#> GSM674229     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674230     2  0.0188      0.983 0.000 0.996 0.000 0.004
#> GSM674231     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674232     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674234     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674235     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674236     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674237     2  0.0469      0.980 0.000 0.988 0.000 0.012
#> GSM674239     2  0.0188      0.983 0.000 0.996 0.000 0.004
#> GSM674240     2  0.0336      0.982 0.000 0.992 0.000 0.008
#> GSM674242     2  0.0336      0.982 0.000 0.992 0.000 0.008
#> GSM674243     2  0.0336      0.982 0.000 0.992 0.000 0.008
#> GSM674244     2  0.1022      0.968 0.000 0.968 0.000 0.032
#> GSM674245     2  0.0336      0.982 0.000 0.992 0.000 0.008
#> GSM674282     1  0.0000      0.849 1.000 0.000 0.000 0.000
#> GSM674284     1  0.1211      0.836 0.960 0.000 0.000 0.040
#> GSM674285     1  0.0000      0.849 1.000 0.000 0.000 0.000
#> GSM674287     1  0.1211      0.836 0.960 0.000 0.000 0.040
#> GSM674288     1  0.3444      0.651 0.816 0.000 0.000 0.184
#> GSM674289     1  0.0000      0.849 1.000 0.000 0.000 0.000
#> GSM674290     1  0.0000      0.849 1.000 0.000 0.000 0.000
#> GSM674291     1  0.0000      0.849 1.000 0.000 0.000 0.000
#> GSM674292     1  0.0000      0.849 1.000 0.000 0.000 0.000
#> GSM674295     1  0.4866     -0.360 0.596 0.000 0.000 0.404
#> GSM674297     1  0.0188      0.849 0.996 0.000 0.000 0.004
#> GSM674298     1  0.0188      0.849 0.996 0.000 0.000 0.004
#> GSM674299     1  0.2011      0.807 0.920 0.000 0.000 0.080
#> GSM674300     1  0.1792      0.817 0.932 0.000 0.000 0.068
#> GSM674301     1  0.0000      0.849 1.000 0.000 0.000 0.000
#> GSM674302     1  0.0000      0.849 1.000 0.000 0.000 0.000
#> GSM674304     1  0.0000      0.849 1.000 0.000 0.000 0.000
#> GSM674305     1  0.0000      0.849 1.000 0.000 0.000 0.000
#> GSM674306     1  0.0000      0.849 1.000 0.000 0.000 0.000
#> GSM674308     1  0.0000      0.849 1.000 0.000 0.000 0.000
#> GSM674309     1  0.3074      0.717 0.848 0.000 0.000 0.152
#> GSM674313     4  0.4746      0.925 0.368 0.000 0.000 0.632
#> GSM674314     1  0.3764      0.570 0.784 0.000 0.000 0.216
#> GSM674315     1  0.0000      0.849 1.000 0.000 0.000 0.000
#> GSM674316     1  0.4830     -0.295 0.608 0.000 0.000 0.392
#> GSM674318     4  0.4730      0.922 0.364 0.000 0.000 0.636
#> GSM674320     4  0.4713      0.917 0.360 0.000 0.000 0.640
#> GSM674323     4  0.4999      0.742 0.492 0.000 0.000 0.508
#> GSM674324     1  0.2704      0.758 0.876 0.000 0.000 0.124
#> GSM674325     4  0.4955      0.856 0.444 0.000 0.000 0.556
#> GSM674327     1  0.3172      0.702 0.840 0.000 0.000 0.160
#> GSM674328     1  0.1389      0.831 0.952 0.000 0.000 0.048
#> GSM674330     1  0.4331      0.311 0.712 0.000 0.000 0.288
#> GSM674331     1  0.2704      0.758 0.876 0.000 0.000 0.124
#> GSM674332     1  0.2868      0.742 0.864 0.000 0.000 0.136
#> GSM674334     1  0.4304      0.329 0.716 0.000 0.000 0.284
#> GSM674335     1  0.4888     -0.399 0.588 0.000 0.000 0.412
#> GSM674345     3  0.1637      0.948 0.000 0.000 0.940 0.060
#> GSM674351     3  0.1022      0.965 0.000 0.000 0.968 0.032
#> GSM674352     3  0.0921      0.967 0.000 0.000 0.972 0.028
#> GSM674359     3  0.4072      0.774 0.000 0.000 0.748 0.252
#> GSM674360     3  0.0657      0.973 0.000 0.004 0.984 0.012
#> GSM674362     3  0.3836      0.845 0.000 0.016 0.816 0.168
#> GSM674369     3  0.0707      0.971 0.000 0.000 0.980 0.020
#> GSM674372     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674374     3  0.0000      0.977 0.000 0.000 1.000 0.000
#> GSM674376     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674377     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674378     3  0.0000      0.977 0.000 0.000 1.000 0.000
#> GSM674383     3  0.0000      0.977 0.000 0.000 1.000 0.000
#> GSM674386     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674387     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674392     3  0.0000      0.977 0.000 0.000 1.000 0.000
#> GSM674396     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674399     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674404     3  0.0188      0.978 0.000 0.000 0.996 0.004
#> GSM674182     2  0.0817      0.973 0.000 0.976 0.000 0.024
#> GSM674188     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674189     2  0.0592      0.978 0.000 0.984 0.000 0.016
#> GSM674196     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674197     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674199     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674207     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674211     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674213     2  0.0188      0.983 0.000 0.996 0.000 0.004
#> GSM674215     2  0.0469      0.982 0.000 0.988 0.000 0.012
#> GSM674216     2  0.0592      0.978 0.000 0.984 0.000 0.016
#> GSM674217     2  0.0336      0.982 0.000 0.992 0.000 0.008
#> GSM674222     2  0.0336      0.982 0.000 0.992 0.000 0.008
#> GSM674224     2  0.0336      0.982 0.000 0.992 0.000 0.008
#> GSM674227     2  0.0336      0.982 0.000 0.992 0.000 0.008
#> GSM674228     2  0.0000      0.984 0.000 1.000 0.000 0.000
#> GSM674233     2  0.0188      0.983 0.000 0.996 0.000 0.004
#> GSM674238     2  0.1637      0.945 0.000 0.940 0.000 0.060
#> GSM674241     2  0.0188      0.983 0.000 0.996 0.000 0.004
#> GSM674283     1  0.0000      0.849 1.000 0.000 0.000 0.000
#> GSM674286     1  0.0000      0.849 1.000 0.000 0.000 0.000
#> GSM674293     1  0.0000      0.849 1.000 0.000 0.000 0.000
#> GSM674294     1  0.0000      0.849 1.000 0.000 0.000 0.000
#> GSM674296     1  0.0000      0.849 1.000 0.000 0.000 0.000
#> GSM674303     1  0.1211      0.836 0.960 0.000 0.000 0.040
#> GSM674307     1  0.0000      0.849 1.000 0.000 0.000 0.000
#> GSM674310     4  0.4730      0.922 0.364 0.000 0.000 0.636
#> GSM674311     1  0.3024      0.723 0.852 0.000 0.000 0.148
#> GSM674312     4  0.4713      0.917 0.360 0.000 0.000 0.640
#> GSM674317     1  0.2081      0.803 0.916 0.000 0.000 0.084
#> GSM674319     4  0.4977      0.827 0.460 0.000 0.000 0.540
#> GSM674321     4  0.4967      0.843 0.452 0.000 0.000 0.548
#> GSM674322     4  0.4746      0.925 0.368 0.000 0.000 0.632
#> GSM674326     4  0.4866      0.903 0.404 0.000 0.000 0.596
#> GSM674329     4  0.4761      0.924 0.372 0.000 0.000 0.628
#> GSM674333     4  0.4761      0.924 0.372 0.000 0.000 0.628

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4    p5
#> GSM674344     5  0.4310     0.2455 0.000 0.004 0.392 0.000 0.604
#> GSM674346     3  0.4331     0.2740 0.000 0.000 0.596 0.004 0.400
#> GSM674347     3  0.0451     0.9287 0.000 0.000 0.988 0.004 0.008
#> GSM674348     3  0.2124     0.8788 0.000 0.000 0.900 0.004 0.096
#> GSM674349     3  0.0865     0.9249 0.000 0.000 0.972 0.004 0.024
#> GSM674350     3  0.1357     0.9126 0.000 0.000 0.948 0.004 0.048
#> GSM674353     3  0.2806     0.8107 0.000 0.000 0.844 0.004 0.152
#> GSM674354     3  0.4375     0.2056 0.000 0.000 0.576 0.004 0.420
#> GSM674355     3  0.0671     0.9277 0.000 0.000 0.980 0.004 0.016
#> GSM674356     3  0.2719     0.8207 0.000 0.000 0.852 0.004 0.144
#> GSM674357     3  0.4251     0.3603 0.000 0.000 0.624 0.004 0.372
#> GSM674358     3  0.1041     0.9214 0.000 0.000 0.964 0.004 0.032
#> GSM674361     3  0.0992     0.9269 0.000 0.000 0.968 0.008 0.024
#> GSM674363     3  0.2563     0.8547 0.000 0.000 0.872 0.008 0.120
#> GSM674364     3  0.1082     0.9255 0.000 0.000 0.964 0.008 0.028
#> GSM674365     3  0.0963     0.9230 0.000 0.000 0.964 0.000 0.036
#> GSM674366     3  0.0451     0.9308 0.000 0.000 0.988 0.008 0.004
#> GSM674367     3  0.0451     0.9308 0.000 0.000 0.988 0.008 0.004
#> GSM674368     3  0.1270     0.9148 0.000 0.000 0.948 0.000 0.052
#> GSM674370     3  0.0451     0.9303 0.000 0.000 0.988 0.008 0.004
#> GSM674371     3  0.0865     0.9263 0.000 0.000 0.972 0.004 0.024
#> GSM674373     3  0.0162     0.9306 0.000 0.000 0.996 0.004 0.000
#> GSM674375     3  0.0671     0.9302 0.000 0.000 0.980 0.004 0.016
#> GSM674379     3  0.1484     0.9180 0.000 0.000 0.944 0.008 0.048
#> GSM674380     3  0.1830     0.9054 0.000 0.000 0.924 0.008 0.068
#> GSM674381     3  0.1557     0.9190 0.000 0.000 0.940 0.008 0.052
#> GSM674382     3  0.1557     0.9159 0.000 0.000 0.940 0.008 0.052
#> GSM674384     3  0.1628     0.9211 0.000 0.000 0.936 0.008 0.056
#> GSM674385     3  0.1168     0.9281 0.000 0.000 0.960 0.008 0.032
#> GSM674388     3  0.0510     0.9288 0.000 0.000 0.984 0.000 0.016
#> GSM674389     3  0.1168     0.9260 0.000 0.000 0.960 0.008 0.032
#> GSM674390     3  0.1041     0.9262 0.000 0.000 0.964 0.004 0.032
#> GSM674391     3  0.1557     0.9159 0.000 0.000 0.940 0.008 0.052
#> GSM674393     3  0.0771     0.9310 0.000 0.000 0.976 0.004 0.020
#> GSM674394     3  0.0404     0.9297 0.000 0.000 0.988 0.000 0.012
#> GSM674395     3  0.0992     0.9298 0.000 0.000 0.968 0.008 0.024
#> GSM674397     3  0.0290     0.9309 0.000 0.000 0.992 0.000 0.008
#> GSM674398     3  0.1845     0.9135 0.000 0.000 0.928 0.016 0.056
#> GSM674400     3  0.0798     0.9297 0.000 0.000 0.976 0.008 0.016
#> GSM674401     3  0.1408     0.9217 0.000 0.000 0.948 0.008 0.044
#> GSM674402     3  0.2439     0.8615 0.000 0.000 0.876 0.004 0.120
#> GSM674403     3  0.0671     0.9285 0.000 0.000 0.980 0.004 0.016
#> GSM674405     3  0.1484     0.9183 0.000 0.000 0.944 0.008 0.048
#> GSM674406     3  0.0898     0.9296 0.000 0.000 0.972 0.008 0.020
#> GSM674407     3  0.1041     0.9262 0.000 0.000 0.964 0.004 0.032
#> GSM674181     5  0.4235     0.3249 0.000 0.424 0.000 0.000 0.576
#> GSM674183     5  0.4161     0.3876 0.000 0.392 0.000 0.000 0.608
#> GSM674184     2  0.3039     0.7874 0.000 0.808 0.000 0.000 0.192
#> GSM674185     2  0.2561     0.8542 0.000 0.856 0.000 0.000 0.144
#> GSM674186     2  0.2011     0.9024 0.000 0.908 0.000 0.004 0.088
#> GSM674187     2  0.2017     0.9101 0.000 0.912 0.000 0.008 0.080
#> GSM674190     2  0.2074     0.8889 0.000 0.896 0.000 0.000 0.104
#> GSM674191     2  0.2179     0.8827 0.000 0.888 0.000 0.000 0.112
#> GSM674192     2  0.0290     0.9339 0.000 0.992 0.000 0.000 0.008
#> GSM674193     2  0.0404     0.9346 0.000 0.988 0.000 0.000 0.012
#> GSM674194     2  0.1908     0.8973 0.000 0.908 0.000 0.000 0.092
#> GSM674195     5  0.4273     0.2740 0.000 0.448 0.000 0.000 0.552
#> GSM674198     2  0.0579     0.9330 0.000 0.984 0.000 0.008 0.008
#> GSM674200     5  0.4430     0.4326 0.000 0.360 0.012 0.000 0.628
#> GSM674201     2  0.2690     0.8349 0.000 0.844 0.000 0.000 0.156
#> GSM674202     2  0.1331     0.9292 0.000 0.952 0.000 0.008 0.040
#> GSM674203     2  0.0898     0.9309 0.000 0.972 0.000 0.008 0.020
#> GSM674204     2  0.0451     0.9333 0.000 0.988 0.000 0.008 0.004
#> GSM674205     2  0.0579     0.9330 0.000 0.984 0.000 0.008 0.008
#> GSM674206     2  0.1430     0.9237 0.000 0.944 0.000 0.004 0.052
#> GSM674208     2  0.0794     0.9296 0.000 0.972 0.000 0.000 0.028
#> GSM674209     2  0.1082     0.9274 0.000 0.964 0.000 0.008 0.028
#> GSM674210     2  0.0992     0.9299 0.000 0.968 0.000 0.008 0.024
#> GSM674212     2  0.1082     0.9308 0.000 0.964 0.000 0.008 0.028
#> GSM674214     2  0.0898     0.9322 0.000 0.972 0.000 0.008 0.020
#> GSM674218     2  0.2864     0.8431 0.000 0.852 0.000 0.012 0.136
#> GSM674219     2  0.2011     0.9037 0.000 0.908 0.000 0.004 0.088
#> GSM674220     2  0.1965     0.9077 0.000 0.904 0.000 0.000 0.096
#> GSM674221     2  0.1894     0.9129 0.000 0.920 0.000 0.008 0.072
#> GSM674223     2  0.0955     0.9312 0.000 0.968 0.000 0.004 0.028
#> GSM674225     2  0.1282     0.9201 0.000 0.952 0.000 0.004 0.044
#> GSM674226     2  0.1082     0.9272 0.000 0.964 0.000 0.008 0.028
#> GSM674229     2  0.0404     0.9329 0.000 0.988 0.000 0.000 0.012
#> GSM674230     2  0.0510     0.9343 0.000 0.984 0.000 0.000 0.016
#> GSM674231     2  0.0671     0.9323 0.000 0.980 0.000 0.004 0.016
#> GSM674232     2  0.0898     0.9309 0.000 0.972 0.000 0.008 0.020
#> GSM674234     2  0.0324     0.9343 0.000 0.992 0.000 0.004 0.004
#> GSM674235     2  0.1082     0.9325 0.000 0.964 0.000 0.008 0.028
#> GSM674236     2  0.0671     0.9347 0.000 0.980 0.000 0.004 0.016
#> GSM674237     2  0.0794     0.9291 0.000 0.972 0.000 0.000 0.028
#> GSM674239     2  0.0609     0.9316 0.000 0.980 0.000 0.000 0.020
#> GSM674240     2  0.2074     0.8873 0.000 0.896 0.000 0.000 0.104
#> GSM674242     2  0.0898     0.9309 0.000 0.972 0.000 0.008 0.020
#> GSM674243     2  0.0992     0.9299 0.000 0.968 0.000 0.008 0.024
#> GSM674244     2  0.1205     0.9252 0.000 0.956 0.000 0.004 0.040
#> GSM674245     2  0.0609     0.9316 0.000 0.980 0.000 0.000 0.020
#> GSM674282     1  0.0290     0.9076 0.992 0.000 0.000 0.000 0.008
#> GSM674284     1  0.1331     0.8910 0.952 0.000 0.000 0.040 0.008
#> GSM674285     1  0.0162     0.9076 0.996 0.000 0.000 0.000 0.004
#> GSM674287     1  0.1168     0.8951 0.960 0.000 0.000 0.032 0.008
#> GSM674288     1  0.4323     0.2774 0.656 0.000 0.000 0.332 0.012
#> GSM674289     1  0.0162     0.9074 0.996 0.000 0.000 0.000 0.004
#> GSM674290     1  0.0290     0.9061 0.992 0.000 0.000 0.000 0.008
#> GSM674291     1  0.0290     0.9061 0.992 0.000 0.000 0.000 0.008
#> GSM674292     1  0.0162     0.9076 0.996 0.000 0.000 0.000 0.004
#> GSM674295     4  0.4464     0.6572 0.408 0.000 0.000 0.584 0.008
#> GSM674297     1  0.0324     0.9069 0.992 0.000 0.000 0.004 0.004
#> GSM674298     1  0.0162     0.9074 0.996 0.000 0.000 0.000 0.004
#> GSM674299     1  0.1768     0.8685 0.924 0.000 0.000 0.072 0.004
#> GSM674300     1  0.1341     0.8829 0.944 0.000 0.000 0.056 0.000
#> GSM674301     1  0.0290     0.9061 0.992 0.000 0.000 0.000 0.008
#> GSM674302     1  0.0290     0.9061 0.992 0.000 0.000 0.000 0.008
#> GSM674304     1  0.0162     0.9076 0.996 0.000 0.000 0.000 0.004
#> GSM674305     1  0.0162     0.9076 0.996 0.000 0.000 0.000 0.004
#> GSM674306     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000
#> GSM674308     1  0.0162     0.9076 0.996 0.000 0.000 0.000 0.004
#> GSM674309     1  0.3123     0.7177 0.812 0.000 0.000 0.184 0.004
#> GSM674313     4  0.2929     0.8567 0.180 0.000 0.000 0.820 0.000
#> GSM674314     1  0.4321    -0.0109 0.600 0.000 0.000 0.396 0.004
#> GSM674315     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000
#> GSM674316     4  0.4268     0.7683 0.344 0.000 0.000 0.648 0.008
#> GSM674318     4  0.2773     0.8483 0.164 0.000 0.000 0.836 0.000
#> GSM674320     4  0.2605     0.8360 0.148 0.000 0.000 0.852 0.000
#> GSM674323     4  0.3861     0.8329 0.284 0.000 0.000 0.712 0.004
#> GSM674324     1  0.2439     0.8160 0.876 0.000 0.000 0.120 0.004
#> GSM674325     4  0.3662     0.8537 0.252 0.000 0.000 0.744 0.004
#> GSM674327     1  0.3550     0.6032 0.760 0.000 0.000 0.236 0.004
#> GSM674328     1  0.1410     0.8798 0.940 0.000 0.000 0.060 0.000
#> GSM674330     4  0.4304     0.4671 0.484 0.000 0.000 0.516 0.000
#> GSM674331     1  0.2536     0.8057 0.868 0.000 0.000 0.128 0.004
#> GSM674332     1  0.3231     0.6968 0.800 0.000 0.000 0.196 0.004
#> GSM674334     4  0.4450     0.4509 0.488 0.000 0.000 0.508 0.004
#> GSM674335     4  0.4182     0.7581 0.352 0.000 0.000 0.644 0.004
#> GSM674345     3  0.1571     0.9060 0.000 0.000 0.936 0.004 0.060
#> GSM674351     3  0.2124     0.8756 0.000 0.000 0.900 0.004 0.096
#> GSM674352     3  0.1831     0.8968 0.000 0.000 0.920 0.004 0.076
#> GSM674359     5  0.4450    -0.0224 0.000 0.000 0.488 0.004 0.508
#> GSM674360     3  0.2179     0.8785 0.000 0.000 0.896 0.004 0.100
#> GSM674362     5  0.5121     0.0584 0.000 0.028 0.468 0.004 0.500
#> GSM674369     3  0.0771     0.9280 0.000 0.000 0.976 0.004 0.020
#> GSM674372     3  0.0771     0.9314 0.000 0.000 0.976 0.004 0.020
#> GSM674374     3  0.0162     0.9306 0.000 0.000 0.996 0.004 0.000
#> GSM674376     3  0.1484     0.9196 0.000 0.000 0.944 0.008 0.048
#> GSM674377     3  0.1830     0.9082 0.000 0.000 0.924 0.008 0.068
#> GSM674378     3  0.0162     0.9306 0.000 0.000 0.996 0.004 0.000
#> GSM674383     3  0.0404     0.9293 0.000 0.000 0.988 0.000 0.012
#> GSM674386     3  0.1697     0.9132 0.000 0.000 0.932 0.008 0.060
#> GSM674387     3  0.1331     0.9218 0.000 0.000 0.952 0.008 0.040
#> GSM674392     3  0.0404     0.9288 0.000 0.000 0.988 0.000 0.012
#> GSM674396     3  0.1740     0.9136 0.000 0.000 0.932 0.012 0.056
#> GSM674399     3  0.1557     0.9159 0.000 0.000 0.940 0.008 0.052
#> GSM674404     3  0.1082     0.9262 0.000 0.000 0.964 0.008 0.028
#> GSM674182     2  0.2516     0.8554 0.000 0.860 0.000 0.000 0.140
#> GSM674188     2  0.1697     0.9203 0.000 0.932 0.000 0.008 0.060
#> GSM674189     2  0.3109     0.7583 0.000 0.800 0.000 0.000 0.200
#> GSM674196     2  0.1331     0.9278 0.000 0.952 0.000 0.008 0.040
#> GSM674197     2  0.0898     0.9322 0.000 0.972 0.000 0.008 0.020
#> GSM674199     2  0.0579     0.9330 0.000 0.984 0.000 0.008 0.008
#> GSM674207     2  0.1444     0.9274 0.000 0.948 0.000 0.012 0.040
#> GSM674211     2  0.0579     0.9331 0.000 0.984 0.000 0.008 0.008
#> GSM674213     2  0.1956     0.9104 0.000 0.916 0.000 0.008 0.076
#> GSM674215     2  0.1478     0.9261 0.000 0.936 0.000 0.000 0.064
#> GSM674216     2  0.0955     0.9281 0.000 0.968 0.000 0.004 0.028
#> GSM674217     2  0.2017     0.9071 0.000 0.912 0.000 0.008 0.080
#> GSM674222     2  0.0671     0.9335 0.000 0.980 0.000 0.004 0.016
#> GSM674224     2  0.0955     0.9309 0.000 0.968 0.000 0.004 0.028
#> GSM674227     2  0.0865     0.9300 0.000 0.972 0.000 0.004 0.024
#> GSM674228     2  0.0290     0.9345 0.000 0.992 0.000 0.000 0.008
#> GSM674233     2  0.1671     0.9137 0.000 0.924 0.000 0.000 0.076
#> GSM674238     2  0.4262     0.0664 0.000 0.560 0.000 0.000 0.440
#> GSM674241     2  0.0703     0.9306 0.000 0.976 0.000 0.000 0.024
#> GSM674283     1  0.0290     0.9076 0.992 0.000 0.000 0.000 0.008
#> GSM674286     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000
#> GSM674293     1  0.0290     0.9061 0.992 0.000 0.000 0.000 0.008
#> GSM674294     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000
#> GSM674296     1  0.0290     0.9061 0.992 0.000 0.000 0.000 0.008
#> GSM674303     1  0.1282     0.8896 0.952 0.000 0.000 0.044 0.004
#> GSM674307     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000
#> GSM674310     4  0.2648     0.8396 0.152 0.000 0.000 0.848 0.000
#> GSM674311     1  0.3010     0.7377 0.824 0.000 0.000 0.172 0.004
#> GSM674312     4  0.2516     0.8277 0.140 0.000 0.000 0.860 0.000
#> GSM674317     1  0.1768     0.8685 0.924 0.000 0.000 0.072 0.004
#> GSM674319     4  0.3561     0.8513 0.260 0.000 0.000 0.740 0.000
#> GSM674321     4  0.3715     0.8509 0.260 0.000 0.000 0.736 0.004
#> GSM674322     4  0.2852     0.8532 0.172 0.000 0.000 0.828 0.000
#> GSM674326     4  0.3424     0.8566 0.240 0.000 0.000 0.760 0.000
#> GSM674329     4  0.2966     0.8575 0.184 0.000 0.000 0.816 0.000
#> GSM674333     4  0.2929     0.8566 0.180 0.000 0.000 0.820 0.000

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3 p4    p5    p6
#> GSM674344     6  0.4238     0.3303 0.000 0.000 0.344 NA 0.000 0.628
#> GSM674346     3  0.4314     0.1837 0.000 0.000 0.536 NA 0.000 0.444
#> GSM674347     3  0.0520     0.9002 0.000 0.000 0.984 NA 0.000 0.008
#> GSM674348     3  0.1663     0.8726 0.000 0.000 0.912 NA 0.000 0.088
#> GSM674349     3  0.0972     0.8988 0.000 0.000 0.964 NA 0.000 0.028
#> GSM674350     3  0.2214     0.8507 0.000 0.000 0.888 NA 0.000 0.096
#> GSM674353     3  0.3665     0.6555 0.000 0.000 0.728 NA 0.000 0.252
#> GSM674354     3  0.4407     0.0174 0.000 0.000 0.492 NA 0.000 0.484
#> GSM674355     3  0.0622     0.8996 0.000 0.000 0.980 NA 0.000 0.012
#> GSM674356     3  0.2805     0.7940 0.000 0.000 0.828 NA 0.000 0.160
#> GSM674357     3  0.4205     0.2716 0.000 0.000 0.564 NA 0.000 0.420
#> GSM674358     3  0.1297     0.8883 0.000 0.000 0.948 NA 0.000 0.040
#> GSM674361     3  0.2461     0.8603 0.000 0.000 0.888 NA 0.004 0.064
#> GSM674363     3  0.3641     0.6902 0.000 0.000 0.748 NA 0.000 0.224
#> GSM674364     3  0.2003     0.8742 0.000 0.000 0.912 NA 0.000 0.044
#> GSM674365     3  0.0692     0.8983 0.000 0.000 0.976 NA 0.000 0.020
#> GSM674366     3  0.0603     0.9019 0.000 0.000 0.980 NA 0.000 0.004
#> GSM674367     3  0.0363     0.9013 0.000 0.000 0.988 NA 0.000 0.000
#> GSM674368     3  0.1462     0.8898 0.000 0.000 0.936 NA 0.000 0.056
#> GSM674370     3  0.0363     0.9021 0.000 0.000 0.988 NA 0.000 0.000
#> GSM674371     3  0.0806     0.8992 0.000 0.000 0.972 NA 0.000 0.020
#> GSM674373     3  0.0632     0.9029 0.000 0.000 0.976 NA 0.000 0.000
#> GSM674375     3  0.0632     0.9013 0.000 0.000 0.976 NA 0.000 0.000
#> GSM674379     3  0.1398     0.8880 0.000 0.000 0.940 NA 0.000 0.008
#> GSM674380     3  0.2070     0.8611 0.000 0.008 0.892 NA 0.000 0.000
#> GSM674381     3  0.0865     0.8990 0.000 0.000 0.964 NA 0.000 0.000
#> GSM674382     3  0.1349     0.8911 0.000 0.000 0.940 NA 0.000 0.004
#> GSM674384     3  0.2631     0.8187 0.000 0.000 0.840 NA 0.000 0.008
#> GSM674385     3  0.3532     0.7819 0.000 0.000 0.796 NA 0.000 0.064
#> GSM674388     3  0.0603     0.9006 0.000 0.000 0.980 NA 0.000 0.016
#> GSM674389     3  0.0632     0.9021 0.000 0.000 0.976 NA 0.000 0.000
#> GSM674390     3  0.0935     0.8969 0.000 0.000 0.964 NA 0.000 0.004
#> GSM674391     3  0.1757     0.8777 0.000 0.000 0.916 NA 0.000 0.008
#> GSM674393     3  0.0405     0.9016 0.000 0.000 0.988 NA 0.000 0.004
#> GSM674394     3  0.0993     0.9012 0.000 0.000 0.964 NA 0.000 0.012
#> GSM674395     3  0.0777     0.9024 0.000 0.000 0.972 NA 0.000 0.004
#> GSM674397     3  0.0458     0.9018 0.000 0.000 0.984 NA 0.000 0.000
#> GSM674398     3  0.2389     0.8466 0.000 0.000 0.864 NA 0.000 0.008
#> GSM674400     3  0.0692     0.9019 0.000 0.000 0.976 NA 0.004 0.000
#> GSM674401     3  0.1296     0.8977 0.000 0.000 0.948 NA 0.004 0.004
#> GSM674402     3  0.4684     0.5401 0.000 0.000 0.656 NA 0.000 0.256
#> GSM674403     3  0.0603     0.8988 0.000 0.000 0.980 NA 0.000 0.016
#> GSM674405     3  0.1462     0.8887 0.000 0.000 0.936 NA 0.000 0.008
#> GSM674406     3  0.0547     0.9004 0.000 0.000 0.980 NA 0.000 0.000
#> GSM674407     3  0.0790     0.8978 0.000 0.000 0.968 NA 0.000 0.000
#> GSM674181     6  0.3898     0.4578 0.000 0.336 0.000 NA 0.000 0.652
#> GSM674183     6  0.3541     0.5636 0.000 0.260 0.000 NA 0.000 0.728
#> GSM674184     2  0.3974     0.6138 0.000 0.680 0.000 NA 0.000 0.296
#> GSM674185     2  0.3699     0.7377 0.000 0.752 0.000 NA 0.000 0.212
#> GSM674186     2  0.2311     0.8523 0.000 0.880 0.000 NA 0.000 0.104
#> GSM674187     2  0.2404     0.8572 0.000 0.884 0.000 NA 0.000 0.080
#> GSM674190     2  0.1663     0.8641 0.000 0.912 0.000 NA 0.000 0.088
#> GSM674191     2  0.2320     0.8358 0.000 0.864 0.000 NA 0.000 0.132
#> GSM674192     2  0.0405     0.8746 0.000 0.988 0.000 NA 0.000 0.008
#> GSM674193     2  0.1616     0.8694 0.000 0.932 0.000 NA 0.000 0.020
#> GSM674194     2  0.1918     0.8625 0.000 0.904 0.000 NA 0.000 0.088
#> GSM674195     6  0.3653     0.5199 0.000 0.300 0.000 NA 0.000 0.692
#> GSM674198     2  0.1219     0.8678 0.000 0.948 0.000 NA 0.000 0.004
#> GSM674200     6  0.3902     0.5876 0.000 0.212 0.012 NA 0.000 0.748
#> GSM674201     2  0.3690     0.6487 0.000 0.700 0.000 NA 0.000 0.288
#> GSM674202     2  0.1845     0.8712 0.000 0.920 0.000 NA 0.000 0.052
#> GSM674203     2  0.1471     0.8663 0.000 0.932 0.000 NA 0.000 0.004
#> GSM674204     2  0.1219     0.8684 0.000 0.948 0.000 NA 0.000 0.004
#> GSM674205     2  0.1124     0.8725 0.000 0.956 0.000 NA 0.000 0.008
#> GSM674206     2  0.3325     0.8295 0.000 0.820 0.000 NA 0.000 0.084
#> GSM674208     2  0.1814     0.8491 0.000 0.900 0.000 NA 0.000 0.000
#> GSM674209     2  0.2613     0.8168 0.000 0.848 0.000 NA 0.000 0.012
#> GSM674210     2  0.1285     0.8695 0.000 0.944 0.000 NA 0.000 0.004
#> GSM674212     2  0.2384     0.8568 0.000 0.888 0.000 NA 0.000 0.048
#> GSM674214     2  0.1895     0.8610 0.000 0.912 0.000 NA 0.000 0.016
#> GSM674218     2  0.5100     0.5165 0.000 0.612 0.000 NA 0.000 0.260
#> GSM674219     2  0.3506     0.7988 0.000 0.792 0.000 NA 0.000 0.156
#> GSM674220     2  0.4214     0.7363 0.000 0.736 0.004 NA 0.000 0.184
#> GSM674221     2  0.3193     0.8276 0.000 0.824 0.000 NA 0.000 0.124
#> GSM674223     2  0.2752     0.8394 0.000 0.856 0.000 NA 0.000 0.036
#> GSM674225     2  0.3798     0.7290 0.000 0.748 0.004 NA 0.000 0.032
#> GSM674226     2  0.2830     0.8152 0.000 0.836 0.000 NA 0.000 0.020
#> GSM674229     2  0.0547     0.8725 0.000 0.980 0.000 NA 0.000 0.000
#> GSM674230     2  0.1934     0.8681 0.000 0.916 0.000 NA 0.000 0.040
#> GSM674231     2  0.2019     0.8497 0.000 0.900 0.000 NA 0.000 0.012
#> GSM674232     2  0.1349     0.8685 0.000 0.940 0.000 NA 0.000 0.004
#> GSM674234     2  0.0777     0.8725 0.000 0.972 0.000 NA 0.000 0.004
#> GSM674235     2  0.1713     0.8719 0.000 0.928 0.000 NA 0.000 0.044
#> GSM674236     2  0.0806     0.8748 0.000 0.972 0.000 NA 0.000 0.020
#> GSM674237     2  0.1610     0.8551 0.000 0.916 0.000 NA 0.000 0.000
#> GSM674239     2  0.1075     0.8658 0.000 0.952 0.000 NA 0.000 0.000
#> GSM674240     2  0.2730     0.8217 0.000 0.836 0.000 NA 0.000 0.152
#> GSM674242     2  0.1349     0.8683 0.000 0.940 0.000 NA 0.000 0.004
#> GSM674243     2  0.2312     0.8367 0.000 0.876 0.000 NA 0.000 0.012
#> GSM674244     2  0.3867     0.7319 0.000 0.744 0.004 NA 0.000 0.036
#> GSM674245     2  0.1088     0.8733 0.000 0.960 0.000 NA 0.000 0.016
#> GSM674282     1  0.0405     0.9168 0.988 0.000 0.000 NA 0.000 0.008
#> GSM674284     1  0.1624     0.8999 0.936 0.000 0.000 NA 0.044 0.012
#> GSM674285     1  0.0260     0.9169 0.992 0.000 0.000 NA 0.000 0.008
#> GSM674287     1  0.1218     0.9083 0.956 0.000 0.000 NA 0.028 0.012
#> GSM674288     1  0.4754     0.1706 0.544 0.000 0.000 NA 0.416 0.016
#> GSM674289     1  0.0291     0.9172 0.992 0.000 0.000 NA 0.000 0.004
#> GSM674290     1  0.0820     0.9111 0.972 0.000 0.000 NA 0.000 0.016
#> GSM674291     1  0.0717     0.9146 0.976 0.000 0.000 NA 0.000 0.016
#> GSM674292     1  0.0603     0.9157 0.980 0.000 0.000 NA 0.000 0.016
#> GSM674295     5  0.3317     0.8413 0.168 0.000 0.000 NA 0.804 0.012
#> GSM674297     1  0.0146     0.9172 0.996 0.000 0.000 NA 0.004 0.000
#> GSM674298     1  0.0146     0.9172 0.996 0.000 0.000 NA 0.004 0.000
#> GSM674299     1  0.2375     0.8774 0.896 0.000 0.000 NA 0.068 0.016
#> GSM674300     1  0.1340     0.9037 0.948 0.000 0.000 NA 0.040 0.008
#> GSM674301     1  0.0622     0.9133 0.980 0.000 0.000 NA 0.000 0.012
#> GSM674302     1  0.0520     0.9132 0.984 0.000 0.000 NA 0.000 0.008
#> GSM674304     1  0.0260     0.9164 0.992 0.000 0.000 NA 0.000 0.008
#> GSM674305     1  0.0146     0.9173 0.996 0.000 0.000 NA 0.000 0.004
#> GSM674306     1  0.0146     0.9173 0.996 0.000 0.000 NA 0.000 0.004
#> GSM674308     1  0.0508     0.9156 0.984 0.000 0.000 NA 0.000 0.012
#> GSM674309     1  0.3586     0.6107 0.712 0.000 0.000 NA 0.280 0.004
#> GSM674313     5  0.1477     0.9057 0.048 0.000 0.000 NA 0.940 0.004
#> GSM674314     5  0.3890     0.4219 0.400 0.000 0.000 NA 0.596 0.004
#> GSM674315     1  0.0146     0.9173 0.996 0.000 0.000 NA 0.000 0.004
#> GSM674316     5  0.1863     0.9051 0.104 0.000 0.000 NA 0.896 0.000
#> GSM674318     5  0.1124     0.8973 0.036 0.000 0.000 NA 0.956 0.000
#> GSM674320     5  0.1049     0.8951 0.032 0.000 0.000 NA 0.960 0.000
#> GSM674323     5  0.1814     0.9075 0.100 0.000 0.000 NA 0.900 0.000
#> GSM674324     1  0.2773     0.7921 0.828 0.000 0.000 NA 0.164 0.004
#> GSM674325     5  0.1610     0.9117 0.084 0.000 0.000 NA 0.916 0.000
#> GSM674327     1  0.3650     0.6247 0.716 0.000 0.000 NA 0.272 0.008
#> GSM674328     1  0.1757     0.8940 0.928 0.000 0.000 NA 0.052 0.008
#> GSM674330     5  0.3690     0.6474 0.308 0.000 0.000 NA 0.684 0.008
#> GSM674331     1  0.2668     0.7892 0.828 0.000 0.000 NA 0.168 0.000
#> GSM674332     1  0.3545     0.6884 0.748 0.000 0.000 NA 0.236 0.008
#> GSM674334     5  0.3398     0.7391 0.252 0.000 0.000 NA 0.740 0.008
#> GSM674335     5  0.2699     0.8872 0.124 0.000 0.000 NA 0.856 0.008
#> GSM674345     3  0.1701     0.8757 0.000 0.000 0.920 NA 0.000 0.072
#> GSM674351     3  0.3189     0.7548 0.000 0.000 0.796 NA 0.000 0.184
#> GSM674352     3  0.2709     0.8137 0.000 0.000 0.848 NA 0.000 0.132
#> GSM674359     6  0.4444     0.0708 0.000 0.000 0.436 NA 0.000 0.536
#> GSM674360     3  0.4131     0.5955 0.000 0.000 0.688 NA 0.000 0.272
#> GSM674362     6  0.5428     0.2791 0.000 0.036 0.368 NA 0.000 0.544
#> GSM674369     3  0.0909     0.9004 0.000 0.000 0.968 NA 0.000 0.020
#> GSM674372     3  0.0692     0.9021 0.000 0.000 0.976 NA 0.000 0.004
#> GSM674374     3  0.0291     0.9016 0.000 0.000 0.992 NA 0.000 0.004
#> GSM674376     3  0.1204     0.8923 0.000 0.000 0.944 NA 0.000 0.000
#> GSM674377     3  0.1970     0.8676 0.000 0.000 0.900 NA 0.000 0.008
#> GSM674378     3  0.0146     0.9010 0.000 0.000 0.996 NA 0.000 0.000
#> GSM674383     3  0.0405     0.8996 0.000 0.000 0.988 NA 0.000 0.008
#> GSM674386     3  0.1753     0.8755 0.000 0.000 0.912 NA 0.004 0.000
#> GSM674387     3  0.1075     0.8929 0.000 0.000 0.952 NA 0.000 0.000
#> GSM674392     3  0.0622     0.9000 0.000 0.000 0.980 NA 0.000 0.012
#> GSM674396     3  0.2006     0.8668 0.000 0.000 0.892 NA 0.000 0.004
#> GSM674399     3  0.1757     0.8760 0.000 0.000 0.916 NA 0.000 0.008
#> GSM674404     3  0.0363     0.9007 0.000 0.000 0.988 NA 0.000 0.000
#> GSM674182     2  0.3290     0.7676 0.000 0.776 0.000 NA 0.000 0.208
#> GSM674188     2  0.1616     0.8713 0.000 0.932 0.000 NA 0.000 0.048
#> GSM674189     2  0.4039     0.4929 0.000 0.632 0.000 NA 0.000 0.352
#> GSM674196     2  0.2046     0.8616 0.000 0.908 0.000 NA 0.000 0.032
#> GSM674197     2  0.1700     0.8667 0.000 0.928 0.000 NA 0.000 0.024
#> GSM674199     2  0.1285     0.8677 0.000 0.944 0.000 NA 0.000 0.004
#> GSM674207     2  0.2457     0.8502 0.000 0.880 0.000 NA 0.000 0.036
#> GSM674211     2  0.1867     0.8622 0.000 0.916 0.000 NA 0.000 0.020
#> GSM674213     2  0.3678     0.8022 0.000 0.788 0.000 NA 0.000 0.128
#> GSM674215     2  0.3922     0.7849 0.000 0.776 0.004 NA 0.000 0.124
#> GSM674216     2  0.1700     0.8586 0.000 0.916 0.000 NA 0.000 0.004
#> GSM674217     2  0.3193     0.8258 0.000 0.824 0.000 NA 0.000 0.124
#> GSM674222     2  0.1168     0.8765 0.000 0.956 0.000 NA 0.000 0.016
#> GSM674224     2  0.2872     0.8185 0.000 0.836 0.000 NA 0.000 0.024
#> GSM674227     2  0.2311     0.8408 0.000 0.880 0.000 NA 0.000 0.016
#> GSM674228     2  0.0891     0.8745 0.000 0.968 0.000 NA 0.000 0.024
#> GSM674233     2  0.2214     0.8538 0.000 0.888 0.000 NA 0.000 0.096
#> GSM674238     6  0.4932     0.3861 0.000 0.356 0.008 NA 0.000 0.580
#> GSM674241     2  0.0937     0.8682 0.000 0.960 0.000 NA 0.000 0.000
#> GSM674283     1  0.0291     0.9172 0.992 0.000 0.000 NA 0.000 0.004
#> GSM674286     1  0.0000     0.9170 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674293     1  0.0717     0.9146 0.976 0.000 0.000 NA 0.000 0.016
#> GSM674294     1  0.0405     0.9168 0.988 0.000 0.000 NA 0.000 0.008
#> GSM674296     1  0.0363     0.9157 0.988 0.000 0.000 NA 0.000 0.012
#> GSM674303     1  0.1196     0.9036 0.952 0.000 0.000 NA 0.040 0.008
#> GSM674307     1  0.0146     0.9173 0.996 0.000 0.000 NA 0.000 0.004
#> GSM674310     5  0.1124     0.8973 0.036 0.000 0.000 NA 0.956 0.000
#> GSM674311     1  0.3437     0.6876 0.752 0.000 0.000 NA 0.236 0.008
#> GSM674312     5  0.1151     0.8955 0.032 0.000 0.000 NA 0.956 0.000
#> GSM674317     1  0.2508     0.8660 0.884 0.000 0.000 NA 0.084 0.016
#> GSM674319     5  0.2169     0.9109 0.080 0.000 0.000 NA 0.900 0.008
#> GSM674321     5  0.1970     0.9103 0.092 0.000 0.000 NA 0.900 0.008
#> GSM674322     5  0.1082     0.9010 0.040 0.000 0.000 NA 0.956 0.000
#> GSM674326     5  0.1501     0.9119 0.076 0.000 0.000 NA 0.924 0.000
#> GSM674329     5  0.1471     0.9101 0.064 0.000 0.000 NA 0.932 0.000
#> GSM674333     5  0.0937     0.9008 0.040 0.000 0.000 NA 0.960 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-CV-NMF-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-CV-NMF-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-CV-NMF-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-CV-NMF-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-CV-NMF-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-CV-NMF-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-CV-NMF-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-CV-NMF-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-CV-NMF-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-CV-NMF-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-CV-NMF-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-CV-NMF-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-CV-NMF-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-CV-NMF-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-CV-NMF-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-CV-NMF-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-CV-NMF-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-CV-NMF-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-CV-NMF-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-CV-NMF-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk CV-NMF-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-CV-NMF-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-CV-NMF-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-CV-NMF-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-CV-NMF-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-CV-NMF-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk CV-NMF-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>          n disease.state(p) specimen(p) k
#> CV:NMF 183           0.9238    1.83e-40 2
#> CV:NMF 183           0.9620    6.15e-78 3
#> CV:NMF 178           0.0924    7.95e-74 4
#> CV:NMF 168           0.3714    1.56e-69 5
#> CV:NMF 172           0.5025    1.73e-69 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


MAD:hclust*

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["MAD", "hclust"]
# you can also extract it by
# res = res_list["MAD:hclust"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#>   Subgroups are detected by 'hclust' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 4.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk MAD-hclust-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk MAD-hclust-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 1.000           0.997       0.998         0.5955 0.750   0.571
#> 4 4 0.948           0.887       0.951         0.0633 0.967   0.900
#> 5 5 0.799           0.774       0.869         0.0728 0.940   0.799
#> 6 6 0.794           0.680       0.843         0.0298 0.985   0.940

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3

There is also optional best \(k\) = 2 3 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette p1    p2    p3
#> GSM674344     3  0.0000      1.000  0 0.000 1.000
#> GSM674346     3  0.0000      1.000  0 0.000 1.000
#> GSM674347     3  0.0000      1.000  0 0.000 1.000
#> GSM674348     3  0.0000      1.000  0 0.000 1.000
#> GSM674349     3  0.0000      1.000  0 0.000 1.000
#> GSM674350     3  0.0000      1.000  0 0.000 1.000
#> GSM674353     3  0.0000      1.000  0 0.000 1.000
#> GSM674354     3  0.0000      1.000  0 0.000 1.000
#> GSM674355     3  0.0000      1.000  0 0.000 1.000
#> GSM674356     3  0.0000      1.000  0 0.000 1.000
#> GSM674357     3  0.0000      1.000  0 0.000 1.000
#> GSM674358     3  0.0000      1.000  0 0.000 1.000
#> GSM674361     3  0.0000      1.000  0 0.000 1.000
#> GSM674363     3  0.0000      1.000  0 0.000 1.000
#> GSM674364     3  0.0000      1.000  0 0.000 1.000
#> GSM674365     3  0.0000      1.000  0 0.000 1.000
#> GSM674366     3  0.0000      1.000  0 0.000 1.000
#> GSM674367     3  0.0000      1.000  0 0.000 1.000
#> GSM674368     3  0.0000      1.000  0 0.000 1.000
#> GSM674370     3  0.0000      1.000  0 0.000 1.000
#> GSM674371     3  0.0000      1.000  0 0.000 1.000
#> GSM674373     3  0.0000      1.000  0 0.000 1.000
#> GSM674375     3  0.0000      1.000  0 0.000 1.000
#> GSM674379     3  0.0000      1.000  0 0.000 1.000
#> GSM674380     3  0.0000      1.000  0 0.000 1.000
#> GSM674381     3  0.0000      1.000  0 0.000 1.000
#> GSM674382     3  0.0000      1.000  0 0.000 1.000
#> GSM674384     3  0.0000      1.000  0 0.000 1.000
#> GSM674385     3  0.0000      1.000  0 0.000 1.000
#> GSM674388     3  0.0000      1.000  0 0.000 1.000
#> GSM674389     3  0.0000      1.000  0 0.000 1.000
#> GSM674390     3  0.0000      1.000  0 0.000 1.000
#> GSM674391     3  0.0000      1.000  0 0.000 1.000
#> GSM674393     3  0.0000      1.000  0 0.000 1.000
#> GSM674394     3  0.0000      1.000  0 0.000 1.000
#> GSM674395     3  0.0000      1.000  0 0.000 1.000
#> GSM674397     3  0.0000      1.000  0 0.000 1.000
#> GSM674398     3  0.0000      1.000  0 0.000 1.000
#> GSM674400     3  0.0000      1.000  0 0.000 1.000
#> GSM674401     3  0.0000      1.000  0 0.000 1.000
#> GSM674402     3  0.0000      1.000  0 0.000 1.000
#> GSM674403     3  0.0000      1.000  0 0.000 1.000
#> GSM674405     3  0.0000      1.000  0 0.000 1.000
#> GSM674406     3  0.0000      1.000  0 0.000 1.000
#> GSM674407     3  0.0000      1.000  0 0.000 1.000
#> GSM674181     2  0.0000      0.995  0 1.000 0.000
#> GSM674183     2  0.0237      0.992  0 0.996 0.004
#> GSM674184     2  0.0237      0.992  0 0.996 0.004
#> GSM674185     2  0.1529      0.963  0 0.960 0.040
#> GSM674186     2  0.0000      0.995  0 1.000 0.000
#> GSM674187     2  0.0000      0.995  0 1.000 0.000
#> GSM674190     2  0.0000      0.995  0 1.000 0.000
#> GSM674191     2  0.0000      0.995  0 1.000 0.000
#> GSM674192     2  0.0000      0.995  0 1.000 0.000
#> GSM674193     2  0.0000      0.995  0 1.000 0.000
#> GSM674194     2  0.0000      0.995  0 1.000 0.000
#> GSM674195     2  0.0237      0.992  0 0.996 0.004
#> GSM674198     2  0.0000      0.995  0 1.000 0.000
#> GSM674200     2  0.1529      0.963  0 0.960 0.040
#> GSM674201     2  0.0000      0.995  0 1.000 0.000
#> GSM674202     2  0.0000      0.995  0 1.000 0.000
#> GSM674203     2  0.0000      0.995  0 1.000 0.000
#> GSM674204     2  0.0000      0.995  0 1.000 0.000
#> GSM674205     2  0.0000      0.995  0 1.000 0.000
#> GSM674206     2  0.0000      0.995  0 1.000 0.000
#> GSM674208     2  0.0000      0.995  0 1.000 0.000
#> GSM674209     2  0.0000      0.995  0 1.000 0.000
#> GSM674210     2  0.0000      0.995  0 1.000 0.000
#> GSM674212     2  0.0000      0.995  0 1.000 0.000
#> GSM674214     2  0.0000      0.995  0 1.000 0.000
#> GSM674218     2  0.0237      0.992  0 0.996 0.004
#> GSM674219     2  0.0000      0.995  0 1.000 0.000
#> GSM674220     2  0.1411      0.966  0 0.964 0.036
#> GSM674221     2  0.0000      0.995  0 1.000 0.000
#> GSM674223     2  0.0000      0.995  0 1.000 0.000
#> GSM674225     2  0.1411      0.966  0 0.964 0.036
#> GSM674226     2  0.0000      0.995  0 1.000 0.000
#> GSM674229     2  0.0000      0.995  0 1.000 0.000
#> GSM674230     2  0.0000      0.995  0 1.000 0.000
#> GSM674231     2  0.0000      0.995  0 1.000 0.000
#> GSM674232     2  0.0000      0.995  0 1.000 0.000
#> GSM674234     2  0.0000      0.995  0 1.000 0.000
#> GSM674235     2  0.0000      0.995  0 1.000 0.000
#> GSM674236     2  0.0000      0.995  0 1.000 0.000
#> GSM674237     2  0.0000      0.995  0 1.000 0.000
#> GSM674239     2  0.0000      0.995  0 1.000 0.000
#> GSM674240     2  0.0000      0.995  0 1.000 0.000
#> GSM674242     2  0.0000      0.995  0 1.000 0.000
#> GSM674243     2  0.0000      0.995  0 1.000 0.000
#> GSM674244     2  0.1411      0.966  0 0.964 0.036
#> GSM674245     2  0.0000      0.995  0 1.000 0.000
#> GSM674282     1  0.0000      1.000  1 0.000 0.000
#> GSM674284     1  0.0000      1.000  1 0.000 0.000
#> GSM674285     1  0.0000      1.000  1 0.000 0.000
#> GSM674287     1  0.0000      1.000  1 0.000 0.000
#> GSM674288     1  0.0000      1.000  1 0.000 0.000
#> GSM674289     1  0.0000      1.000  1 0.000 0.000
#> GSM674290     1  0.0000      1.000  1 0.000 0.000
#> GSM674291     1  0.0000      1.000  1 0.000 0.000
#> GSM674292     1  0.0000      1.000  1 0.000 0.000
#> GSM674295     1  0.0000      1.000  1 0.000 0.000
#> GSM674297     1  0.0000      1.000  1 0.000 0.000
#> GSM674298     1  0.0000      1.000  1 0.000 0.000
#> GSM674299     1  0.0000      1.000  1 0.000 0.000
#> GSM674300     1  0.0000      1.000  1 0.000 0.000
#> GSM674301     1  0.0000      1.000  1 0.000 0.000
#> GSM674302     1  0.0000      1.000  1 0.000 0.000
#> GSM674304     1  0.0000      1.000  1 0.000 0.000
#> GSM674305     1  0.0000      1.000  1 0.000 0.000
#> GSM674306     1  0.0000      1.000  1 0.000 0.000
#> GSM674308     1  0.0000      1.000  1 0.000 0.000
#> GSM674309     1  0.0000      1.000  1 0.000 0.000
#> GSM674313     1  0.0000      1.000  1 0.000 0.000
#> GSM674314     1  0.0000      1.000  1 0.000 0.000
#> GSM674315     1  0.0000      1.000  1 0.000 0.000
#> GSM674316     1  0.0000      1.000  1 0.000 0.000
#> GSM674318     1  0.0000      1.000  1 0.000 0.000
#> GSM674320     1  0.0000      1.000  1 0.000 0.000
#> GSM674323     1  0.0000      1.000  1 0.000 0.000
#> GSM674324     1  0.0000      1.000  1 0.000 0.000
#> GSM674325     1  0.0000      1.000  1 0.000 0.000
#> GSM674327     1  0.0000      1.000  1 0.000 0.000
#> GSM674328     1  0.0000      1.000  1 0.000 0.000
#> GSM674330     1  0.0000      1.000  1 0.000 0.000
#> GSM674331     1  0.0000      1.000  1 0.000 0.000
#> GSM674332     1  0.0000      1.000  1 0.000 0.000
#> GSM674334     1  0.0000      1.000  1 0.000 0.000
#> GSM674335     1  0.0000      1.000  1 0.000 0.000
#> GSM674345     3  0.0000      1.000  0 0.000 1.000
#> GSM674351     3  0.0000      1.000  0 0.000 1.000
#> GSM674352     3  0.0000      1.000  0 0.000 1.000
#> GSM674359     3  0.0000      1.000  0 0.000 1.000
#> GSM674360     3  0.0000      1.000  0 0.000 1.000
#> GSM674362     3  0.0000      1.000  0 0.000 1.000
#> GSM674369     3  0.0000      1.000  0 0.000 1.000
#> GSM674372     3  0.0000      1.000  0 0.000 1.000
#> GSM674374     3  0.0000      1.000  0 0.000 1.000
#> GSM674376     3  0.0000      1.000  0 0.000 1.000
#> GSM674377     3  0.0000      1.000  0 0.000 1.000
#> GSM674378     3  0.0000      1.000  0 0.000 1.000
#> GSM674383     3  0.0000      1.000  0 0.000 1.000
#> GSM674386     3  0.0000      1.000  0 0.000 1.000
#> GSM674387     3  0.0000      1.000  0 0.000 1.000
#> GSM674392     3  0.0000      1.000  0 0.000 1.000
#> GSM674396     3  0.0000      1.000  0 0.000 1.000
#> GSM674399     3  0.0000      1.000  0 0.000 1.000
#> GSM674404     3  0.0000      1.000  0 0.000 1.000
#> GSM674182     2  0.0000      0.995  0 1.000 0.000
#> GSM674188     2  0.0000      0.995  0 1.000 0.000
#> GSM674189     2  0.0237      0.992  0 0.996 0.004
#> GSM674196     2  0.0000      0.995  0 1.000 0.000
#> GSM674197     2  0.0000      0.995  0 1.000 0.000
#> GSM674199     2  0.0000      0.995  0 1.000 0.000
#> GSM674207     2  0.0000      0.995  0 1.000 0.000
#> GSM674211     2  0.0000      0.995  0 1.000 0.000
#> GSM674213     2  0.0000      0.995  0 1.000 0.000
#> GSM674215     2  0.1411      0.966  0 0.964 0.036
#> GSM674216     2  0.0000      0.995  0 1.000 0.000
#> GSM674217     2  0.0000      0.995  0 1.000 0.000
#> GSM674222     2  0.1163      0.973  0 0.972 0.028
#> GSM674224     2  0.0000      0.995  0 1.000 0.000
#> GSM674227     2  0.0000      0.995  0 1.000 0.000
#> GSM674228     2  0.0000      0.995  0 1.000 0.000
#> GSM674233     2  0.0000      0.995  0 1.000 0.000
#> GSM674238     2  0.1529      0.963  0 0.960 0.040
#> GSM674241     2  0.0000      0.995  0 1.000 0.000
#> GSM674283     1  0.0000      1.000  1 0.000 0.000
#> GSM674286     1  0.0000      1.000  1 0.000 0.000
#> GSM674293     1  0.0000      1.000  1 0.000 0.000
#> GSM674294     1  0.0000      1.000  1 0.000 0.000
#> GSM674296     1  0.0000      1.000  1 0.000 0.000
#> GSM674303     1  0.0000      1.000  1 0.000 0.000
#> GSM674307     1  0.0000      1.000  1 0.000 0.000
#> GSM674310     1  0.0000      1.000  1 0.000 0.000
#> GSM674311     1  0.0000      1.000  1 0.000 0.000
#> GSM674312     1  0.0000      1.000  1 0.000 0.000
#> GSM674317     1  0.0000      1.000  1 0.000 0.000
#> GSM674319     1  0.0000      1.000  1 0.000 0.000
#> GSM674321     1  0.0000      1.000  1 0.000 0.000
#> GSM674322     1  0.0000      1.000  1 0.000 0.000
#> GSM674326     1  0.0000      1.000  1 0.000 0.000
#> GSM674329     1  0.0000      1.000  1 0.000 0.000
#> GSM674333     1  0.0000      1.000  1 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette p1    p2    p3    p4
#> GSM674344     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674346     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674347     3  0.0000     0.9906  0 0.000 1.000 0.000
#> GSM674348     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674349     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674350     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674353     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674354     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674355     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674356     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674357     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674358     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674361     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674363     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674364     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674365     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674366     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674367     3  0.0336     0.9903  0 0.000 0.992 0.008
#> GSM674368     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674370     3  0.0817     0.9800  0 0.000 0.976 0.024
#> GSM674371     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674373     3  0.0817     0.9796  0 0.000 0.976 0.024
#> GSM674375     3  0.0188     0.9897  0 0.000 0.996 0.004
#> GSM674379     3  0.1022     0.9751  0 0.000 0.968 0.032
#> GSM674380     3  0.1211     0.9696  0 0.000 0.960 0.040
#> GSM674381     3  0.0469     0.9889  0 0.000 0.988 0.012
#> GSM674382     3  0.1118     0.9723  0 0.000 0.964 0.036
#> GSM674384     3  0.0188     0.9897  0 0.000 0.996 0.004
#> GSM674385     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674388     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674389     3  0.0000     0.9906  0 0.000 1.000 0.000
#> GSM674390     3  0.0817     0.9800  0 0.000 0.976 0.024
#> GSM674391     3  0.1118     0.9723  0 0.000 0.964 0.036
#> GSM674393     3  0.0000     0.9906  0 0.000 1.000 0.000
#> GSM674394     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674395     3  0.0000     0.9906  0 0.000 1.000 0.000
#> GSM674397     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674398     3  0.0188     0.9897  0 0.000 0.996 0.004
#> GSM674400     3  0.0000     0.9906  0 0.000 1.000 0.000
#> GSM674401     3  0.0000     0.9906  0 0.000 1.000 0.000
#> GSM674402     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674403     3  0.0000     0.9906  0 0.000 1.000 0.000
#> GSM674405     3  0.0188     0.9897  0 0.000 0.996 0.004
#> GSM674406     3  0.1022     0.9751  0 0.000 0.968 0.032
#> GSM674407     3  0.1022     0.9751  0 0.000 0.968 0.032
#> GSM674181     2  0.4996    -0.2128  0 0.516 0.000 0.484
#> GSM674183     4  0.4304     0.6735  0 0.284 0.000 0.716
#> GSM674184     4  0.4500     0.6573  0 0.316 0.000 0.684
#> GSM674185     4  0.0707     0.7191  0 0.020 0.000 0.980
#> GSM674186     2  0.3837     0.6463  0 0.776 0.000 0.224
#> GSM674187     2  0.2011     0.8244  0 0.920 0.000 0.080
#> GSM674190     2  0.3726     0.6598  0 0.788 0.000 0.212
#> GSM674191     2  0.3726     0.6598  0 0.788 0.000 0.212
#> GSM674192     2  0.0592     0.8484  0 0.984 0.000 0.016
#> GSM674193     2  0.0817     0.8481  0 0.976 0.000 0.024
#> GSM674194     2  0.4193     0.5651  0 0.732 0.000 0.268
#> GSM674195     4  0.4522     0.6563  0 0.320 0.000 0.680
#> GSM674198     2  0.0000     0.8501  0 1.000 0.000 0.000
#> GSM674200     4  0.0188     0.7123  0 0.004 0.000 0.996
#> GSM674201     2  0.4996    -0.1955  0 0.516 0.000 0.484
#> GSM674202     2  0.3074     0.7398  0 0.848 0.000 0.152
#> GSM674203     2  0.0000     0.8501  0 1.000 0.000 0.000
#> GSM674204     2  0.0000     0.8501  0 1.000 0.000 0.000
#> GSM674205     2  0.0592     0.8484  0 0.984 0.000 0.016
#> GSM674206     2  0.4898     0.1211  0 0.584 0.000 0.416
#> GSM674208     2  0.0000     0.8501  0 1.000 0.000 0.000
#> GSM674209     2  0.0707     0.8489  0 0.980 0.000 0.020
#> GSM674210     2  0.0000     0.8501  0 1.000 0.000 0.000
#> GSM674212     2  0.0000     0.8501  0 1.000 0.000 0.000
#> GSM674214     2  0.0000     0.8501  0 1.000 0.000 0.000
#> GSM674218     4  0.4679     0.6036  0 0.352 0.000 0.648
#> GSM674219     2  0.2921     0.7621  0 0.860 0.000 0.140
#> GSM674220     4  0.4431     0.4983  0 0.304 0.000 0.696
#> GSM674221     2  0.2921     0.7621  0 0.860 0.000 0.140
#> GSM674223     2  0.0817     0.8474  0 0.976 0.000 0.024
#> GSM674225     2  0.4994    -0.0284  0 0.520 0.000 0.480
#> GSM674226     2  0.0817     0.8477  0 0.976 0.000 0.024
#> GSM674229     2  0.0188     0.8497  0 0.996 0.000 0.004
#> GSM674230     2  0.1302     0.8433  0 0.956 0.000 0.044
#> GSM674231     2  0.1474     0.8403  0 0.948 0.000 0.052
#> GSM674232     2  0.0469     0.8466  0 0.988 0.000 0.012
#> GSM674234     2  0.1118     0.8468  0 0.964 0.000 0.036
#> GSM674235     2  0.3074     0.7398  0 0.848 0.000 0.152
#> GSM674236     2  0.3074     0.7398  0 0.848 0.000 0.152
#> GSM674237     2  0.0000     0.8501  0 1.000 0.000 0.000
#> GSM674239     2  0.0000     0.8501  0 1.000 0.000 0.000
#> GSM674240     2  0.4406     0.4630  0 0.700 0.000 0.300
#> GSM674242     2  0.0000     0.8501  0 1.000 0.000 0.000
#> GSM674243     2  0.0921     0.8462  0 0.972 0.000 0.028
#> GSM674244     2  0.4994    -0.0284  0 0.520 0.000 0.480
#> GSM674245     2  0.0921     0.8473  0 0.972 0.000 0.028
#> GSM674282     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674284     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674285     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674287     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674288     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674289     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674290     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674291     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674292     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674295     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674297     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674298     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674299     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674300     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674301     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674302     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674304     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674305     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674306     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674308     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674309     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674313     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674314     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674315     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674316     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674318     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674320     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674323     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674324     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674325     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674327     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674328     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674330     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674331     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674332     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674334     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674335     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674345     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674351     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674352     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674359     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674360     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674362     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674369     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674372     3  0.0000     0.9906  0 0.000 1.000 0.000
#> GSM674374     3  0.0817     0.9796  0 0.000 0.976 0.024
#> GSM674376     3  0.1022     0.9751  0 0.000 0.968 0.032
#> GSM674377     3  0.1211     0.9696  0 0.000 0.960 0.040
#> GSM674378     3  0.0817     0.9796  0 0.000 0.976 0.024
#> GSM674383     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674386     3  0.1118     0.9723  0 0.000 0.964 0.036
#> GSM674387     3  0.1022     0.9751  0 0.000 0.968 0.032
#> GSM674392     3  0.0188     0.9913  0 0.000 0.996 0.004
#> GSM674396     3  0.0188     0.9897  0 0.000 0.996 0.004
#> GSM674399     3  0.0188     0.9897  0 0.000 0.996 0.004
#> GSM674404     3  0.0188     0.9897  0 0.000 0.996 0.004
#> GSM674182     2  0.4989    -0.1627  0 0.528 0.000 0.472
#> GSM674188     2  0.2011     0.8244  0 0.920 0.000 0.080
#> GSM674189     4  0.4830     0.5138  0 0.392 0.000 0.608
#> GSM674196     2  0.0000     0.8501  0 1.000 0.000 0.000
#> GSM674197     2  0.0000     0.8501  0 1.000 0.000 0.000
#> GSM674199     2  0.0000     0.8501  0 1.000 0.000 0.000
#> GSM674207     2  0.0000     0.8501  0 1.000 0.000 0.000
#> GSM674211     2  0.0000     0.8501  0 1.000 0.000 0.000
#> GSM674213     2  0.1792     0.8279  0 0.932 0.000 0.068
#> GSM674215     4  0.2345     0.7214  0 0.100 0.000 0.900
#> GSM674216     2  0.0592     0.8454  0 0.984 0.000 0.016
#> GSM674217     2  0.2921     0.7621  0 0.860 0.000 0.140
#> GSM674222     2  0.4382     0.4868  0 0.704 0.000 0.296
#> GSM674224     2  0.0817     0.8477  0 0.976 0.000 0.024
#> GSM674227     2  0.3074     0.7398  0 0.848 0.000 0.152
#> GSM674228     2  0.1389     0.8413  0 0.952 0.000 0.048
#> GSM674233     2  0.2921     0.7621  0 0.860 0.000 0.140
#> GSM674238     4  0.0188     0.7123  0 0.004 0.000 0.996
#> GSM674241     2  0.0000     0.8501  0 1.000 0.000 0.000
#> GSM674283     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674286     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674293     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674294     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674296     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674303     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674307     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674310     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674311     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674312     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674317     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674319     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674321     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674322     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674326     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674329     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674333     1  0.0000     1.0000  1 0.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4    p5
#> GSM674344     3  0.0290    0.85648 0.000 0.000 0.992 0.008 0.000
#> GSM674346     3  0.0290    0.85648 0.000 0.000 0.992 0.008 0.000
#> GSM674347     4  0.4242    0.68341 0.000 0.000 0.428 0.572 0.000
#> GSM674348     3  0.0404    0.86368 0.000 0.000 0.988 0.012 0.000
#> GSM674349     3  0.0963    0.85803 0.000 0.000 0.964 0.036 0.000
#> GSM674350     3  0.0703    0.86212 0.000 0.000 0.976 0.024 0.000
#> GSM674353     3  0.0703    0.86212 0.000 0.000 0.976 0.024 0.000
#> GSM674354     3  0.0290    0.85648 0.000 0.000 0.992 0.008 0.000
#> GSM674355     3  0.1270    0.84323 0.000 0.000 0.948 0.052 0.000
#> GSM674356     3  0.0290    0.85648 0.000 0.000 0.992 0.008 0.000
#> GSM674357     3  0.0404    0.85783 0.000 0.000 0.988 0.012 0.000
#> GSM674358     3  0.0963    0.85579 0.000 0.000 0.964 0.036 0.000
#> GSM674361     3  0.0609    0.86297 0.000 0.000 0.980 0.020 0.000
#> GSM674363     3  0.0703    0.86290 0.000 0.000 0.976 0.024 0.000
#> GSM674364     3  0.0404    0.85808 0.000 0.000 0.988 0.012 0.000
#> GSM674365     3  0.0510    0.86280 0.000 0.000 0.984 0.016 0.000
#> GSM674366     3  0.2471    0.73521 0.000 0.000 0.864 0.136 0.000
#> GSM674367     3  0.4126   -0.04302 0.000 0.000 0.620 0.380 0.000
#> GSM674368     3  0.0794    0.85864 0.000 0.000 0.972 0.028 0.000
#> GSM674370     4  0.4227    0.70157 0.000 0.000 0.420 0.580 0.000
#> GSM674371     3  0.0609    0.86302 0.000 0.000 0.980 0.020 0.000
#> GSM674373     4  0.4192    0.72054 0.000 0.000 0.404 0.596 0.000
#> GSM674375     4  0.4306    0.54334 0.000 0.000 0.492 0.508 0.000
#> GSM674379     4  0.3561    0.80781 0.000 0.000 0.260 0.740 0.000
#> GSM674380     4  0.2930    0.77581 0.000 0.000 0.164 0.832 0.004
#> GSM674381     3  0.4273   -0.26317 0.000 0.000 0.552 0.448 0.000
#> GSM674382     4  0.2970    0.77893 0.000 0.000 0.168 0.828 0.004
#> GSM674384     3  0.4302   -0.45429 0.000 0.000 0.520 0.480 0.000
#> GSM674385     3  0.1792    0.81884 0.000 0.000 0.916 0.084 0.000
#> GSM674388     3  0.1043    0.85398 0.000 0.000 0.960 0.040 0.000
#> GSM674389     4  0.4307    0.50253 0.000 0.000 0.500 0.500 0.000
#> GSM674390     4  0.4210    0.71467 0.000 0.000 0.412 0.588 0.000
#> GSM674391     4  0.2970    0.77893 0.000 0.000 0.168 0.828 0.004
#> GSM674393     4  0.4210    0.70761 0.000 0.000 0.412 0.588 0.000
#> GSM674394     3  0.2179    0.77088 0.000 0.000 0.888 0.112 0.000
#> GSM674395     3  0.3999    0.07903 0.000 0.000 0.656 0.344 0.000
#> GSM674397     3  0.3143    0.61641 0.000 0.000 0.796 0.204 0.000
#> GSM674398     4  0.3707    0.81403 0.000 0.000 0.284 0.716 0.000
#> GSM674400     4  0.3966    0.79144 0.000 0.000 0.336 0.664 0.000
#> GSM674401     4  0.3932    0.79412 0.000 0.000 0.328 0.672 0.000
#> GSM674402     3  0.0510    0.86085 0.000 0.000 0.984 0.016 0.000
#> GSM674403     4  0.4030    0.78026 0.000 0.000 0.352 0.648 0.000
#> GSM674405     4  0.3752    0.81162 0.000 0.000 0.292 0.708 0.000
#> GSM674406     4  0.3684    0.80818 0.000 0.000 0.280 0.720 0.000
#> GSM674407     4  0.3561    0.80781 0.000 0.000 0.260 0.740 0.000
#> GSM674181     2  0.4306   -0.22314 0.000 0.508 0.000 0.000 0.492
#> GSM674183     5  0.3661    0.67711 0.000 0.276 0.000 0.000 0.724
#> GSM674184     5  0.3837    0.66130 0.000 0.308 0.000 0.000 0.692
#> GSM674185     5  0.1300    0.71786 0.000 0.016 0.000 0.028 0.956
#> GSM674186     2  0.3336    0.64499 0.000 0.772 0.000 0.000 0.228
#> GSM674187     2  0.1732    0.82360 0.000 0.920 0.000 0.000 0.080
#> GSM674190     2  0.3242    0.65836 0.000 0.784 0.000 0.000 0.216
#> GSM674191     2  0.3242    0.65836 0.000 0.784 0.000 0.000 0.216
#> GSM674192     2  0.0609    0.84650 0.000 0.980 0.000 0.000 0.020
#> GSM674193     2  0.0794    0.84617 0.000 0.972 0.000 0.000 0.028
#> GSM674194     2  0.3636    0.56420 0.000 0.728 0.000 0.000 0.272
#> GSM674195     5  0.3857    0.66035 0.000 0.312 0.000 0.000 0.688
#> GSM674198     2  0.0000    0.84839 0.000 1.000 0.000 0.000 0.000
#> GSM674200     5  0.0794    0.70518 0.000 0.000 0.000 0.028 0.972
#> GSM674201     2  0.4306   -0.20635 0.000 0.508 0.000 0.000 0.492
#> GSM674202     2  0.2648    0.73963 0.000 0.848 0.000 0.000 0.152
#> GSM674203     2  0.0000    0.84839 0.000 1.000 0.000 0.000 0.000
#> GSM674204     2  0.0000    0.84839 0.000 1.000 0.000 0.000 0.000
#> GSM674205     2  0.0609    0.84650 0.000 0.980 0.000 0.000 0.020
#> GSM674206     2  0.4235    0.10723 0.000 0.576 0.000 0.000 0.424
#> GSM674208     2  0.0000    0.84839 0.000 1.000 0.000 0.000 0.000
#> GSM674209     2  0.0609    0.84798 0.000 0.980 0.000 0.000 0.020
#> GSM674210     2  0.0000    0.84839 0.000 1.000 0.000 0.000 0.000
#> GSM674212     2  0.0162    0.84853 0.000 0.996 0.000 0.000 0.004
#> GSM674214     2  0.0162    0.84853 0.000 0.996 0.000 0.000 0.004
#> GSM674218     5  0.3999    0.60835 0.000 0.344 0.000 0.000 0.656
#> GSM674219     2  0.2605    0.75509 0.000 0.852 0.000 0.000 0.148
#> GSM674220     5  0.4526    0.49903 0.000 0.300 0.000 0.028 0.672
#> GSM674221     2  0.2605    0.75509 0.000 0.852 0.000 0.000 0.148
#> GSM674223     2  0.0794    0.84539 0.000 0.972 0.000 0.000 0.028
#> GSM674225     2  0.4965   -0.01978 0.000 0.520 0.000 0.028 0.452
#> GSM674226     2  0.0703    0.84663 0.000 0.976 0.000 0.000 0.024
#> GSM674229     2  0.0162    0.84831 0.000 0.996 0.000 0.000 0.004
#> GSM674230     2  0.1121    0.84235 0.000 0.956 0.000 0.000 0.044
#> GSM674231     2  0.1270    0.83942 0.000 0.948 0.000 0.000 0.052
#> GSM674232     2  0.0404    0.84513 0.000 0.988 0.000 0.000 0.012
#> GSM674234     2  0.1043    0.84503 0.000 0.960 0.000 0.000 0.040
#> GSM674235     2  0.2648    0.73963 0.000 0.848 0.000 0.000 0.152
#> GSM674236     2  0.2648    0.73963 0.000 0.848 0.000 0.000 0.152
#> GSM674237     2  0.0000    0.84839 0.000 1.000 0.000 0.000 0.000
#> GSM674239     2  0.0000    0.84839 0.000 1.000 0.000 0.000 0.000
#> GSM674240     2  0.3837    0.45231 0.000 0.692 0.000 0.000 0.308
#> GSM674242     2  0.0000    0.84839 0.000 1.000 0.000 0.000 0.000
#> GSM674243     2  0.0794    0.84577 0.000 0.972 0.000 0.000 0.028
#> GSM674244     2  0.4965   -0.01978 0.000 0.520 0.000 0.028 0.452
#> GSM674245     2  0.0794    0.84630 0.000 0.972 0.000 0.000 0.028
#> GSM674282     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674284     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674285     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674287     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674288     1  0.2505    0.92744 0.888 0.000 0.000 0.092 0.020
#> GSM674289     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674291     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674292     1  0.0162    0.94501 0.996 0.000 0.000 0.004 0.000
#> GSM674295     1  0.3152    0.90832 0.840 0.000 0.000 0.136 0.024
#> GSM674297     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674298     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674299     1  0.2505    0.92744 0.888 0.000 0.000 0.092 0.020
#> GSM674300     1  0.0566    0.94377 0.984 0.000 0.000 0.012 0.004
#> GSM674301     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674302     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674305     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674306     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674308     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674309     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674313     1  0.3326    0.89904 0.824 0.000 0.000 0.152 0.024
#> GSM674314     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674315     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674316     1  0.2915    0.91786 0.860 0.000 0.000 0.116 0.024
#> GSM674318     1  0.2964    0.91632 0.856 0.000 0.000 0.120 0.024
#> GSM674320     1  0.3326    0.89904 0.824 0.000 0.000 0.152 0.024
#> GSM674323     1  0.2964    0.91632 0.856 0.000 0.000 0.120 0.024
#> GSM674324     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674325     1  0.2964    0.91632 0.856 0.000 0.000 0.120 0.024
#> GSM674327     1  0.2915    0.91786 0.860 0.000 0.000 0.116 0.024
#> GSM674328     1  0.0566    0.94377 0.984 0.000 0.000 0.012 0.004
#> GSM674330     1  0.2505    0.92687 0.888 0.000 0.000 0.092 0.020
#> GSM674331     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674332     1  0.2505    0.92687 0.888 0.000 0.000 0.092 0.020
#> GSM674334     1  0.2505    0.92687 0.888 0.000 0.000 0.092 0.020
#> GSM674335     1  0.2964    0.91632 0.856 0.000 0.000 0.120 0.024
#> GSM674345     3  0.0609    0.86319 0.000 0.000 0.980 0.020 0.000
#> GSM674351     3  0.0703    0.86212 0.000 0.000 0.976 0.024 0.000
#> GSM674352     3  0.0703    0.86212 0.000 0.000 0.976 0.024 0.000
#> GSM674359     3  0.0162    0.86102 0.000 0.000 0.996 0.004 0.000
#> GSM674360     3  0.0794    0.85864 0.000 0.000 0.972 0.028 0.000
#> GSM674362     3  0.0290    0.85648 0.000 0.000 0.992 0.008 0.000
#> GSM674369     3  0.0609    0.86302 0.000 0.000 0.980 0.020 0.000
#> GSM674372     3  0.4045    0.00799 0.000 0.000 0.644 0.356 0.000
#> GSM674374     4  0.4192    0.72054 0.000 0.000 0.404 0.596 0.000
#> GSM674376     4  0.3561    0.80781 0.000 0.000 0.260 0.740 0.000
#> GSM674377     4  0.3231    0.79111 0.000 0.000 0.196 0.800 0.004
#> GSM674378     4  0.4182    0.72388 0.000 0.000 0.400 0.600 0.000
#> GSM674383     3  0.0963    0.85707 0.000 0.000 0.964 0.036 0.000
#> GSM674386     4  0.2970    0.77893 0.000 0.000 0.168 0.828 0.004
#> GSM674387     4  0.3561    0.80781 0.000 0.000 0.260 0.740 0.000
#> GSM674392     3  0.3424    0.49017 0.000 0.000 0.760 0.240 0.000
#> GSM674396     4  0.3707    0.81403 0.000 0.000 0.284 0.716 0.000
#> GSM674399     4  0.3707    0.81403 0.000 0.000 0.284 0.716 0.000
#> GSM674404     4  0.3816    0.81229 0.000 0.000 0.304 0.696 0.000
#> GSM674182     2  0.4302   -0.17400 0.000 0.520 0.000 0.000 0.480
#> GSM674188     2  0.1732    0.82360 0.000 0.920 0.000 0.000 0.080
#> GSM674189     5  0.4138    0.51968 0.000 0.384 0.000 0.000 0.616
#> GSM674196     2  0.0000    0.84839 0.000 1.000 0.000 0.000 0.000
#> GSM674197     2  0.0000    0.84839 0.000 1.000 0.000 0.000 0.000
#> GSM674199     2  0.0000    0.84839 0.000 1.000 0.000 0.000 0.000
#> GSM674207     2  0.0162    0.84853 0.000 0.996 0.000 0.000 0.004
#> GSM674211     2  0.0162    0.84853 0.000 0.996 0.000 0.000 0.004
#> GSM674213     2  0.1608    0.82668 0.000 0.928 0.000 0.000 0.072
#> GSM674215     5  0.2740    0.72325 0.000 0.096 0.000 0.028 0.876
#> GSM674216     2  0.0510    0.84397 0.000 0.984 0.000 0.000 0.016
#> GSM674217     2  0.2605    0.75509 0.000 0.852 0.000 0.000 0.148
#> GSM674222     2  0.4229    0.48984 0.000 0.704 0.000 0.020 0.276
#> GSM674224     2  0.0703    0.84663 0.000 0.976 0.000 0.000 0.024
#> GSM674227     2  0.2648    0.73965 0.000 0.848 0.000 0.000 0.152
#> GSM674228     2  0.1197    0.84044 0.000 0.952 0.000 0.000 0.048
#> GSM674233     2  0.2605    0.75509 0.000 0.852 0.000 0.000 0.148
#> GSM674238     5  0.0794    0.70518 0.000 0.000 0.000 0.028 0.972
#> GSM674241     2  0.0000    0.84839 0.000 1.000 0.000 0.000 0.000
#> GSM674283     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674286     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674293     1  0.0162    0.94501 0.996 0.000 0.000 0.004 0.000
#> GSM674294     1  0.0162    0.94501 0.996 0.000 0.000 0.004 0.000
#> GSM674296     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674303     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674307     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674310     1  0.2964    0.91632 0.856 0.000 0.000 0.120 0.024
#> GSM674311     1  0.0000    0.94521 1.000 0.000 0.000 0.000 0.000
#> GSM674312     1  0.3326    0.89904 0.824 0.000 0.000 0.152 0.024
#> GSM674317     1  0.2331    0.93014 0.900 0.000 0.000 0.080 0.020
#> GSM674319     1  0.3326    0.89904 0.824 0.000 0.000 0.152 0.024
#> GSM674321     1  0.2915    0.91786 0.860 0.000 0.000 0.116 0.024
#> GSM674322     1  0.2964    0.91632 0.856 0.000 0.000 0.120 0.024
#> GSM674326     1  0.2964    0.91632 0.856 0.000 0.000 0.120 0.024
#> GSM674329     1  0.3326    0.89904 0.824 0.000 0.000 0.152 0.024
#> GSM674333     1  0.2964    0.91632 0.856 0.000 0.000 0.120 0.024

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4    p5    p6
#> GSM674344     3  0.0260     0.8122 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM674346     3  0.0260     0.8122 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM674347     4  0.6104    -0.3606 0.000 0.000 0.328 0.376 0.296 0.000
#> GSM674348     3  0.0547     0.8168 0.000 0.000 0.980 0.020 0.000 0.000
#> GSM674349     3  0.1176     0.8091 0.000 0.000 0.956 0.024 0.020 0.000
#> GSM674350     3  0.0725     0.8144 0.000 0.000 0.976 0.012 0.012 0.000
#> GSM674353     3  0.0725     0.8144 0.000 0.000 0.976 0.012 0.012 0.000
#> GSM674354     3  0.0260     0.8122 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM674355     3  0.1434     0.7965 0.000 0.000 0.940 0.048 0.012 0.000
#> GSM674356     3  0.0260     0.8122 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM674357     3  0.0405     0.8133 0.000 0.000 0.988 0.004 0.008 0.000
#> GSM674358     3  0.0993     0.8105 0.000 0.000 0.964 0.024 0.012 0.000
#> GSM674361     3  0.0622     0.8148 0.000 0.000 0.980 0.008 0.012 0.000
#> GSM674363     3  0.0725     0.8156 0.000 0.000 0.976 0.012 0.012 0.000
#> GSM674364     3  0.0405     0.8130 0.000 0.000 0.988 0.004 0.008 0.000
#> GSM674365     3  0.0603     0.8159 0.000 0.000 0.980 0.016 0.004 0.000
#> GSM674366     3  0.2581     0.7026 0.000 0.000 0.860 0.120 0.020 0.000
#> GSM674367     3  0.4331    -0.1158 0.000 0.000 0.516 0.464 0.020 0.000
#> GSM674368     3  0.0937     0.8077 0.000 0.000 0.960 0.040 0.000 0.000
#> GSM674370     4  0.3584     0.4815 0.000 0.000 0.308 0.688 0.004 0.000
#> GSM674371     3  0.0717     0.8156 0.000 0.000 0.976 0.016 0.008 0.000
#> GSM674373     4  0.3390     0.5022 0.000 0.000 0.296 0.704 0.000 0.000
#> GSM674375     3  0.5262    -0.2545 0.000 0.000 0.452 0.452 0.096 0.000
#> GSM674379     4  0.2445     0.6108 0.000 0.000 0.108 0.872 0.020 0.000
#> GSM674380     4  0.0777     0.5544 0.000 0.000 0.004 0.972 0.024 0.000
#> GSM674381     4  0.4184     0.1698 0.000 0.000 0.408 0.576 0.016 0.000
#> GSM674382     4  0.0458     0.5539 0.000 0.000 0.000 0.984 0.016 0.000
#> GSM674384     3  0.4338    -0.1019 0.000 0.000 0.492 0.488 0.020 0.000
#> GSM674385     3  0.1908     0.7675 0.000 0.000 0.900 0.096 0.004 0.000
#> GSM674388     3  0.2178     0.6935 0.000 0.000 0.868 0.132 0.000 0.000
#> GSM674389     3  0.5763    -0.3558 0.000 0.000 0.480 0.332 0.188 0.000
#> GSM674390     4  0.3547     0.4911 0.000 0.000 0.300 0.696 0.004 0.000
#> GSM674391     4  0.0458     0.5539 0.000 0.000 0.000 0.984 0.016 0.000
#> GSM674393     4  0.6100    -0.3466 0.000 0.000 0.312 0.384 0.304 0.000
#> GSM674394     3  0.2234     0.7218 0.000 0.000 0.872 0.124 0.004 0.000
#> GSM674395     3  0.4249     0.2434 0.000 0.000 0.640 0.328 0.032 0.000
#> GSM674397     3  0.3201     0.5932 0.000 0.000 0.780 0.208 0.012 0.000
#> GSM674398     4  0.5492     0.1799 0.000 0.000 0.168 0.552 0.280 0.000
#> GSM674400     5  0.5606     0.9680 0.000 0.000 0.324 0.164 0.512 0.000
#> GSM674401     5  0.5558     0.9600 0.000 0.000 0.316 0.160 0.524 0.000
#> GSM674402     3  0.0508     0.8154 0.000 0.000 0.984 0.004 0.012 0.000
#> GSM674403     5  0.5618     0.9524 0.000 0.000 0.340 0.160 0.500 0.000
#> GSM674405     4  0.5799    -0.1446 0.000 0.000 0.184 0.448 0.368 0.000
#> GSM674406     4  0.2907     0.5928 0.000 0.000 0.152 0.828 0.020 0.000
#> GSM674407     4  0.2445     0.6108 0.000 0.000 0.108 0.872 0.020 0.000
#> GSM674181     2  0.3868    -0.2141 0.000 0.508 0.000 0.000 0.000 0.492
#> GSM674183     6  0.3288     0.6675 0.000 0.276 0.000 0.000 0.000 0.724
#> GSM674184     6  0.3446     0.6536 0.000 0.308 0.000 0.000 0.000 0.692
#> GSM674185     6  0.1059     0.6297 0.000 0.016 0.000 0.004 0.016 0.964
#> GSM674186     2  0.2996     0.6423 0.000 0.772 0.000 0.000 0.000 0.228
#> GSM674187     2  0.1757     0.8198 0.000 0.916 0.000 0.000 0.008 0.076
#> GSM674190     2  0.2912     0.6563 0.000 0.784 0.000 0.000 0.000 0.216
#> GSM674191     2  0.2912     0.6563 0.000 0.784 0.000 0.000 0.000 0.216
#> GSM674192     2  0.0547     0.8410 0.000 0.980 0.000 0.000 0.000 0.020
#> GSM674193     2  0.0713     0.8407 0.000 0.972 0.000 0.000 0.000 0.028
#> GSM674194     2  0.3266     0.5631 0.000 0.728 0.000 0.000 0.000 0.272
#> GSM674195     6  0.3464     0.6526 0.000 0.312 0.000 0.000 0.000 0.688
#> GSM674198     2  0.0260     0.8435 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM674200     6  0.0603     0.6128 0.000 0.000 0.000 0.004 0.016 0.980
#> GSM674201     2  0.3868    -0.1975 0.000 0.508 0.000 0.000 0.000 0.492
#> GSM674202     2  0.2950     0.7224 0.000 0.828 0.000 0.000 0.024 0.148
#> GSM674203     2  0.0260     0.8435 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM674204     2  0.0260     0.8435 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM674205     2  0.0547     0.8410 0.000 0.980 0.000 0.000 0.000 0.020
#> GSM674206     2  0.3804     0.1122 0.000 0.576 0.000 0.000 0.000 0.424
#> GSM674208     2  0.0260     0.8435 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM674209     2  0.0547     0.8426 0.000 0.980 0.000 0.000 0.000 0.020
#> GSM674210     2  0.0260     0.8435 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM674212     2  0.0291     0.8439 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM674214     2  0.0291     0.8439 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM674218     6  0.3592     0.6000 0.000 0.344 0.000 0.000 0.000 0.656
#> GSM674219     2  0.2340     0.7512 0.000 0.852 0.000 0.000 0.000 0.148
#> GSM674220     6  0.4035     0.4950 0.000 0.296 0.000 0.004 0.020 0.680
#> GSM674221     2  0.2340     0.7512 0.000 0.852 0.000 0.000 0.000 0.148
#> GSM674223     2  0.0713     0.8401 0.000 0.972 0.000 0.000 0.000 0.028
#> GSM674225     2  0.4593    -0.0716 0.000 0.492 0.000 0.000 0.036 0.472
#> GSM674226     2  0.0632     0.8418 0.000 0.976 0.000 0.000 0.000 0.024
#> GSM674229     2  0.0146     0.8435 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674230     2  0.1007     0.8379 0.000 0.956 0.000 0.000 0.000 0.044
#> GSM674231     2  0.1141     0.8358 0.000 0.948 0.000 0.000 0.000 0.052
#> GSM674232     2  0.0717     0.8385 0.000 0.976 0.000 0.000 0.016 0.008
#> GSM674234     2  0.0937     0.8405 0.000 0.960 0.000 0.000 0.000 0.040
#> GSM674235     2  0.2950     0.7224 0.000 0.828 0.000 0.000 0.024 0.148
#> GSM674236     2  0.2950     0.7224 0.000 0.828 0.000 0.000 0.024 0.148
#> GSM674237     2  0.0363     0.8429 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM674239     2  0.0260     0.8435 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM674240     2  0.3446     0.4546 0.000 0.692 0.000 0.000 0.000 0.308
#> GSM674242     2  0.0260     0.8435 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM674243     2  0.0972     0.8424 0.000 0.964 0.000 0.000 0.008 0.028
#> GSM674244     2  0.4593    -0.0716 0.000 0.492 0.000 0.000 0.036 0.472
#> GSM674245     2  0.0713     0.8416 0.000 0.972 0.000 0.000 0.000 0.028
#> GSM674282     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674284     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674285     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674287     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674288     1  0.3446     0.7781 0.692 0.000 0.000 0.000 0.308 0.000
#> GSM674289     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674291     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674292     1  0.0146     0.8652 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM674295     1  0.3659     0.7538 0.636 0.000 0.000 0.000 0.364 0.000
#> GSM674297     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674298     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674299     1  0.3288     0.7907 0.724 0.000 0.000 0.000 0.276 0.000
#> GSM674300     1  0.0458     0.8634 0.984 0.000 0.000 0.000 0.016 0.000
#> GSM674301     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674302     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674305     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674306     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674308     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674309     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674313     1  0.3756     0.7276 0.600 0.000 0.000 0.000 0.400 0.000
#> GSM674314     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674315     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674316     1  0.3634     0.7576 0.644 0.000 0.000 0.000 0.356 0.000
#> GSM674318     1  0.3659     0.7533 0.636 0.000 0.000 0.000 0.364 0.000
#> GSM674320     1  0.3756     0.7276 0.600 0.000 0.000 0.000 0.400 0.000
#> GSM674323     1  0.3659     0.7533 0.636 0.000 0.000 0.000 0.364 0.000
#> GSM674324     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674325     1  0.3659     0.7533 0.636 0.000 0.000 0.000 0.364 0.000
#> GSM674327     1  0.3620     0.7596 0.648 0.000 0.000 0.000 0.352 0.000
#> GSM674328     1  0.0458     0.8634 0.984 0.000 0.000 0.000 0.016 0.000
#> GSM674330     1  0.2178     0.8381 0.868 0.000 0.000 0.000 0.132 0.000
#> GSM674331     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674332     1  0.2178     0.8381 0.868 0.000 0.000 0.000 0.132 0.000
#> GSM674334     1  0.2178     0.8381 0.868 0.000 0.000 0.000 0.132 0.000
#> GSM674335     1  0.3672     0.7508 0.632 0.000 0.000 0.000 0.368 0.000
#> GSM674345     3  0.0603     0.8133 0.000 0.000 0.980 0.004 0.016 0.000
#> GSM674351     3  0.0725     0.8144 0.000 0.000 0.976 0.012 0.012 0.000
#> GSM674352     3  0.0725     0.8144 0.000 0.000 0.976 0.012 0.012 0.000
#> GSM674359     3  0.0146     0.8147 0.000 0.000 0.996 0.004 0.000 0.000
#> GSM674360     3  0.0937     0.8071 0.000 0.000 0.960 0.040 0.000 0.000
#> GSM674362     3  0.0260     0.8122 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM674369     3  0.0717     0.8156 0.000 0.000 0.976 0.016 0.008 0.000
#> GSM674372     3  0.4438     0.1891 0.000 0.000 0.628 0.328 0.044 0.000
#> GSM674374     4  0.3390     0.5022 0.000 0.000 0.296 0.704 0.000 0.000
#> GSM674376     4  0.2445     0.6108 0.000 0.000 0.108 0.872 0.020 0.000
#> GSM674377     4  0.1320     0.5791 0.000 0.000 0.036 0.948 0.016 0.000
#> GSM674378     4  0.3508     0.5034 0.000 0.000 0.292 0.704 0.004 0.000
#> GSM674383     3  0.1225     0.8076 0.000 0.000 0.952 0.036 0.012 0.000
#> GSM674386     4  0.0547     0.5526 0.000 0.000 0.000 0.980 0.020 0.000
#> GSM674387     4  0.2445     0.6108 0.000 0.000 0.108 0.872 0.020 0.000
#> GSM674392     3  0.3686     0.4857 0.000 0.000 0.748 0.220 0.032 0.000
#> GSM674396     4  0.5492     0.1799 0.000 0.000 0.168 0.552 0.280 0.000
#> GSM674399     4  0.5445     0.2031 0.000 0.000 0.168 0.564 0.268 0.000
#> GSM674404     4  0.5791    -0.0630 0.000 0.000 0.192 0.472 0.336 0.000
#> GSM674182     2  0.3864    -0.1650 0.000 0.520 0.000 0.000 0.000 0.480
#> GSM674188     2  0.1757     0.8198 0.000 0.916 0.000 0.000 0.008 0.076
#> GSM674189     6  0.3717     0.5107 0.000 0.384 0.000 0.000 0.000 0.616
#> GSM674196     2  0.0260     0.8435 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM674197     2  0.0260     0.8435 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM674199     2  0.0260     0.8435 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM674207     2  0.0291     0.8439 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM674211     2  0.0291     0.8439 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM674213     2  0.1444     0.8227 0.000 0.928 0.000 0.000 0.000 0.072
#> GSM674215     6  0.2393     0.6643 0.000 0.092 0.000 0.004 0.020 0.884
#> GSM674216     2  0.0909     0.8360 0.000 0.968 0.000 0.000 0.020 0.012
#> GSM674217     2  0.2340     0.7512 0.000 0.852 0.000 0.000 0.000 0.148
#> GSM674222     2  0.3956     0.4660 0.000 0.684 0.000 0.000 0.024 0.292
#> GSM674224     2  0.0632     0.8418 0.000 0.976 0.000 0.000 0.000 0.024
#> GSM674227     2  0.2950     0.7224 0.000 0.828 0.000 0.000 0.024 0.148
#> GSM674228     2  0.1075     0.8358 0.000 0.952 0.000 0.000 0.000 0.048
#> GSM674233     2  0.2340     0.7512 0.000 0.852 0.000 0.000 0.000 0.148
#> GSM674238     6  0.0603     0.6128 0.000 0.000 0.000 0.004 0.016 0.980
#> GSM674241     2  0.0260     0.8435 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM674283     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674286     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674293     1  0.0146     0.8652 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM674294     1  0.0146     0.8652 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM674296     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674303     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674307     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674310     1  0.3659     0.7533 0.636 0.000 0.000 0.000 0.364 0.000
#> GSM674311     1  0.0000     0.8656 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674312     1  0.3756     0.7276 0.600 0.000 0.000 0.000 0.400 0.000
#> GSM674317     1  0.2562     0.8272 0.828 0.000 0.000 0.000 0.172 0.000
#> GSM674319     1  0.3756     0.7276 0.600 0.000 0.000 0.000 0.400 0.000
#> GSM674321     1  0.3620     0.7596 0.648 0.000 0.000 0.000 0.352 0.000
#> GSM674322     1  0.3659     0.7533 0.636 0.000 0.000 0.000 0.364 0.000
#> GSM674326     1  0.3659     0.7533 0.636 0.000 0.000 0.000 0.364 0.000
#> GSM674329     1  0.3756     0.7276 0.600 0.000 0.000 0.000 0.400 0.000
#> GSM674333     1  0.3672     0.7508 0.632 0.000 0.000 0.000 0.368 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-MAD-hclust-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-MAD-hclust-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-MAD-hclust-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-MAD-hclust-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-MAD-hclust-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-MAD-hclust-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-MAD-hclust-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-MAD-hclust-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-MAD-hclust-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-MAD-hclust-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-MAD-hclust-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-MAD-hclust-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-MAD-hclust-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-MAD-hclust-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-MAD-hclust-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-MAD-hclust-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-MAD-hclust-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-MAD-hclust-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-MAD-hclust-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-MAD-hclust-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk MAD-hclust-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-MAD-hclust-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-MAD-hclust-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-MAD-hclust-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-MAD-hclust-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-MAD-hclust-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk MAD-hclust-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>              n disease.state(p) specimen(p) k
#> MAD:hclust 183            0.924    1.83e-40 2
#> MAD:hclust 183            0.962    6.15e-78 3
#> MAD:hclust 174            0.993    4.15e-72 4
#> MAD:hclust 168            0.974    8.79e-68 5
#> MAD:hclust 157            0.668    1.70e-61 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


MAD:kmeans**

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["MAD", "kmeans"]
# you can also extract it by
# res = res_list["MAD:kmeans"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#>   Subgroups are detected by 'kmeans' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 2.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk MAD-kmeans-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk MAD-kmeans-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 0.709           0.979       0.904         0.4921 0.750   0.571
#> 4 4 0.818           0.868       0.826         0.1176 1.000   1.000
#> 5 5 0.770           0.787       0.743         0.0778 1.000   1.000
#> 6 6 0.739           0.633       0.693         0.0465 0.843   0.527

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 2

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette    p1    p2    p3
#> GSM674344     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674346     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674347     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674348     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674349     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674350     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674353     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674354     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674355     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674356     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674357     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674358     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674361     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674363     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674364     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674365     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674366     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674367     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674368     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674370     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674371     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674373     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674375     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674379     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674380     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674381     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674382     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674384     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674385     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674388     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674389     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674390     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674391     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674393     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674394     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674395     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674397     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674398     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674400     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674401     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674402     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674403     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674405     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674406     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674407     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674181     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674183     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674184     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674185     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674186     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674187     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674190     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674191     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674192     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674193     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674194     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674195     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674198     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674200     2  0.3816      0.770 0.000 0.852 0.148
#> GSM674201     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674202     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674203     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674204     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674205     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674206     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674208     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674209     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674210     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674212     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674214     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674218     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674219     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674220     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674221     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674223     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674225     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674226     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674229     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674230     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674231     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674232     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674234     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674235     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674236     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674237     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674239     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674240     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674242     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674243     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674244     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674245     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674282     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674284     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674285     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674287     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674288     1  0.4605      0.911 0.796 0.000 0.204
#> GSM674289     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674290     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674291     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674292     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674295     1  0.4654      0.910 0.792 0.000 0.208
#> GSM674297     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674298     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674299     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674300     1  0.0592      0.948 0.988 0.000 0.012
#> GSM674301     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674302     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674304     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674305     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674306     1  0.0592      0.948 0.988 0.000 0.012
#> GSM674308     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674309     1  0.0747      0.948 0.984 0.000 0.016
#> GSM674313     1  0.4654      0.910 0.792 0.000 0.208
#> GSM674314     1  0.3879      0.923 0.848 0.000 0.152
#> GSM674315     1  0.0592      0.948 0.988 0.000 0.012
#> GSM674316     1  0.4555      0.912 0.800 0.000 0.200
#> GSM674318     1  0.4654      0.910 0.792 0.000 0.208
#> GSM674320     1  0.4654      0.910 0.792 0.000 0.208
#> GSM674323     1  0.4654      0.910 0.792 0.000 0.208
#> GSM674324     1  0.0237      0.949 0.996 0.000 0.004
#> GSM674325     1  0.4654      0.910 0.792 0.000 0.208
#> GSM674327     1  0.3551      0.928 0.868 0.000 0.132
#> GSM674328     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674330     1  0.3551      0.928 0.868 0.000 0.132
#> GSM674331     1  0.0237      0.949 0.996 0.000 0.004
#> GSM674332     1  0.0747      0.948 0.984 0.000 0.016
#> GSM674334     1  0.3116      0.932 0.892 0.000 0.108
#> GSM674335     1  0.4654      0.910 0.792 0.000 0.208
#> GSM674345     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674351     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674352     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674359     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674360     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674362     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674369     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674372     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674374     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674376     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674377     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674378     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674383     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674386     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674387     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674392     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674396     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674399     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674404     3  0.4654      1.000 0.000 0.208 0.792
#> GSM674182     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674188     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674189     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674196     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674197     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674199     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674207     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674211     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674213     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674215     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674216     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674217     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674222     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674224     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674227     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674228     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674233     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674238     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674241     2  0.0000      0.997 0.000 1.000 0.000
#> GSM674283     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674286     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674293     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674294     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674296     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674303     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674307     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674310     1  0.4654      0.910 0.792 0.000 0.208
#> GSM674311     1  0.0424      0.949 0.992 0.000 0.008
#> GSM674312     1  0.4654      0.910 0.792 0.000 0.208
#> GSM674317     1  0.0000      0.949 1.000 0.000 0.000
#> GSM674319     1  0.4654      0.910 0.792 0.000 0.208
#> GSM674321     1  0.4654      0.910 0.792 0.000 0.208
#> GSM674322     1  0.4654      0.910 0.792 0.000 0.208
#> GSM674326     1  0.4654      0.910 0.792 0.000 0.208
#> GSM674329     1  0.4654      0.910 0.792 0.000 0.208
#> GSM674333     1  0.4654      0.910 0.792 0.000 0.208

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1    p2    p3    p4
#> GSM674344     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674346     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674347     3  0.5995      0.868 0.000 0.096 0.672 0.232
#> GSM674348     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674349     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674350     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674353     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674354     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674355     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674356     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674357     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674358     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674361     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674363     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674364     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674365     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674366     3  0.4834      0.867 0.000 0.096 0.784 0.120
#> GSM674367     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674368     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674370     3  0.4297      0.868 0.000 0.096 0.820 0.084
#> GSM674371     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674373     3  0.4362      0.868 0.000 0.096 0.816 0.088
#> GSM674375     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674379     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674380     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674381     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674382     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674384     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674385     3  0.6025      0.870 0.000 0.096 0.668 0.236
#> GSM674388     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674389     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674390     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674391     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674393     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674394     3  0.5369      0.870 0.000 0.096 0.740 0.164
#> GSM674395     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674397     3  0.5867      0.871 0.000 0.096 0.688 0.216
#> GSM674398     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674400     3  0.2611      0.862 0.000 0.096 0.896 0.008
#> GSM674401     3  0.2611      0.862 0.000 0.096 0.896 0.008
#> GSM674402     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674403     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674405     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674406     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674407     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674181     2  0.1474      0.884 0.000 0.948 0.000 0.052
#> GSM674183     2  0.2469      0.866 0.000 0.892 0.000 0.108
#> GSM674184     2  0.2469      0.866 0.000 0.892 0.000 0.108
#> GSM674185     2  0.2469      0.866 0.000 0.892 0.000 0.108
#> GSM674186     2  0.1389      0.885 0.000 0.952 0.000 0.048
#> GSM674187     2  0.0188      0.891 0.000 0.996 0.000 0.004
#> GSM674190     2  0.1389      0.885 0.000 0.952 0.000 0.048
#> GSM674191     2  0.1557      0.883 0.000 0.944 0.000 0.056
#> GSM674192     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674193     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674194     2  0.2408      0.867 0.000 0.896 0.000 0.104
#> GSM674195     2  0.2469      0.866 0.000 0.892 0.000 0.108
#> GSM674198     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674200     2  0.5817      0.602 0.000 0.676 0.076 0.248
#> GSM674201     2  0.2469      0.866 0.000 0.892 0.000 0.108
#> GSM674202     2  0.1716      0.881 0.000 0.936 0.000 0.064
#> GSM674203     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674204     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674205     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674206     2  0.2345      0.869 0.000 0.900 0.000 0.100
#> GSM674208     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674209     2  0.2760      0.884 0.000 0.872 0.000 0.128
#> GSM674210     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674212     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674214     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674218     2  0.2469      0.866 0.000 0.892 0.000 0.108
#> GSM674219     2  0.1211      0.887 0.000 0.960 0.000 0.040
#> GSM674220     2  0.2469      0.866 0.000 0.892 0.000 0.108
#> GSM674221     2  0.0000      0.891 0.000 1.000 0.000 0.000
#> GSM674223     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674225     2  0.2345      0.869 0.000 0.900 0.000 0.100
#> GSM674226     2  0.3024      0.881 0.000 0.852 0.000 0.148
#> GSM674229     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674230     2  0.0707      0.890 0.000 0.980 0.000 0.020
#> GSM674231     2  0.2281      0.887 0.000 0.904 0.000 0.096
#> GSM674232     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674234     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674235     2  0.0707      0.890 0.000 0.980 0.000 0.020
#> GSM674236     2  0.0817      0.890 0.000 0.976 0.000 0.024
#> GSM674237     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674239     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674240     2  0.0707      0.890 0.000 0.980 0.000 0.020
#> GSM674242     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674243     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674244     2  0.2469      0.866 0.000 0.892 0.000 0.108
#> GSM674245     2  0.0921      0.892 0.000 0.972 0.000 0.028
#> GSM674282     1  0.0336      0.894 0.992 0.000 0.008 0.000
#> GSM674284     1  0.0336      0.894 0.992 0.000 0.008 0.000
#> GSM674285     1  0.0336      0.894 0.992 0.000 0.008 0.000
#> GSM674287     1  0.0336      0.894 0.992 0.000 0.008 0.000
#> GSM674288     1  0.5442      0.823 0.636 0.000 0.028 0.336
#> GSM674289     1  0.0336      0.894 0.992 0.000 0.008 0.000
#> GSM674290     1  0.0336      0.894 0.992 0.000 0.008 0.000
#> GSM674291     1  0.0336      0.894 0.992 0.000 0.008 0.000
#> GSM674292     1  0.0336      0.894 0.992 0.000 0.008 0.000
#> GSM674295     1  0.5582      0.816 0.620 0.000 0.032 0.348
#> GSM674297     1  0.1118      0.892 0.964 0.000 0.036 0.000
#> GSM674298     1  0.1118      0.892 0.964 0.000 0.036 0.000
#> GSM674299     1  0.0336      0.894 0.992 0.000 0.008 0.000
#> GSM674300     1  0.2399      0.892 0.920 0.000 0.048 0.032
#> GSM674301     1  0.0188      0.894 0.996 0.000 0.004 0.000
#> GSM674302     1  0.0188      0.894 0.996 0.000 0.004 0.000
#> GSM674304     1  0.0188      0.894 0.996 0.000 0.004 0.000
#> GSM674305     1  0.0188      0.894 0.996 0.000 0.004 0.000
#> GSM674306     1  0.2483      0.890 0.916 0.000 0.052 0.032
#> GSM674308     1  0.0000      0.894 1.000 0.000 0.000 0.000
#> GSM674309     1  0.2313      0.891 0.924 0.000 0.044 0.032
#> GSM674313     1  0.5790      0.815 0.616 0.000 0.044 0.340
#> GSM674314     1  0.5123      0.853 0.724 0.000 0.044 0.232
#> GSM674315     1  0.2483      0.890 0.916 0.000 0.052 0.032
#> GSM674316     1  0.5492      0.826 0.640 0.000 0.032 0.328
#> GSM674318     1  0.5070      0.817 0.620 0.000 0.008 0.372
#> GSM674320     1  0.5582      0.816 0.620 0.000 0.032 0.348
#> GSM674323     1  0.5070      0.817 0.620 0.000 0.008 0.372
#> GSM674324     1  0.1489      0.892 0.952 0.000 0.044 0.004
#> GSM674325     1  0.5070      0.817 0.620 0.000 0.008 0.372
#> GSM674327     1  0.4877      0.859 0.752 0.000 0.044 0.204
#> GSM674328     1  0.1022      0.894 0.968 0.000 0.032 0.000
#> GSM674330     1  0.4745      0.859 0.756 0.000 0.036 0.208
#> GSM674331     1  0.1489      0.892 0.952 0.000 0.044 0.004
#> GSM674332     1  0.2214      0.891 0.928 0.000 0.044 0.028
#> GSM674334     1  0.4590      0.863 0.772 0.000 0.036 0.192
#> GSM674335     1  0.5511      0.816 0.620 0.000 0.028 0.352
#> GSM674345     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674351     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674352     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674359     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674360     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674362     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674369     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674372     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674374     3  0.3716      0.866 0.000 0.096 0.852 0.052
#> GSM674376     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674377     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674378     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674383     3  0.6464      0.865 0.000 0.096 0.596 0.308
#> GSM674386     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674387     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674392     3  0.5495      0.870 0.000 0.096 0.728 0.176
#> GSM674396     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674399     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674404     3  0.2281      0.861 0.000 0.096 0.904 0.000
#> GSM674182     2  0.1474      0.884 0.000 0.948 0.000 0.052
#> GSM674188     2  0.0707      0.890 0.000 0.980 0.000 0.020
#> GSM674189     2  0.2469      0.866 0.000 0.892 0.000 0.108
#> GSM674196     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674197     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674199     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674207     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674211     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674213     2  0.0188      0.891 0.000 0.996 0.000 0.004
#> GSM674215     2  0.2469      0.866 0.000 0.892 0.000 0.108
#> GSM674216     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674217     2  0.0336      0.891 0.000 0.992 0.000 0.008
#> GSM674222     2  0.1716      0.881 0.000 0.936 0.000 0.064
#> GSM674224     2  0.3074      0.880 0.000 0.848 0.000 0.152
#> GSM674227     2  0.1716      0.881 0.000 0.936 0.000 0.064
#> GSM674228     2  0.0000      0.891 0.000 1.000 0.000 0.000
#> GSM674233     2  0.0188      0.891 0.000 0.996 0.000 0.004
#> GSM674238     2  0.3074      0.835 0.000 0.848 0.000 0.152
#> GSM674241     2  0.3610      0.873 0.000 0.800 0.000 0.200
#> GSM674283     1  0.0336      0.894 0.992 0.000 0.008 0.000
#> GSM674286     1  0.0336      0.894 0.992 0.000 0.008 0.000
#> GSM674293     1  0.0336      0.894 0.992 0.000 0.008 0.000
#> GSM674294     1  0.0336      0.894 0.992 0.000 0.008 0.000
#> GSM674296     1  0.0707      0.893 0.980 0.000 0.020 0.000
#> GSM674303     1  0.0000      0.894 1.000 0.000 0.000 0.000
#> GSM674307     1  0.0707      0.893 0.980 0.000 0.020 0.000
#> GSM674310     1  0.5070      0.817 0.620 0.000 0.008 0.372
#> GSM674311     1  0.1635      0.892 0.948 0.000 0.044 0.008
#> GSM674312     1  0.5582      0.816 0.620 0.000 0.032 0.348
#> GSM674317     1  0.0657      0.894 0.984 0.000 0.012 0.004
#> GSM674319     1  0.5582      0.816 0.620 0.000 0.032 0.348
#> GSM674321     1  0.5070      0.817 0.620 0.000 0.008 0.372
#> GSM674322     1  0.4790      0.816 0.620 0.000 0.000 0.380
#> GSM674326     1  0.5070      0.817 0.620 0.000 0.008 0.372
#> GSM674329     1  0.5511      0.816 0.620 0.000 0.028 0.352
#> GSM674333     1  0.5070      0.816 0.620 0.000 0.008 0.372

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3 p4 p5
#> GSM674344     3  0.6556      0.779 0.000 0.028 0.480 NA NA
#> GSM674346     3  0.6649      0.779 0.000 0.028 0.480 NA NA
#> GSM674347     3  0.6535      0.788 0.000 0.028 0.572 NA NA
#> GSM674348     3  0.6649      0.779 0.000 0.028 0.480 NA NA
#> GSM674349     3  0.6907      0.780 0.000 0.028 0.480 NA NA
#> GSM674350     3  0.6678      0.779 0.000 0.028 0.480 NA NA
#> GSM674353     3  0.6678      0.779 0.000 0.028 0.480 NA NA
#> GSM674354     3  0.6649      0.779 0.000 0.028 0.480 NA NA
#> GSM674355     3  0.6671      0.780 0.000 0.028 0.484 NA NA
#> GSM674356     3  0.6678      0.779 0.000 0.028 0.480 NA NA
#> GSM674357     3  0.6649      0.779 0.000 0.028 0.480 NA NA
#> GSM674358     3  0.6678      0.779 0.000 0.028 0.480 NA NA
#> GSM674361     3  0.6678      0.779 0.000 0.028 0.480 NA NA
#> GSM674363     3  0.6678      0.779 0.000 0.028 0.480 NA NA
#> GSM674364     3  0.6556      0.779 0.000 0.028 0.480 NA NA
#> GSM674365     3  0.6925      0.780 0.000 0.028 0.480 NA NA
#> GSM674366     3  0.5663      0.788 0.000 0.028 0.688 NA NA
#> GSM674367     3  0.1830      0.779 0.000 0.028 0.932 NA NA
#> GSM674368     3  0.6869      0.780 0.000 0.028 0.480 NA NA
#> GSM674370     3  0.3823      0.792 0.000 0.028 0.836 NA NA
#> GSM674371     3  0.6942      0.780 0.000 0.028 0.480 NA NA
#> GSM674373     3  0.3823      0.791 0.000 0.028 0.836 NA NA
#> GSM674375     3  0.1750      0.778 0.000 0.028 0.936 NA NA
#> GSM674379     3  0.0955      0.776 0.000 0.028 0.968 NA NA
#> GSM674380     3  0.1082      0.775 0.000 0.028 0.964 NA NA
#> GSM674381     3  0.1300      0.778 0.000 0.028 0.956 NA NA
#> GSM674382     3  0.0794      0.776 0.000 0.028 0.972 NA NA
#> GSM674384     3  0.1082      0.777 0.000 0.028 0.964 NA NA
#> GSM674385     3  0.5790      0.797 0.000 0.028 0.652 NA NA
#> GSM674388     3  0.6925      0.780 0.000 0.028 0.480 NA NA
#> GSM674389     3  0.1668      0.776 0.000 0.028 0.940 NA NA
#> GSM674390     3  0.0955      0.776 0.000 0.028 0.968 NA NA
#> GSM674391     3  0.0794      0.776 0.000 0.028 0.972 NA NA
#> GSM674393     3  0.2548      0.780 0.000 0.028 0.896 NA NA
#> GSM674394     3  0.5254      0.796 0.000 0.028 0.712 NA NA
#> GSM674395     3  0.1082      0.776 0.000 0.028 0.964 NA NA
#> GSM674397     3  0.5846      0.797 0.000 0.028 0.656 NA NA
#> GSM674398     3  0.1582      0.776 0.000 0.028 0.944 NA NA
#> GSM674400     3  0.3023      0.782 0.000 0.028 0.872 NA NA
#> GSM674401     3  0.3023      0.782 0.000 0.028 0.872 NA NA
#> GSM674402     3  0.6705      0.780 0.000 0.028 0.480 NA NA
#> GSM674403     3  0.7024      0.781 0.000 0.028 0.480 NA NA
#> GSM674405     3  0.1750      0.776 0.000 0.028 0.936 NA NA
#> GSM674406     3  0.0955      0.776 0.000 0.028 0.968 NA NA
#> GSM674407     3  0.0794      0.776 0.000 0.028 0.972 NA NA
#> GSM674181     2  0.2291      0.792 0.000 0.908 0.000 NA NA
#> GSM674183     2  0.4528      0.741 0.000 0.728 0.000 NA NA
#> GSM674184     2  0.4528      0.741 0.000 0.728 0.000 NA NA
#> GSM674185     2  0.4588      0.740 0.000 0.720 0.000 NA NA
#> GSM674186     2  0.2278      0.794 0.000 0.908 0.000 NA NA
#> GSM674187     2  0.0162      0.805 0.000 0.996 0.000 NA NA
#> GSM674190     2  0.2278      0.794 0.000 0.908 0.000 NA NA
#> GSM674191     2  0.2491      0.791 0.000 0.896 0.000 NA NA
#> GSM674192     2  0.4288      0.775 0.000 0.612 0.000 NA NA
#> GSM674193     2  0.4009      0.787 0.000 0.684 0.000 NA NA
#> GSM674194     2  0.3888      0.759 0.000 0.800 0.000 NA NA
#> GSM674195     2  0.4528      0.741 0.000 0.728 0.000 NA NA
#> GSM674198     2  0.4150      0.774 0.000 0.612 0.000 NA NA
#> GSM674200     2  0.6362      0.591 0.000 0.572 0.012 NA NA
#> GSM674201     2  0.4035      0.753 0.000 0.784 0.000 NA NA
#> GSM674202     2  0.3944      0.777 0.000 0.788 0.000 NA NA
#> GSM674203     2  0.4171      0.773 0.000 0.604 0.000 NA NA
#> GSM674204     2  0.4138      0.774 0.000 0.616 0.000 NA NA
#> GSM674205     2  0.4138      0.774 0.000 0.616 0.000 NA NA
#> GSM674206     2  0.3601      0.766 0.000 0.820 0.000 NA NA
#> GSM674208     2  0.4171      0.773 0.000 0.604 0.000 NA NA
#> GSM674209     2  0.3430      0.802 0.000 0.776 0.000 NA NA
#> GSM674210     2  0.4150      0.774 0.000 0.612 0.000 NA NA
#> GSM674212     2  0.4114      0.776 0.000 0.624 0.000 NA NA
#> GSM674214     2  0.4126      0.776 0.000 0.620 0.000 NA NA
#> GSM674218     2  0.4528      0.741 0.000 0.728 0.000 NA NA
#> GSM674219     2  0.1211      0.800 0.000 0.960 0.000 NA NA
#> GSM674220     2  0.5059      0.741 0.000 0.668 0.000 NA NA
#> GSM674221     2  0.0162      0.805 0.000 0.996 0.000 NA NA
#> GSM674223     2  0.4009      0.786 0.000 0.684 0.000 NA NA
#> GSM674225     2  0.5066      0.745 0.000 0.676 0.000 NA NA
#> GSM674226     2  0.3994      0.803 0.000 0.772 0.000 NA NA
#> GSM674229     2  0.4101      0.777 0.000 0.628 0.000 NA NA
#> GSM674230     2  0.2390      0.802 0.000 0.896 0.000 NA NA
#> GSM674231     2  0.3280      0.807 0.000 0.812 0.000 NA NA
#> GSM674232     2  0.4761      0.778 0.000 0.616 0.000 NA NA
#> GSM674234     2  0.3983      0.782 0.000 0.660 0.000 NA NA
#> GSM674235     2  0.2712      0.799 0.000 0.880 0.000 NA NA
#> GSM674236     2  0.2850      0.798 0.000 0.872 0.000 NA NA
#> GSM674237     2  0.4171      0.773 0.000 0.604 0.000 NA NA
#> GSM674239     2  0.4138      0.774 0.000 0.616 0.000 NA NA
#> GSM674240     2  0.1741      0.798 0.000 0.936 0.000 NA NA
#> GSM674242     2  0.4171      0.773 0.000 0.604 0.000 NA NA
#> GSM674243     2  0.4029      0.785 0.000 0.680 0.000 NA NA
#> GSM674244     2  0.5117      0.743 0.000 0.672 0.000 NA NA
#> GSM674245     2  0.2676      0.803 0.000 0.884 0.000 NA NA
#> GSM674282     1  0.4304      0.847 0.516 0.000 0.000 NA NA
#> GSM674284     1  0.4448      0.847 0.516 0.000 0.000 NA NA
#> GSM674285     1  0.4591      0.847 0.516 0.000 0.004 NA NA
#> GSM674287     1  0.4304      0.847 0.516 0.000 0.000 NA NA
#> GSM674288     1  0.1670      0.753 0.936 0.000 0.000 NA NA
#> GSM674289     1  0.4304      0.847 0.516 0.000 0.000 NA NA
#> GSM674290     1  0.4448      0.847 0.516 0.000 0.004 NA NA
#> GSM674291     1  0.4304      0.847 0.516 0.000 0.000 NA NA
#> GSM674292     1  0.4304      0.847 0.516 0.000 0.000 NA NA
#> GSM674295     1  0.0992      0.739 0.968 0.000 0.008 NA NA
#> GSM674297     1  0.5856      0.845 0.516 0.000 0.008 NA NA
#> GSM674298     1  0.5856      0.845 0.516 0.000 0.008 NA NA
#> GSM674299     1  0.4304      0.847 0.516 0.000 0.000 NA NA
#> GSM674300     1  0.5533      0.846 0.540 0.000 0.004 NA NA
#> GSM674301     1  0.4992      0.848 0.516 0.000 0.008 NA NA
#> GSM674302     1  0.5148      0.847 0.516 0.000 0.008 NA NA
#> GSM674304     1  0.5148      0.847 0.516 0.000 0.008 NA NA
#> GSM674305     1  0.5148      0.847 0.516 0.000 0.008 NA NA
#> GSM674306     1  0.6079      0.842 0.540 0.000 0.012 NA NA
#> GSM674308     1  0.5111      0.848 0.516 0.000 0.004 NA NA
#> GSM674309     1  0.5606      0.845 0.556 0.000 0.000 NA NA
#> GSM674313     1  0.1757      0.738 0.936 0.000 0.012 NA NA
#> GSM674314     1  0.3849      0.791 0.808 0.000 0.000 NA NA
#> GSM674315     1  0.6079      0.842 0.540 0.000 0.012 NA NA
#> GSM674316     1  0.1809      0.754 0.928 0.000 0.000 NA NA
#> GSM674318     1  0.0162      0.740 0.996 0.000 0.004 NA NA
#> GSM674320     1  0.1106      0.739 0.964 0.000 0.012 NA NA
#> GSM674323     1  0.0000      0.740 1.000 0.000 0.000 NA NA
#> GSM674324     1  0.5670      0.845 0.528 0.000 0.000 NA NA
#> GSM674325     1  0.0000      0.740 1.000 0.000 0.000 NA NA
#> GSM674327     1  0.4452      0.800 0.760 0.000 0.004 NA NA
#> GSM674328     1  0.5174      0.848 0.520 0.000 0.004 NA NA
#> GSM674330     1  0.3994      0.797 0.792 0.000 0.000 NA NA
#> GSM674331     1  0.5670      0.845 0.528 0.000 0.000 NA NA
#> GSM674332     1  0.5606      0.845 0.556 0.000 0.000 NA NA
#> GSM674334     1  0.4238      0.804 0.768 0.000 0.000 NA NA
#> GSM674335     1  0.0992      0.739 0.968 0.000 0.008 NA NA
#> GSM674345     3  0.6827      0.780 0.000 0.028 0.480 NA NA
#> GSM674351     3  0.6678      0.779 0.000 0.028 0.480 NA NA
#> GSM674352     3  0.6678      0.779 0.000 0.028 0.480 NA NA
#> GSM674359     3  0.6649      0.779 0.000 0.028 0.480 NA NA
#> GSM674360     3  0.6705      0.780 0.000 0.028 0.480 NA NA
#> GSM674362     3  0.6556      0.779 0.000 0.028 0.480 NA NA
#> GSM674369     3  0.6925      0.780 0.000 0.028 0.480 NA NA
#> GSM674372     3  0.2430      0.782 0.000 0.028 0.912 NA NA
#> GSM674374     3  0.3432      0.789 0.000 0.028 0.860 NA NA
#> GSM674376     3  0.0794      0.776 0.000 0.028 0.972 NA NA
#> GSM674377     3  0.1195      0.778 0.000 0.028 0.960 NA NA
#> GSM674378     3  0.1668      0.779 0.000 0.028 0.940 NA NA
#> GSM674383     3  0.6942      0.780 0.000 0.028 0.480 NA NA
#> GSM674386     3  0.1668      0.776 0.000 0.028 0.940 NA NA
#> GSM674387     3  0.0794      0.776 0.000 0.028 0.972 NA NA
#> GSM674392     3  0.5579      0.796 0.000 0.028 0.676 NA NA
#> GSM674396     3  0.1668      0.776 0.000 0.028 0.940 NA NA
#> GSM674399     3  0.1668      0.776 0.000 0.028 0.940 NA NA
#> GSM674404     3  0.1668      0.776 0.000 0.028 0.940 NA NA
#> GSM674182     2  0.2221      0.793 0.000 0.912 0.000 NA NA
#> GSM674188     2  0.0579      0.804 0.000 0.984 0.000 NA NA
#> GSM674189     2  0.4558      0.742 0.000 0.724 0.000 NA NA
#> GSM674196     2  0.4138      0.774 0.000 0.616 0.000 NA NA
#> GSM674197     2  0.4138      0.774 0.000 0.616 0.000 NA NA
#> GSM674199     2  0.4150      0.774 0.000 0.612 0.000 NA NA
#> GSM674207     2  0.4126      0.776 0.000 0.620 0.000 NA NA
#> GSM674211     2  0.4114      0.776 0.000 0.624 0.000 NA NA
#> GSM674213     2  0.0290      0.805 0.000 0.992 0.000 NA NA
#> GSM674215     2  0.5059      0.741 0.000 0.668 0.000 NA NA
#> GSM674216     2  0.5260      0.778 0.000 0.604 0.000 NA NA
#> GSM674217     2  0.0162      0.804 0.000 0.996 0.000 NA NA
#> GSM674222     2  0.4238      0.772 0.000 0.756 0.000 NA NA
#> GSM674224     2  0.3491      0.800 0.000 0.768 0.000 NA NA
#> GSM674227     2  0.3904      0.778 0.000 0.792 0.000 NA NA
#> GSM674228     2  0.1907      0.807 0.000 0.928 0.000 NA NA
#> GSM674233     2  0.0162      0.804 0.000 0.996 0.000 NA NA
#> GSM674238     2  0.5423      0.686 0.000 0.652 0.000 NA NA
#> GSM674241     2  0.4150      0.774 0.000 0.612 0.000 NA NA
#> GSM674283     1  0.4591      0.847 0.516 0.000 0.004 NA NA
#> GSM674286     1  0.4448      0.847 0.516 0.000 0.004 NA NA
#> GSM674293     1  0.4304      0.847 0.516 0.000 0.000 NA NA
#> GSM674294     1  0.4304      0.847 0.516 0.000 0.000 NA NA
#> GSM674296     1  0.5770      0.846 0.516 0.000 0.008 NA NA
#> GSM674303     1  0.5178      0.848 0.516 0.000 0.004 NA NA
#> GSM674307     1  0.5770      0.846 0.516 0.000 0.008 NA NA
#> GSM674310     1  0.0162      0.740 0.996 0.000 0.004 NA NA
#> GSM674311     1  0.5654      0.845 0.536 0.000 0.000 NA NA
#> GSM674312     1  0.1106      0.739 0.964 0.000 0.012 NA NA
#> GSM674317     1  0.4653      0.848 0.516 0.000 0.000 NA NA
#> GSM674319     1  0.0992      0.739 0.968 0.000 0.008 NA NA
#> GSM674321     1  0.0000      0.740 1.000 0.000 0.000 NA NA
#> GSM674322     1  0.0451      0.739 0.988 0.000 0.004 NA NA
#> GSM674326     1  0.0162      0.740 0.996 0.000 0.004 NA NA
#> GSM674329     1  0.0992      0.739 0.968 0.000 0.008 NA NA
#> GSM674333     1  0.0451      0.739 0.988 0.000 0.004 NA NA

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4    p5    p6
#> GSM674344     3  0.4161    0.90872 0.000 0.000 0.608 0.376 0.004 0.012
#> GSM674346     3  0.4591    0.90411 0.000 0.000 0.588 0.376 0.024 0.012
#> GSM674347     4  0.5984   -0.63985 0.000 0.000 0.412 0.460 0.076 0.052
#> GSM674348     3  0.4752    0.90342 0.000 0.000 0.580 0.376 0.020 0.024
#> GSM674349     3  0.5560    0.88112 0.000 0.000 0.528 0.376 0.052 0.044
#> GSM674350     3  0.4894    0.89597 0.000 0.000 0.572 0.376 0.028 0.024
#> GSM674353     3  0.4894    0.89597 0.000 0.000 0.572 0.376 0.028 0.024
#> GSM674354     3  0.4518    0.90299 0.000 0.000 0.592 0.376 0.020 0.012
#> GSM674355     3  0.4904    0.89344 0.000 0.000 0.568 0.380 0.028 0.024
#> GSM674356     3  0.4601    0.90541 0.000 0.000 0.588 0.376 0.016 0.020
#> GSM674357     3  0.4518    0.90299 0.000 0.000 0.592 0.376 0.020 0.012
#> GSM674358     3  0.4894    0.89597 0.000 0.000 0.572 0.376 0.028 0.024
#> GSM674361     3  0.4963    0.89421 0.000 0.000 0.568 0.376 0.028 0.028
#> GSM674363     3  0.4821    0.89811 0.000 0.000 0.576 0.376 0.028 0.020
#> GSM674364     3  0.4161    0.90791 0.000 0.000 0.608 0.376 0.004 0.012
#> GSM674365     3  0.5665    0.87267 0.000 0.000 0.520 0.376 0.056 0.048
#> GSM674366     4  0.5225    0.27985 0.000 0.000 0.204 0.672 0.064 0.060
#> GSM674367     4  0.1418    0.80495 0.000 0.000 0.000 0.944 0.032 0.024
#> GSM674368     3  0.5641    0.86027 0.000 0.000 0.508 0.392 0.048 0.052
#> GSM674370     4  0.3461    0.66750 0.000 0.000 0.092 0.832 0.044 0.032
#> GSM674371     3  0.5717    0.87276 0.000 0.000 0.516 0.376 0.056 0.052
#> GSM674373     4  0.3317    0.65826 0.000 0.000 0.104 0.836 0.036 0.024
#> GSM674375     4  0.1498    0.81447 0.000 0.000 0.000 0.940 0.028 0.032
#> GSM674379     4  0.0260    0.81703 0.000 0.000 0.000 0.992 0.000 0.008
#> GSM674380     4  0.0405    0.81393 0.000 0.000 0.000 0.988 0.008 0.004
#> GSM674381     4  0.0820    0.81019 0.000 0.000 0.000 0.972 0.016 0.012
#> GSM674382     4  0.0291    0.81674 0.000 0.000 0.000 0.992 0.004 0.004
#> GSM674384     4  0.0976    0.81476 0.000 0.000 0.008 0.968 0.016 0.008
#> GSM674385     4  0.5241   -0.49671 0.000 0.000 0.400 0.528 0.024 0.048
#> GSM674388     3  0.5672    0.86932 0.000 0.000 0.516 0.380 0.056 0.048
#> GSM674389     4  0.1794    0.80711 0.000 0.000 0.000 0.924 0.040 0.036
#> GSM674390     4  0.0291    0.81460 0.000 0.000 0.000 0.992 0.004 0.004
#> GSM674391     4  0.0291    0.81674 0.000 0.000 0.000 0.992 0.004 0.004
#> GSM674393     4  0.3127    0.76774 0.000 0.000 0.020 0.852 0.084 0.044
#> GSM674394     4  0.5121   -0.13246 0.000 0.000 0.320 0.604 0.036 0.040
#> GSM674395     4  0.0909    0.81655 0.000 0.000 0.000 0.968 0.012 0.020
#> GSM674397     4  0.5247   -0.43506 0.000 0.000 0.364 0.560 0.044 0.032
#> GSM674398     4  0.1649    0.80960 0.000 0.000 0.000 0.932 0.036 0.032
#> GSM674400     4  0.3637    0.74298 0.000 0.000 0.032 0.820 0.096 0.052
#> GSM674401     4  0.3637    0.74298 0.000 0.000 0.032 0.820 0.096 0.052
#> GSM674402     3  0.5004    0.88500 0.000 0.000 0.572 0.368 0.036 0.024
#> GSM674403     3  0.5932    0.84900 0.000 0.000 0.504 0.368 0.076 0.052
#> GSM674405     4  0.1720    0.80843 0.000 0.000 0.000 0.928 0.040 0.032
#> GSM674406     4  0.0291    0.81460 0.000 0.000 0.000 0.992 0.004 0.004
#> GSM674407     4  0.0000    0.81586 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674181     6  0.4611    0.56310 0.000 0.392 0.016 0.012 0.004 0.576
#> GSM674183     6  0.5939    0.70866 0.000 0.288 0.068 0.012 0.052 0.580
#> GSM674184     6  0.5992    0.70832 0.000 0.288 0.068 0.012 0.056 0.576
#> GSM674185     6  0.5990    0.70573 0.000 0.276 0.072 0.012 0.056 0.584
#> GSM674186     6  0.4729    0.54347 0.000 0.400 0.016 0.012 0.008 0.564
#> GSM674187     2  0.5670   -0.24104 0.000 0.484 0.040 0.012 0.036 0.428
#> GSM674190     6  0.4545    0.54664 0.000 0.400 0.012 0.012 0.004 0.572
#> GSM674191     6  0.4519    0.56828 0.000 0.388 0.012 0.012 0.004 0.584
#> GSM674192     2  0.1699    0.66965 0.000 0.936 0.040 0.012 0.004 0.008
#> GSM674193     2  0.3654    0.61033 0.000 0.824 0.048 0.012 0.016 0.100
#> GSM674194     6  0.4490    0.68108 0.000 0.296 0.012 0.012 0.016 0.664
#> GSM674195     6  0.5992    0.70832 0.000 0.288 0.068 0.012 0.056 0.576
#> GSM674198     2  0.0870    0.67609 0.000 0.972 0.004 0.012 0.012 0.000
#> GSM674200     6  0.6516    0.58893 0.000 0.180 0.152 0.024 0.060 0.584
#> GSM674201     6  0.4553    0.69788 0.000 0.292 0.020 0.012 0.012 0.664
#> GSM674202     6  0.7364    0.51479 0.000 0.332 0.084 0.012 0.204 0.368
#> GSM674203     2  0.1414    0.66781 0.000 0.952 0.004 0.012 0.020 0.012
#> GSM674204     2  0.0653    0.67769 0.000 0.980 0.004 0.012 0.004 0.000
#> GSM674205     2  0.0870    0.67780 0.000 0.972 0.012 0.012 0.004 0.000
#> GSM674206     6  0.4216    0.68101 0.000 0.296 0.008 0.012 0.008 0.676
#> GSM674208     2  0.1167    0.66849 0.000 0.960 0.000 0.012 0.020 0.008
#> GSM674209     2  0.4885    0.45832 0.000 0.708 0.060 0.012 0.024 0.196
#> GSM674210     2  0.0870    0.67762 0.000 0.972 0.012 0.012 0.004 0.000
#> GSM674212     2  0.1691    0.67212 0.000 0.940 0.028 0.012 0.008 0.012
#> GSM674214     2  0.1672    0.67157 0.000 0.940 0.028 0.012 0.016 0.004
#> GSM674218     6  0.6084    0.70689 0.000 0.288 0.076 0.012 0.056 0.568
#> GSM674219     6  0.5502    0.36930 0.000 0.440 0.032 0.012 0.032 0.484
#> GSM674220     6  0.7445    0.62983 0.000 0.276 0.108 0.012 0.196 0.408
#> GSM674221     2  0.5554   -0.21166 0.000 0.492 0.036 0.012 0.032 0.428
#> GSM674223     2  0.3401    0.61604 0.000 0.832 0.048 0.012 0.004 0.104
#> GSM674225     6  0.7516    0.59342 0.000 0.296 0.100 0.012 0.224 0.368
#> GSM674226     2  0.5990    0.38365 0.000 0.632 0.080 0.012 0.088 0.188
#> GSM674229     2  0.1616    0.67249 0.000 0.940 0.020 0.012 0.000 0.028
#> GSM674230     2  0.6868   -0.30870 0.000 0.428 0.052 0.012 0.160 0.348
#> GSM674231     2  0.5398    0.37279 0.000 0.660 0.064 0.012 0.040 0.224
#> GSM674232     2  0.2799    0.62379 0.000 0.880 0.028 0.012 0.068 0.012
#> GSM674234     2  0.3182    0.63938 0.000 0.856 0.040 0.012 0.012 0.080
#> GSM674235     2  0.7205   -0.36191 0.000 0.400 0.072 0.012 0.192 0.324
#> GSM674236     2  0.7274   -0.40328 0.000 0.388 0.076 0.012 0.200 0.324
#> GSM674237     2  0.1251    0.66653 0.000 0.956 0.000 0.012 0.024 0.008
#> GSM674239     2  0.0363    0.67801 0.000 0.988 0.000 0.012 0.000 0.000
#> GSM674240     6  0.5220    0.33809 0.000 0.460 0.036 0.012 0.012 0.480
#> GSM674242     2  0.1498    0.66580 0.000 0.948 0.004 0.012 0.024 0.012
#> GSM674243     2  0.3091    0.63196 0.000 0.856 0.044 0.012 0.004 0.084
#> GSM674244     6  0.7487    0.60280 0.000 0.292 0.100 0.012 0.216 0.380
#> GSM674245     2  0.6807   -0.17745 0.000 0.464 0.052 0.012 0.160 0.312
#> GSM674282     1  0.0260    0.80669 0.992 0.000 0.008 0.000 0.000 0.000
#> GSM674284     1  0.0405    0.80863 0.988 0.000 0.008 0.000 0.000 0.004
#> GSM674285     1  0.0653    0.80866 0.980 0.004 0.012 0.000 0.000 0.004
#> GSM674287     1  0.0260    0.80669 0.992 0.000 0.008 0.000 0.000 0.000
#> GSM674288     1  0.5149   -0.82459 0.472 0.000 0.048 0.000 0.464 0.016
#> GSM674289     1  0.0260    0.80669 0.992 0.000 0.008 0.000 0.000 0.000
#> GSM674290     1  0.0603    0.80709 0.980 0.004 0.016 0.000 0.000 0.000
#> GSM674291     1  0.0260    0.80669 0.992 0.000 0.008 0.000 0.000 0.000
#> GSM674292     1  0.0260    0.80669 0.992 0.000 0.008 0.000 0.000 0.000
#> GSM674295     5  0.5533    0.90137 0.392 0.000 0.080 0.000 0.508 0.020
#> GSM674297     1  0.2795    0.77422 0.856 0.000 0.044 0.000 0.000 0.100
#> GSM674298     1  0.2795    0.77422 0.856 0.000 0.044 0.000 0.000 0.100
#> GSM674299     1  0.0508    0.80570 0.984 0.000 0.012 0.000 0.000 0.004
#> GSM674300     1  0.3635    0.73350 0.832 0.008 0.040 0.000 0.040 0.080
#> GSM674301     1  0.1268    0.80807 0.952 0.004 0.036 0.000 0.000 0.008
#> GSM674302     1  0.1464    0.80692 0.944 0.004 0.036 0.000 0.000 0.016
#> GSM674304     1  0.1552    0.80625 0.940 0.004 0.036 0.000 0.000 0.020
#> GSM674305     1  0.1464    0.80692 0.944 0.004 0.036 0.000 0.000 0.016
#> GSM674306     1  0.4522    0.69415 0.764 0.008 0.068 0.000 0.040 0.120
#> GSM674308     1  0.1485    0.80846 0.944 0.004 0.028 0.000 0.000 0.024
#> GSM674309     1  0.4142    0.70569 0.784 0.004 0.040 0.000 0.044 0.128
#> GSM674313     5  0.5732    0.87810 0.380 0.000 0.088 0.000 0.504 0.028
#> GSM674314     1  0.6255   -0.34584 0.512 0.004 0.040 0.000 0.316 0.128
#> GSM674315     1  0.4522    0.69415 0.764 0.008 0.068 0.000 0.040 0.120
#> GSM674316     5  0.5774    0.75262 0.408 0.000 0.024 0.000 0.472 0.096
#> GSM674318     5  0.4435    0.90828 0.392 0.000 0.004 0.000 0.580 0.024
#> GSM674320     5  0.5417    0.90321 0.392 0.000 0.076 0.000 0.516 0.016
#> GSM674323     5  0.4504    0.90613 0.392 0.000 0.004 0.000 0.576 0.028
#> GSM674324     1  0.3523    0.74050 0.812 0.000 0.040 0.000 0.016 0.132
#> GSM674325     5  0.4437    0.90272 0.392 0.000 0.000 0.000 0.576 0.032
#> GSM674327     1  0.6096   -0.19850 0.544 0.004 0.040 0.000 0.296 0.116
#> GSM674328     1  0.2011    0.79231 0.912 0.000 0.020 0.000 0.004 0.064
#> GSM674330     1  0.5889   -0.16353 0.556 0.000 0.044 0.000 0.300 0.100
#> GSM674331     1  0.3549    0.74114 0.812 0.000 0.044 0.000 0.016 0.128
#> GSM674332     1  0.4171    0.69892 0.776 0.000 0.044 0.000 0.048 0.132
#> GSM674334     1  0.5740   -0.00296 0.584 0.000 0.040 0.000 0.276 0.100
#> GSM674335     5  0.5459    0.90316 0.392 0.000 0.080 0.000 0.512 0.016
#> GSM674345     3  0.5395    0.88920 0.000 0.000 0.540 0.376 0.044 0.040
#> GSM674351     3  0.4894    0.89597 0.000 0.000 0.572 0.376 0.028 0.024
#> GSM674352     3  0.4894    0.89597 0.000 0.000 0.572 0.376 0.028 0.024
#> GSM674359     3  0.5011    0.89814 0.000 0.000 0.564 0.376 0.020 0.040
#> GSM674360     3  0.4744    0.90415 0.000 0.000 0.580 0.376 0.016 0.028
#> GSM674362     3  0.4026    0.90775 0.000 0.000 0.612 0.376 0.000 0.012
#> GSM674369     3  0.5667    0.87345 0.000 0.000 0.520 0.376 0.052 0.052
#> GSM674372     4  0.3431    0.73600 0.000 0.000 0.060 0.840 0.052 0.048
#> GSM674374     4  0.2854    0.71827 0.000 0.000 0.068 0.872 0.036 0.024
#> GSM674376     4  0.0146    0.81635 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM674377     4  0.0725    0.81048 0.000 0.000 0.000 0.976 0.012 0.012
#> GSM674378     4  0.1003    0.80745 0.000 0.000 0.000 0.964 0.020 0.016
#> GSM674383     3  0.5672    0.86932 0.000 0.000 0.516 0.380 0.056 0.048
#> GSM674386     4  0.1720    0.80843 0.000 0.000 0.000 0.928 0.040 0.032
#> GSM674387     4  0.0000    0.81586 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674392     4  0.5322   -0.48277 0.000 0.000 0.400 0.524 0.036 0.040
#> GSM674396     4  0.1720    0.80843 0.000 0.000 0.000 0.928 0.040 0.032
#> GSM674399     4  0.1720    0.80843 0.000 0.000 0.000 0.928 0.040 0.032
#> GSM674404     4  0.1794    0.80711 0.000 0.000 0.000 0.924 0.040 0.036
#> GSM674182     6  0.4545    0.54459 0.000 0.400 0.012 0.012 0.004 0.572
#> GSM674188     2  0.5839   -0.35170 0.000 0.452 0.040 0.012 0.048 0.448
#> GSM674189     6  0.6233    0.70766 0.000 0.288 0.072 0.012 0.072 0.556
#> GSM674196     2  0.0653    0.67769 0.000 0.980 0.004 0.012 0.004 0.000
#> GSM674197     2  0.0653    0.67769 0.000 0.980 0.004 0.012 0.004 0.000
#> GSM674199     2  0.0870    0.67609 0.000 0.972 0.004 0.012 0.012 0.000
#> GSM674207     2  0.1672    0.67157 0.000 0.940 0.028 0.012 0.016 0.004
#> GSM674211     2  0.1483    0.67411 0.000 0.944 0.036 0.012 0.008 0.000
#> GSM674213     2  0.5554   -0.21166 0.000 0.492 0.036 0.012 0.032 0.428
#> GSM674215     6  0.7445    0.62983 0.000 0.276 0.108 0.012 0.196 0.408
#> GSM674216     2  0.3861    0.54354 0.000 0.796 0.040 0.012 0.140 0.012
#> GSM674217     2  0.5497   -0.22152 0.000 0.492 0.032 0.012 0.032 0.432
#> GSM674222     6  0.7509    0.52534 0.000 0.336 0.100 0.012 0.212 0.340
#> GSM674224     2  0.4605    0.49843 0.000 0.732 0.060 0.012 0.016 0.180
#> GSM674227     6  0.7321    0.51115 0.000 0.340 0.080 0.012 0.200 0.368
#> GSM674228     2  0.6458   -0.07198 0.000 0.512 0.068 0.012 0.088 0.320
#> GSM674233     2  0.5497   -0.22152 0.000 0.492 0.032 0.012 0.032 0.432
#> GSM674238     6  0.6177    0.67823 0.000 0.248 0.096 0.012 0.060 0.584
#> GSM674241     2  0.0767    0.67773 0.000 0.976 0.008 0.012 0.004 0.000
#> GSM674283     1  0.0748    0.80902 0.976 0.004 0.016 0.000 0.000 0.004
#> GSM674286     1  0.0363    0.80699 0.988 0.000 0.012 0.000 0.000 0.000
#> GSM674293     1  0.0260    0.80669 0.992 0.000 0.008 0.000 0.000 0.000
#> GSM674294     1  0.0260    0.80669 0.992 0.000 0.008 0.000 0.000 0.000
#> GSM674296     1  0.2407    0.79385 0.892 0.004 0.048 0.000 0.000 0.056
#> GSM674303     1  0.1857    0.80439 0.924 0.004 0.028 0.000 0.000 0.044
#> GSM674307     1  0.2407    0.79385 0.892 0.004 0.048 0.000 0.000 0.056
#> GSM674310     5  0.4435    0.90828 0.392 0.000 0.004 0.000 0.580 0.024
#> GSM674311     1  0.3608    0.73656 0.808 0.000 0.040 0.000 0.020 0.132
#> GSM674312     5  0.5417    0.90321 0.392 0.000 0.076 0.000 0.516 0.016
#> GSM674317     1  0.1167    0.80585 0.960 0.000 0.012 0.000 0.008 0.020
#> GSM674319     5  0.5533    0.90137 0.392 0.000 0.080 0.000 0.508 0.020
#> GSM674321     5  0.4504    0.90613 0.392 0.000 0.004 0.000 0.576 0.028
#> GSM674322     5  0.4284    0.91217 0.392 0.000 0.016 0.000 0.588 0.004
#> GSM674326     5  0.4435    0.90828 0.392 0.000 0.004 0.000 0.580 0.024
#> GSM674329     5  0.5336    0.90471 0.392 0.000 0.076 0.000 0.520 0.012
#> GSM674333     5  0.4150    0.91276 0.392 0.000 0.016 0.000 0.592 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-MAD-kmeans-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-MAD-kmeans-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-MAD-kmeans-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-MAD-kmeans-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-MAD-kmeans-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-MAD-kmeans-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-MAD-kmeans-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-MAD-kmeans-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-MAD-kmeans-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-MAD-kmeans-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-MAD-kmeans-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-MAD-kmeans-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-MAD-kmeans-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-MAD-kmeans-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-MAD-kmeans-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-MAD-kmeans-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-MAD-kmeans-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-MAD-kmeans-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-MAD-kmeans-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-MAD-kmeans-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk MAD-kmeans-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-MAD-kmeans-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-MAD-kmeans-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-MAD-kmeans-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-MAD-kmeans-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-MAD-kmeans-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk MAD-kmeans-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>              n disease.state(p) specimen(p) k
#> MAD:kmeans 183            0.924    1.83e-40 2
#> MAD:kmeans 183            0.962    6.15e-78 3
#> MAD:kmeans 183            0.962    6.15e-78 4
#> MAD:kmeans 183            0.962    6.15e-78 5
#> MAD:kmeans 155            0.633    1.19e-60 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


MAD:skmeans*

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["MAD", "skmeans"]
# you can also extract it by
# res = res_list["MAD:skmeans"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#>   Subgroups are detected by 'skmeans' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 5.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk MAD-skmeans-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk MAD-skmeans-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 1.000           1.000       1.000         0.5958 0.750   0.571
#> 4 4 0.998           0.953       0.960         0.0904 0.939   0.815
#> 5 5 0.939           0.928       0.954         0.0681 0.949   0.812
#> 6 6 0.854           0.794       0.882         0.0315 0.998   0.991

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3 4

There is also optional best \(k\) = 2 3 4 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette p1 p2 p3
#> GSM674344     3       0          1  0  0  1
#> GSM674346     3       0          1  0  0  1
#> GSM674347     3       0          1  0  0  1
#> GSM674348     3       0          1  0  0  1
#> GSM674349     3       0          1  0  0  1
#> GSM674350     3       0          1  0  0  1
#> GSM674353     3       0          1  0  0  1
#> GSM674354     3       0          1  0  0  1
#> GSM674355     3       0          1  0  0  1
#> GSM674356     3       0          1  0  0  1
#> GSM674357     3       0          1  0  0  1
#> GSM674358     3       0          1  0  0  1
#> GSM674361     3       0          1  0  0  1
#> GSM674363     3       0          1  0  0  1
#> GSM674364     3       0          1  0  0  1
#> GSM674365     3       0          1  0  0  1
#> GSM674366     3       0          1  0  0  1
#> GSM674367     3       0          1  0  0  1
#> GSM674368     3       0          1  0  0  1
#> GSM674370     3       0          1  0  0  1
#> GSM674371     3       0          1  0  0  1
#> GSM674373     3       0          1  0  0  1
#> GSM674375     3       0          1  0  0  1
#> GSM674379     3       0          1  0  0  1
#> GSM674380     3       0          1  0  0  1
#> GSM674381     3       0          1  0  0  1
#> GSM674382     3       0          1  0  0  1
#> GSM674384     3       0          1  0  0  1
#> GSM674385     3       0          1  0  0  1
#> GSM674388     3       0          1  0  0  1
#> GSM674389     3       0          1  0  0  1
#> GSM674390     3       0          1  0  0  1
#> GSM674391     3       0          1  0  0  1
#> GSM674393     3       0          1  0  0  1
#> GSM674394     3       0          1  0  0  1
#> GSM674395     3       0          1  0  0  1
#> GSM674397     3       0          1  0  0  1
#> GSM674398     3       0          1  0  0  1
#> GSM674400     3       0          1  0  0  1
#> GSM674401     3       0          1  0  0  1
#> GSM674402     3       0          1  0  0  1
#> GSM674403     3       0          1  0  0  1
#> GSM674405     3       0          1  0  0  1
#> GSM674406     3       0          1  0  0  1
#> GSM674407     3       0          1  0  0  1
#> GSM674181     2       0          1  0  1  0
#> GSM674183     2       0          1  0  1  0
#> GSM674184     2       0          1  0  1  0
#> GSM674185     2       0          1  0  1  0
#> GSM674186     2       0          1  0  1  0
#> GSM674187     2       0          1  0  1  0
#> GSM674190     2       0          1  0  1  0
#> GSM674191     2       0          1  0  1  0
#> GSM674192     2       0          1  0  1  0
#> GSM674193     2       0          1  0  1  0
#> GSM674194     2       0          1  0  1  0
#> GSM674195     2       0          1  0  1  0
#> GSM674198     2       0          1  0  1  0
#> GSM674200     2       0          1  0  1  0
#> GSM674201     2       0          1  0  1  0
#> GSM674202     2       0          1  0  1  0
#> GSM674203     2       0          1  0  1  0
#> GSM674204     2       0          1  0  1  0
#> GSM674205     2       0          1  0  1  0
#> GSM674206     2       0          1  0  1  0
#> GSM674208     2       0          1  0  1  0
#> GSM674209     2       0          1  0  1  0
#> GSM674210     2       0          1  0  1  0
#> GSM674212     2       0          1  0  1  0
#> GSM674214     2       0          1  0  1  0
#> GSM674218     2       0          1  0  1  0
#> GSM674219     2       0          1  0  1  0
#> GSM674220     2       0          1  0  1  0
#> GSM674221     2       0          1  0  1  0
#> GSM674223     2       0          1  0  1  0
#> GSM674225     2       0          1  0  1  0
#> GSM674226     2       0          1  0  1  0
#> GSM674229     2       0          1  0  1  0
#> GSM674230     2       0          1  0  1  0
#> GSM674231     2       0          1  0  1  0
#> GSM674232     2       0          1  0  1  0
#> GSM674234     2       0          1  0  1  0
#> GSM674235     2       0          1  0  1  0
#> GSM674236     2       0          1  0  1  0
#> GSM674237     2       0          1  0  1  0
#> GSM674239     2       0          1  0  1  0
#> GSM674240     2       0          1  0  1  0
#> GSM674242     2       0          1  0  1  0
#> GSM674243     2       0          1  0  1  0
#> GSM674244     2       0          1  0  1  0
#> GSM674245     2       0          1  0  1  0
#> GSM674282     1       0          1  1  0  0
#> GSM674284     1       0          1  1  0  0
#> GSM674285     1       0          1  1  0  0
#> GSM674287     1       0          1  1  0  0
#> GSM674288     1       0          1  1  0  0
#> GSM674289     1       0          1  1  0  0
#> GSM674290     1       0          1  1  0  0
#> GSM674291     1       0          1  1  0  0
#> GSM674292     1       0          1  1  0  0
#> GSM674295     1       0          1  1  0  0
#> GSM674297     1       0          1  1  0  0
#> GSM674298     1       0          1  1  0  0
#> GSM674299     1       0          1  1  0  0
#> GSM674300     1       0          1  1  0  0
#> GSM674301     1       0          1  1  0  0
#> GSM674302     1       0          1  1  0  0
#> GSM674304     1       0          1  1  0  0
#> GSM674305     1       0          1  1  0  0
#> GSM674306     1       0          1  1  0  0
#> GSM674308     1       0          1  1  0  0
#> GSM674309     1       0          1  1  0  0
#> GSM674313     1       0          1  1  0  0
#> GSM674314     1       0          1  1  0  0
#> GSM674315     1       0          1  1  0  0
#> GSM674316     1       0          1  1  0  0
#> GSM674318     1       0          1  1  0  0
#> GSM674320     1       0          1  1  0  0
#> GSM674323     1       0          1  1  0  0
#> GSM674324     1       0          1  1  0  0
#> GSM674325     1       0          1  1  0  0
#> GSM674327     1       0          1  1  0  0
#> GSM674328     1       0          1  1  0  0
#> GSM674330     1       0          1  1  0  0
#> GSM674331     1       0          1  1  0  0
#> GSM674332     1       0          1  1  0  0
#> GSM674334     1       0          1  1  0  0
#> GSM674335     1       0          1  1  0  0
#> GSM674345     3       0          1  0  0  1
#> GSM674351     3       0          1  0  0  1
#> GSM674352     3       0          1  0  0  1
#> GSM674359     3       0          1  0  0  1
#> GSM674360     3       0          1  0  0  1
#> GSM674362     3       0          1  0  0  1
#> GSM674369     3       0          1  0  0  1
#> GSM674372     3       0          1  0  0  1
#> GSM674374     3       0          1  0  0  1
#> GSM674376     3       0          1  0  0  1
#> GSM674377     3       0          1  0  0  1
#> GSM674378     3       0          1  0  0  1
#> GSM674383     3       0          1  0  0  1
#> GSM674386     3       0          1  0  0  1
#> GSM674387     3       0          1  0  0  1
#> GSM674392     3       0          1  0  0  1
#> GSM674396     3       0          1  0  0  1
#> GSM674399     3       0          1  0  0  1
#> GSM674404     3       0          1  0  0  1
#> GSM674182     2       0          1  0  1  0
#> GSM674188     2       0          1  0  1  0
#> GSM674189     2       0          1  0  1  0
#> GSM674196     2       0          1  0  1  0
#> GSM674197     2       0          1  0  1  0
#> GSM674199     2       0          1  0  1  0
#> GSM674207     2       0          1  0  1  0
#> GSM674211     2       0          1  0  1  0
#> GSM674213     2       0          1  0  1  0
#> GSM674215     2       0          1  0  1  0
#> GSM674216     2       0          1  0  1  0
#> GSM674217     2       0          1  0  1  0
#> GSM674222     2       0          1  0  1  0
#> GSM674224     2       0          1  0  1  0
#> GSM674227     2       0          1  0  1  0
#> GSM674228     2       0          1  0  1  0
#> GSM674233     2       0          1  0  1  0
#> GSM674238     2       0          1  0  1  0
#> GSM674241     2       0          1  0  1  0
#> GSM674283     1       0          1  1  0  0
#> GSM674286     1       0          1  1  0  0
#> GSM674293     1       0          1  1  0  0
#> GSM674294     1       0          1  1  0  0
#> GSM674296     1       0          1  1  0  0
#> GSM674303     1       0          1  1  0  0
#> GSM674307     1       0          1  1  0  0
#> GSM674310     1       0          1  1  0  0
#> GSM674311     1       0          1  1  0  0
#> GSM674312     1       0          1  1  0  0
#> GSM674317     1       0          1  1  0  0
#> GSM674319     1       0          1  1  0  0
#> GSM674321     1       0          1  1  0  0
#> GSM674322     1       0          1  1  0  0
#> GSM674326     1       0          1  1  0  0
#> GSM674329     1       0          1  1  0  0
#> GSM674333     1       0          1  1  0  0

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1    p2    p3    p4
#> GSM674344     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674346     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674347     4  0.3688     0.6809 0.000 0.000 0.208 0.792
#> GSM674348     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674349     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674350     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674353     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674354     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674355     4  0.0188     0.9554 0.000 0.000 0.004 0.996
#> GSM674356     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674357     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674358     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674361     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674363     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674364     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674365     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674366     3  0.4907     0.4141 0.000 0.000 0.580 0.420
#> GSM674367     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674368     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674370     3  0.3074     0.9039 0.000 0.000 0.848 0.152
#> GSM674371     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674373     3  0.3486     0.8619 0.000 0.000 0.812 0.188
#> GSM674375     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674379     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674380     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674381     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674382     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674384     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674385     4  0.4830     0.1975 0.000 0.000 0.392 0.608
#> GSM674388     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674389     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674390     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674391     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674393     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674394     3  0.4790     0.5385 0.000 0.000 0.620 0.380
#> GSM674395     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674397     3  0.4996     0.2404 0.000 0.000 0.516 0.484
#> GSM674398     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674400     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674401     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674402     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674403     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674405     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674406     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674407     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674181     2  0.2216     0.9484 0.000 0.908 0.092 0.000
#> GSM674183     2  0.2216     0.9484 0.000 0.908 0.092 0.000
#> GSM674184     2  0.2216     0.9484 0.000 0.908 0.092 0.000
#> GSM674185     2  0.2216     0.9484 0.000 0.908 0.092 0.000
#> GSM674186     2  0.2011     0.9531 0.000 0.920 0.080 0.000
#> GSM674187     2  0.0592     0.9737 0.000 0.984 0.016 0.000
#> GSM674190     2  0.2081     0.9516 0.000 0.916 0.084 0.000
#> GSM674191     2  0.2149     0.9500 0.000 0.912 0.088 0.000
#> GSM674192     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674193     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674194     2  0.2081     0.9516 0.000 0.916 0.084 0.000
#> GSM674195     2  0.2216     0.9484 0.000 0.908 0.092 0.000
#> GSM674198     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674200     2  0.2216     0.9484 0.000 0.908 0.092 0.000
#> GSM674201     2  0.2216     0.9484 0.000 0.908 0.092 0.000
#> GSM674202     2  0.0188     0.9759 0.000 0.996 0.004 0.000
#> GSM674203     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674204     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674205     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674206     2  0.2216     0.9484 0.000 0.908 0.092 0.000
#> GSM674208     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674209     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674210     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674212     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674214     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674218     2  0.2216     0.9484 0.000 0.908 0.092 0.000
#> GSM674219     2  0.1211     0.9675 0.000 0.960 0.040 0.000
#> GSM674220     2  0.2216     0.9484 0.000 0.908 0.092 0.000
#> GSM674221     2  0.0592     0.9737 0.000 0.984 0.016 0.000
#> GSM674223     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674225     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674226     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674229     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674230     2  0.0336     0.9752 0.000 0.992 0.008 0.000
#> GSM674231     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674232     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674234     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674235     2  0.0188     0.9759 0.000 0.996 0.004 0.000
#> GSM674236     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674237     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674239     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674240     2  0.1716     0.9595 0.000 0.936 0.064 0.000
#> GSM674242     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674243     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674244     2  0.0469     0.9748 0.000 0.988 0.012 0.000
#> GSM674245     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674282     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674284     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674285     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674287     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674288     1  0.0188     0.9978 0.996 0.000 0.004 0.000
#> GSM674289     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674290     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674291     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674292     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674295     1  0.0188     0.9978 0.996 0.000 0.004 0.000
#> GSM674297     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674298     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674299     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674300     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674301     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674302     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674304     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674305     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674306     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674308     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674309     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674313     1  0.0188     0.9978 0.996 0.000 0.004 0.000
#> GSM674314     1  0.0188     0.9978 0.996 0.000 0.004 0.000
#> GSM674315     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674316     1  0.0188     0.9978 0.996 0.000 0.004 0.000
#> GSM674318     1  0.0188     0.9978 0.996 0.000 0.004 0.000
#> GSM674320     1  0.0188     0.9978 0.996 0.000 0.004 0.000
#> GSM674323     1  0.0188     0.9978 0.996 0.000 0.004 0.000
#> GSM674324     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674325     1  0.0188     0.9978 0.996 0.000 0.004 0.000
#> GSM674327     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674328     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674330     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674331     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674332     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674334     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674335     1  0.0188     0.9978 0.996 0.000 0.004 0.000
#> GSM674345     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674351     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674352     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674359     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674360     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674362     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674369     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674372     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674374     3  0.2530     0.9431 0.000 0.000 0.888 0.112
#> GSM674376     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674377     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674378     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674383     4  0.0000     0.9594 0.000 0.000 0.000 1.000
#> GSM674386     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674387     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674392     4  0.4907     0.0958 0.000 0.000 0.420 0.580
#> GSM674396     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674399     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674404     3  0.2281     0.9571 0.000 0.000 0.904 0.096
#> GSM674182     2  0.2216     0.9484 0.000 0.908 0.092 0.000
#> GSM674188     2  0.0592     0.9737 0.000 0.984 0.016 0.000
#> GSM674189     2  0.2216     0.9484 0.000 0.908 0.092 0.000
#> GSM674196     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674197     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674199     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674207     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674211     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674213     2  0.1022     0.9697 0.000 0.968 0.032 0.000
#> GSM674215     2  0.2216     0.9484 0.000 0.908 0.092 0.000
#> GSM674216     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674217     2  0.1118     0.9686 0.000 0.964 0.036 0.000
#> GSM674222     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674224     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674227     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674228     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674233     2  0.1118     0.9686 0.000 0.964 0.036 0.000
#> GSM674238     2  0.2216     0.9484 0.000 0.908 0.092 0.000
#> GSM674241     2  0.0000     0.9764 0.000 1.000 0.000 0.000
#> GSM674283     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674286     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674293     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674294     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674296     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674303     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674307     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674310     1  0.0188     0.9978 0.996 0.000 0.004 0.000
#> GSM674311     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674312     1  0.0188     0.9978 0.996 0.000 0.004 0.000
#> GSM674317     1  0.0000     0.9989 1.000 0.000 0.000 0.000
#> GSM674319     1  0.0188     0.9978 0.996 0.000 0.004 0.000
#> GSM674321     1  0.0188     0.9978 0.996 0.000 0.004 0.000
#> GSM674322     1  0.0188     0.9978 0.996 0.000 0.004 0.000
#> GSM674326     1  0.0188     0.9978 0.996 0.000 0.004 0.000
#> GSM674329     1  0.0188     0.9978 0.996 0.000 0.004 0.000
#> GSM674333     1  0.0188     0.9978 0.996 0.000 0.004 0.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4    p5
#> GSM674344     5  0.0290    0.94214 0.000 0.000 0.000 0.008 0.992
#> GSM674346     5  0.0404    0.94211 0.000 0.000 0.000 0.012 0.988
#> GSM674347     5  0.4284    0.66115 0.000 0.000 0.224 0.040 0.736
#> GSM674348     5  0.0510    0.94159 0.000 0.000 0.000 0.016 0.984
#> GSM674349     5  0.0963    0.93766 0.000 0.000 0.000 0.036 0.964
#> GSM674350     5  0.0290    0.94153 0.000 0.000 0.000 0.008 0.992
#> GSM674353     5  0.0290    0.94153 0.000 0.000 0.000 0.008 0.992
#> GSM674354     5  0.0290    0.94193 0.000 0.000 0.000 0.008 0.992
#> GSM674355     5  0.0451    0.94028 0.000 0.000 0.004 0.008 0.988
#> GSM674356     5  0.0609    0.94085 0.000 0.000 0.000 0.020 0.980
#> GSM674357     5  0.0290    0.94193 0.000 0.000 0.000 0.008 0.992
#> GSM674358     5  0.0290    0.94153 0.000 0.000 0.000 0.008 0.992
#> GSM674361     5  0.0290    0.94153 0.000 0.000 0.000 0.008 0.992
#> GSM674363     5  0.0162    0.94207 0.000 0.000 0.000 0.004 0.996
#> GSM674364     5  0.0162    0.94234 0.000 0.000 0.000 0.004 0.996
#> GSM674365     5  0.1270    0.93389 0.000 0.000 0.000 0.052 0.948
#> GSM674366     3  0.5019    0.45185 0.000 0.000 0.632 0.052 0.316
#> GSM674367     3  0.0609    0.94308 0.000 0.000 0.980 0.020 0.000
#> GSM674368     5  0.1364    0.93422 0.000 0.000 0.012 0.036 0.952
#> GSM674370     3  0.2036    0.90153 0.000 0.000 0.920 0.024 0.056
#> GSM674371     5  0.1197    0.93383 0.000 0.000 0.000 0.048 0.952
#> GSM674373     3  0.2505    0.86235 0.000 0.000 0.888 0.020 0.092
#> GSM674375     3  0.0510    0.94624 0.000 0.000 0.984 0.016 0.000
#> GSM674379     3  0.0000    0.94673 0.000 0.000 1.000 0.000 0.000
#> GSM674380     3  0.0000    0.94673 0.000 0.000 1.000 0.000 0.000
#> GSM674381     3  0.0162    0.94619 0.000 0.000 0.996 0.004 0.000
#> GSM674382     3  0.0000    0.94673 0.000 0.000 1.000 0.000 0.000
#> GSM674384     3  0.0566    0.94654 0.000 0.000 0.984 0.012 0.004
#> GSM674385     5  0.4930    0.18101 0.000 0.000 0.424 0.028 0.548
#> GSM674388     5  0.1270    0.93389 0.000 0.000 0.000 0.052 0.948
#> GSM674389     3  0.0609    0.94548 0.000 0.000 0.980 0.020 0.000
#> GSM674390     3  0.0000    0.94673 0.000 0.000 1.000 0.000 0.000
#> GSM674391     3  0.0000    0.94673 0.000 0.000 1.000 0.000 0.000
#> GSM674393     3  0.1251    0.93716 0.000 0.000 0.956 0.036 0.008
#> GSM674394     3  0.4419    0.54570 0.000 0.000 0.668 0.020 0.312
#> GSM674395     3  0.0510    0.94627 0.000 0.000 0.984 0.016 0.000
#> GSM674397     3  0.4697    0.32886 0.000 0.000 0.592 0.020 0.388
#> GSM674398     3  0.0510    0.94624 0.000 0.000 0.984 0.016 0.000
#> GSM674400     3  0.1522    0.93169 0.000 0.000 0.944 0.044 0.012
#> GSM674401     3  0.1522    0.93169 0.000 0.000 0.944 0.044 0.012
#> GSM674402     5  0.0404    0.94134 0.000 0.000 0.000 0.012 0.988
#> GSM674403     5  0.1270    0.93233 0.000 0.000 0.000 0.052 0.948
#> GSM674405     3  0.0510    0.94624 0.000 0.000 0.984 0.016 0.000
#> GSM674406     3  0.0000    0.94673 0.000 0.000 1.000 0.000 0.000
#> GSM674407     3  0.0000    0.94673 0.000 0.000 1.000 0.000 0.000
#> GSM674181     4  0.2732    0.93883 0.000 0.160 0.000 0.840 0.000
#> GSM674183     4  0.2179    0.95515 0.000 0.112 0.000 0.888 0.000
#> GSM674184     4  0.2179    0.95515 0.000 0.112 0.000 0.888 0.000
#> GSM674185     4  0.2179    0.95515 0.000 0.112 0.000 0.888 0.000
#> GSM674186     4  0.3661    0.81525 0.000 0.276 0.000 0.724 0.000
#> GSM674187     2  0.1341    0.91362 0.000 0.944 0.000 0.056 0.000
#> GSM674190     4  0.3305    0.88655 0.000 0.224 0.000 0.776 0.000
#> GSM674191     4  0.3003    0.92164 0.000 0.188 0.000 0.812 0.000
#> GSM674192     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674193     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674194     4  0.3210    0.90038 0.000 0.212 0.000 0.788 0.000
#> GSM674195     4  0.2179    0.95515 0.000 0.112 0.000 0.888 0.000
#> GSM674198     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674200     4  0.2179    0.95515 0.000 0.112 0.000 0.888 0.000
#> GSM674201     4  0.2179    0.95515 0.000 0.112 0.000 0.888 0.000
#> GSM674202     2  0.0162    0.95796 0.000 0.996 0.000 0.004 0.000
#> GSM674203     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674204     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674205     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674206     4  0.2561    0.94703 0.000 0.144 0.000 0.856 0.000
#> GSM674208     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674209     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674210     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674212     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674214     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674218     4  0.2179    0.95515 0.000 0.112 0.000 0.888 0.000
#> GSM674219     2  0.3305    0.68130 0.000 0.776 0.000 0.224 0.000
#> GSM674220     4  0.2179    0.95515 0.000 0.112 0.000 0.888 0.000
#> GSM674221     2  0.1478    0.90572 0.000 0.936 0.000 0.064 0.000
#> GSM674223     2  0.0162    0.95778 0.000 0.996 0.000 0.004 0.000
#> GSM674225     2  0.1341    0.91095 0.000 0.944 0.000 0.056 0.000
#> GSM674226     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674229     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674230     2  0.0290    0.95521 0.000 0.992 0.000 0.008 0.000
#> GSM674231     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674232     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674234     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674235     2  0.0162    0.95796 0.000 0.996 0.000 0.004 0.000
#> GSM674236     2  0.0162    0.95796 0.000 0.996 0.000 0.004 0.000
#> GSM674237     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674239     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674240     2  0.4268   -0.00224 0.000 0.556 0.000 0.444 0.000
#> GSM674242     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674243     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674244     2  0.1671    0.89414 0.000 0.924 0.000 0.076 0.000
#> GSM674245     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674282     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674284     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674285     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674287     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674288     1  0.0963    0.97923 0.964 0.000 0.000 0.036 0.000
#> GSM674289     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674291     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674292     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674295     1  0.0963    0.97923 0.964 0.000 0.000 0.036 0.000
#> GSM674297     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674298     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674299     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674300     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674301     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674302     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674305     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674306     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674308     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674309     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674313     1  0.0963    0.97923 0.964 0.000 0.000 0.036 0.000
#> GSM674314     1  0.0404    0.98681 0.988 0.000 0.000 0.012 0.000
#> GSM674315     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674316     1  0.0880    0.98060 0.968 0.000 0.000 0.032 0.000
#> GSM674318     1  0.0963    0.97923 0.964 0.000 0.000 0.036 0.000
#> GSM674320     1  0.0963    0.97923 0.964 0.000 0.000 0.036 0.000
#> GSM674323     1  0.0963    0.97923 0.964 0.000 0.000 0.036 0.000
#> GSM674324     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674325     1  0.0963    0.97923 0.964 0.000 0.000 0.036 0.000
#> GSM674327     1  0.0290    0.98780 0.992 0.000 0.000 0.008 0.000
#> GSM674328     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674330     1  0.0404    0.98681 0.988 0.000 0.000 0.012 0.000
#> GSM674331     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674332     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674334     1  0.0404    0.98681 0.988 0.000 0.000 0.012 0.000
#> GSM674335     1  0.0963    0.97923 0.964 0.000 0.000 0.036 0.000
#> GSM674345     5  0.0963    0.93766 0.000 0.000 0.000 0.036 0.964
#> GSM674351     5  0.0290    0.94153 0.000 0.000 0.000 0.008 0.992
#> GSM674352     5  0.0290    0.94153 0.000 0.000 0.000 0.008 0.992
#> GSM674359     5  0.0703    0.94043 0.000 0.000 0.000 0.024 0.976
#> GSM674360     5  0.0609    0.94127 0.000 0.000 0.000 0.020 0.980
#> GSM674362     5  0.0162    0.94234 0.000 0.000 0.000 0.004 0.996
#> GSM674369     5  0.1270    0.93389 0.000 0.000 0.000 0.052 0.948
#> GSM674372     3  0.1310    0.93751 0.000 0.000 0.956 0.024 0.020
#> GSM674374     3  0.1216    0.92924 0.000 0.000 0.960 0.020 0.020
#> GSM674376     3  0.0000    0.94673 0.000 0.000 1.000 0.000 0.000
#> GSM674377     3  0.0290    0.94520 0.000 0.000 0.992 0.008 0.000
#> GSM674378     3  0.0290    0.94508 0.000 0.000 0.992 0.008 0.000
#> GSM674383     5  0.1121    0.93491 0.000 0.000 0.000 0.044 0.956
#> GSM674386     3  0.0510    0.94624 0.000 0.000 0.984 0.016 0.000
#> GSM674387     3  0.0000    0.94673 0.000 0.000 1.000 0.000 0.000
#> GSM674392     5  0.4787    0.15206 0.000 0.000 0.432 0.020 0.548
#> GSM674396     3  0.0510    0.94624 0.000 0.000 0.984 0.016 0.000
#> GSM674399     3  0.0510    0.94624 0.000 0.000 0.984 0.016 0.000
#> GSM674404     3  0.0609    0.94548 0.000 0.000 0.980 0.020 0.000
#> GSM674182     4  0.2929    0.92736 0.000 0.180 0.000 0.820 0.000
#> GSM674188     2  0.1197    0.92119 0.000 0.952 0.000 0.048 0.000
#> GSM674189     4  0.2179    0.95515 0.000 0.112 0.000 0.888 0.000
#> GSM674196     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674197     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674199     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674207     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674211     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674213     2  0.2929    0.75528 0.000 0.820 0.000 0.180 0.000
#> GSM674215     4  0.2773    0.93042 0.000 0.164 0.000 0.836 0.000
#> GSM674216     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674217     2  0.2966    0.74893 0.000 0.816 0.000 0.184 0.000
#> GSM674222     2  0.0162    0.95796 0.000 0.996 0.000 0.004 0.000
#> GSM674224     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674227     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674228     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674233     2  0.3003    0.74289 0.000 0.812 0.000 0.188 0.000
#> GSM674238     4  0.2179    0.95515 0.000 0.112 0.000 0.888 0.000
#> GSM674241     2  0.0000    0.96013 0.000 1.000 0.000 0.000 0.000
#> GSM674283     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674286     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674293     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674294     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674296     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674303     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674307     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674310     1  0.0963    0.97923 0.964 0.000 0.000 0.036 0.000
#> GSM674311     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674312     1  0.0963    0.97923 0.964 0.000 0.000 0.036 0.000
#> GSM674317     1  0.0000    0.98961 1.000 0.000 0.000 0.000 0.000
#> GSM674319     1  0.0963    0.97923 0.964 0.000 0.000 0.036 0.000
#> GSM674321     1  0.0963    0.97923 0.964 0.000 0.000 0.036 0.000
#> GSM674322     1  0.0963    0.97923 0.964 0.000 0.000 0.036 0.000
#> GSM674326     1  0.0963    0.97923 0.964 0.000 0.000 0.036 0.000
#> GSM674329     1  0.0963    0.97923 0.964 0.000 0.000 0.036 0.000
#> GSM674333     1  0.0963    0.97923 0.964 0.000 0.000 0.036 0.000

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4    p5    p6
#> GSM674344     3  0.0713     0.7579 0.000 0.000 0.972 0.000 0.028 0.000
#> GSM674346     3  0.0363     0.7578 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM674347     3  0.5026     0.2110 0.000 0.000 0.656 0.180 0.160 0.004
#> GSM674348     3  0.1863     0.7347 0.000 0.000 0.896 0.000 0.104 0.000
#> GSM674349     3  0.3409     0.5865 0.000 0.000 0.700 0.000 0.300 0.000
#> GSM674350     3  0.0632     0.7495 0.000 0.000 0.976 0.000 0.024 0.000
#> GSM674353     3  0.0363     0.7549 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM674354     3  0.0260     0.7571 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM674355     3  0.1074     0.7390 0.000 0.000 0.960 0.012 0.028 0.000
#> GSM674356     3  0.2003     0.7287 0.000 0.000 0.884 0.000 0.116 0.000
#> GSM674357     3  0.0260     0.7571 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM674358     3  0.0363     0.7549 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM674361     3  0.0547     0.7516 0.000 0.000 0.980 0.000 0.020 0.000
#> GSM674363     3  0.0000     0.7572 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM674364     3  0.0937     0.7578 0.000 0.000 0.960 0.000 0.040 0.000
#> GSM674365     3  0.3765     0.4607 0.000 0.000 0.596 0.000 0.404 0.000
#> GSM674366     5  0.5919     0.0000 0.000 0.000 0.212 0.364 0.424 0.000
#> GSM674367     4  0.2340     0.7084 0.000 0.000 0.000 0.852 0.148 0.000
#> GSM674368     3  0.4378     0.4460 0.000 0.000 0.600 0.032 0.368 0.000
#> GSM674370     4  0.3744     0.5685 0.000 0.000 0.052 0.764 0.184 0.000
#> GSM674371     3  0.3747     0.4605 0.000 0.000 0.604 0.000 0.396 0.000
#> GSM674373     4  0.3101     0.6525 0.000 0.000 0.032 0.820 0.148 0.000
#> GSM674375     4  0.1700     0.8168 0.000 0.000 0.000 0.916 0.080 0.004
#> GSM674379     4  0.0508     0.8230 0.000 0.000 0.000 0.984 0.012 0.004
#> GSM674380     4  0.0632     0.8202 0.000 0.000 0.000 0.976 0.024 0.000
#> GSM674381     4  0.1610     0.7883 0.000 0.000 0.000 0.916 0.084 0.000
#> GSM674382     4  0.0146     0.8241 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM674384     4  0.1780     0.8142 0.000 0.000 0.028 0.924 0.048 0.000
#> GSM674385     3  0.5807    -0.3515 0.000 0.000 0.440 0.376 0.184 0.000
#> GSM674388     3  0.3774     0.4562 0.000 0.000 0.592 0.000 0.408 0.000
#> GSM674389     4  0.1753     0.8079 0.000 0.000 0.000 0.912 0.084 0.004
#> GSM674390     4  0.0458     0.8217 0.000 0.000 0.000 0.984 0.016 0.000
#> GSM674391     4  0.0458     0.8218 0.000 0.000 0.000 0.984 0.016 0.000
#> GSM674393     4  0.3352     0.6660 0.000 0.000 0.008 0.776 0.208 0.008
#> GSM674394     4  0.5034    -0.0898 0.000 0.000 0.404 0.520 0.076 0.000
#> GSM674395     4  0.1501     0.8166 0.000 0.000 0.000 0.924 0.076 0.000
#> GSM674397     4  0.5303    -0.1631 0.000 0.000 0.204 0.600 0.196 0.000
#> GSM674398     4  0.1471     0.8164 0.000 0.000 0.000 0.932 0.064 0.004
#> GSM674400     4  0.4130     0.4090 0.000 0.000 0.016 0.664 0.312 0.008
#> GSM674401     4  0.4244     0.3682 0.000 0.000 0.020 0.652 0.320 0.008
#> GSM674402     3  0.1007     0.7461 0.000 0.000 0.956 0.000 0.044 0.000
#> GSM674403     3  0.3930     0.4167 0.000 0.000 0.576 0.000 0.420 0.004
#> GSM674405     4  0.1643     0.8146 0.000 0.000 0.000 0.924 0.068 0.008
#> GSM674406     4  0.0458     0.8216 0.000 0.000 0.000 0.984 0.016 0.000
#> GSM674407     4  0.0458     0.8216 0.000 0.000 0.000 0.984 0.016 0.000
#> GSM674181     6  0.2846     0.8521 0.000 0.084 0.000 0.000 0.060 0.856
#> GSM674183     6  0.0260     0.8709 0.000 0.008 0.000 0.000 0.000 0.992
#> GSM674184     6  0.0260     0.8709 0.000 0.008 0.000 0.000 0.000 0.992
#> GSM674185     6  0.0520     0.8687 0.000 0.008 0.000 0.000 0.008 0.984
#> GSM674186     6  0.4066     0.7507 0.000 0.204 0.000 0.000 0.064 0.732
#> GSM674187     2  0.3920     0.7734 0.000 0.768 0.000 0.000 0.112 0.120
#> GSM674190     6  0.3706     0.7925 0.000 0.172 0.000 0.000 0.056 0.772
#> GSM674191     6  0.3276     0.8301 0.000 0.132 0.000 0.000 0.052 0.816
#> GSM674192     2  0.1265     0.8775 0.000 0.948 0.000 0.000 0.044 0.008
#> GSM674193     2  0.1398     0.8779 0.000 0.940 0.000 0.000 0.052 0.008
#> GSM674194     6  0.3513     0.8189 0.000 0.144 0.000 0.000 0.060 0.796
#> GSM674195     6  0.0260     0.8709 0.000 0.008 0.000 0.000 0.000 0.992
#> GSM674198     2  0.0363     0.8828 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM674200     6  0.0520     0.8687 0.000 0.008 0.000 0.000 0.008 0.984
#> GSM674201     6  0.1176     0.8724 0.000 0.020 0.000 0.000 0.024 0.956
#> GSM674202     2  0.3217     0.7984 0.000 0.768 0.000 0.000 0.224 0.008
#> GSM674203     2  0.0547     0.8821 0.000 0.980 0.000 0.000 0.020 0.000
#> GSM674204     2  0.0363     0.8830 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM674205     2  0.0937     0.8788 0.000 0.960 0.000 0.000 0.040 0.000
#> GSM674206     6  0.2724     0.8566 0.000 0.084 0.000 0.000 0.052 0.864
#> GSM674208     2  0.0713     0.8812 0.000 0.972 0.000 0.000 0.028 0.000
#> GSM674209     2  0.1584     0.8756 0.000 0.928 0.000 0.000 0.064 0.008
#> GSM674210     2  0.0363     0.8830 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM674212     2  0.0937     0.8831 0.000 0.960 0.000 0.000 0.040 0.000
#> GSM674214     2  0.0713     0.8839 0.000 0.972 0.000 0.000 0.028 0.000
#> GSM674218     6  0.0260     0.8709 0.000 0.008 0.000 0.000 0.000 0.992
#> GSM674219     2  0.4704     0.6169 0.000 0.664 0.000 0.000 0.100 0.236
#> GSM674220     6  0.3161     0.7471 0.000 0.008 0.000 0.000 0.216 0.776
#> GSM674221     2  0.3658     0.7927 0.000 0.792 0.000 0.000 0.104 0.104
#> GSM674223     2  0.1625     0.8729 0.000 0.928 0.000 0.000 0.060 0.012
#> GSM674225     2  0.4495     0.7027 0.000 0.672 0.000 0.000 0.256 0.072
#> GSM674226     2  0.1444     0.8834 0.000 0.928 0.000 0.000 0.072 0.000
#> GSM674229     2  0.0260     0.8838 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM674230     2  0.3168     0.8273 0.000 0.804 0.000 0.000 0.172 0.024
#> GSM674231     2  0.1462     0.8775 0.000 0.936 0.000 0.000 0.056 0.008
#> GSM674232     2  0.1663     0.8677 0.000 0.912 0.000 0.000 0.088 0.000
#> GSM674234     2  0.0937     0.8788 0.000 0.960 0.000 0.000 0.040 0.000
#> GSM674235     2  0.3103     0.8142 0.000 0.784 0.000 0.000 0.208 0.008
#> GSM674236     2  0.3271     0.7965 0.000 0.760 0.000 0.000 0.232 0.008
#> GSM674237     2  0.0937     0.8785 0.000 0.960 0.000 0.000 0.040 0.000
#> GSM674239     2  0.0458     0.8830 0.000 0.984 0.000 0.000 0.016 0.000
#> GSM674240     2  0.4991     0.2131 0.000 0.524 0.000 0.000 0.072 0.404
#> GSM674242     2  0.0937     0.8785 0.000 0.960 0.000 0.000 0.040 0.000
#> GSM674243     2  0.0937     0.8800 0.000 0.960 0.000 0.000 0.040 0.000
#> GSM674244     2  0.5065     0.6432 0.000 0.616 0.000 0.000 0.260 0.124
#> GSM674245     2  0.2260     0.8515 0.000 0.860 0.000 0.000 0.140 0.000
#> GSM674282     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674284     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674285     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674287     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674288     1  0.1957     0.9211 0.888 0.000 0.000 0.000 0.112 0.000
#> GSM674289     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674291     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674292     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674295     1  0.2219     0.9105 0.864 0.000 0.000 0.000 0.136 0.000
#> GSM674297     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674298     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674299     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674300     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674301     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674302     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674305     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674306     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674308     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674309     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674313     1  0.2219     0.9105 0.864 0.000 0.000 0.000 0.136 0.000
#> GSM674314     1  0.0865     0.9493 0.964 0.000 0.000 0.000 0.036 0.000
#> GSM674315     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674316     1  0.1814     0.9260 0.900 0.000 0.000 0.000 0.100 0.000
#> GSM674318     1  0.2219     0.9105 0.864 0.000 0.000 0.000 0.136 0.000
#> GSM674320     1  0.2219     0.9105 0.864 0.000 0.000 0.000 0.136 0.000
#> GSM674323     1  0.2219     0.9105 0.864 0.000 0.000 0.000 0.136 0.000
#> GSM674324     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674325     1  0.2219     0.9105 0.864 0.000 0.000 0.000 0.136 0.000
#> GSM674327     1  0.0632     0.9529 0.976 0.000 0.000 0.000 0.024 0.000
#> GSM674328     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674330     1  0.0713     0.9518 0.972 0.000 0.000 0.000 0.028 0.000
#> GSM674331     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674332     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674334     1  0.0790     0.9505 0.968 0.000 0.000 0.000 0.032 0.000
#> GSM674335     1  0.2219     0.9105 0.864 0.000 0.000 0.000 0.136 0.000
#> GSM674345     3  0.3126     0.6351 0.000 0.000 0.752 0.000 0.248 0.000
#> GSM674351     3  0.0363     0.7549 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM674352     3  0.0363     0.7549 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM674359     3  0.2631     0.6968 0.000 0.000 0.820 0.000 0.180 0.000
#> GSM674360     3  0.2219     0.7220 0.000 0.000 0.864 0.000 0.136 0.000
#> GSM674362     3  0.0713     0.7575 0.000 0.000 0.972 0.000 0.028 0.000
#> GSM674369     3  0.3765     0.4607 0.000 0.000 0.596 0.000 0.404 0.000
#> GSM674372     4  0.3821     0.6301 0.000 0.000 0.148 0.772 0.080 0.000
#> GSM674374     4  0.2340     0.7087 0.000 0.000 0.000 0.852 0.148 0.000
#> GSM674376     4  0.0260     0.8238 0.000 0.000 0.000 0.992 0.008 0.000
#> GSM674377     4  0.1204     0.8042 0.000 0.000 0.000 0.944 0.056 0.000
#> GSM674378     4  0.1765     0.7722 0.000 0.000 0.000 0.904 0.096 0.000
#> GSM674383     3  0.3747     0.4605 0.000 0.000 0.604 0.000 0.396 0.000
#> GSM674386     4  0.1588     0.8153 0.000 0.000 0.000 0.924 0.072 0.004
#> GSM674387     4  0.0363     0.8222 0.000 0.000 0.000 0.988 0.012 0.000
#> GSM674392     3  0.4783    -0.0591 0.000 0.000 0.616 0.308 0.076 0.000
#> GSM674396     4  0.1531     0.8153 0.000 0.000 0.000 0.928 0.068 0.004
#> GSM674399     4  0.1531     0.8153 0.000 0.000 0.000 0.928 0.068 0.004
#> GSM674404     4  0.1644     0.8124 0.000 0.000 0.000 0.920 0.076 0.004
#> GSM674182     6  0.3354     0.8297 0.000 0.128 0.000 0.000 0.060 0.812
#> GSM674188     2  0.3834     0.7822 0.000 0.776 0.000 0.000 0.108 0.116
#> GSM674189     6  0.1049     0.8719 0.000 0.008 0.000 0.000 0.032 0.960
#> GSM674196     2  0.0260     0.8831 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM674197     2  0.0260     0.8831 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM674199     2  0.0363     0.8828 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM674207     2  0.0790     0.8841 0.000 0.968 0.000 0.000 0.032 0.000
#> GSM674211     2  0.1141     0.8790 0.000 0.948 0.000 0.000 0.052 0.000
#> GSM674213     2  0.4374     0.6916 0.000 0.712 0.000 0.000 0.096 0.192
#> GSM674215     6  0.4255     0.7004 0.000 0.068 0.000 0.000 0.224 0.708
#> GSM674216     2  0.2631     0.8189 0.000 0.820 0.000 0.000 0.180 0.000
#> GSM674217     2  0.4599     0.6531 0.000 0.684 0.000 0.000 0.104 0.212
#> GSM674222     2  0.3421     0.7755 0.000 0.736 0.000 0.000 0.256 0.008
#> GSM674224     2  0.1327     0.8789 0.000 0.936 0.000 0.000 0.064 0.000
#> GSM674227     2  0.2912     0.8046 0.000 0.784 0.000 0.000 0.216 0.000
#> GSM674228     2  0.1643     0.8768 0.000 0.924 0.000 0.000 0.068 0.008
#> GSM674233     2  0.4599     0.6544 0.000 0.684 0.000 0.000 0.104 0.212
#> GSM674238     6  0.0520     0.8687 0.000 0.008 0.000 0.000 0.008 0.984
#> GSM674241     2  0.0458     0.8830 0.000 0.984 0.000 0.000 0.016 0.000
#> GSM674283     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674286     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674293     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674294     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674296     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674303     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674307     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674310     1  0.2219     0.9105 0.864 0.000 0.000 0.000 0.136 0.000
#> GSM674311     1  0.0000     0.9590 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674312     1  0.2219     0.9105 0.864 0.000 0.000 0.000 0.136 0.000
#> GSM674317     1  0.0146     0.9581 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM674319     1  0.2219     0.9105 0.864 0.000 0.000 0.000 0.136 0.000
#> GSM674321     1  0.2219     0.9105 0.864 0.000 0.000 0.000 0.136 0.000
#> GSM674322     1  0.2219     0.9105 0.864 0.000 0.000 0.000 0.136 0.000
#> GSM674326     1  0.2219     0.9105 0.864 0.000 0.000 0.000 0.136 0.000
#> GSM674329     1  0.2219     0.9105 0.864 0.000 0.000 0.000 0.136 0.000
#> GSM674333     1  0.2219     0.9105 0.864 0.000 0.000 0.000 0.136 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-MAD-skmeans-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-MAD-skmeans-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-MAD-skmeans-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-MAD-skmeans-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-MAD-skmeans-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-MAD-skmeans-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-MAD-skmeans-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-MAD-skmeans-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-MAD-skmeans-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-MAD-skmeans-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-MAD-skmeans-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-MAD-skmeans-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-MAD-skmeans-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-MAD-skmeans-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-MAD-skmeans-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-MAD-skmeans-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-MAD-skmeans-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-MAD-skmeans-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-MAD-skmeans-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-MAD-skmeans-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk MAD-skmeans-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-MAD-skmeans-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-MAD-skmeans-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-MAD-skmeans-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-MAD-skmeans-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-MAD-skmeans-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk MAD-skmeans-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>               n disease.state(p) specimen(p) k
#> MAD:skmeans 183            0.924    1.83e-40 2
#> MAD:skmeans 183            0.962    6.15e-78 3
#> MAD:skmeans 179            0.973    2.96e-74 4
#> MAD:skmeans 178            0.930    4.74e-72 5
#> MAD:skmeans 167            0.901    2.35e-67 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


MAD:pam*

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["MAD", "pam"]
# you can also extract it by
# res = res_list["MAD:pam"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#>   Subgroups are detected by 'pam' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 6.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk MAD-pam-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk MAD-pam-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 1.000           0.994       0.997         0.5956 0.750   0.571
#> 4 4 0.969           0.909       0.950         0.0932 0.933   0.799
#> 5 5 0.856           0.810       0.856         0.0705 0.937   0.771
#> 6 6 0.918           0.862       0.936         0.0625 0.938   0.722

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3 4

There is also optional best \(k\) = 2 3 4 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette p1    p2    p3
#> GSM674344     3  0.4887      0.709  0 0.228 0.772
#> GSM674346     3  0.0000      0.992  0 0.000 1.000
#> GSM674347     3  0.0000      0.992  0 0.000 1.000
#> GSM674348     3  0.0000      0.992  0 0.000 1.000
#> GSM674349     3  0.0000      0.992  0 0.000 1.000
#> GSM674350     3  0.0000      0.992  0 0.000 1.000
#> GSM674353     3  0.0000      0.992  0 0.000 1.000
#> GSM674354     3  0.0000      0.992  0 0.000 1.000
#> GSM674355     3  0.0000      0.992  0 0.000 1.000
#> GSM674356     3  0.0000      0.992  0 0.000 1.000
#> GSM674357     3  0.0000      0.992  0 0.000 1.000
#> GSM674358     3  0.0000      0.992  0 0.000 1.000
#> GSM674361     3  0.0000      0.992  0 0.000 1.000
#> GSM674363     3  0.0000      0.992  0 0.000 1.000
#> GSM674364     3  0.0000      0.992  0 0.000 1.000
#> GSM674365     3  0.0000      0.992  0 0.000 1.000
#> GSM674366     3  0.0000      0.992  0 0.000 1.000
#> GSM674367     3  0.0000      0.992  0 0.000 1.000
#> GSM674368     3  0.0000      0.992  0 0.000 1.000
#> GSM674370     3  0.0000      0.992  0 0.000 1.000
#> GSM674371     3  0.0000      0.992  0 0.000 1.000
#> GSM674373     3  0.0000      0.992  0 0.000 1.000
#> GSM674375     3  0.0000      0.992  0 0.000 1.000
#> GSM674379     3  0.0000      0.992  0 0.000 1.000
#> GSM674380     3  0.0000      0.992  0 0.000 1.000
#> GSM674381     3  0.0000      0.992  0 0.000 1.000
#> GSM674382     3  0.0000      0.992  0 0.000 1.000
#> GSM674384     3  0.0000      0.992  0 0.000 1.000
#> GSM674385     3  0.0000      0.992  0 0.000 1.000
#> GSM674388     3  0.0000      0.992  0 0.000 1.000
#> GSM674389     3  0.0000      0.992  0 0.000 1.000
#> GSM674390     3  0.0000      0.992  0 0.000 1.000
#> GSM674391     3  0.0000      0.992  0 0.000 1.000
#> GSM674393     3  0.0000      0.992  0 0.000 1.000
#> GSM674394     3  0.0000      0.992  0 0.000 1.000
#> GSM674395     3  0.0000      0.992  0 0.000 1.000
#> GSM674397     3  0.0000      0.992  0 0.000 1.000
#> GSM674398     3  0.0000      0.992  0 0.000 1.000
#> GSM674400     3  0.0000      0.992  0 0.000 1.000
#> GSM674401     3  0.0000      0.992  0 0.000 1.000
#> GSM674402     3  0.0000      0.992  0 0.000 1.000
#> GSM674403     3  0.0000      0.992  0 0.000 1.000
#> GSM674405     3  0.0000      0.992  0 0.000 1.000
#> GSM674406     3  0.0000      0.992  0 0.000 1.000
#> GSM674407     3  0.0000      0.992  0 0.000 1.000
#> GSM674181     2  0.0000      1.000  0 1.000 0.000
#> GSM674183     2  0.0000      1.000  0 1.000 0.000
#> GSM674184     2  0.0000      1.000  0 1.000 0.000
#> GSM674185     2  0.0000      1.000  0 1.000 0.000
#> GSM674186     2  0.0000      1.000  0 1.000 0.000
#> GSM674187     2  0.0000      1.000  0 1.000 0.000
#> GSM674190     2  0.0000      1.000  0 1.000 0.000
#> GSM674191     2  0.0000      1.000  0 1.000 0.000
#> GSM674192     2  0.0000      1.000  0 1.000 0.000
#> GSM674193     2  0.0000      1.000  0 1.000 0.000
#> GSM674194     2  0.0000      1.000  0 1.000 0.000
#> GSM674195     2  0.0000      1.000  0 1.000 0.000
#> GSM674198     2  0.0000      1.000  0 1.000 0.000
#> GSM674200     2  0.0237      0.996  0 0.996 0.004
#> GSM674201     2  0.0000      1.000  0 1.000 0.000
#> GSM674202     2  0.0000      1.000  0 1.000 0.000
#> GSM674203     2  0.0000      1.000  0 1.000 0.000
#> GSM674204     2  0.0000      1.000  0 1.000 0.000
#> GSM674205     2  0.0000      1.000  0 1.000 0.000
#> GSM674206     2  0.0000      1.000  0 1.000 0.000
#> GSM674208     2  0.0000      1.000  0 1.000 0.000
#> GSM674209     2  0.0000      1.000  0 1.000 0.000
#> GSM674210     2  0.0000      1.000  0 1.000 0.000
#> GSM674212     2  0.0000      1.000  0 1.000 0.000
#> GSM674214     2  0.0000      1.000  0 1.000 0.000
#> GSM674218     2  0.0000      1.000  0 1.000 0.000
#> GSM674219     2  0.0000      1.000  0 1.000 0.000
#> GSM674220     2  0.0000      1.000  0 1.000 0.000
#> GSM674221     2  0.0000      1.000  0 1.000 0.000
#> GSM674223     2  0.0000      1.000  0 1.000 0.000
#> GSM674225     2  0.0000      1.000  0 1.000 0.000
#> GSM674226     2  0.0000      1.000  0 1.000 0.000
#> GSM674229     2  0.0000      1.000  0 1.000 0.000
#> GSM674230     2  0.0000      1.000  0 1.000 0.000
#> GSM674231     2  0.0000      1.000  0 1.000 0.000
#> GSM674232     2  0.0000      1.000  0 1.000 0.000
#> GSM674234     2  0.0000      1.000  0 1.000 0.000
#> GSM674235     2  0.0000      1.000  0 1.000 0.000
#> GSM674236     2  0.0000      1.000  0 1.000 0.000
#> GSM674237     2  0.0000      1.000  0 1.000 0.000
#> GSM674239     2  0.0000      1.000  0 1.000 0.000
#> GSM674240     2  0.0000      1.000  0 1.000 0.000
#> GSM674242     2  0.0000      1.000  0 1.000 0.000
#> GSM674243     2  0.0000      1.000  0 1.000 0.000
#> GSM674244     2  0.0000      1.000  0 1.000 0.000
#> GSM674245     2  0.0000      1.000  0 1.000 0.000
#> GSM674282     1  0.0000      1.000  1 0.000 0.000
#> GSM674284     1  0.0000      1.000  1 0.000 0.000
#> GSM674285     1  0.0000      1.000  1 0.000 0.000
#> GSM674287     1  0.0000      1.000  1 0.000 0.000
#> GSM674288     1  0.0000      1.000  1 0.000 0.000
#> GSM674289     1  0.0000      1.000  1 0.000 0.000
#> GSM674290     1  0.0000      1.000  1 0.000 0.000
#> GSM674291     1  0.0000      1.000  1 0.000 0.000
#> GSM674292     1  0.0000      1.000  1 0.000 0.000
#> GSM674295     1  0.0000      1.000  1 0.000 0.000
#> GSM674297     1  0.0000      1.000  1 0.000 0.000
#> GSM674298     1  0.0000      1.000  1 0.000 0.000
#> GSM674299     1  0.0000      1.000  1 0.000 0.000
#> GSM674300     1  0.0000      1.000  1 0.000 0.000
#> GSM674301     1  0.0000      1.000  1 0.000 0.000
#> GSM674302     1  0.0000      1.000  1 0.000 0.000
#> GSM674304     1  0.0000      1.000  1 0.000 0.000
#> GSM674305     1  0.0000      1.000  1 0.000 0.000
#> GSM674306     1  0.0000      1.000  1 0.000 0.000
#> GSM674308     1  0.0000      1.000  1 0.000 0.000
#> GSM674309     1  0.0000      1.000  1 0.000 0.000
#> GSM674313     1  0.0000      1.000  1 0.000 0.000
#> GSM674314     1  0.0000      1.000  1 0.000 0.000
#> GSM674315     1  0.0000      1.000  1 0.000 0.000
#> GSM674316     1  0.0000      1.000  1 0.000 0.000
#> GSM674318     1  0.0000      1.000  1 0.000 0.000
#> GSM674320     1  0.0000      1.000  1 0.000 0.000
#> GSM674323     1  0.0000      1.000  1 0.000 0.000
#> GSM674324     1  0.0000      1.000  1 0.000 0.000
#> GSM674325     1  0.0000      1.000  1 0.000 0.000
#> GSM674327     1  0.0000      1.000  1 0.000 0.000
#> GSM674328     1  0.0000      1.000  1 0.000 0.000
#> GSM674330     1  0.0000      1.000  1 0.000 0.000
#> GSM674331     1  0.0000      1.000  1 0.000 0.000
#> GSM674332     1  0.0000      1.000  1 0.000 0.000
#> GSM674334     1  0.0000      1.000  1 0.000 0.000
#> GSM674335     1  0.0000      1.000  1 0.000 0.000
#> GSM674345     3  0.0000      0.992  0 0.000 1.000
#> GSM674351     3  0.0000      0.992  0 0.000 1.000
#> GSM674352     3  0.0000      0.992  0 0.000 1.000
#> GSM674359     3  0.0000      0.992  0 0.000 1.000
#> GSM674360     3  0.0000      0.992  0 0.000 1.000
#> GSM674362     3  0.4974      0.696  0 0.236 0.764
#> GSM674369     3  0.0000      0.992  0 0.000 1.000
#> GSM674372     3  0.0000      0.992  0 0.000 1.000
#> GSM674374     3  0.0000      0.992  0 0.000 1.000
#> GSM674376     3  0.0000      0.992  0 0.000 1.000
#> GSM674377     3  0.0000      0.992  0 0.000 1.000
#> GSM674378     3  0.0000      0.992  0 0.000 1.000
#> GSM674383     3  0.0000      0.992  0 0.000 1.000
#> GSM674386     3  0.0000      0.992  0 0.000 1.000
#> GSM674387     3  0.0000      0.992  0 0.000 1.000
#> GSM674392     3  0.0000      0.992  0 0.000 1.000
#> GSM674396     3  0.0000      0.992  0 0.000 1.000
#> GSM674399     3  0.0000      0.992  0 0.000 1.000
#> GSM674404     3  0.0000      0.992  0 0.000 1.000
#> GSM674182     2  0.0000      1.000  0 1.000 0.000
#> GSM674188     2  0.0000      1.000  0 1.000 0.000
#> GSM674189     2  0.0000      1.000  0 1.000 0.000
#> GSM674196     2  0.0000      1.000  0 1.000 0.000
#> GSM674197     2  0.0000      1.000  0 1.000 0.000
#> GSM674199     2  0.0000      1.000  0 1.000 0.000
#> GSM674207     2  0.0000      1.000  0 1.000 0.000
#> GSM674211     2  0.0000      1.000  0 1.000 0.000
#> GSM674213     2  0.0000      1.000  0 1.000 0.000
#> GSM674215     2  0.0000      1.000  0 1.000 0.000
#> GSM674216     2  0.0000      1.000  0 1.000 0.000
#> GSM674217     2  0.0000      1.000  0 1.000 0.000
#> GSM674222     2  0.0000      1.000  0 1.000 0.000
#> GSM674224     2  0.0000      1.000  0 1.000 0.000
#> GSM674227     2  0.0000      1.000  0 1.000 0.000
#> GSM674228     2  0.0000      1.000  0 1.000 0.000
#> GSM674233     2  0.0000      1.000  0 1.000 0.000
#> GSM674238     2  0.0000      1.000  0 1.000 0.000
#> GSM674241     2  0.0000      1.000  0 1.000 0.000
#> GSM674283     1  0.0000      1.000  1 0.000 0.000
#> GSM674286     1  0.0000      1.000  1 0.000 0.000
#> GSM674293     1  0.0000      1.000  1 0.000 0.000
#> GSM674294     1  0.0000      1.000  1 0.000 0.000
#> GSM674296     1  0.0000      1.000  1 0.000 0.000
#> GSM674303     1  0.0000      1.000  1 0.000 0.000
#> GSM674307     1  0.0000      1.000  1 0.000 0.000
#> GSM674310     1  0.0000      1.000  1 0.000 0.000
#> GSM674311     1  0.0000      1.000  1 0.000 0.000
#> GSM674312     1  0.0000      1.000  1 0.000 0.000
#> GSM674317     1  0.0000      1.000  1 0.000 0.000
#> GSM674319     1  0.0000      1.000  1 0.000 0.000
#> GSM674321     1  0.0000      1.000  1 0.000 0.000
#> GSM674322     1  0.0000      1.000  1 0.000 0.000
#> GSM674326     1  0.0000      1.000  1 0.000 0.000
#> GSM674329     1  0.0000      1.000  1 0.000 0.000
#> GSM674333     1  0.0000      1.000  1 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette p1    p2    p3    p4
#> GSM674344     3  0.0336     0.8411  0 0.008 0.992 0.000
#> GSM674346     3  0.0336     0.8453  0 0.000 0.992 0.008
#> GSM674347     4  0.4888     0.2730  0 0.000 0.412 0.588
#> GSM674348     3  0.0817     0.8442  0 0.000 0.976 0.024
#> GSM674349     3  0.0336     0.8453  0 0.000 0.992 0.008
#> GSM674350     3  0.1118     0.8452  0 0.000 0.964 0.036
#> GSM674353     3  0.1118     0.8452  0 0.000 0.964 0.036
#> GSM674354     3  0.1118     0.8452  0 0.000 0.964 0.036
#> GSM674355     3  0.4250     0.5649  0 0.000 0.724 0.276
#> GSM674356     3  0.0336     0.8453  0 0.000 0.992 0.008
#> GSM674357     3  0.0817     0.8463  0 0.000 0.976 0.024
#> GSM674358     3  0.1118     0.8452  0 0.000 0.964 0.036
#> GSM674361     3  0.1118     0.8452  0 0.000 0.964 0.036
#> GSM674363     3  0.1118     0.8452  0 0.000 0.964 0.036
#> GSM674364     3  0.0336     0.8453  0 0.000 0.992 0.008
#> GSM674365     3  0.0817     0.8428  0 0.000 0.976 0.024
#> GSM674366     4  0.4877     0.3225  0 0.000 0.408 0.592
#> GSM674367     4  0.1792     0.9192  0 0.000 0.068 0.932
#> GSM674368     3  0.4996     0.0227  0 0.000 0.516 0.484
#> GSM674370     4  0.1792     0.9211  0 0.000 0.068 0.932
#> GSM674371     3  0.4454     0.5297  0 0.000 0.692 0.308
#> GSM674373     4  0.3219     0.8172  0 0.000 0.164 0.836
#> GSM674375     4  0.1474     0.9270  0 0.000 0.052 0.948
#> GSM674379     4  0.1637     0.9235  0 0.000 0.060 0.940
#> GSM674380     4  0.1474     0.9270  0 0.000 0.052 0.948
#> GSM674381     4  0.2011     0.9112  0 0.000 0.080 0.920
#> GSM674382     4  0.1474     0.9270  0 0.000 0.052 0.948
#> GSM674384     4  0.1474     0.9270  0 0.000 0.052 0.948
#> GSM674385     3  0.1389     0.8303  0 0.000 0.952 0.048
#> GSM674388     3  0.4356     0.5548  0 0.000 0.708 0.292
#> GSM674389     4  0.1474     0.9270  0 0.000 0.052 0.948
#> GSM674390     4  0.1474     0.9270  0 0.000 0.052 0.948
#> GSM674391     4  0.1474     0.9270  0 0.000 0.052 0.948
#> GSM674393     3  0.4713     0.4417  0 0.000 0.640 0.360
#> GSM674394     4  0.4643     0.4921  0 0.000 0.344 0.656
#> GSM674395     4  0.4679     0.4733  0 0.000 0.352 0.648
#> GSM674397     3  0.4992     0.0967  0 0.000 0.524 0.476
#> GSM674398     4  0.1474     0.9270  0 0.000 0.052 0.948
#> GSM674400     4  0.2149     0.9081  0 0.000 0.088 0.912
#> GSM674401     4  0.3219     0.8292  0 0.000 0.164 0.836
#> GSM674402     3  0.1118     0.8452  0 0.000 0.964 0.036
#> GSM674403     3  0.1022     0.8390  0 0.000 0.968 0.032
#> GSM674405     4  0.1474     0.9270  0 0.000 0.052 0.948
#> GSM674406     4  0.1474     0.9270  0 0.000 0.052 0.948
#> GSM674407     4  0.1474     0.9270  0 0.000 0.052 0.948
#> GSM674181     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674183     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674184     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674185     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674186     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674187     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674190     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674191     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674192     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674193     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674194     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674195     2  0.0188     0.9752  0 0.996 0.004 0.000
#> GSM674198     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674200     3  0.4977     0.1276  0 0.460 0.540 0.000
#> GSM674201     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674202     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674203     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674204     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674205     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674206     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674208     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674209     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674210     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674212     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674214     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674218     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674219     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674220     2  0.0336     0.9729  0 0.992 0.000 0.008
#> GSM674221     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674223     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674225     2  0.0336     0.9729  0 0.992 0.000 0.008
#> GSM674226     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674229     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674230     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674231     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674232     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674234     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674235     2  0.1635     0.9662  0 0.948 0.008 0.044
#> GSM674236     2  0.1722     0.9653  0 0.944 0.008 0.048
#> GSM674237     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674239     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674240     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674242     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674243     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674244     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674245     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674282     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674284     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674285     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674287     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674288     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674289     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674290     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674291     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674292     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674295     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674297     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674298     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674299     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674300     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674301     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674302     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674304     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674305     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674306     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674308     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674309     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674313     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674314     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674315     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674316     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674318     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674320     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674323     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674324     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674325     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674327     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674328     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674330     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674331     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674332     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674334     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674335     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674345     3  0.0336     0.8453  0 0.000 0.992 0.008
#> GSM674351     3  0.1118     0.8452  0 0.000 0.964 0.036
#> GSM674352     3  0.1118     0.8452  0 0.000 0.964 0.036
#> GSM674359     3  0.0336     0.8453  0 0.000 0.992 0.008
#> GSM674360     3  0.0336     0.8453  0 0.000 0.992 0.008
#> GSM674362     3  0.0336     0.8411  0 0.008 0.992 0.000
#> GSM674369     3  0.4431     0.5364  0 0.000 0.696 0.304
#> GSM674372     4  0.2760     0.8570  0 0.000 0.128 0.872
#> GSM674374     4  0.2011     0.9112  0 0.000 0.080 0.920
#> GSM674376     4  0.1474     0.9270  0 0.000 0.052 0.948
#> GSM674377     4  0.2011     0.9112  0 0.000 0.080 0.920
#> GSM674378     4  0.1557     0.9250  0 0.000 0.056 0.944
#> GSM674383     3  0.4605     0.4767  0 0.000 0.664 0.336
#> GSM674386     4  0.1474     0.9270  0 0.000 0.052 0.948
#> GSM674387     4  0.1474     0.9270  0 0.000 0.052 0.948
#> GSM674392     3  0.4643     0.4197  0 0.000 0.656 0.344
#> GSM674396     4  0.1474     0.9270  0 0.000 0.052 0.948
#> GSM674399     4  0.1474     0.9270  0 0.000 0.052 0.948
#> GSM674404     4  0.1474     0.9270  0 0.000 0.052 0.948
#> GSM674182     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674188     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674189     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674196     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674197     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674199     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674207     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674211     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674213     2  0.0336     0.9759  0 0.992 0.000 0.008
#> GSM674215     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674216     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674217     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674222     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674224     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674227     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674228     2  0.1356     0.9691  0 0.960 0.008 0.032
#> GSM674233     2  0.0000     0.9773  0 1.000 0.000 0.000
#> GSM674238     2  0.3266     0.7914  0 0.832 0.168 0.000
#> GSM674241     2  0.1807     0.9643  0 0.940 0.008 0.052
#> GSM674283     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674286     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674293     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674294     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674296     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674303     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674307     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674310     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674311     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674312     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674317     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674319     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674321     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674322     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674326     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674329     1  0.0000     1.0000  1 0.000 0.000 0.000
#> GSM674333     1  0.0000     1.0000  1 0.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4    p5
#> GSM674344     5  0.0000     0.8891 0.000 0.000 0.000 0.000 1.000
#> GSM674346     5  0.0000     0.8891 0.000 0.000 0.000 0.000 1.000
#> GSM674347     3  0.4291     0.0255 0.000 0.000 0.536 0.000 0.464
#> GSM674348     5  0.0404     0.8870 0.000 0.000 0.012 0.000 0.988
#> GSM674349     5  0.0000     0.8891 0.000 0.000 0.000 0.000 1.000
#> GSM674350     5  0.0404     0.8894 0.000 0.000 0.012 0.000 0.988
#> GSM674353     5  0.0404     0.8894 0.000 0.000 0.012 0.000 0.988
#> GSM674354     5  0.0404     0.8894 0.000 0.000 0.012 0.000 0.988
#> GSM674355     5  0.3837     0.5230 0.000 0.000 0.308 0.000 0.692
#> GSM674356     5  0.0000     0.8891 0.000 0.000 0.000 0.000 1.000
#> GSM674357     5  0.0162     0.8894 0.000 0.000 0.004 0.000 0.996
#> GSM674358     5  0.0404     0.8894 0.000 0.000 0.012 0.000 0.988
#> GSM674361     5  0.0404     0.8894 0.000 0.000 0.012 0.000 0.988
#> GSM674363     5  0.0404     0.8894 0.000 0.000 0.012 0.000 0.988
#> GSM674364     5  0.0000     0.8891 0.000 0.000 0.000 0.000 1.000
#> GSM674365     5  0.0510     0.8844 0.000 0.000 0.016 0.000 0.984
#> GSM674366     3  0.4074     0.3675 0.000 0.000 0.636 0.000 0.364
#> GSM674367     3  0.0000     0.9129 0.000 0.000 1.000 0.000 0.000
#> GSM674368     3  0.4307    -0.0677 0.000 0.000 0.504 0.000 0.496
#> GSM674370     3  0.0290     0.9089 0.000 0.000 0.992 0.000 0.008
#> GSM674371     5  0.3752     0.5940 0.000 0.000 0.292 0.000 0.708
#> GSM674373     3  0.2074     0.8221 0.000 0.000 0.896 0.000 0.104
#> GSM674375     3  0.0000     0.9129 0.000 0.000 1.000 0.000 0.000
#> GSM674379     3  0.0290     0.9091 0.000 0.000 0.992 0.000 0.008
#> GSM674380     3  0.0000     0.9129 0.000 0.000 1.000 0.000 0.000
#> GSM674381     3  0.0404     0.9069 0.000 0.000 0.988 0.000 0.012
#> GSM674382     3  0.0000     0.9129 0.000 0.000 1.000 0.000 0.000
#> GSM674384     3  0.0000     0.9129 0.000 0.000 1.000 0.000 0.000
#> GSM674385     5  0.1410     0.8523 0.000 0.000 0.060 0.000 0.940
#> GSM674388     5  0.3707     0.6057 0.000 0.000 0.284 0.000 0.716
#> GSM674389     3  0.0000     0.9129 0.000 0.000 1.000 0.000 0.000
#> GSM674390     3  0.0000     0.9129 0.000 0.000 1.000 0.000 0.000
#> GSM674391     3  0.0000     0.9129 0.000 0.000 1.000 0.000 0.000
#> GSM674393     5  0.3966     0.5205 0.000 0.000 0.336 0.000 0.664
#> GSM674394     3  0.3752     0.5423 0.000 0.000 0.708 0.000 0.292
#> GSM674395     3  0.3837     0.5130 0.000 0.000 0.692 0.000 0.308
#> GSM674397     5  0.4283     0.1996 0.000 0.000 0.456 0.000 0.544
#> GSM674398     3  0.0000     0.9129 0.000 0.000 1.000 0.000 0.000
#> GSM674400     3  0.0609     0.9031 0.000 0.000 0.980 0.000 0.020
#> GSM674401     3  0.2561     0.7807 0.000 0.000 0.856 0.000 0.144
#> GSM674402     5  0.0404     0.8894 0.000 0.000 0.012 0.000 0.988
#> GSM674403     5  0.0703     0.8797 0.000 0.000 0.024 0.000 0.976
#> GSM674405     3  0.0000     0.9129 0.000 0.000 1.000 0.000 0.000
#> GSM674406     3  0.0000     0.9129 0.000 0.000 1.000 0.000 0.000
#> GSM674407     3  0.0000     0.9129 0.000 0.000 1.000 0.000 0.000
#> GSM674181     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674183     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674184     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674185     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674186     2  0.0609     0.8798 0.000 0.980 0.000 0.020 0.000
#> GSM674187     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674190     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674191     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674192     2  0.3177     0.4705 0.000 0.792 0.000 0.208 0.000
#> GSM674193     2  0.1544     0.8189 0.000 0.932 0.000 0.068 0.000
#> GSM674194     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674195     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674198     4  0.4219     0.9879 0.000 0.416 0.000 0.584 0.000
#> GSM674200     2  0.4304     0.0501 0.000 0.516 0.000 0.000 0.484
#> GSM674201     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674202     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674203     4  0.4219     0.9879 0.000 0.416 0.000 0.584 0.000
#> GSM674204     4  0.4219     0.9879 0.000 0.416 0.000 0.584 0.000
#> GSM674205     4  0.4219     0.9879 0.000 0.416 0.000 0.584 0.000
#> GSM674206     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674208     4  0.4219     0.9879 0.000 0.416 0.000 0.584 0.000
#> GSM674209     2  0.1197     0.8495 0.000 0.952 0.000 0.048 0.000
#> GSM674210     4  0.4219     0.9879 0.000 0.416 0.000 0.584 0.000
#> GSM674212     4  0.4283     0.9286 0.000 0.456 0.000 0.544 0.000
#> GSM674214     4  0.4219     0.9879 0.000 0.416 0.000 0.584 0.000
#> GSM674218     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674219     2  0.0162     0.8940 0.000 0.996 0.000 0.004 0.000
#> GSM674220     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674221     2  0.0404     0.8881 0.000 0.988 0.000 0.012 0.000
#> GSM674223     2  0.0880     0.8692 0.000 0.968 0.000 0.032 0.000
#> GSM674225     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674226     2  0.0290     0.8920 0.000 0.992 0.000 0.008 0.000
#> GSM674229     4  0.4278     0.9359 0.000 0.452 0.000 0.548 0.000
#> GSM674230     2  0.0162     0.8940 0.000 0.996 0.000 0.004 0.000
#> GSM674231     2  0.1043     0.8588 0.000 0.960 0.000 0.040 0.000
#> GSM674232     4  0.4219     0.9879 0.000 0.416 0.000 0.584 0.000
#> GSM674234     4  0.4235     0.9796 0.000 0.424 0.000 0.576 0.000
#> GSM674235     2  0.4305    -0.8161 0.000 0.512 0.000 0.488 0.000
#> GSM674236     2  0.4297    -0.7727 0.000 0.528 0.000 0.472 0.000
#> GSM674237     4  0.4219     0.9879 0.000 0.416 0.000 0.584 0.000
#> GSM674239     4  0.4219     0.9879 0.000 0.416 0.000 0.584 0.000
#> GSM674240     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674242     4  0.4219     0.9879 0.000 0.416 0.000 0.584 0.000
#> GSM674243     2  0.0880     0.8709 0.000 0.968 0.000 0.032 0.000
#> GSM674244     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674245     2  0.0162     0.8940 0.000 0.996 0.000 0.004 0.000
#> GSM674282     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674284     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674285     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674287     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674288     1  0.3480     0.8044 0.752 0.000 0.000 0.248 0.000
#> GSM674289     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674291     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674292     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674295     1  0.4210     0.7778 0.588 0.000 0.000 0.412 0.000
#> GSM674297     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674298     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674299     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674300     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674301     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674302     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674305     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674306     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674308     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674309     1  0.4219     0.7767 0.584 0.000 0.000 0.416 0.000
#> GSM674313     1  0.4219     0.7767 0.584 0.000 0.000 0.416 0.000
#> GSM674314     1  0.4219     0.7767 0.584 0.000 0.000 0.416 0.000
#> GSM674315     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674316     1  0.4219     0.7767 0.584 0.000 0.000 0.416 0.000
#> GSM674318     1  0.4219     0.7767 0.584 0.000 0.000 0.416 0.000
#> GSM674320     1  0.4219     0.7767 0.584 0.000 0.000 0.416 0.000
#> GSM674323     1  0.4219     0.7767 0.584 0.000 0.000 0.416 0.000
#> GSM674324     1  0.4138     0.7834 0.616 0.000 0.000 0.384 0.000
#> GSM674325     1  0.4219     0.7767 0.584 0.000 0.000 0.416 0.000
#> GSM674327     1  0.1197     0.8317 0.952 0.000 0.000 0.048 0.000
#> GSM674328     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674330     1  0.4219     0.7767 0.584 0.000 0.000 0.416 0.000
#> GSM674331     1  0.3366     0.8083 0.768 0.000 0.000 0.232 0.000
#> GSM674332     1  0.1792     0.8276 0.916 0.000 0.000 0.084 0.000
#> GSM674334     1  0.4201     0.7788 0.592 0.000 0.000 0.408 0.000
#> GSM674335     1  0.4219     0.7767 0.584 0.000 0.000 0.416 0.000
#> GSM674345     5  0.0000     0.8891 0.000 0.000 0.000 0.000 1.000
#> GSM674351     5  0.0404     0.8894 0.000 0.000 0.012 0.000 0.988
#> GSM674352     5  0.0404     0.8894 0.000 0.000 0.012 0.000 0.988
#> GSM674359     5  0.0000     0.8891 0.000 0.000 0.000 0.000 1.000
#> GSM674360     5  0.0000     0.8891 0.000 0.000 0.000 0.000 1.000
#> GSM674362     5  0.0000     0.8891 0.000 0.000 0.000 0.000 1.000
#> GSM674369     5  0.3730     0.6001 0.000 0.000 0.288 0.000 0.712
#> GSM674372     3  0.2280     0.8013 0.000 0.000 0.880 0.000 0.120
#> GSM674374     3  0.0404     0.9069 0.000 0.000 0.988 0.000 0.012
#> GSM674376     3  0.0000     0.9129 0.000 0.000 1.000 0.000 0.000
#> GSM674377     3  0.0404     0.9069 0.000 0.000 0.988 0.000 0.012
#> GSM674378     3  0.0162     0.9111 0.000 0.000 0.996 0.000 0.004
#> GSM674383     5  0.3913     0.5390 0.000 0.000 0.324 0.000 0.676
#> GSM674386     3  0.0000     0.9129 0.000 0.000 1.000 0.000 0.000
#> GSM674387     3  0.0000     0.9129 0.000 0.000 1.000 0.000 0.000
#> GSM674392     5  0.3966     0.4578 0.000 0.000 0.336 0.000 0.664
#> GSM674396     3  0.0000     0.9129 0.000 0.000 1.000 0.000 0.000
#> GSM674399     3  0.0000     0.9129 0.000 0.000 1.000 0.000 0.000
#> GSM674404     3  0.0000     0.9129 0.000 0.000 1.000 0.000 0.000
#> GSM674182     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674188     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674189     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674196     4  0.4219     0.9879 0.000 0.416 0.000 0.584 0.000
#> GSM674197     4  0.4219     0.9879 0.000 0.416 0.000 0.584 0.000
#> GSM674199     4  0.4219     0.9879 0.000 0.416 0.000 0.584 0.000
#> GSM674207     4  0.4227     0.9837 0.000 0.420 0.000 0.580 0.000
#> GSM674211     4  0.4227     0.9838 0.000 0.420 0.000 0.580 0.000
#> GSM674213     2  0.0510     0.8855 0.000 0.984 0.000 0.016 0.000
#> GSM674215     2  0.0000     0.8957 0.000 1.000 0.000 0.000 0.000
#> GSM674216     4  0.4219     0.9879 0.000 0.416 0.000 0.584 0.000
#> GSM674217     2  0.0794     0.8693 0.000 0.972 0.000 0.028 0.000
#> GSM674222     2  0.0703     0.8771 0.000 0.976 0.000 0.024 0.000
#> GSM674224     2  0.0794     0.8727 0.000 0.972 0.000 0.028 0.000
#> GSM674227     2  0.1043     0.8570 0.000 0.960 0.000 0.040 0.000
#> GSM674228     2  0.4268    -0.7044 0.000 0.556 0.000 0.444 0.000
#> GSM674233     2  0.0162     0.8940 0.000 0.996 0.000 0.004 0.000
#> GSM674238     2  0.0510     0.8745 0.000 0.984 0.000 0.000 0.016
#> GSM674241     4  0.4278     0.9359 0.000 0.452 0.000 0.548 0.000
#> GSM674283     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674286     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674293     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674294     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674296     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674303     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674307     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674310     1  0.4219     0.7767 0.584 0.000 0.000 0.416 0.000
#> GSM674311     1  0.4192     0.7796 0.596 0.000 0.000 0.404 0.000
#> GSM674312     1  0.4219     0.7767 0.584 0.000 0.000 0.416 0.000
#> GSM674317     1  0.0000     0.8366 1.000 0.000 0.000 0.000 0.000
#> GSM674319     1  0.4219     0.7767 0.584 0.000 0.000 0.416 0.000
#> GSM674321     1  0.4219     0.7767 0.584 0.000 0.000 0.416 0.000
#> GSM674322     1  0.4219     0.7767 0.584 0.000 0.000 0.416 0.000
#> GSM674326     1  0.4219     0.7767 0.584 0.000 0.000 0.416 0.000
#> GSM674329     1  0.4219     0.7767 0.584 0.000 0.000 0.416 0.000
#> GSM674333     1  0.4219     0.7767 0.584 0.000 0.000 0.416 0.000

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4    p5    p6
#> GSM674344     3  0.0146     0.8766 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM674346     3  0.0000     0.8768 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM674347     4  0.4258    -0.0575 0.000 0.000 0.468 0.516 0.016 0.000
#> GSM674348     3  0.0405     0.8762 0.000 0.000 0.988 0.008 0.004 0.000
#> GSM674349     3  0.0146     0.8766 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM674350     3  0.0603     0.8748 0.000 0.000 0.980 0.004 0.016 0.000
#> GSM674353     3  0.0603     0.8748 0.000 0.000 0.980 0.004 0.016 0.000
#> GSM674354     3  0.0291     0.8767 0.000 0.000 0.992 0.004 0.004 0.000
#> GSM674355     3  0.3853     0.5137 0.000 0.000 0.680 0.304 0.016 0.000
#> GSM674356     3  0.0000     0.8768 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM674357     3  0.0000     0.8768 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM674358     3  0.0603     0.8748 0.000 0.000 0.980 0.004 0.016 0.000
#> GSM674361     3  0.0603     0.8748 0.000 0.000 0.980 0.004 0.016 0.000
#> GSM674363     3  0.0603     0.8748 0.000 0.000 0.980 0.004 0.016 0.000
#> GSM674364     3  0.0146     0.8766 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM674365     3  0.0508     0.8741 0.000 0.000 0.984 0.012 0.004 0.000
#> GSM674366     4  0.3769     0.3483 0.000 0.000 0.356 0.640 0.004 0.000
#> GSM674367     4  0.0000     0.9251 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674368     3  0.3999     0.0911 0.000 0.000 0.500 0.496 0.004 0.000
#> GSM674370     4  0.0717     0.9165 0.000 0.000 0.008 0.976 0.016 0.000
#> GSM674371     3  0.3468     0.6162 0.000 0.000 0.712 0.284 0.004 0.000
#> GSM674373     4  0.2263     0.8305 0.000 0.000 0.100 0.884 0.016 0.000
#> GSM674375     4  0.0000     0.9251 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674379     4  0.0000     0.9251 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674380     4  0.0260     0.9233 0.000 0.000 0.000 0.992 0.008 0.000
#> GSM674381     4  0.0405     0.9204 0.000 0.000 0.008 0.988 0.004 0.000
#> GSM674382     4  0.0260     0.9233 0.000 0.000 0.000 0.992 0.008 0.000
#> GSM674384     4  0.0458     0.9205 0.000 0.000 0.000 0.984 0.016 0.000
#> GSM674385     3  0.1411     0.8431 0.000 0.000 0.936 0.060 0.004 0.000
#> GSM674388     3  0.3426     0.6267 0.000 0.000 0.720 0.276 0.004 0.000
#> GSM674389     4  0.0458     0.9205 0.000 0.000 0.000 0.984 0.016 0.000
#> GSM674390     4  0.0000     0.9251 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674391     4  0.0000     0.9251 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674393     3  0.3531     0.5535 0.000 0.000 0.672 0.328 0.000 0.000
#> GSM674394     4  0.3758     0.5476 0.000 0.000 0.284 0.700 0.016 0.000
#> GSM674395     4  0.3835     0.5174 0.000 0.000 0.300 0.684 0.016 0.000
#> GSM674397     3  0.3838     0.2598 0.000 0.000 0.552 0.448 0.000 0.000
#> GSM674398     4  0.0000     0.9251 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674400     4  0.0458     0.9177 0.000 0.000 0.016 0.984 0.000 0.000
#> GSM674401     4  0.2340     0.7754 0.000 0.000 0.148 0.852 0.000 0.000
#> GSM674402     3  0.0603     0.8748 0.000 0.000 0.980 0.004 0.016 0.000
#> GSM674403     3  0.0777     0.8682 0.000 0.000 0.972 0.024 0.004 0.000
#> GSM674405     4  0.0000     0.9251 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674406     4  0.0000     0.9251 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674407     4  0.0000     0.9251 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674181     6  0.0000     0.9412 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM674183     6  0.0520     0.9401 0.000 0.008 0.000 0.000 0.008 0.984
#> GSM674184     6  0.0260     0.9411 0.000 0.000 0.000 0.000 0.008 0.992
#> GSM674185     6  0.0520     0.9401 0.000 0.008 0.000 0.000 0.008 0.984
#> GSM674186     6  0.1757     0.8892 0.000 0.076 0.000 0.000 0.008 0.916
#> GSM674187     6  0.0713     0.9344 0.000 0.028 0.000 0.000 0.000 0.972
#> GSM674190     6  0.0000     0.9412 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM674191     6  0.0000     0.9412 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM674192     2  0.3823     0.1915 0.000 0.564 0.000 0.000 0.000 0.436
#> GSM674193     6  0.3198     0.6621 0.000 0.260 0.000 0.000 0.000 0.740
#> GSM674194     6  0.0260     0.9411 0.000 0.000 0.000 0.000 0.008 0.992
#> GSM674195     6  0.0260     0.9411 0.000 0.000 0.000 0.000 0.008 0.992
#> GSM674198     2  0.0260     0.8886 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674200     6  0.4274     0.2533 0.000 0.008 0.424 0.000 0.008 0.560
#> GSM674201     6  0.0000     0.9412 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM674202     6  0.0260     0.9404 0.000 0.008 0.000 0.000 0.000 0.992
#> GSM674203     2  0.0000     0.8882 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674204     2  0.0260     0.8886 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674205     2  0.0260     0.8886 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674206     6  0.0000     0.9412 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM674208     2  0.0000     0.8882 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674209     6  0.2697     0.7679 0.000 0.188 0.000 0.000 0.000 0.812
#> GSM674210     2  0.0260     0.8886 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674212     2  0.2883     0.7524 0.000 0.788 0.000 0.000 0.000 0.212
#> GSM674214     2  0.0000     0.8882 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674218     6  0.0260     0.9411 0.000 0.000 0.000 0.000 0.008 0.992
#> GSM674219     6  0.0260     0.9403 0.000 0.008 0.000 0.000 0.000 0.992
#> GSM674220     6  0.0520     0.9401 0.000 0.008 0.000 0.000 0.008 0.984
#> GSM674221     6  0.0547     0.9348 0.000 0.020 0.000 0.000 0.000 0.980
#> GSM674223     6  0.1327     0.9039 0.000 0.064 0.000 0.000 0.000 0.936
#> GSM674225     6  0.0520     0.9401 0.000 0.008 0.000 0.000 0.008 0.984
#> GSM674226     6  0.0363     0.9394 0.000 0.012 0.000 0.000 0.000 0.988
#> GSM674229     2  0.2823     0.7598 0.000 0.796 0.000 0.000 0.000 0.204
#> GSM674230     6  0.0260     0.9403 0.000 0.008 0.000 0.000 0.000 0.992
#> GSM674231     6  0.2941     0.7286 0.000 0.220 0.000 0.000 0.000 0.780
#> GSM674232     2  0.0146     0.8886 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674234     2  0.1267     0.8720 0.000 0.940 0.000 0.000 0.000 0.060
#> GSM674235     2  0.3706     0.4947 0.000 0.620 0.000 0.000 0.000 0.380
#> GSM674236     2  0.3634     0.5381 0.000 0.644 0.000 0.000 0.000 0.356
#> GSM674237     2  0.0000     0.8882 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674239     2  0.0458     0.8863 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM674240     6  0.0000     0.9412 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM674242     2  0.0000     0.8882 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674243     6  0.2454     0.8060 0.000 0.160 0.000 0.000 0.000 0.840
#> GSM674244     6  0.0520     0.9401 0.000 0.008 0.000 0.000 0.008 0.984
#> GSM674245     6  0.0363     0.9393 0.000 0.012 0.000 0.000 0.000 0.988
#> GSM674282     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674284     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674285     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674287     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674288     1  0.3789     0.2297 0.584 0.000 0.000 0.000 0.416 0.000
#> GSM674289     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674291     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674292     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674295     5  0.0790     0.9670 0.032 0.000 0.000 0.000 0.968 0.000
#> GSM674297     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674298     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674299     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674300     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674301     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674302     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674305     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674306     1  0.0146     0.9751 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM674308     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674309     5  0.0713     0.9695 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674313     5  0.0713     0.9695 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674314     5  0.0713     0.9695 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674315     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674316     5  0.0713     0.9695 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674318     5  0.0713     0.9695 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674320     5  0.0713     0.9695 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674323     5  0.0713     0.9695 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674324     5  0.1327     0.9396 0.064 0.000 0.000 0.000 0.936 0.000
#> GSM674325     5  0.0713     0.9695 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674327     1  0.2378     0.7983 0.848 0.000 0.000 0.000 0.152 0.000
#> GSM674328     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674330     5  0.0713     0.9695 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674331     5  0.2996     0.7381 0.228 0.000 0.000 0.000 0.772 0.000
#> GSM674332     5  0.3774     0.3633 0.408 0.000 0.000 0.000 0.592 0.000
#> GSM674334     5  0.0865     0.9643 0.036 0.000 0.000 0.000 0.964 0.000
#> GSM674335     5  0.0713     0.9695 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674345     3  0.0000     0.8768 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM674351     3  0.0603     0.8748 0.000 0.000 0.980 0.004 0.016 0.000
#> GSM674352     3  0.0291     0.8767 0.000 0.000 0.992 0.004 0.004 0.000
#> GSM674359     3  0.0146     0.8766 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM674360     3  0.0146     0.8766 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM674362     3  0.0146     0.8766 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM674369     3  0.3448     0.6216 0.000 0.000 0.716 0.280 0.004 0.000
#> GSM674372     4  0.2538     0.7987 0.000 0.000 0.124 0.860 0.016 0.000
#> GSM674374     4  0.0146     0.9233 0.000 0.000 0.004 0.996 0.000 0.000
#> GSM674376     4  0.0000     0.9251 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674377     4  0.0146     0.9233 0.000 0.000 0.004 0.996 0.000 0.000
#> GSM674378     4  0.0603     0.9188 0.000 0.000 0.004 0.980 0.016 0.000
#> GSM674383     3  0.3601     0.5732 0.000 0.000 0.684 0.312 0.004 0.000
#> GSM674386     4  0.0000     0.9251 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674387     4  0.0000     0.9251 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674392     3  0.3922     0.4756 0.000 0.000 0.664 0.320 0.016 0.000
#> GSM674396     4  0.0000     0.9251 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674399     4  0.0000     0.9251 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674404     4  0.0458     0.9205 0.000 0.000 0.000 0.984 0.016 0.000
#> GSM674182     6  0.0000     0.9412 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM674188     6  0.0000     0.9412 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM674189     6  0.0405     0.9409 0.000 0.004 0.000 0.000 0.008 0.988
#> GSM674196     2  0.0260     0.8886 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674197     2  0.0260     0.8886 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674199     2  0.0000     0.8882 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674207     2  0.0458     0.8880 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM674211     2  0.1141     0.8741 0.000 0.948 0.000 0.000 0.000 0.052
#> GSM674213     6  0.0547     0.9360 0.000 0.020 0.000 0.000 0.000 0.980
#> GSM674215     6  0.0520     0.9401 0.000 0.008 0.000 0.000 0.008 0.984
#> GSM674216     2  0.0000     0.8882 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674217     6  0.0713     0.9287 0.000 0.028 0.000 0.000 0.000 0.972
#> GSM674222     6  0.1267     0.9120 0.000 0.060 0.000 0.000 0.000 0.940
#> GSM674224     6  0.1075     0.9164 0.000 0.048 0.000 0.000 0.000 0.952
#> GSM674227     6  0.3076     0.6987 0.000 0.240 0.000 0.000 0.000 0.760
#> GSM674228     2  0.3810     0.4071 0.000 0.572 0.000 0.000 0.000 0.428
#> GSM674233     6  0.0260     0.9403 0.000 0.008 0.000 0.000 0.000 0.992
#> GSM674238     6  0.0520     0.9401 0.000 0.008 0.000 0.000 0.008 0.984
#> GSM674241     2  0.2793     0.7634 0.000 0.800 0.000 0.000 0.000 0.200
#> GSM674283     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674286     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674293     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674294     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674296     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674303     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674307     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674310     5  0.0713     0.9695 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674311     5  0.0937     0.9609 0.040 0.000 0.000 0.000 0.960 0.000
#> GSM674312     5  0.0713     0.9695 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674317     1  0.0000     0.9788 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674319     5  0.0713     0.9695 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674321     5  0.0713     0.9695 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674322     5  0.0713     0.9695 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674326     5  0.0713     0.9695 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674329     5  0.0713     0.9695 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674333     5  0.0713     0.9695 0.028 0.000 0.000 0.000 0.972 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-MAD-pam-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-MAD-pam-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-MAD-pam-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-MAD-pam-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-MAD-pam-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-MAD-pam-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-MAD-pam-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-MAD-pam-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-MAD-pam-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-MAD-pam-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-MAD-pam-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-MAD-pam-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-MAD-pam-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-MAD-pam-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-MAD-pam-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-MAD-pam-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-MAD-pam-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-MAD-pam-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-MAD-pam-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-MAD-pam-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk MAD-pam-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-MAD-pam-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-MAD-pam-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-MAD-pam-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-MAD-pam-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-MAD-pam-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk MAD-pam-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>           n disease.state(p) specimen(p) k
#> MAD:pam 183            0.924    1.83e-40 2
#> MAD:pam 183            0.962    6.15e-78 3
#> MAD:pam 173            0.881    1.11e-71 4
#> MAD:pam 173            0.980    6.47e-70 5
#> MAD:pam 172            0.940    7.47e-68 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


MAD:mclust*

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["MAD", "mclust"]
# you can also extract it by
# res = res_list["MAD:mclust"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#>   Subgroups are detected by 'mclust' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 6.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk MAD-mclust-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk MAD-mclust-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 1.000           1.000       1.000         0.5958 0.750   0.571
#> 4 4 0.965           0.921       0.956         0.0490 0.979   0.937
#> 5 5 0.855           0.800       0.873         0.0544 0.978   0.930
#> 6 6 0.924           0.905       0.939         0.0375 0.950   0.828

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3 4

There is also optional best \(k\) = 2 3 4 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette p1 p2 p3
#> GSM674344     3       0          1  0  0  1
#> GSM674346     3       0          1  0  0  1
#> GSM674347     3       0          1  0  0  1
#> GSM674348     3       0          1  0  0  1
#> GSM674349     3       0          1  0  0  1
#> GSM674350     3       0          1  0  0  1
#> GSM674353     3       0          1  0  0  1
#> GSM674354     3       0          1  0  0  1
#> GSM674355     3       0          1  0  0  1
#> GSM674356     3       0          1  0  0  1
#> GSM674357     3       0          1  0  0  1
#> GSM674358     3       0          1  0  0  1
#> GSM674361     3       0          1  0  0  1
#> GSM674363     3       0          1  0  0  1
#> GSM674364     3       0          1  0  0  1
#> GSM674365     3       0          1  0  0  1
#> GSM674366     3       0          1  0  0  1
#> GSM674367     3       0          1  0  0  1
#> GSM674368     3       0          1  0  0  1
#> GSM674370     3       0          1  0  0  1
#> GSM674371     3       0          1  0  0  1
#> GSM674373     3       0          1  0  0  1
#> GSM674375     3       0          1  0  0  1
#> GSM674379     3       0          1  0  0  1
#> GSM674380     3       0          1  0  0  1
#> GSM674381     3       0          1  0  0  1
#> GSM674382     3       0          1  0  0  1
#> GSM674384     3       0          1  0  0  1
#> GSM674385     3       0          1  0  0  1
#> GSM674388     3       0          1  0  0  1
#> GSM674389     3       0          1  0  0  1
#> GSM674390     3       0          1  0  0  1
#> GSM674391     3       0          1  0  0  1
#> GSM674393     3       0          1  0  0  1
#> GSM674394     3       0          1  0  0  1
#> GSM674395     3       0          1  0  0  1
#> GSM674397     3       0          1  0  0  1
#> GSM674398     3       0          1  0  0  1
#> GSM674400     3       0          1  0  0  1
#> GSM674401     3       0          1  0  0  1
#> GSM674402     3       0          1  0  0  1
#> GSM674403     3       0          1  0  0  1
#> GSM674405     3       0          1  0  0  1
#> GSM674406     3       0          1  0  0  1
#> GSM674407     3       0          1  0  0  1
#> GSM674181     2       0          1  0  1  0
#> GSM674183     2       0          1  0  1  0
#> GSM674184     2       0          1  0  1  0
#> GSM674185     2       0          1  0  1  0
#> GSM674186     2       0          1  0  1  0
#> GSM674187     2       0          1  0  1  0
#> GSM674190     2       0          1  0  1  0
#> GSM674191     2       0          1  0  1  0
#> GSM674192     2       0          1  0  1  0
#> GSM674193     2       0          1  0  1  0
#> GSM674194     2       0          1  0  1  0
#> GSM674195     2       0          1  0  1  0
#> GSM674198     2       0          1  0  1  0
#> GSM674200     2       0          1  0  1  0
#> GSM674201     2       0          1  0  1  0
#> GSM674202     2       0          1  0  1  0
#> GSM674203     2       0          1  0  1  0
#> GSM674204     2       0          1  0  1  0
#> GSM674205     2       0          1  0  1  0
#> GSM674206     2       0          1  0  1  0
#> GSM674208     2       0          1  0  1  0
#> GSM674209     2       0          1  0  1  0
#> GSM674210     2       0          1  0  1  0
#> GSM674212     2       0          1  0  1  0
#> GSM674214     2       0          1  0  1  0
#> GSM674218     2       0          1  0  1  0
#> GSM674219     2       0          1  0  1  0
#> GSM674220     2       0          1  0  1  0
#> GSM674221     2       0          1  0  1  0
#> GSM674223     2       0          1  0  1  0
#> GSM674225     2       0          1  0  1  0
#> GSM674226     2       0          1  0  1  0
#> GSM674229     2       0          1  0  1  0
#> GSM674230     2       0          1  0  1  0
#> GSM674231     2       0          1  0  1  0
#> GSM674232     2       0          1  0  1  0
#> GSM674234     2       0          1  0  1  0
#> GSM674235     2       0          1  0  1  0
#> GSM674236     2       0          1  0  1  0
#> GSM674237     2       0          1  0  1  0
#> GSM674239     2       0          1  0  1  0
#> GSM674240     2       0          1  0  1  0
#> GSM674242     2       0          1  0  1  0
#> GSM674243     2       0          1  0  1  0
#> GSM674244     2       0          1  0  1  0
#> GSM674245     2       0          1  0  1  0
#> GSM674282     1       0          1  1  0  0
#> GSM674284     1       0          1  1  0  0
#> GSM674285     1       0          1  1  0  0
#> GSM674287     1       0          1  1  0  0
#> GSM674288     1       0          1  1  0  0
#> GSM674289     1       0          1  1  0  0
#> GSM674290     1       0          1  1  0  0
#> GSM674291     1       0          1  1  0  0
#> GSM674292     1       0          1  1  0  0
#> GSM674295     1       0          1  1  0  0
#> GSM674297     1       0          1  1  0  0
#> GSM674298     1       0          1  1  0  0
#> GSM674299     1       0          1  1  0  0
#> GSM674300     1       0          1  1  0  0
#> GSM674301     1       0          1  1  0  0
#> GSM674302     1       0          1  1  0  0
#> GSM674304     1       0          1  1  0  0
#> GSM674305     1       0          1  1  0  0
#> GSM674306     1       0          1  1  0  0
#> GSM674308     1       0          1  1  0  0
#> GSM674309     1       0          1  1  0  0
#> GSM674313     1       0          1  1  0  0
#> GSM674314     1       0          1  1  0  0
#> GSM674315     1       0          1  1  0  0
#> GSM674316     1       0          1  1  0  0
#> GSM674318     1       0          1  1  0  0
#> GSM674320     1       0          1  1  0  0
#> GSM674323     1       0          1  1  0  0
#> GSM674324     1       0          1  1  0  0
#> GSM674325     1       0          1  1  0  0
#> GSM674327     1       0          1  1  0  0
#> GSM674328     1       0          1  1  0  0
#> GSM674330     1       0          1  1  0  0
#> GSM674331     1       0          1  1  0  0
#> GSM674332     1       0          1  1  0  0
#> GSM674334     1       0          1  1  0  0
#> GSM674335     1       0          1  1  0  0
#> GSM674345     3       0          1  0  0  1
#> GSM674351     3       0          1  0  0  1
#> GSM674352     3       0          1  0  0  1
#> GSM674359     3       0          1  0  0  1
#> GSM674360     3       0          1  0  0  1
#> GSM674362     3       0          1  0  0  1
#> GSM674369     3       0          1  0  0  1
#> GSM674372     3       0          1  0  0  1
#> GSM674374     3       0          1  0  0  1
#> GSM674376     3       0          1  0  0  1
#> GSM674377     3       0          1  0  0  1
#> GSM674378     3       0          1  0  0  1
#> GSM674383     3       0          1  0  0  1
#> GSM674386     3       0          1  0  0  1
#> GSM674387     3       0          1  0  0  1
#> GSM674392     3       0          1  0  0  1
#> GSM674396     3       0          1  0  0  1
#> GSM674399     3       0          1  0  0  1
#> GSM674404     3       0          1  0  0  1
#> GSM674182     2       0          1  0  1  0
#> GSM674188     2       0          1  0  1  0
#> GSM674189     2       0          1  0  1  0
#> GSM674196     2       0          1  0  1  0
#> GSM674197     2       0          1  0  1  0
#> GSM674199     2       0          1  0  1  0
#> GSM674207     2       0          1  0  1  0
#> GSM674211     2       0          1  0  1  0
#> GSM674213     2       0          1  0  1  0
#> GSM674215     2       0          1  0  1  0
#> GSM674216     2       0          1  0  1  0
#> GSM674217     2       0          1  0  1  0
#> GSM674222     2       0          1  0  1  0
#> GSM674224     2       0          1  0  1  0
#> GSM674227     2       0          1  0  1  0
#> GSM674228     2       0          1  0  1  0
#> GSM674233     2       0          1  0  1  0
#> GSM674238     2       0          1  0  1  0
#> GSM674241     2       0          1  0  1  0
#> GSM674283     1       0          1  1  0  0
#> GSM674286     1       0          1  1  0  0
#> GSM674293     1       0          1  1  0  0
#> GSM674294     1       0          1  1  0  0
#> GSM674296     1       0          1  1  0  0
#> GSM674303     1       0          1  1  0  0
#> GSM674307     1       0          1  1  0  0
#> GSM674310     1       0          1  1  0  0
#> GSM674311     1       0          1  1  0  0
#> GSM674312     1       0          1  1  0  0
#> GSM674317     1       0          1  1  0  0
#> GSM674319     1       0          1  1  0  0
#> GSM674321     1       0          1  1  0  0
#> GSM674322     1       0          1  1  0  0
#> GSM674326     1       0          1  1  0  0
#> GSM674329     1       0          1  1  0  0
#> GSM674333     1       0          1  1  0  0

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1    p2    p3    p4
#> GSM674344     3  0.4933    -0.1705 0.000 0.000 0.568 0.432
#> GSM674346     4  0.4477     0.8380 0.000 0.000 0.312 0.688
#> GSM674347     3  0.0707     0.9292 0.000 0.000 0.980 0.020
#> GSM674348     3  0.0336     0.9322 0.000 0.000 0.992 0.008
#> GSM674349     3  0.4643     0.2341 0.000 0.000 0.656 0.344
#> GSM674350     3  0.0707     0.9275 0.000 0.000 0.980 0.020
#> GSM674353     3  0.1022     0.9203 0.000 0.000 0.968 0.032
#> GSM674354     3  0.0336     0.9322 0.000 0.000 0.992 0.008
#> GSM674355     3  0.0336     0.9322 0.000 0.000 0.992 0.008
#> GSM674356     3  0.0336     0.9322 0.000 0.000 0.992 0.008
#> GSM674357     3  0.2647     0.8111 0.000 0.000 0.880 0.120
#> GSM674358     3  0.1211     0.9141 0.000 0.000 0.960 0.040
#> GSM674361     3  0.0336     0.9322 0.000 0.000 0.992 0.008
#> GSM674363     3  0.0707     0.9275 0.000 0.000 0.980 0.020
#> GSM674364     3  0.0188     0.9330 0.000 0.000 0.996 0.004
#> GSM674365     3  0.3688     0.6403 0.000 0.000 0.792 0.208
#> GSM674366     3  0.0188     0.9334 0.000 0.000 0.996 0.004
#> GSM674367     3  0.0000     0.9333 0.000 0.000 1.000 0.000
#> GSM674368     3  0.0469     0.9321 0.000 0.000 0.988 0.012
#> GSM674370     3  0.0000     0.9333 0.000 0.000 1.000 0.000
#> GSM674371     3  0.0592     0.9309 0.000 0.000 0.984 0.016
#> GSM674373     3  0.0336     0.9326 0.000 0.000 0.992 0.008
#> GSM674375     3  0.0000     0.9333 0.000 0.000 1.000 0.000
#> GSM674379     3  0.0592     0.9279 0.000 0.000 0.984 0.016
#> GSM674380     3  0.1824     0.8827 0.000 0.004 0.936 0.060
#> GSM674381     3  0.0592     0.9314 0.000 0.000 0.984 0.016
#> GSM674382     3  0.0592     0.9279 0.000 0.000 0.984 0.016
#> GSM674384     3  0.0188     0.9326 0.000 0.000 0.996 0.004
#> GSM674385     3  0.0336     0.9326 0.000 0.000 0.992 0.008
#> GSM674388     3  0.3266     0.7220 0.000 0.000 0.832 0.168
#> GSM674389     3  0.0000     0.9333 0.000 0.000 1.000 0.000
#> GSM674390     3  0.0336     0.9332 0.000 0.000 0.992 0.008
#> GSM674391     3  0.0592     0.9279 0.000 0.000 0.984 0.016
#> GSM674393     3  0.0469     0.9322 0.000 0.000 0.988 0.012
#> GSM674394     3  0.0188     0.9330 0.000 0.000 0.996 0.004
#> GSM674395     3  0.0000     0.9333 0.000 0.000 1.000 0.000
#> GSM674397     3  0.0000     0.9333 0.000 0.000 1.000 0.000
#> GSM674398     3  0.0592     0.9279 0.000 0.000 0.984 0.016
#> GSM674400     4  0.4477     0.8324 0.000 0.000 0.312 0.688
#> GSM674401     4  0.3356     0.8637 0.000 0.000 0.176 0.824
#> GSM674402     4  0.3311     0.8710 0.000 0.000 0.172 0.828
#> GSM674403     4  0.3266     0.8683 0.000 0.000 0.168 0.832
#> GSM674405     3  0.4817     0.0531 0.000 0.000 0.612 0.388
#> GSM674406     3  0.0000     0.9333 0.000 0.000 1.000 0.000
#> GSM674407     3  0.0707     0.9262 0.000 0.000 0.980 0.020
#> GSM674181     2  0.2647     0.8850 0.000 0.880 0.000 0.120
#> GSM674183     2  0.3873     0.7737 0.000 0.772 0.000 0.228
#> GSM674184     2  0.1302     0.9550 0.000 0.956 0.000 0.044
#> GSM674185     2  0.0469     0.9723 0.000 0.988 0.000 0.012
#> GSM674186     2  0.0707     0.9682 0.000 0.980 0.000 0.020
#> GSM674187     2  0.1118     0.9598 0.000 0.964 0.000 0.036
#> GSM674190     2  0.0336     0.9725 0.000 0.992 0.000 0.008
#> GSM674191     2  0.0188     0.9734 0.000 0.996 0.000 0.004
#> GSM674192     2  0.0469     0.9716 0.000 0.988 0.000 0.012
#> GSM674193     2  0.0188     0.9734 0.000 0.996 0.000 0.004
#> GSM674194     2  0.1302     0.9550 0.000 0.956 0.000 0.044
#> GSM674195     2  0.3486     0.8221 0.000 0.812 0.000 0.188
#> GSM674198     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674200     2  0.3975     0.7576 0.000 0.760 0.000 0.240
#> GSM674201     2  0.1118     0.9598 0.000 0.964 0.000 0.036
#> GSM674202     2  0.0469     0.9735 0.000 0.988 0.000 0.012
#> GSM674203     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674204     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674205     2  0.0188     0.9734 0.000 0.996 0.000 0.004
#> GSM674206     2  0.0469     0.9713 0.000 0.988 0.000 0.012
#> GSM674208     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674209     2  0.1302     0.9550 0.000 0.956 0.000 0.044
#> GSM674210     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674212     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674214     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674218     2  0.1474     0.9508 0.000 0.948 0.000 0.052
#> GSM674219     2  0.0000     0.9740 0.000 1.000 0.000 0.000
#> GSM674220     2  0.0592     0.9723 0.000 0.984 0.000 0.016
#> GSM674221     2  0.0188     0.9734 0.000 0.996 0.000 0.004
#> GSM674223     2  0.0188     0.9734 0.000 0.996 0.000 0.004
#> GSM674225     2  0.0817     0.9685 0.000 0.976 0.000 0.024
#> GSM674226     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674229     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674230     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674231     2  0.0188     0.9734 0.000 0.996 0.000 0.004
#> GSM674232     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674234     2  0.0188     0.9734 0.000 0.996 0.000 0.004
#> GSM674235     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674236     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674237     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674239     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674240     2  0.0469     0.9713 0.000 0.988 0.000 0.012
#> GSM674242     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674243     2  0.3123     0.8451 0.000 0.844 0.000 0.156
#> GSM674244     2  0.0707     0.9705 0.000 0.980 0.000 0.020
#> GSM674245     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674282     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674284     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674285     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674287     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674288     1  0.2011     0.9542 0.920 0.000 0.000 0.080
#> GSM674289     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674290     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674291     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674292     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674295     1  0.2149     0.9503 0.912 0.000 0.000 0.088
#> GSM674297     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674298     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674299     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674300     1  0.2011     0.9542 0.920 0.000 0.000 0.080
#> GSM674301     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674302     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674304     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674305     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674306     1  0.2011     0.9542 0.920 0.000 0.000 0.080
#> GSM674308     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674309     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674313     1  0.2216     0.9481 0.908 0.000 0.000 0.092
#> GSM674314     1  0.2011     0.9542 0.920 0.000 0.000 0.080
#> GSM674315     1  0.2011     0.9542 0.920 0.000 0.000 0.080
#> GSM674316     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674318     1  0.2011     0.9542 0.920 0.000 0.000 0.080
#> GSM674320     1  0.2081     0.9523 0.916 0.000 0.000 0.084
#> GSM674323     1  0.2011     0.9542 0.920 0.000 0.000 0.080
#> GSM674324     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674325     1  0.2011     0.9542 0.920 0.000 0.000 0.080
#> GSM674327     1  0.2011     0.9542 0.920 0.000 0.000 0.080
#> GSM674328     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674330     1  0.1022     0.9631 0.968 0.000 0.000 0.032
#> GSM674331     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674332     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674334     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674335     1  0.2011     0.9542 0.920 0.000 0.000 0.080
#> GSM674345     4  0.4585     0.8133 0.000 0.000 0.332 0.668
#> GSM674351     3  0.1474     0.9025 0.000 0.000 0.948 0.052
#> GSM674352     3  0.1389     0.9068 0.000 0.000 0.952 0.048
#> GSM674359     3  0.4977    -0.2801 0.000 0.000 0.540 0.460
#> GSM674360     3  0.0817     0.9265 0.000 0.000 0.976 0.024
#> GSM674362     3  0.0921     0.9237 0.000 0.000 0.972 0.028
#> GSM674369     3  0.0469     0.9321 0.000 0.000 0.988 0.012
#> GSM674372     3  0.0592     0.9310 0.000 0.000 0.984 0.016
#> GSM674374     3  0.0000     0.9333 0.000 0.000 1.000 0.000
#> GSM674376     3  0.0592     0.9279 0.000 0.000 0.984 0.016
#> GSM674377     3  0.0921     0.9209 0.000 0.000 0.972 0.028
#> GSM674378     3  0.0000     0.9333 0.000 0.000 1.000 0.000
#> GSM674383     3  0.0000     0.9333 0.000 0.000 1.000 0.000
#> GSM674386     3  0.0592     0.9279 0.000 0.000 0.984 0.016
#> GSM674387     3  0.1302     0.9114 0.000 0.000 0.956 0.044
#> GSM674392     3  0.0336     0.9322 0.000 0.000 0.992 0.008
#> GSM674396     3  0.0592     0.9279 0.000 0.000 0.984 0.016
#> GSM674399     3  0.0817     0.9239 0.000 0.000 0.976 0.024
#> GSM674404     3  0.0921     0.9237 0.000 0.000 0.972 0.028
#> GSM674182     2  0.0469     0.9713 0.000 0.988 0.000 0.012
#> GSM674188     2  0.0707     0.9684 0.000 0.980 0.000 0.020
#> GSM674189     2  0.1302     0.9550 0.000 0.956 0.000 0.044
#> GSM674196     2  0.0000     0.9740 0.000 1.000 0.000 0.000
#> GSM674197     2  0.0000     0.9740 0.000 1.000 0.000 0.000
#> GSM674199     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674207     2  0.0000     0.9740 0.000 1.000 0.000 0.000
#> GSM674211     2  0.0000     0.9740 0.000 1.000 0.000 0.000
#> GSM674213     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674215     2  0.0469     0.9735 0.000 0.988 0.000 0.012
#> GSM674216     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674217     2  0.0817     0.9663 0.000 0.976 0.000 0.024
#> GSM674222     2  0.0592     0.9722 0.000 0.984 0.000 0.016
#> GSM674224     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674227     2  0.0469     0.9735 0.000 0.988 0.000 0.012
#> GSM674228     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674233     2  0.0188     0.9734 0.000 0.996 0.000 0.004
#> GSM674238     2  0.3400     0.8319 0.000 0.820 0.000 0.180
#> GSM674241     2  0.0336     0.9744 0.000 0.992 0.000 0.008
#> GSM674283     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674286     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674293     1  0.2011     0.9542 0.920 0.000 0.000 0.080
#> GSM674294     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674296     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674303     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674307     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674310     1  0.2011     0.9542 0.920 0.000 0.000 0.080
#> GSM674311     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674312     1  0.2216     0.9481 0.908 0.000 0.000 0.092
#> GSM674317     1  0.0000     0.9682 1.000 0.000 0.000 0.000
#> GSM674319     1  0.2149     0.9503 0.912 0.000 0.000 0.088
#> GSM674321     1  0.2011     0.9542 0.920 0.000 0.000 0.080
#> GSM674322     1  0.2011     0.9542 0.920 0.000 0.000 0.080
#> GSM674326     1  0.2011     0.9542 0.920 0.000 0.000 0.080
#> GSM674329     1  0.2011     0.9542 0.920 0.000 0.000 0.080
#> GSM674333     1  0.2011     0.9542 0.920 0.000 0.000 0.080

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4    p5
#> GSM674344     3  0.2648     0.8508 0.000 0.000 0.848 0.000 0.152
#> GSM674346     5  0.3242     0.8404 0.000 0.000 0.216 0.000 0.784
#> GSM674347     3  0.2377     0.8762 0.000 0.000 0.872 0.000 0.128
#> GSM674348     3  0.1671     0.8935 0.000 0.000 0.924 0.000 0.076
#> GSM674349     3  0.3816     0.5212 0.000 0.000 0.696 0.000 0.304
#> GSM674350     3  0.2516     0.8619 0.000 0.000 0.860 0.000 0.140
#> GSM674353     3  0.2773     0.8430 0.000 0.000 0.836 0.000 0.164
#> GSM674354     3  0.1908     0.8901 0.000 0.000 0.908 0.000 0.092
#> GSM674355     3  0.2127     0.8860 0.000 0.000 0.892 0.000 0.108
#> GSM674356     3  0.1792     0.8915 0.000 0.000 0.916 0.000 0.084
#> GSM674357     3  0.2377     0.8705 0.000 0.000 0.872 0.000 0.128
#> GSM674358     3  0.2813     0.8393 0.000 0.000 0.832 0.000 0.168
#> GSM674361     3  0.2230     0.8783 0.000 0.000 0.884 0.000 0.116
#> GSM674363     3  0.2648     0.8524 0.000 0.000 0.848 0.000 0.152
#> GSM674364     3  0.1270     0.9015 0.000 0.000 0.948 0.000 0.052
#> GSM674365     3  0.1965     0.8906 0.000 0.000 0.904 0.000 0.096
#> GSM674366     3  0.0290     0.9051 0.000 0.000 0.992 0.000 0.008
#> GSM674367     3  0.0162     0.9052 0.000 0.000 0.996 0.000 0.004
#> GSM674368     3  0.1341     0.9036 0.000 0.000 0.944 0.000 0.056
#> GSM674370     3  0.0404     0.9059 0.000 0.000 0.988 0.000 0.012
#> GSM674371     3  0.1671     0.8935 0.000 0.000 0.924 0.000 0.076
#> GSM674373     3  0.0290     0.9046 0.000 0.000 0.992 0.000 0.008
#> GSM674375     3  0.0404     0.9053 0.000 0.000 0.988 0.000 0.012
#> GSM674379     3  0.1628     0.8807 0.000 0.000 0.936 0.008 0.056
#> GSM674380     3  0.2233     0.8584 0.000 0.000 0.904 0.016 0.080
#> GSM674381     3  0.1043     0.8943 0.000 0.000 0.960 0.000 0.040
#> GSM674382     3  0.1704     0.8745 0.000 0.000 0.928 0.004 0.068
#> GSM674384     3  0.0510     0.9013 0.000 0.000 0.984 0.000 0.016
#> GSM674385     3  0.0609     0.9060 0.000 0.000 0.980 0.000 0.020
#> GSM674388     3  0.1671     0.8935 0.000 0.000 0.924 0.000 0.076
#> GSM674389     3  0.0703     0.9030 0.000 0.000 0.976 0.000 0.024
#> GSM674390     3  0.0693     0.9022 0.000 0.000 0.980 0.008 0.012
#> GSM674391     3  0.1697     0.8783 0.000 0.000 0.932 0.008 0.060
#> GSM674393     3  0.1908     0.8941 0.000 0.000 0.908 0.000 0.092
#> GSM674394     3  0.0609     0.9063 0.000 0.000 0.980 0.000 0.020
#> GSM674395     3  0.0290     0.9036 0.000 0.000 0.992 0.000 0.008
#> GSM674397     3  0.0290     0.9051 0.000 0.000 0.992 0.000 0.008
#> GSM674398     3  0.1764     0.8751 0.000 0.000 0.928 0.008 0.064
#> GSM674400     5  0.3990     0.8240 0.000 0.000 0.308 0.004 0.688
#> GSM674401     5  0.3461     0.7997 0.000 0.000 0.224 0.004 0.772
#> GSM674402     5  0.2561     0.8226 0.000 0.000 0.144 0.000 0.856
#> GSM674403     5  0.2605     0.8266 0.000 0.000 0.148 0.000 0.852
#> GSM674405     5  0.4403     0.7160 0.000 0.000 0.384 0.008 0.608
#> GSM674406     3  0.0510     0.9013 0.000 0.000 0.984 0.000 0.016
#> GSM674407     3  0.1270     0.8855 0.000 0.000 0.948 0.000 0.052
#> GSM674181     2  0.4364     0.5077 0.000 0.768 0.000 0.120 0.112
#> GSM674183     4  0.6273     0.8662 0.000 0.316 0.000 0.512 0.172
#> GSM674184     2  0.4909    -0.4012 0.000 0.560 0.000 0.412 0.028
#> GSM674185     2  0.2012     0.8449 0.000 0.920 0.000 0.060 0.020
#> GSM674186     2  0.1205     0.8788 0.000 0.956 0.000 0.040 0.004
#> GSM674187     2  0.2124     0.8012 0.000 0.900 0.000 0.096 0.004
#> GSM674190     2  0.0794     0.8912 0.000 0.972 0.000 0.028 0.000
#> GSM674191     2  0.0162     0.9052 0.000 0.996 0.000 0.004 0.000
#> GSM674192     2  0.0880     0.8922 0.000 0.968 0.000 0.032 0.000
#> GSM674193     2  0.0880     0.8895 0.000 0.968 0.000 0.032 0.000
#> GSM674194     2  0.4540     0.0621 0.000 0.656 0.000 0.320 0.024
#> GSM674195     4  0.6122     0.8549 0.000 0.348 0.000 0.512 0.140
#> GSM674198     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674200     4  0.6529     0.7090 0.000 0.228 0.004 0.512 0.256
#> GSM674201     2  0.4558     0.0466 0.000 0.652 0.000 0.324 0.024
#> GSM674202     2  0.0865     0.8935 0.000 0.972 0.000 0.004 0.024
#> GSM674203     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674204     2  0.2189     0.7929 0.000 0.904 0.000 0.084 0.012
#> GSM674205     2  0.0162     0.9052 0.000 0.996 0.000 0.004 0.000
#> GSM674206     2  0.0955     0.8896 0.000 0.968 0.000 0.028 0.004
#> GSM674208     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674209     2  0.4183     0.0960 0.000 0.668 0.000 0.324 0.008
#> GSM674210     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674212     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674214     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674218     2  0.5049    -0.6587 0.000 0.484 0.000 0.484 0.032
#> GSM674219     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674220     2  0.1106     0.8880 0.000 0.964 0.000 0.012 0.024
#> GSM674221     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674223     2  0.0794     0.8889 0.000 0.972 0.000 0.028 0.000
#> GSM674225     2  0.0992     0.8910 0.000 0.968 0.000 0.008 0.024
#> GSM674226     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674229     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674230     2  0.0162     0.9052 0.000 0.996 0.000 0.004 0.000
#> GSM674231     2  0.0162     0.9052 0.000 0.996 0.000 0.004 0.000
#> GSM674232     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674234     2  0.0703     0.8954 0.000 0.976 0.000 0.024 0.000
#> GSM674235     2  0.0162     0.9052 0.000 0.996 0.000 0.004 0.000
#> GSM674236     2  0.0162     0.9052 0.000 0.996 0.000 0.004 0.000
#> GSM674237     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674239     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674240     2  0.1410     0.8611 0.000 0.940 0.000 0.060 0.000
#> GSM674242     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674243     2  0.5968    -0.3825 0.000 0.576 0.000 0.268 0.156
#> GSM674244     2  0.0955     0.8907 0.000 0.968 0.000 0.004 0.028
#> GSM674245     2  0.0162     0.9052 0.000 0.996 0.000 0.004 0.000
#> GSM674282     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674284     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674285     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674287     1  0.4294     0.7935 0.532 0.000 0.000 0.468 0.000
#> GSM674288     1  0.0794     0.6872 0.972 0.000 0.000 0.028 0.000
#> GSM674289     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674290     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674291     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674292     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674295     1  0.0510     0.6753 0.984 0.000 0.000 0.000 0.016
#> GSM674297     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674298     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674299     1  0.4287     0.7927 0.540 0.000 0.000 0.460 0.000
#> GSM674300     1  0.0162     0.6732 0.996 0.000 0.000 0.000 0.004
#> GSM674301     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674302     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674304     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674305     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674306     1  0.0162     0.6732 0.996 0.000 0.000 0.000 0.004
#> GSM674308     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674309     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674313     1  0.0609     0.6723 0.980 0.000 0.000 0.000 0.020
#> GSM674314     1  0.0000     0.6759 1.000 0.000 0.000 0.000 0.000
#> GSM674315     1  0.0162     0.6732 0.996 0.000 0.000 0.000 0.004
#> GSM674316     1  0.4294     0.7941 0.532 0.000 0.000 0.468 0.000
#> GSM674318     1  0.0000     0.6759 1.000 0.000 0.000 0.000 0.000
#> GSM674320     1  0.0510     0.6753 0.984 0.000 0.000 0.000 0.016
#> GSM674323     1  0.0609     0.6844 0.980 0.000 0.000 0.020 0.000
#> GSM674324     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674325     1  0.0794     0.6872 0.972 0.000 0.000 0.028 0.000
#> GSM674327     1  0.0000     0.6759 1.000 0.000 0.000 0.000 0.000
#> GSM674328     1  0.4294     0.7940 0.532 0.000 0.000 0.468 0.000
#> GSM674330     1  0.4060     0.7693 0.640 0.000 0.000 0.360 0.000
#> GSM674331     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674332     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674334     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674335     1  0.0794     0.6872 0.972 0.000 0.000 0.028 0.000
#> GSM674345     5  0.3424     0.8361 0.000 0.000 0.240 0.000 0.760
#> GSM674351     3  0.3003     0.8173 0.000 0.000 0.812 0.000 0.188
#> GSM674352     3  0.2852     0.8347 0.000 0.000 0.828 0.000 0.172
#> GSM674359     3  0.3366     0.7314 0.000 0.000 0.768 0.000 0.232
#> GSM674360     3  0.2020     0.8906 0.000 0.000 0.900 0.000 0.100
#> GSM674362     3  0.1965     0.8896 0.000 0.000 0.904 0.000 0.096
#> GSM674369     3  0.1341     0.9041 0.000 0.000 0.944 0.000 0.056
#> GSM674372     3  0.2471     0.8684 0.000 0.000 0.864 0.000 0.136
#> GSM674374     3  0.0290     0.9034 0.000 0.000 0.992 0.000 0.008
#> GSM674376     3  0.1571     0.8790 0.000 0.000 0.936 0.004 0.060
#> GSM674377     3  0.2233     0.8584 0.000 0.000 0.904 0.016 0.080
#> GSM674378     3  0.0162     0.9042 0.000 0.000 0.996 0.000 0.004
#> GSM674383     3  0.1121     0.9034 0.000 0.000 0.956 0.000 0.044
#> GSM674386     3  0.1704     0.8745 0.000 0.000 0.928 0.004 0.068
#> GSM674387     3  0.2179     0.8331 0.000 0.000 0.888 0.000 0.112
#> GSM674392     3  0.2230     0.8783 0.000 0.000 0.884 0.000 0.116
#> GSM674396     3  0.1571     0.8799 0.000 0.000 0.936 0.004 0.060
#> GSM674399     3  0.1697     0.8783 0.000 0.000 0.932 0.008 0.060
#> GSM674404     3  0.1478     0.8845 0.000 0.000 0.936 0.000 0.064
#> GSM674182     2  0.1410     0.8611 0.000 0.940 0.000 0.060 0.000
#> GSM674188     2  0.1282     0.8748 0.000 0.952 0.000 0.044 0.004
#> GSM674189     4  0.4906     0.5857 0.000 0.480 0.000 0.496 0.024
#> GSM674196     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674197     2  0.0162     0.9052 0.000 0.996 0.000 0.004 0.000
#> GSM674199     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674207     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674211     2  0.0162     0.9052 0.000 0.996 0.000 0.004 0.000
#> GSM674213     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674215     2  0.0865     0.8935 0.000 0.972 0.000 0.004 0.024
#> GSM674216     2  0.0162     0.9052 0.000 0.996 0.000 0.000 0.004
#> GSM674217     2  0.1410     0.8609 0.000 0.940 0.000 0.060 0.000
#> GSM674222     2  0.0771     0.8966 0.000 0.976 0.000 0.004 0.020
#> GSM674224     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674227     2  0.0865     0.8935 0.000 0.972 0.000 0.004 0.024
#> GSM674228     2  0.0162     0.9052 0.000 0.996 0.000 0.004 0.000
#> GSM674233     2  0.0290     0.9036 0.000 0.992 0.000 0.008 0.000
#> GSM674238     4  0.6357     0.8706 0.000 0.324 0.004 0.512 0.160
#> GSM674241     2  0.0000     0.9061 0.000 1.000 0.000 0.000 0.000
#> GSM674283     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674286     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674293     1  0.0000     0.6759 1.000 0.000 0.000 0.000 0.000
#> GSM674294     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674296     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674303     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674307     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674310     1  0.0000     0.6759 1.000 0.000 0.000 0.000 0.000
#> GSM674311     1  0.4297     0.7944 0.528 0.000 0.000 0.472 0.000
#> GSM674312     1  0.0510     0.6753 0.984 0.000 0.000 0.000 0.016
#> GSM674317     1  0.4235     0.7852 0.576 0.000 0.000 0.424 0.000
#> GSM674319     1  0.0510     0.6753 0.984 0.000 0.000 0.000 0.016
#> GSM674321     1  0.0000     0.6759 1.000 0.000 0.000 0.000 0.000
#> GSM674322     1  0.0510     0.6829 0.984 0.000 0.000 0.016 0.000
#> GSM674326     1  0.0000     0.6759 1.000 0.000 0.000 0.000 0.000
#> GSM674329     1  0.0000     0.6759 1.000 0.000 0.000 0.000 0.000
#> GSM674333     1  0.0703     0.6858 0.976 0.000 0.000 0.024 0.000

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4    p5    p6
#> GSM674344     3  0.1686      0.929 0.000 0.000 0.924 0.064 0.000 0.012
#> GSM674346     4  0.2491      0.801 0.000 0.000 0.164 0.836 0.000 0.000
#> GSM674347     3  0.0458      0.964 0.000 0.000 0.984 0.016 0.000 0.000
#> GSM674348     3  0.0363      0.963 0.000 0.000 0.988 0.012 0.000 0.000
#> GSM674349     3  0.3175      0.558 0.000 0.000 0.744 0.256 0.000 0.000
#> GSM674350     3  0.0790      0.956 0.000 0.000 0.968 0.032 0.000 0.000
#> GSM674353     3  0.1075      0.947 0.000 0.000 0.952 0.048 0.000 0.000
#> GSM674354     3  0.0790      0.959 0.000 0.000 0.968 0.032 0.000 0.000
#> GSM674355     3  0.0363      0.963 0.000 0.000 0.988 0.012 0.000 0.000
#> GSM674356     3  0.0458      0.962 0.000 0.000 0.984 0.016 0.000 0.000
#> GSM674357     3  0.1267      0.937 0.000 0.000 0.940 0.060 0.000 0.000
#> GSM674358     3  0.0937      0.952 0.000 0.000 0.960 0.040 0.000 0.000
#> GSM674361     3  0.0260      0.963 0.000 0.000 0.992 0.008 0.000 0.000
#> GSM674363     3  0.0937      0.951 0.000 0.000 0.960 0.040 0.000 0.000
#> GSM674364     3  0.0458      0.962 0.000 0.000 0.984 0.016 0.000 0.000
#> GSM674365     3  0.0547      0.962 0.000 0.000 0.980 0.020 0.000 0.000
#> GSM674366     3  0.0146      0.963 0.000 0.000 0.996 0.004 0.000 0.000
#> GSM674367     3  0.0146      0.963 0.000 0.000 0.996 0.004 0.000 0.000
#> GSM674368     3  0.0993      0.957 0.000 0.000 0.964 0.024 0.000 0.012
#> GSM674370     3  0.0146      0.963 0.000 0.000 0.996 0.004 0.000 0.000
#> GSM674371     3  0.0363      0.963 0.000 0.000 0.988 0.012 0.000 0.000
#> GSM674373     3  0.0458      0.963 0.000 0.000 0.984 0.016 0.000 0.000
#> GSM674375     3  0.0260      0.963 0.000 0.000 0.992 0.008 0.000 0.000
#> GSM674379     3  0.1261      0.949 0.000 0.000 0.952 0.024 0.024 0.000
#> GSM674380     3  0.2116      0.925 0.000 0.000 0.916 0.024 0.024 0.036
#> GSM674381     3  0.0717      0.961 0.000 0.000 0.976 0.016 0.008 0.000
#> GSM674382     3  0.1261      0.949 0.000 0.000 0.952 0.024 0.024 0.000
#> GSM674384     3  0.0146      0.963 0.000 0.000 0.996 0.004 0.000 0.000
#> GSM674385     3  0.0363      0.963 0.000 0.000 0.988 0.012 0.000 0.000
#> GSM674388     3  0.0260      0.963 0.000 0.000 0.992 0.008 0.000 0.000
#> GSM674389     3  0.0820      0.957 0.000 0.000 0.972 0.016 0.012 0.000
#> GSM674390     3  0.0881      0.961 0.000 0.000 0.972 0.008 0.012 0.008
#> GSM674391     3  0.1261      0.949 0.000 0.000 0.952 0.024 0.024 0.000
#> GSM674393     3  0.0260      0.964 0.000 0.000 0.992 0.008 0.000 0.000
#> GSM674394     3  0.0000      0.964 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM674395     3  0.0260      0.963 0.000 0.000 0.992 0.008 0.000 0.000
#> GSM674397     3  0.0363      0.963 0.000 0.000 0.988 0.012 0.000 0.000
#> GSM674398     3  0.1261      0.949 0.000 0.000 0.952 0.024 0.024 0.000
#> GSM674400     4  0.2883      0.787 0.000 0.000 0.212 0.788 0.000 0.000
#> GSM674401     4  0.2146      0.759 0.000 0.000 0.116 0.880 0.000 0.004
#> GSM674402     4  0.1908      0.756 0.000 0.000 0.096 0.900 0.000 0.004
#> GSM674403     4  0.1908      0.755 0.000 0.000 0.096 0.900 0.000 0.004
#> GSM674405     4  0.4088      0.597 0.000 0.000 0.368 0.616 0.016 0.000
#> GSM674406     3  0.0260      0.963 0.000 0.000 0.992 0.008 0.000 0.000
#> GSM674407     3  0.0993      0.954 0.000 0.000 0.964 0.024 0.012 0.000
#> GSM674181     2  0.4383      0.636 0.000 0.716 0.000 0.108 0.000 0.176
#> GSM674183     6  0.2667      0.816 0.000 0.020 0.000 0.128 0.000 0.852
#> GSM674184     2  0.3843      0.195 0.000 0.548 0.000 0.000 0.000 0.452
#> GSM674185     2  0.1327      0.912 0.000 0.936 0.000 0.000 0.000 0.064
#> GSM674186     2  0.2092      0.866 0.000 0.876 0.000 0.000 0.000 0.124
#> GSM674187     2  0.2003      0.872 0.000 0.884 0.000 0.000 0.000 0.116
#> GSM674190     2  0.1387      0.904 0.000 0.932 0.000 0.000 0.000 0.068
#> GSM674191     2  0.1501      0.901 0.000 0.924 0.000 0.000 0.000 0.076
#> GSM674192     2  0.1720      0.918 0.000 0.928 0.000 0.032 0.000 0.040
#> GSM674193     2  0.1444      0.904 0.000 0.928 0.000 0.000 0.000 0.072
#> GSM674194     2  0.2793      0.777 0.000 0.800 0.000 0.000 0.000 0.200
#> GSM674195     6  0.2706      0.830 0.000 0.036 0.000 0.104 0.000 0.860
#> GSM674198     2  0.0790      0.923 0.000 0.968 0.000 0.032 0.000 0.000
#> GSM674200     6  0.2667      0.816 0.000 0.020 0.000 0.128 0.000 0.852
#> GSM674201     2  0.3198      0.690 0.000 0.740 0.000 0.000 0.000 0.260
#> GSM674202     2  0.0790      0.920 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM674203     2  0.1320      0.919 0.000 0.948 0.000 0.036 0.000 0.016
#> GSM674204     2  0.4823      0.148 0.000 0.552 0.000 0.060 0.000 0.388
#> GSM674205     2  0.1049      0.923 0.000 0.960 0.000 0.032 0.000 0.008
#> GSM674206     2  0.1863      0.884 0.000 0.896 0.000 0.000 0.000 0.104
#> GSM674208     2  0.0790      0.923 0.000 0.968 0.000 0.032 0.000 0.000
#> GSM674209     2  0.3727      0.425 0.000 0.612 0.000 0.000 0.000 0.388
#> GSM674210     2  0.0547      0.924 0.000 0.980 0.000 0.020 0.000 0.000
#> GSM674212     2  0.0790      0.923 0.000 0.968 0.000 0.032 0.000 0.000
#> GSM674214     2  0.0790      0.923 0.000 0.968 0.000 0.032 0.000 0.000
#> GSM674218     6  0.2915      0.724 0.000 0.184 0.000 0.008 0.000 0.808
#> GSM674219     2  0.0000      0.923 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674220     2  0.1204      0.914 0.000 0.944 0.000 0.000 0.000 0.056
#> GSM674221     2  0.1327      0.903 0.000 0.936 0.000 0.000 0.000 0.064
#> GSM674223     2  0.1265      0.918 0.000 0.948 0.000 0.008 0.000 0.044
#> GSM674225     2  0.1700      0.896 0.000 0.916 0.000 0.004 0.000 0.080
#> GSM674226     2  0.0000      0.923 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674229     2  0.0790      0.923 0.000 0.968 0.000 0.032 0.000 0.000
#> GSM674230     2  0.0000      0.923 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674231     2  0.0363      0.923 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM674232     2  0.1151      0.920 0.000 0.956 0.000 0.032 0.000 0.012
#> GSM674234     2  0.0937      0.916 0.000 0.960 0.000 0.000 0.000 0.040
#> GSM674235     2  0.0000      0.923 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674236     2  0.0000      0.923 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674237     2  0.1245      0.920 0.000 0.952 0.000 0.032 0.000 0.016
#> GSM674239     2  0.0790      0.923 0.000 0.968 0.000 0.032 0.000 0.000
#> GSM674240     2  0.1327      0.907 0.000 0.936 0.000 0.000 0.000 0.064
#> GSM674242     2  0.1320      0.918 0.000 0.948 0.000 0.036 0.000 0.016
#> GSM674243     6  0.3878      0.789 0.000 0.112 0.000 0.116 0.000 0.772
#> GSM674244     2  0.1219      0.915 0.000 0.948 0.000 0.004 0.000 0.048
#> GSM674245     2  0.0000      0.923 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674282     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674284     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674285     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674287     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674288     5  0.2597      0.831 0.176 0.000 0.000 0.000 0.824 0.000
#> GSM674289     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674291     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674292     1  0.0146      0.984 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM674295     5  0.1780      0.910 0.028 0.000 0.000 0.028 0.932 0.012
#> GSM674297     1  0.0146      0.984 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM674298     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674299     1  0.0458      0.975 0.984 0.000 0.000 0.000 0.016 0.000
#> GSM674300     5  0.0713      0.919 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674301     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674302     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674305     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674306     5  0.0713      0.919 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674308     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674309     1  0.0146      0.984 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM674313     5  0.1851      0.903 0.024 0.000 0.000 0.036 0.928 0.012
#> GSM674314     5  0.1501      0.910 0.076 0.000 0.000 0.000 0.924 0.000
#> GSM674315     5  0.0713      0.919 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674316     1  0.0260      0.981 0.992 0.000 0.000 0.000 0.008 0.000
#> GSM674318     5  0.1141      0.921 0.052 0.000 0.000 0.000 0.948 0.000
#> GSM674320     5  0.1780      0.910 0.028 0.000 0.000 0.028 0.932 0.012
#> GSM674323     5  0.1765      0.901 0.096 0.000 0.000 0.000 0.904 0.000
#> GSM674324     1  0.0146      0.984 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM674325     5  0.3244      0.718 0.268 0.000 0.000 0.000 0.732 0.000
#> GSM674327     5  0.0713      0.919 0.028 0.000 0.000 0.000 0.972 0.000
#> GSM674328     1  0.0458      0.975 0.984 0.000 0.000 0.000 0.016 0.000
#> GSM674330     1  0.3023      0.660 0.768 0.000 0.000 0.000 0.232 0.000
#> GSM674331     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674332     1  0.0790      0.957 0.968 0.000 0.000 0.000 0.032 0.000
#> GSM674334     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674335     5  0.3330      0.696 0.284 0.000 0.000 0.000 0.716 0.000
#> GSM674345     4  0.3050      0.770 0.000 0.000 0.236 0.764 0.000 0.000
#> GSM674351     3  0.1007      0.949 0.000 0.000 0.956 0.044 0.000 0.000
#> GSM674352     3  0.1007      0.949 0.000 0.000 0.956 0.044 0.000 0.000
#> GSM674359     3  0.1910      0.888 0.000 0.000 0.892 0.108 0.000 0.000
#> GSM674360     3  0.0547      0.962 0.000 0.000 0.980 0.020 0.000 0.000
#> GSM674362     3  0.0777      0.960 0.000 0.000 0.972 0.024 0.000 0.004
#> GSM674369     3  0.0547      0.962 0.000 0.000 0.980 0.020 0.000 0.000
#> GSM674372     3  0.0458      0.964 0.000 0.000 0.984 0.016 0.000 0.000
#> GSM674374     3  0.0363      0.963 0.000 0.000 0.988 0.012 0.000 0.000
#> GSM674376     3  0.1176      0.951 0.000 0.000 0.956 0.024 0.020 0.000
#> GSM674377     3  0.1886      0.938 0.000 0.000 0.928 0.024 0.024 0.024
#> GSM674378     3  0.0146      0.963 0.000 0.000 0.996 0.004 0.000 0.000
#> GSM674383     3  0.0363      0.963 0.000 0.000 0.988 0.012 0.000 0.000
#> GSM674386     3  0.1261      0.949 0.000 0.000 0.952 0.024 0.024 0.000
#> GSM674387     3  0.2263      0.874 0.000 0.000 0.884 0.100 0.016 0.000
#> GSM674392     3  0.0260      0.963 0.000 0.000 0.992 0.008 0.000 0.000
#> GSM674396     3  0.1261      0.949 0.000 0.000 0.952 0.024 0.024 0.000
#> GSM674399     3  0.1261      0.949 0.000 0.000 0.952 0.024 0.024 0.000
#> GSM674404     3  0.1297      0.947 0.000 0.000 0.948 0.040 0.012 0.000
#> GSM674182     2  0.1444      0.903 0.000 0.928 0.000 0.000 0.000 0.072
#> GSM674188     2  0.1765      0.886 0.000 0.904 0.000 0.000 0.000 0.096
#> GSM674189     6  0.2941      0.672 0.000 0.220 0.000 0.000 0.000 0.780
#> GSM674196     2  0.0790      0.923 0.000 0.968 0.000 0.032 0.000 0.000
#> GSM674197     2  0.0790      0.923 0.000 0.968 0.000 0.032 0.000 0.000
#> GSM674199     2  0.0790      0.923 0.000 0.968 0.000 0.032 0.000 0.000
#> GSM674207     2  0.0000      0.923 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674211     2  0.0790      0.923 0.000 0.968 0.000 0.032 0.000 0.000
#> GSM674213     2  0.0000      0.923 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674215     2  0.1075      0.916 0.000 0.952 0.000 0.000 0.000 0.048
#> GSM674216     2  0.1320      0.919 0.000 0.948 0.000 0.036 0.000 0.016
#> GSM674217     2  0.2135      0.863 0.000 0.872 0.000 0.000 0.000 0.128
#> GSM674222     2  0.1219      0.915 0.000 0.948 0.000 0.004 0.000 0.048
#> GSM674224     2  0.0000      0.923 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674227     2  0.0790      0.920 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM674228     2  0.0000      0.923 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674233     2  0.1714      0.890 0.000 0.908 0.000 0.000 0.000 0.092
#> GSM674238     6  0.2726      0.828 0.000 0.032 0.000 0.112 0.000 0.856
#> GSM674241     2  0.0790      0.923 0.000 0.968 0.000 0.032 0.000 0.000
#> GSM674283     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674286     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674293     5  0.1910      0.894 0.108 0.000 0.000 0.000 0.892 0.000
#> GSM674294     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674296     1  0.0146      0.984 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM674303     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674307     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674310     5  0.0790      0.921 0.032 0.000 0.000 0.000 0.968 0.000
#> GSM674311     1  0.0000      0.986 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674312     5  0.1780      0.910 0.028 0.000 0.000 0.028 0.932 0.012
#> GSM674317     1  0.1141      0.937 0.948 0.000 0.000 0.000 0.052 0.000
#> GSM674319     5  0.1857      0.911 0.032 0.000 0.000 0.028 0.928 0.012
#> GSM674321     5  0.1267      0.918 0.060 0.000 0.000 0.000 0.940 0.000
#> GSM674322     5  0.2003      0.888 0.116 0.000 0.000 0.000 0.884 0.000
#> GSM674326     5  0.0790      0.921 0.032 0.000 0.000 0.000 0.968 0.000
#> GSM674329     5  0.0865      0.921 0.036 0.000 0.000 0.000 0.964 0.000
#> GSM674333     5  0.2340      0.859 0.148 0.000 0.000 0.000 0.852 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-MAD-mclust-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-MAD-mclust-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-MAD-mclust-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-MAD-mclust-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-MAD-mclust-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-MAD-mclust-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-MAD-mclust-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-MAD-mclust-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-MAD-mclust-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-MAD-mclust-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-MAD-mclust-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-MAD-mclust-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-MAD-mclust-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-MAD-mclust-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-MAD-mclust-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-MAD-mclust-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-MAD-mclust-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-MAD-mclust-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-MAD-mclust-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-MAD-mclust-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk MAD-mclust-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-MAD-mclust-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-MAD-mclust-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-MAD-mclust-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-MAD-mclust-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-MAD-mclust-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk MAD-mclust-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>              n disease.state(p) specimen(p) k
#> MAD:mclust 183            0.924    1.83e-40 2
#> MAD:mclust 183            0.962    6.15e-78 3
#> MAD:mclust 179            0.888    2.96e-74 4
#> MAD:mclust 177            0.891    1.27e-71 5
#> MAD:mclust 180            0.777    3.00e-71 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


MAD:NMF*

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["MAD", "NMF"]
# you can also extract it by
# res = res_list["MAD:NMF"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#>   Subgroups are detected by 'NMF' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 4.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk MAD-NMF-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk MAD-NMF-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 1.000           0.999       1.000         0.5958 0.750   0.571
#> 4 4 0.925           0.873       0.937         0.0542 0.974   0.922
#> 5 5 0.867           0.873       0.919         0.0232 0.980   0.935
#> 6 6 0.793           0.796       0.864         0.0354 1.000   1.000

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3

There is also optional best \(k\) = 2 3 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette p1    p2    p3
#> GSM674344     3  0.0000      1.000  0 0.000 1.000
#> GSM674346     3  0.0000      1.000  0 0.000 1.000
#> GSM674347     3  0.0000      1.000  0 0.000 1.000
#> GSM674348     3  0.0000      1.000  0 0.000 1.000
#> GSM674349     3  0.0000      1.000  0 0.000 1.000
#> GSM674350     3  0.0000      1.000  0 0.000 1.000
#> GSM674353     3  0.0000      1.000  0 0.000 1.000
#> GSM674354     3  0.0000      1.000  0 0.000 1.000
#> GSM674355     3  0.0000      1.000  0 0.000 1.000
#> GSM674356     3  0.0000      1.000  0 0.000 1.000
#> GSM674357     3  0.0000      1.000  0 0.000 1.000
#> GSM674358     3  0.0000      1.000  0 0.000 1.000
#> GSM674361     3  0.0000      1.000  0 0.000 1.000
#> GSM674363     3  0.0000      1.000  0 0.000 1.000
#> GSM674364     3  0.0000      1.000  0 0.000 1.000
#> GSM674365     3  0.0000      1.000  0 0.000 1.000
#> GSM674366     3  0.0000      1.000  0 0.000 1.000
#> GSM674367     3  0.0000      1.000  0 0.000 1.000
#> GSM674368     3  0.0000      1.000  0 0.000 1.000
#> GSM674370     3  0.0000      1.000  0 0.000 1.000
#> GSM674371     3  0.0000      1.000  0 0.000 1.000
#> GSM674373     3  0.0000      1.000  0 0.000 1.000
#> GSM674375     3  0.0000      1.000  0 0.000 1.000
#> GSM674379     3  0.0000      1.000  0 0.000 1.000
#> GSM674380     3  0.0000      1.000  0 0.000 1.000
#> GSM674381     3  0.0000      1.000  0 0.000 1.000
#> GSM674382     3  0.0000      1.000  0 0.000 1.000
#> GSM674384     3  0.0000      1.000  0 0.000 1.000
#> GSM674385     3  0.0000      1.000  0 0.000 1.000
#> GSM674388     3  0.0000      1.000  0 0.000 1.000
#> GSM674389     3  0.0000      1.000  0 0.000 1.000
#> GSM674390     3  0.0000      1.000  0 0.000 1.000
#> GSM674391     3  0.0000      1.000  0 0.000 1.000
#> GSM674393     3  0.0000      1.000  0 0.000 1.000
#> GSM674394     3  0.0000      1.000  0 0.000 1.000
#> GSM674395     3  0.0000      1.000  0 0.000 1.000
#> GSM674397     3  0.0000      1.000  0 0.000 1.000
#> GSM674398     3  0.0000      1.000  0 0.000 1.000
#> GSM674400     3  0.0000      1.000  0 0.000 1.000
#> GSM674401     3  0.0000      1.000  0 0.000 1.000
#> GSM674402     3  0.0000      1.000  0 0.000 1.000
#> GSM674403     3  0.0000      1.000  0 0.000 1.000
#> GSM674405     3  0.0000      1.000  0 0.000 1.000
#> GSM674406     3  0.0000      1.000  0 0.000 1.000
#> GSM674407     3  0.0000      1.000  0 0.000 1.000
#> GSM674181     2  0.0000      0.999  0 1.000 0.000
#> GSM674183     2  0.0000      0.999  0 1.000 0.000
#> GSM674184     2  0.0000      0.999  0 1.000 0.000
#> GSM674185     2  0.0000      0.999  0 1.000 0.000
#> GSM674186     2  0.0000      0.999  0 1.000 0.000
#> GSM674187     2  0.0000      0.999  0 1.000 0.000
#> GSM674190     2  0.0000      0.999  0 1.000 0.000
#> GSM674191     2  0.0000      0.999  0 1.000 0.000
#> GSM674192     2  0.0000      0.999  0 1.000 0.000
#> GSM674193     2  0.0000      0.999  0 1.000 0.000
#> GSM674194     2  0.0000      0.999  0 1.000 0.000
#> GSM674195     2  0.0000      0.999  0 1.000 0.000
#> GSM674198     2  0.0000      0.999  0 1.000 0.000
#> GSM674200     2  0.1289      0.967  0 0.968 0.032
#> GSM674201     2  0.0000      0.999  0 1.000 0.000
#> GSM674202     2  0.0000      0.999  0 1.000 0.000
#> GSM674203     2  0.0000      0.999  0 1.000 0.000
#> GSM674204     2  0.0000      0.999  0 1.000 0.000
#> GSM674205     2  0.0000      0.999  0 1.000 0.000
#> GSM674206     2  0.0000      0.999  0 1.000 0.000
#> GSM674208     2  0.0000      0.999  0 1.000 0.000
#> GSM674209     2  0.0000      0.999  0 1.000 0.000
#> GSM674210     2  0.0000      0.999  0 1.000 0.000
#> GSM674212     2  0.0000      0.999  0 1.000 0.000
#> GSM674214     2  0.0000      0.999  0 1.000 0.000
#> GSM674218     2  0.0000      0.999  0 1.000 0.000
#> GSM674219     2  0.0000      0.999  0 1.000 0.000
#> GSM674220     2  0.0000      0.999  0 1.000 0.000
#> GSM674221     2  0.0000      0.999  0 1.000 0.000
#> GSM674223     2  0.0000      0.999  0 1.000 0.000
#> GSM674225     2  0.0000      0.999  0 1.000 0.000
#> GSM674226     2  0.0000      0.999  0 1.000 0.000
#> GSM674229     2  0.0000      0.999  0 1.000 0.000
#> GSM674230     2  0.0000      0.999  0 1.000 0.000
#> GSM674231     2  0.0000      0.999  0 1.000 0.000
#> GSM674232     2  0.0000      0.999  0 1.000 0.000
#> GSM674234     2  0.0000      0.999  0 1.000 0.000
#> GSM674235     2  0.0000      0.999  0 1.000 0.000
#> GSM674236     2  0.0000      0.999  0 1.000 0.000
#> GSM674237     2  0.0000      0.999  0 1.000 0.000
#> GSM674239     2  0.0000      0.999  0 1.000 0.000
#> GSM674240     2  0.0000      0.999  0 1.000 0.000
#> GSM674242     2  0.0000      0.999  0 1.000 0.000
#> GSM674243     2  0.0000      0.999  0 1.000 0.000
#> GSM674244     2  0.0000      0.999  0 1.000 0.000
#> GSM674245     2  0.0000      0.999  0 1.000 0.000
#> GSM674282     1  0.0000      1.000  1 0.000 0.000
#> GSM674284     1  0.0000      1.000  1 0.000 0.000
#> GSM674285     1  0.0000      1.000  1 0.000 0.000
#> GSM674287     1  0.0000      1.000  1 0.000 0.000
#> GSM674288     1  0.0000      1.000  1 0.000 0.000
#> GSM674289     1  0.0000      1.000  1 0.000 0.000
#> GSM674290     1  0.0000      1.000  1 0.000 0.000
#> GSM674291     1  0.0000      1.000  1 0.000 0.000
#> GSM674292     1  0.0000      1.000  1 0.000 0.000
#> GSM674295     1  0.0000      1.000  1 0.000 0.000
#> GSM674297     1  0.0000      1.000  1 0.000 0.000
#> GSM674298     1  0.0000      1.000  1 0.000 0.000
#> GSM674299     1  0.0000      1.000  1 0.000 0.000
#> GSM674300     1  0.0000      1.000  1 0.000 0.000
#> GSM674301     1  0.0000      1.000  1 0.000 0.000
#> GSM674302     1  0.0000      1.000  1 0.000 0.000
#> GSM674304     1  0.0000      1.000  1 0.000 0.000
#> GSM674305     1  0.0000      1.000  1 0.000 0.000
#> GSM674306     1  0.0000      1.000  1 0.000 0.000
#> GSM674308     1  0.0000      1.000  1 0.000 0.000
#> GSM674309     1  0.0000      1.000  1 0.000 0.000
#> GSM674313     1  0.0000      1.000  1 0.000 0.000
#> GSM674314     1  0.0000      1.000  1 0.000 0.000
#> GSM674315     1  0.0000      1.000  1 0.000 0.000
#> GSM674316     1  0.0000      1.000  1 0.000 0.000
#> GSM674318     1  0.0000      1.000  1 0.000 0.000
#> GSM674320     1  0.0000      1.000  1 0.000 0.000
#> GSM674323     1  0.0000      1.000  1 0.000 0.000
#> GSM674324     1  0.0000      1.000  1 0.000 0.000
#> GSM674325     1  0.0000      1.000  1 0.000 0.000
#> GSM674327     1  0.0000      1.000  1 0.000 0.000
#> GSM674328     1  0.0000      1.000  1 0.000 0.000
#> GSM674330     1  0.0000      1.000  1 0.000 0.000
#> GSM674331     1  0.0000      1.000  1 0.000 0.000
#> GSM674332     1  0.0000      1.000  1 0.000 0.000
#> GSM674334     1  0.0000      1.000  1 0.000 0.000
#> GSM674335     1  0.0000      1.000  1 0.000 0.000
#> GSM674345     3  0.0000      1.000  0 0.000 1.000
#> GSM674351     3  0.0000      1.000  0 0.000 1.000
#> GSM674352     3  0.0000      1.000  0 0.000 1.000
#> GSM674359     3  0.0000      1.000  0 0.000 1.000
#> GSM674360     3  0.0000      1.000  0 0.000 1.000
#> GSM674362     3  0.0000      1.000  0 0.000 1.000
#> GSM674369     3  0.0000      1.000  0 0.000 1.000
#> GSM674372     3  0.0000      1.000  0 0.000 1.000
#> GSM674374     3  0.0000      1.000  0 0.000 1.000
#> GSM674376     3  0.0000      1.000  0 0.000 1.000
#> GSM674377     3  0.0000      1.000  0 0.000 1.000
#> GSM674378     3  0.0000      1.000  0 0.000 1.000
#> GSM674383     3  0.0000      1.000  0 0.000 1.000
#> GSM674386     3  0.0000      1.000  0 0.000 1.000
#> GSM674387     3  0.0000      1.000  0 0.000 1.000
#> GSM674392     3  0.0000      1.000  0 0.000 1.000
#> GSM674396     3  0.0000      1.000  0 0.000 1.000
#> GSM674399     3  0.0000      1.000  0 0.000 1.000
#> GSM674404     3  0.0000      1.000  0 0.000 1.000
#> GSM674182     2  0.0000      0.999  0 1.000 0.000
#> GSM674188     2  0.0000      0.999  0 1.000 0.000
#> GSM674189     2  0.0000      0.999  0 1.000 0.000
#> GSM674196     2  0.0000      0.999  0 1.000 0.000
#> GSM674197     2  0.0000      0.999  0 1.000 0.000
#> GSM674199     2  0.0000      0.999  0 1.000 0.000
#> GSM674207     2  0.0000      0.999  0 1.000 0.000
#> GSM674211     2  0.0000      0.999  0 1.000 0.000
#> GSM674213     2  0.0000      0.999  0 1.000 0.000
#> GSM674215     2  0.0000      0.999  0 1.000 0.000
#> GSM674216     2  0.0000      0.999  0 1.000 0.000
#> GSM674217     2  0.0000      0.999  0 1.000 0.000
#> GSM674222     2  0.0000      0.999  0 1.000 0.000
#> GSM674224     2  0.0000      0.999  0 1.000 0.000
#> GSM674227     2  0.0000      0.999  0 1.000 0.000
#> GSM674228     2  0.0000      0.999  0 1.000 0.000
#> GSM674233     2  0.0000      0.999  0 1.000 0.000
#> GSM674238     2  0.0892      0.979  0 0.980 0.020
#> GSM674241     2  0.0000      0.999  0 1.000 0.000
#> GSM674283     1  0.0000      1.000  1 0.000 0.000
#> GSM674286     1  0.0000      1.000  1 0.000 0.000
#> GSM674293     1  0.0000      1.000  1 0.000 0.000
#> GSM674294     1  0.0000      1.000  1 0.000 0.000
#> GSM674296     1  0.0000      1.000  1 0.000 0.000
#> GSM674303     1  0.0000      1.000  1 0.000 0.000
#> GSM674307     1  0.0000      1.000  1 0.000 0.000
#> GSM674310     1  0.0000      1.000  1 0.000 0.000
#> GSM674311     1  0.0000      1.000  1 0.000 0.000
#> GSM674312     1  0.0000      1.000  1 0.000 0.000
#> GSM674317     1  0.0000      1.000  1 0.000 0.000
#> GSM674319     1  0.0000      1.000  1 0.000 0.000
#> GSM674321     1  0.0000      1.000  1 0.000 0.000
#> GSM674322     1  0.0000      1.000  1 0.000 0.000
#> GSM674326     1  0.0000      1.000  1 0.000 0.000
#> GSM674329     1  0.0000      1.000  1 0.000 0.000
#> GSM674333     1  0.0000      1.000  1 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1    p2    p3    p4
#> GSM674344     4  0.4991     0.5970 0.000 0.004 0.388 0.608
#> GSM674346     4  0.4999     0.4725 0.000 0.000 0.492 0.508
#> GSM674347     3  0.0707     0.8408 0.000 0.000 0.980 0.020
#> GSM674348     3  0.2589     0.7591 0.000 0.000 0.884 0.116
#> GSM674349     3  0.1940     0.8031 0.000 0.000 0.924 0.076
#> GSM674350     3  0.1867     0.8068 0.000 0.000 0.928 0.072
#> GSM674353     3  0.4008     0.5172 0.000 0.000 0.756 0.244
#> GSM674354     4  0.4992     0.5167 0.000 0.000 0.476 0.524
#> GSM674355     3  0.0817     0.8392 0.000 0.000 0.976 0.024
#> GSM674356     3  0.4193     0.4480 0.000 0.000 0.732 0.268
#> GSM674357     3  0.4955    -0.3289 0.000 0.000 0.556 0.444
#> GSM674358     3  0.1389     0.8258 0.000 0.000 0.952 0.048
#> GSM674361     3  0.0921     0.8375 0.000 0.000 0.972 0.028
#> GSM674363     3  0.4331     0.3830 0.000 0.000 0.712 0.288
#> GSM674364     3  0.0817     0.8392 0.000 0.000 0.976 0.024
#> GSM674365     3  0.1022     0.8355 0.000 0.000 0.968 0.032
#> GSM674366     3  0.0188     0.8456 0.000 0.000 0.996 0.004
#> GSM674367     3  0.0817     0.8444 0.000 0.000 0.976 0.024
#> GSM674368     3  0.1118     0.8341 0.000 0.000 0.964 0.036
#> GSM674370     3  0.0000     0.8451 0.000 0.000 1.000 0.000
#> GSM674371     3  0.1637     0.8172 0.000 0.000 0.940 0.060
#> GSM674373     3  0.0336     0.8457 0.000 0.000 0.992 0.008
#> GSM674375     3  0.0707     0.8448 0.000 0.000 0.980 0.020
#> GSM674379     3  0.3486     0.7349 0.000 0.000 0.812 0.188
#> GSM674380     3  0.4690     0.5950 0.000 0.012 0.712 0.276
#> GSM674381     3  0.2469     0.8060 0.000 0.000 0.892 0.108
#> GSM674382     3  0.3801     0.6970 0.000 0.000 0.780 0.220
#> GSM674384     3  0.1940     0.8247 0.000 0.000 0.924 0.076
#> GSM674385     3  0.0336     0.8461 0.000 0.000 0.992 0.008
#> GSM674388     3  0.0921     0.8375 0.000 0.000 0.972 0.028
#> GSM674389     3  0.1389     0.8375 0.000 0.000 0.952 0.048
#> GSM674390     3  0.2589     0.8002 0.000 0.000 0.884 0.116
#> GSM674391     3  0.4134     0.6418 0.000 0.000 0.740 0.260
#> GSM674393     3  0.0000     0.8451 0.000 0.000 1.000 0.000
#> GSM674394     3  0.0188     0.8447 0.000 0.000 0.996 0.004
#> GSM674395     3  0.0817     0.8448 0.000 0.000 0.976 0.024
#> GSM674397     3  0.0188     0.8457 0.000 0.000 0.996 0.004
#> GSM674398     3  0.3074     0.7716 0.000 0.000 0.848 0.152
#> GSM674400     3  0.0817     0.8452 0.000 0.000 0.976 0.024
#> GSM674401     3  0.1118     0.8418 0.000 0.000 0.964 0.036
#> GSM674402     3  0.3123     0.7100 0.000 0.000 0.844 0.156
#> GSM674403     3  0.1637     0.8170 0.000 0.000 0.940 0.060
#> GSM674405     3  0.2530     0.8038 0.000 0.000 0.888 0.112
#> GSM674406     3  0.1474     0.8360 0.000 0.000 0.948 0.052
#> GSM674407     3  0.2589     0.8002 0.000 0.000 0.884 0.116
#> GSM674181     2  0.4790     0.4005 0.000 0.620 0.000 0.380
#> GSM674183     4  0.4989    -0.0972 0.000 0.472 0.000 0.528
#> GSM674184     2  0.0707     0.9581 0.000 0.980 0.000 0.020
#> GSM674185     2  0.0336     0.9638 0.000 0.992 0.000 0.008
#> GSM674186     2  0.0336     0.9637 0.000 0.992 0.000 0.008
#> GSM674187     2  0.0188     0.9648 0.000 0.996 0.000 0.004
#> GSM674190     2  0.1022     0.9503 0.000 0.968 0.000 0.032
#> GSM674191     2  0.0592     0.9603 0.000 0.984 0.000 0.016
#> GSM674192     2  0.0188     0.9648 0.000 0.996 0.000 0.004
#> GSM674193     2  0.0188     0.9648 0.000 0.996 0.000 0.004
#> GSM674194     2  0.0592     0.9604 0.000 0.984 0.000 0.016
#> GSM674195     2  0.4898     0.3005 0.000 0.584 0.000 0.416
#> GSM674198     2  0.0000     0.9653 0.000 1.000 0.000 0.000
#> GSM674200     4  0.6752     0.4778 0.000 0.280 0.132 0.588
#> GSM674201     2  0.0921     0.9533 0.000 0.972 0.000 0.028
#> GSM674202     2  0.0336     0.9644 0.000 0.992 0.000 0.008
#> GSM674203     2  0.0469     0.9633 0.000 0.988 0.000 0.012
#> GSM674204     2  0.0000     0.9653 0.000 1.000 0.000 0.000
#> GSM674205     2  0.0188     0.9648 0.000 0.996 0.000 0.004
#> GSM674206     2  0.0336     0.9638 0.000 0.992 0.000 0.008
#> GSM674208     2  0.0469     0.9633 0.000 0.988 0.000 0.012
#> GSM674209     2  0.0188     0.9648 0.000 0.996 0.000 0.004
#> GSM674210     2  0.0336     0.9644 0.000 0.992 0.000 0.008
#> GSM674212     2  0.0188     0.9650 0.000 0.996 0.000 0.004
#> GSM674214     2  0.0469     0.9633 0.000 0.988 0.000 0.012
#> GSM674218     2  0.1211     0.9440 0.000 0.960 0.000 0.040
#> GSM674219     2  0.0000     0.9653 0.000 1.000 0.000 0.000
#> GSM674220     2  0.0817     0.9575 0.000 0.976 0.000 0.024
#> GSM674221     2  0.0000     0.9653 0.000 1.000 0.000 0.000
#> GSM674223     2  0.0336     0.9637 0.000 0.992 0.000 0.008
#> GSM674225     2  0.3024     0.8260 0.000 0.852 0.000 0.148
#> GSM674226     2  0.0469     0.9633 0.000 0.988 0.000 0.012
#> GSM674229     2  0.0000     0.9653 0.000 1.000 0.000 0.000
#> GSM674230     2  0.0469     0.9633 0.000 0.988 0.000 0.012
#> GSM674231     2  0.0000     0.9653 0.000 1.000 0.000 0.000
#> GSM674232     2  0.0707     0.9598 0.000 0.980 0.000 0.020
#> GSM674234     2  0.0188     0.9648 0.000 0.996 0.000 0.004
#> GSM674235     2  0.0469     0.9633 0.000 0.988 0.000 0.012
#> GSM674236     2  0.0592     0.9617 0.000 0.984 0.000 0.016
#> GSM674237     2  0.0707     0.9598 0.000 0.980 0.000 0.020
#> GSM674239     2  0.0336     0.9644 0.000 0.992 0.000 0.008
#> GSM674240     2  0.0817     0.9556 0.000 0.976 0.000 0.024
#> GSM674242     2  0.0707     0.9598 0.000 0.980 0.000 0.020
#> GSM674243     2  0.0188     0.9648 0.000 0.996 0.000 0.004
#> GSM674244     2  0.1474     0.9354 0.000 0.948 0.000 0.052
#> GSM674245     2  0.0592     0.9617 0.000 0.984 0.000 0.016
#> GSM674282     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674284     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674285     1  0.0188     0.9950 0.996 0.000 0.000 0.004
#> GSM674287     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674288     1  0.0188     0.9952 0.996 0.000 0.000 0.004
#> GSM674289     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674290     1  0.0188     0.9950 0.996 0.000 0.000 0.004
#> GSM674291     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674292     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674295     1  0.0469     0.9916 0.988 0.000 0.000 0.012
#> GSM674297     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674298     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674299     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674300     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674301     1  0.0188     0.9950 0.996 0.000 0.000 0.004
#> GSM674302     1  0.0188     0.9950 0.996 0.000 0.000 0.004
#> GSM674304     1  0.0188     0.9950 0.996 0.000 0.000 0.004
#> GSM674305     1  0.0188     0.9950 0.996 0.000 0.000 0.004
#> GSM674306     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674308     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674309     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674313     1  0.1118     0.9738 0.964 0.000 0.000 0.036
#> GSM674314     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674315     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674316     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674318     1  0.0336     0.9936 0.992 0.000 0.000 0.008
#> GSM674320     1  0.0707     0.9865 0.980 0.000 0.000 0.020
#> GSM674323     1  0.0336     0.9936 0.992 0.000 0.000 0.008
#> GSM674324     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674325     1  0.0336     0.9936 0.992 0.000 0.000 0.008
#> GSM674327     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674328     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674330     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674331     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674332     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674334     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674335     1  0.0336     0.9936 0.992 0.000 0.000 0.008
#> GSM674345     3  0.4040     0.5065 0.000 0.000 0.752 0.248
#> GSM674351     3  0.3764     0.5859 0.000 0.000 0.784 0.216
#> GSM674352     3  0.3074     0.7073 0.000 0.000 0.848 0.152
#> GSM674359     4  0.4941     0.5863 0.000 0.000 0.436 0.564
#> GSM674360     3  0.3569     0.6384 0.000 0.000 0.804 0.196
#> GSM674362     4  0.4933     0.5902 0.000 0.000 0.432 0.568
#> GSM674369     3  0.2530     0.7640 0.000 0.000 0.888 0.112
#> GSM674372     3  0.0000     0.8451 0.000 0.000 1.000 0.000
#> GSM674374     3  0.0469     0.8455 0.000 0.000 0.988 0.012
#> GSM674376     3  0.3172     0.7640 0.000 0.000 0.840 0.160
#> GSM674377     3  0.4072     0.6529 0.000 0.000 0.748 0.252
#> GSM674378     3  0.0817     0.8445 0.000 0.000 0.976 0.024
#> GSM674383     3  0.0707     0.8408 0.000 0.000 0.980 0.020
#> GSM674386     3  0.3649     0.7169 0.000 0.000 0.796 0.204
#> GSM674387     3  0.3123     0.7679 0.000 0.000 0.844 0.156
#> GSM674392     3  0.0707     0.8408 0.000 0.000 0.980 0.020
#> GSM674396     3  0.3074     0.7716 0.000 0.000 0.848 0.152
#> GSM674399     3  0.3649     0.7169 0.000 0.000 0.796 0.204
#> GSM674404     3  0.1637     0.8325 0.000 0.000 0.940 0.060
#> GSM674182     2  0.0817     0.9556 0.000 0.976 0.000 0.024
#> GSM674188     2  0.0188     0.9648 0.000 0.996 0.000 0.004
#> GSM674189     2  0.2011     0.9047 0.000 0.920 0.000 0.080
#> GSM674196     2  0.0000     0.9653 0.000 1.000 0.000 0.000
#> GSM674197     2  0.0000     0.9653 0.000 1.000 0.000 0.000
#> GSM674199     2  0.0000     0.9653 0.000 1.000 0.000 0.000
#> GSM674207     2  0.0000     0.9653 0.000 1.000 0.000 0.000
#> GSM674211     2  0.0000     0.9653 0.000 1.000 0.000 0.000
#> GSM674213     2  0.0188     0.9650 0.000 0.996 0.000 0.004
#> GSM674215     2  0.0707     0.9598 0.000 0.980 0.000 0.020
#> GSM674216     2  0.1022     0.9521 0.000 0.968 0.000 0.032
#> GSM674217     2  0.0592     0.9603 0.000 0.984 0.000 0.016
#> GSM674222     2  0.1302     0.9425 0.000 0.956 0.000 0.044
#> GSM674224     2  0.0188     0.9650 0.000 0.996 0.000 0.004
#> GSM674227     2  0.0469     0.9633 0.000 0.988 0.000 0.012
#> GSM674228     2  0.0336     0.9644 0.000 0.992 0.000 0.008
#> GSM674233     2  0.0469     0.9622 0.000 0.988 0.000 0.012
#> GSM674238     2  0.5436     0.3848 0.000 0.620 0.024 0.356
#> GSM674241     2  0.0336     0.9644 0.000 0.992 0.000 0.008
#> GSM674283     1  0.0188     0.9950 0.996 0.000 0.000 0.004
#> GSM674286     1  0.0188     0.9950 0.996 0.000 0.000 0.004
#> GSM674293     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674294     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674296     1  0.0188     0.9950 0.996 0.000 0.000 0.004
#> GSM674303     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674307     1  0.0188     0.9950 0.996 0.000 0.000 0.004
#> GSM674310     1  0.0469     0.9916 0.988 0.000 0.000 0.012
#> GSM674311     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674312     1  0.0707     0.9865 0.980 0.000 0.000 0.020
#> GSM674317     1  0.0000     0.9963 1.000 0.000 0.000 0.000
#> GSM674319     1  0.0592     0.9892 0.984 0.000 0.000 0.016
#> GSM674321     1  0.0336     0.9936 0.992 0.000 0.000 0.008
#> GSM674322     1  0.0336     0.9936 0.992 0.000 0.000 0.008
#> GSM674326     1  0.0336     0.9936 0.992 0.000 0.000 0.008
#> GSM674329     1  0.0592     0.9892 0.984 0.000 0.000 0.016
#> GSM674333     1  0.0336     0.9936 0.992 0.000 0.000 0.008

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4 p5
#> GSM674344     4  0.3742      0.649 0.000 0.004 0.188 0.788 NA
#> GSM674346     4  0.4171      0.465 0.000 0.000 0.396 0.604 NA
#> GSM674347     3  0.1211      0.885 0.000 0.000 0.960 0.024 NA
#> GSM674348     3  0.2230      0.827 0.000 0.000 0.884 0.116 NA
#> GSM674349     3  0.1557      0.877 0.000 0.000 0.940 0.052 NA
#> GSM674350     3  0.2848      0.776 0.000 0.000 0.840 0.156 NA
#> GSM674353     3  0.4088      0.321 0.000 0.000 0.632 0.368 NA
#> GSM674354     4  0.4161      0.474 0.000 0.000 0.392 0.608 NA
#> GSM674355     3  0.1124      0.880 0.000 0.000 0.960 0.036 NA
#> GSM674356     3  0.3550      0.660 0.000 0.000 0.760 0.236 NA
#> GSM674357     4  0.4268      0.354 0.000 0.000 0.444 0.556 NA
#> GSM674358     3  0.1478      0.868 0.000 0.000 0.936 0.064 NA
#> GSM674361     3  0.2233      0.836 0.000 0.000 0.892 0.104 NA
#> GSM674363     3  0.3949      0.436 0.000 0.000 0.668 0.332 NA
#> GSM674364     3  0.1502      0.872 0.000 0.000 0.940 0.056 NA
#> GSM674365     3  0.0794      0.883 0.000 0.000 0.972 0.028 NA
#> GSM674366     3  0.1403      0.886 0.000 0.000 0.952 0.024 NA
#> GSM674367     3  0.1493      0.883 0.000 0.000 0.948 0.028 NA
#> GSM674368     3  0.1430      0.878 0.000 0.000 0.944 0.052 NA
#> GSM674370     3  0.0451      0.888 0.000 0.000 0.988 0.008 NA
#> GSM674371     3  0.1211      0.884 0.000 0.000 0.960 0.024 NA
#> GSM674373     3  0.1216      0.885 0.000 0.000 0.960 0.020 NA
#> GSM674375     3  0.0798      0.888 0.000 0.000 0.976 0.008 NA
#> GSM674379     3  0.2813      0.839 0.000 0.000 0.876 0.040 NA
#> GSM674380     3  0.4491      0.736 0.000 0.024 0.776 0.052 NA
#> GSM674381     3  0.2074      0.871 0.000 0.000 0.920 0.036 NA
#> GSM674382     3  0.2927      0.838 0.000 0.000 0.868 0.040 NA
#> GSM674384     3  0.1579      0.884 0.000 0.000 0.944 0.024 NA
#> GSM674385     3  0.2719      0.857 0.000 0.000 0.884 0.068 NA
#> GSM674388     3  0.0955      0.883 0.000 0.000 0.968 0.028 NA
#> GSM674389     3  0.1012      0.888 0.000 0.000 0.968 0.012 NA
#> GSM674390     3  0.2221      0.867 0.000 0.000 0.912 0.036 NA
#> GSM674391     3  0.3521      0.793 0.000 0.000 0.820 0.040 NA
#> GSM674393     3  0.1117      0.885 0.000 0.000 0.964 0.020 NA
#> GSM674394     3  0.1915      0.882 0.000 0.000 0.928 0.040 NA
#> GSM674395     3  0.1549      0.886 0.000 0.000 0.944 0.016 NA
#> GSM674397     3  0.0451      0.886 0.000 0.000 0.988 0.008 NA
#> GSM674398     3  0.2491      0.861 0.000 0.000 0.896 0.036 NA
#> GSM674400     3  0.1211      0.885 0.000 0.000 0.960 0.024 NA
#> GSM674401     3  0.1216      0.887 0.000 0.000 0.960 0.020 NA
#> GSM674402     4  0.4965      0.293 0.000 0.000 0.452 0.520 NA
#> GSM674403     3  0.1877      0.870 0.000 0.000 0.924 0.064 NA
#> GSM674405     3  0.2067      0.873 0.000 0.000 0.920 0.032 NA
#> GSM674406     3  0.1403      0.882 0.000 0.000 0.952 0.024 NA
#> GSM674407     3  0.2209      0.867 0.000 0.000 0.912 0.032 NA
#> GSM674181     4  0.4497      0.209 0.000 0.424 0.000 0.568 NA
#> GSM674183     4  0.3461      0.593 0.000 0.224 0.000 0.772 NA
#> GSM674184     2  0.2660      0.856 0.000 0.864 0.000 0.128 NA
#> GSM674185     2  0.2236      0.911 0.000 0.908 0.000 0.068 NA
#> GSM674186     2  0.0609      0.961 0.000 0.980 0.000 0.020 NA
#> GSM674187     2  0.0290      0.965 0.000 0.992 0.000 0.008 NA
#> GSM674190     2  0.1043      0.950 0.000 0.960 0.000 0.040 NA
#> GSM674191     2  0.1043      0.950 0.000 0.960 0.000 0.040 NA
#> GSM674192     2  0.0451      0.965 0.000 0.988 0.000 0.008 NA
#> GSM674193     2  0.0290      0.965 0.000 0.992 0.000 0.008 NA
#> GSM674194     2  0.0609      0.961 0.000 0.980 0.000 0.020 NA
#> GSM674195     4  0.4270      0.439 0.000 0.336 0.004 0.656 NA
#> GSM674198     2  0.0579      0.964 0.000 0.984 0.000 0.008 NA
#> GSM674200     4  0.4703      0.666 0.000 0.096 0.096 0.776 NA
#> GSM674201     2  0.2389      0.874 0.000 0.880 0.000 0.116 NA
#> GSM674202     2  0.0451      0.965 0.000 0.988 0.000 0.008 NA
#> GSM674203     2  0.0693      0.962 0.000 0.980 0.000 0.012 NA
#> GSM674204     2  0.0290      0.965 0.000 0.992 0.000 0.000 NA
#> GSM674205     2  0.0324      0.965 0.000 0.992 0.000 0.004 NA
#> GSM674206     2  0.0963      0.953 0.000 0.964 0.000 0.036 NA
#> GSM674208     2  0.0693      0.962 0.000 0.980 0.000 0.012 NA
#> GSM674209     2  0.0404      0.964 0.000 0.988 0.000 0.012 NA
#> GSM674210     2  0.0693      0.962 0.000 0.980 0.000 0.012 NA
#> GSM674212     2  0.0451      0.965 0.000 0.988 0.000 0.004 NA
#> GSM674214     2  0.0693      0.962 0.000 0.980 0.000 0.012 NA
#> GSM674218     2  0.4016      0.613 0.000 0.716 0.000 0.272 NA
#> GSM674219     2  0.0703      0.959 0.000 0.976 0.000 0.024 NA
#> GSM674220     2  0.2149      0.919 0.000 0.916 0.000 0.048 NA
#> GSM674221     2  0.0566      0.965 0.000 0.984 0.000 0.012 NA
#> GSM674223     2  0.0609      0.961 0.000 0.980 0.000 0.020 NA
#> GSM674225     2  0.2806      0.878 0.000 0.888 0.008 0.052 NA
#> GSM674226     2  0.0000      0.965 0.000 1.000 0.000 0.000 NA
#> GSM674229     2  0.0162      0.965 0.000 0.996 0.000 0.000 NA
#> GSM674230     2  0.0162      0.966 0.000 0.996 0.000 0.004 NA
#> GSM674231     2  0.0290      0.965 0.000 0.992 0.000 0.008 NA
#> GSM674232     2  0.0693      0.962 0.000 0.980 0.000 0.012 NA
#> GSM674234     2  0.0324      0.965 0.000 0.992 0.000 0.004 NA
#> GSM674235     2  0.0324      0.965 0.000 0.992 0.000 0.004 NA
#> GSM674236     2  0.0693      0.963 0.000 0.980 0.000 0.012 NA
#> GSM674237     2  0.0693      0.962 0.000 0.980 0.000 0.012 NA
#> GSM674239     2  0.0162      0.965 0.000 0.996 0.000 0.000 NA
#> GSM674240     2  0.0880      0.955 0.000 0.968 0.000 0.032 NA
#> GSM674242     2  0.0693      0.962 0.000 0.980 0.000 0.012 NA
#> GSM674243     2  0.0290      0.965 0.000 0.992 0.000 0.008 NA
#> GSM674244     2  0.1493      0.941 0.000 0.948 0.000 0.028 NA
#> GSM674245     2  0.0290      0.965 0.000 0.992 0.000 0.008 NA
#> GSM674282     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674284     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674285     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674287     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674288     1  0.2424      0.910 0.868 0.000 0.000 0.000 NA
#> GSM674289     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674290     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674291     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674292     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674295     1  0.2773      0.895 0.836 0.000 0.000 0.000 NA
#> GSM674297     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674298     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674299     1  0.0290      0.949 0.992 0.000 0.000 0.000 NA
#> GSM674300     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674301     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674302     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674304     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674305     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674306     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674308     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674309     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674313     1  0.2852      0.891 0.828 0.000 0.000 0.000 NA
#> GSM674314     1  0.1608      0.932 0.928 0.000 0.000 0.000 NA
#> GSM674315     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674316     1  0.2179      0.918 0.888 0.000 0.000 0.000 NA
#> GSM674318     1  0.2773      0.895 0.836 0.000 0.000 0.000 NA
#> GSM674320     1  0.3177      0.865 0.792 0.000 0.000 0.000 NA
#> GSM674323     1  0.2648      0.901 0.848 0.000 0.000 0.000 NA
#> GSM674324     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674325     1  0.2648      0.901 0.848 0.000 0.000 0.000 NA
#> GSM674327     1  0.0609      0.947 0.980 0.000 0.000 0.000 NA
#> GSM674328     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674330     1  0.1732      0.930 0.920 0.000 0.000 0.000 NA
#> GSM674331     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674332     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674334     1  0.1341      0.937 0.944 0.000 0.000 0.000 NA
#> GSM674335     1  0.2605      0.903 0.852 0.000 0.000 0.000 NA
#> GSM674345     3  0.3209      0.749 0.000 0.000 0.812 0.180 NA
#> GSM674351     3  0.3837      0.499 0.000 0.000 0.692 0.308 NA
#> GSM674352     3  0.3003      0.730 0.000 0.000 0.812 0.188 NA
#> GSM674359     4  0.3783      0.628 0.000 0.000 0.252 0.740 NA
#> GSM674360     3  0.4276      0.280 0.000 0.000 0.616 0.380 NA
#> GSM674362     4  0.3756      0.634 0.000 0.000 0.248 0.744 NA
#> GSM674369     3  0.1364      0.883 0.000 0.000 0.952 0.036 NA
#> GSM674372     3  0.0771      0.885 0.000 0.000 0.976 0.020 NA
#> GSM674374     3  0.1211      0.886 0.000 0.000 0.960 0.016 NA
#> GSM674376     3  0.2554      0.858 0.000 0.000 0.892 0.036 NA
#> GSM674377     3  0.3601      0.781 0.000 0.000 0.820 0.052 NA
#> GSM674378     3  0.1493      0.882 0.000 0.000 0.948 0.024 NA
#> GSM674383     3  0.0703      0.884 0.000 0.000 0.976 0.024 NA
#> GSM674386     3  0.2754      0.844 0.000 0.000 0.880 0.040 NA
#> GSM674387     3  0.2616      0.854 0.000 0.000 0.888 0.036 NA
#> GSM674392     3  0.1251      0.881 0.000 0.000 0.956 0.036 NA
#> GSM674396     3  0.2359      0.861 0.000 0.000 0.904 0.036 NA
#> GSM674399     3  0.2871      0.840 0.000 0.000 0.872 0.040 NA
#> GSM674404     3  0.1012      0.888 0.000 0.000 0.968 0.012 NA
#> GSM674182     2  0.0963      0.953 0.000 0.964 0.000 0.036 NA
#> GSM674188     2  0.0290      0.965 0.000 0.992 0.000 0.008 NA
#> GSM674189     2  0.3932      0.501 0.000 0.672 0.000 0.328 NA
#> GSM674196     2  0.0290      0.965 0.000 0.992 0.000 0.000 NA
#> GSM674197     2  0.0162      0.965 0.000 0.996 0.000 0.000 NA
#> GSM674199     2  0.0579      0.964 0.000 0.984 0.000 0.008 NA
#> GSM674207     2  0.0404      0.965 0.000 0.988 0.000 0.000 NA
#> GSM674211     2  0.0693      0.962 0.000 0.980 0.000 0.012 NA
#> GSM674213     2  0.0566      0.965 0.000 0.984 0.000 0.012 NA
#> GSM674215     2  0.1386      0.948 0.000 0.952 0.000 0.016 NA
#> GSM674216     2  0.0807      0.960 0.000 0.976 0.000 0.012 NA
#> GSM674217     2  0.0955      0.959 0.000 0.968 0.000 0.028 NA
#> GSM674222     2  0.1012      0.955 0.000 0.968 0.000 0.020 NA
#> GSM674224     2  0.0162      0.965 0.000 0.996 0.000 0.004 NA
#> GSM674227     2  0.0290      0.965 0.000 0.992 0.000 0.008 NA
#> GSM674228     2  0.0162      0.965 0.000 0.996 0.000 0.000 NA
#> GSM674233     2  0.0880      0.955 0.000 0.968 0.000 0.032 NA
#> GSM674238     4  0.4870      0.544 0.000 0.276 0.016 0.680 NA
#> GSM674241     2  0.0579      0.964 0.000 0.984 0.000 0.008 NA
#> GSM674283     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674286     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674293     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674294     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674296     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674303     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674307     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674310     1  0.2891      0.888 0.824 0.000 0.000 0.000 NA
#> GSM674311     1  0.0000      0.951 1.000 0.000 0.000 0.000 NA
#> GSM674312     1  0.3242      0.859 0.784 0.000 0.000 0.000 NA
#> GSM674317     1  0.0794      0.945 0.972 0.000 0.000 0.000 NA
#> GSM674319     1  0.2813      0.893 0.832 0.000 0.000 0.000 NA
#> GSM674321     1  0.2690      0.899 0.844 0.000 0.000 0.000 NA
#> GSM674322     1  0.2852      0.891 0.828 0.000 0.000 0.000 NA
#> GSM674326     1  0.2561      0.905 0.856 0.000 0.000 0.000 NA
#> GSM674329     1  0.2852      0.891 0.828 0.000 0.000 0.000 NA
#> GSM674333     1  0.2813      0.893 0.832 0.000 0.000 0.000 NA

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3 p4    p5    p6
#> GSM674344     6  0.2678      0.651 0.000 0.000 0.116 NA 0.004 0.860
#> GSM674346     6  0.3592      0.434 0.000 0.000 0.344 NA 0.000 0.656
#> GSM674347     3  0.2375      0.835 0.000 0.000 0.896 NA 0.008 0.036
#> GSM674348     3  0.3468      0.668 0.000 0.000 0.712 NA 0.000 0.284
#> GSM674349     3  0.3201      0.798 0.000 0.000 0.820 NA 0.008 0.148
#> GSM674350     3  0.3314      0.701 0.000 0.000 0.740 NA 0.000 0.256
#> GSM674353     3  0.3828      0.306 0.000 0.000 0.560 NA 0.000 0.440
#> GSM674354     6  0.3706      0.354 0.000 0.000 0.380 NA 0.000 0.620
#> GSM674355     3  0.2306      0.831 0.000 0.000 0.888 NA 0.004 0.092
#> GSM674356     3  0.3563      0.586 0.000 0.000 0.664 NA 0.000 0.336
#> GSM674357     6  0.3717      0.343 0.000 0.000 0.384 NA 0.000 0.616
#> GSM674358     3  0.2584      0.808 0.000 0.000 0.848 NA 0.004 0.144
#> GSM674361     3  0.3053      0.788 0.000 0.000 0.812 NA 0.004 0.172
#> GSM674363     3  0.3797      0.371 0.000 0.000 0.580 NA 0.000 0.420
#> GSM674364     3  0.2191      0.821 0.000 0.000 0.876 NA 0.000 0.120
#> GSM674365     3  0.2450      0.822 0.000 0.000 0.868 NA 0.000 0.116
#> GSM674366     3  0.2349      0.832 0.000 0.000 0.892 NA 0.008 0.020
#> GSM674367     3  0.1411      0.839 0.000 0.000 0.936 NA 0.000 0.004
#> GSM674368     3  0.2946      0.794 0.000 0.000 0.812 NA 0.000 0.176
#> GSM674370     3  0.1857      0.840 0.000 0.000 0.924 NA 0.004 0.028
#> GSM674371     3  0.3074      0.822 0.000 0.000 0.856 NA 0.016 0.068
#> GSM674373     3  0.2088      0.842 0.000 0.000 0.904 NA 0.000 0.028
#> GSM674375     3  0.0520      0.843 0.000 0.000 0.984 NA 0.000 0.008
#> GSM674379     3  0.1866      0.822 0.000 0.000 0.908 NA 0.008 0.000
#> GSM674380     3  0.4117      0.630 0.000 0.036 0.704 NA 0.004 0.000
#> GSM674381     3  0.0777      0.840 0.000 0.000 0.972 NA 0.000 0.004
#> GSM674382     3  0.2442      0.798 0.000 0.000 0.852 NA 0.000 0.004
#> GSM674384     3  0.2002      0.832 0.000 0.000 0.908 NA 0.004 0.012
#> GSM674385     3  0.4233      0.707 0.000 0.000 0.724 NA 0.004 0.064
#> GSM674388     3  0.2218      0.827 0.000 0.000 0.884 NA 0.000 0.104
#> GSM674389     3  0.0858      0.841 0.000 0.000 0.968 NA 0.000 0.004
#> GSM674390     3  0.1462      0.839 0.000 0.000 0.936 NA 0.008 0.000
#> GSM674391     3  0.2597      0.772 0.000 0.000 0.824 NA 0.000 0.000
#> GSM674393     3  0.2164      0.836 0.000 0.000 0.908 NA 0.012 0.020
#> GSM674394     3  0.3276      0.805 0.000 0.000 0.816 NA 0.000 0.052
#> GSM674395     3  0.2662      0.814 0.000 0.000 0.856 NA 0.000 0.024
#> GSM674397     3  0.1053      0.843 0.000 0.000 0.964 NA 0.004 0.012
#> GSM674398     3  0.2848      0.775 0.000 0.000 0.816 NA 0.000 0.008
#> GSM674400     3  0.2036      0.834 0.000 0.000 0.912 NA 0.008 0.016
#> GSM674401     3  0.2647      0.819 0.000 0.000 0.876 NA 0.020 0.016
#> GSM674402     6  0.4355      0.216 0.000 0.000 0.420 NA 0.000 0.556
#> GSM674403     3  0.3559      0.782 0.000 0.000 0.800 NA 0.012 0.152
#> GSM674405     3  0.2199      0.821 0.000 0.000 0.892 NA 0.020 0.000
#> GSM674406     3  0.0935      0.841 0.000 0.000 0.964 NA 0.004 0.000
#> GSM674407     3  0.1700      0.831 0.000 0.000 0.916 NA 0.000 0.004
#> GSM674181     6  0.4799      0.208 0.000 0.356 0.000 NA 0.012 0.592
#> GSM674183     6  0.3472      0.650 0.000 0.100 0.000 NA 0.000 0.808
#> GSM674184     2  0.5238      0.497 0.000 0.580 0.000 NA 0.000 0.292
#> GSM674185     2  0.5143      0.591 0.000 0.612 0.000 NA 0.000 0.140
#> GSM674186     2  0.1794      0.895 0.000 0.924 0.000 NA 0.000 0.036
#> GSM674187     2  0.0622      0.910 0.000 0.980 0.000 NA 0.000 0.012
#> GSM674190     2  0.2110      0.884 0.000 0.900 0.000 NA 0.004 0.084
#> GSM674191     2  0.2506      0.872 0.000 0.880 0.000 NA 0.000 0.068
#> GSM674192     2  0.0551      0.911 0.000 0.984 0.000 NA 0.008 0.004
#> GSM674193     2  0.0820      0.909 0.000 0.972 0.000 NA 0.016 0.012
#> GSM674194     2  0.2152      0.888 0.000 0.904 0.000 NA 0.004 0.068
#> GSM674195     6  0.4390      0.567 0.000 0.176 0.000 NA 0.004 0.724
#> GSM674198     2  0.0508      0.909 0.000 0.984 0.000 NA 0.012 0.000
#> GSM674200     6  0.4202      0.657 0.000 0.032 0.028 NA 0.012 0.772
#> GSM674201     2  0.4960      0.524 0.000 0.600 0.000 NA 0.000 0.308
#> GSM674202     2  0.0777      0.910 0.000 0.972 0.000 NA 0.000 0.004
#> GSM674203     2  0.0622      0.909 0.000 0.980 0.000 NA 0.008 0.000
#> GSM674204     2  0.0508      0.909 0.000 0.984 0.000 NA 0.012 0.000
#> GSM674205     2  0.0692      0.908 0.000 0.976 0.000 NA 0.020 0.000
#> GSM674206     2  0.3017      0.847 0.000 0.844 0.000 NA 0.000 0.072
#> GSM674208     2  0.0622      0.910 0.000 0.980 0.000 NA 0.008 0.000
#> GSM674209     2  0.0653      0.911 0.000 0.980 0.000 NA 0.004 0.012
#> GSM674210     2  0.0603      0.908 0.000 0.980 0.000 NA 0.016 0.000
#> GSM674212     2  0.0363      0.910 0.000 0.988 0.000 NA 0.000 0.000
#> GSM674214     2  0.0725      0.908 0.000 0.976 0.000 NA 0.012 0.000
#> GSM674218     2  0.5290      0.299 0.000 0.504 0.000 NA 0.000 0.392
#> GSM674219     2  0.2660      0.862 0.000 0.868 0.000 NA 0.000 0.048
#> GSM674220     2  0.5092      0.550 0.000 0.588 0.008 NA 0.000 0.076
#> GSM674221     2  0.0914      0.909 0.000 0.968 0.000 NA 0.000 0.016
#> GSM674223     2  0.1225      0.904 0.000 0.952 0.000 NA 0.012 0.036
#> GSM674225     2  0.4792      0.585 0.000 0.624 0.032 NA 0.000 0.024
#> GSM674226     2  0.1049      0.908 0.000 0.960 0.000 NA 0.000 0.008
#> GSM674229     2  0.0146      0.910 0.000 0.996 0.000 NA 0.000 0.000
#> GSM674230     2  0.1807      0.896 0.000 0.920 0.000 NA 0.000 0.020
#> GSM674231     2  0.0405      0.911 0.000 0.988 0.000 NA 0.000 0.008
#> GSM674232     2  0.0458      0.910 0.000 0.984 0.000 NA 0.000 0.000
#> GSM674234     2  0.0363      0.910 0.000 0.988 0.000 NA 0.012 0.000
#> GSM674235     2  0.0692      0.910 0.000 0.976 0.000 NA 0.000 0.004
#> GSM674236     2  0.0777      0.910 0.000 0.972 0.000 NA 0.000 0.004
#> GSM674237     2  0.0363      0.910 0.000 0.988 0.000 NA 0.000 0.000
#> GSM674239     2  0.0146      0.910 0.000 0.996 0.000 NA 0.000 0.000
#> GSM674240     2  0.2600      0.867 0.000 0.876 0.000 NA 0.004 0.084
#> GSM674242     2  0.0692      0.909 0.000 0.976 0.000 NA 0.004 0.000
#> GSM674243     2  0.0862      0.909 0.000 0.972 0.000 NA 0.016 0.008
#> GSM674244     2  0.4489      0.608 0.000 0.632 0.008 NA 0.000 0.032
#> GSM674245     2  0.1152      0.906 0.000 0.952 0.000 NA 0.000 0.004
#> GSM674282     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674284     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674285     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674287     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674288     1  0.2823      0.824 0.796 0.000 0.000 NA 0.204 0.000
#> GSM674289     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674290     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674291     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674292     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674295     1  0.3499      0.772 0.680 0.000 0.000 NA 0.320 0.000
#> GSM674297     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674298     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674299     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674300     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674301     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674302     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674304     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674305     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674306     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674308     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674309     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674313     1  0.3706      0.731 0.620 0.000 0.000 NA 0.380 0.000
#> GSM674314     1  0.3266      0.796 0.728 0.000 0.000 NA 0.272 0.000
#> GSM674315     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674316     1  0.3390      0.784 0.704 0.000 0.000 NA 0.296 0.000
#> GSM674318     1  0.3684      0.737 0.628 0.000 0.000 NA 0.372 0.000
#> GSM674320     1  0.3833      0.671 0.556 0.000 0.000 NA 0.444 0.000
#> GSM674323     1  0.3464      0.776 0.688 0.000 0.000 NA 0.312 0.000
#> GSM674324     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674325     1  0.3482      0.774 0.684 0.000 0.000 NA 0.316 0.000
#> GSM674327     1  0.1327      0.868 0.936 0.000 0.000 NA 0.064 0.000
#> GSM674328     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674330     1  0.2883      0.820 0.788 0.000 0.000 NA 0.212 0.000
#> GSM674331     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674332     1  0.0363      0.882 0.988 0.000 0.000 NA 0.012 0.000
#> GSM674334     1  0.2996      0.814 0.772 0.000 0.000 NA 0.228 0.000
#> GSM674335     1  0.3446      0.778 0.692 0.000 0.000 NA 0.308 0.000
#> GSM674345     3  0.3936      0.665 0.000 0.000 0.700 NA 0.004 0.276
#> GSM674351     3  0.3727      0.460 0.000 0.000 0.612 NA 0.000 0.388
#> GSM674352     3  0.3468      0.661 0.000 0.000 0.712 NA 0.000 0.284
#> GSM674359     6  0.3152      0.621 0.000 0.000 0.196 NA 0.008 0.792
#> GSM674360     3  0.3823      0.314 0.000 0.000 0.564 NA 0.000 0.436
#> GSM674362     6  0.2838      0.632 0.000 0.000 0.188 NA 0.000 0.808
#> GSM674369     3  0.3543      0.791 0.000 0.000 0.812 NA 0.012 0.124
#> GSM674372     3  0.1788      0.841 0.000 0.000 0.928 NA 0.004 0.040
#> GSM674374     3  0.1461      0.846 0.000 0.000 0.940 NA 0.000 0.016
#> GSM674376     3  0.2100      0.816 0.000 0.000 0.884 NA 0.000 0.004
#> GSM674377     3  0.2706      0.782 0.000 0.000 0.832 NA 0.008 0.000
#> GSM674378     3  0.1082      0.844 0.000 0.000 0.956 NA 0.004 0.000
#> GSM674383     3  0.2221      0.833 0.000 0.000 0.896 NA 0.000 0.072
#> GSM674386     3  0.2118      0.819 0.000 0.000 0.888 NA 0.008 0.000
#> GSM674387     3  0.2278      0.807 0.000 0.000 0.868 NA 0.000 0.004
#> GSM674392     3  0.2393      0.832 0.000 0.000 0.884 NA 0.004 0.092
#> GSM674396     3  0.1970      0.825 0.000 0.000 0.900 NA 0.008 0.000
#> GSM674399     3  0.2431      0.807 0.000 0.000 0.860 NA 0.008 0.000
#> GSM674404     3  0.1049      0.841 0.000 0.000 0.960 NA 0.000 0.008
#> GSM674182     2  0.3112      0.844 0.000 0.840 0.000 NA 0.004 0.104
#> GSM674188     2  0.0622      0.910 0.000 0.980 0.000 NA 0.000 0.012
#> GSM674189     2  0.4903      0.407 0.000 0.552 0.000 NA 0.000 0.380
#> GSM674196     2  0.0603      0.908 0.000 0.980 0.000 NA 0.016 0.000
#> GSM674197     2  0.0146      0.910 0.000 0.996 0.000 NA 0.004 0.000
#> GSM674199     2  0.0603      0.908 0.000 0.980 0.000 NA 0.016 0.000
#> GSM674207     2  0.1168      0.901 0.000 0.956 0.000 NA 0.028 0.000
#> GSM674211     2  0.0520      0.909 0.000 0.984 0.000 NA 0.008 0.000
#> GSM674213     2  0.1682      0.897 0.000 0.928 0.000 NA 0.000 0.020
#> GSM674215     2  0.4408      0.662 0.000 0.664 0.000 NA 0.000 0.056
#> GSM674216     2  0.0547      0.909 0.000 0.980 0.000 NA 0.000 0.000
#> GSM674217     2  0.1788      0.897 0.000 0.928 0.000 NA 0.004 0.040
#> GSM674222     2  0.2006      0.878 0.000 0.892 0.000 NA 0.000 0.004
#> GSM674224     2  0.0909      0.909 0.000 0.968 0.000 NA 0.000 0.012
#> GSM674227     2  0.0632      0.911 0.000 0.976 0.000 NA 0.000 0.000
#> GSM674228     2  0.0508      0.910 0.000 0.984 0.000 NA 0.000 0.004
#> GSM674233     2  0.2190      0.881 0.000 0.900 0.000 NA 0.000 0.060
#> GSM674238     6  0.4637      0.620 0.000 0.136 0.008 NA 0.000 0.712
#> GSM674241     2  0.0146      0.910 0.000 0.996 0.000 NA 0.000 0.000
#> GSM674283     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674286     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674293     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674294     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674296     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674303     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674307     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674310     1  0.3756      0.715 0.600 0.000 0.000 NA 0.400 0.000
#> GSM674311     1  0.0000      0.884 1.000 0.000 0.000 NA 0.000 0.000
#> GSM674312     1  0.3847      0.658 0.544 0.000 0.000 NA 0.456 0.000
#> GSM674317     1  0.0937      0.875 0.960 0.000 0.000 NA 0.040 0.000
#> GSM674319     1  0.3620      0.752 0.648 0.000 0.000 NA 0.352 0.000
#> GSM674321     1  0.3482      0.774 0.684 0.000 0.000 NA 0.316 0.000
#> GSM674322     1  0.3706      0.731 0.620 0.000 0.000 NA 0.380 0.000
#> GSM674326     1  0.3482      0.774 0.684 0.000 0.000 NA 0.316 0.000
#> GSM674329     1  0.3684      0.737 0.628 0.000 0.000 NA 0.372 0.000
#> GSM674333     1  0.3695      0.734 0.624 0.000 0.000 NA 0.376 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-MAD-NMF-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-MAD-NMF-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-MAD-NMF-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-MAD-NMF-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-MAD-NMF-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-MAD-NMF-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-MAD-NMF-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-MAD-NMF-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-MAD-NMF-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-MAD-NMF-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-MAD-NMF-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-MAD-NMF-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-MAD-NMF-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-MAD-NMF-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-MAD-NMF-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-MAD-NMF-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-MAD-NMF-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-MAD-NMF-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-MAD-NMF-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-MAD-NMF-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk MAD-NMF-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-MAD-NMF-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-MAD-NMF-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-MAD-NMF-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-MAD-NMF-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-MAD-NMF-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk MAD-NMF-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>           n disease.state(p) specimen(p) k
#> MAD:NMF 183            0.924    1.83e-40 2
#> MAD:NMF 183            0.962    6.15e-78 3
#> MAD:NMF 174            0.869    4.15e-72 4
#> MAD:NMF 173            0.747    8.43e-70 5
#> MAD:NMF 171            0.882    1.15e-68 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


ATC:hclust*

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["ATC", "hclust"]
# you can also extract it by
# res = res_list["ATC:hclust"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#>   Subgroups are detected by 'hclust' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 4.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk ATC-hclust-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk ATC-hclust-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 1.000           0.976       0.989         0.5937 0.751   0.571
#> 4 4 0.902           0.888       0.950         0.0431 0.974   0.920
#> 5 5 0.836           0.823       0.913         0.0365 0.988   0.962
#> 6 6 0.820           0.769       0.881         0.0276 0.983   0.942

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3

There is also optional best \(k\) = 2 3 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette p1    p2    p3
#> GSM674344     3  0.0000      0.989  0 0.000 1.000
#> GSM674346     3  0.0000      0.989  0 0.000 1.000
#> GSM674347     3  0.0000      0.989  0 0.000 1.000
#> GSM674348     3  0.0000      0.989  0 0.000 1.000
#> GSM674349     3  0.0000      0.989  0 0.000 1.000
#> GSM674350     3  0.0000      0.989  0 0.000 1.000
#> GSM674353     3  0.0000      0.989  0 0.000 1.000
#> GSM674354     3  0.0000      0.989  0 0.000 1.000
#> GSM674355     3  0.0000      0.989  0 0.000 1.000
#> GSM674356     3  0.0000      0.989  0 0.000 1.000
#> GSM674357     3  0.0000      0.989  0 0.000 1.000
#> GSM674358     3  0.0000      0.989  0 0.000 1.000
#> GSM674361     3  0.0000      0.989  0 0.000 1.000
#> GSM674363     3  0.0000      0.989  0 0.000 1.000
#> GSM674364     3  0.0237      0.986  0 0.004 0.996
#> GSM674365     3  0.0000      0.989  0 0.000 1.000
#> GSM674366     3  0.0000      0.989  0 0.000 1.000
#> GSM674367     3  0.0000      0.989  0 0.000 1.000
#> GSM674368     3  0.0000      0.989  0 0.000 1.000
#> GSM674370     3  0.0000      0.989  0 0.000 1.000
#> GSM674371     3  0.0000      0.989  0 0.000 1.000
#> GSM674373     3  0.0000      0.989  0 0.000 1.000
#> GSM674375     3  0.0000      0.989  0 0.000 1.000
#> GSM674379     3  0.0000      0.989  0 0.000 1.000
#> GSM674380     2  0.5988      0.437  0 0.632 0.368
#> GSM674381     3  0.0000      0.989  0 0.000 1.000
#> GSM674382     3  0.0000      0.989  0 0.000 1.000
#> GSM674384     3  0.0000      0.989  0 0.000 1.000
#> GSM674385     3  0.0747      0.975  0 0.016 0.984
#> GSM674388     3  0.0000      0.989  0 0.000 1.000
#> GSM674389     3  0.0000      0.989  0 0.000 1.000
#> GSM674390     3  0.0000      0.989  0 0.000 1.000
#> GSM674391     3  0.0000      0.989  0 0.000 1.000
#> GSM674393     3  0.0000      0.989  0 0.000 1.000
#> GSM674394     3  0.0000      0.989  0 0.000 1.000
#> GSM674395     3  0.0000      0.989  0 0.000 1.000
#> GSM674397     3  0.0000      0.989  0 0.000 1.000
#> GSM674398     3  0.0000      0.989  0 0.000 1.000
#> GSM674400     3  0.0000      0.989  0 0.000 1.000
#> GSM674401     3  0.0000      0.989  0 0.000 1.000
#> GSM674402     3  0.0000      0.989  0 0.000 1.000
#> GSM674403     3  0.0000      0.989  0 0.000 1.000
#> GSM674405     3  0.0000      0.989  0 0.000 1.000
#> GSM674406     3  0.0000      0.989  0 0.000 1.000
#> GSM674407     3  0.0000      0.989  0 0.000 1.000
#> GSM674181     2  0.0000      0.978  0 1.000 0.000
#> GSM674183     3  0.1860      0.939  0 0.052 0.948
#> GSM674184     2  0.3340      0.873  0 0.880 0.120
#> GSM674185     2  0.3267      0.877  0 0.884 0.116
#> GSM674186     2  0.0000      0.978  0 1.000 0.000
#> GSM674187     2  0.0000      0.978  0 1.000 0.000
#> GSM674190     2  0.0000      0.978  0 1.000 0.000
#> GSM674191     2  0.0000      0.978  0 1.000 0.000
#> GSM674192     2  0.0000      0.978  0 1.000 0.000
#> GSM674193     2  0.0000      0.978  0 1.000 0.000
#> GSM674194     2  0.0000      0.978  0 1.000 0.000
#> GSM674195     3  0.6204      0.239  0 0.424 0.576
#> GSM674198     2  0.0000      0.978  0 1.000 0.000
#> GSM674200     3  0.0000      0.989  0 0.000 1.000
#> GSM674201     2  0.1643      0.946  0 0.956 0.044
#> GSM674202     2  0.0000      0.978  0 1.000 0.000
#> GSM674203     2  0.0000      0.978  0 1.000 0.000
#> GSM674204     2  0.0000      0.978  0 1.000 0.000
#> GSM674205     2  0.0000      0.978  0 1.000 0.000
#> GSM674206     2  0.2796      0.902  0 0.908 0.092
#> GSM674208     2  0.0000      0.978  0 1.000 0.000
#> GSM674209     2  0.0000      0.978  0 1.000 0.000
#> GSM674210     2  0.0000      0.978  0 1.000 0.000
#> GSM674212     2  0.0000      0.978  0 1.000 0.000
#> GSM674214     2  0.0000      0.978  0 1.000 0.000
#> GSM674218     2  0.3482      0.863  0 0.872 0.128
#> GSM674219     2  0.0000      0.978  0 1.000 0.000
#> GSM674220     2  0.3752      0.843  0 0.856 0.144
#> GSM674221     2  0.0000      0.978  0 1.000 0.000
#> GSM674223     2  0.0000      0.978  0 1.000 0.000
#> GSM674225     2  0.3267      0.875  0 0.884 0.116
#> GSM674226     2  0.0000      0.978  0 1.000 0.000
#> GSM674229     2  0.0000      0.978  0 1.000 0.000
#> GSM674230     2  0.0000      0.978  0 1.000 0.000
#> GSM674231     2  0.0000      0.978  0 1.000 0.000
#> GSM674232     2  0.0000      0.978  0 1.000 0.000
#> GSM674234     2  0.0000      0.978  0 1.000 0.000
#> GSM674235     2  0.0000      0.978  0 1.000 0.000
#> GSM674236     2  0.0000      0.978  0 1.000 0.000
#> GSM674237     2  0.0000      0.978  0 1.000 0.000
#> GSM674239     2  0.0000      0.978  0 1.000 0.000
#> GSM674240     2  0.0000      0.978  0 1.000 0.000
#> GSM674242     2  0.0000      0.978  0 1.000 0.000
#> GSM674243     2  0.0000      0.978  0 1.000 0.000
#> GSM674244     2  0.0000      0.978  0 1.000 0.000
#> GSM674245     2  0.0000      0.978  0 1.000 0.000
#> GSM674282     1  0.0000      1.000  1 0.000 0.000
#> GSM674284     1  0.0000      1.000  1 0.000 0.000
#> GSM674285     1  0.0000      1.000  1 0.000 0.000
#> GSM674287     1  0.0000      1.000  1 0.000 0.000
#> GSM674288     1  0.0000      1.000  1 0.000 0.000
#> GSM674289     1  0.0000      1.000  1 0.000 0.000
#> GSM674290     1  0.0000      1.000  1 0.000 0.000
#> GSM674291     1  0.0000      1.000  1 0.000 0.000
#> GSM674292     1  0.0000      1.000  1 0.000 0.000
#> GSM674295     1  0.0000      1.000  1 0.000 0.000
#> GSM674297     1  0.0000      1.000  1 0.000 0.000
#> GSM674298     1  0.0000      1.000  1 0.000 0.000
#> GSM674299     1  0.0000      1.000  1 0.000 0.000
#> GSM674300     1  0.0000      1.000  1 0.000 0.000
#> GSM674301     1  0.0000      1.000  1 0.000 0.000
#> GSM674302     1  0.0000      1.000  1 0.000 0.000
#> GSM674304     1  0.0000      1.000  1 0.000 0.000
#> GSM674305     1  0.0000      1.000  1 0.000 0.000
#> GSM674306     1  0.0000      1.000  1 0.000 0.000
#> GSM674308     1  0.0000      1.000  1 0.000 0.000
#> GSM674309     1  0.0000      1.000  1 0.000 0.000
#> GSM674313     1  0.0000      1.000  1 0.000 0.000
#> GSM674314     1  0.0000      1.000  1 0.000 0.000
#> GSM674315     1  0.0000      1.000  1 0.000 0.000
#> GSM674316     1  0.0000      1.000  1 0.000 0.000
#> GSM674318     1  0.0000      1.000  1 0.000 0.000
#> GSM674320     1  0.0000      1.000  1 0.000 0.000
#> GSM674323     1  0.0000      1.000  1 0.000 0.000
#> GSM674324     1  0.0000      1.000  1 0.000 0.000
#> GSM674325     1  0.0000      1.000  1 0.000 0.000
#> GSM674327     1  0.0000      1.000  1 0.000 0.000
#> GSM674328     1  0.0000      1.000  1 0.000 0.000
#> GSM674330     1  0.0000      1.000  1 0.000 0.000
#> GSM674331     1  0.0000      1.000  1 0.000 0.000
#> GSM674332     1  0.0000      1.000  1 0.000 0.000
#> GSM674334     1  0.0000      1.000  1 0.000 0.000
#> GSM674335     1  0.0000      1.000  1 0.000 0.000
#> GSM674345     3  0.0000      0.989  0 0.000 1.000
#> GSM674351     3  0.0000      0.989  0 0.000 1.000
#> GSM674352     3  0.0000      0.989  0 0.000 1.000
#> GSM674359     3  0.0000      0.989  0 0.000 1.000
#> GSM674360     3  0.0237      0.986  0 0.004 0.996
#> GSM674362     3  0.0237      0.986  0 0.004 0.996
#> GSM674369     3  0.0000      0.989  0 0.000 1.000
#> GSM674372     3  0.0000      0.989  0 0.000 1.000
#> GSM674374     3  0.0000      0.989  0 0.000 1.000
#> GSM674376     3  0.0000      0.989  0 0.000 1.000
#> GSM674377     3  0.1860      0.938  0 0.052 0.948
#> GSM674378     3  0.0000      0.989  0 0.000 1.000
#> GSM674383     3  0.0000      0.989  0 0.000 1.000
#> GSM674386     3  0.0000      0.989  0 0.000 1.000
#> GSM674387     3  0.0000      0.989  0 0.000 1.000
#> GSM674392     3  0.0000      0.989  0 0.000 1.000
#> GSM674396     3  0.0000      0.989  0 0.000 1.000
#> GSM674399     3  0.0000      0.989  0 0.000 1.000
#> GSM674404     3  0.0000      0.989  0 0.000 1.000
#> GSM674182     2  0.0237      0.976  0 0.996 0.004
#> GSM674188     2  0.0000      0.978  0 1.000 0.000
#> GSM674189     2  0.2165      0.928  0 0.936 0.064
#> GSM674196     2  0.0000      0.978  0 1.000 0.000
#> GSM674197     2  0.0000      0.978  0 1.000 0.000
#> GSM674199     2  0.0000      0.978  0 1.000 0.000
#> GSM674207     2  0.0000      0.978  0 1.000 0.000
#> GSM674211     2  0.0000      0.978  0 1.000 0.000
#> GSM674213     2  0.0000      0.978  0 1.000 0.000
#> GSM674215     2  0.0424      0.973  0 0.992 0.008
#> GSM674216     2  0.0000      0.978  0 1.000 0.000
#> GSM674217     2  0.0000      0.978  0 1.000 0.000
#> GSM674222     2  0.2165      0.928  0 0.936 0.064
#> GSM674224     2  0.0000      0.978  0 1.000 0.000
#> GSM674227     2  0.0000      0.978  0 1.000 0.000
#> GSM674228     2  0.0000      0.978  0 1.000 0.000
#> GSM674233     2  0.0000      0.978  0 1.000 0.000
#> GSM674238     3  0.3816      0.821  0 0.148 0.852
#> GSM674241     2  0.0000      0.978  0 1.000 0.000
#> GSM674283     1  0.0000      1.000  1 0.000 0.000
#> GSM674286     1  0.0000      1.000  1 0.000 0.000
#> GSM674293     1  0.0000      1.000  1 0.000 0.000
#> GSM674294     1  0.0000      1.000  1 0.000 0.000
#> GSM674296     1  0.0000      1.000  1 0.000 0.000
#> GSM674303     1  0.0000      1.000  1 0.000 0.000
#> GSM674307     1  0.0000      1.000  1 0.000 0.000
#> GSM674310     1  0.0000      1.000  1 0.000 0.000
#> GSM674311     1  0.0000      1.000  1 0.000 0.000
#> GSM674312     1  0.0000      1.000  1 0.000 0.000
#> GSM674317     1  0.0000      1.000  1 0.000 0.000
#> GSM674319     1  0.0000      1.000  1 0.000 0.000
#> GSM674321     1  0.0000      1.000  1 0.000 0.000
#> GSM674322     1  0.0000      1.000  1 0.000 0.000
#> GSM674326     1  0.0000      1.000  1 0.000 0.000
#> GSM674329     1  0.0000      1.000  1 0.000 0.000
#> GSM674333     1  0.0000      1.000  1 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1    p2    p3    p4
#> GSM674344     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674346     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674347     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674348     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674349     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674350     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674353     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674354     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674355     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674356     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674357     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674358     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674361     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674363     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674364     3  0.0188      0.982 0.000 0.004 0.996 0.000
#> GSM674365     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674366     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674367     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674368     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674370     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674371     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674373     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674375     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674379     3  0.0336      0.981 0.000 0.000 0.992 0.008
#> GSM674380     2  0.5127      0.435 0.000 0.632 0.356 0.012
#> GSM674381     3  0.0188      0.983 0.000 0.000 0.996 0.004
#> GSM674382     3  0.0469      0.979 0.000 0.000 0.988 0.012
#> GSM674384     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674385     3  0.0779      0.968 0.000 0.016 0.980 0.004
#> GSM674388     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674389     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674390     3  0.0188      0.983 0.000 0.000 0.996 0.004
#> GSM674391     3  0.0469      0.979 0.000 0.000 0.988 0.012
#> GSM674393     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674394     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674395     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674397     3  0.0188      0.983 0.000 0.000 0.996 0.004
#> GSM674398     3  0.0336      0.981 0.000 0.000 0.992 0.008
#> GSM674400     3  0.0188      0.983 0.000 0.000 0.996 0.004
#> GSM674401     3  0.0188      0.983 0.000 0.000 0.996 0.004
#> GSM674402     3  0.0188      0.983 0.000 0.000 0.996 0.004
#> GSM674403     3  0.0188      0.983 0.000 0.000 0.996 0.004
#> GSM674405     3  0.0336      0.981 0.000 0.000 0.992 0.008
#> GSM674406     3  0.0188      0.983 0.000 0.000 0.996 0.004
#> GSM674407     3  0.0336      0.981 0.000 0.000 0.992 0.008
#> GSM674181     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674183     3  0.1474      0.926 0.000 0.052 0.948 0.000
#> GSM674184     2  0.2647      0.843 0.000 0.880 0.120 0.000
#> GSM674185     2  0.2589      0.848 0.000 0.884 0.116 0.000
#> GSM674186     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674187     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674190     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674191     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674192     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674193     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674194     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674195     3  0.4916      0.242 0.000 0.424 0.576 0.000
#> GSM674198     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674200     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674201     2  0.1302      0.932 0.000 0.956 0.044 0.000
#> GSM674202     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674203     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674204     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674205     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674206     2  0.2216      0.878 0.000 0.908 0.092 0.000
#> GSM674208     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674209     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674210     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674212     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674214     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674218     2  0.2760      0.832 0.000 0.872 0.128 0.000
#> GSM674219     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674220     2  0.3271      0.814 0.000 0.856 0.132 0.012
#> GSM674221     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674223     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674225     2  0.2799      0.850 0.000 0.884 0.108 0.008
#> GSM674226     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674229     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674230     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674231     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674232     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674234     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674235     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674236     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674237     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674239     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674240     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674242     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674243     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674244     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674245     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674282     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674284     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674285     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674287     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674288     1  0.4888      0.206 0.588 0.000 0.000 0.412
#> GSM674289     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674290     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674291     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674292     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674295     4  0.4713      0.601 0.360 0.000 0.000 0.640
#> GSM674297     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674298     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674299     1  0.2973      0.757 0.856 0.000 0.000 0.144
#> GSM674300     1  0.4679      0.425 0.648 0.000 0.000 0.352
#> GSM674301     1  0.1474      0.821 0.948 0.000 0.000 0.052
#> GSM674302     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674304     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674305     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674306     1  0.3074      0.732 0.848 0.000 0.000 0.152
#> GSM674308     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674309     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674313     4  0.0592      0.723 0.016 0.000 0.000 0.984
#> GSM674314     1  0.0817      0.838 0.976 0.000 0.000 0.024
#> GSM674315     1  0.3074      0.732 0.848 0.000 0.000 0.152
#> GSM674316     1  0.4888      0.231 0.588 0.000 0.000 0.412
#> GSM674318     4  0.3074      0.801 0.152 0.000 0.000 0.848
#> GSM674320     4  0.4193      0.748 0.268 0.000 0.000 0.732
#> GSM674323     1  0.4898      0.218 0.584 0.000 0.000 0.416
#> GSM674324     1  0.0817      0.840 0.976 0.000 0.000 0.024
#> GSM674325     1  0.4888      0.231 0.588 0.000 0.000 0.412
#> GSM674327     1  0.4697      0.414 0.644 0.000 0.000 0.356
#> GSM674328     1  0.2868      0.765 0.864 0.000 0.000 0.136
#> GSM674330     1  0.2647      0.777 0.880 0.000 0.000 0.120
#> GSM674331     1  0.0817      0.840 0.976 0.000 0.000 0.024
#> GSM674332     1  0.3610      0.691 0.800 0.000 0.000 0.200
#> GSM674334     1  0.3610      0.691 0.800 0.000 0.000 0.200
#> GSM674335     1  0.3610      0.691 0.800 0.000 0.000 0.200
#> GSM674345     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674351     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674352     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674359     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674360     3  0.0188      0.982 0.000 0.004 0.996 0.000
#> GSM674362     3  0.0188      0.982 0.000 0.004 0.996 0.000
#> GSM674369     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674372     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674374     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674376     3  0.0336      0.981 0.000 0.000 0.992 0.008
#> GSM674377     3  0.1938      0.920 0.000 0.052 0.936 0.012
#> GSM674378     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674383     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674386     3  0.0469      0.979 0.000 0.000 0.988 0.012
#> GSM674387     3  0.0336      0.981 0.000 0.000 0.992 0.008
#> GSM674392     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> GSM674396     3  0.0336      0.981 0.000 0.000 0.992 0.008
#> GSM674399     3  0.0336      0.981 0.000 0.000 0.992 0.008
#> GSM674404     3  0.0336      0.981 0.000 0.000 0.992 0.008
#> GSM674182     2  0.0188      0.970 0.000 0.996 0.004 0.000
#> GSM674188     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674189     2  0.1716      0.910 0.000 0.936 0.064 0.000
#> GSM674196     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674197     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674199     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674207     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674211     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674213     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674215     2  0.0336      0.966 0.000 0.992 0.008 0.000
#> GSM674216     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674217     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674222     2  0.1938      0.914 0.000 0.936 0.052 0.012
#> GSM674224     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674227     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674228     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674233     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674238     3  0.3024      0.793 0.000 0.148 0.852 0.000
#> GSM674241     2  0.0000      0.973 0.000 1.000 0.000 0.000
#> GSM674283     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674286     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674293     1  0.2589      0.770 0.884 0.000 0.000 0.116
#> GSM674294     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674296     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674303     1  0.0817      0.840 0.976 0.000 0.000 0.024
#> GSM674307     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674310     4  0.3074      0.801 0.152 0.000 0.000 0.848
#> GSM674311     1  0.0000      0.847 1.000 0.000 0.000 0.000
#> GSM674312     4  0.0707      0.725 0.020 0.000 0.000 0.980
#> GSM674317     1  0.3123      0.747 0.844 0.000 0.000 0.156
#> GSM674319     4  0.4961      0.387 0.448 0.000 0.000 0.552
#> GSM674321     1  0.4746      0.363 0.632 0.000 0.000 0.368
#> GSM674322     4  0.4164      0.746 0.264 0.000 0.000 0.736
#> GSM674326     4  0.3074      0.801 0.152 0.000 0.000 0.848
#> GSM674329     4  0.4193      0.748 0.268 0.000 0.000 0.732
#> GSM674333     1  0.4804      0.334 0.616 0.000 0.000 0.384

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4    p5
#> GSM674344     3  0.1043      0.833 0.000 0.000 0.960 0.000 0.040
#> GSM674346     3  0.1043      0.833 0.000 0.000 0.960 0.000 0.040
#> GSM674347     3  0.0794      0.852 0.000 0.000 0.972 0.000 0.028
#> GSM674348     3  0.1043      0.833 0.000 0.000 0.960 0.000 0.040
#> GSM674349     3  0.1043      0.852 0.000 0.000 0.960 0.000 0.040
#> GSM674350     3  0.0000      0.850 0.000 0.000 1.000 0.000 0.000
#> GSM674353     3  0.0000      0.850 0.000 0.000 1.000 0.000 0.000
#> GSM674354     3  0.0000      0.850 0.000 0.000 1.000 0.000 0.000
#> GSM674355     3  0.0000      0.850 0.000 0.000 1.000 0.000 0.000
#> GSM674356     3  0.0000      0.850 0.000 0.000 1.000 0.000 0.000
#> GSM674357     3  0.0000      0.850 0.000 0.000 1.000 0.000 0.000
#> GSM674358     3  0.0000      0.850 0.000 0.000 1.000 0.000 0.000
#> GSM674361     3  0.0000      0.850 0.000 0.000 1.000 0.000 0.000
#> GSM674363     3  0.0000      0.850 0.000 0.000 1.000 0.000 0.000
#> GSM674364     3  0.0162      0.850 0.000 0.004 0.996 0.000 0.000
#> GSM674365     3  0.1341      0.850 0.000 0.000 0.944 0.000 0.056
#> GSM674366     3  0.1544      0.848 0.000 0.000 0.932 0.000 0.068
#> GSM674367     3  0.2329      0.828 0.000 0.000 0.876 0.000 0.124
#> GSM674368     3  0.0703      0.842 0.000 0.000 0.976 0.000 0.024
#> GSM674370     3  0.1732      0.846 0.000 0.000 0.920 0.000 0.080
#> GSM674371     3  0.0703      0.842 0.000 0.000 0.976 0.000 0.024
#> GSM674373     3  0.2471      0.815 0.000 0.000 0.864 0.000 0.136
#> GSM674375     3  0.2852      0.777 0.000 0.000 0.828 0.000 0.172
#> GSM674379     3  0.3177      0.733 0.000 0.000 0.792 0.000 0.208
#> GSM674380     2  0.5565      0.351 0.000 0.632 0.240 0.000 0.128
#> GSM674381     3  0.2690      0.796 0.000 0.000 0.844 0.000 0.156
#> GSM674382     5  0.3774      1.000 0.000 0.000 0.296 0.000 0.704
#> GSM674384     3  0.2471      0.811 0.000 0.000 0.864 0.000 0.136
#> GSM674385     3  0.3264      0.774 0.000 0.016 0.820 0.000 0.164
#> GSM674388     3  0.1121      0.836 0.000 0.000 0.956 0.000 0.044
#> GSM674389     3  0.2424      0.812 0.000 0.000 0.868 0.000 0.132
#> GSM674390     3  0.2732      0.805 0.000 0.000 0.840 0.000 0.160
#> GSM674391     5  0.3774      1.000 0.000 0.000 0.296 0.000 0.704
#> GSM674393     3  0.2230      0.822 0.000 0.000 0.884 0.000 0.116
#> GSM674394     3  0.2561      0.803 0.000 0.000 0.856 0.000 0.144
#> GSM674395     3  0.2424      0.812 0.000 0.000 0.868 0.000 0.132
#> GSM674397     3  0.2127      0.839 0.000 0.000 0.892 0.000 0.108
#> GSM674398     3  0.3366      0.696 0.000 0.000 0.768 0.000 0.232
#> GSM674400     3  0.1792      0.806 0.000 0.000 0.916 0.000 0.084
#> GSM674401     3  0.1792      0.806 0.000 0.000 0.916 0.000 0.084
#> GSM674402     3  0.1792      0.806 0.000 0.000 0.916 0.000 0.084
#> GSM674403     3  0.1792      0.806 0.000 0.000 0.916 0.000 0.084
#> GSM674405     3  0.3366      0.696 0.000 0.000 0.768 0.000 0.232
#> GSM674406     3  0.2561      0.816 0.000 0.000 0.856 0.000 0.144
#> GSM674407     3  0.3210      0.727 0.000 0.000 0.788 0.000 0.212
#> GSM674181     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674183     3  0.2300      0.769 0.000 0.052 0.908 0.000 0.040
#> GSM674184     2  0.2735      0.857 0.000 0.880 0.084 0.000 0.036
#> GSM674185     2  0.2676      0.862 0.000 0.884 0.080 0.000 0.036
#> GSM674186     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674187     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674190     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674191     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674192     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674193     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674194     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674195     3  0.5137     -0.101 0.000 0.424 0.536 0.000 0.040
#> GSM674198     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674200     3  0.1043      0.833 0.000 0.000 0.960 0.000 0.040
#> GSM674201     2  0.1281      0.941 0.000 0.956 0.032 0.000 0.012
#> GSM674202     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674203     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674204     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674205     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674206     2  0.2278      0.890 0.000 0.908 0.060 0.000 0.032
#> GSM674208     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674209     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674210     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674212     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674214     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674218     2  0.2850      0.845 0.000 0.872 0.092 0.000 0.036
#> GSM674219     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674220     2  0.3090      0.846 0.000 0.856 0.040 0.000 0.104
#> GSM674221     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674223     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674225     2  0.2561      0.879 0.000 0.884 0.020 0.000 0.096
#> GSM674226     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674229     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674230     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674231     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674232     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674234     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674235     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674236     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674237     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674239     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674240     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674242     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674243     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674244     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674245     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674282     1  0.0000      0.842 1.000 0.000 0.000 0.000 0.000
#> GSM674284     1  0.0000      0.842 1.000 0.000 0.000 0.000 0.000
#> GSM674285     1  0.0000      0.842 1.000 0.000 0.000 0.000 0.000
#> GSM674287     1  0.0000      0.842 1.000 0.000 0.000 0.000 0.000
#> GSM674288     1  0.4256      0.156 0.564 0.000 0.000 0.436 0.000
#> GSM674289     1  0.0000      0.842 1.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0000      0.842 1.000 0.000 0.000 0.000 0.000
#> GSM674291     1  0.0000      0.842 1.000 0.000 0.000 0.000 0.000
#> GSM674292     1  0.0000      0.842 1.000 0.000 0.000 0.000 0.000
#> GSM674295     4  0.4235      0.605 0.336 0.000 0.000 0.656 0.008
#> GSM674297     1  0.0000      0.842 1.000 0.000 0.000 0.000 0.000
#> GSM674298     1  0.0000      0.842 1.000 0.000 0.000 0.000 0.000
#> GSM674299     1  0.2605      0.750 0.852 0.000 0.000 0.148 0.000
#> GSM674300     1  0.5911      0.412 0.596 0.000 0.000 0.228 0.176
#> GSM674301     1  0.1478      0.808 0.936 0.000 0.000 0.000 0.064
#> GSM674302     1  0.0000      0.842 1.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0000      0.842 1.000 0.000 0.000 0.000 0.000
#> GSM674305     1  0.0000      0.842 1.000 0.000 0.000 0.000 0.000
#> GSM674306     1  0.3419      0.695 0.804 0.000 0.000 0.016 0.180
#> GSM674308     1  0.0000      0.842 1.000 0.000 0.000 0.000 0.000
#> GSM674309     1  0.0162      0.841 0.996 0.000 0.000 0.004 0.000
#> GSM674313     4  0.1270      0.658 0.000 0.000 0.000 0.948 0.052
#> GSM674314     1  0.0865      0.832 0.972 0.000 0.000 0.004 0.024
#> GSM674315     1  0.3419      0.695 0.804 0.000 0.000 0.016 0.180
#> GSM674316     1  0.4268      0.158 0.556 0.000 0.000 0.444 0.000
#> GSM674318     4  0.2230      0.799 0.116 0.000 0.000 0.884 0.000
#> GSM674320     4  0.3988      0.741 0.252 0.000 0.000 0.732 0.016
#> GSM674323     1  0.4273      0.143 0.552 0.000 0.000 0.448 0.000
#> GSM674324     1  0.0794      0.833 0.972 0.000 0.000 0.028 0.000
#> GSM674325     1  0.4268      0.158 0.556 0.000 0.000 0.444 0.000
#> GSM674327     1  0.5941      0.403 0.592 0.000 0.000 0.228 0.180
#> GSM674328     1  0.2516      0.757 0.860 0.000 0.000 0.140 0.000
#> GSM674330     1  0.2424      0.764 0.868 0.000 0.000 0.132 0.000
#> GSM674331     1  0.0794      0.833 0.972 0.000 0.000 0.028 0.000
#> GSM674332     1  0.3242      0.675 0.784 0.000 0.000 0.216 0.000
#> GSM674334     1  0.3242      0.675 0.784 0.000 0.000 0.216 0.000
#> GSM674335     1  0.3242      0.675 0.784 0.000 0.000 0.216 0.000
#> GSM674345     3  0.1043      0.833 0.000 0.000 0.960 0.000 0.040
#> GSM674351     3  0.0000      0.850 0.000 0.000 1.000 0.000 0.000
#> GSM674352     3  0.0000      0.850 0.000 0.000 1.000 0.000 0.000
#> GSM674359     3  0.1043      0.833 0.000 0.000 0.960 0.000 0.040
#> GSM674360     3  0.0162      0.850 0.000 0.004 0.996 0.000 0.000
#> GSM674362     3  0.0162      0.850 0.000 0.004 0.996 0.000 0.000
#> GSM674369     3  0.0703      0.842 0.000 0.000 0.976 0.000 0.024
#> GSM674372     3  0.2424      0.812 0.000 0.000 0.868 0.000 0.132
#> GSM674374     3  0.2471      0.815 0.000 0.000 0.864 0.000 0.136
#> GSM674376     3  0.3210      0.727 0.000 0.000 0.788 0.000 0.212
#> GSM674377     3  0.4575      0.575 0.000 0.052 0.712 0.000 0.236
#> GSM674378     3  0.2377      0.820 0.000 0.000 0.872 0.000 0.128
#> GSM674383     3  0.0703      0.842 0.000 0.000 0.976 0.000 0.024
#> GSM674386     5  0.3774      1.000 0.000 0.000 0.296 0.000 0.704
#> GSM674387     3  0.3210      0.727 0.000 0.000 0.788 0.000 0.212
#> GSM674392     3  0.1792      0.839 0.000 0.000 0.916 0.000 0.084
#> GSM674396     3  0.3366      0.696 0.000 0.000 0.768 0.000 0.232
#> GSM674399     3  0.3366      0.696 0.000 0.000 0.768 0.000 0.232
#> GSM674404     3  0.3366      0.696 0.000 0.000 0.768 0.000 0.232
#> GSM674182     2  0.0162      0.974 0.000 0.996 0.004 0.000 0.000
#> GSM674188     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674189     2  0.1725      0.919 0.000 0.936 0.044 0.000 0.020
#> GSM674196     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674197     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674199     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674207     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674211     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674213     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674215     2  0.0290      0.970 0.000 0.992 0.008 0.000 0.000
#> GSM674216     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674217     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674222     2  0.1628      0.928 0.000 0.936 0.008 0.000 0.056
#> GSM674224     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674227     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674228     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674233     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674238     3  0.3608      0.538 0.000 0.148 0.812 0.000 0.040
#> GSM674241     2  0.0000      0.977 0.000 1.000 0.000 0.000 0.000
#> GSM674283     1  0.0000      0.842 1.000 0.000 0.000 0.000 0.000
#> GSM674286     1  0.0000      0.842 1.000 0.000 0.000 0.000 0.000
#> GSM674293     1  0.2909      0.738 0.848 0.000 0.000 0.012 0.140
#> GSM674294     1  0.0000      0.842 1.000 0.000 0.000 0.000 0.000
#> GSM674296     1  0.0000      0.842 1.000 0.000 0.000 0.000 0.000
#> GSM674303     1  0.0794      0.833 0.972 0.000 0.000 0.028 0.000
#> GSM674307     1  0.0000      0.842 1.000 0.000 0.000 0.000 0.000
#> GSM674310     4  0.2230      0.799 0.116 0.000 0.000 0.884 0.000
#> GSM674311     1  0.0162      0.841 0.996 0.000 0.000 0.004 0.000
#> GSM674312     4  0.1043      0.661 0.000 0.000 0.000 0.960 0.040
#> GSM674317     1  0.2773      0.737 0.836 0.000 0.000 0.164 0.000
#> GSM674319     4  0.4510      0.369 0.432 0.000 0.000 0.560 0.008
#> GSM674321     1  0.4171      0.308 0.604 0.000 0.000 0.396 0.000
#> GSM674322     4  0.3336      0.753 0.228 0.000 0.000 0.772 0.000
#> GSM674326     4  0.2230      0.799 0.116 0.000 0.000 0.884 0.000
#> GSM674329     4  0.3988      0.741 0.252 0.000 0.000 0.732 0.016
#> GSM674333     1  0.4227      0.249 0.580 0.000 0.000 0.420 0.000

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4    p5 p6
#> GSM674344     3  0.2136     0.7569 0.000 0.000 0.904 0.048 0.000 NA
#> GSM674346     3  0.2136     0.7569 0.000 0.000 0.904 0.048 0.000 NA
#> GSM674347     3  0.1082     0.8020 0.000 0.000 0.956 0.040 0.000 NA
#> GSM674348     3  0.2070     0.7596 0.000 0.000 0.908 0.048 0.000 NA
#> GSM674349     3  0.1461     0.8000 0.000 0.000 0.940 0.044 0.000 NA
#> GSM674350     3  0.0000     0.8008 0.000 0.000 1.000 0.000 0.000 NA
#> GSM674353     3  0.0000     0.8008 0.000 0.000 1.000 0.000 0.000 NA
#> GSM674354     3  0.0146     0.8002 0.000 0.000 0.996 0.004 0.000 NA
#> GSM674355     3  0.0146     0.8012 0.000 0.000 0.996 0.004 0.000 NA
#> GSM674356     3  0.0146     0.8002 0.000 0.000 0.996 0.004 0.000 NA
#> GSM674357     3  0.0000     0.8008 0.000 0.000 1.000 0.000 0.000 NA
#> GSM674358     3  0.0146     0.8012 0.000 0.000 0.996 0.004 0.000 NA
#> GSM674361     3  0.0146     0.8002 0.000 0.000 0.996 0.004 0.000 NA
#> GSM674363     3  0.0146     0.8002 0.000 0.000 0.996 0.004 0.000 NA
#> GSM674364     3  0.0291     0.8000 0.000 0.004 0.992 0.004 0.000 NA
#> GSM674365     3  0.1444     0.8010 0.000 0.000 0.928 0.072 0.000 NA
#> GSM674366     3  0.1714     0.7983 0.000 0.000 0.908 0.092 0.000 NA
#> GSM674367     3  0.2491     0.7784 0.000 0.000 0.836 0.164 0.000 NA
#> GSM674368     3  0.0865     0.7959 0.000 0.000 0.964 0.036 0.000 NA
#> GSM674370     3  0.1863     0.7965 0.000 0.000 0.896 0.104 0.000 NA
#> GSM674371     3  0.0865     0.7959 0.000 0.000 0.964 0.036 0.000 NA
#> GSM674373     3  0.2562     0.7659 0.000 0.000 0.828 0.172 0.000 NA
#> GSM674375     3  0.2883     0.7355 0.000 0.000 0.788 0.212 0.000 NA
#> GSM674379     3  0.3409     0.6430 0.000 0.000 0.700 0.300 0.000 NA
#> GSM674380     2  0.5078     0.4008 0.000 0.632 0.160 0.208 0.000 NA
#> GSM674381     3  0.2912     0.7341 0.000 0.000 0.784 0.216 0.000 NA
#> GSM674382     4  0.2135     1.0000 0.000 0.000 0.128 0.872 0.000 NA
#> GSM674384     3  0.2491     0.7676 0.000 0.000 0.836 0.164 0.000 NA
#> GSM674385     3  0.3261     0.7316 0.000 0.016 0.780 0.204 0.000 NA
#> GSM674388     3  0.2197     0.7617 0.000 0.000 0.900 0.056 0.000 NA
#> GSM674389     3  0.2562     0.7623 0.000 0.000 0.828 0.172 0.000 NA
#> GSM674390     3  0.3023     0.7356 0.000 0.000 0.768 0.232 0.000 NA
#> GSM674391     4  0.2135     1.0000 0.000 0.000 0.128 0.872 0.000 NA
#> GSM674393     3  0.2340     0.7737 0.000 0.000 0.852 0.148 0.000 NA
#> GSM674394     3  0.2562     0.7626 0.000 0.000 0.828 0.172 0.000 NA
#> GSM674395     3  0.2527     0.7640 0.000 0.000 0.832 0.168 0.000 NA
#> GSM674397     3  0.2597     0.7728 0.000 0.000 0.824 0.176 0.000 NA
#> GSM674398     3  0.3634     0.5625 0.000 0.000 0.644 0.356 0.000 NA
#> GSM674400     3  0.4916     0.1298 0.000 0.000 0.520 0.064 0.000 NA
#> GSM674401     3  0.4916     0.1298 0.000 0.000 0.520 0.064 0.000 NA
#> GSM674402     3  0.4916     0.1298 0.000 0.000 0.520 0.064 0.000 NA
#> GSM674403     3  0.4916     0.1298 0.000 0.000 0.520 0.064 0.000 NA
#> GSM674405     3  0.3634     0.5625 0.000 0.000 0.644 0.356 0.000 NA
#> GSM674406     3  0.2883     0.7495 0.000 0.000 0.788 0.212 0.000 NA
#> GSM674407     3  0.3464     0.6272 0.000 0.000 0.688 0.312 0.000 NA
#> GSM674181     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674183     3  0.3181     0.7114 0.000 0.052 0.856 0.048 0.000 NA
#> GSM674184     2  0.2474     0.8574 0.000 0.880 0.080 0.040 0.000 NA
#> GSM674185     2  0.2420     0.8622 0.000 0.884 0.076 0.040 0.000 NA
#> GSM674186     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674187     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674190     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674191     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674192     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674193     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674194     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674195     3  0.5400     0.0309 0.000 0.424 0.496 0.048 0.000 NA
#> GSM674198     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674200     3  0.2136     0.7569 0.000 0.000 0.904 0.048 0.000 NA
#> GSM674201     2  0.1151     0.9402 0.000 0.956 0.032 0.012 0.000 NA
#> GSM674202     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674203     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674204     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674205     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674206     2  0.2058     0.8908 0.000 0.908 0.056 0.036 0.000 NA
#> GSM674208     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674209     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674210     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674212     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674214     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674218     2  0.2579     0.8466 0.000 0.872 0.088 0.040 0.000 NA
#> GSM674219     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674220     2  0.2726     0.8453 0.000 0.856 0.032 0.112 0.000 NA
#> GSM674221     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674223     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674225     2  0.2218     0.8752 0.000 0.884 0.012 0.104 0.000 NA
#> GSM674226     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674229     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674230     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674231     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674232     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674234     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674235     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674236     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674237     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674239     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674240     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674242     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674243     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674244     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674245     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674282     1  0.0000     0.8469 1.000 0.000 0.000 0.000 0.000 NA
#> GSM674284     1  0.0000     0.8469 1.000 0.000 0.000 0.000 0.000 NA
#> GSM674285     1  0.0000     0.8469 1.000 0.000 0.000 0.000 0.000 NA
#> GSM674287     1  0.0000     0.8469 1.000 0.000 0.000 0.000 0.000 NA
#> GSM674288     5  0.4381     0.3606 0.440 0.000 0.000 0.000 0.536 NA
#> GSM674289     1  0.0000     0.8469 1.000 0.000 0.000 0.000 0.000 NA
#> GSM674290     1  0.0000     0.8469 1.000 0.000 0.000 0.000 0.000 NA
#> GSM674291     1  0.0363     0.8429 0.988 0.000 0.000 0.000 0.012 NA
#> GSM674292     1  0.0000     0.8469 1.000 0.000 0.000 0.000 0.000 NA
#> GSM674295     5  0.4881     0.6263 0.232 0.000 0.000 0.000 0.648 NA
#> GSM674297     1  0.0000     0.8469 1.000 0.000 0.000 0.000 0.000 NA
#> GSM674298     1  0.0000     0.8469 1.000 0.000 0.000 0.000 0.000 NA
#> GSM674299     1  0.3244     0.5432 0.732 0.000 0.000 0.000 0.268 NA
#> GSM674300     1  0.6592    -0.1259 0.448 0.000 0.000 0.068 0.348 NA
#> GSM674301     1  0.1633     0.8023 0.932 0.000 0.000 0.024 0.000 NA
#> GSM674302     1  0.0000     0.8469 1.000 0.000 0.000 0.000 0.000 NA
#> GSM674304     1  0.0000     0.8469 1.000 0.000 0.000 0.000 0.000 NA
#> GSM674305     1  0.0000     0.8469 1.000 0.000 0.000 0.000 0.000 NA
#> GSM674306     1  0.4024     0.6384 0.776 0.000 0.000 0.068 0.016 NA
#> GSM674308     1  0.0000     0.8469 1.000 0.000 0.000 0.000 0.000 NA
#> GSM674309     1  0.0632     0.8384 0.976 0.000 0.000 0.000 0.024 NA
#> GSM674313     5  0.4238     0.2675 0.000 0.000 0.000 0.016 0.540 NA
#> GSM674314     1  0.1448     0.8264 0.948 0.000 0.000 0.012 0.024 NA
#> GSM674315     1  0.4024     0.6384 0.776 0.000 0.000 0.068 0.016 NA
#> GSM674316     5  0.3804     0.4051 0.424 0.000 0.000 0.000 0.576 NA
#> GSM674318     5  0.1367     0.5431 0.012 0.000 0.000 0.000 0.944 NA
#> GSM674320     5  0.4354     0.6450 0.144 0.000 0.000 0.000 0.724 NA
#> GSM674323     5  0.3797     0.4126 0.420 0.000 0.000 0.000 0.580 NA
#> GSM674324     1  0.1387     0.8063 0.932 0.000 0.000 0.000 0.068 NA
#> GSM674325     5  0.3804     0.4051 0.424 0.000 0.000 0.000 0.576 NA
#> GSM674327     1  0.6619    -0.1357 0.444 0.000 0.000 0.068 0.348 NA
#> GSM674328     1  0.3023     0.6052 0.768 0.000 0.000 0.000 0.232 NA
#> GSM674330     1  0.3215     0.5927 0.756 0.000 0.000 0.000 0.240 NA
#> GSM674331     1  0.1387     0.8063 0.932 0.000 0.000 0.000 0.068 NA
#> GSM674332     1  0.3756     0.3473 0.644 0.000 0.000 0.000 0.352 NA
#> GSM674334     1  0.3756     0.3473 0.644 0.000 0.000 0.000 0.352 NA
#> GSM674335     1  0.3756     0.3473 0.644 0.000 0.000 0.000 0.352 NA
#> GSM674345     3  0.2136     0.7569 0.000 0.000 0.904 0.048 0.000 NA
#> GSM674351     3  0.0000     0.8008 0.000 0.000 1.000 0.000 0.000 NA
#> GSM674352     3  0.0000     0.8008 0.000 0.000 1.000 0.000 0.000 NA
#> GSM674359     3  0.2136     0.7569 0.000 0.000 0.904 0.048 0.000 NA
#> GSM674360     3  0.0291     0.8000 0.000 0.004 0.992 0.004 0.000 NA
#> GSM674362     3  0.0291     0.8000 0.000 0.004 0.992 0.004 0.000 NA
#> GSM674369     3  0.0865     0.7959 0.000 0.000 0.964 0.036 0.000 NA
#> GSM674372     3  0.2527     0.7640 0.000 0.000 0.832 0.168 0.000 NA
#> GSM674374     3  0.2562     0.7659 0.000 0.000 0.828 0.172 0.000 NA
#> GSM674376     3  0.3464     0.6269 0.000 0.000 0.688 0.312 0.000 NA
#> GSM674377     3  0.4553     0.5094 0.000 0.052 0.620 0.328 0.000 NA
#> GSM674378     3  0.2527     0.7681 0.000 0.000 0.832 0.168 0.000 NA
#> GSM674383     3  0.0937     0.7987 0.000 0.000 0.960 0.040 0.000 NA
#> GSM674386     4  0.2135     1.0000 0.000 0.000 0.128 0.872 0.000 NA
#> GSM674387     3  0.3464     0.6272 0.000 0.000 0.688 0.312 0.000 NA
#> GSM674392     3  0.1910     0.7882 0.000 0.000 0.892 0.108 0.000 NA
#> GSM674396     3  0.3634     0.5625 0.000 0.000 0.644 0.356 0.000 NA
#> GSM674399     3  0.3634     0.5625 0.000 0.000 0.644 0.356 0.000 NA
#> GSM674404     3  0.3634     0.5625 0.000 0.000 0.644 0.356 0.000 NA
#> GSM674182     2  0.0146     0.9740 0.000 0.996 0.004 0.000 0.000 NA
#> GSM674188     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674189     2  0.1564     0.9204 0.000 0.936 0.040 0.024 0.000 NA
#> GSM674196     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674197     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674199     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674207     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674211     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674213     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674215     2  0.0260     0.9707 0.000 0.992 0.008 0.000 0.000 NA
#> GSM674216     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674217     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674222     2  0.1411     0.9264 0.000 0.936 0.004 0.060 0.000 NA
#> GSM674224     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674227     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674228     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674233     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674238     3  0.3844     0.6024 0.000 0.148 0.788 0.040 0.000 NA
#> GSM674241     2  0.0000     0.9776 0.000 1.000 0.000 0.000 0.000 NA
#> GSM674283     1  0.0000     0.8469 1.000 0.000 0.000 0.000 0.000 NA
#> GSM674286     1  0.0000     0.8469 1.000 0.000 0.000 0.000 0.000 NA
#> GSM674293     1  0.3836     0.6868 0.804 0.000 0.000 0.056 0.032 NA
#> GSM674294     1  0.0000     0.8469 1.000 0.000 0.000 0.000 0.000 NA
#> GSM674296     1  0.0000     0.8469 1.000 0.000 0.000 0.000 0.000 NA
#> GSM674303     1  0.1387     0.8063 0.932 0.000 0.000 0.000 0.068 NA
#> GSM674307     1  0.0000     0.8469 1.000 0.000 0.000 0.000 0.000 NA
#> GSM674310     5  0.1367     0.5431 0.012 0.000 0.000 0.000 0.944 NA
#> GSM674311     1  0.0632     0.8384 0.976 0.000 0.000 0.000 0.024 NA
#> GSM674312     5  0.4147     0.2748 0.000 0.000 0.000 0.012 0.552 NA
#> GSM674317     1  0.3330     0.5135 0.716 0.000 0.000 0.000 0.284 NA
#> GSM674319     5  0.5268     0.5310 0.332 0.000 0.000 0.000 0.552 NA
#> GSM674321     5  0.3991     0.2801 0.472 0.000 0.000 0.000 0.524 NA
#> GSM674322     5  0.2527     0.6219 0.108 0.000 0.000 0.000 0.868 NA
#> GSM674326     5  0.1367     0.5431 0.012 0.000 0.000 0.000 0.944 NA
#> GSM674329     5  0.4354     0.6450 0.144 0.000 0.000 0.000 0.724 NA
#> GSM674333     5  0.3961     0.3436 0.440 0.000 0.000 0.000 0.556 NA

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-ATC-hclust-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-ATC-hclust-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-ATC-hclust-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-ATC-hclust-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-ATC-hclust-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-ATC-hclust-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-ATC-hclust-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-ATC-hclust-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-ATC-hclust-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-ATC-hclust-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-ATC-hclust-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-ATC-hclust-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-ATC-hclust-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-ATC-hclust-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-ATC-hclust-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-ATC-hclust-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-ATC-hclust-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-ATC-hclust-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-ATC-hclust-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-ATC-hclust-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk ATC-hclust-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-ATC-hclust-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-ATC-hclust-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-ATC-hclust-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-ATC-hclust-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-ATC-hclust-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk ATC-hclust-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>              n disease.state(p) specimen(p) k
#> ATC:hclust 183            0.924    1.83e-40 2
#> ATC:hclust 181            0.974    1.51e-73 3
#> ATC:hclust 172            0.359    6.39e-68 4
#> ATC:hclust 172            0.520    3.46e-66 5
#> ATC:hclust 164            0.413    7.79e-63 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


ATC:kmeans**

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["ATC", "kmeans"]
# you can also extract it by
# res = res_list["ATC:kmeans"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#>   Subgroups are detected by 'kmeans' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 2.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk ATC-kmeans-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk ATC-kmeans-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 0.709           0.980       0.902         0.4878 0.750   0.571
#> 4 4 0.819           0.851       0.826         0.1420 0.992   0.977
#> 5 5 0.798           0.740       0.732         0.0656 0.879   0.635
#> 6 6 0.747           0.786       0.782         0.0506 0.915   0.638

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 2

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette    p1    p2    p3
#> GSM674344     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674346     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674347     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674348     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674349     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674350     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674353     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674354     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674355     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674356     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674357     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674358     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674361     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674363     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674364     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674365     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674366     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674367     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674368     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674370     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674371     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674373     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674375     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674379     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674380     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674381     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674382     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674384     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674385     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674388     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674389     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674390     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674391     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674393     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674394     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674395     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674397     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674398     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674400     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674401     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674402     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674403     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674405     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674406     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674407     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674181     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674183     2  0.5178      0.946 0.000 0.744 0.256
#> GSM674184     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674185     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674186     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674187     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674190     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674191     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674192     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674193     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674194     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674195     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674198     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674200     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674201     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674202     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674203     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674204     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674205     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674206     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674208     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674209     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674210     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674212     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674214     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674218     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674219     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674220     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674221     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674223     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674225     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674226     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674229     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674230     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674231     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674232     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674234     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674235     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674236     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674237     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674239     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674240     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674242     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674243     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674244     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674245     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674282     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674284     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674285     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674287     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674288     1  0.4750      0.906 0.784 0.216 0.000
#> GSM674289     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674290     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674291     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674292     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674295     1  0.4750      0.906 0.784 0.216 0.000
#> GSM674297     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674298     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674299     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674300     1  0.2959      0.933 0.900 0.100 0.000
#> GSM674301     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674302     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674304     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674305     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674306     1  0.2448      0.938 0.924 0.076 0.000
#> GSM674308     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674309     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674313     1  0.4750      0.906 0.784 0.216 0.000
#> GSM674314     1  0.3752      0.924 0.856 0.144 0.000
#> GSM674315     1  0.2448      0.938 0.924 0.076 0.000
#> GSM674316     1  0.4750      0.906 0.784 0.216 0.000
#> GSM674318     1  0.4750      0.906 0.784 0.216 0.000
#> GSM674320     1  0.4750      0.906 0.784 0.216 0.000
#> GSM674323     1  0.4750      0.906 0.784 0.216 0.000
#> GSM674324     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674325     1  0.4750      0.906 0.784 0.216 0.000
#> GSM674327     1  0.4750      0.906 0.784 0.216 0.000
#> GSM674328     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674330     1  0.1031      0.946 0.976 0.024 0.000
#> GSM674331     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674332     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674334     1  0.0892      0.946 0.980 0.020 0.000
#> GSM674335     1  0.2537      0.937 0.920 0.080 0.000
#> GSM674345     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674351     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674352     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674359     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674360     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674362     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674369     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674372     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674374     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674376     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674377     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674378     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674383     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674386     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674387     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674392     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674396     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674399     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674404     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674182     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674188     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674189     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674196     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674197     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674199     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674207     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674211     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674213     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674215     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674216     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674217     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674222     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674224     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674227     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674228     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674233     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674238     3  0.0000      1.000 0.000 0.000 1.000
#> GSM674241     2  0.4750      0.999 0.000 0.784 0.216
#> GSM674283     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674286     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674293     1  0.1643      0.943 0.956 0.044 0.000
#> GSM674294     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674296     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674303     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674307     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674310     1  0.4750      0.906 0.784 0.216 0.000
#> GSM674311     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674312     1  0.4750      0.906 0.784 0.216 0.000
#> GSM674317     1  0.0000      0.948 1.000 0.000 0.000
#> GSM674319     1  0.4399      0.912 0.812 0.188 0.000
#> GSM674321     1  0.4750      0.906 0.784 0.216 0.000
#> GSM674322     1  0.4750      0.906 0.784 0.216 0.000
#> GSM674326     1  0.4750      0.906 0.784 0.216 0.000
#> GSM674329     1  0.4750      0.906 0.784 0.216 0.000
#> GSM674333     1  0.4750      0.906 0.784 0.216 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1    p2    p3 p4
#> GSM674344     3  0.5720      0.869 0.000 0.052 0.652 NA
#> GSM674346     3  0.5649      0.873 0.000 0.052 0.664 NA
#> GSM674347     3  0.5599      0.874 0.000 0.052 0.672 NA
#> GSM674348     3  0.5673      0.872 0.000 0.052 0.660 NA
#> GSM674349     3  0.5649      0.873 0.000 0.052 0.664 NA
#> GSM674350     3  0.5649      0.873 0.000 0.052 0.664 NA
#> GSM674353     3  0.5649      0.873 0.000 0.052 0.664 NA
#> GSM674354     3  0.5697      0.871 0.000 0.052 0.656 NA
#> GSM674355     3  0.5491      0.874 0.000 0.052 0.688 NA
#> GSM674356     3  0.5697      0.871 0.000 0.052 0.656 NA
#> GSM674357     3  0.5649      0.873 0.000 0.052 0.664 NA
#> GSM674358     3  0.5649      0.873 0.000 0.052 0.664 NA
#> GSM674361     3  0.5649      0.873 0.000 0.052 0.664 NA
#> GSM674363     3  0.5649      0.873 0.000 0.052 0.664 NA
#> GSM674364     3  0.5697      0.871 0.000 0.052 0.656 NA
#> GSM674365     3  0.5697      0.871 0.000 0.052 0.656 NA
#> GSM674366     3  0.5649      0.873 0.000 0.052 0.664 NA
#> GSM674367     3  0.1661      0.861 0.000 0.052 0.944 NA
#> GSM674368     3  0.5720      0.869 0.000 0.052 0.652 NA
#> GSM674370     3  0.5624      0.873 0.000 0.052 0.668 NA
#> GSM674371     3  0.5697      0.871 0.000 0.052 0.656 NA
#> GSM674373     3  0.1938      0.858 0.000 0.052 0.936 NA
#> GSM674375     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674379     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674380     3  0.1938      0.858 0.000 0.052 0.936 NA
#> GSM674381     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674382     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674384     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674385     3  0.1938      0.858 0.000 0.052 0.936 NA
#> GSM674388     3  0.5573      0.874 0.000 0.052 0.676 NA
#> GSM674389     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674390     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674391     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674393     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674394     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674395     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674397     3  0.1938      0.858 0.000 0.052 0.936 NA
#> GSM674398     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674400     3  0.5624      0.873 0.000 0.052 0.668 NA
#> GSM674401     3  0.5624      0.873 0.000 0.052 0.668 NA
#> GSM674402     3  0.5649      0.873 0.000 0.052 0.664 NA
#> GSM674403     3  0.5649      0.873 0.000 0.052 0.664 NA
#> GSM674405     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674406     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674407     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674181     2  0.2973      0.838 0.000 0.856 0.000 NA
#> GSM674183     2  0.5013      0.436 0.000 0.688 0.020 NA
#> GSM674184     2  0.0469      0.807 0.000 0.988 0.000 NA
#> GSM674185     2  0.0592      0.805 0.000 0.984 0.000 NA
#> GSM674186     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674187     2  0.4661      0.847 0.000 0.652 0.000 NA
#> GSM674190     2  0.4304      0.847 0.000 0.716 0.000 NA
#> GSM674191     2  0.3219      0.842 0.000 0.836 0.000 NA
#> GSM674192     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674193     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674194     2  0.0000      0.812 0.000 1.000 0.000 NA
#> GSM674195     2  0.1716      0.771 0.000 0.936 0.000 NA
#> GSM674198     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674200     3  0.5764      0.865 0.000 0.052 0.644 NA
#> GSM674201     2  0.0336      0.809 0.000 0.992 0.000 NA
#> GSM674202     2  0.0000      0.812 0.000 1.000 0.000 NA
#> GSM674203     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674204     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674205     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674206     2  0.0336      0.809 0.000 0.992 0.000 NA
#> GSM674208     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674209     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674210     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674212     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674214     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674218     2  0.0707      0.803 0.000 0.980 0.000 NA
#> GSM674219     2  0.0188      0.810 0.000 0.996 0.000 NA
#> GSM674220     2  0.0707      0.803 0.000 0.980 0.000 NA
#> GSM674221     2  0.3172      0.841 0.000 0.840 0.000 NA
#> GSM674223     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674225     2  0.0469      0.807 0.000 0.988 0.000 NA
#> GSM674226     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674229     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674230     2  0.0000      0.812 0.000 1.000 0.000 NA
#> GSM674231     2  0.0000      0.812 0.000 1.000 0.000 NA
#> GSM674232     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674234     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674235     2  0.0000      0.812 0.000 1.000 0.000 NA
#> GSM674236     2  0.0000      0.812 0.000 1.000 0.000 NA
#> GSM674237     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674239     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674240     2  0.3311      0.842 0.000 0.828 0.000 NA
#> GSM674242     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674243     2  0.3726      0.845 0.000 0.788 0.000 NA
#> GSM674244     2  0.0000      0.812 0.000 1.000 0.000 NA
#> GSM674245     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674282     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674284     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674285     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674287     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674288     1  0.4814      0.839 0.676 0.000 0.008 NA
#> GSM674289     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674290     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674291     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674292     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674295     1  0.5085      0.839 0.676 0.000 0.020 NA
#> GSM674297     1  0.0469      0.908 0.988 0.000 0.012 NA
#> GSM674298     1  0.0469      0.908 0.988 0.000 0.012 NA
#> GSM674299     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674300     1  0.3647      0.883 0.832 0.000 0.016 NA
#> GSM674301     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674302     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674304     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674305     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674306     1  0.3616      0.889 0.852 0.000 0.036 NA
#> GSM674308     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674309     1  0.0895      0.907 0.976 0.000 0.020 NA
#> GSM674313     1  0.5161      0.839 0.676 0.000 0.024 NA
#> GSM674314     1  0.4781      0.866 0.752 0.000 0.036 NA
#> GSM674315     1  0.3616      0.889 0.852 0.000 0.036 NA
#> GSM674316     1  0.4543      0.839 0.676 0.000 0.000 NA
#> GSM674318     1  0.4543      0.839 0.676 0.000 0.000 NA
#> GSM674320     1  0.5003      0.839 0.676 0.000 0.016 NA
#> GSM674323     1  0.4543      0.839 0.676 0.000 0.000 NA
#> GSM674324     1  0.0895      0.907 0.976 0.000 0.020 NA
#> GSM674325     1  0.4543      0.839 0.676 0.000 0.000 NA
#> GSM674327     1  0.5003      0.840 0.676 0.000 0.016 NA
#> GSM674328     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674330     1  0.1913      0.905 0.940 0.000 0.020 NA
#> GSM674331     1  0.0895      0.907 0.976 0.000 0.020 NA
#> GSM674332     1  0.0895      0.907 0.976 0.000 0.020 NA
#> GSM674334     1  0.1913      0.905 0.940 0.000 0.020 NA
#> GSM674335     1  0.3638      0.887 0.848 0.000 0.032 NA
#> GSM674345     3  0.5649      0.873 0.000 0.052 0.664 NA
#> GSM674351     3  0.5649      0.873 0.000 0.052 0.664 NA
#> GSM674352     3  0.5649      0.873 0.000 0.052 0.664 NA
#> GSM674359     3  0.5697      0.871 0.000 0.052 0.656 NA
#> GSM674360     3  0.5697      0.871 0.000 0.052 0.656 NA
#> GSM674362     3  0.5720      0.869 0.000 0.052 0.652 NA
#> GSM674369     3  0.5720      0.869 0.000 0.052 0.652 NA
#> GSM674372     3  0.1661      0.861 0.000 0.052 0.944 NA
#> GSM674374     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674376     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674377     3  0.1938      0.858 0.000 0.052 0.936 NA
#> GSM674378     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674383     3  0.5697      0.871 0.000 0.052 0.656 NA
#> GSM674386     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674387     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674392     3  0.2578      0.864 0.000 0.052 0.912 NA
#> GSM674396     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674399     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674404     3  0.1474      0.861 0.000 0.052 0.948 NA
#> GSM674182     2  0.3219      0.841 0.000 0.836 0.000 NA
#> GSM674188     2  0.3356      0.843 0.000 0.824 0.000 NA
#> GSM674189     2  0.0469      0.807 0.000 0.988 0.000 NA
#> GSM674196     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674197     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674199     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674207     2  0.4605      0.847 0.000 0.664 0.000 NA
#> GSM674211     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674213     2  0.3486      0.843 0.000 0.812 0.000 NA
#> GSM674215     2  0.0469      0.807 0.000 0.988 0.000 NA
#> GSM674216     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674217     2  0.0000      0.812 0.000 1.000 0.000 NA
#> GSM674222     2  0.0000      0.812 0.000 1.000 0.000 NA
#> GSM674224     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674227     2  0.0000      0.812 0.000 1.000 0.000 NA
#> GSM674228     2  0.0000      0.812 0.000 1.000 0.000 NA
#> GSM674233     2  0.0000      0.812 0.000 1.000 0.000 NA
#> GSM674238     2  0.7790     -0.357 0.000 0.424 0.272 NA
#> GSM674241     2  0.4761      0.846 0.000 0.628 0.000 NA
#> GSM674283     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674286     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674293     1  0.2222      0.900 0.924 0.000 0.016 NA
#> GSM674294     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674296     1  0.0469      0.908 0.988 0.000 0.012 NA
#> GSM674303     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674307     1  0.0469      0.908 0.988 0.000 0.012 NA
#> GSM674310     1  0.4543      0.839 0.676 0.000 0.000 NA
#> GSM674311     1  0.0895      0.907 0.976 0.000 0.020 NA
#> GSM674312     1  0.5003      0.839 0.676 0.000 0.016 NA
#> GSM674317     1  0.0000      0.909 1.000 0.000 0.000 NA
#> GSM674319     1  0.4857      0.846 0.700 0.000 0.016 NA
#> GSM674321     1  0.4543      0.839 0.676 0.000 0.000 NA
#> GSM674322     1  0.4699      0.839 0.676 0.000 0.004 NA
#> GSM674326     1  0.4543      0.839 0.676 0.000 0.000 NA
#> GSM674329     1  0.5003      0.839 0.676 0.000 0.016 NA
#> GSM674333     1  0.4699      0.839 0.676 0.000 0.004 NA

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4    p5
#> GSM674344     3  0.2104     0.7881 0.000 0.000 0.916 0.024 0.060
#> GSM674346     3  0.1124     0.8078 0.000 0.000 0.960 0.004 0.036
#> GSM674347     3  0.0671     0.8003 0.000 0.000 0.980 0.016 0.004
#> GSM674348     3  0.1670     0.8066 0.000 0.000 0.936 0.012 0.052
#> GSM674349     3  0.1282     0.8078 0.000 0.000 0.952 0.004 0.044
#> GSM674350     3  0.0000     0.8114 0.000 0.000 1.000 0.000 0.000
#> GSM674353     3  0.0000     0.8114 0.000 0.000 1.000 0.000 0.000
#> GSM674354     3  0.0992     0.8109 0.000 0.000 0.968 0.008 0.024
#> GSM674355     3  0.0566     0.8060 0.000 0.000 0.984 0.012 0.004
#> GSM674356     3  0.1331     0.8097 0.000 0.000 0.952 0.008 0.040
#> GSM674357     3  0.0000     0.8114 0.000 0.000 1.000 0.000 0.000
#> GSM674358     3  0.0000     0.8114 0.000 0.000 1.000 0.000 0.000
#> GSM674361     3  0.0162     0.8114 0.000 0.000 0.996 0.000 0.004
#> GSM674363     3  0.0000     0.8114 0.000 0.000 1.000 0.000 0.000
#> GSM674364     3  0.1168     0.8087 0.000 0.000 0.960 0.008 0.032
#> GSM674365     3  0.1484     0.8088 0.000 0.000 0.944 0.008 0.048
#> GSM674366     3  0.1626     0.8062 0.000 0.000 0.940 0.016 0.044
#> GSM674367     3  0.4826    -0.9121 0.000 0.000 0.508 0.472 0.020
#> GSM674368     3  0.1845     0.8012 0.000 0.000 0.928 0.016 0.056
#> GSM674370     3  0.1485     0.8054 0.000 0.000 0.948 0.020 0.032
#> GSM674371     3  0.1557     0.8061 0.000 0.000 0.940 0.008 0.052
#> GSM674373     4  0.4650     0.9569 0.000 0.000 0.468 0.520 0.012
#> GSM674375     4  0.4559     0.9600 0.000 0.000 0.480 0.512 0.008
#> GSM674379     4  0.4555     0.9593 0.000 0.000 0.472 0.520 0.008
#> GSM674380     4  0.5153     0.8816 0.000 0.000 0.436 0.524 0.040
#> GSM674381     4  0.5047     0.9488 0.000 0.000 0.472 0.496 0.032
#> GSM674382     4  0.4980     0.9517 0.000 0.000 0.484 0.488 0.028
#> GSM674384     3  0.4906    -0.9362 0.000 0.000 0.496 0.480 0.024
#> GSM674385     4  0.5047     0.9314 0.000 0.000 0.472 0.496 0.032
#> GSM674388     3  0.2491     0.7803 0.000 0.000 0.896 0.036 0.068
#> GSM674389     3  0.4656    -0.9308 0.000 0.000 0.508 0.480 0.012
#> GSM674390     4  0.4827     0.9536 0.000 0.000 0.476 0.504 0.020
#> GSM674391     4  0.4980     0.9517 0.000 0.000 0.484 0.488 0.028
#> GSM674393     3  0.4650    -0.9123 0.000 0.000 0.520 0.468 0.012
#> GSM674394     4  0.4659     0.9465 0.000 0.000 0.492 0.496 0.012
#> GSM674395     4  0.4659     0.9465 0.000 0.000 0.492 0.496 0.012
#> GSM674397     4  0.5048     0.9324 0.000 0.000 0.476 0.492 0.032
#> GSM674398     4  0.4448     0.9615 0.000 0.000 0.480 0.516 0.004
#> GSM674400     3  0.1357     0.7979 0.000 0.000 0.948 0.004 0.048
#> GSM674401     3  0.1357     0.7979 0.000 0.000 0.948 0.004 0.048
#> GSM674402     3  0.1124     0.8003 0.000 0.000 0.960 0.004 0.036
#> GSM674403     3  0.1502     0.8002 0.000 0.000 0.940 0.004 0.056
#> GSM674405     4  0.4559     0.9623 0.000 0.000 0.480 0.512 0.008
#> GSM674406     4  0.4744     0.9612 0.000 0.000 0.476 0.508 0.016
#> GSM674407     4  0.4448     0.9614 0.000 0.000 0.480 0.516 0.004
#> GSM674181     2  0.5423     0.3831 0.000 0.700 0.024 0.096 0.180
#> GSM674183     2  0.6153     0.4658 0.000 0.648 0.204 0.080 0.068
#> GSM674184     2  0.2264     0.7391 0.000 0.912 0.024 0.060 0.004
#> GSM674185     2  0.2321     0.7384 0.000 0.912 0.024 0.056 0.008
#> GSM674186     5  0.5504     0.9289 0.000 0.400 0.024 0.028 0.548
#> GSM674187     2  0.6048    -0.7613 0.000 0.468 0.024 0.060 0.448
#> GSM674190     2  0.5194    -0.5518 0.000 0.552 0.024 0.012 0.412
#> GSM674191     2  0.4572     0.2351 0.000 0.708 0.024 0.012 0.256
#> GSM674192     5  0.4734     0.9528 0.000 0.372 0.024 0.000 0.604
#> GSM674193     5  0.5186     0.9309 0.000 0.408 0.024 0.012 0.556
#> GSM674194     2  0.1393     0.7423 0.000 0.956 0.024 0.012 0.008
#> GSM674195     2  0.4019     0.6577 0.000 0.828 0.064 0.060 0.048
#> GSM674198     5  0.5361     0.9490 0.000 0.372 0.024 0.024 0.580
#> GSM674200     3  0.3019     0.7175 0.000 0.016 0.880 0.048 0.056
#> GSM674201     2  0.2396     0.7411 0.000 0.904 0.024 0.068 0.004
#> GSM674202     2  0.1901     0.7462 0.000 0.932 0.024 0.040 0.004
#> GSM674203     5  0.4734     0.9528 0.000 0.372 0.024 0.000 0.604
#> GSM674204     5  0.5512     0.9443 0.000 0.372 0.024 0.032 0.572
#> GSM674205     5  0.5193     0.9515 0.000 0.372 0.024 0.016 0.588
#> GSM674206     2  0.1564     0.7465 0.000 0.948 0.024 0.024 0.004
#> GSM674208     5  0.4746     0.9510 0.000 0.376 0.024 0.000 0.600
#> GSM674209     5  0.5253     0.9378 0.000 0.396 0.024 0.016 0.564
#> GSM674210     5  0.4734     0.9528 0.000 0.372 0.024 0.000 0.604
#> GSM674212     5  0.5948     0.9262 0.000 0.372 0.024 0.060 0.544
#> GSM674214     5  0.5948     0.9262 0.000 0.372 0.024 0.060 0.544
#> GSM674218     2  0.2537     0.7337 0.000 0.904 0.024 0.056 0.016
#> GSM674219     2  0.1579     0.7405 0.000 0.944 0.024 0.032 0.000
#> GSM674220     2  0.3497     0.7072 0.000 0.852 0.024 0.084 0.040
#> GSM674221     2  0.5410     0.2976 0.000 0.692 0.024 0.080 0.204
#> GSM674223     5  0.5253     0.9378 0.000 0.396 0.024 0.016 0.564
#> GSM674225     2  0.2703     0.7312 0.000 0.896 0.024 0.060 0.020
#> GSM674226     5  0.5170     0.9388 0.000 0.400 0.024 0.012 0.564
#> GSM674229     5  0.4734     0.9528 0.000 0.372 0.024 0.000 0.604
#> GSM674230     2  0.1710     0.7413 0.000 0.944 0.024 0.020 0.012
#> GSM674231     2  0.1153     0.7451 0.000 0.964 0.024 0.008 0.004
#> GSM674232     5  0.5253     0.9212 0.000 0.396 0.024 0.016 0.564
#> GSM674234     5  0.4734     0.9528 0.000 0.372 0.024 0.000 0.604
#> GSM674235     2  0.1653     0.7451 0.000 0.944 0.024 0.028 0.004
#> GSM674236     2  0.1653     0.7451 0.000 0.944 0.024 0.028 0.004
#> GSM674237     5  0.4746     0.9510 0.000 0.376 0.024 0.000 0.600
#> GSM674239     5  0.4734     0.9528 0.000 0.372 0.024 0.000 0.604
#> GSM674240     2  0.5710     0.1542 0.000 0.652 0.024 0.084 0.240
#> GSM674242     5  0.4746     0.9510 0.000 0.376 0.024 0.000 0.600
#> GSM674243     2  0.5355    -0.0958 0.000 0.632 0.024 0.036 0.308
#> GSM674244     2  0.1901     0.7418 0.000 0.932 0.024 0.040 0.004
#> GSM674245     5  0.5170     0.9388 0.000 0.400 0.024 0.012 0.564
#> GSM674282     1  0.0451     0.8656 0.988 0.008 0.000 0.000 0.004
#> GSM674284     1  0.0290     0.8658 0.992 0.000 0.000 0.000 0.008
#> GSM674285     1  0.0324     0.8653 0.992 0.004 0.000 0.000 0.004
#> GSM674287     1  0.0451     0.8656 0.988 0.008 0.000 0.000 0.004
#> GSM674288     1  0.6284     0.7654 0.576 0.012 0.000 0.252 0.160
#> GSM674289     1  0.0451     0.8656 0.988 0.008 0.000 0.000 0.004
#> GSM674290     1  0.0324     0.8653 0.992 0.004 0.000 0.000 0.004
#> GSM674291     1  0.0579     0.8656 0.984 0.008 0.000 0.000 0.008
#> GSM674292     1  0.0451     0.8656 0.988 0.008 0.000 0.000 0.004
#> GSM674295     1  0.6295     0.7645 0.576 0.012 0.000 0.248 0.164
#> GSM674297     1  0.1043     0.8638 0.960 0.000 0.000 0.000 0.040
#> GSM674298     1  0.1043     0.8638 0.960 0.000 0.000 0.000 0.040
#> GSM674299     1  0.0693     0.8659 0.980 0.008 0.000 0.000 0.012
#> GSM674300     1  0.4777     0.8256 0.748 0.008 0.000 0.116 0.128
#> GSM674301     1  0.0162     0.8653 0.996 0.004 0.000 0.000 0.000
#> GSM674302     1  0.0162     0.8653 0.996 0.004 0.000 0.000 0.000
#> GSM674304     1  0.0162     0.8653 0.996 0.004 0.000 0.000 0.000
#> GSM674305     1  0.0162     0.8653 0.996 0.004 0.000 0.000 0.000
#> GSM674306     1  0.4415     0.8342 0.768 0.008 0.000 0.064 0.160
#> GSM674308     1  0.0162     0.8653 0.996 0.004 0.000 0.000 0.000
#> GSM674309     1  0.1798     0.8608 0.928 0.004 0.000 0.004 0.064
#> GSM674313     1  0.6179     0.7623 0.572 0.004 0.000 0.244 0.180
#> GSM674314     1  0.5142     0.8181 0.704 0.008 0.000 0.096 0.192
#> GSM674315     1  0.4415     0.8342 0.768 0.008 0.000 0.064 0.160
#> GSM674316     1  0.5923     0.7631 0.572 0.000 0.000 0.288 0.140
#> GSM674318     1  0.5843     0.7604 0.572 0.000 0.000 0.304 0.124
#> GSM674320     1  0.6087     0.7602 0.572 0.004 0.000 0.276 0.148
#> GSM674323     1  0.5843     0.7604 0.572 0.000 0.000 0.304 0.124
#> GSM674324     1  0.1478     0.8613 0.936 0.000 0.000 0.000 0.064
#> GSM674325     1  0.5940     0.7629 0.572 0.000 0.000 0.284 0.144
#> GSM674327     1  0.6152     0.7629 0.572 0.004 0.000 0.256 0.168
#> GSM674328     1  0.0579     0.8659 0.984 0.008 0.000 0.000 0.008
#> GSM674330     1  0.2130     0.8604 0.908 0.000 0.000 0.012 0.080
#> GSM674331     1  0.1704     0.8608 0.928 0.000 0.000 0.004 0.068
#> GSM674332     1  0.1608     0.8609 0.928 0.000 0.000 0.000 0.072
#> GSM674334     1  0.2130     0.8604 0.908 0.000 0.000 0.012 0.080
#> GSM674335     1  0.3981     0.8441 0.800 0.004 0.000 0.060 0.136
#> GSM674345     3  0.1124     0.8078 0.000 0.000 0.960 0.004 0.036
#> GSM674351     3  0.0000     0.8114 0.000 0.000 1.000 0.000 0.000
#> GSM674352     3  0.0000     0.8114 0.000 0.000 1.000 0.000 0.000
#> GSM674359     3  0.1628     0.8056 0.000 0.000 0.936 0.008 0.056
#> GSM674360     3  0.1082     0.8099 0.000 0.000 0.964 0.008 0.028
#> GSM674362     3  0.1281     0.8071 0.000 0.000 0.956 0.012 0.032
#> GSM674369     3  0.1557     0.8061 0.000 0.000 0.940 0.008 0.052
#> GSM674372     3  0.4637    -0.8791 0.000 0.000 0.536 0.452 0.012
#> GSM674374     4  0.4653     0.9582 0.000 0.000 0.472 0.516 0.012
#> GSM674376     4  0.4448     0.9614 0.000 0.000 0.480 0.516 0.004
#> GSM674377     4  0.5168     0.9128 0.000 0.000 0.452 0.508 0.040
#> GSM674378     4  0.4656     0.9596 0.000 0.000 0.480 0.508 0.012
#> GSM674383     3  0.1331     0.8079 0.000 0.000 0.952 0.008 0.040
#> GSM674386     4  0.4978     0.9480 0.000 0.000 0.476 0.496 0.028
#> GSM674387     4  0.4559     0.9600 0.000 0.000 0.480 0.512 0.008
#> GSM674392     3  0.4446    -0.7369 0.000 0.000 0.592 0.400 0.008
#> GSM674396     4  0.4448     0.9615 0.000 0.000 0.480 0.516 0.004
#> GSM674399     4  0.4559     0.9623 0.000 0.000 0.480 0.512 0.008
#> GSM674404     4  0.4449     0.9610 0.000 0.000 0.484 0.512 0.004
#> GSM674182     2  0.5550     0.2592 0.000 0.676 0.024 0.084 0.216
#> GSM674188     2  0.5291     0.2068 0.000 0.684 0.024 0.056 0.236
#> GSM674189     2  0.2053     0.7422 0.000 0.924 0.024 0.048 0.004
#> GSM674196     5  0.5512     0.9443 0.000 0.372 0.024 0.032 0.572
#> GSM674197     5  0.5361     0.9490 0.000 0.372 0.024 0.024 0.580
#> GSM674199     5  0.5361     0.9490 0.000 0.372 0.024 0.024 0.580
#> GSM674207     5  0.6268     0.8224 0.000 0.416 0.024 0.080 0.480
#> GSM674211     5  0.5948     0.9262 0.000 0.372 0.024 0.060 0.544
#> GSM674213     2  0.5754     0.0709 0.000 0.640 0.024 0.080 0.256
#> GSM674215     2  0.2522     0.7388 0.000 0.896 0.024 0.076 0.004
#> GSM674216     5  0.5339     0.9162 0.000 0.396 0.024 0.020 0.560
#> GSM674217     2  0.2766     0.7031 0.000 0.884 0.024 0.084 0.008
#> GSM674222     2  0.2467     0.7395 0.000 0.908 0.024 0.052 0.016
#> GSM674224     5  0.5262     0.9370 0.000 0.400 0.024 0.016 0.560
#> GSM674227     2  0.1739     0.7452 0.000 0.940 0.024 0.032 0.004
#> GSM674228     2  0.1739     0.7385 0.000 0.940 0.024 0.032 0.004
#> GSM674233     2  0.1780     0.7365 0.000 0.940 0.024 0.028 0.008
#> GSM674238     2  0.6385     0.1895 0.000 0.528 0.360 0.060 0.052
#> GSM674241     5  0.4734     0.9528 0.000 0.372 0.024 0.000 0.604
#> GSM674283     1  0.0324     0.8653 0.992 0.004 0.000 0.000 0.004
#> GSM674286     1  0.0324     0.8653 0.992 0.004 0.000 0.000 0.004
#> GSM674293     1  0.3018     0.8516 0.872 0.008 0.000 0.036 0.084
#> GSM674294     1  0.0579     0.8656 0.984 0.008 0.000 0.000 0.008
#> GSM674296     1  0.0771     0.8650 0.976 0.004 0.000 0.000 0.020
#> GSM674303     1  0.0324     0.8656 0.992 0.004 0.000 0.000 0.004
#> GSM674307     1  0.0771     0.8650 0.976 0.004 0.000 0.000 0.020
#> GSM674310     1  0.5843     0.7604 0.572 0.000 0.000 0.304 0.124
#> GSM674311     1  0.1798     0.8608 0.928 0.004 0.000 0.004 0.064
#> GSM674312     1  0.6087     0.7602 0.572 0.004 0.000 0.276 0.148
#> GSM674317     1  0.0693     0.8659 0.980 0.008 0.000 0.000 0.012
#> GSM674319     1  0.6023     0.7798 0.616 0.012 0.000 0.224 0.148
#> GSM674321     1  0.5864     0.7606 0.572 0.000 0.000 0.300 0.128
#> GSM674322     1  0.5843     0.7604 0.572 0.000 0.000 0.304 0.124
#> GSM674326     1  0.5843     0.7604 0.572 0.000 0.000 0.304 0.124
#> GSM674329     1  0.6071     0.7603 0.572 0.004 0.000 0.280 0.144
#> GSM674333     1  0.5885     0.7604 0.572 0.000 0.000 0.296 0.132

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4    p5    p6
#> GSM674344     3  0.2577     0.8985 0.000 0.000 0.888 0.016 0.056 0.040
#> GSM674346     3  0.2209     0.9118 0.000 0.000 0.900 0.004 0.072 0.024
#> GSM674347     3  0.1173     0.9171 0.000 0.000 0.960 0.016 0.016 0.008
#> GSM674348     3  0.2265     0.9117 0.000 0.000 0.896 0.004 0.076 0.024
#> GSM674349     3  0.2039     0.9145 0.000 0.000 0.908 0.004 0.072 0.016
#> GSM674350     3  0.0767     0.9196 0.000 0.000 0.976 0.004 0.012 0.008
#> GSM674353     3  0.0767     0.9196 0.000 0.000 0.976 0.004 0.012 0.008
#> GSM674354     3  0.1092     0.9215 0.000 0.000 0.960 0.000 0.020 0.020
#> GSM674355     3  0.1409     0.9080 0.000 0.000 0.948 0.032 0.012 0.008
#> GSM674356     3  0.1257     0.9215 0.000 0.000 0.952 0.000 0.028 0.020
#> GSM674357     3  0.0870     0.9207 0.000 0.000 0.972 0.004 0.012 0.012
#> GSM674358     3  0.0862     0.9191 0.000 0.000 0.972 0.004 0.016 0.008
#> GSM674361     3  0.1053     0.9194 0.000 0.000 0.964 0.004 0.020 0.012
#> GSM674363     3  0.0622     0.9203 0.000 0.000 0.980 0.000 0.012 0.008
#> GSM674364     3  0.1401     0.9168 0.000 0.000 0.948 0.004 0.020 0.028
#> GSM674365     3  0.2006     0.9160 0.000 0.000 0.904 0.000 0.080 0.016
#> GSM674366     3  0.2103     0.9121 0.000 0.000 0.912 0.012 0.056 0.020
#> GSM674367     4  0.4873     0.8325 0.000 0.000 0.376 0.572 0.036 0.016
#> GSM674368     3  0.2263     0.9086 0.000 0.000 0.900 0.004 0.060 0.036
#> GSM674370     3  0.2039     0.9149 0.000 0.000 0.916 0.020 0.052 0.012
#> GSM674371     3  0.1789     0.9150 0.000 0.000 0.924 0.000 0.044 0.032
#> GSM674373     4  0.4626     0.9260 0.000 0.000 0.292 0.652 0.044 0.012
#> GSM674375     4  0.4225     0.9394 0.000 0.000 0.276 0.688 0.016 0.020
#> GSM674379     4  0.3855     0.9397 0.000 0.000 0.276 0.704 0.016 0.004
#> GSM674380     4  0.4884     0.8830 0.000 0.000 0.244 0.672 0.052 0.032
#> GSM674381     4  0.4416     0.9299 0.000 0.000 0.288 0.668 0.032 0.012
#> GSM674382     4  0.4225     0.9371 0.000 0.000 0.276 0.688 0.020 0.016
#> GSM674384     4  0.4530     0.9289 0.000 0.000 0.308 0.648 0.020 0.024
#> GSM674385     4  0.4453     0.9259 0.000 0.000 0.296 0.660 0.012 0.032
#> GSM674388     3  0.3815     0.8423 0.000 0.000 0.808 0.056 0.100 0.036
#> GSM674389     4  0.4254     0.9191 0.000 0.000 0.312 0.656 0.004 0.028
#> GSM674390     4  0.4245     0.9357 0.000 0.000 0.280 0.684 0.020 0.016
#> GSM674391     4  0.4138     0.9376 0.000 0.000 0.276 0.692 0.020 0.012
#> GSM674393     4  0.4302     0.8952 0.000 0.000 0.344 0.628 0.004 0.024
#> GSM674394     4  0.4130     0.9291 0.000 0.000 0.300 0.672 0.004 0.024
#> GSM674395     4  0.4165     0.9246 0.000 0.000 0.308 0.664 0.004 0.024
#> GSM674397     4  0.4693     0.9121 0.000 0.000 0.312 0.636 0.028 0.024
#> GSM674398     4  0.3961     0.9390 0.000 0.000 0.276 0.700 0.008 0.016
#> GSM674400     3  0.3438     0.8468 0.000 0.000 0.820 0.012 0.120 0.048
#> GSM674401     3  0.3438     0.8468 0.000 0.000 0.820 0.012 0.120 0.048
#> GSM674402     3  0.3296     0.8497 0.000 0.000 0.828 0.008 0.116 0.048
#> GSM674403     3  0.3587     0.8486 0.000 0.000 0.804 0.008 0.132 0.056
#> GSM674405     4  0.3874     0.9393 0.000 0.000 0.276 0.704 0.008 0.012
#> GSM674406     4  0.4097     0.9374 0.000 0.000 0.284 0.688 0.016 0.012
#> GSM674407     4  0.3961     0.9393 0.000 0.000 0.276 0.700 0.016 0.008
#> GSM674181     6  0.6420     0.3582 0.000 0.412 0.004 0.060 0.100 0.424
#> GSM674183     6  0.6735     0.5582 0.000 0.060 0.164 0.084 0.096 0.596
#> GSM674184     6  0.5396     0.8124 0.000 0.248 0.004 0.064 0.044 0.640
#> GSM674185     6  0.5353     0.8088 0.000 0.240 0.004 0.064 0.044 0.648
#> GSM674186     2  0.2971     0.7910 0.000 0.868 0.004 0.020 0.072 0.036
#> GSM674187     2  0.4835     0.6356 0.000 0.724 0.004 0.032 0.088 0.152
#> GSM674190     2  0.4910     0.3668 0.000 0.640 0.004 0.008 0.064 0.284
#> GSM674191     2  0.5256    -0.1084 0.000 0.524 0.004 0.008 0.064 0.400
#> GSM674192     2  0.0146     0.8192 0.000 0.996 0.004 0.000 0.000 0.000
#> GSM674193     2  0.2599     0.7919 0.000 0.888 0.004 0.008 0.052 0.048
#> GSM674194     6  0.4521     0.8112 0.000 0.256 0.004 0.012 0.040 0.688
#> GSM674195     6  0.5773     0.7481 0.000 0.176 0.044 0.064 0.048 0.668
#> GSM674198     2  0.0964     0.8183 0.000 0.968 0.004 0.012 0.016 0.000
#> GSM674200     3  0.4185     0.7929 0.000 0.000 0.780 0.060 0.116 0.044
#> GSM674201     6  0.5257     0.8204 0.000 0.248 0.004 0.068 0.032 0.648
#> GSM674202     6  0.4310     0.8319 0.000 0.252 0.004 0.024 0.016 0.704
#> GSM674203     2  0.0405     0.8189 0.000 0.988 0.004 0.000 0.008 0.000
#> GSM674204     2  0.1053     0.8176 0.000 0.964 0.004 0.012 0.020 0.000
#> GSM674205     2  0.0964     0.8183 0.000 0.968 0.004 0.012 0.016 0.000
#> GSM674206     6  0.3633     0.8300 0.000 0.252 0.004 0.012 0.000 0.732
#> GSM674208     2  0.0146     0.8192 0.000 0.996 0.004 0.000 0.000 0.000
#> GSM674209     2  0.2408     0.7994 0.000 0.896 0.004 0.008 0.068 0.024
#> GSM674210     2  0.0653     0.8188 0.000 0.980 0.004 0.004 0.012 0.000
#> GSM674212     2  0.2113     0.8091 0.000 0.908 0.004 0.028 0.060 0.000
#> GSM674214     2  0.2052     0.8098 0.000 0.912 0.004 0.028 0.056 0.000
#> GSM674218     6  0.5200     0.8071 0.000 0.232 0.004 0.056 0.044 0.664
#> GSM674219     6  0.5007     0.8025 0.000 0.252 0.004 0.032 0.048 0.664
#> GSM674220     6  0.5701     0.7883 0.000 0.212 0.004 0.088 0.060 0.636
#> GSM674221     6  0.6140     0.4213 0.000 0.396 0.004 0.052 0.080 0.468
#> GSM674223     2  0.2369     0.8007 0.000 0.900 0.004 0.008 0.060 0.028
#> GSM674225     6  0.5779     0.8069 0.000 0.252 0.004 0.056 0.080 0.608
#> GSM674226     2  0.2753     0.7930 0.000 0.876 0.004 0.012 0.080 0.028
#> GSM674229     2  0.0436     0.8190 0.000 0.988 0.004 0.004 0.004 0.000
#> GSM674230     6  0.5287     0.8040 0.000 0.272 0.004 0.024 0.072 0.628
#> GSM674231     6  0.4231     0.8238 0.000 0.264 0.004 0.004 0.032 0.696
#> GSM674232     2  0.2484     0.7722 0.000 0.896 0.004 0.012 0.032 0.056
#> GSM674234     2  0.0291     0.8198 0.000 0.992 0.004 0.004 0.000 0.000
#> GSM674235     6  0.4406     0.8288 0.000 0.256 0.004 0.016 0.028 0.696
#> GSM674236     6  0.4689     0.8246 0.000 0.256 0.004 0.020 0.040 0.680
#> GSM674237     2  0.0146     0.8192 0.000 0.996 0.004 0.000 0.000 0.000
#> GSM674239     2  0.0146     0.8192 0.000 0.996 0.004 0.000 0.000 0.000
#> GSM674240     2  0.6311    -0.2219 0.000 0.460 0.004 0.052 0.100 0.384
#> GSM674242     2  0.0653     0.8188 0.000 0.980 0.004 0.004 0.012 0.000
#> GSM674243     2  0.5402     0.1348 0.000 0.588 0.004 0.028 0.060 0.320
#> GSM674244     6  0.5936     0.7995 0.000 0.256 0.004 0.040 0.116 0.584
#> GSM674245     2  0.2358     0.8026 0.000 0.896 0.004 0.012 0.076 0.012
#> GSM674282     1  0.0291     0.8462 0.992 0.000 0.000 0.004 0.000 0.004
#> GSM674284     1  0.0000     0.8477 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674285     1  0.0000     0.8477 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674287     1  0.0291     0.8462 0.992 0.000 0.000 0.004 0.000 0.004
#> GSM674288     5  0.5306     0.9362 0.428 0.000 0.000 0.056 0.496 0.020
#> GSM674289     1  0.0291     0.8462 0.992 0.000 0.000 0.004 0.000 0.004
#> GSM674290     1  0.0000     0.8477 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674291     1  0.0291     0.8462 0.992 0.000 0.000 0.004 0.000 0.004
#> GSM674292     1  0.0291     0.8462 0.992 0.000 0.000 0.004 0.000 0.004
#> GSM674295     5  0.5444     0.9277 0.428 0.000 0.000 0.068 0.484 0.020
#> GSM674297     1  0.1245     0.8303 0.952 0.000 0.000 0.016 0.000 0.032
#> GSM674298     1  0.1245     0.8303 0.952 0.000 0.000 0.016 0.000 0.032
#> GSM674299     1  0.0520     0.8443 0.984 0.000 0.000 0.008 0.000 0.008
#> GSM674300     1  0.4733    -0.0263 0.668 0.000 0.000 0.024 0.264 0.044
#> GSM674301     1  0.0000     0.8477 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674302     1  0.0000     0.8477 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0146     0.8474 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM674305     1  0.0000     0.8477 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674306     1  0.5409     0.2804 0.668 0.000 0.000 0.056 0.172 0.104
#> GSM674308     1  0.0000     0.8477 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674309     1  0.2658     0.7758 0.876 0.000 0.000 0.036 0.008 0.080
#> GSM674313     5  0.5330     0.9363 0.428 0.004 0.000 0.060 0.496 0.012
#> GSM674314     1  0.5989    -0.2641 0.568 0.000 0.000 0.048 0.264 0.120
#> GSM674315     1  0.5409     0.2804 0.668 0.000 0.000 0.056 0.172 0.104
#> GSM674316     5  0.4566     0.9456 0.428 0.000 0.000 0.004 0.540 0.028
#> GSM674318     5  0.3944     0.9544 0.428 0.000 0.000 0.004 0.568 0.000
#> GSM674320     5  0.5194     0.9392 0.428 0.004 0.000 0.056 0.504 0.008
#> GSM674323     5  0.4045     0.9535 0.428 0.000 0.000 0.000 0.564 0.008
#> GSM674324     1  0.2476     0.7847 0.888 0.000 0.000 0.032 0.008 0.072
#> GSM674325     5  0.4631     0.9459 0.428 0.000 0.000 0.004 0.536 0.032
#> GSM674327     5  0.4976     0.9281 0.428 0.000 0.000 0.020 0.520 0.032
#> GSM674328     1  0.0405     0.8470 0.988 0.000 0.000 0.004 0.000 0.008
#> GSM674330     1  0.3649     0.7005 0.820 0.000 0.000 0.032 0.056 0.092
#> GSM674331     1  0.2476     0.7847 0.888 0.000 0.000 0.032 0.008 0.072
#> GSM674332     1  0.2639     0.7759 0.876 0.000 0.000 0.032 0.008 0.084
#> GSM674334     1  0.3360     0.7292 0.840 0.000 0.000 0.032 0.044 0.084
#> GSM674335     1  0.5301     0.2569 0.680 0.000 0.000 0.068 0.172 0.080
#> GSM674345     3  0.2126     0.9120 0.000 0.000 0.904 0.004 0.072 0.020
#> GSM674351     3  0.0767     0.9196 0.000 0.000 0.976 0.004 0.012 0.008
#> GSM674352     3  0.0767     0.9196 0.000 0.000 0.976 0.004 0.012 0.008
#> GSM674359     3  0.2122     0.9112 0.000 0.000 0.900 0.000 0.076 0.024
#> GSM674360     3  0.1257     0.9186 0.000 0.000 0.952 0.000 0.020 0.028
#> GSM674362     3  0.1675     0.9119 0.000 0.000 0.936 0.008 0.024 0.032
#> GSM674369     3  0.1863     0.9143 0.000 0.000 0.920 0.000 0.044 0.036
#> GSM674372     4  0.4570     0.8434 0.000 0.000 0.376 0.588 0.008 0.028
#> GSM674374     4  0.4608     0.9273 0.000 0.000 0.288 0.656 0.044 0.012
#> GSM674376     4  0.3672     0.9398 0.000 0.000 0.276 0.712 0.008 0.004
#> GSM674377     4  0.4691     0.9057 0.000 0.000 0.256 0.676 0.044 0.024
#> GSM674378     4  0.4263     0.9374 0.000 0.000 0.276 0.684 0.032 0.008
#> GSM674383     3  0.1418     0.9171 0.000 0.000 0.944 0.000 0.032 0.024
#> GSM674386     4  0.4225     0.9371 0.000 0.000 0.276 0.688 0.020 0.016
#> GSM674387     4  0.4143     0.9396 0.000 0.000 0.276 0.692 0.016 0.016
#> GSM674392     4  0.4493     0.6428 0.000 0.000 0.484 0.492 0.008 0.016
#> GSM674396     4  0.3961     0.9390 0.000 0.000 0.276 0.700 0.008 0.016
#> GSM674399     4  0.3874     0.9393 0.000 0.000 0.276 0.704 0.008 0.012
#> GSM674404     4  0.3767     0.9393 0.000 0.000 0.276 0.708 0.004 0.012
#> GSM674182     2  0.6311    -0.2219 0.000 0.460 0.004 0.052 0.100 0.384
#> GSM674188     2  0.5794    -0.2827 0.000 0.456 0.004 0.028 0.076 0.436
#> GSM674189     6  0.4844     0.8233 0.000 0.244 0.004 0.036 0.036 0.680
#> GSM674196     2  0.1053     0.8176 0.000 0.964 0.004 0.012 0.020 0.000
#> GSM674197     2  0.0964     0.8183 0.000 0.968 0.004 0.012 0.016 0.000
#> GSM674199     2  0.0964     0.8183 0.000 0.968 0.004 0.012 0.016 0.000
#> GSM674207     2  0.4804     0.6442 0.000 0.740 0.004 0.048 0.096 0.112
#> GSM674211     2  0.2113     0.8091 0.000 0.908 0.004 0.028 0.060 0.000
#> GSM674213     2  0.6237    -0.1315 0.000 0.480 0.004 0.056 0.088 0.372
#> GSM674215     6  0.5866     0.8122 0.000 0.248 0.004 0.068 0.076 0.604
#> GSM674216     2  0.2807     0.7624 0.000 0.880 0.004 0.020 0.040 0.056
#> GSM674217     6  0.5669     0.7617 0.000 0.252 0.004 0.048 0.080 0.616
#> GSM674222     6  0.5271     0.8180 0.000 0.256 0.004 0.040 0.056 0.644
#> GSM674224     2  0.2753     0.7930 0.000 0.876 0.004 0.012 0.080 0.028
#> GSM674227     6  0.4667     0.8224 0.000 0.264 0.004 0.020 0.036 0.676
#> GSM674228     6  0.5095     0.8059 0.000 0.256 0.004 0.036 0.048 0.656
#> GSM674233     6  0.5014     0.7976 0.000 0.252 0.004 0.036 0.044 0.664
#> GSM674238     6  0.5511     0.4255 0.000 0.000 0.264 0.064 0.056 0.616
#> GSM674241     2  0.0291     0.8196 0.000 0.992 0.004 0.000 0.004 0.000
#> GSM674283     1  0.0000     0.8477 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674286     1  0.0000     0.8477 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674293     1  0.2955     0.6697 0.860 0.000 0.000 0.016 0.088 0.036
#> GSM674294     1  0.0291     0.8462 0.992 0.000 0.000 0.004 0.000 0.004
#> GSM674296     1  0.0993     0.8362 0.964 0.000 0.000 0.012 0.000 0.024
#> GSM674303     1  0.0146     0.8474 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM674307     1  0.0993     0.8362 0.964 0.000 0.000 0.012 0.000 0.024
#> GSM674310     5  0.3944     0.9544 0.428 0.000 0.000 0.004 0.568 0.000
#> GSM674311     1  0.2658     0.7758 0.876 0.000 0.000 0.036 0.008 0.080
#> GSM674312     5  0.5194     0.9392 0.428 0.004 0.000 0.056 0.504 0.008
#> GSM674317     1  0.0520     0.8443 0.984 0.000 0.000 0.008 0.000 0.008
#> GSM674319     1  0.5379    -0.8554 0.472 0.000 0.000 0.068 0.444 0.016
#> GSM674321     5  0.4136     0.9539 0.428 0.000 0.000 0.000 0.560 0.012
#> GSM674322     5  0.4045     0.9545 0.428 0.000 0.000 0.008 0.564 0.000
#> GSM674326     5  0.3944     0.9544 0.428 0.000 0.000 0.004 0.568 0.000
#> GSM674329     5  0.5312     0.9407 0.428 0.004 0.000 0.052 0.500 0.016
#> GSM674333     5  0.4370     0.9552 0.428 0.000 0.000 0.012 0.552 0.008

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-ATC-kmeans-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-ATC-kmeans-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-ATC-kmeans-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-ATC-kmeans-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-ATC-kmeans-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-ATC-kmeans-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-ATC-kmeans-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-ATC-kmeans-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-ATC-kmeans-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-ATC-kmeans-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-ATC-kmeans-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-ATC-kmeans-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-ATC-kmeans-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-ATC-kmeans-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-ATC-kmeans-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-ATC-kmeans-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-ATC-kmeans-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-ATC-kmeans-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-ATC-kmeans-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-ATC-kmeans-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk ATC-kmeans-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-ATC-kmeans-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-ATC-kmeans-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-ATC-kmeans-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-ATC-kmeans-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-ATC-kmeans-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk ATC-kmeans-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>              n disease.state(p) specimen(p) k
#> ATC:kmeans 183            0.924    1.83e-40 2
#> ATC:kmeans 183            0.942    1.46e-75 3
#> ATC:kmeans 181            0.951    7.33e-76 4
#> ATC:kmeans 165            0.871    2.86e-65 5
#> ATC:kmeans 167            0.733    1.43e-64 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


ATC:skmeans*

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["ATC", "skmeans"]
# you can also extract it by
# res = res_list["ATC:skmeans"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#>   Subgroups are detected by 'skmeans' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 5.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk ATC-skmeans-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk ATC-skmeans-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 1.000           0.996       0.998         0.5956 0.750   0.571
#> 4 4 1.000           0.992       0.994         0.0961 0.935   0.804
#> 5 5 0.921           0.823       0.903         0.0343 0.985   0.944
#> 6 6 0.847           0.856       0.907         0.0346 0.954   0.826

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3 4

There is also optional best \(k\) = 2 3 4 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette p1    p2    p3
#> GSM674344     3   0.000      0.995  0 0.000 1.000
#> GSM674346     3   0.000      0.995  0 0.000 1.000
#> GSM674347     3   0.000      0.995  0 0.000 1.000
#> GSM674348     3   0.000      0.995  0 0.000 1.000
#> GSM674349     3   0.000      0.995  0 0.000 1.000
#> GSM674350     3   0.000      0.995  0 0.000 1.000
#> GSM674353     3   0.000      0.995  0 0.000 1.000
#> GSM674354     3   0.000      0.995  0 0.000 1.000
#> GSM674355     3   0.000      0.995  0 0.000 1.000
#> GSM674356     3   0.000      0.995  0 0.000 1.000
#> GSM674357     3   0.000      0.995  0 0.000 1.000
#> GSM674358     3   0.000      0.995  0 0.000 1.000
#> GSM674361     3   0.000      0.995  0 0.000 1.000
#> GSM674363     3   0.000      0.995  0 0.000 1.000
#> GSM674364     3   0.000      0.995  0 0.000 1.000
#> GSM674365     3   0.000      0.995  0 0.000 1.000
#> GSM674366     3   0.000      0.995  0 0.000 1.000
#> GSM674367     3   0.000      0.995  0 0.000 1.000
#> GSM674368     3   0.000      0.995  0 0.000 1.000
#> GSM674370     3   0.000      0.995  0 0.000 1.000
#> GSM674371     3   0.000      0.995  0 0.000 1.000
#> GSM674373     3   0.000      0.995  0 0.000 1.000
#> GSM674375     3   0.000      0.995  0 0.000 1.000
#> GSM674379     3   0.000      0.995  0 0.000 1.000
#> GSM674380     3   0.000      0.995  0 0.000 1.000
#> GSM674381     3   0.000      0.995  0 0.000 1.000
#> GSM674382     3   0.000      0.995  0 0.000 1.000
#> GSM674384     3   0.000      0.995  0 0.000 1.000
#> GSM674385     3   0.000      0.995  0 0.000 1.000
#> GSM674388     3   0.000      0.995  0 0.000 1.000
#> GSM674389     3   0.000      0.995  0 0.000 1.000
#> GSM674390     3   0.000      0.995  0 0.000 1.000
#> GSM674391     3   0.000      0.995  0 0.000 1.000
#> GSM674393     3   0.000      0.995  0 0.000 1.000
#> GSM674394     3   0.000      0.995  0 0.000 1.000
#> GSM674395     3   0.000      0.995  0 0.000 1.000
#> GSM674397     3   0.000      0.995  0 0.000 1.000
#> GSM674398     3   0.000      0.995  0 0.000 1.000
#> GSM674400     3   0.000      0.995  0 0.000 1.000
#> GSM674401     3   0.000      0.995  0 0.000 1.000
#> GSM674402     3   0.000      0.995  0 0.000 1.000
#> GSM674403     3   0.000      0.995  0 0.000 1.000
#> GSM674405     3   0.000      0.995  0 0.000 1.000
#> GSM674406     3   0.000      0.995  0 0.000 1.000
#> GSM674407     3   0.000      0.995  0 0.000 1.000
#> GSM674181     2   0.000      1.000  0 1.000 0.000
#> GSM674183     2   0.000      1.000  0 1.000 0.000
#> GSM674184     2   0.000      1.000  0 1.000 0.000
#> GSM674185     2   0.000      1.000  0 1.000 0.000
#> GSM674186     2   0.000      1.000  0 1.000 0.000
#> GSM674187     2   0.000      1.000  0 1.000 0.000
#> GSM674190     2   0.000      1.000  0 1.000 0.000
#> GSM674191     2   0.000      1.000  0 1.000 0.000
#> GSM674192     2   0.000      1.000  0 1.000 0.000
#> GSM674193     2   0.000      1.000  0 1.000 0.000
#> GSM674194     2   0.000      1.000  0 1.000 0.000
#> GSM674195     2   0.000      1.000  0 1.000 0.000
#> GSM674198     2   0.000      1.000  0 1.000 0.000
#> GSM674200     3   0.000      0.995  0 0.000 1.000
#> GSM674201     2   0.000      1.000  0 1.000 0.000
#> GSM674202     2   0.000      1.000  0 1.000 0.000
#> GSM674203     2   0.000      1.000  0 1.000 0.000
#> GSM674204     2   0.000      1.000  0 1.000 0.000
#> GSM674205     2   0.000      1.000  0 1.000 0.000
#> GSM674206     2   0.000      1.000  0 1.000 0.000
#> GSM674208     2   0.000      1.000  0 1.000 0.000
#> GSM674209     2   0.000      1.000  0 1.000 0.000
#> GSM674210     2   0.000      1.000  0 1.000 0.000
#> GSM674212     2   0.000      1.000  0 1.000 0.000
#> GSM674214     2   0.000      1.000  0 1.000 0.000
#> GSM674218     2   0.000      1.000  0 1.000 0.000
#> GSM674219     2   0.000      1.000  0 1.000 0.000
#> GSM674220     2   0.000      1.000  0 1.000 0.000
#> GSM674221     2   0.000      1.000  0 1.000 0.000
#> GSM674223     2   0.000      1.000  0 1.000 0.000
#> GSM674225     2   0.000      1.000  0 1.000 0.000
#> GSM674226     2   0.000      1.000  0 1.000 0.000
#> GSM674229     2   0.000      1.000  0 1.000 0.000
#> GSM674230     2   0.000      1.000  0 1.000 0.000
#> GSM674231     2   0.000      1.000  0 1.000 0.000
#> GSM674232     2   0.000      1.000  0 1.000 0.000
#> GSM674234     2   0.000      1.000  0 1.000 0.000
#> GSM674235     2   0.000      1.000  0 1.000 0.000
#> GSM674236     2   0.000      1.000  0 1.000 0.000
#> GSM674237     2   0.000      1.000  0 1.000 0.000
#> GSM674239     2   0.000      1.000  0 1.000 0.000
#> GSM674240     2   0.000      1.000  0 1.000 0.000
#> GSM674242     2   0.000      1.000  0 1.000 0.000
#> GSM674243     2   0.000      1.000  0 1.000 0.000
#> GSM674244     2   0.000      1.000  0 1.000 0.000
#> GSM674245     2   0.000      1.000  0 1.000 0.000
#> GSM674282     1   0.000      1.000  1 0.000 0.000
#> GSM674284     1   0.000      1.000  1 0.000 0.000
#> GSM674285     1   0.000      1.000  1 0.000 0.000
#> GSM674287     1   0.000      1.000  1 0.000 0.000
#> GSM674288     1   0.000      1.000  1 0.000 0.000
#> GSM674289     1   0.000      1.000  1 0.000 0.000
#> GSM674290     1   0.000      1.000  1 0.000 0.000
#> GSM674291     1   0.000      1.000  1 0.000 0.000
#> GSM674292     1   0.000      1.000  1 0.000 0.000
#> GSM674295     1   0.000      1.000  1 0.000 0.000
#> GSM674297     1   0.000      1.000  1 0.000 0.000
#> GSM674298     1   0.000      1.000  1 0.000 0.000
#> GSM674299     1   0.000      1.000  1 0.000 0.000
#> GSM674300     1   0.000      1.000  1 0.000 0.000
#> GSM674301     1   0.000      1.000  1 0.000 0.000
#> GSM674302     1   0.000      1.000  1 0.000 0.000
#> GSM674304     1   0.000      1.000  1 0.000 0.000
#> GSM674305     1   0.000      1.000  1 0.000 0.000
#> GSM674306     1   0.000      1.000  1 0.000 0.000
#> GSM674308     1   0.000      1.000  1 0.000 0.000
#> GSM674309     1   0.000      1.000  1 0.000 0.000
#> GSM674313     1   0.000      1.000  1 0.000 0.000
#> GSM674314     1   0.000      1.000  1 0.000 0.000
#> GSM674315     1   0.000      1.000  1 0.000 0.000
#> GSM674316     1   0.000      1.000  1 0.000 0.000
#> GSM674318     1   0.000      1.000  1 0.000 0.000
#> GSM674320     1   0.000      1.000  1 0.000 0.000
#> GSM674323     1   0.000      1.000  1 0.000 0.000
#> GSM674324     1   0.000      1.000  1 0.000 0.000
#> GSM674325     1   0.000      1.000  1 0.000 0.000
#> GSM674327     1   0.000      1.000  1 0.000 0.000
#> GSM674328     1   0.000      1.000  1 0.000 0.000
#> GSM674330     1   0.000      1.000  1 0.000 0.000
#> GSM674331     1   0.000      1.000  1 0.000 0.000
#> GSM674332     1   0.000      1.000  1 0.000 0.000
#> GSM674334     1   0.000      1.000  1 0.000 0.000
#> GSM674335     1   0.000      1.000  1 0.000 0.000
#> GSM674345     3   0.000      0.995  0 0.000 1.000
#> GSM674351     3   0.000      0.995  0 0.000 1.000
#> GSM674352     3   0.000      0.995  0 0.000 1.000
#> GSM674359     3   0.000      0.995  0 0.000 1.000
#> GSM674360     3   0.000      0.995  0 0.000 1.000
#> GSM674362     3   0.000      0.995  0 0.000 1.000
#> GSM674369     3   0.000      0.995  0 0.000 1.000
#> GSM674372     3   0.000      0.995  0 0.000 1.000
#> GSM674374     3   0.000      0.995  0 0.000 1.000
#> GSM674376     3   0.000      0.995  0 0.000 1.000
#> GSM674377     3   0.000      0.995  0 0.000 1.000
#> GSM674378     3   0.000      0.995  0 0.000 1.000
#> GSM674383     3   0.000      0.995  0 0.000 1.000
#> GSM674386     3   0.000      0.995  0 0.000 1.000
#> GSM674387     3   0.000      0.995  0 0.000 1.000
#> GSM674392     3   0.000      0.995  0 0.000 1.000
#> GSM674396     3   0.000      0.995  0 0.000 1.000
#> GSM674399     3   0.000      0.995  0 0.000 1.000
#> GSM674404     3   0.000      0.995  0 0.000 1.000
#> GSM674182     2   0.000      1.000  0 1.000 0.000
#> GSM674188     2   0.000      1.000  0 1.000 0.000
#> GSM674189     2   0.000      1.000  0 1.000 0.000
#> GSM674196     2   0.000      1.000  0 1.000 0.000
#> GSM674197     2   0.000      1.000  0 1.000 0.000
#> GSM674199     2   0.000      1.000  0 1.000 0.000
#> GSM674207     2   0.000      1.000  0 1.000 0.000
#> GSM674211     2   0.000      1.000  0 1.000 0.000
#> GSM674213     2   0.000      1.000  0 1.000 0.000
#> GSM674215     2   0.000      1.000  0 1.000 0.000
#> GSM674216     2   0.000      1.000  0 1.000 0.000
#> GSM674217     2   0.000      1.000  0 1.000 0.000
#> GSM674222     2   0.000      1.000  0 1.000 0.000
#> GSM674224     2   0.000      1.000  0 1.000 0.000
#> GSM674227     2   0.000      1.000  0 1.000 0.000
#> GSM674228     2   0.000      1.000  0 1.000 0.000
#> GSM674233     2   0.000      1.000  0 1.000 0.000
#> GSM674238     3   0.553      0.580  0 0.296 0.704
#> GSM674241     2   0.000      1.000  0 1.000 0.000
#> GSM674283     1   0.000      1.000  1 0.000 0.000
#> GSM674286     1   0.000      1.000  1 0.000 0.000
#> GSM674293     1   0.000      1.000  1 0.000 0.000
#> GSM674294     1   0.000      1.000  1 0.000 0.000
#> GSM674296     1   0.000      1.000  1 0.000 0.000
#> GSM674303     1   0.000      1.000  1 0.000 0.000
#> GSM674307     1   0.000      1.000  1 0.000 0.000
#> GSM674310     1   0.000      1.000  1 0.000 0.000
#> GSM674311     1   0.000      1.000  1 0.000 0.000
#> GSM674312     1   0.000      1.000  1 0.000 0.000
#> GSM674317     1   0.000      1.000  1 0.000 0.000
#> GSM674319     1   0.000      1.000  1 0.000 0.000
#> GSM674321     1   0.000      1.000  1 0.000 0.000
#> GSM674322     1   0.000      1.000  1 0.000 0.000
#> GSM674326     1   0.000      1.000  1 0.000 0.000
#> GSM674329     1   0.000      1.000  1 0.000 0.000
#> GSM674333     1   0.000      1.000  1 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette p1    p2    p3    p4
#> GSM674344     3  0.0000      0.984  0 0.000 1.000 0.000
#> GSM674346     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674347     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674348     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674349     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674350     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674353     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674354     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674355     3  0.0469      0.980  0 0.000 0.988 0.012
#> GSM674356     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674357     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674358     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674361     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674363     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674364     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674365     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674366     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674367     4  0.1022      0.973  0 0.000 0.032 0.968
#> GSM674368     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674370     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674371     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674373     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674375     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674379     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674380     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674381     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674382     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674384     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674385     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674388     3  0.1118      0.956  0 0.000 0.964 0.036
#> GSM674389     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674390     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674391     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674393     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674394     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674395     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674397     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674398     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674400     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674401     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674402     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674403     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674405     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674406     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674407     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674181     2  0.0188      0.996  0 0.996 0.004 0.000
#> GSM674183     2  0.0524      0.991  0 0.988 0.004 0.008
#> GSM674184     2  0.0524      0.991  0 0.988 0.004 0.008
#> GSM674185     2  0.0524      0.991  0 0.988 0.004 0.008
#> GSM674186     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674187     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674190     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674191     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674192     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674193     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674194     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674195     2  0.0524      0.991  0 0.988 0.004 0.008
#> GSM674198     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674200     3  0.0336      0.976  0 0.000 0.992 0.008
#> GSM674201     2  0.0524      0.991  0 0.988 0.004 0.008
#> GSM674202     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674203     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674204     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674205     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674206     2  0.0524      0.991  0 0.988 0.004 0.008
#> GSM674208     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674209     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674210     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674212     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674214     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674218     2  0.0524      0.991  0 0.988 0.004 0.008
#> GSM674219     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674220     2  0.0524      0.991  0 0.988 0.004 0.008
#> GSM674221     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674223     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674225     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674226     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674229     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674230     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674231     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674232     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674234     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674235     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674236     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674237     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674239     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674240     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674242     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674243     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674244     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674245     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674282     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674284     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674285     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674287     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674288     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674289     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674290     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674291     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674292     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674295     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674297     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674298     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674299     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674300     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674301     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674302     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674304     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674305     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674306     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674308     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674309     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674313     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674314     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674315     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674316     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674318     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674320     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674323     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674324     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674325     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674327     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674328     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674330     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674331     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674332     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674334     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674335     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674345     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674351     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674352     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674359     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674360     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674362     3  0.0000      0.984  0 0.000 1.000 0.000
#> GSM674369     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674372     4  0.1474      0.953  0 0.000 0.052 0.948
#> GSM674374     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674376     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674377     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674378     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674383     3  0.0188      0.987  0 0.000 0.996 0.004
#> GSM674386     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674387     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674392     4  0.2868      0.856  0 0.000 0.136 0.864
#> GSM674396     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674399     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674404     4  0.0336      0.993  0 0.000 0.008 0.992
#> GSM674182     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674188     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674189     2  0.0524      0.991  0 0.988 0.004 0.008
#> GSM674196     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674197     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674199     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674207     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674211     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674213     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674215     2  0.0336      0.994  0 0.992 0.000 0.008
#> GSM674216     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674217     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674222     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674224     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674227     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674228     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674233     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674238     3  0.4697      0.569  0 0.296 0.696 0.008
#> GSM674241     2  0.0000      0.998  0 1.000 0.000 0.000
#> GSM674283     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674286     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674293     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674294     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674296     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674303     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674307     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674310     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674311     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674312     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674317     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674319     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674321     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674322     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674326     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674329     1  0.0000      1.000  1 0.000 0.000 0.000
#> GSM674333     1  0.0000      1.000  1 0.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4    p5
#> GSM674344     4  0.4307     0.6919 0.000 0.000 0.000 0.500 0.500
#> GSM674346     5  0.4304    -0.6862 0.000 0.000 0.000 0.484 0.516
#> GSM674347     4  0.4440     0.7105 0.000 0.000 0.004 0.528 0.468
#> GSM674348     4  0.4304     0.6906 0.000 0.000 0.000 0.516 0.484
#> GSM674349     4  0.4304     0.6906 0.000 0.000 0.000 0.516 0.484
#> GSM674350     5  0.4307    -0.7463 0.000 0.000 0.000 0.500 0.500
#> GSM674353     4  0.4306     0.7155 0.000 0.000 0.000 0.508 0.492
#> GSM674354     4  0.4304     0.7200 0.000 0.000 0.000 0.516 0.484
#> GSM674355     4  0.4655     0.7034 0.000 0.000 0.012 0.512 0.476
#> GSM674356     4  0.4304     0.7183 0.000 0.000 0.000 0.516 0.484
#> GSM674357     4  0.4305     0.7151 0.000 0.000 0.000 0.512 0.488
#> GSM674358     4  0.4450     0.7168 0.000 0.000 0.004 0.508 0.488
#> GSM674361     4  0.4450     0.7109 0.000 0.000 0.004 0.508 0.488
#> GSM674363     4  0.4307     0.7063 0.000 0.000 0.000 0.500 0.500
#> GSM674364     4  0.4449     0.7080 0.000 0.000 0.004 0.512 0.484
#> GSM674365     4  0.4306     0.7003 0.000 0.000 0.000 0.508 0.492
#> GSM674366     4  0.4552     0.6887 0.000 0.000 0.008 0.524 0.468
#> GSM674367     3  0.3194     0.8207 0.000 0.000 0.832 0.148 0.020
#> GSM674368     4  0.4440     0.6993 0.000 0.000 0.004 0.528 0.468
#> GSM674370     4  0.4653     0.6858 0.000 0.000 0.012 0.516 0.472
#> GSM674371     4  0.4297     0.7143 0.000 0.000 0.000 0.528 0.472
#> GSM674373     3  0.0794     0.9627 0.000 0.000 0.972 0.028 0.000
#> GSM674375     3  0.0609     0.9651 0.000 0.000 0.980 0.020 0.000
#> GSM674379     3  0.0404     0.9667 0.000 0.000 0.988 0.012 0.000
#> GSM674380     3  0.0510     0.9655 0.000 0.000 0.984 0.016 0.000
#> GSM674381     3  0.0807     0.9631 0.000 0.000 0.976 0.012 0.012
#> GSM674382     3  0.0324     0.9667 0.000 0.000 0.992 0.004 0.004
#> GSM674384     3  0.1012     0.9606 0.000 0.000 0.968 0.020 0.012
#> GSM674385     3  0.0807     0.9635 0.000 0.000 0.976 0.012 0.012
#> GSM674388     5  0.5778    -0.3972 0.000 0.000 0.088 0.448 0.464
#> GSM674389     3  0.0566     0.9657 0.000 0.000 0.984 0.004 0.012
#> GSM674390     3  0.0404     0.9667 0.000 0.000 0.988 0.012 0.000
#> GSM674391     3  0.0162     0.9670 0.000 0.000 0.996 0.004 0.000
#> GSM674393     3  0.1522     0.9414 0.000 0.000 0.944 0.044 0.012
#> GSM674394     3  0.0566     0.9657 0.000 0.000 0.984 0.004 0.012
#> GSM674395     3  0.0566     0.9657 0.000 0.000 0.984 0.004 0.012
#> GSM674397     3  0.1544     0.9365 0.000 0.000 0.932 0.068 0.000
#> GSM674398     3  0.0451     0.9663 0.000 0.000 0.988 0.004 0.008
#> GSM674400     5  0.0162     0.3507 0.000 0.000 0.004 0.000 0.996
#> GSM674401     5  0.0162     0.3507 0.000 0.000 0.004 0.000 0.996
#> GSM674402     5  0.0290     0.3498 0.000 0.000 0.000 0.008 0.992
#> GSM674403     5  0.0290     0.3500 0.000 0.000 0.000 0.008 0.992
#> GSM674405     3  0.0324     0.9666 0.000 0.000 0.992 0.004 0.004
#> GSM674406     3  0.0609     0.9654 0.000 0.000 0.980 0.020 0.000
#> GSM674407     3  0.0404     0.9664 0.000 0.000 0.988 0.012 0.000
#> GSM674181     2  0.2605     0.8701 0.000 0.852 0.000 0.148 0.000
#> GSM674183     2  0.4610     0.6597 0.000 0.556 0.000 0.432 0.012
#> GSM674184     2  0.4242     0.6777 0.000 0.572 0.000 0.428 0.000
#> GSM674185     2  0.4242     0.6777 0.000 0.572 0.000 0.428 0.000
#> GSM674186     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674187     2  0.0880     0.9057 0.000 0.968 0.000 0.032 0.000
#> GSM674190     2  0.1043     0.9055 0.000 0.960 0.000 0.040 0.000
#> GSM674191     2  0.1851     0.8959 0.000 0.912 0.000 0.088 0.000
#> GSM674192     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674193     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674194     2  0.2561     0.8771 0.000 0.856 0.000 0.144 0.000
#> GSM674195     2  0.4242     0.6777 0.000 0.572 0.000 0.428 0.000
#> GSM674198     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674200     4  0.3109    -0.0198 0.000 0.000 0.000 0.800 0.200
#> GSM674201     2  0.4242     0.6777 0.000 0.572 0.000 0.428 0.000
#> GSM674202     2  0.3003     0.8560 0.000 0.812 0.000 0.188 0.000
#> GSM674203     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674204     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674205     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674206     2  0.4171     0.7056 0.000 0.604 0.000 0.396 0.000
#> GSM674208     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674209     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674210     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674212     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674214     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674218     2  0.4242     0.6777 0.000 0.572 0.000 0.428 0.000
#> GSM674219     2  0.3109     0.8505 0.000 0.800 0.000 0.200 0.000
#> GSM674220     2  0.4242     0.6777 0.000 0.572 0.000 0.428 0.000
#> GSM674221     2  0.1270     0.9035 0.000 0.948 0.000 0.052 0.000
#> GSM674223     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674225     2  0.3796     0.7787 0.000 0.700 0.000 0.300 0.000
#> GSM674226     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674229     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674230     2  0.2424     0.8808 0.000 0.868 0.000 0.132 0.000
#> GSM674231     2  0.2424     0.8808 0.000 0.868 0.000 0.132 0.000
#> GSM674232     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674234     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674235     2  0.2516     0.8785 0.000 0.860 0.000 0.140 0.000
#> GSM674236     2  0.2424     0.8808 0.000 0.868 0.000 0.132 0.000
#> GSM674237     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674239     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674240     2  0.1121     0.9048 0.000 0.956 0.000 0.044 0.000
#> GSM674242     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674243     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674244     2  0.1851     0.8964 0.000 0.912 0.000 0.088 0.000
#> GSM674245     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674282     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674284     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674285     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674287     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674288     1  0.0510     0.9897 0.984 0.000 0.000 0.016 0.000
#> GSM674289     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674291     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674292     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674295     1  0.0609     0.9883 0.980 0.000 0.000 0.020 0.000
#> GSM674297     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674298     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674299     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674300     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674301     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674302     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674305     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674306     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674308     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674309     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674313     1  0.0609     0.9883 0.980 0.000 0.000 0.020 0.000
#> GSM674314     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674315     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674316     1  0.0609     0.9883 0.980 0.000 0.000 0.020 0.000
#> GSM674318     1  0.0609     0.9883 0.980 0.000 0.000 0.020 0.000
#> GSM674320     1  0.0609     0.9883 0.980 0.000 0.000 0.020 0.000
#> GSM674323     1  0.0609     0.9883 0.980 0.000 0.000 0.020 0.000
#> GSM674324     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674325     1  0.0609     0.9883 0.980 0.000 0.000 0.020 0.000
#> GSM674327     1  0.0510     0.9897 0.984 0.000 0.000 0.016 0.000
#> GSM674328     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674330     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674331     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674332     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674334     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674335     1  0.0290     0.9923 0.992 0.000 0.000 0.008 0.000
#> GSM674345     5  0.4304    -0.6862 0.000 0.000 0.000 0.484 0.516
#> GSM674351     4  0.4307     0.7063 0.000 0.000 0.000 0.500 0.500
#> GSM674352     5  0.4307    -0.7463 0.000 0.000 0.000 0.500 0.500
#> GSM674359     5  0.4302    -0.6846 0.000 0.000 0.000 0.480 0.520
#> GSM674360     4  0.4306     0.7128 0.000 0.000 0.000 0.508 0.492
#> GSM674362     4  0.4306     0.7128 0.000 0.000 0.000 0.508 0.492
#> GSM674369     4  0.4297     0.7143 0.000 0.000 0.000 0.528 0.472
#> GSM674372     3  0.2580     0.8855 0.000 0.000 0.892 0.064 0.044
#> GSM674374     3  0.0880     0.9611 0.000 0.000 0.968 0.032 0.000
#> GSM674376     3  0.0404     0.9664 0.000 0.000 0.988 0.012 0.000
#> GSM674377     3  0.0609     0.9654 0.000 0.000 0.980 0.020 0.000
#> GSM674378     3  0.0794     0.9627 0.000 0.000 0.972 0.028 0.000
#> GSM674383     4  0.4305     0.7029 0.000 0.000 0.000 0.512 0.488
#> GSM674386     3  0.0324     0.9667 0.000 0.000 0.992 0.004 0.004
#> GSM674387     3  0.0404     0.9664 0.000 0.000 0.988 0.012 0.000
#> GSM674392     3  0.5139     0.4715 0.000 0.000 0.648 0.280 0.072
#> GSM674396     3  0.0324     0.9666 0.000 0.000 0.992 0.004 0.004
#> GSM674399     3  0.0324     0.9666 0.000 0.000 0.992 0.004 0.004
#> GSM674404     3  0.0162     0.9667 0.000 0.000 0.996 0.000 0.004
#> GSM674182     2  0.1270     0.9037 0.000 0.948 0.000 0.052 0.000
#> GSM674188     2  0.1478     0.9016 0.000 0.936 0.000 0.064 0.000
#> GSM674189     2  0.4242     0.6777 0.000 0.572 0.000 0.428 0.000
#> GSM674196     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674197     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674199     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674207     2  0.0404     0.9070 0.000 0.988 0.000 0.012 0.000
#> GSM674211     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674213     2  0.1341     0.9029 0.000 0.944 0.000 0.056 0.000
#> GSM674215     2  0.4242     0.6777 0.000 0.572 0.000 0.428 0.000
#> GSM674216     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674217     2  0.1851     0.8966 0.000 0.912 0.000 0.088 0.000
#> GSM674222     2  0.2929     0.8591 0.000 0.820 0.000 0.180 0.000
#> GSM674224     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674227     2  0.2424     0.8808 0.000 0.868 0.000 0.132 0.000
#> GSM674228     2  0.1732     0.8978 0.000 0.920 0.000 0.080 0.000
#> GSM674233     2  0.2561     0.8771 0.000 0.856 0.000 0.144 0.000
#> GSM674238     4  0.4215    -0.0720 0.000 0.168 0.000 0.768 0.064
#> GSM674241     2  0.0000     0.9079 0.000 1.000 0.000 0.000 0.000
#> GSM674283     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674286     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674293     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674294     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674296     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674303     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674307     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674310     1  0.0609     0.9883 0.980 0.000 0.000 0.020 0.000
#> GSM674311     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674312     1  0.0609     0.9883 0.980 0.000 0.000 0.020 0.000
#> GSM674317     1  0.0000     0.9946 1.000 0.000 0.000 0.000 0.000
#> GSM674319     1  0.0609     0.9883 0.980 0.000 0.000 0.020 0.000
#> GSM674321     1  0.0609     0.9883 0.980 0.000 0.000 0.020 0.000
#> GSM674322     1  0.0609     0.9883 0.980 0.000 0.000 0.020 0.000
#> GSM674326     1  0.0609     0.9883 0.980 0.000 0.000 0.020 0.000
#> GSM674329     1  0.0609     0.9883 0.980 0.000 0.000 0.020 0.000
#> GSM674333     1  0.0609     0.9883 0.980 0.000 0.000 0.020 0.000

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4    p5    p6
#> GSM674344     3  0.2134     0.8860 0.000 0.000 0.904 0.000 0.052 0.044
#> GSM674346     3  0.2747     0.8537 0.000 0.000 0.860 0.000 0.096 0.044
#> GSM674347     3  0.1350     0.9046 0.000 0.000 0.952 0.020 0.020 0.008
#> GSM674348     3  0.2948     0.8588 0.000 0.000 0.848 0.000 0.092 0.060
#> GSM674349     3  0.2625     0.8771 0.000 0.000 0.872 0.000 0.072 0.056
#> GSM674350     3  0.0363     0.9080 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM674353     3  0.0363     0.9080 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM674354     3  0.0146     0.9110 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM674355     3  0.0909     0.9054 0.000 0.000 0.968 0.012 0.020 0.000
#> GSM674356     3  0.0790     0.9115 0.000 0.000 0.968 0.000 0.032 0.000
#> GSM674357     3  0.0260     0.9088 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM674358     3  0.0363     0.9080 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM674361     3  0.1036     0.9060 0.000 0.000 0.964 0.004 0.024 0.008
#> GSM674363     3  0.0363     0.9080 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM674364     3  0.1503     0.9000 0.000 0.000 0.944 0.008 0.032 0.016
#> GSM674365     3  0.2721     0.8845 0.000 0.000 0.868 0.004 0.088 0.040
#> GSM674366     3  0.3174     0.8531 0.000 0.000 0.836 0.004 0.104 0.056
#> GSM674367     4  0.5523     0.4985 0.000 0.000 0.280 0.604 0.068 0.048
#> GSM674368     3  0.2398     0.8917 0.000 0.000 0.888 0.004 0.080 0.028
#> GSM674370     3  0.2675     0.8869 0.000 0.000 0.876 0.008 0.076 0.040
#> GSM674371     3  0.2344     0.8936 0.000 0.000 0.892 0.004 0.076 0.028
#> GSM674373     4  0.2113     0.8830 0.000 0.000 0.004 0.908 0.028 0.060
#> GSM674375     4  0.0993     0.9011 0.000 0.000 0.000 0.964 0.012 0.024
#> GSM674379     4  0.1498     0.9004 0.000 0.000 0.000 0.940 0.028 0.032
#> GSM674380     4  0.3183     0.8465 0.000 0.000 0.000 0.828 0.112 0.060
#> GSM674381     4  0.2575     0.8839 0.000 0.000 0.004 0.880 0.072 0.044
#> GSM674382     4  0.2201     0.8861 0.000 0.000 0.000 0.900 0.052 0.048
#> GSM674384     4  0.2620     0.8850 0.000 0.000 0.040 0.888 0.048 0.024
#> GSM674385     4  0.1528     0.8972 0.000 0.000 0.016 0.944 0.028 0.012
#> GSM674388     3  0.5790     0.5123 0.000 0.000 0.632 0.176 0.124 0.068
#> GSM674389     4  0.0717     0.9001 0.000 0.000 0.008 0.976 0.016 0.000
#> GSM674390     4  0.2129     0.8889 0.000 0.000 0.000 0.904 0.056 0.040
#> GSM674391     4  0.2070     0.8884 0.000 0.000 0.000 0.908 0.044 0.048
#> GSM674393     4  0.3310     0.7903 0.000 0.000 0.132 0.824 0.028 0.016
#> GSM674394     4  0.0964     0.8992 0.000 0.000 0.012 0.968 0.016 0.004
#> GSM674395     4  0.0976     0.8997 0.000 0.000 0.008 0.968 0.016 0.008
#> GSM674397     4  0.3643     0.8342 0.000 0.000 0.080 0.824 0.052 0.044
#> GSM674398     4  0.0508     0.9022 0.000 0.000 0.000 0.984 0.012 0.004
#> GSM674400     5  0.2823     0.9801 0.000 0.000 0.204 0.000 0.796 0.000
#> GSM674401     5  0.2902     0.9766 0.000 0.000 0.196 0.000 0.800 0.004
#> GSM674402     5  0.2883     0.9757 0.000 0.000 0.212 0.000 0.788 0.000
#> GSM674403     5  0.2730     0.9593 0.000 0.000 0.192 0.000 0.808 0.000
#> GSM674405     4  0.0405     0.9023 0.000 0.000 0.000 0.988 0.008 0.004
#> GSM674406     4  0.2316     0.8933 0.000 0.000 0.016 0.904 0.040 0.040
#> GSM674407     4  0.0806     0.9022 0.000 0.000 0.000 0.972 0.008 0.020
#> GSM674181     2  0.3714     0.4029 0.000 0.656 0.000 0.000 0.004 0.340
#> GSM674183     6  0.3152     0.8372 0.000 0.196 0.008 0.000 0.004 0.792
#> GSM674184     6  0.3240     0.8881 0.000 0.244 0.000 0.000 0.004 0.752
#> GSM674185     6  0.3240     0.8881 0.000 0.244 0.000 0.000 0.004 0.752
#> GSM674186     2  0.0363     0.8665 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM674187     2  0.1141     0.8534 0.000 0.948 0.000 0.000 0.000 0.052
#> GSM674190     2  0.1387     0.8466 0.000 0.932 0.000 0.000 0.000 0.068
#> GSM674191     2  0.2416     0.7868 0.000 0.844 0.000 0.000 0.000 0.156
#> GSM674192     2  0.0000     0.8681 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674193     2  0.0146     0.8677 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674194     2  0.3126     0.6781 0.000 0.752 0.000 0.000 0.000 0.248
#> GSM674195     6  0.3240     0.8881 0.000 0.244 0.000 0.000 0.004 0.752
#> GSM674198     2  0.0000     0.8681 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674200     6  0.4517     0.0216 0.000 0.000 0.292 0.000 0.060 0.648
#> GSM674201     6  0.3101     0.8868 0.000 0.244 0.000 0.000 0.000 0.756
#> GSM674202     2  0.4446     0.3751 0.000 0.612 0.000 0.000 0.040 0.348
#> GSM674203     2  0.0000     0.8681 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674204     2  0.0000     0.8681 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674205     2  0.0000     0.8681 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674206     6  0.3489     0.8222 0.000 0.288 0.000 0.000 0.004 0.708
#> GSM674208     2  0.0000     0.8681 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674209     2  0.0146     0.8677 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674210     2  0.0000     0.8681 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674212     2  0.0146     0.8669 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM674214     2  0.0146     0.8669 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM674218     6  0.3240     0.8881 0.000 0.244 0.000 0.000 0.004 0.752
#> GSM674219     2  0.3881     0.2950 0.000 0.600 0.000 0.000 0.004 0.396
#> GSM674220     6  0.4110     0.8664 0.000 0.236 0.000 0.000 0.052 0.712
#> GSM674221     2  0.2146     0.8183 0.000 0.880 0.000 0.000 0.004 0.116
#> GSM674223     2  0.0000     0.8681 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674225     2  0.4829    -0.0567 0.000 0.520 0.000 0.000 0.056 0.424
#> GSM674226     2  0.0291     0.8670 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM674229     2  0.0000     0.8681 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674230     2  0.3766     0.6774 0.000 0.748 0.000 0.000 0.040 0.212
#> GSM674231     2  0.2994     0.7202 0.000 0.788 0.000 0.000 0.004 0.208
#> GSM674232     2  0.1398     0.8427 0.000 0.940 0.000 0.000 0.052 0.008
#> GSM674234     2  0.0000     0.8681 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674235     2  0.4085     0.6356 0.000 0.716 0.000 0.000 0.052 0.232
#> GSM674236     2  0.4007     0.6506 0.000 0.728 0.000 0.000 0.052 0.220
#> GSM674237     2  0.0000     0.8681 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674239     2  0.0000     0.8681 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674240     2  0.2006     0.8240 0.000 0.892 0.000 0.000 0.004 0.104
#> GSM674242     2  0.0000     0.8681 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674243     2  0.0000     0.8681 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674244     2  0.3176     0.7607 0.000 0.812 0.000 0.000 0.032 0.156
#> GSM674245     2  0.0146     0.8677 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674282     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674284     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674285     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674287     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674288     1  0.2221     0.9171 0.896 0.000 0.000 0.000 0.032 0.072
#> GSM674289     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674291     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674292     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674295     1  0.2680     0.9000 0.860 0.000 0.000 0.000 0.032 0.108
#> GSM674297     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674298     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674299     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674300     1  0.0146     0.9559 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM674301     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674302     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674305     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674306     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674308     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674309     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674313     1  0.2680     0.9000 0.860 0.000 0.000 0.000 0.032 0.108
#> GSM674314     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674315     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674316     1  0.2633     0.9021 0.864 0.000 0.000 0.000 0.032 0.104
#> GSM674318     1  0.2680     0.9000 0.860 0.000 0.000 0.000 0.032 0.108
#> GSM674320     1  0.2680     0.9000 0.860 0.000 0.000 0.000 0.032 0.108
#> GSM674323     1  0.2680     0.9000 0.860 0.000 0.000 0.000 0.032 0.108
#> GSM674324     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674325     1  0.2680     0.9000 0.860 0.000 0.000 0.000 0.032 0.108
#> GSM674327     1  0.1890     0.9258 0.916 0.000 0.000 0.000 0.024 0.060
#> GSM674328     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674330     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674331     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674332     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674334     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674335     1  0.1480     0.9353 0.940 0.000 0.000 0.000 0.020 0.040
#> GSM674345     3  0.2647     0.8597 0.000 0.000 0.868 0.000 0.088 0.044
#> GSM674351     3  0.0363     0.9080 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM674352     3  0.0363     0.9080 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM674359     3  0.2889     0.8455 0.000 0.000 0.848 0.000 0.108 0.044
#> GSM674360     3  0.1176     0.9090 0.000 0.000 0.956 0.000 0.024 0.020
#> GSM674362     3  0.0820     0.9078 0.000 0.000 0.972 0.000 0.016 0.012
#> GSM674369     3  0.2344     0.8936 0.000 0.000 0.892 0.004 0.076 0.028
#> GSM674372     4  0.3316     0.7679 0.000 0.000 0.152 0.812 0.028 0.008
#> GSM674374     4  0.2113     0.8830 0.000 0.000 0.004 0.908 0.028 0.060
#> GSM674376     4  0.0806     0.9032 0.000 0.000 0.000 0.972 0.008 0.020
#> GSM674377     4  0.2263     0.8894 0.000 0.000 0.000 0.896 0.056 0.048
#> GSM674378     4  0.1890     0.8899 0.000 0.000 0.008 0.924 0.024 0.044
#> GSM674383     3  0.2373     0.8931 0.000 0.000 0.888 0.004 0.084 0.024
#> GSM674386     4  0.2201     0.8861 0.000 0.000 0.000 0.900 0.052 0.048
#> GSM674387     4  0.0820     0.9017 0.000 0.000 0.000 0.972 0.012 0.016
#> GSM674392     4  0.4338     0.0952 0.000 0.000 0.484 0.496 0.020 0.000
#> GSM674396     4  0.0508     0.9022 0.000 0.000 0.000 0.984 0.012 0.004
#> GSM674399     4  0.0508     0.9028 0.000 0.000 0.000 0.984 0.012 0.004
#> GSM674404     4  0.0260     0.9028 0.000 0.000 0.000 0.992 0.008 0.000
#> GSM674182     2  0.2234     0.8102 0.000 0.872 0.000 0.000 0.004 0.124
#> GSM674188     2  0.2178     0.8098 0.000 0.868 0.000 0.000 0.000 0.132
#> GSM674189     6  0.3101     0.8868 0.000 0.244 0.000 0.000 0.000 0.756
#> GSM674196     2  0.0000     0.8681 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674197     2  0.0000     0.8681 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674199     2  0.0000     0.8681 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674207     2  0.0603     0.8620 0.000 0.980 0.000 0.000 0.004 0.016
#> GSM674211     2  0.0146     0.8669 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM674213     2  0.2482     0.7950 0.000 0.848 0.000 0.000 0.004 0.148
#> GSM674215     6  0.3934     0.8544 0.000 0.260 0.000 0.000 0.032 0.708
#> GSM674216     2  0.1462     0.8402 0.000 0.936 0.000 0.000 0.056 0.008
#> GSM674217     2  0.2933     0.7400 0.000 0.796 0.000 0.000 0.004 0.200
#> GSM674222     2  0.4463     0.4872 0.000 0.652 0.000 0.000 0.056 0.292
#> GSM674224     2  0.0146     0.8677 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674227     2  0.4038     0.6505 0.000 0.728 0.000 0.000 0.056 0.216
#> GSM674228     2  0.2442     0.7981 0.000 0.852 0.000 0.000 0.004 0.144
#> GSM674233     2  0.3405     0.6348 0.000 0.724 0.000 0.000 0.004 0.272
#> GSM674238     6  0.3947     0.6410 0.000 0.096 0.116 0.000 0.008 0.780
#> GSM674241     2  0.0000     0.8681 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674283     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674286     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674293     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674294     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674296     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674303     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674307     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674310     1  0.2680     0.9000 0.860 0.000 0.000 0.000 0.032 0.108
#> GSM674311     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674312     1  0.2680     0.9000 0.860 0.000 0.000 0.000 0.032 0.108
#> GSM674317     1  0.0000     0.9573 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674319     1  0.2633     0.9021 0.864 0.000 0.000 0.000 0.032 0.104
#> GSM674321     1  0.2680     0.9000 0.860 0.000 0.000 0.000 0.032 0.108
#> GSM674322     1  0.2680     0.9000 0.860 0.000 0.000 0.000 0.032 0.108
#> GSM674326     1  0.2680     0.9000 0.860 0.000 0.000 0.000 0.032 0.108
#> GSM674329     1  0.2680     0.9000 0.860 0.000 0.000 0.000 0.032 0.108
#> GSM674333     1  0.2680     0.9000 0.860 0.000 0.000 0.000 0.032 0.108

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-ATC-skmeans-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-ATC-skmeans-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-ATC-skmeans-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-ATC-skmeans-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-ATC-skmeans-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-ATC-skmeans-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-ATC-skmeans-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-ATC-skmeans-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-ATC-skmeans-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-ATC-skmeans-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-ATC-skmeans-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-ATC-skmeans-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-ATC-skmeans-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-ATC-skmeans-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-ATC-skmeans-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-ATC-skmeans-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-ATC-skmeans-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-ATC-skmeans-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-ATC-skmeans-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-ATC-skmeans-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk ATC-skmeans-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-ATC-skmeans-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-ATC-skmeans-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-ATC-skmeans-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-ATC-skmeans-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-ATC-skmeans-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk ATC-skmeans-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>               n disease.state(p) specimen(p) k
#> ATC:skmeans 183            0.924    1.83e-40 2
#> ATC:skmeans 183            0.942    1.46e-75 3
#> ATC:skmeans 183            0.833    1.12e-73 4
#> ATC:skmeans 170            0.799    2.16e-70 5
#> ATC:skmeans 175            0.823    3.98e-69 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


ATC:pam**

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["ATC", "pam"]
# you can also extract it by
# res = res_list["ATC:pam"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#>   Subgroups are detected by 'pam' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk ATC-pam-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk ATC-pam-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 1.000           0.997       0.999         0.5953 0.750   0.571
#> 4 4 0.862           0.859       0.879         0.0945 0.923   0.772
#> 5 5 0.900           0.875       0.938         0.0676 0.937   0.770
#> 6 6 0.840           0.842       0.902         0.0647 0.916   0.643

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2

There is also optional best \(k\) = 2 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette p1    p2    p3
#> GSM674344     3  0.0000      0.999  0 0.000 1.000
#> GSM674346     3  0.0000      0.999  0 0.000 1.000
#> GSM674347     3  0.0000      0.999  0 0.000 1.000
#> GSM674348     3  0.0000      0.999  0 0.000 1.000
#> GSM674349     3  0.0000      0.999  0 0.000 1.000
#> GSM674350     3  0.0000      0.999  0 0.000 1.000
#> GSM674353     3  0.0000      0.999  0 0.000 1.000
#> GSM674354     3  0.0000      0.999  0 0.000 1.000
#> GSM674355     3  0.0000      0.999  0 0.000 1.000
#> GSM674356     3  0.0000      0.999  0 0.000 1.000
#> GSM674357     3  0.0000      0.999  0 0.000 1.000
#> GSM674358     3  0.0000      0.999  0 0.000 1.000
#> GSM674361     3  0.0000      0.999  0 0.000 1.000
#> GSM674363     3  0.0000      0.999  0 0.000 1.000
#> GSM674364     3  0.0000      0.999  0 0.000 1.000
#> GSM674365     3  0.0000      0.999  0 0.000 1.000
#> GSM674366     3  0.0000      0.999  0 0.000 1.000
#> GSM674367     3  0.0000      0.999  0 0.000 1.000
#> GSM674368     3  0.0000      0.999  0 0.000 1.000
#> GSM674370     3  0.0000      0.999  0 0.000 1.000
#> GSM674371     3  0.0000      0.999  0 0.000 1.000
#> GSM674373     3  0.0000      0.999  0 0.000 1.000
#> GSM674375     3  0.0000      0.999  0 0.000 1.000
#> GSM674379     3  0.0000      0.999  0 0.000 1.000
#> GSM674380     3  0.0000      0.999  0 0.000 1.000
#> GSM674381     3  0.0000      0.999  0 0.000 1.000
#> GSM674382     3  0.0000      0.999  0 0.000 1.000
#> GSM674384     3  0.0000      0.999  0 0.000 1.000
#> GSM674385     3  0.0000      0.999  0 0.000 1.000
#> GSM674388     3  0.0000      0.999  0 0.000 1.000
#> GSM674389     3  0.0000      0.999  0 0.000 1.000
#> GSM674390     3  0.0000      0.999  0 0.000 1.000
#> GSM674391     3  0.0000      0.999  0 0.000 1.000
#> GSM674393     3  0.0000      0.999  0 0.000 1.000
#> GSM674394     3  0.0000      0.999  0 0.000 1.000
#> GSM674395     3  0.0000      0.999  0 0.000 1.000
#> GSM674397     3  0.0000      0.999  0 0.000 1.000
#> GSM674398     3  0.0000      0.999  0 0.000 1.000
#> GSM674400     3  0.0000      0.999  0 0.000 1.000
#> GSM674401     3  0.0000      0.999  0 0.000 1.000
#> GSM674402     3  0.0000      0.999  0 0.000 1.000
#> GSM674403     3  0.0000      0.999  0 0.000 1.000
#> GSM674405     3  0.0000      0.999  0 0.000 1.000
#> GSM674406     3  0.0000      0.999  0 0.000 1.000
#> GSM674407     3  0.0000      0.999  0 0.000 1.000
#> GSM674181     2  0.0000      0.997  0 1.000 0.000
#> GSM674183     2  0.2165      0.933  0 0.936 0.064
#> GSM674184     2  0.0000      0.997  0 1.000 0.000
#> GSM674185     2  0.0000      0.997  0 1.000 0.000
#> GSM674186     2  0.0000      0.997  0 1.000 0.000
#> GSM674187     2  0.0000      0.997  0 1.000 0.000
#> GSM674190     2  0.0000      0.997  0 1.000 0.000
#> GSM674191     2  0.0000      0.997  0 1.000 0.000
#> GSM674192     2  0.0000      0.997  0 1.000 0.000
#> GSM674193     2  0.0000      0.997  0 1.000 0.000
#> GSM674194     2  0.0000      0.997  0 1.000 0.000
#> GSM674195     2  0.1753      0.949  0 0.952 0.048
#> GSM674198     2  0.0000      0.997  0 1.000 0.000
#> GSM674200     3  0.0000      0.999  0 0.000 1.000
#> GSM674201     2  0.0000      0.997  0 1.000 0.000
#> GSM674202     2  0.0000      0.997  0 1.000 0.000
#> GSM674203     2  0.0000      0.997  0 1.000 0.000
#> GSM674204     2  0.0000      0.997  0 1.000 0.000
#> GSM674205     2  0.0000      0.997  0 1.000 0.000
#> GSM674206     2  0.0000      0.997  0 1.000 0.000
#> GSM674208     2  0.0000      0.997  0 1.000 0.000
#> GSM674209     2  0.0000      0.997  0 1.000 0.000
#> GSM674210     2  0.0000      0.997  0 1.000 0.000
#> GSM674212     2  0.0000      0.997  0 1.000 0.000
#> GSM674214     2  0.0000      0.997  0 1.000 0.000
#> GSM674218     2  0.0000      0.997  0 1.000 0.000
#> GSM674219     2  0.0000      0.997  0 1.000 0.000
#> GSM674220     2  0.2625      0.911  0 0.916 0.084
#> GSM674221     2  0.0000      0.997  0 1.000 0.000
#> GSM674223     2  0.0000      0.997  0 1.000 0.000
#> GSM674225     2  0.0000      0.997  0 1.000 0.000
#> GSM674226     2  0.0000      0.997  0 1.000 0.000
#> GSM674229     2  0.0000      0.997  0 1.000 0.000
#> GSM674230     2  0.0000      0.997  0 1.000 0.000
#> GSM674231     2  0.0000      0.997  0 1.000 0.000
#> GSM674232     2  0.0000      0.997  0 1.000 0.000
#> GSM674234     2  0.0000      0.997  0 1.000 0.000
#> GSM674235     2  0.0000      0.997  0 1.000 0.000
#> GSM674236     2  0.0000      0.997  0 1.000 0.000
#> GSM674237     2  0.0000      0.997  0 1.000 0.000
#> GSM674239     2  0.0000      0.997  0 1.000 0.000
#> GSM674240     2  0.0000      0.997  0 1.000 0.000
#> GSM674242     2  0.0000      0.997  0 1.000 0.000
#> GSM674243     2  0.0000      0.997  0 1.000 0.000
#> GSM674244     2  0.0000      0.997  0 1.000 0.000
#> GSM674245     2  0.0000      0.997  0 1.000 0.000
#> GSM674282     1  0.0000      1.000  1 0.000 0.000
#> GSM674284     1  0.0000      1.000  1 0.000 0.000
#> GSM674285     1  0.0000      1.000  1 0.000 0.000
#> GSM674287     1  0.0000      1.000  1 0.000 0.000
#> GSM674288     1  0.0000      1.000  1 0.000 0.000
#> GSM674289     1  0.0000      1.000  1 0.000 0.000
#> GSM674290     1  0.0000      1.000  1 0.000 0.000
#> GSM674291     1  0.0000      1.000  1 0.000 0.000
#> GSM674292     1  0.0000      1.000  1 0.000 0.000
#> GSM674295     1  0.0000      1.000  1 0.000 0.000
#> GSM674297     1  0.0000      1.000  1 0.000 0.000
#> GSM674298     1  0.0000      1.000  1 0.000 0.000
#> GSM674299     1  0.0000      1.000  1 0.000 0.000
#> GSM674300     1  0.0000      1.000  1 0.000 0.000
#> GSM674301     1  0.0000      1.000  1 0.000 0.000
#> GSM674302     1  0.0000      1.000  1 0.000 0.000
#> GSM674304     1  0.0000      1.000  1 0.000 0.000
#> GSM674305     1  0.0000      1.000  1 0.000 0.000
#> GSM674306     1  0.0000      1.000  1 0.000 0.000
#> GSM674308     1  0.0000      1.000  1 0.000 0.000
#> GSM674309     1  0.0000      1.000  1 0.000 0.000
#> GSM674313     1  0.0000      1.000  1 0.000 0.000
#> GSM674314     1  0.0000      1.000  1 0.000 0.000
#> GSM674315     1  0.0000      1.000  1 0.000 0.000
#> GSM674316     1  0.0000      1.000  1 0.000 0.000
#> GSM674318     1  0.0000      1.000  1 0.000 0.000
#> GSM674320     1  0.0000      1.000  1 0.000 0.000
#> GSM674323     1  0.0000      1.000  1 0.000 0.000
#> GSM674324     1  0.0000      1.000  1 0.000 0.000
#> GSM674325     1  0.0000      1.000  1 0.000 0.000
#> GSM674327     1  0.0000      1.000  1 0.000 0.000
#> GSM674328     1  0.0000      1.000  1 0.000 0.000
#> GSM674330     1  0.0000      1.000  1 0.000 0.000
#> GSM674331     1  0.0000      1.000  1 0.000 0.000
#> GSM674332     1  0.0000      1.000  1 0.000 0.000
#> GSM674334     1  0.0000      1.000  1 0.000 0.000
#> GSM674335     1  0.0000      1.000  1 0.000 0.000
#> GSM674345     3  0.0000      0.999  0 0.000 1.000
#> GSM674351     3  0.0000      0.999  0 0.000 1.000
#> GSM674352     3  0.0000      0.999  0 0.000 1.000
#> GSM674359     3  0.0000      0.999  0 0.000 1.000
#> GSM674360     3  0.0000      0.999  0 0.000 1.000
#> GSM674362     3  0.0000      0.999  0 0.000 1.000
#> GSM674369     3  0.1643      0.954  0 0.044 0.956
#> GSM674372     3  0.0000      0.999  0 0.000 1.000
#> GSM674374     3  0.0000      0.999  0 0.000 1.000
#> GSM674376     3  0.0000      0.999  0 0.000 1.000
#> GSM674377     3  0.0424      0.991  0 0.008 0.992
#> GSM674378     3  0.0000      0.999  0 0.000 1.000
#> GSM674383     3  0.0000      0.999  0 0.000 1.000
#> GSM674386     3  0.0000      0.999  0 0.000 1.000
#> GSM674387     3  0.0000      0.999  0 0.000 1.000
#> GSM674392     3  0.0000      0.999  0 0.000 1.000
#> GSM674396     3  0.0000      0.999  0 0.000 1.000
#> GSM674399     3  0.0000      0.999  0 0.000 1.000
#> GSM674404     3  0.0000      0.999  0 0.000 1.000
#> GSM674182     2  0.0000      0.997  0 1.000 0.000
#> GSM674188     2  0.0000      0.997  0 1.000 0.000
#> GSM674189     2  0.0000      0.997  0 1.000 0.000
#> GSM674196     2  0.0000      0.997  0 1.000 0.000
#> GSM674197     2  0.0000      0.997  0 1.000 0.000
#> GSM674199     2  0.0000      0.997  0 1.000 0.000
#> GSM674207     2  0.0000      0.997  0 1.000 0.000
#> GSM674211     2  0.0000      0.997  0 1.000 0.000
#> GSM674213     2  0.0000      0.997  0 1.000 0.000
#> GSM674215     2  0.0000      0.997  0 1.000 0.000
#> GSM674216     2  0.0000      0.997  0 1.000 0.000
#> GSM674217     2  0.0000      0.997  0 1.000 0.000
#> GSM674222     2  0.0000      0.997  0 1.000 0.000
#> GSM674224     2  0.0000      0.997  0 1.000 0.000
#> GSM674227     2  0.0000      0.997  0 1.000 0.000
#> GSM674228     2  0.0000      0.997  0 1.000 0.000
#> GSM674233     2  0.0000      0.997  0 1.000 0.000
#> GSM674238     3  0.0892      0.979  0 0.020 0.980
#> GSM674241     2  0.0000      0.997  0 1.000 0.000
#> GSM674283     1  0.0000      1.000  1 0.000 0.000
#> GSM674286     1  0.0000      1.000  1 0.000 0.000
#> GSM674293     1  0.0000      1.000  1 0.000 0.000
#> GSM674294     1  0.0000      1.000  1 0.000 0.000
#> GSM674296     1  0.0000      1.000  1 0.000 0.000
#> GSM674303     1  0.0000      1.000  1 0.000 0.000
#> GSM674307     1  0.0000      1.000  1 0.000 0.000
#> GSM674310     1  0.0000      1.000  1 0.000 0.000
#> GSM674311     1  0.0000      1.000  1 0.000 0.000
#> GSM674312     1  0.0000      1.000  1 0.000 0.000
#> GSM674317     1  0.0000      1.000  1 0.000 0.000
#> GSM674319     1  0.0000      1.000  1 0.000 0.000
#> GSM674321     1  0.0000      1.000  1 0.000 0.000
#> GSM674322     1  0.0000      1.000  1 0.000 0.000
#> GSM674326     1  0.0000      1.000  1 0.000 0.000
#> GSM674329     1  0.0000      1.000  1 0.000 0.000
#> GSM674333     1  0.0000      1.000  1 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1    p2    p3    p4
#> GSM674344     4  0.4103      0.914 0.000 0.000 0.256 0.744
#> GSM674346     4  0.4103      0.914 0.000 0.000 0.256 0.744
#> GSM674347     4  0.4967      0.597 0.000 0.000 0.452 0.548
#> GSM674348     4  0.4304      0.895 0.000 0.000 0.284 0.716
#> GSM674349     4  0.4134      0.912 0.000 0.000 0.260 0.740
#> GSM674350     4  0.4103      0.914 0.000 0.000 0.256 0.744
#> GSM674353     4  0.4103      0.914 0.000 0.000 0.256 0.744
#> GSM674354     4  0.4103      0.914 0.000 0.000 0.256 0.744
#> GSM674355     4  0.4972      0.558 0.000 0.000 0.456 0.544
#> GSM674356     4  0.4250      0.902 0.000 0.000 0.276 0.724
#> GSM674357     4  0.4103      0.914 0.000 0.000 0.256 0.744
#> GSM674358     4  0.4103      0.914 0.000 0.000 0.256 0.744
#> GSM674361     4  0.4164      0.909 0.000 0.000 0.264 0.736
#> GSM674363     4  0.4103      0.914 0.000 0.000 0.256 0.744
#> GSM674364     4  0.4866      0.727 0.000 0.000 0.404 0.596
#> GSM674365     4  0.4605      0.835 0.000 0.000 0.336 0.664
#> GSM674366     3  0.4955     -0.321 0.000 0.000 0.556 0.444
#> GSM674367     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674368     3  0.4843     -0.147 0.000 0.000 0.604 0.396
#> GSM674370     3  0.0336      0.846 0.000 0.000 0.992 0.008
#> GSM674371     4  0.4817      0.760 0.000 0.000 0.388 0.612
#> GSM674373     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674375     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674379     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674380     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674381     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674382     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674384     3  0.0592      0.839 0.000 0.000 0.984 0.016
#> GSM674385     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674388     4  0.4855      0.737 0.000 0.000 0.400 0.600
#> GSM674389     3  0.2589      0.721 0.000 0.000 0.884 0.116
#> GSM674390     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674391     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674393     4  0.4193      0.907 0.000 0.000 0.268 0.732
#> GSM674394     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674395     3  0.4454      0.316 0.000 0.000 0.692 0.308
#> GSM674397     3  0.4855     -0.166 0.000 0.000 0.600 0.400
#> GSM674398     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674400     4  0.4907      0.651 0.000 0.000 0.420 0.580
#> GSM674401     4  0.4134      0.912 0.000 0.000 0.260 0.740
#> GSM674402     4  0.4103      0.914 0.000 0.000 0.256 0.744
#> GSM674403     4  0.4103      0.914 0.000 0.000 0.256 0.744
#> GSM674405     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674406     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674407     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674181     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674183     4  0.5387      0.268 0.000 0.400 0.016 0.584
#> GSM674184     2  0.0921      0.956 0.000 0.972 0.000 0.028
#> GSM674185     2  0.3764      0.727 0.000 0.784 0.216 0.000
#> GSM674186     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674187     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674190     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674191     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674192     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674193     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674194     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674195     2  0.5050      0.313 0.000 0.588 0.004 0.408
#> GSM674198     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674200     4  0.4103      0.914 0.000 0.000 0.256 0.744
#> GSM674201     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674202     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674203     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674204     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674205     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674206     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674208     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674209     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674210     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674212     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674214     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674218     2  0.0817      0.960 0.000 0.976 0.000 0.024
#> GSM674219     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674220     3  0.4804      0.259 0.000 0.384 0.616 0.000
#> GSM674221     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674223     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674225     2  0.4817      0.399 0.000 0.612 0.388 0.000
#> GSM674226     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674229     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674230     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674231     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674232     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674234     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674235     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674236     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674237     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674239     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674240     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674242     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674243     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674244     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674245     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674282     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674284     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674285     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674287     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674288     1  0.2530      0.900 0.888 0.000 0.000 0.112
#> GSM674289     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674290     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674291     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674292     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674295     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674297     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674298     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674299     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674300     1  0.2704      0.900 0.876 0.000 0.000 0.124
#> GSM674301     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674302     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674304     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674305     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674306     1  0.0921      0.894 0.972 0.000 0.000 0.028
#> GSM674308     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674309     1  0.2760      0.898 0.872 0.000 0.000 0.128
#> GSM674313     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674314     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674315     1  0.1302      0.896 0.956 0.000 0.000 0.044
#> GSM674316     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674318     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674320     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674323     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674324     1  0.3688      0.901 0.792 0.000 0.000 0.208
#> GSM674325     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674327     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674328     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674330     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674331     1  0.2921      0.899 0.860 0.000 0.000 0.140
#> GSM674332     1  0.2081      0.899 0.916 0.000 0.000 0.084
#> GSM674334     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674335     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674345     4  0.4103      0.914 0.000 0.000 0.256 0.744
#> GSM674351     4  0.4103      0.914 0.000 0.000 0.256 0.744
#> GSM674352     4  0.4103      0.914 0.000 0.000 0.256 0.744
#> GSM674359     4  0.4103      0.914 0.000 0.000 0.256 0.744
#> GSM674360     4  0.4103      0.914 0.000 0.000 0.256 0.744
#> GSM674362     4  0.4103      0.914 0.000 0.000 0.256 0.744
#> GSM674369     3  0.5220     -0.254 0.000 0.008 0.568 0.424
#> GSM674372     3  0.4277      0.398 0.000 0.000 0.720 0.280
#> GSM674374     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674376     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674377     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674378     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674383     4  0.4500      0.862 0.000 0.000 0.316 0.684
#> GSM674386     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674387     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674392     3  0.4989     -0.351 0.000 0.000 0.528 0.472
#> GSM674396     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674399     3  0.0000      0.853 0.000 0.000 1.000 0.000
#> GSM674404     3  0.0336      0.846 0.000 0.000 0.992 0.008
#> GSM674182     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674188     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674189     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674196     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674197     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674199     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674207     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674211     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674213     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674215     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674216     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674217     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674222     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674224     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674227     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674228     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674233     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674238     4  0.4737      0.892 0.000 0.020 0.252 0.728
#> GSM674241     2  0.0000      0.982 0.000 1.000 0.000 0.000
#> GSM674283     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674286     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674293     1  0.3172      0.902 0.840 0.000 0.000 0.160
#> GSM674294     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674296     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674303     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674307     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674310     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674311     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674312     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674317     1  0.4103      0.899 0.744 0.000 0.000 0.256
#> GSM674319     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674321     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674322     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674326     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674329     1  0.0000      0.891 1.000 0.000 0.000 0.000
#> GSM674333     1  0.0000      0.891 1.000 0.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4    p5
#> GSM674344     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000
#> GSM674346     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000
#> GSM674347     3  0.3913      0.629 0.000 0.000 0.676 0.000 0.324
#> GSM674348     3  0.0880      0.847 0.000 0.000 0.968 0.000 0.032
#> GSM674349     3  0.0162      0.851 0.000 0.000 0.996 0.000 0.004
#> GSM674350     3  0.2127      0.827 0.000 0.000 0.892 0.000 0.108
#> GSM674353     3  0.2127      0.827 0.000 0.000 0.892 0.000 0.108
#> GSM674354     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000
#> GSM674355     3  0.4030      0.522 0.000 0.000 0.648 0.000 0.352
#> GSM674356     3  0.0794      0.848 0.000 0.000 0.972 0.000 0.028
#> GSM674357     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000
#> GSM674358     3  0.2020      0.831 0.000 0.000 0.900 0.000 0.100
#> GSM674361     3  0.2230      0.823 0.000 0.000 0.884 0.000 0.116
#> GSM674363     3  0.0290      0.852 0.000 0.000 0.992 0.000 0.008
#> GSM674364     3  0.2929      0.757 0.000 0.000 0.820 0.000 0.180
#> GSM674365     3  0.1908      0.822 0.000 0.000 0.908 0.000 0.092
#> GSM674366     3  0.4030      0.503 0.000 0.000 0.648 0.000 0.352
#> GSM674367     5  0.2230      0.843 0.000 0.000 0.116 0.000 0.884
#> GSM674368     3  0.4182      0.405 0.000 0.000 0.600 0.000 0.400
#> GSM674370     5  0.0609      0.916 0.000 0.000 0.020 0.000 0.980
#> GSM674371     3  0.2690      0.779 0.000 0.000 0.844 0.000 0.156
#> GSM674373     5  0.2280      0.840 0.000 0.000 0.120 0.000 0.880
#> GSM674375     5  0.0404      0.919 0.000 0.000 0.012 0.000 0.988
#> GSM674379     5  0.0404      0.919 0.000 0.000 0.012 0.000 0.988
#> GSM674380     5  0.1671      0.880 0.000 0.000 0.076 0.000 0.924
#> GSM674381     5  0.0963      0.908 0.000 0.000 0.036 0.000 0.964
#> GSM674382     5  0.0404      0.919 0.000 0.000 0.012 0.000 0.988
#> GSM674384     5  0.1270      0.892 0.000 0.000 0.052 0.000 0.948
#> GSM674385     5  0.1544      0.891 0.000 0.000 0.068 0.000 0.932
#> GSM674388     3  0.2966      0.753 0.000 0.000 0.816 0.000 0.184
#> GSM674389     5  0.2773      0.765 0.000 0.000 0.164 0.000 0.836
#> GSM674390     5  0.0404      0.919 0.000 0.000 0.012 0.000 0.988
#> GSM674391     5  0.0404      0.919 0.000 0.000 0.012 0.000 0.988
#> GSM674393     3  0.2471      0.823 0.000 0.000 0.864 0.000 0.136
#> GSM674394     5  0.0703      0.914 0.000 0.000 0.024 0.000 0.976
#> GSM674395     5  0.4101      0.355 0.000 0.000 0.372 0.000 0.628
#> GSM674397     3  0.4235      0.344 0.000 0.000 0.576 0.000 0.424
#> GSM674398     5  0.0404      0.919 0.000 0.000 0.012 0.000 0.988
#> GSM674400     3  0.3774      0.626 0.000 0.000 0.704 0.000 0.296
#> GSM674401     3  0.1965      0.836 0.000 0.000 0.904 0.000 0.096
#> GSM674402     3  0.2127      0.827 0.000 0.000 0.892 0.000 0.108
#> GSM674403     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000
#> GSM674405     5  0.0404      0.919 0.000 0.000 0.012 0.000 0.988
#> GSM674406     5  0.0404      0.919 0.000 0.000 0.012 0.000 0.988
#> GSM674407     5  0.0404      0.919 0.000 0.000 0.012 0.000 0.988
#> GSM674181     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674183     3  0.3242      0.646 0.000 0.216 0.784 0.000 0.000
#> GSM674184     2  0.0794      0.952 0.000 0.972 0.028 0.000 0.000
#> GSM674185     2  0.3305      0.699 0.000 0.776 0.000 0.000 0.224
#> GSM674186     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674187     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674190     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674191     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674192     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674193     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674194     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674195     2  0.4249      0.206 0.000 0.568 0.432 0.000 0.000
#> GSM674198     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674200     3  0.1851      0.836 0.000 0.000 0.912 0.000 0.088
#> GSM674201     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674202     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674203     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674204     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674205     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674206     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674208     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674209     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674210     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674212     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674214     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674218     2  0.0794      0.952 0.000 0.972 0.028 0.000 0.000
#> GSM674219     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674220     5  0.3999      0.464 0.000 0.344 0.000 0.000 0.656
#> GSM674221     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674223     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674225     2  0.4192      0.305 0.000 0.596 0.000 0.000 0.404
#> GSM674226     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674229     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674230     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674231     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674232     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674234     2  0.0404      0.972 0.000 0.988 0.000 0.000 0.012
#> GSM674235     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674236     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674237     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674239     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674240     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674242     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674243     2  0.0324      0.973 0.004 0.992 0.000 0.000 0.004
#> GSM674244     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674245     2  0.0566      0.972 0.004 0.984 0.000 0.000 0.012
#> GSM674282     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674284     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674285     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674287     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674288     4  0.4015      0.433 0.348 0.000 0.000 0.652 0.000
#> GSM674289     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674290     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674291     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674292     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674295     1  0.0404      0.925 0.988 0.000 0.000 0.012 0.000
#> GSM674297     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674298     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674299     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674300     4  0.3177      0.721 0.208 0.000 0.000 0.792 0.000
#> GSM674301     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674302     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674304     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674305     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674306     1  0.3983      0.508 0.660 0.000 0.000 0.340 0.000
#> GSM674308     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674309     1  0.3177      0.751 0.792 0.000 0.000 0.208 0.000
#> GSM674313     1  0.0290      0.925 0.992 0.000 0.000 0.008 0.000
#> GSM674314     1  0.0290      0.925 0.992 0.000 0.000 0.008 0.000
#> GSM674315     1  0.3508      0.674 0.748 0.000 0.000 0.252 0.000
#> GSM674316     1  0.0290      0.925 0.992 0.000 0.000 0.008 0.000
#> GSM674318     1  0.0290      0.925 0.992 0.000 0.000 0.008 0.000
#> GSM674320     1  0.0290      0.925 0.992 0.000 0.000 0.008 0.000
#> GSM674323     1  0.0290      0.925 0.992 0.000 0.000 0.008 0.000
#> GSM674324     1  0.4219      0.376 0.584 0.000 0.000 0.416 0.000
#> GSM674325     1  0.0290      0.925 0.992 0.000 0.000 0.008 0.000
#> GSM674327     1  0.0290      0.925 0.992 0.000 0.000 0.008 0.000
#> GSM674328     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674330     1  0.0703      0.921 0.976 0.000 0.000 0.024 0.000
#> GSM674331     1  0.3274      0.736 0.780 0.000 0.000 0.220 0.000
#> GSM674332     1  0.3949      0.542 0.668 0.000 0.000 0.332 0.000
#> GSM674334     1  0.0703      0.921 0.976 0.000 0.000 0.024 0.000
#> GSM674335     1  0.0703      0.921 0.976 0.000 0.000 0.024 0.000
#> GSM674345     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000
#> GSM674351     3  0.2127      0.827 0.000 0.000 0.892 0.000 0.108
#> GSM674352     3  0.0290      0.852 0.000 0.000 0.992 0.000 0.008
#> GSM674359     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000
#> GSM674360     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000
#> GSM674362     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000
#> GSM674369     3  0.4088      0.474 0.000 0.000 0.632 0.000 0.368
#> GSM674372     5  0.3966      0.447 0.000 0.000 0.336 0.000 0.664
#> GSM674374     5  0.2280      0.842 0.000 0.000 0.120 0.000 0.880
#> GSM674376     5  0.0404      0.919 0.000 0.000 0.012 0.000 0.988
#> GSM674377     5  0.2280      0.840 0.000 0.000 0.120 0.000 0.880
#> GSM674378     5  0.0404      0.919 0.000 0.000 0.012 0.000 0.988
#> GSM674383     3  0.1732      0.839 0.000 0.000 0.920 0.000 0.080
#> GSM674386     5  0.0404      0.919 0.000 0.000 0.012 0.000 0.988
#> GSM674387     5  0.0404      0.919 0.000 0.000 0.012 0.000 0.988
#> GSM674392     3  0.4192      0.391 0.000 0.000 0.596 0.000 0.404
#> GSM674396     5  0.0404      0.919 0.000 0.000 0.012 0.000 0.988
#> GSM674399     5  0.0404      0.919 0.000 0.000 0.012 0.000 0.988
#> GSM674404     5  0.0609      0.915 0.000 0.000 0.020 0.000 0.980
#> GSM674182     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674188     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674189     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674196     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674197     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674199     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674207     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674211     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674213     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674215     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674216     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674217     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674222     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674224     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674227     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674228     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674233     2  0.0000      0.973 0.000 1.000 0.000 0.000 0.000
#> GSM674238     3  0.0798      0.848 0.000 0.016 0.976 0.000 0.008
#> GSM674241     2  0.0693      0.971 0.008 0.980 0.000 0.000 0.012
#> GSM674283     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674286     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674293     4  0.2471      0.824 0.136 0.000 0.000 0.864 0.000
#> GSM674294     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674296     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674303     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674307     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674310     1  0.0290      0.925 0.992 0.000 0.000 0.008 0.000
#> GSM674311     1  0.0703      0.921 0.976 0.000 0.000 0.024 0.000
#> GSM674312     1  0.0290      0.925 0.992 0.000 0.000 0.008 0.000
#> GSM674317     4  0.0000      0.971 0.000 0.000 0.000 1.000 0.000
#> GSM674319     1  0.0703      0.921 0.976 0.000 0.000 0.024 0.000
#> GSM674321     1  0.0290      0.925 0.992 0.000 0.000 0.008 0.000
#> GSM674322     1  0.0290      0.925 0.992 0.000 0.000 0.008 0.000
#> GSM674326     1  0.0290      0.925 0.992 0.000 0.000 0.008 0.000
#> GSM674329     1  0.0290      0.925 0.992 0.000 0.000 0.008 0.000
#> GSM674333     1  0.0609      0.922 0.980 0.000 0.000 0.020 0.000

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4    p5    p6
#> GSM674344     3  0.0000     0.8439 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM674346     3  0.0260     0.8442 0.000 0.008 0.992 0.000 0.000 0.000
#> GSM674347     3  0.4067     0.3349 0.000 0.008 0.548 0.444 0.000 0.000
#> GSM674348     3  0.0790     0.8360 0.000 0.000 0.968 0.032 0.000 0.000
#> GSM674349     3  0.0260     0.8427 0.000 0.000 0.992 0.008 0.000 0.000
#> GSM674350     3  0.2212     0.8309 0.000 0.008 0.880 0.112 0.000 0.000
#> GSM674353     3  0.2212     0.8309 0.000 0.008 0.880 0.112 0.000 0.000
#> GSM674354     3  0.0000     0.8439 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM674355     3  0.3217     0.7502 0.000 0.008 0.768 0.224 0.000 0.000
#> GSM674356     3  0.0790     0.8362 0.000 0.000 0.968 0.032 0.000 0.000
#> GSM674357     3  0.0000     0.8439 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM674358     3  0.2118     0.8339 0.000 0.008 0.888 0.104 0.000 0.000
#> GSM674361     3  0.2346     0.8276 0.000 0.008 0.868 0.124 0.000 0.000
#> GSM674363     3  0.0520     0.8454 0.000 0.008 0.984 0.008 0.000 0.000
#> GSM674364     3  0.3409     0.5383 0.000 0.000 0.700 0.300 0.000 0.000
#> GSM674365     3  0.2664     0.7101 0.000 0.000 0.816 0.184 0.000 0.000
#> GSM674366     4  0.3531     0.5748 0.000 0.000 0.328 0.672 0.000 0.000
#> GSM674367     4  0.1910     0.8494 0.000 0.000 0.108 0.892 0.000 0.000
#> GSM674368     4  0.3482     0.5945 0.000 0.000 0.316 0.684 0.000 0.000
#> GSM674370     4  0.0260     0.9072 0.000 0.000 0.008 0.992 0.000 0.000
#> GSM674371     3  0.3647     0.3949 0.000 0.000 0.640 0.360 0.000 0.000
#> GSM674373     4  0.1957     0.8463 0.000 0.000 0.112 0.888 0.000 0.000
#> GSM674375     4  0.0000     0.9108 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674379     4  0.0000     0.9108 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674380     4  0.2020     0.8405 0.000 0.000 0.008 0.896 0.000 0.096
#> GSM674381     4  0.0632     0.9021 0.000 0.000 0.024 0.976 0.000 0.000
#> GSM674382     4  0.0000     0.9108 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674384     4  0.1327     0.8629 0.000 0.000 0.064 0.936 0.000 0.000
#> GSM674385     4  0.1387     0.8834 0.000 0.000 0.068 0.932 0.000 0.000
#> GSM674388     3  0.3695     0.3486 0.000 0.000 0.624 0.376 0.000 0.000
#> GSM674389     4  0.3575     0.4766 0.000 0.008 0.284 0.708 0.000 0.000
#> GSM674390     4  0.0000     0.9108 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674391     4  0.0000     0.9108 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674393     3  0.2416     0.8211 0.000 0.000 0.844 0.156 0.000 0.000
#> GSM674394     4  0.0713     0.8957 0.000 0.000 0.028 0.972 0.000 0.000
#> GSM674395     3  0.3741     0.6173 0.000 0.008 0.672 0.320 0.000 0.000
#> GSM674397     4  0.3221     0.6788 0.000 0.000 0.264 0.736 0.000 0.000
#> GSM674398     4  0.0000     0.9108 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674400     3  0.2669     0.8115 0.000 0.008 0.836 0.156 0.000 0.000
#> GSM674401     3  0.2070     0.8380 0.000 0.008 0.892 0.100 0.000 0.000
#> GSM674402     3  0.2212     0.8309 0.000 0.008 0.880 0.112 0.000 0.000
#> GSM674403     3  0.0260     0.8442 0.000 0.008 0.992 0.000 0.000 0.000
#> GSM674405     4  0.0000     0.9108 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674406     4  0.0000     0.9108 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674407     4  0.0000     0.9108 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674181     6  0.2491     0.8612 0.000 0.164 0.000 0.000 0.000 0.836
#> GSM674183     6  0.2178     0.7676 0.000 0.000 0.132 0.000 0.000 0.868
#> GSM674184     6  0.2454     0.8630 0.000 0.160 0.000 0.000 0.000 0.840
#> GSM674185     6  0.0000     0.8595 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM674186     6  0.2491     0.8612 0.000 0.164 0.000 0.000 0.000 0.836
#> GSM674187     6  0.2854     0.8478 0.000 0.208 0.000 0.000 0.000 0.792
#> GSM674190     6  0.2854     0.8478 0.000 0.208 0.000 0.000 0.000 0.792
#> GSM674191     6  0.2491     0.8630 0.000 0.164 0.000 0.000 0.000 0.836
#> GSM674192     2  0.1610     0.9030 0.000 0.916 0.000 0.000 0.000 0.084
#> GSM674193     6  0.2854     0.8478 0.000 0.208 0.000 0.000 0.000 0.792
#> GSM674194     6  0.2454     0.8630 0.000 0.160 0.000 0.000 0.000 0.840
#> GSM674195     6  0.2593     0.8655 0.000 0.148 0.008 0.000 0.000 0.844
#> GSM674198     2  0.0790     0.9300 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM674200     3  0.2588     0.8333 0.000 0.008 0.876 0.092 0.000 0.024
#> GSM674201     6  0.1610     0.8756 0.000 0.084 0.000 0.000 0.000 0.916
#> GSM674202     6  0.0260     0.8620 0.000 0.008 0.000 0.000 0.000 0.992
#> GSM674203     2  0.0790     0.9300 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM674204     2  0.1141     0.9210 0.000 0.948 0.000 0.000 0.000 0.052
#> GSM674205     2  0.0790     0.9300 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM674206     6  0.0458     0.8663 0.000 0.016 0.000 0.000 0.000 0.984
#> GSM674208     2  0.0790     0.9300 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM674209     2  0.1610     0.9030 0.000 0.916 0.000 0.000 0.000 0.084
#> GSM674210     2  0.0790     0.9300 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM674212     2  0.0790     0.9300 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM674214     2  0.0790     0.9300 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM674218     6  0.0000     0.8595 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM674219     6  0.0000     0.8595 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM674220     6  0.3817     0.0878 0.000 0.000 0.000 0.432 0.000 0.568
#> GSM674221     6  0.1765     0.8739 0.000 0.096 0.000 0.000 0.000 0.904
#> GSM674223     6  0.2527     0.8654 0.000 0.168 0.000 0.000 0.000 0.832
#> GSM674225     6  0.0000     0.8595 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM674226     6  0.2854     0.8478 0.000 0.208 0.000 0.000 0.000 0.792
#> GSM674229     2  0.0865     0.9291 0.000 0.964 0.000 0.000 0.000 0.036
#> GSM674230     6  0.1075     0.8681 0.000 0.048 0.000 0.000 0.000 0.952
#> GSM674231     6  0.1007     0.8668 0.000 0.044 0.000 0.000 0.000 0.956
#> GSM674232     2  0.3126     0.7701 0.000 0.752 0.000 0.000 0.000 0.248
#> GSM674234     2  0.2597     0.8161 0.000 0.824 0.000 0.000 0.000 0.176
#> GSM674235     6  0.1007     0.8668 0.000 0.044 0.000 0.000 0.000 0.956
#> GSM674236     6  0.1007     0.8668 0.000 0.044 0.000 0.000 0.000 0.956
#> GSM674237     2  0.2730     0.7949 0.000 0.808 0.000 0.000 0.000 0.192
#> GSM674239     2  0.1556     0.9059 0.000 0.920 0.000 0.000 0.000 0.080
#> GSM674240     6  0.2854     0.8478 0.000 0.208 0.000 0.000 0.000 0.792
#> GSM674242     2  0.0790     0.9300 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM674243     2  0.3862     0.2494 0.000 0.524 0.000 0.000 0.000 0.476
#> GSM674244     6  0.2416     0.8651 0.000 0.156 0.000 0.000 0.000 0.844
#> GSM674245     2  0.2378     0.8299 0.000 0.848 0.000 0.000 0.000 0.152
#> GSM674282     1  0.0000     0.9645 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674284     1  0.0458     0.9635 0.984 0.016 0.000 0.000 0.000 0.000
#> GSM674285     1  0.0458     0.9635 0.984 0.016 0.000 0.000 0.000 0.000
#> GSM674287     1  0.0000     0.9645 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674288     1  0.3531     0.4832 0.672 0.000 0.000 0.000 0.328 0.000
#> GSM674289     1  0.0000     0.9645 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0000     0.9645 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674291     1  0.0000     0.9645 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674292     1  0.0000     0.9645 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674295     5  0.0363     0.9201 0.012 0.000 0.000 0.000 0.988 0.000
#> GSM674297     1  0.0632     0.9614 0.976 0.024 0.000 0.000 0.000 0.000
#> GSM674298     1  0.0632     0.9614 0.976 0.024 0.000 0.000 0.000 0.000
#> GSM674299     1  0.0000     0.9645 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674300     1  0.2793     0.7448 0.800 0.000 0.000 0.000 0.200 0.000
#> GSM674301     1  0.0260     0.9645 0.992 0.008 0.000 0.000 0.000 0.000
#> GSM674302     1  0.0632     0.9614 0.976 0.024 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0363     0.9638 0.988 0.012 0.000 0.000 0.000 0.000
#> GSM674305     1  0.0146     0.9645 0.996 0.004 0.000 0.000 0.000 0.000
#> GSM674306     5  0.3578     0.4908 0.340 0.000 0.000 0.000 0.660 0.000
#> GSM674308     1  0.0458     0.9636 0.984 0.016 0.000 0.000 0.000 0.000
#> GSM674309     5  0.3202     0.7682 0.176 0.024 0.000 0.000 0.800 0.000
#> GSM674313     5  0.0000     0.9222 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674314     5  0.0458     0.9192 0.000 0.016 0.000 0.000 0.984 0.000
#> GSM674315     5  0.3126     0.6685 0.248 0.000 0.000 0.000 0.752 0.000
#> GSM674316     5  0.0000     0.9222 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674318     5  0.0000     0.9222 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674320     5  0.0000     0.9222 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674323     5  0.0000     0.9222 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674324     5  0.4283     0.4118 0.384 0.024 0.000 0.000 0.592 0.000
#> GSM674325     5  0.0000     0.9222 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674327     5  0.0000     0.9222 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674328     1  0.0000     0.9645 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674330     5  0.0993     0.9137 0.012 0.024 0.000 0.000 0.964 0.000
#> GSM674331     5  0.3301     0.7547 0.188 0.024 0.000 0.000 0.788 0.000
#> GSM674332     5  0.4078     0.5317 0.320 0.024 0.000 0.000 0.656 0.000
#> GSM674334     5  0.0935     0.9131 0.032 0.004 0.000 0.000 0.964 0.000
#> GSM674335     5  0.0993     0.9137 0.012 0.024 0.000 0.000 0.964 0.000
#> GSM674345     3  0.0000     0.8439 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM674351     3  0.2212     0.8309 0.000 0.008 0.880 0.112 0.000 0.000
#> GSM674352     3  0.0520     0.8454 0.000 0.008 0.984 0.008 0.000 0.000
#> GSM674359     3  0.0000     0.8439 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM674360     3  0.0000     0.8439 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM674362     3  0.0000     0.8439 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM674369     4  0.3499     0.5882 0.000 0.000 0.320 0.680 0.000 0.000
#> GSM674372     3  0.4057     0.3997 0.000 0.008 0.556 0.436 0.000 0.000
#> GSM674374     4  0.2048     0.8442 0.000 0.000 0.120 0.880 0.000 0.000
#> GSM674376     4  0.0000     0.9108 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674377     4  0.1957     0.8463 0.000 0.000 0.112 0.888 0.000 0.000
#> GSM674378     4  0.0000     0.9108 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674383     3  0.2416     0.7692 0.000 0.000 0.844 0.156 0.000 0.000
#> GSM674386     4  0.0000     0.9108 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674387     4  0.0000     0.9108 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674392     3  0.3271     0.7493 0.000 0.008 0.760 0.232 0.000 0.000
#> GSM674396     4  0.0000     0.9108 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674399     4  0.0000     0.9108 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM674404     4  0.0260     0.9065 0.000 0.000 0.008 0.992 0.000 0.000
#> GSM674182     6  0.2527     0.8609 0.000 0.168 0.000 0.000 0.000 0.832
#> GSM674188     6  0.2823     0.8503 0.000 0.204 0.000 0.000 0.000 0.796
#> GSM674189     6  0.2378     0.8665 0.000 0.152 0.000 0.000 0.000 0.848
#> GSM674196     2  0.0790     0.9300 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM674197     2  0.0790     0.9300 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM674199     2  0.0937     0.9274 0.000 0.960 0.000 0.000 0.000 0.040
#> GSM674207     2  0.0865     0.9291 0.000 0.964 0.000 0.000 0.000 0.036
#> GSM674211     2  0.0790     0.9300 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM674213     6  0.2664     0.8588 0.000 0.184 0.000 0.000 0.000 0.816
#> GSM674215     6  0.0000     0.8595 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM674216     2  0.2969     0.7836 0.000 0.776 0.000 0.000 0.000 0.224
#> GSM674217     6  0.1204     0.8702 0.000 0.056 0.000 0.000 0.000 0.944
#> GSM674222     6  0.1007     0.8668 0.000 0.044 0.000 0.000 0.000 0.956
#> GSM674224     6  0.2854     0.8478 0.000 0.208 0.000 0.000 0.000 0.792
#> GSM674227     6  0.1007     0.8668 0.000 0.044 0.000 0.000 0.000 0.956
#> GSM674228     6  0.1141     0.8643 0.000 0.052 0.000 0.000 0.000 0.948
#> GSM674233     6  0.1007     0.8668 0.000 0.044 0.000 0.000 0.000 0.956
#> GSM674238     3  0.3923     0.4283 0.000 0.000 0.620 0.008 0.000 0.372
#> GSM674241     2  0.1327     0.9158 0.000 0.936 0.000 0.000 0.000 0.064
#> GSM674283     1  0.0363     0.9639 0.988 0.012 0.000 0.000 0.000 0.000
#> GSM674286     1  0.0000     0.9645 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674293     1  0.2178     0.8361 0.868 0.000 0.000 0.000 0.132 0.000
#> GSM674294     1  0.0000     0.9645 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674296     1  0.0632     0.9614 0.976 0.024 0.000 0.000 0.000 0.000
#> GSM674303     1  0.0632     0.9614 0.976 0.024 0.000 0.000 0.000 0.000
#> GSM674307     1  0.0632     0.9614 0.976 0.024 0.000 0.000 0.000 0.000
#> GSM674310     5  0.0000     0.9222 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674311     5  0.0993     0.9137 0.012 0.024 0.000 0.000 0.964 0.000
#> GSM674312     5  0.0000     0.9222 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674317     1  0.0363     0.9639 0.988 0.012 0.000 0.000 0.000 0.000
#> GSM674319     5  0.0993     0.9137 0.012 0.024 0.000 0.000 0.964 0.000
#> GSM674321     5  0.0000     0.9222 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674322     5  0.0000     0.9222 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674326     5  0.0000     0.9222 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674329     5  0.0000     0.9222 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM674333     5  0.0632     0.9170 0.024 0.000 0.000 0.000 0.976 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-ATC-pam-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-ATC-pam-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-ATC-pam-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-ATC-pam-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-ATC-pam-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-ATC-pam-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-ATC-pam-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-ATC-pam-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-ATC-pam-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-ATC-pam-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-ATC-pam-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-ATC-pam-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-ATC-pam-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-ATC-pam-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-ATC-pam-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-ATC-pam-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-ATC-pam-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-ATC-pam-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-ATC-pam-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-ATC-pam-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk ATC-pam-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-ATC-pam-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-ATC-pam-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-ATC-pam-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-ATC-pam-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-ATC-pam-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk ATC-pam-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>           n disease.state(p) specimen(p) k
#> ATC:pam 183            0.924    1.83e-40 2
#> ATC:pam 183            0.942    1.46e-75 3
#> ATC:pam 172            0.901    6.69e-69 4
#> ATC:pam 172            0.896    3.86e-66 5
#> ATC:pam 172            0.983    1.10e-66 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


ATC:mclust*

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["ATC", "mclust"]
# you can also extract it by
# res = res_list["ATC:mclust"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#>   Subgroups are detected by 'mclust' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 5.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk ATC-mclust-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk ATC-mclust-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 1.000           0.986       0.994         0.5956 0.750   0.571
#> 4 4 0.915           0.937       0.917         0.0584 0.949   0.848
#> 5 5 0.915           0.869       0.938         0.0596 0.964   0.875
#> 6 6 0.787           0.751       0.860         0.0320 0.982   0.930

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3 4

There is also optional best \(k\) = 2 3 4 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette p1    p2    p3
#> GSM674344     3  0.0000     0.9911  0 0.000 1.000
#> GSM674346     3  0.0000     0.9911  0 0.000 1.000
#> GSM674347     3  0.0000     0.9911  0 0.000 1.000
#> GSM674348     3  0.0000     0.9911  0 0.000 1.000
#> GSM674349     3  0.0000     0.9911  0 0.000 1.000
#> GSM674350     3  0.0000     0.9911  0 0.000 1.000
#> GSM674353     3  0.0000     0.9911  0 0.000 1.000
#> GSM674354     3  0.0000     0.9911  0 0.000 1.000
#> GSM674355     3  0.0000     0.9911  0 0.000 1.000
#> GSM674356     3  0.0000     0.9911  0 0.000 1.000
#> GSM674357     3  0.0000     0.9911  0 0.000 1.000
#> GSM674358     3  0.0000     0.9911  0 0.000 1.000
#> GSM674361     3  0.0000     0.9911  0 0.000 1.000
#> GSM674363     3  0.0000     0.9911  0 0.000 1.000
#> GSM674364     3  0.0000     0.9911  0 0.000 1.000
#> GSM674365     3  0.0000     0.9911  0 0.000 1.000
#> GSM674366     3  0.0000     0.9911  0 0.000 1.000
#> GSM674367     3  0.0000     0.9911  0 0.000 1.000
#> GSM674368     3  0.0000     0.9911  0 0.000 1.000
#> GSM674370     3  0.0000     0.9911  0 0.000 1.000
#> GSM674371     3  0.0000     0.9911  0 0.000 1.000
#> GSM674373     3  0.0000     0.9911  0 0.000 1.000
#> GSM674375     3  0.0000     0.9911  0 0.000 1.000
#> GSM674379     3  0.0000     0.9911  0 0.000 1.000
#> GSM674380     2  0.6299     0.0763  0 0.524 0.476
#> GSM674381     3  0.0000     0.9911  0 0.000 1.000
#> GSM674382     3  0.0000     0.9911  0 0.000 1.000
#> GSM674384     3  0.0000     0.9911  0 0.000 1.000
#> GSM674385     3  0.0237     0.9880  0 0.004 0.996
#> GSM674388     3  0.0000     0.9911  0 0.000 1.000
#> GSM674389     3  0.0000     0.9911  0 0.000 1.000
#> GSM674390     3  0.0000     0.9911  0 0.000 1.000
#> GSM674391     3  0.0000     0.9911  0 0.000 1.000
#> GSM674393     3  0.0000     0.9911  0 0.000 1.000
#> GSM674394     3  0.0000     0.9911  0 0.000 1.000
#> GSM674395     3  0.0000     0.9911  0 0.000 1.000
#> GSM674397     3  0.0000     0.9911  0 0.000 1.000
#> GSM674398     3  0.0000     0.9911  0 0.000 1.000
#> GSM674400     3  0.0237     0.9881  0 0.004 0.996
#> GSM674401     3  0.0237     0.9881  0 0.004 0.996
#> GSM674402     3  0.0237     0.9881  0 0.004 0.996
#> GSM674403     3  0.0237     0.9881  0 0.004 0.996
#> GSM674405     3  0.0000     0.9911  0 0.000 1.000
#> GSM674406     3  0.0000     0.9911  0 0.000 1.000
#> GSM674407     3  0.0000     0.9911  0 0.000 1.000
#> GSM674181     2  0.0000     0.9921  0 1.000 0.000
#> GSM674183     2  0.0000     0.9921  0 1.000 0.000
#> GSM674184     2  0.0000     0.9921  0 1.000 0.000
#> GSM674185     2  0.0000     0.9921  0 1.000 0.000
#> GSM674186     2  0.0000     0.9921  0 1.000 0.000
#> GSM674187     2  0.0000     0.9921  0 1.000 0.000
#> GSM674190     2  0.0000     0.9921  0 1.000 0.000
#> GSM674191     2  0.0000     0.9921  0 1.000 0.000
#> GSM674192     2  0.0000     0.9921  0 1.000 0.000
#> GSM674193     2  0.0000     0.9921  0 1.000 0.000
#> GSM674194     2  0.0000     0.9921  0 1.000 0.000
#> GSM674195     2  0.0000     0.9921  0 1.000 0.000
#> GSM674198     2  0.0000     0.9921  0 1.000 0.000
#> GSM674200     3  0.0237     0.9881  0 0.004 0.996
#> GSM674201     2  0.0000     0.9921  0 1.000 0.000
#> GSM674202     2  0.0000     0.9921  0 1.000 0.000
#> GSM674203     2  0.0000     0.9921  0 1.000 0.000
#> GSM674204     2  0.0000     0.9921  0 1.000 0.000
#> GSM674205     2  0.0000     0.9921  0 1.000 0.000
#> GSM674206     2  0.0000     0.9921  0 1.000 0.000
#> GSM674208     2  0.0000     0.9921  0 1.000 0.000
#> GSM674209     2  0.0000     0.9921  0 1.000 0.000
#> GSM674210     2  0.0000     0.9921  0 1.000 0.000
#> GSM674212     2  0.0000     0.9921  0 1.000 0.000
#> GSM674214     2  0.0000     0.9921  0 1.000 0.000
#> GSM674218     2  0.0000     0.9921  0 1.000 0.000
#> GSM674219     2  0.0000     0.9921  0 1.000 0.000
#> GSM674220     2  0.0000     0.9921  0 1.000 0.000
#> GSM674221     2  0.0000     0.9921  0 1.000 0.000
#> GSM674223     2  0.0000     0.9921  0 1.000 0.000
#> GSM674225     2  0.0000     0.9921  0 1.000 0.000
#> GSM674226     2  0.0000     0.9921  0 1.000 0.000
#> GSM674229     2  0.0000     0.9921  0 1.000 0.000
#> GSM674230     2  0.0000     0.9921  0 1.000 0.000
#> GSM674231     2  0.0000     0.9921  0 1.000 0.000
#> GSM674232     2  0.0000     0.9921  0 1.000 0.000
#> GSM674234     2  0.0000     0.9921  0 1.000 0.000
#> GSM674235     2  0.0000     0.9921  0 1.000 0.000
#> GSM674236     2  0.0000     0.9921  0 1.000 0.000
#> GSM674237     2  0.0000     0.9921  0 1.000 0.000
#> GSM674239     2  0.0000     0.9921  0 1.000 0.000
#> GSM674240     2  0.0000     0.9921  0 1.000 0.000
#> GSM674242     2  0.0000     0.9921  0 1.000 0.000
#> GSM674243     2  0.0000     0.9921  0 1.000 0.000
#> GSM674244     2  0.0000     0.9921  0 1.000 0.000
#> GSM674245     2  0.0000     0.9921  0 1.000 0.000
#> GSM674282     1  0.0000     1.0000  1 0.000 0.000
#> GSM674284     1  0.0000     1.0000  1 0.000 0.000
#> GSM674285     1  0.0000     1.0000  1 0.000 0.000
#> GSM674287     1  0.0000     1.0000  1 0.000 0.000
#> GSM674288     1  0.0000     1.0000  1 0.000 0.000
#> GSM674289     1  0.0000     1.0000  1 0.000 0.000
#> GSM674290     1  0.0000     1.0000  1 0.000 0.000
#> GSM674291     1  0.0000     1.0000  1 0.000 0.000
#> GSM674292     1  0.0000     1.0000  1 0.000 0.000
#> GSM674295     1  0.0000     1.0000  1 0.000 0.000
#> GSM674297     1  0.0000     1.0000  1 0.000 0.000
#> GSM674298     1  0.0000     1.0000  1 0.000 0.000
#> GSM674299     1  0.0000     1.0000  1 0.000 0.000
#> GSM674300     1  0.0000     1.0000  1 0.000 0.000
#> GSM674301     1  0.0000     1.0000  1 0.000 0.000
#> GSM674302     1  0.0000     1.0000  1 0.000 0.000
#> GSM674304     1  0.0000     1.0000  1 0.000 0.000
#> GSM674305     1  0.0000     1.0000  1 0.000 0.000
#> GSM674306     1  0.0000     1.0000  1 0.000 0.000
#> GSM674308     1  0.0000     1.0000  1 0.000 0.000
#> GSM674309     1  0.0000     1.0000  1 0.000 0.000
#> GSM674313     1  0.0000     1.0000  1 0.000 0.000
#> GSM674314     1  0.0000     1.0000  1 0.000 0.000
#> GSM674315     1  0.0000     1.0000  1 0.000 0.000
#> GSM674316     1  0.0000     1.0000  1 0.000 0.000
#> GSM674318     1  0.0000     1.0000  1 0.000 0.000
#> GSM674320     1  0.0000     1.0000  1 0.000 0.000
#> GSM674323     1  0.0000     1.0000  1 0.000 0.000
#> GSM674324     1  0.0000     1.0000  1 0.000 0.000
#> GSM674325     1  0.0000     1.0000  1 0.000 0.000
#> GSM674327     1  0.0000     1.0000  1 0.000 0.000
#> GSM674328     1  0.0000     1.0000  1 0.000 0.000
#> GSM674330     1  0.0000     1.0000  1 0.000 0.000
#> GSM674331     1  0.0000     1.0000  1 0.000 0.000
#> GSM674332     1  0.0000     1.0000  1 0.000 0.000
#> GSM674334     1  0.0000     1.0000  1 0.000 0.000
#> GSM674335     1  0.0000     1.0000  1 0.000 0.000
#> GSM674345     3  0.0000     0.9911  0 0.000 1.000
#> GSM674351     3  0.0000     0.9911  0 0.000 1.000
#> GSM674352     3  0.0000     0.9911  0 0.000 1.000
#> GSM674359     3  0.0000     0.9911  0 0.000 1.000
#> GSM674360     3  0.0000     0.9911  0 0.000 1.000
#> GSM674362     3  0.1860     0.9409  0 0.052 0.948
#> GSM674369     3  0.0747     0.9771  0 0.016 0.984
#> GSM674372     3  0.0000     0.9911  0 0.000 1.000
#> GSM674374     3  0.0000     0.9911  0 0.000 1.000
#> GSM674376     3  0.0000     0.9911  0 0.000 1.000
#> GSM674377     3  0.4750     0.7265  0 0.216 0.784
#> GSM674378     3  0.0000     0.9911  0 0.000 1.000
#> GSM674383     3  0.0000     0.9911  0 0.000 1.000
#> GSM674386     3  0.0000     0.9911  0 0.000 1.000
#> GSM674387     3  0.0000     0.9911  0 0.000 1.000
#> GSM674392     3  0.0000     0.9911  0 0.000 1.000
#> GSM674396     3  0.0000     0.9911  0 0.000 1.000
#> GSM674399     3  0.0000     0.9911  0 0.000 1.000
#> GSM674404     3  0.0000     0.9911  0 0.000 1.000
#> GSM674182     2  0.0000     0.9921  0 1.000 0.000
#> GSM674188     2  0.0000     0.9921  0 1.000 0.000
#> GSM674189     2  0.0000     0.9921  0 1.000 0.000
#> GSM674196     2  0.0000     0.9921  0 1.000 0.000
#> GSM674197     2  0.0000     0.9921  0 1.000 0.000
#> GSM674199     2  0.0000     0.9921  0 1.000 0.000
#> GSM674207     2  0.0000     0.9921  0 1.000 0.000
#> GSM674211     2  0.0000     0.9921  0 1.000 0.000
#> GSM674213     2  0.0000     0.9921  0 1.000 0.000
#> GSM674215     2  0.0000     0.9921  0 1.000 0.000
#> GSM674216     2  0.0000     0.9921  0 1.000 0.000
#> GSM674217     2  0.0000     0.9921  0 1.000 0.000
#> GSM674222     2  0.0000     0.9921  0 1.000 0.000
#> GSM674224     2  0.0000     0.9921  0 1.000 0.000
#> GSM674227     2  0.0000     0.9921  0 1.000 0.000
#> GSM674228     2  0.0000     0.9921  0 1.000 0.000
#> GSM674233     2  0.0000     0.9921  0 1.000 0.000
#> GSM674238     3  0.5016     0.6880  0 0.240 0.760
#> GSM674241     2  0.0000     0.9921  0 1.000 0.000
#> GSM674283     1  0.0000     1.0000  1 0.000 0.000
#> GSM674286     1  0.0000     1.0000  1 0.000 0.000
#> GSM674293     1  0.0000     1.0000  1 0.000 0.000
#> GSM674294     1  0.0000     1.0000  1 0.000 0.000
#> GSM674296     1  0.0000     1.0000  1 0.000 0.000
#> GSM674303     1  0.0000     1.0000  1 0.000 0.000
#> GSM674307     1  0.0000     1.0000  1 0.000 0.000
#> GSM674310     1  0.0000     1.0000  1 0.000 0.000
#> GSM674311     1  0.0000     1.0000  1 0.000 0.000
#> GSM674312     1  0.0000     1.0000  1 0.000 0.000
#> GSM674317     1  0.0000     1.0000  1 0.000 0.000
#> GSM674319     1  0.0000     1.0000  1 0.000 0.000
#> GSM674321     1  0.0000     1.0000  1 0.000 0.000
#> GSM674322     1  0.0000     1.0000  1 0.000 0.000
#> GSM674326     1  0.0000     1.0000  1 0.000 0.000
#> GSM674329     1  0.0000     1.0000  1 0.000 0.000
#> GSM674333     1  0.0000     1.0000  1 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1    p2    p3    p4
#> GSM674344     3  0.1940      0.912 0.076 0.000 0.924 0.000
#> GSM674346     3  0.3266      0.850 0.168 0.000 0.832 0.000
#> GSM674347     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674348     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674349     3  0.0707      0.943 0.020 0.000 0.980 0.000
#> GSM674350     3  0.0188      0.950 0.004 0.000 0.996 0.000
#> GSM674353     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674354     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674355     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674356     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674357     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674358     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674361     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674363     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674364     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674365     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674366     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674367     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674368     3  0.2011      0.890 0.000 0.080 0.920 0.000
#> GSM674370     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674371     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674373     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674375     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674379     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674380     3  0.6033      0.669 0.116 0.204 0.680 0.000
#> GSM674381     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674382     3  0.0188      0.950 0.004 0.000 0.996 0.000
#> GSM674384     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674385     3  0.0524      0.946 0.008 0.004 0.988 0.000
#> GSM674388     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674389     3  0.0188      0.950 0.004 0.000 0.996 0.000
#> GSM674390     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674391     3  0.0188      0.950 0.004 0.000 0.996 0.000
#> GSM674393     3  0.0188      0.950 0.004 0.000 0.996 0.000
#> GSM674394     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674395     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674397     3  0.0592      0.941 0.000 0.016 0.984 0.000
#> GSM674398     3  0.0336      0.949 0.008 0.000 0.992 0.000
#> GSM674400     3  0.4222      0.769 0.272 0.000 0.728 0.000
#> GSM674401     3  0.4730      0.679 0.364 0.000 0.636 0.000
#> GSM674402     3  0.4500      0.728 0.316 0.000 0.684 0.000
#> GSM674403     3  0.4697      0.687 0.356 0.000 0.644 0.000
#> GSM674405     3  0.1557      0.923 0.056 0.000 0.944 0.000
#> GSM674406     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674407     3  0.0188      0.950 0.004 0.000 0.996 0.000
#> GSM674181     2  0.3649      0.806 0.204 0.796 0.000 0.000
#> GSM674183     2  0.4546      0.738 0.256 0.732 0.012 0.000
#> GSM674184     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674185     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674186     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674187     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674190     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674191     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674192     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674193     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674194     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674195     2  0.0336      0.980 0.008 0.992 0.000 0.000
#> GSM674198     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674200     3  0.4500      0.726 0.316 0.000 0.684 0.000
#> GSM674201     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674202     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674203     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674204     2  0.0921      0.967 0.028 0.972 0.000 0.000
#> GSM674205     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674206     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674208     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674209     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674210     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674212     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674214     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674218     2  0.0469      0.978 0.012 0.988 0.000 0.000
#> GSM674219     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674220     2  0.0921      0.968 0.028 0.972 0.000 0.000
#> GSM674221     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674223     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674225     2  0.2530      0.901 0.112 0.888 0.000 0.000
#> GSM674226     2  0.0188      0.983 0.004 0.996 0.000 0.000
#> GSM674229     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674230     2  0.0188      0.983 0.004 0.996 0.000 0.000
#> GSM674231     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674232     2  0.0188      0.983 0.004 0.996 0.000 0.000
#> GSM674234     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674235     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674236     2  0.0188      0.983 0.004 0.996 0.000 0.000
#> GSM674237     2  0.0188      0.983 0.004 0.996 0.000 0.000
#> GSM674239     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674240     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674242     2  0.0188      0.983 0.004 0.996 0.000 0.000
#> GSM674243     2  0.4431      0.697 0.304 0.696 0.000 0.000
#> GSM674244     2  0.0469      0.979 0.012 0.988 0.000 0.000
#> GSM674245     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674282     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674284     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674285     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674287     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674288     4  0.0592      0.957 0.016 0.000 0.000 0.984
#> GSM674289     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674290     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674291     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674292     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674295     4  0.0000      0.964 0.000 0.000 0.000 1.000
#> GSM674297     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674298     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674299     1  0.4996      0.805 0.516 0.000 0.000 0.484
#> GSM674300     4  0.0188      0.964 0.004 0.000 0.000 0.996
#> GSM674301     1  0.4804      0.954 0.616 0.000 0.000 0.384
#> GSM674302     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674304     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674305     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674306     4  0.0592      0.957 0.016 0.000 0.000 0.984
#> GSM674308     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674309     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674313     4  0.0000      0.964 0.000 0.000 0.000 1.000
#> GSM674314     4  0.0707      0.957 0.020 0.000 0.000 0.980
#> GSM674315     4  0.0188      0.964 0.004 0.000 0.000 0.996
#> GSM674316     4  0.0592      0.957 0.016 0.000 0.000 0.984
#> GSM674318     4  0.0188      0.962 0.004 0.000 0.000 0.996
#> GSM674320     4  0.0188      0.962 0.004 0.000 0.000 0.996
#> GSM674323     4  0.0188      0.964 0.004 0.000 0.000 0.996
#> GSM674324     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674325     4  0.0592      0.957 0.016 0.000 0.000 0.984
#> GSM674327     4  0.0921      0.955 0.028 0.000 0.000 0.972
#> GSM674328     1  0.4992      0.820 0.524 0.000 0.000 0.476
#> GSM674330     4  0.1940      0.856 0.076 0.000 0.000 0.924
#> GSM674331     1  0.4776      0.962 0.624 0.000 0.000 0.376
#> GSM674332     1  0.4776      0.962 0.624 0.000 0.000 0.376
#> GSM674334     1  0.4996      0.807 0.516 0.000 0.000 0.484
#> GSM674335     4  0.4222      0.204 0.272 0.000 0.000 0.728
#> GSM674345     3  0.3528      0.832 0.192 0.000 0.808 0.000
#> GSM674351     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674352     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674359     3  0.3074      0.861 0.152 0.000 0.848 0.000
#> GSM674360     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674362     3  0.1489      0.919 0.004 0.044 0.952 0.000
#> GSM674369     3  0.2760      0.843 0.000 0.128 0.872 0.000
#> GSM674372     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674374     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674376     3  0.0188      0.950 0.004 0.000 0.996 0.000
#> GSM674377     3  0.5705      0.690 0.092 0.204 0.704 0.000
#> GSM674378     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674383     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674386     3  0.0188      0.950 0.004 0.000 0.996 0.000
#> GSM674387     3  0.0188      0.950 0.004 0.000 0.996 0.000
#> GSM674392     3  0.0000      0.951 0.000 0.000 1.000 0.000
#> GSM674396     3  0.0188      0.950 0.004 0.000 0.996 0.000
#> GSM674399     3  0.0188      0.950 0.004 0.000 0.996 0.000
#> GSM674404     3  0.0188      0.950 0.004 0.000 0.996 0.000
#> GSM674182     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674188     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674189     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674196     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674197     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674199     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674207     2  0.1474      0.949 0.052 0.948 0.000 0.000
#> GSM674211     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674213     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674215     2  0.0188      0.983 0.004 0.996 0.000 0.000
#> GSM674216     2  0.0336      0.981 0.008 0.992 0.000 0.000
#> GSM674217     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674222     2  0.1389      0.954 0.048 0.952 0.000 0.000
#> GSM674224     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674227     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674228     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674233     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674238     3  0.5767      0.600 0.060 0.280 0.660 0.000
#> GSM674241     2  0.0000      0.985 0.000 1.000 0.000 0.000
#> GSM674283     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674286     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674293     4  0.0592      0.957 0.016 0.000 0.000 0.984
#> GSM674294     1  0.4989      0.821 0.528 0.000 0.000 0.472
#> GSM674296     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674303     1  0.4790      0.959 0.620 0.000 0.000 0.380
#> GSM674307     1  0.4761      0.965 0.628 0.000 0.000 0.372
#> GSM674310     4  0.0188      0.962 0.004 0.000 0.000 0.996
#> GSM674311     1  0.4817      0.950 0.612 0.000 0.000 0.388
#> GSM674312     4  0.0188      0.962 0.004 0.000 0.000 0.996
#> GSM674317     1  0.5000      0.779 0.504 0.000 0.000 0.496
#> GSM674319     4  0.0000      0.964 0.000 0.000 0.000 1.000
#> GSM674321     4  0.0000      0.964 0.000 0.000 0.000 1.000
#> GSM674322     4  0.0000      0.964 0.000 0.000 0.000 1.000
#> GSM674326     4  0.0188      0.962 0.004 0.000 0.000 0.996
#> GSM674329     4  0.0000      0.964 0.000 0.000 0.000 1.000
#> GSM674333     4  0.0000      0.964 0.000 0.000 0.000 1.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3    p4    p5
#> GSM674344     3  0.3003      0.734 0.000 0.000 0.812 0.000 0.188
#> GSM674346     5  0.4030      0.498 0.000 0.000 0.352 0.000 0.648
#> GSM674347     3  0.0609      0.924 0.000 0.000 0.980 0.000 0.020
#> GSM674348     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674349     3  0.3366      0.666 0.000 0.000 0.768 0.000 0.232
#> GSM674350     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674353     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674354     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674355     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674356     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674357     3  0.0404      0.928 0.000 0.000 0.988 0.000 0.012
#> GSM674358     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674361     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674363     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674364     3  0.0703      0.924 0.000 0.000 0.976 0.000 0.024
#> GSM674365     3  0.0162      0.931 0.000 0.000 0.996 0.000 0.004
#> GSM674366     3  0.0162      0.931 0.000 0.000 0.996 0.000 0.004
#> GSM674367     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674368     3  0.1282      0.907 0.000 0.004 0.952 0.000 0.044
#> GSM674370     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674371     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674373     3  0.0510      0.928 0.000 0.000 0.984 0.000 0.016
#> GSM674375     3  0.0290      0.930 0.000 0.000 0.992 0.000 0.008
#> GSM674379     3  0.0794      0.925 0.000 0.000 0.972 0.000 0.028
#> GSM674380     3  0.6321     -0.143 0.000 0.160 0.464 0.000 0.376
#> GSM674381     3  0.0404      0.930 0.000 0.000 0.988 0.000 0.012
#> GSM674382     3  0.3452      0.652 0.000 0.000 0.756 0.000 0.244
#> GSM674384     3  0.0404      0.930 0.000 0.000 0.988 0.000 0.012
#> GSM674385     3  0.0963      0.919 0.000 0.000 0.964 0.000 0.036
#> GSM674388     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674389     3  0.0510      0.928 0.000 0.000 0.984 0.000 0.016
#> GSM674390     3  0.0290      0.930 0.000 0.000 0.992 0.000 0.008
#> GSM674391     3  0.3424      0.660 0.000 0.000 0.760 0.000 0.240
#> GSM674393     3  0.1043      0.914 0.000 0.000 0.960 0.000 0.040
#> GSM674394     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674395     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674397     3  0.0880      0.919 0.000 0.000 0.968 0.000 0.032
#> GSM674398     3  0.0794      0.925 0.000 0.000 0.972 0.000 0.028
#> GSM674400     5  0.1732      0.708 0.000 0.000 0.080 0.000 0.920
#> GSM674401     5  0.0609      0.688 0.000 0.000 0.020 0.000 0.980
#> GSM674402     5  0.1270      0.707 0.000 0.000 0.052 0.000 0.948
#> GSM674403     5  0.0703      0.691 0.000 0.000 0.024 0.000 0.976
#> GSM674405     3  0.4114      0.357 0.000 0.000 0.624 0.000 0.376
#> GSM674406     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674407     3  0.0510      0.928 0.000 0.000 0.984 0.000 0.016
#> GSM674181     2  0.4182      0.350 0.000 0.600 0.000 0.000 0.400
#> GSM674183     5  0.4135      0.394 0.000 0.340 0.004 0.000 0.656
#> GSM674184     2  0.0162      0.967 0.000 0.996 0.000 0.000 0.004
#> GSM674185     2  0.0290      0.966 0.000 0.992 0.000 0.000 0.008
#> GSM674186     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674187     2  0.0162      0.967 0.000 0.996 0.000 0.000 0.004
#> GSM674190     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674191     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674192     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674193     2  0.0162      0.967 0.000 0.996 0.000 0.000 0.004
#> GSM674194     2  0.0162      0.967 0.000 0.996 0.000 0.000 0.004
#> GSM674195     2  0.3816      0.575 0.000 0.696 0.000 0.000 0.304
#> GSM674198     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674200     5  0.1544      0.709 0.000 0.000 0.068 0.000 0.932
#> GSM674201     2  0.0162      0.967 0.000 0.996 0.000 0.000 0.004
#> GSM674202     2  0.0162      0.967 0.000 0.996 0.000 0.000 0.004
#> GSM674203     2  0.0162      0.966 0.000 0.996 0.000 0.000 0.004
#> GSM674204     2  0.1341      0.928 0.000 0.944 0.000 0.000 0.056
#> GSM674205     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674206     2  0.0162      0.967 0.000 0.996 0.000 0.000 0.004
#> GSM674208     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674209     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674210     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674212     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674214     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674218     2  0.1908      0.893 0.000 0.908 0.000 0.000 0.092
#> GSM674219     2  0.0162      0.967 0.000 0.996 0.000 0.000 0.004
#> GSM674220     2  0.3612      0.700 0.000 0.764 0.008 0.000 0.228
#> GSM674221     2  0.0162      0.967 0.000 0.996 0.000 0.000 0.004
#> GSM674223     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674225     2  0.3932      0.525 0.000 0.672 0.000 0.000 0.328
#> GSM674226     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674229     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674230     2  0.0162      0.966 0.000 0.996 0.000 0.000 0.004
#> GSM674231     2  0.0162      0.967 0.000 0.996 0.000 0.000 0.004
#> GSM674232     2  0.0162      0.966 0.000 0.996 0.000 0.000 0.004
#> GSM674234     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674235     2  0.0162      0.967 0.000 0.996 0.000 0.000 0.004
#> GSM674236     2  0.0162      0.966 0.000 0.996 0.000 0.000 0.004
#> GSM674237     2  0.0510      0.959 0.000 0.984 0.000 0.000 0.016
#> GSM674239     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674240     2  0.0162      0.967 0.000 0.996 0.000 0.000 0.004
#> GSM674242     2  0.0703      0.953 0.000 0.976 0.000 0.000 0.024
#> GSM674243     5  0.4101      0.316 0.000 0.372 0.000 0.000 0.628
#> GSM674244     2  0.0880      0.947 0.000 0.968 0.000 0.000 0.032
#> GSM674245     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674282     1  0.0162      0.917 0.996 0.000 0.000 0.004 0.000
#> GSM674284     1  0.0000      0.916 1.000 0.000 0.000 0.000 0.000
#> GSM674285     1  0.0000      0.916 1.000 0.000 0.000 0.000 0.000
#> GSM674287     1  0.1410      0.903 0.940 0.000 0.000 0.060 0.000
#> GSM674288     4  0.2516      0.881 0.140 0.000 0.000 0.860 0.000
#> GSM674289     1  0.0000      0.916 1.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0290      0.918 0.992 0.000 0.000 0.008 0.000
#> GSM674291     1  0.0963      0.913 0.964 0.000 0.000 0.036 0.000
#> GSM674292     1  0.1908      0.883 0.908 0.000 0.000 0.092 0.000
#> GSM674295     4  0.0794      0.917 0.028 0.000 0.000 0.972 0.000
#> GSM674297     1  0.0162      0.917 0.996 0.000 0.000 0.004 0.000
#> GSM674298     1  0.0162      0.917 0.996 0.000 0.000 0.004 0.000
#> GSM674299     1  0.3480      0.710 0.752 0.000 0.000 0.248 0.000
#> GSM674300     4  0.1410      0.920 0.060 0.000 0.000 0.940 0.000
#> GSM674301     1  0.2074      0.873 0.896 0.000 0.000 0.104 0.000
#> GSM674302     1  0.0000      0.916 1.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0162      0.917 0.996 0.000 0.000 0.004 0.000
#> GSM674305     1  0.0000      0.916 1.000 0.000 0.000 0.000 0.000
#> GSM674306     4  0.1965      0.908 0.096 0.000 0.000 0.904 0.000
#> GSM674308     1  0.1043      0.914 0.960 0.000 0.000 0.040 0.000
#> GSM674309     1  0.1197      0.910 0.952 0.000 0.000 0.048 0.000
#> GSM674313     4  0.0324      0.911 0.004 0.000 0.000 0.992 0.004
#> GSM674314     4  0.2516      0.882 0.140 0.000 0.000 0.860 0.000
#> GSM674315     4  0.1544      0.918 0.068 0.000 0.000 0.932 0.000
#> GSM674316     4  0.2561      0.877 0.144 0.000 0.000 0.856 0.000
#> GSM674318     4  0.0162      0.908 0.000 0.000 0.000 0.996 0.004
#> GSM674320     4  0.0451      0.913 0.008 0.000 0.000 0.988 0.004
#> GSM674323     4  0.0963      0.920 0.036 0.000 0.000 0.964 0.000
#> GSM674324     1  0.0162      0.917 0.996 0.000 0.000 0.004 0.000
#> GSM674325     4  0.2516      0.881 0.140 0.000 0.000 0.860 0.000
#> GSM674327     4  0.2124      0.908 0.096 0.000 0.000 0.900 0.004
#> GSM674328     1  0.3143      0.774 0.796 0.000 0.000 0.204 0.000
#> GSM674330     4  0.2773      0.854 0.164 0.000 0.000 0.836 0.000
#> GSM674331     1  0.1732      0.892 0.920 0.000 0.000 0.080 0.000
#> GSM674332     1  0.1792      0.886 0.916 0.000 0.000 0.084 0.000
#> GSM674334     1  0.4101      0.443 0.628 0.000 0.000 0.372 0.000
#> GSM674335     4  0.4138      0.408 0.384 0.000 0.000 0.616 0.000
#> GSM674345     5  0.4045      0.492 0.000 0.000 0.356 0.000 0.644
#> GSM674351     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674352     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674359     5  0.4201      0.376 0.000 0.000 0.408 0.000 0.592
#> GSM674360     3  0.0404      0.929 0.000 0.000 0.988 0.000 0.012
#> GSM674362     3  0.1197      0.907 0.000 0.000 0.952 0.000 0.048
#> GSM674369     3  0.2124      0.869 0.000 0.028 0.916 0.000 0.056
#> GSM674372     3  0.0510      0.928 0.000 0.000 0.984 0.000 0.016
#> GSM674374     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674376     3  0.0510      0.928 0.000 0.000 0.984 0.000 0.016
#> GSM674377     3  0.5243      0.471 0.000 0.132 0.680 0.000 0.188
#> GSM674378     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674383     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674386     3  0.0880      0.923 0.000 0.000 0.968 0.000 0.032
#> GSM674387     3  0.0510      0.928 0.000 0.000 0.984 0.000 0.016
#> GSM674392     3  0.0000      0.932 0.000 0.000 1.000 0.000 0.000
#> GSM674396     3  0.0794      0.925 0.000 0.000 0.972 0.000 0.028
#> GSM674399     3  0.0794      0.925 0.000 0.000 0.972 0.000 0.028
#> GSM674404     3  0.0510      0.928 0.000 0.000 0.984 0.000 0.016
#> GSM674182     2  0.0162      0.967 0.000 0.996 0.000 0.000 0.004
#> GSM674188     2  0.0162      0.967 0.000 0.996 0.000 0.000 0.004
#> GSM674189     2  0.0162      0.967 0.000 0.996 0.000 0.000 0.004
#> GSM674196     2  0.0162      0.967 0.000 0.996 0.000 0.000 0.004
#> GSM674197     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674199     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674207     2  0.2230      0.866 0.000 0.884 0.000 0.000 0.116
#> GSM674211     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674213     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674215     2  0.0404      0.964 0.000 0.988 0.000 0.000 0.012
#> GSM674216     2  0.0794      0.951 0.000 0.972 0.000 0.000 0.028
#> GSM674217     2  0.0162      0.967 0.000 0.996 0.000 0.000 0.004
#> GSM674222     2  0.2020      0.882 0.000 0.900 0.000 0.000 0.100
#> GSM674224     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674227     2  0.0404      0.964 0.000 0.988 0.000 0.000 0.012
#> GSM674228     2  0.0162      0.967 0.000 0.996 0.000 0.000 0.004
#> GSM674233     2  0.0162      0.967 0.000 0.996 0.000 0.000 0.004
#> GSM674238     3  0.6542     -0.254 0.000 0.200 0.428 0.000 0.372
#> GSM674241     2  0.0000      0.968 0.000 1.000 0.000 0.000 0.000
#> GSM674283     1  0.0703      0.917 0.976 0.000 0.000 0.024 0.000
#> GSM674286     1  0.0404      0.918 0.988 0.000 0.000 0.012 0.000
#> GSM674293     4  0.2074      0.904 0.104 0.000 0.000 0.896 0.000
#> GSM674294     1  0.3752      0.626 0.708 0.000 0.000 0.292 0.000
#> GSM674296     1  0.0404      0.918 0.988 0.000 0.000 0.012 0.000
#> GSM674303     1  0.0963      0.915 0.964 0.000 0.000 0.036 0.000
#> GSM674307     1  0.0000      0.916 1.000 0.000 0.000 0.000 0.000
#> GSM674310     4  0.0162      0.908 0.000 0.000 0.000 0.996 0.004
#> GSM674311     1  0.2127      0.875 0.892 0.000 0.000 0.108 0.000
#> GSM674312     4  0.0451      0.913 0.008 0.000 0.000 0.988 0.004
#> GSM674317     1  0.4015      0.517 0.652 0.000 0.000 0.348 0.000
#> GSM674319     4  0.1478      0.918 0.064 0.000 0.000 0.936 0.000
#> GSM674321     4  0.1478      0.920 0.064 0.000 0.000 0.936 0.000
#> GSM674322     4  0.0290      0.913 0.008 0.000 0.000 0.992 0.000
#> GSM674326     4  0.0000      0.908 0.000 0.000 0.000 1.000 0.000
#> GSM674329     4  0.0290      0.913 0.008 0.000 0.000 0.992 0.000
#> GSM674333     4  0.0404      0.915 0.012 0.000 0.000 0.988 0.000

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4    p5    p6
#> GSM674344     3  0.4193     0.5475 0.000 0.000 0.684 0.272 0.000 0.044
#> GSM674346     4  0.4312     0.6893 0.000 0.000 0.272 0.676 0.000 0.052
#> GSM674347     3  0.2046     0.8660 0.000 0.000 0.908 0.060 0.000 0.032
#> GSM674348     3  0.1434     0.8720 0.000 0.000 0.940 0.012 0.000 0.048
#> GSM674349     3  0.4674     0.3283 0.000 0.000 0.608 0.332 0.000 0.060
#> GSM674350     3  0.0717     0.8816 0.000 0.000 0.976 0.016 0.000 0.008
#> GSM674353     3  0.0858     0.8784 0.000 0.000 0.968 0.004 0.000 0.028
#> GSM674354     3  0.2145     0.8538 0.000 0.000 0.900 0.028 0.000 0.072
#> GSM674355     3  0.0547     0.8807 0.000 0.000 0.980 0.020 0.000 0.000
#> GSM674356     3  0.2350     0.8465 0.000 0.000 0.888 0.036 0.000 0.076
#> GSM674357     3  0.1010     0.8741 0.000 0.000 0.960 0.036 0.000 0.004
#> GSM674358     3  0.0363     0.8811 0.000 0.000 0.988 0.012 0.000 0.000
#> GSM674361     3  0.0146     0.8801 0.000 0.000 0.996 0.004 0.000 0.000
#> GSM674363     3  0.0935     0.8786 0.000 0.000 0.964 0.004 0.000 0.032
#> GSM674364     3  0.3017     0.8152 0.000 0.000 0.844 0.072 0.000 0.084
#> GSM674365     3  0.1765     0.8679 0.000 0.000 0.924 0.024 0.000 0.052
#> GSM674366     3  0.2129     0.8653 0.000 0.000 0.904 0.056 0.000 0.040
#> GSM674367     3  0.0146     0.8794 0.000 0.000 0.996 0.004 0.000 0.000
#> GSM674368     3  0.4309     0.7260 0.000 0.020 0.760 0.104 0.000 0.116
#> GSM674370     3  0.0508     0.8801 0.000 0.000 0.984 0.004 0.000 0.012
#> GSM674371     3  0.2488     0.8413 0.000 0.000 0.880 0.044 0.000 0.076
#> GSM674373     3  0.2897     0.8223 0.000 0.000 0.852 0.060 0.000 0.088
#> GSM674375     3  0.1196     0.8734 0.000 0.000 0.952 0.040 0.000 0.008
#> GSM674379     3  0.1088     0.8778 0.000 0.000 0.960 0.024 0.000 0.016
#> GSM674380     6  0.7007    -0.0828 0.000 0.124 0.308 0.136 0.000 0.432
#> GSM674381     3  0.1225     0.8786 0.000 0.000 0.952 0.036 0.000 0.012
#> GSM674382     3  0.2692     0.7717 0.000 0.000 0.840 0.148 0.000 0.012
#> GSM674384     3  0.0692     0.8803 0.000 0.000 0.976 0.020 0.000 0.004
#> GSM674385     3  0.3063     0.8095 0.000 0.000 0.840 0.068 0.000 0.092
#> GSM674388     3  0.1367     0.8721 0.000 0.000 0.944 0.012 0.000 0.044
#> GSM674389     3  0.1196     0.8731 0.000 0.000 0.952 0.040 0.000 0.008
#> GSM674390     3  0.0820     0.8786 0.000 0.000 0.972 0.012 0.000 0.016
#> GSM674391     3  0.2730     0.7666 0.000 0.000 0.836 0.152 0.000 0.012
#> GSM674393     3  0.1812     0.8455 0.000 0.000 0.912 0.080 0.000 0.008
#> GSM674394     3  0.0260     0.8795 0.000 0.000 0.992 0.008 0.000 0.000
#> GSM674395     3  0.0603     0.8787 0.000 0.000 0.980 0.016 0.000 0.004
#> GSM674397     3  0.3225     0.8026 0.000 0.000 0.828 0.080 0.000 0.092
#> GSM674398     3  0.1245     0.8753 0.000 0.000 0.952 0.032 0.000 0.016
#> GSM674400     4  0.3270     0.7650 0.000 0.000 0.120 0.820 0.000 0.060
#> GSM674401     4  0.2837     0.7196 0.000 0.000 0.056 0.856 0.000 0.088
#> GSM674402     4  0.2487     0.7705 0.000 0.000 0.092 0.876 0.000 0.032
#> GSM674403     4  0.2088     0.7435 0.000 0.000 0.068 0.904 0.000 0.028
#> GSM674405     3  0.4272     0.4656 0.000 0.000 0.668 0.288 0.000 0.044
#> GSM674406     3  0.0458     0.8810 0.000 0.000 0.984 0.016 0.000 0.000
#> GSM674407     3  0.1049     0.8743 0.000 0.000 0.960 0.032 0.000 0.008
#> GSM674181     2  0.4339     0.3873 0.000 0.684 0.000 0.256 0.000 0.060
#> GSM674183     2  0.5400    -0.1098 0.000 0.488 0.008 0.416 0.000 0.088
#> GSM674184     2  0.0865     0.7958 0.000 0.964 0.000 0.000 0.000 0.036
#> GSM674185     2  0.1075     0.7941 0.000 0.952 0.000 0.000 0.000 0.048
#> GSM674186     2  0.2340     0.8037 0.000 0.852 0.000 0.000 0.000 0.148
#> GSM674187     2  0.1663     0.8121 0.000 0.912 0.000 0.000 0.000 0.088
#> GSM674190     2  0.2219     0.8064 0.000 0.864 0.000 0.000 0.000 0.136
#> GSM674191     2  0.1765     0.8112 0.000 0.904 0.000 0.000 0.000 0.096
#> GSM674192     2  0.2300     0.8054 0.000 0.856 0.000 0.000 0.000 0.144
#> GSM674193     2  0.1387     0.8076 0.000 0.932 0.000 0.000 0.000 0.068
#> GSM674194     2  0.0260     0.8027 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674195     2  0.3858     0.5757 0.000 0.780 0.004 0.132 0.000 0.084
#> GSM674198     2  0.2340     0.8007 0.000 0.852 0.000 0.000 0.000 0.148
#> GSM674200     4  0.2706     0.7593 0.000 0.000 0.104 0.860 0.000 0.036
#> GSM674201     2  0.0547     0.7978 0.000 0.980 0.000 0.000 0.000 0.020
#> GSM674202     2  0.0937     0.7967 0.000 0.960 0.000 0.000 0.000 0.040
#> GSM674203     2  0.3499     0.6746 0.000 0.680 0.000 0.000 0.000 0.320
#> GSM674204     2  0.3295     0.7414 0.000 0.816 0.000 0.056 0.000 0.128
#> GSM674205     2  0.2135     0.8092 0.000 0.872 0.000 0.000 0.000 0.128
#> GSM674206     2  0.0260     0.8028 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674208     2  0.3076     0.7606 0.000 0.760 0.000 0.000 0.000 0.240
#> GSM674209     2  0.2092     0.8103 0.000 0.876 0.000 0.000 0.000 0.124
#> GSM674210     2  0.2793     0.7822 0.000 0.800 0.000 0.000 0.000 0.200
#> GSM674212     2  0.2664     0.7876 0.000 0.816 0.000 0.000 0.000 0.184
#> GSM674214     2  0.2562     0.7901 0.000 0.828 0.000 0.000 0.000 0.172
#> GSM674218     2  0.1807     0.7639 0.000 0.920 0.000 0.020 0.000 0.060
#> GSM674219     2  0.0260     0.8016 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM674220     2  0.4745    -0.1683 0.000 0.552 0.020 0.020 0.000 0.408
#> GSM674221     2  0.0632     0.8065 0.000 0.976 0.000 0.000 0.000 0.024
#> GSM674223     2  0.1863     0.8101 0.000 0.896 0.000 0.000 0.000 0.104
#> GSM674225     6  0.4946    -0.0764 0.000 0.404 0.000 0.068 0.000 0.528
#> GSM674226     2  0.2762     0.7766 0.000 0.804 0.000 0.000 0.000 0.196
#> GSM674229     2  0.2260     0.8055 0.000 0.860 0.000 0.000 0.000 0.140
#> GSM674230     2  0.2527     0.7599 0.000 0.832 0.000 0.000 0.000 0.168
#> GSM674231     2  0.0632     0.8037 0.000 0.976 0.000 0.000 0.000 0.024
#> GSM674232     2  0.3371     0.6646 0.000 0.708 0.000 0.000 0.000 0.292
#> GSM674234     2  0.2300     0.8032 0.000 0.856 0.000 0.000 0.000 0.144
#> GSM674235     2  0.0865     0.8062 0.000 0.964 0.000 0.000 0.000 0.036
#> GSM674236     2  0.2762     0.7199 0.000 0.804 0.000 0.000 0.000 0.196
#> GSM674237     2  0.3634     0.6183 0.000 0.644 0.000 0.000 0.000 0.356
#> GSM674239     2  0.2854     0.7799 0.000 0.792 0.000 0.000 0.000 0.208
#> GSM674240     2  0.0000     0.8032 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674242     2  0.3647     0.6111 0.000 0.640 0.000 0.000 0.000 0.360
#> GSM674243     2  0.5706    -0.0726 0.000 0.488 0.000 0.336 0.000 0.176
#> GSM674244     2  0.3872     0.3371 0.000 0.604 0.000 0.004 0.000 0.392
#> GSM674245     2  0.2416     0.7990 0.000 0.844 0.000 0.000 0.000 0.156
#> GSM674282     1  0.0146     0.9168 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM674284     1  0.0000     0.9158 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674285     1  0.0000     0.9158 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674287     1  0.0865     0.9104 0.964 0.000 0.000 0.000 0.036 0.000
#> GSM674288     5  0.4945     0.6978 0.292 0.000 0.000 0.004 0.620 0.084
#> GSM674289     1  0.0000     0.9158 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674290     1  0.0000     0.9158 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674291     1  0.0713     0.9145 0.972 0.000 0.000 0.000 0.028 0.000
#> GSM674292     1  0.1367     0.9025 0.944 0.000 0.000 0.000 0.044 0.012
#> GSM674295     5  0.0692     0.7709 0.020 0.000 0.000 0.000 0.976 0.004
#> GSM674297     1  0.0000     0.9158 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674298     1  0.0146     0.9168 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM674299     1  0.2790     0.8087 0.840 0.000 0.000 0.000 0.140 0.020
#> GSM674300     5  0.4431     0.7720 0.200 0.000 0.000 0.004 0.712 0.084
#> GSM674301     1  0.2006     0.8586 0.892 0.000 0.000 0.000 0.104 0.004
#> GSM674302     1  0.0000     0.9158 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674304     1  0.0146     0.9166 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM674305     1  0.0000     0.9158 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674306     5  0.4729     0.7271 0.264 0.000 0.000 0.008 0.660 0.068
#> GSM674308     1  0.0713     0.9155 0.972 0.000 0.000 0.000 0.028 0.000
#> GSM674309     1  0.0858     0.9133 0.968 0.000 0.000 0.000 0.028 0.004
#> GSM674313     5  0.2058     0.7392 0.012 0.000 0.000 0.008 0.908 0.072
#> GSM674314     5  0.4894     0.6929 0.300 0.000 0.000 0.008 0.624 0.068
#> GSM674315     5  0.4340     0.7611 0.224 0.000 0.000 0.004 0.708 0.064
#> GSM674316     5  0.4993     0.6799 0.304 0.000 0.000 0.004 0.608 0.084
#> GSM674318     5  0.1082     0.7525 0.004 0.000 0.000 0.000 0.956 0.040
#> GSM674320     5  0.1889     0.7551 0.020 0.000 0.000 0.004 0.920 0.056
#> GSM674323     5  0.3354     0.7925 0.168 0.000 0.000 0.000 0.796 0.036
#> GSM674324     1  0.0146     0.9168 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM674325     5  0.4945     0.6978 0.292 0.000 0.000 0.004 0.620 0.084
#> GSM674327     5  0.4991     0.7301 0.252 0.000 0.000 0.008 0.644 0.096
#> GSM674328     1  0.2667     0.8249 0.852 0.000 0.000 0.000 0.128 0.020
#> GSM674330     5  0.4993     0.6799 0.304 0.000 0.000 0.004 0.608 0.084
#> GSM674331     1  0.1501     0.8882 0.924 0.000 0.000 0.000 0.076 0.000
#> GSM674332     1  0.1524     0.8933 0.932 0.000 0.000 0.000 0.060 0.008
#> GSM674334     1  0.3628     0.5819 0.720 0.000 0.000 0.004 0.268 0.008
#> GSM674335     1  0.4829     0.0109 0.544 0.000 0.000 0.004 0.404 0.048
#> GSM674345     4  0.4291     0.6769 0.000 0.000 0.292 0.664 0.000 0.044
#> GSM674351     3  0.0935     0.8786 0.000 0.000 0.964 0.004 0.000 0.032
#> GSM674352     3  0.0909     0.8813 0.000 0.000 0.968 0.012 0.000 0.020
#> GSM674359     4  0.4092     0.6121 0.000 0.000 0.344 0.636 0.000 0.020
#> GSM674360     3  0.2680     0.8328 0.000 0.000 0.868 0.056 0.000 0.076
#> GSM674362     3  0.4213     0.7366 0.000 0.024 0.772 0.104 0.000 0.100
#> GSM674369     3  0.5750     0.4943 0.000 0.140 0.648 0.092 0.000 0.120
#> GSM674372     3  0.0972     0.8781 0.000 0.000 0.964 0.028 0.000 0.008
#> GSM674374     3  0.1434     0.8720 0.000 0.000 0.940 0.012 0.000 0.048
#> GSM674376     3  0.1334     0.8732 0.000 0.000 0.948 0.032 0.000 0.020
#> GSM674377     3  0.6666    -0.2703 0.000 0.092 0.436 0.112 0.000 0.360
#> GSM674378     3  0.0146     0.8794 0.000 0.000 0.996 0.004 0.000 0.000
#> GSM674383     3  0.2365     0.8471 0.000 0.000 0.888 0.040 0.000 0.072
#> GSM674386     3  0.1421     0.8736 0.000 0.000 0.944 0.028 0.000 0.028
#> GSM674387     3  0.1196     0.8724 0.000 0.000 0.952 0.040 0.000 0.008
#> GSM674392     3  0.0363     0.8802 0.000 0.000 0.988 0.012 0.000 0.000
#> GSM674396     3  0.1334     0.8742 0.000 0.000 0.948 0.032 0.000 0.020
#> GSM674399     3  0.1334     0.8742 0.000 0.000 0.948 0.032 0.000 0.020
#> GSM674404     3  0.1334     0.8726 0.000 0.000 0.948 0.032 0.000 0.020
#> GSM674182     2  0.0146     0.8043 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM674188     2  0.1204     0.8099 0.000 0.944 0.000 0.000 0.000 0.056
#> GSM674189     2  0.0865     0.7958 0.000 0.964 0.000 0.000 0.000 0.036
#> GSM674196     2  0.1765     0.8068 0.000 0.904 0.000 0.000 0.000 0.096
#> GSM674197     2  0.2454     0.7977 0.000 0.840 0.000 0.000 0.000 0.160
#> GSM674199     2  0.1957     0.8080 0.000 0.888 0.000 0.000 0.000 0.112
#> GSM674207     2  0.3261     0.7026 0.000 0.824 0.000 0.072 0.000 0.104
#> GSM674211     2  0.2454     0.8014 0.000 0.840 0.000 0.000 0.000 0.160
#> GSM674213     2  0.1444     0.8114 0.000 0.928 0.000 0.000 0.000 0.072
#> GSM674215     2  0.3151     0.5646 0.000 0.748 0.000 0.000 0.000 0.252
#> GSM674216     2  0.3872     0.4783 0.000 0.604 0.000 0.004 0.000 0.392
#> GSM674217     2  0.0000     0.8032 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674222     2  0.4314     0.0187 0.000 0.536 0.000 0.020 0.000 0.444
#> GSM674224     2  0.2219     0.8058 0.000 0.864 0.000 0.000 0.000 0.136
#> GSM674227     2  0.1610     0.7778 0.000 0.916 0.000 0.000 0.000 0.084
#> GSM674228     2  0.0363     0.8016 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM674233     2  0.0000     0.8032 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM674238     3  0.7292    -0.3859 0.000 0.300 0.364 0.228 0.000 0.108
#> GSM674241     2  0.2793     0.7824 0.000 0.800 0.000 0.000 0.000 0.200
#> GSM674283     1  0.0790     0.9138 0.968 0.000 0.000 0.000 0.032 0.000
#> GSM674286     1  0.0146     0.9168 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM674293     5  0.4663     0.7192 0.272 0.000 0.000 0.004 0.656 0.068
#> GSM674294     1  0.3014     0.7483 0.804 0.000 0.000 0.000 0.184 0.012
#> GSM674296     1  0.0146     0.9168 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM674303     1  0.1007     0.9088 0.956 0.000 0.000 0.000 0.044 0.000
#> GSM674307     1  0.0000     0.9158 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM674310     5  0.1462     0.7384 0.000 0.000 0.000 0.008 0.936 0.056
#> GSM674311     1  0.1644     0.8874 0.920 0.000 0.000 0.000 0.076 0.004
#> GSM674312     5  0.2339     0.7441 0.020 0.000 0.000 0.012 0.896 0.072
#> GSM674317     1  0.3284     0.7234 0.784 0.000 0.000 0.000 0.196 0.020
#> GSM674319     5  0.1895     0.7835 0.072 0.000 0.000 0.000 0.912 0.016
#> GSM674321     5  0.2997     0.7960 0.096 0.000 0.000 0.000 0.844 0.060
#> GSM674322     5  0.0692     0.7709 0.020 0.000 0.000 0.000 0.976 0.004
#> GSM674326     5  0.0458     0.7586 0.000 0.000 0.000 0.000 0.984 0.016
#> GSM674329     5  0.0777     0.7732 0.024 0.000 0.000 0.000 0.972 0.004
#> GSM674333     5  0.3361     0.7969 0.108 0.000 0.000 0.000 0.816 0.076

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-ATC-mclust-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-ATC-mclust-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-ATC-mclust-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-ATC-mclust-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-ATC-mclust-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-ATC-mclust-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-ATC-mclust-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-ATC-mclust-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-ATC-mclust-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-ATC-mclust-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-ATC-mclust-get-signatures-1

get_signatures(res, k = 3)
#> Error in mat[ceiling(1:nr/h_ratio), ceiling(1:nc/w_ratio), drop = FALSE]: subscript out of bounds

plot of chunk tab-ATC-mclust-get-signatures-2

get_signatures(res, k = 4)
#> Error in mat[ceiling(1:nr/h_ratio), ceiling(1:nc/w_ratio), drop = FALSE]: subscript out of bounds

plot of chunk tab-ATC-mclust-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-ATC-mclust-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-ATC-mclust-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-ATC-mclust-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-ATC-mclust-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-ATC-mclust-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-ATC-mclust-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-ATC-mclust-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk ATC-mclust-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-ATC-mclust-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-ATC-mclust-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-ATC-mclust-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-ATC-mclust-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-ATC-mclust-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk ATC-mclust-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>              n disease.state(p) specimen(p) k
#> ATC:mclust 183            0.924    1.83e-40 2
#> ATC:mclust 182            0.936    4.00e-75 3
#> ATC:mclust 182            0.771    3.41e-73 4
#> ATC:mclust 171            0.533    4.42e-68 5
#> ATC:mclust 168            0.874    1.08e-66 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


ATC:NMF**

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["ATC", "NMF"]
# you can also extract it by
# res = res_list["ATC:NMF"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 23299 rows and 183 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#>   Subgroups are detected by 'NMF' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 2.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk ATC-NMF-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk ATC-NMF-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.4189 0.582   0.582
#> 3 3 0.696           0.748       0.878         0.3783 0.792   0.643
#> 4 4 0.813           0.915       0.923         0.1438 0.839   0.629
#> 5 5 0.732           0.704       0.855         0.0744 0.959   0.878
#> 6 6 0.653           0.704       0.795         0.0386 0.957   0.861

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 2

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>           class entropy silhouette p1 p2
#> GSM674344     2       0          1  0  1
#> GSM674346     2       0          1  0  1
#> GSM674347     2       0          1  0  1
#> GSM674348     2       0          1  0  1
#> GSM674349     2       0          1  0  1
#> GSM674350     2       0          1  0  1
#> GSM674353     2       0          1  0  1
#> GSM674354     2       0          1  0  1
#> GSM674355     2       0          1  0  1
#> GSM674356     2       0          1  0  1
#> GSM674357     2       0          1  0  1
#> GSM674358     2       0          1  0  1
#> GSM674361     2       0          1  0  1
#> GSM674363     2       0          1  0  1
#> GSM674364     2       0          1  0  1
#> GSM674365     2       0          1  0  1
#> GSM674366     2       0          1  0  1
#> GSM674367     2       0          1  0  1
#> GSM674368     2       0          1  0  1
#> GSM674370     2       0          1  0  1
#> GSM674371     2       0          1  0  1
#> GSM674373     2       0          1  0  1
#> GSM674375     2       0          1  0  1
#> GSM674379     2       0          1  0  1
#> GSM674380     2       0          1  0  1
#> GSM674381     2       0          1  0  1
#> GSM674382     2       0          1  0  1
#> GSM674384     2       0          1  0  1
#> GSM674385     2       0          1  0  1
#> GSM674388     2       0          1  0  1
#> GSM674389     2       0          1  0  1
#> GSM674390     2       0          1  0  1
#> GSM674391     2       0          1  0  1
#> GSM674393     2       0          1  0  1
#> GSM674394     2       0          1  0  1
#> GSM674395     2       0          1  0  1
#> GSM674397     2       0          1  0  1
#> GSM674398     2       0          1  0  1
#> GSM674400     2       0          1  0  1
#> GSM674401     2       0          1  0  1
#> GSM674402     2       0          1  0  1
#> GSM674403     2       0          1  0  1
#> GSM674405     2       0          1  0  1
#> GSM674406     2       0          1  0  1
#> GSM674407     2       0          1  0  1
#> GSM674181     2       0          1  0  1
#> GSM674183     2       0          1  0  1
#> GSM674184     2       0          1  0  1
#> GSM674185     2       0          1  0  1
#> GSM674186     2       0          1  0  1
#> GSM674187     2       0          1  0  1
#> GSM674190     2       0          1  0  1
#> GSM674191     2       0          1  0  1
#> GSM674192     2       0          1  0  1
#> GSM674193     2       0          1  0  1
#> GSM674194     2       0          1  0  1
#> GSM674195     2       0          1  0  1
#> GSM674198     2       0          1  0  1
#> GSM674200     2       0          1  0  1
#> GSM674201     2       0          1  0  1
#> GSM674202     2       0          1  0  1
#> GSM674203     2       0          1  0  1
#> GSM674204     2       0          1  0  1
#> GSM674205     2       0          1  0  1
#> GSM674206     2       0          1  0  1
#> GSM674208     2       0          1  0  1
#> GSM674209     2       0          1  0  1
#> GSM674210     2       0          1  0  1
#> GSM674212     2       0          1  0  1
#> GSM674214     2       0          1  0  1
#> GSM674218     2       0          1  0  1
#> GSM674219     2       0          1  0  1
#> GSM674220     2       0          1  0  1
#> GSM674221     2       0          1  0  1
#> GSM674223     2       0          1  0  1
#> GSM674225     2       0          1  0  1
#> GSM674226     2       0          1  0  1
#> GSM674229     2       0          1  0  1
#> GSM674230     2       0          1  0  1
#> GSM674231     2       0          1  0  1
#> GSM674232     2       0          1  0  1
#> GSM674234     2       0          1  0  1
#> GSM674235     2       0          1  0  1
#> GSM674236     2       0          1  0  1
#> GSM674237     2       0          1  0  1
#> GSM674239     2       0          1  0  1
#> GSM674240     2       0          1  0  1
#> GSM674242     2       0          1  0  1
#> GSM674243     2       0          1  0  1
#> GSM674244     2       0          1  0  1
#> GSM674245     2       0          1  0  1
#> GSM674282     1       0          1  1  0
#> GSM674284     1       0          1  1  0
#> GSM674285     1       0          1  1  0
#> GSM674287     1       0          1  1  0
#> GSM674288     1       0          1  1  0
#> GSM674289     1       0          1  1  0
#> GSM674290     1       0          1  1  0
#> GSM674291     1       0          1  1  0
#> GSM674292     1       0          1  1  0
#> GSM674295     1       0          1  1  0
#> GSM674297     1       0          1  1  0
#> GSM674298     1       0          1  1  0
#> GSM674299     1       0          1  1  0
#> GSM674300     1       0          1  1  0
#> GSM674301     1       0          1  1  0
#> GSM674302     1       0          1  1  0
#> GSM674304     1       0          1  1  0
#> GSM674305     1       0          1  1  0
#> GSM674306     1       0          1  1  0
#> GSM674308     1       0          1  1  0
#> GSM674309     1       0          1  1  0
#> GSM674313     1       0          1  1  0
#> GSM674314     1       0          1  1  0
#> GSM674315     1       0          1  1  0
#> GSM674316     1       0          1  1  0
#> GSM674318     1       0          1  1  0
#> GSM674320     1       0          1  1  0
#> GSM674323     1       0          1  1  0
#> GSM674324     1       0          1  1  0
#> GSM674325     1       0          1  1  0
#> GSM674327     1       0          1  1  0
#> GSM674328     1       0          1  1  0
#> GSM674330     1       0          1  1  0
#> GSM674331     1       0          1  1  0
#> GSM674332     1       0          1  1  0
#> GSM674334     1       0          1  1  0
#> GSM674335     1       0          1  1  0
#> GSM674345     2       0          1  0  1
#> GSM674351     2       0          1  0  1
#> GSM674352     2       0          1  0  1
#> GSM674359     2       0          1  0  1
#> GSM674360     2       0          1  0  1
#> GSM674362     2       0          1  0  1
#> GSM674369     2       0          1  0  1
#> GSM674372     2       0          1  0  1
#> GSM674374     2       0          1  0  1
#> GSM674376     2       0          1  0  1
#> GSM674377     2       0          1  0  1
#> GSM674378     2       0          1  0  1
#> GSM674383     2       0          1  0  1
#> GSM674386     2       0          1  0  1
#> GSM674387     2       0          1  0  1
#> GSM674392     2       0          1  0  1
#> GSM674396     2       0          1  0  1
#> GSM674399     2       0          1  0  1
#> GSM674404     2       0          1  0  1
#> GSM674182     2       0          1  0  1
#> GSM674188     2       0          1  0  1
#> GSM674189     2       0          1  0  1
#> GSM674196     2       0          1  0  1
#> GSM674197     2       0          1  0  1
#> GSM674199     2       0          1  0  1
#> GSM674207     2       0          1  0  1
#> GSM674211     2       0          1  0  1
#> GSM674213     2       0          1  0  1
#> GSM674215     2       0          1  0  1
#> GSM674216     2       0          1  0  1
#> GSM674217     2       0          1  0  1
#> GSM674222     2       0          1  0  1
#> GSM674224     2       0          1  0  1
#> GSM674227     2       0          1  0  1
#> GSM674228     2       0          1  0  1
#> GSM674233     2       0          1  0  1
#> GSM674238     2       0          1  0  1
#> GSM674241     2       0          1  0  1
#> GSM674283     1       0          1  1  0
#> GSM674286     1       0          1  1  0
#> GSM674293     1       0          1  1  0
#> GSM674294     1       0          1  1  0
#> GSM674296     1       0          1  1  0
#> GSM674303     1       0          1  1  0
#> GSM674307     1       0          1  1  0
#> GSM674310     1       0          1  1  0
#> GSM674311     1       0          1  1  0
#> GSM674312     1       0          1  1  0
#> GSM674317     1       0          1  1  0
#> GSM674319     1       0          1  1  0
#> GSM674321     1       0          1  1  0
#> GSM674322     1       0          1  1  0
#> GSM674326     1       0          1  1  0
#> GSM674329     1       0          1  1  0
#> GSM674333     1       0          1  1  0

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>           class entropy silhouette p1    p2    p3
#> GSM674344     2  0.4605     0.5270  0 0.796 0.204
#> GSM674346     3  0.5363     0.8280  0 0.276 0.724
#> GSM674347     3  0.6235     0.7520  0 0.436 0.564
#> GSM674348     2  0.6302    -0.5457  0 0.520 0.480
#> GSM674349     3  0.6274     0.7145  0 0.456 0.544
#> GSM674350     3  0.5948     0.8373  0 0.360 0.640
#> GSM674353     3  0.6026     0.8252  0 0.376 0.624
#> GSM674354     2  0.6026    -0.1187  0 0.624 0.376
#> GSM674355     3  0.5706     0.8456  0 0.320 0.680
#> GSM674356     2  0.5968    -0.0572  0 0.636 0.364
#> GSM674357     3  0.5859     0.8449  0 0.344 0.656
#> GSM674358     3  0.5706     0.8456  0 0.320 0.680
#> GSM674361     2  0.6299    -0.5323  0 0.524 0.476
#> GSM674363     2  0.6309    -0.6109  0 0.500 0.500
#> GSM674364     2  0.4974     0.4460  0 0.764 0.236
#> GSM674365     2  0.6204    -0.3365  0 0.576 0.424
#> GSM674366     3  0.6309     0.5960  0 0.500 0.500
#> GSM674367     3  0.6307     0.6334  0 0.488 0.512
#> GSM674368     2  0.3038     0.7118  0 0.896 0.104
#> GSM674370     3  0.6079     0.8140  0 0.388 0.612
#> GSM674371     2  0.5810     0.0862  0 0.664 0.336
#> GSM674373     2  0.5760     0.1233  0 0.672 0.328
#> GSM674375     3  0.5431     0.8328  0 0.284 0.716
#> GSM674379     3  0.6252     0.7383  0 0.444 0.556
#> GSM674380     2  0.2711     0.7335  0 0.912 0.088
#> GSM674381     2  0.6308    -0.5854  0 0.508 0.492
#> GSM674382     3  0.5397     0.8306  0 0.280 0.720
#> GSM674384     2  0.6235    -0.3855  0 0.564 0.436
#> GSM674385     2  0.5760     0.1232  0 0.672 0.328
#> GSM674388     2  0.6299    -0.5319  0 0.524 0.476
#> GSM674389     3  0.5058     0.7998  0 0.244 0.756
#> GSM674390     2  0.6154    -0.2685  0 0.592 0.408
#> GSM674391     3  0.5650     0.8439  0 0.312 0.688
#> GSM674393     3  0.5859     0.8448  0 0.344 0.656
#> GSM674394     3  0.6260     0.7306  0 0.448 0.552
#> GSM674395     3  0.5216     0.8152  0 0.260 0.740
#> GSM674397     2  0.4702     0.5081  0 0.788 0.212
#> GSM674398     3  0.6291     0.6881  0 0.468 0.532
#> GSM674400     3  0.4750     0.7710  0 0.216 0.784
#> GSM674401     3  0.5291     0.8226  0 0.268 0.732
#> GSM674402     3  0.4062     0.7127  0 0.164 0.836
#> GSM674403     3  0.4399     0.7410  0 0.188 0.812
#> GSM674405     3  0.6062     0.8177  0 0.384 0.616
#> GSM674406     3  0.6299     0.6672  0 0.476 0.524
#> GSM674407     3  0.5291     0.8221  0 0.268 0.732
#> GSM674181     2  0.0000     0.8305  0 1.000 0.000
#> GSM674183     2  0.0237     0.8268  0 0.996 0.004
#> GSM674184     2  0.0000     0.8305  0 1.000 0.000
#> GSM674185     2  0.0000     0.8305  0 1.000 0.000
#> GSM674186     2  0.0000     0.8305  0 1.000 0.000
#> GSM674187     2  0.0000     0.8305  0 1.000 0.000
#> GSM674190     2  0.0000     0.8305  0 1.000 0.000
#> GSM674191     2  0.0000     0.8305  0 1.000 0.000
#> GSM674192     2  0.0000     0.8305  0 1.000 0.000
#> GSM674193     2  0.0000     0.8305  0 1.000 0.000
#> GSM674194     2  0.0000     0.8305  0 1.000 0.000
#> GSM674195     2  0.0000     0.8305  0 1.000 0.000
#> GSM674198     2  0.0000     0.8305  0 1.000 0.000
#> GSM674200     2  0.5529     0.2538  0 0.704 0.296
#> GSM674201     2  0.0000     0.8305  0 1.000 0.000
#> GSM674202     2  0.0000     0.8305  0 1.000 0.000
#> GSM674203     2  0.0000     0.8305  0 1.000 0.000
#> GSM674204     2  0.0000     0.8305  0 1.000 0.000
#> GSM674205     2  0.0000     0.8305  0 1.000 0.000
#> GSM674206     2  0.0000     0.8305  0 1.000 0.000
#> GSM674208     2  0.0000     0.8305  0 1.000 0.000
#> GSM674209     2  0.0000     0.8305  0 1.000 0.000
#> GSM674210     2  0.0000     0.8305  0 1.000 0.000
#> GSM674212     2  0.0000     0.8305  0 1.000 0.000
#> GSM674214     2  0.0000     0.8305  0 1.000 0.000
#> GSM674218     2  0.0000     0.8305  0 1.000 0.000
#> GSM674219     2  0.0000     0.8305  0 1.000 0.000
#> GSM674220     2  0.0000     0.8305  0 1.000 0.000
#> GSM674221     2  0.0000     0.8305  0 1.000 0.000
#> GSM674223     2  0.0000     0.8305  0 1.000 0.000
#> GSM674225     2  0.0000     0.8305  0 1.000 0.000
#> GSM674226     2  0.0000     0.8305  0 1.000 0.000
#> GSM674229     2  0.0000     0.8305  0 1.000 0.000
#> GSM674230     2  0.0000     0.8305  0 1.000 0.000
#> GSM674231     2  0.0000     0.8305  0 1.000 0.000
#> GSM674232     2  0.0000     0.8305  0 1.000 0.000
#> GSM674234     2  0.0000     0.8305  0 1.000 0.000
#> GSM674235     2  0.0000     0.8305  0 1.000 0.000
#> GSM674236     2  0.0000     0.8305  0 1.000 0.000
#> GSM674237     2  0.0000     0.8305  0 1.000 0.000
#> GSM674239     2  0.0000     0.8305  0 1.000 0.000
#> GSM674240     2  0.0000     0.8305  0 1.000 0.000
#> GSM674242     2  0.0000     0.8305  0 1.000 0.000
#> GSM674243     2  0.0000     0.8305  0 1.000 0.000
#> GSM674244     2  0.0000     0.8305  0 1.000 0.000
#> GSM674245     2  0.0000     0.8305  0 1.000 0.000
#> GSM674282     1  0.0000     1.0000  1 0.000 0.000
#> GSM674284     1  0.0000     1.0000  1 0.000 0.000
#> GSM674285     1  0.0000     1.0000  1 0.000 0.000
#> GSM674287     1  0.0000     1.0000  1 0.000 0.000
#> GSM674288     1  0.0000     1.0000  1 0.000 0.000
#> GSM674289     1  0.0000     1.0000  1 0.000 0.000
#> GSM674290     1  0.0000     1.0000  1 0.000 0.000
#> GSM674291     1  0.0000     1.0000  1 0.000 0.000
#> GSM674292     1  0.0000     1.0000  1 0.000 0.000
#> GSM674295     1  0.0000     1.0000  1 0.000 0.000
#> GSM674297     1  0.0000     1.0000  1 0.000 0.000
#> GSM674298     1  0.0000     1.0000  1 0.000 0.000
#> GSM674299     1  0.0000     1.0000  1 0.000 0.000
#> GSM674300     1  0.0000     1.0000  1 0.000 0.000
#> GSM674301     1  0.0000     1.0000  1 0.000 0.000
#> GSM674302     1  0.0000     1.0000  1 0.000 0.000
#> GSM674304     1  0.0000     1.0000  1 0.000 0.000
#> GSM674305     1  0.0000     1.0000  1 0.000 0.000
#> GSM674306     1  0.0000     1.0000  1 0.000 0.000
#> GSM674308     1  0.0000     1.0000  1 0.000 0.000
#> GSM674309     1  0.0000     1.0000  1 0.000 0.000
#> GSM674313     1  0.0000     1.0000  1 0.000 0.000
#> GSM674314     1  0.0000     1.0000  1 0.000 0.000
#> GSM674315     1  0.0000     1.0000  1 0.000 0.000
#> GSM674316     1  0.0000     1.0000  1 0.000 0.000
#> GSM674318     1  0.0000     1.0000  1 0.000 0.000
#> GSM674320     1  0.0000     1.0000  1 0.000 0.000
#> GSM674323     1  0.0000     1.0000  1 0.000 0.000
#> GSM674324     1  0.0000     1.0000  1 0.000 0.000
#> GSM674325     1  0.0000     1.0000  1 0.000 0.000
#> GSM674327     1  0.0000     1.0000  1 0.000 0.000
#> GSM674328     1  0.0000     1.0000  1 0.000 0.000
#> GSM674330     1  0.0000     1.0000  1 0.000 0.000
#> GSM674331     1  0.0000     1.0000  1 0.000 0.000
#> GSM674332     1  0.0000     1.0000  1 0.000 0.000
#> GSM674334     1  0.0000     1.0000  1 0.000 0.000
#> GSM674335     1  0.0000     1.0000  1 0.000 0.000
#> GSM674345     3  0.5926     0.8400  0 0.356 0.644
#> GSM674351     3  0.6235     0.7525  0 0.436 0.564
#> GSM674352     3  0.5926     0.8397  0 0.356 0.644
#> GSM674359     2  0.6204    -0.3367  0 0.576 0.424
#> GSM674360     2  0.5948    -0.0365  0 0.640 0.360
#> GSM674362     2  0.3816     0.6411  0 0.852 0.148
#> GSM674369     2  0.2711     0.7335  0 0.912 0.088
#> GSM674372     3  0.5465     0.8346  0 0.288 0.712
#> GSM674374     2  0.6295    -0.5181  0 0.528 0.472
#> GSM674376     3  0.5706     0.8456  0 0.320 0.680
#> GSM674377     2  0.3192     0.7003  0 0.888 0.112
#> GSM674378     3  0.6299     0.6673  0 0.476 0.524
#> GSM674383     2  0.5968    -0.0572  0 0.636 0.364
#> GSM674386     2  0.6260    -0.4321  0 0.552 0.448
#> GSM674387     3  0.4062     0.7127  0 0.164 0.836
#> GSM674392     3  0.5835     0.8456  0 0.340 0.660
#> GSM674396     3  0.5835     0.8457  0 0.340 0.660
#> GSM674399     3  0.6180     0.7808  0 0.416 0.584
#> GSM674404     3  0.4399     0.7412  0 0.188 0.812
#> GSM674182     2  0.0000     0.8305  0 1.000 0.000
#> GSM674188     2  0.0000     0.8305  0 1.000 0.000
#> GSM674189     2  0.0000     0.8305  0 1.000 0.000
#> GSM674196     2  0.0000     0.8305  0 1.000 0.000
#> GSM674197     2  0.0000     0.8305  0 1.000 0.000
#> GSM674199     2  0.0000     0.8305  0 1.000 0.000
#> GSM674207     2  0.0000     0.8305  0 1.000 0.000
#> GSM674211     2  0.0000     0.8305  0 1.000 0.000
#> GSM674213     2  0.0000     0.8305  0 1.000 0.000
#> GSM674215     2  0.0000     0.8305  0 1.000 0.000
#> GSM674216     2  0.0000     0.8305  0 1.000 0.000
#> GSM674217     2  0.0000     0.8305  0 1.000 0.000
#> GSM674222     2  0.0000     0.8305  0 1.000 0.000
#> GSM674224     2  0.0000     0.8305  0 1.000 0.000
#> GSM674227     2  0.0000     0.8305  0 1.000 0.000
#> GSM674228     2  0.0000     0.8305  0 1.000 0.000
#> GSM674233     2  0.0000     0.8305  0 1.000 0.000
#> GSM674238     2  0.3267     0.6942  0 0.884 0.116
#> GSM674241     2  0.0000     0.8305  0 1.000 0.000
#> GSM674283     1  0.0000     1.0000  1 0.000 0.000
#> GSM674286     1  0.0000     1.0000  1 0.000 0.000
#> GSM674293     1  0.0000     1.0000  1 0.000 0.000
#> GSM674294     1  0.0000     1.0000  1 0.000 0.000
#> GSM674296     1  0.0000     1.0000  1 0.000 0.000
#> GSM674303     1  0.0000     1.0000  1 0.000 0.000
#> GSM674307     1  0.0000     1.0000  1 0.000 0.000
#> GSM674310     1  0.0000     1.0000  1 0.000 0.000
#> GSM674311     1  0.0000     1.0000  1 0.000 0.000
#> GSM674312     1  0.0000     1.0000  1 0.000 0.000
#> GSM674317     1  0.0000     1.0000  1 0.000 0.000
#> GSM674319     1  0.0000     1.0000  1 0.000 0.000
#> GSM674321     1  0.0000     1.0000  1 0.000 0.000
#> GSM674322     1  0.0000     1.0000  1 0.000 0.000
#> GSM674326     1  0.0000     1.0000  1 0.000 0.000
#> GSM674329     1  0.0000     1.0000  1 0.000 0.000
#> GSM674333     1  0.0000     1.0000  1 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>           class entropy silhouette    p1    p2    p3 p4
#> GSM674344     3  0.4908      0.745 0.000 0.292 0.692 NA
#> GSM674346     3  0.2413      0.900 0.000 0.064 0.916 NA
#> GSM674347     3  0.2011      0.906 0.000 0.080 0.920 NA
#> GSM674348     3  0.2928      0.906 0.000 0.108 0.880 NA
#> GSM674349     3  0.2867      0.906 0.000 0.104 0.884 NA
#> GSM674350     3  0.2412      0.907 0.000 0.084 0.908 NA
#> GSM674353     3  0.2542      0.906 0.000 0.084 0.904 NA
#> GSM674354     3  0.3529      0.890 0.000 0.152 0.836 NA
#> GSM674355     3  0.1637      0.900 0.000 0.060 0.940 NA
#> GSM674356     3  0.3428      0.894 0.000 0.144 0.844 NA
#> GSM674357     3  0.2329      0.904 0.000 0.072 0.916 NA
#> GSM674358     3  0.1716      0.902 0.000 0.064 0.936 NA
#> GSM674361     3  0.3529      0.891 0.000 0.152 0.836 NA
#> GSM674363     3  0.3217      0.902 0.000 0.128 0.860 NA
#> GSM674364     3  0.4804      0.769 0.000 0.276 0.708 NA
#> GSM674365     3  0.3377      0.896 0.000 0.140 0.848 NA
#> GSM674366     3  0.2530      0.906 0.000 0.112 0.888 NA
#> GSM674367     3  0.2654      0.907 0.000 0.108 0.888 NA
#> GSM674368     3  0.4722      0.739 0.000 0.300 0.692 NA
#> GSM674370     3  0.2412      0.907 0.000 0.084 0.908 NA
#> GSM674371     3  0.3577      0.888 0.000 0.156 0.832 NA
#> GSM674373     3  0.3196      0.898 0.000 0.136 0.856 NA
#> GSM674375     3  0.2101      0.900 0.000 0.060 0.928 NA
#> GSM674379     3  0.4513      0.888 0.000 0.120 0.804 NA
#> GSM674380     2  0.4267      0.700 0.000 0.788 0.188 NA
#> GSM674381     3  0.3278      0.905 0.000 0.116 0.864 NA
#> GSM674382     3  0.5861      0.729 0.000 0.060 0.644 NA
#> GSM674384     3  0.5291      0.852 0.000 0.180 0.740 NA
#> GSM674385     3  0.4764      0.832 0.000 0.220 0.748 NA
#> GSM674388     3  0.3047      0.905 0.000 0.116 0.872 NA
#> GSM674389     3  0.2565      0.895 0.000 0.056 0.912 NA
#> GSM674390     3  0.3606      0.899 0.000 0.132 0.844 NA
#> GSM674391     3  0.6098      0.697 0.000 0.068 0.616 NA
#> GSM674393     3  0.2402      0.905 0.000 0.076 0.912 NA
#> GSM674394     3  0.2546      0.907 0.000 0.092 0.900 NA
#> GSM674395     3  0.2300      0.901 0.000 0.064 0.920 NA
#> GSM674397     3  0.5069      0.704 0.000 0.320 0.664 NA
#> GSM674398     3  0.5763      0.836 0.000 0.132 0.712 NA
#> GSM674400     3  0.1637      0.900 0.000 0.060 0.940 NA
#> GSM674401     3  0.1902      0.902 0.000 0.064 0.932 NA
#> GSM674402     3  0.1975      0.893 0.000 0.048 0.936 NA
#> GSM674403     3  0.2399      0.889 0.000 0.048 0.920 NA
#> GSM674405     3  0.4301      0.859 0.000 0.064 0.816 NA
#> GSM674406     3  0.2593      0.907 0.000 0.104 0.892 NA
#> GSM674407     3  0.2214      0.888 0.000 0.044 0.928 NA
#> GSM674181     2  0.2675      0.855 0.000 0.892 0.100 NA
#> GSM674183     2  0.5508     -0.219 0.000 0.508 0.476 NA
#> GSM674184     2  0.1305      0.938 0.000 0.960 0.036 NA
#> GSM674185     2  0.0336      0.964 0.000 0.992 0.008 NA
#> GSM674186     2  0.0000      0.965 0.000 1.000 0.000 NA
#> GSM674187     2  0.0188      0.966 0.000 0.996 0.004 NA
#> GSM674190     2  0.0188      0.966 0.000 0.996 0.004 NA
#> GSM674191     2  0.0188      0.966 0.000 0.996 0.004 NA
#> GSM674192     2  0.0376      0.966 0.000 0.992 0.004 NA
#> GSM674193     2  0.0376      0.966 0.000 0.992 0.004 NA
#> GSM674194     2  0.0188      0.966 0.000 0.996 0.004 NA
#> GSM674195     2  0.4746      0.447 0.000 0.688 0.304 NA
#> GSM674198     2  0.0000      0.965 0.000 1.000 0.000 NA
#> GSM674200     3  0.4579      0.846 0.000 0.200 0.768 NA
#> GSM674201     2  0.1398      0.933 0.000 0.956 0.040 NA
#> GSM674202     2  0.0188      0.966 0.000 0.996 0.004 NA
#> GSM674203     2  0.0188      0.965 0.000 0.996 0.000 NA
#> GSM674204     2  0.0000      0.965 0.000 1.000 0.000 NA
#> GSM674205     2  0.0000      0.965 0.000 1.000 0.000 NA
#> GSM674206     2  0.0376      0.966 0.000 0.992 0.004 NA
#> GSM674208     2  0.0376      0.966 0.000 0.992 0.004 NA
#> GSM674209     2  0.0376      0.966 0.000 0.992 0.004 NA
#> GSM674210     2  0.0376      0.966 0.000 0.992 0.004 NA
#> GSM674212     2  0.0188      0.965 0.000 0.996 0.000 NA
#> GSM674214     2  0.0000      0.965 0.000 1.000 0.000 NA
#> GSM674218     2  0.0804      0.962 0.000 0.980 0.012 NA
#> GSM674219     2  0.0000      0.965 0.000 1.000 0.000 NA
#> GSM674220     2  0.1938      0.917 0.000 0.936 0.052 NA
#> GSM674221     2  0.0000      0.965 0.000 1.000 0.000 NA
#> GSM674223     2  0.0376      0.966 0.000 0.992 0.004 NA
#> GSM674225     2  0.1837      0.934 0.000 0.944 0.028 NA
#> GSM674226     2  0.0524      0.965 0.000 0.988 0.004 NA
#> GSM674229     2  0.0188      0.965 0.000 0.996 0.000 NA
#> GSM674230     2  0.0524      0.965 0.000 0.988 0.004 NA
#> GSM674231     2  0.0376      0.966 0.000 0.992 0.004 NA
#> GSM674232     2  0.0524      0.965 0.000 0.988 0.004 NA
#> GSM674234     2  0.0188      0.966 0.000 0.996 0.004 NA
#> GSM674235     2  0.0376      0.966 0.000 0.992 0.004 NA
#> GSM674236     2  0.0524      0.965 0.000 0.988 0.004 NA
#> GSM674237     2  0.0524      0.965 0.000 0.988 0.004 NA
#> GSM674239     2  0.0376      0.966 0.000 0.992 0.004 NA
#> GSM674240     2  0.0000      0.965 0.000 1.000 0.000 NA
#> GSM674242     2  0.0524      0.965 0.000 0.988 0.004 NA
#> GSM674243     2  0.0188      0.962 0.000 0.996 0.000 NA
#> GSM674244     2  0.0804      0.961 0.000 0.980 0.008 NA
#> GSM674245     2  0.0672      0.963 0.000 0.984 0.008 NA
#> GSM674282     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674284     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674285     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674287     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674288     1  0.1211      0.973 0.960 0.000 0.000 NA
#> GSM674289     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674290     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674291     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674292     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674295     1  0.1940      0.962 0.924 0.000 0.000 NA
#> GSM674297     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674298     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674299     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674300     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674301     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674302     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674304     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674305     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674306     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674308     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674309     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674313     1  0.2149      0.957 0.912 0.000 0.000 NA
#> GSM674314     1  0.0707      0.978 0.980 0.000 0.000 NA
#> GSM674315     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674316     1  0.1716      0.966 0.936 0.000 0.000 NA
#> GSM674318     1  0.2011      0.960 0.920 0.000 0.000 NA
#> GSM674320     1  0.2149      0.957 0.912 0.000 0.000 NA
#> GSM674323     1  0.2011      0.960 0.920 0.000 0.000 NA
#> GSM674324     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674325     1  0.1940      0.962 0.924 0.000 0.000 NA
#> GSM674327     1  0.0707      0.978 0.980 0.000 0.000 NA
#> GSM674328     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674330     1  0.0817      0.977 0.976 0.000 0.000 NA
#> GSM674331     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674332     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674334     1  0.0921      0.977 0.972 0.000 0.000 NA
#> GSM674335     1  0.1302      0.972 0.956 0.000 0.000 NA
#> GSM674345     3  0.2450      0.903 0.000 0.072 0.912 NA
#> GSM674351     3  0.2546      0.907 0.000 0.092 0.900 NA
#> GSM674352     3  0.2473      0.905 0.000 0.080 0.908 NA
#> GSM674359     3  0.4289      0.867 0.000 0.172 0.796 NA
#> GSM674360     3  0.3583      0.873 0.000 0.180 0.816 NA
#> GSM674362     3  0.4897      0.689 0.000 0.332 0.660 NA
#> GSM674369     3  0.4973      0.658 0.000 0.348 0.644 NA
#> GSM674372     3  0.2179      0.902 0.000 0.064 0.924 NA
#> GSM674374     3  0.2859      0.906 0.000 0.112 0.880 NA
#> GSM674376     3  0.3245      0.889 0.000 0.064 0.880 NA
#> GSM674377     2  0.4855      0.530 0.000 0.712 0.268 NA
#> GSM674378     3  0.2654      0.907 0.000 0.108 0.888 NA
#> GSM674383     3  0.3024      0.893 0.000 0.148 0.852 NA
#> GSM674386     3  0.7803      0.415 0.000 0.316 0.416 NA
#> GSM674387     3  0.1936      0.877 0.000 0.028 0.940 NA
#> GSM674392     3  0.2198      0.904 0.000 0.072 0.920 NA
#> GSM674396     3  0.5522      0.805 0.000 0.080 0.716 NA
#> GSM674399     3  0.6275      0.787 0.000 0.136 0.660 NA
#> GSM674404     3  0.3013      0.863 0.000 0.032 0.888 NA
#> GSM674182     2  0.0657      0.956 0.000 0.984 0.012 NA
#> GSM674188     2  0.0188      0.966 0.000 0.996 0.004 NA
#> GSM674189     2  0.0336      0.964 0.000 0.992 0.008 NA
#> GSM674196     2  0.0000      0.965 0.000 1.000 0.000 NA
#> GSM674197     2  0.0000      0.965 0.000 1.000 0.000 NA
#> GSM674199     2  0.0000      0.965 0.000 1.000 0.000 NA
#> GSM674207     2  0.0469      0.959 0.000 0.988 0.012 NA
#> GSM674211     2  0.0000      0.965 0.000 1.000 0.000 NA
#> GSM674213     2  0.0000      0.965 0.000 1.000 0.000 NA
#> GSM674215     2  0.0937      0.958 0.000 0.976 0.012 NA
#> GSM674216     2  0.0657      0.964 0.000 0.984 0.004 NA
#> GSM674217     2  0.0188      0.964 0.000 0.996 0.004 NA
#> GSM674222     2  0.0804      0.961 0.000 0.980 0.008 NA
#> GSM674224     2  0.0524      0.965 0.000 0.988 0.004 NA
#> GSM674227     2  0.0524      0.965 0.000 0.988 0.004 NA
#> GSM674228     2  0.0188      0.966 0.000 0.996 0.004 NA
#> GSM674233     2  0.0336      0.964 0.000 0.992 0.008 NA
#> GSM674238     3  0.4990      0.652 0.000 0.352 0.640 NA
#> GSM674241     2  0.0376      0.966 0.000 0.992 0.004 NA
#> GSM674283     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674286     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674293     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674294     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674296     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674303     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674307     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674310     1  0.2011      0.960 0.920 0.000 0.000 NA
#> GSM674311     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674312     1  0.2149      0.957 0.912 0.000 0.000 NA
#> GSM674317     1  0.0000      0.982 1.000 0.000 0.000 NA
#> GSM674319     1  0.2011      0.960 0.920 0.000 0.000 NA
#> GSM674321     1  0.2011      0.960 0.920 0.000 0.000 NA
#> GSM674322     1  0.2011      0.960 0.920 0.000 0.000 NA
#> GSM674326     1  0.2011      0.960 0.920 0.000 0.000 NA
#> GSM674329     1  0.2011      0.960 0.920 0.000 0.000 NA
#> GSM674333     1  0.2011      0.960 0.920 0.000 0.000 NA

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>           class entropy silhouette    p1    p2    p3 p4    p5
#> GSM674344     3  0.3962   0.526163 0.000 0.088 0.800 NA 0.112
#> GSM674346     3  0.2331   0.575117 0.000 0.020 0.900 NA 0.080
#> GSM674347     3  0.3326   0.493789 0.000 0.024 0.824 NA 0.152
#> GSM674348     3  0.2793   0.582574 0.000 0.036 0.876 NA 0.088
#> GSM674349     3  0.2511   0.585153 0.000 0.028 0.892 NA 0.080
#> GSM674350     3  0.1661   0.592736 0.000 0.036 0.940 NA 0.024
#> GSM674353     3  0.1386   0.592795 0.000 0.032 0.952 NA 0.016
#> GSM674354     3  0.2331   0.587801 0.000 0.080 0.900 NA 0.020
#> GSM674355     3  0.3398   0.404467 0.000 0.004 0.780 NA 0.216
#> GSM674356     3  0.1981   0.592502 0.000 0.064 0.920 NA 0.016
#> GSM674357     3  0.1493   0.593517 0.000 0.028 0.948 NA 0.024
#> GSM674358     3  0.2625   0.542568 0.000 0.016 0.876 NA 0.108
#> GSM674361     3  0.5295   0.351505 0.000 0.096 0.684 NA 0.212
#> GSM674363     3  0.2171   0.592328 0.000 0.064 0.912 NA 0.024
#> GSM674364     3  0.6031   0.179252 0.000 0.244 0.576 NA 0.180
#> GSM674365     3  0.2036   0.594234 0.000 0.056 0.920 NA 0.024
#> GSM674366     3  0.3165   0.544775 0.000 0.036 0.848 NA 0.116
#> GSM674367     3  0.4552   0.283591 0.000 0.040 0.696 NA 0.264
#> GSM674368     3  0.4125   0.477403 0.000 0.172 0.772 NA 0.056
#> GSM674370     3  0.2915   0.556426 0.000 0.024 0.860 NA 0.116
#> GSM674371     3  0.1809   0.595263 0.000 0.060 0.928 NA 0.012
#> GSM674373     3  0.6087   0.069910 0.000 0.148 0.572 NA 0.276
#> GSM674375     3  0.4297   0.256627 0.000 0.020 0.692 NA 0.288
#> GSM674379     5  0.6002   0.736273 0.000 0.088 0.408 NA 0.496
#> GSM674380     2  0.6408  -0.251115 0.000 0.440 0.172 NA 0.388
#> GSM674381     3  0.5097   0.054497 0.000 0.056 0.624 NA 0.320
#> GSM674382     5  0.5319   0.779950 0.000 0.044 0.360 NA 0.588
#> GSM674384     3  0.6267  -0.467735 0.000 0.148 0.448 NA 0.404
#> GSM674385     3  0.6420  -0.437788 0.000 0.176 0.448 NA 0.376
#> GSM674388     3  0.3262   0.568272 0.000 0.036 0.840 NA 0.124
#> GSM674389     3  0.4416  -0.010886 0.000 0.012 0.632 NA 0.356
#> GSM674390     3  0.5934  -0.445074 0.000 0.108 0.496 NA 0.396
#> GSM674391     5  0.5448   0.754226 0.000 0.068 0.300 NA 0.624
#> GSM674393     3  0.4637   0.189750 0.000 0.036 0.672 NA 0.292
#> GSM674394     3  0.4728   0.194399 0.000 0.040 0.664 NA 0.296
#> GSM674395     3  0.4318   0.212238 0.000 0.020 0.688 NA 0.292
#> GSM674397     3  0.6536  -0.344056 0.000 0.216 0.464 NA 0.320
#> GSM674398     5  0.6120   0.770303 0.000 0.092 0.392 NA 0.504
#> GSM674400     3  0.2511   0.552295 0.000 0.016 0.892 NA 0.088
#> GSM674401     3  0.3050   0.563984 0.000 0.024 0.876 NA 0.076
#> GSM674402     3  0.2139   0.578658 0.000 0.032 0.916 NA 0.052
#> GSM674403     3  0.2616   0.551084 0.000 0.020 0.880 NA 0.100
#> GSM674405     5  0.5352   0.712793 0.000 0.044 0.428 NA 0.524
#> GSM674406     3  0.4597   0.287443 0.000 0.044 0.696 NA 0.260
#> GSM674407     3  0.5041  -0.304160 0.000 0.028 0.564 NA 0.404
#> GSM674181     2  0.5144   0.496773 0.000 0.632 0.304 NA 0.064
#> GSM674183     3  0.5571   0.207517 0.000 0.348 0.568 NA 0.084
#> GSM674184     2  0.3012   0.858034 0.000 0.860 0.104 NA 0.036
#> GSM674185     2  0.1845   0.911647 0.000 0.928 0.056 NA 0.016
#> GSM674186     2  0.1195   0.920225 0.000 0.960 0.028 NA 0.012
#> GSM674187     2  0.1549   0.919864 0.000 0.944 0.040 NA 0.016
#> GSM674190     2  0.1386   0.919336 0.000 0.952 0.032 NA 0.016
#> GSM674191     2  0.1124   0.922074 0.000 0.960 0.036 NA 0.004
#> GSM674192     2  0.0693   0.921654 0.000 0.980 0.012 NA 0.008
#> GSM674193     2  0.1012   0.921255 0.000 0.968 0.020 NA 0.012
#> GSM674194     2  0.1568   0.915748 0.000 0.944 0.036 NA 0.020
#> GSM674195     3  0.5602   0.000244 0.000 0.464 0.472 NA 0.060
#> GSM674198     2  0.0609   0.921172 0.000 0.980 0.020 NA 0.000
#> GSM674200     3  0.3865   0.528015 0.000 0.092 0.808 NA 0.100
#> GSM674201     2  0.4149   0.733992 0.000 0.768 0.188 NA 0.040
#> GSM674202     2  0.1568   0.919323 0.000 0.944 0.036 NA 0.020
#> GSM674203     2  0.0451   0.919384 0.000 0.988 0.004 NA 0.008
#> GSM674204     2  0.1012   0.920222 0.000 0.968 0.020 NA 0.012
#> GSM674205     2  0.1018   0.920530 0.000 0.968 0.016 NA 0.016
#> GSM674206     2  0.1493   0.918778 0.000 0.948 0.028 NA 0.024
#> GSM674208     2  0.1211   0.920863 0.000 0.960 0.016 NA 0.024
#> GSM674209     2  0.0798   0.921213 0.000 0.976 0.008 NA 0.016
#> GSM674210     2  0.1364   0.909854 0.000 0.952 0.012 NA 0.036
#> GSM674212     2  0.1469   0.914590 0.000 0.948 0.016 NA 0.036
#> GSM674214     2  0.1661   0.914271 0.000 0.940 0.024 NA 0.036
#> GSM674218     2  0.2835   0.876190 0.000 0.880 0.080 NA 0.036
#> GSM674219     2  0.1830   0.912932 0.000 0.932 0.040 NA 0.028
#> GSM674220     2  0.3667   0.800299 0.000 0.812 0.048 NA 0.140
#> GSM674221     2  0.1579   0.916923 0.000 0.944 0.032 NA 0.024
#> GSM674223     2  0.1195   0.919907 0.000 0.960 0.028 NA 0.012
#> GSM674225     2  0.3141   0.818318 0.000 0.832 0.016 NA 0.152
#> GSM674226     2  0.1043   0.912292 0.000 0.960 0.000 NA 0.040
#> GSM674229     2  0.0566   0.921510 0.000 0.984 0.012 NA 0.004
#> GSM674230     2  0.1597   0.914346 0.000 0.940 0.012 NA 0.048
#> GSM674231     2  0.1403   0.919404 0.000 0.952 0.024 NA 0.024
#> GSM674232     2  0.1282   0.911665 0.000 0.952 0.004 NA 0.044
#> GSM674234     2  0.0510   0.921423 0.000 0.984 0.016 NA 0.000
#> GSM674235     2  0.0992   0.923675 0.000 0.968 0.024 NA 0.008
#> GSM674236     2  0.0992   0.919008 0.000 0.968 0.008 NA 0.024
#> GSM674237     2  0.0880   0.914710 0.000 0.968 0.000 NA 0.032
#> GSM674239     2  0.0912   0.921438 0.000 0.972 0.012 NA 0.016
#> GSM674240     2  0.2359   0.901997 0.000 0.904 0.060 NA 0.036
#> GSM674242     2  0.1522   0.906788 0.000 0.944 0.012 NA 0.044
#> GSM674243     2  0.2125   0.902755 0.000 0.920 0.052 NA 0.024
#> GSM674244     2  0.2233   0.882645 0.000 0.904 0.016 NA 0.080
#> GSM674245     2  0.1597   0.904882 0.000 0.940 0.012 NA 0.048
#> GSM674282     1  0.0162   0.948755 0.996 0.000 0.000 NA 0.000
#> GSM674284     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674285     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674287     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674288     1  0.2561   0.915858 0.856 0.000 0.000 NA 0.000
#> GSM674289     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674290     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674291     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674292     1  0.0162   0.948755 0.996 0.000 0.000 NA 0.000
#> GSM674295     1  0.2690   0.911509 0.844 0.000 0.000 NA 0.000
#> GSM674297     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674298     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674299     1  0.0290   0.948456 0.992 0.000 0.000 NA 0.000
#> GSM674300     1  0.0290   0.948586 0.992 0.000 0.000 NA 0.000
#> GSM674301     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674302     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674304     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674305     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674306     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674308     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674309     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674313     1  0.2813   0.905946 0.832 0.000 0.000 NA 0.000
#> GSM674314     1  0.2011   0.930798 0.908 0.000 0.000 NA 0.004
#> GSM674315     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674316     1  0.2848   0.909038 0.840 0.000 0.000 NA 0.004
#> GSM674318     1  0.2890   0.907135 0.836 0.000 0.000 NA 0.004
#> GSM674320     1  0.2813   0.905946 0.832 0.000 0.000 NA 0.000
#> GSM674323     1  0.2848   0.908914 0.840 0.000 0.000 NA 0.004
#> GSM674324     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674325     1  0.2890   0.907135 0.836 0.000 0.000 NA 0.004
#> GSM674327     1  0.1892   0.932811 0.916 0.000 0.000 NA 0.004
#> GSM674328     1  0.0162   0.948755 0.996 0.000 0.000 NA 0.000
#> GSM674330     1  0.2020   0.928276 0.900 0.000 0.000 NA 0.000
#> GSM674331     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674332     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674334     1  0.2471   0.917721 0.864 0.000 0.000 NA 0.000
#> GSM674335     1  0.2561   0.915850 0.856 0.000 0.000 NA 0.000
#> GSM674345     3  0.2293   0.574277 0.000 0.016 0.900 NA 0.084
#> GSM674351     3  0.1918   0.592763 0.000 0.036 0.928 NA 0.036
#> GSM674352     3  0.1399   0.590292 0.000 0.028 0.952 NA 0.020
#> GSM674359     3  0.3780   0.532338 0.000 0.072 0.812 NA 0.116
#> GSM674360     3  0.2813   0.569881 0.000 0.108 0.868 NA 0.024
#> GSM674362     3  0.4394   0.411228 0.000 0.228 0.732 NA 0.036
#> GSM674369     3  0.4136   0.452976 0.000 0.188 0.764 NA 0.048
#> GSM674372     3  0.4157   0.311627 0.000 0.020 0.716 NA 0.264
#> GSM674374     3  0.5231   0.362119 0.000 0.080 0.680 NA 0.232
#> GSM674376     3  0.5114  -0.578406 0.000 0.036 0.488 NA 0.476
#> GSM674377     2  0.6513  -0.334042 0.000 0.424 0.192 NA 0.384
#> GSM674378     3  0.5524   0.229713 0.000 0.092 0.628 NA 0.276
#> GSM674383     3  0.2592   0.583090 0.000 0.056 0.892 NA 0.052
#> GSM674386     5  0.6603   0.633993 0.000 0.192 0.272 NA 0.524
#> GSM674387     3  0.4849  -0.358802 0.000 0.016 0.548 NA 0.432
#> GSM674392     3  0.3999   0.359484 0.000 0.020 0.740 NA 0.240
#> GSM674396     5  0.5567   0.801633 0.000 0.052 0.368 NA 0.568
#> GSM674399     5  0.5887   0.801985 0.000 0.100 0.344 NA 0.552
#> GSM674404     3  0.4945  -0.422964 0.000 0.020 0.536 NA 0.440
#> GSM674182     2  0.2754   0.874427 0.000 0.880 0.080 NA 0.040
#> GSM674188     2  0.1251   0.921989 0.000 0.956 0.036 NA 0.008
#> GSM674189     2  0.2036   0.910001 0.000 0.920 0.056 NA 0.024
#> GSM674196     2  0.1485   0.919540 0.000 0.948 0.032 NA 0.020
#> GSM674197     2  0.0955   0.922594 0.000 0.968 0.028 NA 0.004
#> GSM674199     2  0.0609   0.921172 0.000 0.980 0.020 NA 0.000
#> GSM674207     2  0.3267   0.847481 0.000 0.844 0.112 NA 0.044
#> GSM674211     2  0.1403   0.918234 0.000 0.952 0.024 NA 0.024
#> GSM674213     2  0.1836   0.913265 0.000 0.932 0.032 NA 0.036
#> GSM674215     2  0.2685   0.867227 0.000 0.880 0.028 NA 0.092
#> GSM674216     2  0.1768   0.896865 0.000 0.924 0.004 NA 0.072
#> GSM674217     2  0.2491   0.897056 0.000 0.896 0.068 NA 0.036
#> GSM674222     2  0.2707   0.864002 0.000 0.876 0.024 NA 0.100
#> GSM674224     2  0.0609   0.917733 0.000 0.980 0.000 NA 0.020
#> GSM674227     2  0.2230   0.904587 0.000 0.912 0.044 NA 0.044
#> GSM674228     2  0.0671   0.921609 0.000 0.980 0.016 NA 0.004
#> GSM674233     2  0.1800   0.913584 0.000 0.932 0.048 NA 0.020
#> GSM674238     3  0.4359   0.439549 0.000 0.196 0.752 NA 0.048
#> GSM674241     2  0.0404   0.918162 0.000 0.988 0.000 NA 0.012
#> GSM674283     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674286     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674293     1  0.0162   0.948755 0.996 0.000 0.000 NA 0.000
#> GSM674294     1  0.0162   0.948755 0.996 0.000 0.000 NA 0.000
#> GSM674296     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674303     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674307     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674310     1  0.2890   0.907135 0.836 0.000 0.000 NA 0.004
#> GSM674311     1  0.0000   0.949508 1.000 0.000 0.000 NA 0.000
#> GSM674312     1  0.2929   0.899522 0.820 0.000 0.000 NA 0.000
#> GSM674317     1  0.0703   0.946127 0.976 0.000 0.000 NA 0.000
#> GSM674319     1  0.2813   0.905946 0.832 0.000 0.000 NA 0.000
#> GSM674321     1  0.2890   0.907135 0.836 0.000 0.000 NA 0.004
#> GSM674322     1  0.2813   0.905946 0.832 0.000 0.000 NA 0.000
#> GSM674326     1  0.2890   0.907135 0.836 0.000 0.000 NA 0.004
#> GSM674329     1  0.2813   0.905946 0.832 0.000 0.000 NA 0.000
#> GSM674333     1  0.2813   0.905946 0.832 0.000 0.000 NA 0.000

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>           class entropy silhouette    p1    p2    p3    p4 p5 p6
#> GSM674344     3  0.3419    0.57862 0.000 0.084 0.812 0.000 NA NA
#> GSM674346     3  0.2466    0.61744 0.000 0.024 0.896 0.028 NA NA
#> GSM674347     3  0.4083    0.44266 0.000 0.020 0.688 0.284 NA NA
#> GSM674348     3  0.4394    0.58673 0.000 0.048 0.768 0.088 NA NA
#> GSM674349     3  0.3721    0.61887 0.000 0.048 0.820 0.072 NA NA
#> GSM674350     3  0.2685    0.63360 0.000 0.036 0.880 0.068 NA NA
#> GSM674353     3  0.1970    0.63461 0.000 0.028 0.920 0.044 NA NA
#> GSM674354     3  0.2624    0.63216 0.000 0.068 0.884 0.020 NA NA
#> GSM674355     3  0.3954    0.42820 0.000 0.016 0.684 0.296 NA NA
#> GSM674356     3  0.2541    0.63691 0.000 0.052 0.892 0.032 NA NA
#> GSM674357     3  0.2074    0.63627 0.000 0.036 0.912 0.048 NA NA
#> GSM674358     3  0.3406    0.57202 0.000 0.020 0.792 0.180 NA NA
#> GSM674361     3  0.6422    0.33441 0.000 0.124 0.580 0.180 NA NA
#> GSM674363     3  0.3329    0.62311 0.000 0.072 0.844 0.032 NA NA
#> GSM674364     3  0.6531    0.18324 0.000 0.292 0.504 0.108 NA NA
#> GSM674365     3  0.3083    0.63527 0.000 0.052 0.860 0.060 NA NA
#> GSM674366     3  0.4252    0.51837 0.000 0.040 0.724 0.220 NA NA
#> GSM674367     3  0.4936    0.12875 0.000 0.036 0.540 0.408 NA NA
#> GSM674368     3  0.5169    0.48949 0.000 0.168 0.692 0.064 NA NA
#> GSM674370     3  0.4653    0.49613 0.000 0.024 0.700 0.220 NA NA
#> GSM674371     3  0.2978    0.63590 0.000 0.056 0.860 0.072 NA NA
#> GSM674373     4  0.7074    0.40291 0.000 0.136 0.316 0.416 NA NA
#> GSM674375     3  0.5147   -0.13535 0.000 0.016 0.480 0.456 NA NA
#> GSM674379     4  0.4830    0.65551 0.000 0.084 0.204 0.692 NA NA
#> GSM674380     4  0.6258    0.41772 0.000 0.368 0.100 0.472 NA NA
#> GSM674381     3  0.5379   -0.12575 0.000 0.068 0.472 0.444 NA NA
#> GSM674382     4  0.5528    0.59269 0.000 0.052 0.224 0.636 NA NA
#> GSM674384     4  0.6905    0.33283 0.000 0.168 0.368 0.384 NA NA
#> GSM674385     4  0.6636    0.37163 0.000 0.192 0.368 0.396 NA NA
#> GSM674388     3  0.4946    0.52107 0.000 0.044 0.704 0.176 NA NA
#> GSM674389     3  0.4935   -0.11517 0.000 0.020 0.496 0.456 NA NA
#> GSM674390     4  0.5426    0.55248 0.000 0.096 0.312 0.576 NA NA
#> GSM674391     4  0.3958    0.63899 0.000 0.060 0.128 0.788 NA NA
#> GSM674393     3  0.4584    0.00993 0.000 0.028 0.524 0.444 NA NA
#> GSM674394     3  0.4833    0.15478 0.000 0.036 0.556 0.396 NA NA
#> GSM674395     3  0.4637    0.13752 0.000 0.028 0.556 0.408 NA NA
#> GSM674397     4  0.6521    0.46552 0.000 0.216 0.320 0.432 NA NA
#> GSM674398     4  0.4678    0.66278 0.000 0.096 0.156 0.724 NA NA
#> GSM674400     3  0.3232    0.57483 0.000 0.008 0.812 0.160 NA NA
#> GSM674401     3  0.4002    0.59838 0.000 0.028 0.816 0.056 NA NA
#> GSM674402     3  0.3003    0.60942 0.000 0.024 0.872 0.028 NA NA
#> GSM674403     3  0.2582    0.61055 0.000 0.028 0.892 0.008 NA NA
#> GSM674405     4  0.4151    0.65369 0.000 0.052 0.192 0.744 NA NA
#> GSM674406     3  0.5112    0.09120 0.000 0.048 0.524 0.412 NA NA
#> GSM674407     4  0.4854    0.49317 0.000 0.016 0.328 0.612 NA NA
#> GSM674181     2  0.5562    0.44229 0.000 0.552 0.308 0.008 NA NA
#> GSM674183     3  0.5455    0.27022 0.000 0.264 0.564 0.000 NA NA
#> GSM674184     2  0.3955    0.81208 0.000 0.784 0.112 0.012 NA NA
#> GSM674185     2  0.2340    0.88662 0.000 0.896 0.044 0.004 NA NA
#> GSM674186     2  0.2377    0.88408 0.000 0.892 0.024 0.008 NA NA
#> GSM674187     2  0.2420    0.88213 0.000 0.888 0.032 0.004 NA NA
#> GSM674190     2  0.2001    0.88389 0.000 0.912 0.048 0.000 NA NA
#> GSM674191     2  0.1720    0.89323 0.000 0.928 0.040 0.000 NA NA
#> GSM674192     2  0.0993    0.89239 0.000 0.964 0.024 0.000 NA NA
#> GSM674193     2  0.1421    0.88943 0.000 0.944 0.028 0.000 NA NA
#> GSM674194     2  0.1995    0.89010 0.000 0.912 0.052 0.000 NA NA
#> GSM674195     3  0.5370    0.06925 0.000 0.428 0.480 0.008 NA NA
#> GSM674198     2  0.1492    0.89410 0.000 0.940 0.024 0.000 NA NA
#> GSM674200     3  0.3705    0.57625 0.000 0.076 0.816 0.004 NA NA
#> GSM674201     2  0.4156    0.73528 0.000 0.732 0.188 0.000 NA NA
#> GSM674202     2  0.1864    0.89679 0.000 0.924 0.032 0.004 NA NA
#> GSM674203     2  0.0291    0.89106 0.000 0.992 0.004 0.004 NA NA
#> GSM674204     2  0.2066    0.88757 0.000 0.904 0.024 0.000 NA NA
#> GSM674205     2  0.1418    0.89353 0.000 0.944 0.032 0.000 NA NA
#> GSM674206     2  0.2527    0.86856 0.000 0.884 0.048 0.004 NA NA
#> GSM674208     2  0.1944    0.87735 0.000 0.924 0.024 0.016 NA NA
#> GSM674209     2  0.1353    0.89058 0.000 0.952 0.012 0.012 NA NA
#> GSM674210     2  0.1777    0.88530 0.000 0.928 0.004 0.024 NA NA
#> GSM674212     2  0.3072    0.86587 0.000 0.856 0.024 0.036 NA NA
#> GSM674214     2  0.3270    0.86456 0.000 0.844 0.028 0.040 NA NA
#> GSM674218     2  0.4267    0.76470 0.000 0.764 0.132 0.024 NA NA
#> GSM674219     2  0.2763    0.87263 0.000 0.868 0.036 0.008 NA NA
#> GSM674220     2  0.4255    0.73285 0.000 0.772 0.048 0.128 NA NA
#> GSM674221     2  0.2679    0.87402 0.000 0.868 0.032 0.004 NA NA
#> GSM674223     2  0.2134    0.87663 0.000 0.904 0.052 0.000 NA NA
#> GSM674225     2  0.4027    0.71693 0.000 0.768 0.012 0.156 NA NA
#> GSM674226     2  0.1901    0.87484 0.000 0.924 0.008 0.040 NA NA
#> GSM674229     2  0.0622    0.89237 0.000 0.980 0.012 0.000 NA NA
#> GSM674230     2  0.1787    0.88138 0.000 0.932 0.016 0.020 NA NA
#> GSM674231     2  0.2649    0.86441 0.000 0.876 0.052 0.004 NA NA
#> GSM674232     2  0.1269    0.88603 0.000 0.956 0.012 0.012 NA NA
#> GSM674234     2  0.0909    0.89589 0.000 0.968 0.020 0.000 NA NA
#> GSM674235     2  0.1401    0.89742 0.000 0.948 0.028 0.004 NA NA
#> GSM674236     2  0.0881    0.89093 0.000 0.972 0.008 0.008 NA NA
#> GSM674237     2  0.1679    0.88000 0.000 0.936 0.016 0.012 NA NA
#> GSM674239     2  0.1167    0.88688 0.000 0.960 0.012 0.008 NA NA
#> GSM674240     2  0.3482    0.84841 0.000 0.812 0.068 0.004 NA NA
#> GSM674242     2  0.2325    0.87695 0.000 0.900 0.008 0.048 NA NA
#> GSM674243     2  0.2966    0.85086 0.000 0.848 0.076 0.000 NA NA
#> GSM674244     2  0.3652    0.80552 0.000 0.808 0.016 0.120 NA NA
#> GSM674245     2  0.2760    0.86317 0.000 0.872 0.008 0.068 NA NA
#> GSM674282     1  0.0291    0.88294 0.992 0.000 0.000 0.000 NA NA
#> GSM674284     1  0.0146    0.88294 0.996 0.000 0.000 0.000 NA NA
#> GSM674285     1  0.0000    0.88236 1.000 0.000 0.000 0.000 NA NA
#> GSM674287     1  0.0260    0.88318 0.992 0.000 0.000 0.000 NA NA
#> GSM674288     1  0.3528    0.80884 0.700 0.000 0.000 0.000 NA NA
#> GSM674289     1  0.0000    0.88236 1.000 0.000 0.000 0.000 NA NA
#> GSM674290     1  0.0146    0.88151 0.996 0.000 0.000 0.000 NA NA
#> GSM674291     1  0.0146    0.88258 0.996 0.000 0.000 0.000 NA NA
#> GSM674292     1  0.0405    0.88299 0.988 0.000 0.000 0.000 NA NA
#> GSM674295     1  0.3584    0.80555 0.688 0.000 0.000 0.000 NA NA
#> GSM674297     1  0.0146    0.88234 0.996 0.000 0.000 0.000 NA NA
#> GSM674298     1  0.0146    0.88234 0.996 0.000 0.000 0.000 NA NA
#> GSM674299     1  0.1531    0.87371 0.928 0.000 0.000 0.000 NA NA
#> GSM674300     1  0.0713    0.88186 0.972 0.000 0.000 0.000 NA NA
#> GSM674301     1  0.0000    0.88236 1.000 0.000 0.000 0.000 NA NA
#> GSM674302     1  0.0146    0.88151 0.996 0.000 0.000 0.000 NA NA
#> GSM674304     1  0.0363    0.88111 0.988 0.000 0.000 0.000 NA NA
#> GSM674305     1  0.0260    0.88169 0.992 0.000 0.000 0.000 NA NA
#> GSM674306     1  0.0632    0.88200 0.976 0.000 0.000 0.000 NA NA
#> GSM674308     1  0.0000    0.88236 1.000 0.000 0.000 0.000 NA NA
#> GSM674309     1  0.0713    0.88183 0.972 0.000 0.000 0.000 NA NA
#> GSM674313     1  0.3769    0.78186 0.640 0.000 0.000 0.000 NA NA
#> GSM674314     1  0.2883    0.83994 0.788 0.000 0.000 0.000 NA NA
#> GSM674315     1  0.0547    0.88274 0.980 0.000 0.000 0.000 NA NA
#> GSM674316     1  0.3578    0.79363 0.660 0.000 0.000 0.000 NA NA
#> GSM674318     1  0.3706    0.77230 0.620 0.000 0.000 0.000 NA NA
#> GSM674320     1  0.3672    0.77706 0.632 0.000 0.000 0.000 NA NA
#> GSM674323     1  0.3634    0.78580 0.644 0.000 0.000 0.000 NA NA
#> GSM674324     1  0.0458    0.88271 0.984 0.000 0.000 0.000 NA NA
#> GSM674325     1  0.3659    0.78222 0.636 0.000 0.000 0.000 NA NA
#> GSM674327     1  0.2664    0.84779 0.816 0.000 0.000 0.000 NA NA
#> GSM674328     1  0.0632    0.88245 0.976 0.000 0.000 0.000 NA NA
#> GSM674330     1  0.2762    0.84402 0.804 0.000 0.000 0.000 NA NA
#> GSM674331     1  0.0632    0.88239 0.976 0.000 0.000 0.000 NA NA
#> GSM674332     1  0.0000    0.88236 1.000 0.000 0.000 0.000 NA NA
#> GSM674334     1  0.3221    0.82280 0.736 0.000 0.000 0.000 NA NA
#> GSM674335     1  0.3565    0.80744 0.692 0.000 0.000 0.000 NA NA
#> GSM674345     3  0.3077    0.62033 0.000 0.032 0.860 0.040 NA NA
#> GSM674351     3  0.3255    0.63039 0.000 0.044 0.848 0.076 NA NA
#> GSM674352     3  0.2480    0.62769 0.000 0.028 0.896 0.048 NA NA
#> GSM674359     3  0.3127    0.59682 0.000 0.056 0.840 0.004 NA NA
#> GSM674360     3  0.4066    0.58617 0.000 0.112 0.788 0.036 NA NA
#> GSM674362     3  0.5084    0.38930 0.000 0.244 0.648 0.016 NA NA
#> GSM674369     3  0.4310    0.50166 0.000 0.188 0.740 0.024 NA NA
#> GSM674372     3  0.4579    0.22201 0.000 0.028 0.584 0.380 NA NA
#> GSM674374     3  0.6756   -0.14430 0.000 0.088 0.448 0.328 NA NA
#> GSM674376     4  0.4193    0.59536 0.000 0.028 0.276 0.688 NA NA
#> GSM674377     4  0.5824    0.45194 0.000 0.344 0.092 0.528 NA NA
#> GSM674378     4  0.6529    0.27472 0.000 0.084 0.404 0.412 NA NA
#> GSM674383     3  0.3566    0.61308 0.000 0.076 0.812 0.104 NA NA
#> GSM674386     4  0.5904    0.57750 0.000 0.204 0.140 0.604 NA NA
#> GSM674387     4  0.4564    0.53635 0.000 0.012 0.292 0.656 NA NA
#> GSM674392     3  0.4492    0.31538 0.000 0.036 0.620 0.340 NA NA
#> GSM674396     4  0.4146    0.64624 0.000 0.052 0.152 0.768 NA NA
#> GSM674399     4  0.4551    0.66186 0.000 0.088 0.152 0.736 NA NA
#> GSM674404     4  0.4515    0.45924 0.000 0.008 0.356 0.608 NA NA
#> GSM674182     2  0.3972    0.81303 0.000 0.772 0.120 0.004 NA NA
#> GSM674188     2  0.1788    0.89262 0.000 0.928 0.028 0.004 NA NA
#> GSM674189     2  0.3032    0.84350 0.000 0.840 0.104 0.000 NA NA
#> GSM674196     2  0.2702    0.87718 0.000 0.868 0.036 0.004 NA NA
#> GSM674197     2  0.1716    0.89330 0.000 0.932 0.028 0.004 NA NA
#> GSM674199     2  0.1528    0.89154 0.000 0.936 0.016 0.000 NA NA
#> GSM674207     2  0.4332    0.77374 0.000 0.744 0.128 0.008 NA NA
#> GSM674211     2  0.2894    0.87143 0.000 0.864 0.020 0.028 NA NA
#> GSM674213     2  0.3514    0.85667 0.000 0.828 0.040 0.036 NA NA
#> GSM674215     2  0.4405    0.76414 0.000 0.756 0.036 0.140 NA NA
#> GSM674216     2  0.2251    0.86289 0.000 0.904 0.008 0.052 NA NA
#> GSM674217     2  0.3502    0.84358 0.000 0.812 0.076 0.004 NA NA
#> GSM674222     2  0.3124    0.82005 0.000 0.848 0.016 0.096 NA NA
#> GSM674224     2  0.1426    0.88692 0.000 0.948 0.008 0.016 NA NA
#> GSM674227     2  0.3017    0.85291 0.000 0.860 0.060 0.016 NA NA
#> GSM674228     2  0.1257    0.89702 0.000 0.952 0.028 0.000 NA NA
#> GSM674233     2  0.2653    0.88223 0.000 0.876 0.056 0.004 NA NA
#> GSM674238     3  0.4164    0.50347 0.000 0.184 0.744 0.008 NA NA
#> GSM674241     2  0.0551    0.89027 0.000 0.984 0.004 0.004 NA NA
#> GSM674283     1  0.0000    0.88236 1.000 0.000 0.000 0.000 NA NA
#> GSM674286     1  0.0000    0.88236 1.000 0.000 0.000 0.000 NA NA
#> GSM674293     1  0.0146    0.88258 0.996 0.000 0.000 0.000 NA NA
#> GSM674294     1  0.0603    0.88235 0.980 0.000 0.000 0.000 NA NA
#> GSM674296     1  0.0363    0.88111 0.988 0.000 0.000 0.000 NA NA
#> GSM674303     1  0.0000    0.88236 1.000 0.000 0.000 0.000 NA NA
#> GSM674307     1  0.0260    0.88147 0.992 0.000 0.000 0.000 NA NA
#> GSM674310     1  0.3684    0.77723 0.628 0.000 0.000 0.000 NA NA
#> GSM674311     1  0.0713    0.88183 0.972 0.000 0.000 0.000 NA NA
#> GSM674312     1  0.3830    0.76971 0.620 0.000 0.000 0.000 NA NA
#> GSM674317     1  0.1753    0.87064 0.912 0.000 0.000 0.000 NA NA
#> GSM674319     1  0.3728    0.78853 0.652 0.000 0.000 0.000 NA NA
#> GSM674321     1  0.3659    0.78204 0.636 0.000 0.000 0.000 NA NA
#> GSM674322     1  0.3672    0.77974 0.632 0.000 0.000 0.000 NA NA
#> GSM674326     1  0.3659    0.78170 0.636 0.000 0.000 0.000 NA NA
#> GSM674329     1  0.3659    0.78051 0.636 0.000 0.000 0.000 NA NA
#> GSM674333     1  0.3647    0.78136 0.640 0.000 0.000 0.000 NA NA

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-ATC-NMF-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-ATC-NMF-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-ATC-NMF-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-ATC-NMF-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-ATC-NMF-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-ATC-NMF-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-ATC-NMF-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-ATC-NMF-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-ATC-NMF-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-ATC-NMF-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-ATC-NMF-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-ATC-NMF-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-ATC-NMF-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-ATC-NMF-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-ATC-NMF-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-ATC-NMF-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-ATC-NMF-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-ATC-NMF-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-ATC-NMF-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-ATC-NMF-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk ATC-NMF-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-ATC-NMF-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-ATC-NMF-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-ATC-NMF-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-ATC-NMF-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-ATC-NMF-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk ATC-NMF-collect-classes

Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.

test_to_known_factors(res)
#>           n disease.state(p) specimen(p) k
#> ATC:NMF 183            0.924    1.83e-40 2
#> ATC:NMF 163            0.964    6.65e-61 3
#> ATC:NMF 180            0.943    7.30e-72 4
#> ATC:NMF 149            0.791    5.61e-60 5
#> ATC:NMF 153            0.761    1.80e-60 6

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.

Session info

sessionInfo()
#> R version 3.6.0 (2019-04-26)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#> 
#> Matrix products: default
#> BLAS:   /usr/lib64/libblas.so.3.4.2
#> LAPACK: /usr/lib64/liblapack.so.3.4.2
#> 
#> locale:
#>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8       
#>  [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
#>  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
#> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] grid      stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] genefilter_1.66.0    ComplexHeatmap_2.3.1 markdown_1.1         knitr_1.26          
#> [5] GetoptLong_0.1.7     cola_1.3.2          
#> 
#> loaded via a namespace (and not attached):
#>  [1] circlize_0.4.8       shape_1.4.4          xfun_0.11            slam_0.1-46         
#>  [5] lattice_0.20-38      splines_3.6.0        colorspace_1.4-1     vctrs_0.2.0         
#>  [9] stats4_3.6.0         blob_1.2.0           XML_3.98-1.20        survival_2.44-1.1   
#> [13] rlang_0.4.2          pillar_1.4.2         DBI_1.0.0            BiocGenerics_0.30.0 
#> [17] bit64_0.9-7          RColorBrewer_1.1-2   matrixStats_0.55.0   stringr_1.4.0       
#> [21] GlobalOptions_0.1.1  evaluate_0.14        memoise_1.1.0        Biobase_2.44.0      
#> [25] IRanges_2.18.3       parallel_3.6.0       AnnotationDbi_1.46.1 highr_0.8           
#> [29] Rcpp_1.0.3           xtable_1.8-4         backports_1.1.5      S4Vectors_0.22.1    
#> [33] annotate_1.62.0      skmeans_0.2-11       bit_1.1-14           microbenchmark_1.4-7
#> [37] brew_1.0-6           impute_1.58.0        rjson_0.2.20         png_0.1-7           
#> [41] digest_0.6.23        stringi_1.4.3        polyclip_1.10-0      clue_0.3-57         
#> [45] tools_3.6.0          bitops_1.0-6         magrittr_1.5         eulerr_6.0.0        
#> [49] RCurl_1.95-4.12      RSQLite_2.1.4        tibble_2.1.3         cluster_2.1.0       
#> [53] crayon_1.3.4         pkgconfig_2.0.3      zeallot_0.1.0        Matrix_1.2-17       
#> [57] xml2_1.2.2           httr_1.4.1           R6_2.4.1             mclust_5.4.5        
#> [61] compiler_3.6.0