Date: 2019-12-25 23:55:09 CET, cola version: 1.3.2
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All available functions which can be applied to this res_list object:
res_list
#> A 'ConsensusPartitionList' object with 24 methods.
#> On a matrix with 714 rows and 185 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)
Dimension of the input matrix:
mat = get_matrix(res_list)
dim(mat)
#> [1] 714 185
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, ylab = "value", cluster_columns = TRUE, show_column_names = FALSE,
mc.cores = 4)
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:pam | 2 | 1.000 | 0.997 | 0.999 | ** | |
| SD:mclust | 2 | 1.000 | 1.000 | 1.000 | ** | |
| CV:kmeans | 3 | 1.000 | 0.967 | 0.979 | ** | |
| CV:skmeans | 2 | 1.000 | 0.980 | 0.992 | ** | |
| CV:NMF | 2 | 1.000 | 0.991 | 0.996 | ** | |
| MAD:kmeans | 2 | 1.000 | 0.998 | 0.998 | ** | |
| MAD:pam | 2 | 1.000 | 0.991 | 0.995 | ** | |
| MAD:mclust | 2 | 1.000 | 1.000 | 1.000 | ** | |
| SD:skmeans | 4 | 0.955 | 0.930 | 0.970 | ** | 2,3 |
| MAD:skmeans | 4 | 0.947 | 0.933 | 0.970 | * | 2,3 |
| ATC:kmeans | 3 | 0.938 | 0.920 | 0.970 | * | 2 |
| ATC:skmeans | 3 | 0.936 | 0.932 | 0.970 | * | 2 |
| MAD:NMF | 4 | 0.933 | 0.912 | 0.956 | * | 2 |
| ATC:pam | 4 | 0.924 | 0.924 | 0.967 | * | 2 |
| SD:NMF | 4 | 0.904 | 0.885 | 0.947 | * | 2 |
| CV:mclust | 2 | 0.827 | 0.905 | 0.955 | ||
| ATC:mclust | 2 | 0.818 | 0.914 | 0.963 | ||
| CV:pam | 2 | 0.702 | 0.876 | 0.934 | ||
| CV:hclust | 3 | 0.588 | 0.724 | 0.881 | ||
| SD:hclust | 3 | 0.542 | 0.865 | 0.898 | ||
| MAD:hclust | 3 | 0.345 | 0.830 | 0.826 | ||
| ATC:NMF | 2 | 0.259 | 0.761 | 0.836 | ||
| ATC:hclust | NA | NA | NA | NA |
**: 1-PAC > 0.95, *: 1-PAC > 0.9
Cumulative distribution function curves of consensus matrix for all methods.
collect_plots(res_list, fun = plot_ecdf)
Consensus heatmaps for all methods. (What is a consensus heatmap?)
collect_plots(res_list, k = 2, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 3, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 4, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 5, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 6, fun = consensus_heatmap, mc.cores = 4)
Membership heatmaps for all methods. (What is a membership heatmap?)
collect_plots(res_list, k = 2, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 3, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 4, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 5, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 6, fun = membership_heatmap, mc.cores = 4)
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)
collect_plots(res_list, k = 3, fun = get_signatures, mc.cores = 4)
collect_plots(res_list, k = 4, fun = get_signatures, mc.cores = 4)
collect_plots(res_list, k = 5, fun = get_signatures, mc.cores = 4)
collect_plots(res_list, k = 6, fun = get_signatures, mc.cores = 4)
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 1.000 0.995 0.998 0.493 0.508 0.508
#> CV:NMF 2 1.000 0.991 0.996 0.494 0.508 0.508
#> MAD:NMF 2 1.000 0.994 0.997 0.493 0.508 0.508
#> ATC:NMF 2 0.259 0.761 0.836 0.490 0.508 0.508
#> SD:skmeans 2 1.000 1.000 1.000 0.493 0.508 0.508
#> CV:skmeans 2 1.000 0.980 0.992 0.488 0.510 0.510
#> MAD:skmeans 2 1.000 1.000 1.000 0.493 0.508 0.508
#> ATC:skmeans 2 0.955 0.944 0.978 0.472 0.533 0.533
#> SD:mclust 2 1.000 1.000 1.000 0.493 0.508 0.508
#> CV:mclust 2 0.827 0.905 0.955 0.491 0.510 0.510
#> MAD:mclust 2 1.000 1.000 1.000 0.493 0.508 0.508
#> ATC:mclust 2 0.818 0.914 0.963 0.500 0.498 0.498
#> SD:kmeans 2 1.000 1.000 1.000 0.492 0.508 0.508
#> CV:kmeans 2 0.881 0.928 0.970 0.328 0.685 0.685
#> MAD:kmeans 2 1.000 0.998 0.998 0.493 0.508 0.508
#> ATC:kmeans 2 1.000 0.988 0.995 0.300 0.705 0.705
#> SD:pam 2 1.000 0.997 0.999 0.493 0.508 0.508
#> CV:pam 2 0.702 0.876 0.934 0.487 0.504 0.504
#> MAD:pam 2 1.000 0.991 0.995 0.493 0.508 0.508
#> ATC:pam 2 0.910 0.925 0.969 0.447 0.559 0.559
#> SD:hclust 2 0.475 0.867 0.857 0.366 0.508 0.508
#> CV:hclust 2 0.752 0.847 0.938 0.212 0.815 0.815
#> MAD:hclust 2 0.523 0.581 0.847 0.343 0.727 0.727
#> ATC:hclust 2 0.850 0.924 0.963 0.234 0.757 0.757
get_stats(res_list, k = 3)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 3 0.732 0.828 0.793 0.265 0.841 0.687
#> CV:NMF 3 0.675 0.705 0.837 0.282 0.854 0.713
#> MAD:NMF 3 0.736 0.843 0.797 0.272 0.835 0.675
#> ATC:NMF 3 0.327 0.593 0.746 0.265 0.900 0.805
#> SD:skmeans 3 1.000 0.979 0.990 0.333 0.835 0.676
#> CV:skmeans 3 0.807 0.875 0.937 0.319 0.766 0.570
#> MAD:skmeans 3 1.000 0.980 0.991 0.333 0.836 0.677
#> ATC:skmeans 3 0.936 0.932 0.970 0.218 0.875 0.770
#> SD:mclust 3 0.690 0.760 0.873 0.239 0.856 0.724
#> CV:mclust 3 0.862 0.879 0.936 0.241 0.810 0.646
#> MAD:mclust 3 0.656 0.561 0.747 0.285 0.856 0.717
#> ATC:mclust 3 0.802 0.817 0.904 0.230 0.889 0.778
#> SD:kmeans 3 0.742 0.879 0.801 0.251 0.827 0.662
#> CV:kmeans 3 1.000 0.967 0.979 0.699 0.673 0.549
#> MAD:kmeans 3 0.748 0.886 0.784 0.251 0.835 0.675
#> ATC:kmeans 3 0.938 0.920 0.970 0.798 0.674 0.559
#> SD:pam 3 0.721 0.855 0.818 0.288 0.835 0.675
#> CV:pam 3 0.728 0.857 0.929 0.302 0.809 0.639
#> MAD:pam 3 0.737 0.910 0.896 0.305 0.835 0.676
#> ATC:pam 3 0.873 0.916 0.963 0.237 0.770 0.628
#> SD:hclust 3 0.542 0.865 0.898 0.501 0.938 0.878
#> CV:hclust 3 0.588 0.724 0.881 0.965 0.685 0.622
#> MAD:hclust 3 0.345 0.830 0.826 0.487 0.638 0.530
#> ATC:hclust 3 0.760 0.863 0.948 0.336 0.941 0.922
get_stats(res_list, k = 4)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 4 0.904 0.885 0.947 0.1682 0.887 0.690
#> CV:NMF 4 0.746 0.796 0.890 0.1389 0.849 0.617
#> MAD:NMF 4 0.933 0.912 0.956 0.1656 0.900 0.717
#> ATC:NMF 4 0.437 0.596 0.713 0.1421 0.807 0.580
#> SD:skmeans 4 0.955 0.930 0.970 0.1347 0.912 0.743
#> CV:skmeans 4 0.831 0.884 0.933 0.1566 0.783 0.467
#> MAD:skmeans 4 0.947 0.933 0.970 0.1330 0.913 0.746
#> ATC:skmeans 4 0.730 0.675 0.845 0.1713 0.945 0.873
#> SD:mclust 4 0.883 0.859 0.936 0.2185 0.793 0.515
#> CV:mclust 4 0.627 0.606 0.786 0.1426 0.948 0.861
#> MAD:mclust 4 0.833 0.868 0.934 0.1684 0.805 0.522
#> ATC:mclust 4 0.623 0.717 0.822 0.1325 0.911 0.779
#> SD:kmeans 4 0.682 0.872 0.869 0.1392 0.921 0.774
#> CV:kmeans 4 0.755 0.903 0.880 0.2455 0.829 0.613
#> MAD:kmeans 4 0.831 0.873 0.870 0.1475 0.909 0.744
#> ATC:kmeans 4 0.665 0.733 0.848 0.1729 0.884 0.754
#> SD:pam 4 0.869 0.844 0.932 0.1620 0.888 0.687
#> CV:pam 4 0.647 0.765 0.852 0.0659 0.987 0.965
#> MAD:pam 4 0.869 0.867 0.939 0.1443 0.918 0.760
#> ATC:pam 4 0.924 0.924 0.967 0.1048 0.938 0.863
#> SD:hclust 4 0.681 0.766 0.818 0.1219 0.992 0.982
#> CV:hclust 4 0.591 0.706 0.874 0.0433 0.978 0.960
#> MAD:hclust 4 0.358 0.449 0.761 0.1747 0.983 0.963
#> ATC:hclust 4 0.714 0.831 0.929 0.0364 0.988 0.984
get_stats(res_list, k = 5)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 5 0.801 0.707 0.855 0.0531 0.986 0.948
#> CV:NMF 5 0.761 0.721 0.846 0.0550 0.946 0.808
#> MAD:NMF 5 0.815 0.609 0.857 0.0432 0.965 0.875
#> ATC:NMF 5 0.521 0.573 0.709 0.0879 0.790 0.445
#> SD:skmeans 5 0.873 0.836 0.894 0.0461 0.973 0.894
#> CV:skmeans 5 0.756 0.693 0.789 0.0581 0.954 0.825
#> MAD:skmeans 5 0.875 0.874 0.912 0.0433 0.972 0.893
#> ATC:skmeans 5 0.727 0.736 0.792 0.0786 0.815 0.531
#> SD:mclust 5 0.827 0.805 0.860 0.0415 0.967 0.874
#> CV:mclust 5 0.565 0.502 0.701 0.0637 0.888 0.685
#> MAD:mclust 5 0.788 0.768 0.858 0.0413 0.963 0.856
#> ATC:mclust 5 0.603 0.647 0.755 0.0699 0.956 0.866
#> SD:kmeans 5 0.801 0.814 0.848 0.0714 0.995 0.983
#> CV:kmeans 5 0.677 0.816 0.837 0.0757 0.994 0.978
#> MAD:kmeans 5 0.786 0.754 0.809 0.0646 0.946 0.808
#> ATC:kmeans 5 0.657 0.646 0.796 0.0811 0.934 0.832
#> SD:pam 5 0.779 0.680 0.843 0.0517 0.952 0.820
#> CV:pam 5 0.682 0.800 0.867 0.0925 0.852 0.603
#> MAD:pam 5 0.769 0.632 0.828 0.0487 0.954 0.831
#> ATC:pam 5 0.725 0.604 0.832 0.1325 0.892 0.725
#> SD:hclust 5 0.635 0.759 0.767 0.0962 0.837 0.629
#> CV:hclust 5 0.639 0.714 0.866 0.0932 0.931 0.874
#> MAD:hclust 5 0.351 0.648 0.736 0.0787 0.849 0.654
#> ATC:hclust 5 0.702 0.796 0.915 0.0357 0.989 0.984
get_stats(res_list, k = 6)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 6 0.788 0.692 0.825 0.0383 0.933 0.749
#> CV:NMF 6 0.786 0.748 0.850 0.0379 0.957 0.826
#> MAD:NMF 6 0.796 0.656 0.827 0.0290 0.945 0.800
#> ATC:NMF 6 0.582 0.566 0.705 0.0323 0.975 0.900
#> SD:skmeans 6 0.839 0.816 0.888 0.0417 0.957 0.817
#> CV:skmeans 6 0.788 0.773 0.803 0.0449 0.906 0.615
#> MAD:skmeans 6 0.853 0.806 0.899 0.0440 0.950 0.787
#> ATC:skmeans 6 0.789 0.841 0.874 0.0565 0.920 0.690
#> SD:mclust 6 0.856 0.821 0.885 0.0277 0.968 0.866
#> CV:mclust 6 0.585 0.436 0.690 0.0339 0.941 0.796
#> MAD:mclust 6 0.819 0.806 0.876 0.0376 0.964 0.844
#> ATC:mclust 6 0.628 0.565 0.726 0.0477 0.939 0.799
#> SD:kmeans 6 0.748 0.671 0.803 0.0393 0.943 0.795
#> CV:kmeans 6 0.707 0.583 0.750 0.0464 0.952 0.824
#> MAD:kmeans 6 0.753 0.680 0.813 0.0360 0.952 0.809
#> ATC:kmeans 6 0.638 0.283 0.669 0.0614 0.855 0.629
#> SD:pam 6 0.741 0.622 0.751 0.0373 0.901 0.625
#> CV:pam 6 0.743 0.776 0.879 0.0317 0.989 0.957
#> MAD:pam 6 0.745 0.571 0.741 0.0370 0.906 0.643
#> ATC:pam 6 0.710 0.755 0.825 0.0395 0.909 0.704
#> SD:hclust 6 0.644 0.723 0.790 0.0550 0.964 0.875
#> CV:hclust 6 0.555 0.765 0.863 0.0672 0.893 0.798
#> MAD:hclust 6 0.390 0.685 0.767 0.0444 0.896 0.686
#> ATC:hclust 6 0.667 0.779 0.900 0.0706 0.995 0.992
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)
collect_stats(res_list, k = 3)
collect_stats(res_list, k = 4)
collect_stats(res_list, k = 5)
collect_stats(res_list, k = 6)
Collect partitions from all methods:
collect_classes(res_list, k = 2)
collect_classes(res_list, k = 3)
collect_classes(res_list, k = 4)
collect_classes(res_list, k = 5)
collect_classes(res_list, k = 6)
Overlap of top rows from different top-row methods:
top_rows_overlap(res_list, top_n = 71, method = "euler")
top_rows_overlap(res_list, top_n = 142, method = "euler")
top_rows_overlap(res_list, top_n = 214, method = "euler")
top_rows_overlap(res_list, top_n = 286, method = "euler")
top_rows_overlap(res_list, top_n = 357, method = "euler")
Also visualize the correspondance of rankings between different top-row methods:
top_rows_overlap(res_list, top_n = 71, method = "correspondance")
top_rows_overlap(res_list, top_n = 142, method = "correspondance")
top_rows_overlap(res_list, top_n = 214, method = "correspondance")
top_rows_overlap(res_list, top_n = 286, method = "correspondance")
top_rows_overlap(res_list, top_n = 357, method = "correspondance")
Heatmaps of the top rows:
top_rows_heatmap(res_list, top_n = 71)
top_rows_heatmap(res_list, top_n = 142)
top_rows_heatmap(res_list, top_n = 214)
top_rows_heatmap(res_list, top_n = 286)
top_rows_heatmap(res_list, top_n = 357)
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.475 0.867 0.857 0.3663 0.508 0.508
#> 3 3 0.542 0.865 0.898 0.5009 0.938 0.878
#> 4 4 0.681 0.766 0.818 0.1219 0.992 0.982
#> 5 5 0.635 0.759 0.767 0.0962 0.837 0.629
#> 6 6 0.644 0.723 0.790 0.0550 0.964 0.875
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0.9754 0.745 0.408 0.592
#> SRR1044416 2 0.9993 0.714 0.484 0.516
#> SRR1044417 2 0.9993 0.714 0.484 0.516
#> SRR1044418 2 0.9993 0.714 0.484 0.516
#> SRR1044420 2 0.9977 0.727 0.472 0.528
#> SRR1044419 2 0.9580 0.748 0.380 0.620
#> SRR1044421 2 0.9988 0.719 0.480 0.520
#> SRR1044422 2 0.9954 0.733 0.460 0.540
#> SRR1044423 2 0.9954 0.733 0.460 0.540
#> SRR1044424 2 0.9970 0.729 0.468 0.532
#> SRR1044425 1 0.0000 0.995 1.000 0.000
#> SRR1044426 1 0.0000 0.995 1.000 0.000
#> SRR1044427 1 0.0000 0.995 1.000 0.000
#> SRR1044428 1 0.0000 0.995 1.000 0.000
#> SRR1044429 1 0.0000 0.995 1.000 0.000
#> SRR1044430 1 0.0000 0.995 1.000 0.000
#> SRR1044431 1 0.0000 0.995 1.000 0.000
#> SRR1044433 1 0.2043 0.950 0.968 0.032
#> SRR1044432 1 0.0000 0.995 1.000 0.000
#> SRR1044434 1 0.0000 0.995 1.000 0.000
#> SRR1044435 1 0.0000 0.995 1.000 0.000
#> SRR1044436 1 0.0000 0.995 1.000 0.000
#> SRR1044437 1 0.0000 0.995 1.000 0.000
#> SRR1044439 1 0.0000 0.995 1.000 0.000
#> SRR1044438 1 0.0000 0.995 1.000 0.000
#> SRR1044440 1 0.0000 0.995 1.000 0.000
#> SRR1044441 1 0.0000 0.995 1.000 0.000
#> SRR1044442 1 0.2043 0.950 0.968 0.032
#> SRR1044443 1 0.2043 0.950 0.968 0.032
#> SRR1044444 1 0.0000 0.995 1.000 0.000
#> SRR1044445 1 0.0000 0.995 1.000 0.000
#> SRR1044446 2 0.3114 0.637 0.056 0.944
#> SRR1044447 2 0.9552 0.744 0.376 0.624
#> SRR1044449 2 0.0000 0.612 0.000 1.000
#> SRR1044448 2 0.0376 0.614 0.004 0.996
#> SRR1044450 2 0.0672 0.616 0.008 0.992
#> SRR1044451 2 0.9129 0.738 0.328 0.672
#> SRR1044452 2 0.0000 0.612 0.000 1.000
#> SRR1044453 2 0.0000 0.612 0.000 1.000
#> SRR1044454 2 0.0000 0.612 0.000 1.000
#> SRR1044455 2 0.9866 0.738 0.432 0.568
#> SRR1044456 2 0.9993 0.714 0.484 0.516
#> SRR1044457 2 0.8713 0.730 0.292 0.708
#> SRR1044458 2 0.9393 0.745 0.356 0.644
#> SRR1044459 2 0.6973 0.695 0.188 0.812
#> SRR1044460 2 0.9977 0.727 0.472 0.528
#> SRR1044461 2 0.9522 0.748 0.372 0.628
#> SRR1044462 1 0.0000 0.995 1.000 0.000
#> SRR1044463 1 0.0000 0.995 1.000 0.000
#> SRR1044464 1 0.0000 0.995 1.000 0.000
#> SRR1044466 1 0.0000 0.995 1.000 0.000
#> SRR1044465 1 0.0000 0.995 1.000 0.000
#> SRR1044467 1 0.0000 0.995 1.000 0.000
#> SRR1044468 2 0.9963 0.732 0.464 0.536
#> SRR1044469 2 0.5294 0.662 0.120 0.880
#> SRR1044470 1 0.0000 0.995 1.000 0.000
#> SRR1044471 1 0.0000 0.995 1.000 0.000
#> SRR1044472 1 0.0000 0.995 1.000 0.000
#> SRR1044473 1 0.0000 0.995 1.000 0.000
#> SRR1044474 2 0.9993 0.714 0.484 0.516
#> SRR1044475 2 0.3733 0.640 0.072 0.928
#> SRR1044476 2 0.9552 0.748 0.376 0.624
#> SRR1044477 2 0.9993 0.714 0.484 0.516
#> SRR1044478 2 0.9608 0.748 0.384 0.616
#> SRR1044479 2 0.9993 0.714 0.484 0.516
#> SRR1044480 1 0.0000 0.995 1.000 0.000
#> SRR1044481 1 0.0000 0.995 1.000 0.000
#> SRR1044482 2 0.9993 0.714 0.484 0.516
#> SRR1044483 1 0.0000 0.995 1.000 0.000
#> SRR1044484 1 0.0000 0.995 1.000 0.000
#> SRR1044486 1 0.0000 0.995 1.000 0.000
#> SRR1044485 2 0.9983 0.723 0.476 0.524
#> SRR1044487 2 0.9993 0.714 0.484 0.516
#> SRR1044488 2 0.9977 0.727 0.472 0.528
#> SRR1044489 2 0.9977 0.727 0.472 0.528
#> SRR1044490 1 0.0000 0.995 1.000 0.000
#> SRR1044491 1 0.0000 0.995 1.000 0.000
#> SRR1044492 1 0.0000 0.995 1.000 0.000
#> SRR1044493 1 0.0000 0.995 1.000 0.000
#> SRR1044494 2 0.9993 0.714 0.484 0.516
#> SRR1044496 2 0.9993 0.714 0.484 0.516
#> SRR1044495 2 0.9993 0.714 0.484 0.516
#> SRR1044497 1 0.0000 0.995 1.000 0.000
#> SRR1044499 2 0.6048 0.673 0.148 0.852
#> SRR1044498 1 0.0000 0.995 1.000 0.000
#> SRR1044500 2 0.9977 0.727 0.472 0.528
#> SRR1044501 2 0.9427 0.746 0.360 0.640
#> SRR1044502 2 0.8327 0.722 0.264 0.736
#> SRR1044503 1 0.0000 0.995 1.000 0.000
#> SRR1044504 1 0.0000 0.995 1.000 0.000
#> SRR1044505 1 0.0000 0.995 1.000 0.000
#> SRR1044506 1 0.0000 0.995 1.000 0.000
#> SRR1044507 1 0.2043 0.950 0.968 0.032
#> SRR1044508 1 0.2043 0.950 0.968 0.032
#> SRR1044509 1 0.2043 0.950 0.968 0.032
#> SRR1044510 2 0.0000 0.612 0.000 1.000
#> SRR1044511 2 0.0000 0.612 0.000 1.000
#> SRR1044512 2 0.0000 0.612 0.000 1.000
#> SRR1044513 2 0.9635 0.745 0.388 0.612
#> SRR1044514 2 0.0000 0.612 0.000 1.000
#> SRR1044515 2 0.9608 0.745 0.384 0.616
#> SRR1044516 2 0.9970 0.729 0.468 0.532
#> SRR1044517 2 0.0000 0.612 0.000 1.000
#> SRR1044518 2 0.0000 0.612 0.000 1.000
#> SRR1044519 2 0.0376 0.614 0.004 0.996
#> SRR1044520 2 0.0376 0.614 0.004 0.996
#> SRR1044521 2 0.9977 0.727 0.472 0.528
#> SRR1044522 2 0.9993 0.714 0.484 0.516
#> SRR1044523 2 0.9954 0.732 0.460 0.540
#> SRR1044524 2 0.7528 0.706 0.216 0.784
#> SRR1044525 1 0.0000 0.995 1.000 0.000
#> SRR1044526 1 0.0000 0.995 1.000 0.000
#> SRR1044527 2 0.9963 0.730 0.464 0.536
#> SRR1044528 2 0.9996 0.706 0.488 0.512
#> SRR1044529 2 0.9993 0.714 0.484 0.516
#> SRR1044530 1 0.0000 0.995 1.000 0.000
#> SRR1044531 1 0.0000 0.995 1.000 0.000
#> SRR1044533 1 0.0000 0.995 1.000 0.000
#> SRR1044532 1 0.0000 0.995 1.000 0.000
#> SRR1044534 2 0.9977 0.727 0.472 0.528
#> SRR1044535 2 0.7376 0.703 0.208 0.792
#> SRR1044536 2 0.9977 0.727 0.472 0.528
#> SRR1044537 1 0.0000 0.995 1.000 0.000
#> SRR1044538 1 0.0000 0.995 1.000 0.000
#> SRR1044539 1 0.0000 0.995 1.000 0.000
#> SRR1044540 1 0.0000 0.995 1.000 0.000
#> SRR1044541 2 0.7056 0.696 0.192 0.808
#> SRR1044542 1 0.0000 0.995 1.000 0.000
#> SRR1044543 1 0.0000 0.995 1.000 0.000
#> SRR1044544 2 0.8608 0.727 0.284 0.716
#> SRR1044545 1 0.0000 0.995 1.000 0.000
#> SRR1044546 1 0.0000 0.995 1.000 0.000
#> SRR1044547 1 0.0000 0.995 1.000 0.000
#> SRR1044548 1 0.0000 0.995 1.000 0.000
#> SRR1044549 2 0.9954 0.732 0.460 0.540
#> SRR1044550 2 0.9977 0.727 0.472 0.528
#> SRR1044551 2 0.9988 0.719 0.480 0.520
#> SRR1044552 1 0.0000 0.995 1.000 0.000
#> SRR1044553 1 0.0000 0.995 1.000 0.000
#> SRR1044554 1 0.0000 0.995 1.000 0.000
#> SRR1044555 2 0.7528 0.706 0.216 0.784
#> SRR1044556 1 0.0000 0.995 1.000 0.000
#> SRR1044557 1 0.0000 0.995 1.000 0.000
#> SRR1044558 1 0.0000 0.995 1.000 0.000
#> SRR1044559 1 0.0000 0.995 1.000 0.000
#> SRR1044561 1 0.0000 0.995 1.000 0.000
#> SRR1044560 2 0.9491 0.747 0.368 0.632
#> SRR1044562 1 0.0000 0.995 1.000 0.000
#> SRR1044563 1 0.0000 0.995 1.000 0.000
#> SRR1044564 1 0.0000 0.995 1.000 0.000
#> SRR1044565 2 0.9993 0.714 0.484 0.516
#> SRR1044566 2 0.9522 0.748 0.372 0.628
#> SRR1044567 1 0.0000 0.995 1.000 0.000
#> SRR1044568 1 0.0000 0.995 1.000 0.000
#> SRR1044569 1 0.0000 0.995 1.000 0.000
#> SRR1044570 1 0.0000 0.995 1.000 0.000
#> SRR1044571 1 0.0000 0.995 1.000 0.000
#> SRR1044572 1 0.0000 0.995 1.000 0.000
#> SRR1044573 1 0.0000 0.995 1.000 0.000
#> SRR1044574 1 0.0000 0.995 1.000 0.000
#> SRR1044575 1 0.0000 0.995 1.000 0.000
#> SRR1044576 2 0.9993 0.714 0.484 0.516
#> SRR1044577 2 0.9993 0.714 0.484 0.516
#> SRR1044578 2 0.9993 0.714 0.484 0.516
#> SRR1044579 1 0.0000 0.995 1.000 0.000
#> SRR1044580 1 0.0000 0.995 1.000 0.000
#> SRR1044581 1 0.0000 0.995 1.000 0.000
#> SRR1044582 1 0.0000 0.995 1.000 0.000
#> SRR1044583 1 0.0000 0.995 1.000 0.000
#> SRR1044584 1 0.0000 0.995 1.000 0.000
#> SRR1044585 1 0.0000 0.995 1.000 0.000
#> SRR1044586 1 0.0000 0.995 1.000 0.000
#> SRR1044587 1 0.0000 0.995 1.000 0.000
#> SRR1044588 1 0.0000 0.995 1.000 0.000
#> SRR1044589 1 0.0000 0.995 1.000 0.000
#> SRR1044590 1 0.0000 0.995 1.000 0.000
#> SRR1044591 1 0.0000 0.995 1.000 0.000
#> SRR1044592 1 0.2043 0.950 0.968 0.032
#> SRR1044593 1 0.0000 0.995 1.000 0.000
#> SRR1044594 1 0.0000 0.995 1.000 0.000
#> SRR1044595 1 0.2043 0.950 0.968 0.032
#> SRR1044596 1 0.2043 0.950 0.968 0.032
#> SRR1044597 1 0.2236 0.943 0.964 0.036
#> SRR1044598 1 0.0000 0.995 1.000 0.000
#> SRR1044599 1 0.0000 0.995 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.2152 0.8406 0.036 0.948 0.016
#> SRR1044416 2 0.2878 0.8790 0.096 0.904 0.000
#> SRR1044417 2 0.2878 0.8790 0.096 0.904 0.000
#> SRR1044418 2 0.2878 0.8790 0.096 0.904 0.000
#> SRR1044420 2 0.2625 0.8812 0.084 0.916 0.000
#> SRR1044419 2 0.2918 0.8224 0.032 0.924 0.044
#> SRR1044421 2 0.2796 0.8800 0.092 0.908 0.000
#> SRR1044422 2 0.2682 0.8775 0.076 0.920 0.004
#> SRR1044423 2 0.2682 0.8775 0.076 0.920 0.004
#> SRR1044424 2 0.2537 0.8798 0.080 0.920 0.000
#> SRR1044425 1 0.1015 0.9356 0.980 0.008 0.012
#> SRR1044426 1 0.1877 0.9364 0.956 0.012 0.032
#> SRR1044427 1 0.0237 0.9360 0.996 0.004 0.000
#> SRR1044428 1 0.1315 0.9321 0.972 0.008 0.020
#> SRR1044429 1 0.0983 0.9360 0.980 0.004 0.016
#> SRR1044430 1 0.1315 0.9321 0.972 0.008 0.020
#> SRR1044431 1 0.1337 0.9347 0.972 0.012 0.016
#> SRR1044433 1 0.5603 0.8467 0.804 0.136 0.060
#> SRR1044432 1 0.1315 0.9321 0.972 0.008 0.020
#> SRR1044434 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044435 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044436 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044437 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044439 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044438 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044440 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044441 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044442 1 0.5471 0.8554 0.812 0.128 0.060
#> SRR1044443 1 0.5603 0.8467 0.804 0.136 0.060
#> SRR1044444 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044445 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044446 3 0.4887 0.8654 0.000 0.228 0.772
#> SRR1044447 2 0.6264 0.7265 0.068 0.764 0.168
#> SRR1044449 3 0.3941 0.9038 0.000 0.156 0.844
#> SRR1044448 3 0.4062 0.9048 0.000 0.164 0.836
#> SRR1044450 3 0.4121 0.9041 0.000 0.168 0.832
#> SRR1044451 2 0.6201 0.6536 0.044 0.748 0.208
#> SRR1044452 3 0.4931 0.8669 0.000 0.232 0.768
#> SRR1044453 3 0.4931 0.8669 0.000 0.232 0.768
#> SRR1044454 3 0.4931 0.8669 0.000 0.232 0.768
#> SRR1044455 2 0.2846 0.8551 0.056 0.924 0.020
#> SRR1044456 2 0.2878 0.8790 0.096 0.904 0.000
#> SRR1044457 2 0.3686 0.6756 0.000 0.860 0.140
#> SRR1044458 2 0.3181 0.7981 0.024 0.912 0.064
#> SRR1044459 2 0.6267 -0.1956 0.000 0.548 0.452
#> SRR1044460 2 0.2625 0.8812 0.084 0.916 0.000
#> SRR1044461 2 0.3337 0.8124 0.032 0.908 0.060
#> SRR1044462 1 0.2564 0.9331 0.936 0.028 0.036
#> SRR1044463 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044464 1 0.3039 0.9302 0.920 0.036 0.044
#> SRR1044466 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044465 1 0.1315 0.9321 0.972 0.008 0.020
#> SRR1044467 1 0.1315 0.9321 0.972 0.008 0.020
#> SRR1044468 2 0.3043 0.8806 0.084 0.908 0.008
#> SRR1044469 3 0.6305 0.4339 0.000 0.484 0.516
#> SRR1044470 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044471 1 0.1482 0.9312 0.968 0.012 0.020
#> SRR1044472 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044473 1 0.1482 0.9312 0.968 0.012 0.020
#> SRR1044474 2 0.2878 0.8790 0.096 0.904 0.000
#> SRR1044475 3 0.6215 0.5635 0.000 0.428 0.572
#> SRR1044476 2 0.2550 0.8144 0.024 0.936 0.040
#> SRR1044477 2 0.2878 0.8790 0.096 0.904 0.000
#> SRR1044478 2 0.3148 0.8253 0.036 0.916 0.048
#> SRR1044479 2 0.2878 0.8790 0.096 0.904 0.000
#> SRR1044480 1 0.2297 0.9326 0.944 0.020 0.036
#> SRR1044481 1 0.0237 0.9356 0.996 0.004 0.000
#> SRR1044482 2 0.2878 0.8790 0.096 0.904 0.000
#> SRR1044483 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044484 1 0.0661 0.9355 0.988 0.004 0.008
#> SRR1044486 1 0.0848 0.9357 0.984 0.008 0.008
#> SRR1044485 2 0.2711 0.8807 0.088 0.912 0.000
#> SRR1044487 2 0.2878 0.8790 0.096 0.904 0.000
#> SRR1044488 2 0.2625 0.8812 0.084 0.916 0.000
#> SRR1044489 2 0.2625 0.8812 0.084 0.916 0.000
#> SRR1044490 1 0.1315 0.9321 0.972 0.008 0.020
#> SRR1044491 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044492 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044493 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044494 2 0.2878 0.8790 0.096 0.904 0.000
#> SRR1044496 2 0.2878 0.8790 0.096 0.904 0.000
#> SRR1044495 2 0.2878 0.8790 0.096 0.904 0.000
#> SRR1044497 1 0.3583 0.9262 0.900 0.044 0.056
#> SRR1044499 2 0.6204 -0.1675 0.000 0.576 0.424
#> SRR1044498 1 0.0848 0.9359 0.984 0.008 0.008
#> SRR1044500 2 0.2625 0.8812 0.084 0.916 0.000
#> SRR1044501 2 0.3083 0.8016 0.024 0.916 0.060
#> SRR1044502 2 0.6379 0.5579 0.032 0.712 0.256
#> SRR1044503 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044504 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044505 1 0.1129 0.9366 0.976 0.020 0.004
#> SRR1044506 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044507 1 0.5403 0.8597 0.816 0.124 0.060
#> SRR1044508 1 0.5603 0.8467 0.804 0.136 0.060
#> SRR1044509 1 0.5603 0.8467 0.804 0.136 0.060
#> SRR1044510 3 0.2711 0.8968 0.000 0.088 0.912
#> SRR1044511 3 0.2711 0.8977 0.000 0.088 0.912
#> SRR1044512 3 0.2711 0.8977 0.000 0.088 0.912
#> SRR1044513 2 0.6034 0.7542 0.068 0.780 0.152
#> SRR1044514 3 0.2711 0.8977 0.000 0.088 0.912
#> SRR1044515 2 0.6093 0.7491 0.068 0.776 0.156
#> SRR1044516 2 0.2537 0.8798 0.080 0.920 0.000
#> SRR1044517 3 0.2711 0.8968 0.000 0.088 0.912
#> SRR1044518 3 0.2711 0.8977 0.000 0.088 0.912
#> SRR1044519 3 0.4062 0.9048 0.000 0.164 0.836
#> SRR1044520 3 0.4062 0.9048 0.000 0.164 0.836
#> SRR1044521 2 0.2625 0.8812 0.084 0.916 0.000
#> SRR1044522 2 0.2878 0.8790 0.096 0.904 0.000
#> SRR1044523 2 0.4316 0.8621 0.088 0.868 0.044
#> SRR1044524 2 0.5621 0.3576 0.000 0.692 0.308
#> SRR1044525 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044526 1 0.0892 0.9365 0.980 0.020 0.000
#> SRR1044527 2 0.4206 0.8644 0.088 0.872 0.040
#> SRR1044528 2 0.3112 0.8762 0.096 0.900 0.004
#> SRR1044529 2 0.2878 0.8790 0.096 0.904 0.000
#> SRR1044530 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044531 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044533 1 0.1170 0.9333 0.976 0.008 0.016
#> SRR1044532 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044534 2 0.2625 0.8812 0.084 0.916 0.000
#> SRR1044535 2 0.5678 0.3362 0.000 0.684 0.316
#> SRR1044536 2 0.2625 0.8812 0.084 0.916 0.000
#> SRR1044537 1 0.1919 0.9354 0.956 0.024 0.020
#> SRR1044538 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044539 1 0.3572 0.9261 0.900 0.040 0.060
#> SRR1044540 1 0.1315 0.9321 0.972 0.008 0.020
#> SRR1044541 2 0.6140 -0.0112 0.000 0.596 0.404
#> SRR1044542 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044543 1 0.1129 0.9324 0.976 0.004 0.020
#> SRR1044544 2 0.3941 0.6522 0.000 0.844 0.156
#> SRR1044545 1 0.3572 0.9261 0.900 0.040 0.060
#> SRR1044546 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044547 1 0.3572 0.9261 0.900 0.040 0.060
#> SRR1044548 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044549 2 0.4316 0.8621 0.088 0.868 0.044
#> SRR1044550 2 0.2625 0.8812 0.084 0.916 0.000
#> SRR1044551 2 0.2796 0.8800 0.092 0.908 0.000
#> SRR1044552 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044553 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044554 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044555 2 0.5621 0.3576 0.000 0.692 0.308
#> SRR1044556 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044557 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044558 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044559 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044561 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044560 2 0.2773 0.8095 0.024 0.928 0.048
#> SRR1044562 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044563 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044564 1 0.2187 0.9368 0.948 0.024 0.028
#> SRR1044565 2 0.2878 0.8790 0.096 0.904 0.000
#> SRR1044566 2 0.2793 0.8168 0.028 0.928 0.044
#> SRR1044567 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044568 1 0.2564 0.9330 0.936 0.028 0.036
#> SRR1044569 1 0.1315 0.9321 0.972 0.008 0.020
#> SRR1044570 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044571 1 0.1315 0.9321 0.972 0.008 0.020
#> SRR1044572 1 0.1315 0.9321 0.972 0.008 0.020
#> SRR1044573 1 0.1482 0.9312 0.968 0.012 0.020
#> SRR1044574 1 0.1315 0.9321 0.972 0.008 0.020
#> SRR1044575 1 0.1482 0.9312 0.968 0.012 0.020
#> SRR1044576 2 0.2878 0.8790 0.096 0.904 0.000
#> SRR1044577 2 0.2878 0.8790 0.096 0.904 0.000
#> SRR1044578 2 0.2878 0.8790 0.096 0.904 0.000
#> SRR1044579 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044580 1 0.0424 0.9361 0.992 0.008 0.000
#> SRR1044581 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044582 1 0.0661 0.9355 0.988 0.004 0.008
#> SRR1044583 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044584 1 0.0424 0.9361 0.992 0.008 0.000
#> SRR1044585 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044586 1 0.0829 0.9358 0.984 0.004 0.012
#> SRR1044587 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044588 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044589 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044590 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044591 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044592 1 0.5603 0.8467 0.804 0.136 0.060
#> SRR1044593 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044594 1 0.3683 0.9253 0.896 0.044 0.060
#> SRR1044595 1 0.5603 0.8467 0.804 0.136 0.060
#> SRR1044596 1 0.5471 0.8554 0.812 0.128 0.060
#> SRR1044597 1 0.4261 0.8376 0.848 0.140 0.012
#> SRR1044598 1 0.1337 0.9329 0.972 0.012 0.016
#> SRR1044599 1 0.1337 0.9329 0.972 0.012 0.016
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 2 0.1488 0.841 0.012 0.956 0.032 0.000
#> SRR1044416 2 0.1637 0.880 0.060 0.940 0.000 0.000
#> SRR1044417 2 0.1637 0.880 0.060 0.940 0.000 0.000
#> SRR1044418 2 0.1637 0.880 0.060 0.940 0.000 0.000
#> SRR1044420 2 0.1389 0.882 0.048 0.952 0.000 0.000
#> SRR1044419 2 0.2287 0.823 0.012 0.924 0.060 0.004
#> SRR1044421 2 0.1557 0.881 0.056 0.944 0.000 0.000
#> SRR1044422 2 0.1398 0.877 0.040 0.956 0.004 0.000
#> SRR1044423 2 0.1398 0.877 0.040 0.956 0.004 0.000
#> SRR1044424 2 0.1302 0.880 0.044 0.956 0.000 0.000
#> SRR1044425 1 0.1854 0.813 0.940 0.012 0.000 0.048
#> SRR1044426 1 0.2593 0.811 0.904 0.016 0.000 0.080
#> SRR1044427 1 0.1890 0.813 0.936 0.008 0.000 0.056
#> SRR1044428 1 0.2111 0.785 0.932 0.024 0.000 0.044
#> SRR1044429 1 0.1722 0.814 0.944 0.008 0.000 0.048
#> SRR1044430 1 0.2111 0.783 0.932 0.024 0.000 0.044
#> SRR1044431 1 0.2255 0.814 0.920 0.012 0.000 0.068
#> SRR1044433 1 0.6494 0.718 0.572 0.088 0.000 0.340
#> SRR1044432 1 0.2214 0.780 0.928 0.028 0.000 0.044
#> SRR1044434 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044435 1 0.4800 0.782 0.656 0.004 0.000 0.340
#> SRR1044436 1 0.4819 0.780 0.652 0.004 0.000 0.344
#> SRR1044437 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044439 1 0.4819 0.780 0.652 0.004 0.000 0.344
#> SRR1044438 1 0.4746 0.791 0.688 0.008 0.000 0.304
#> SRR1044440 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044441 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044442 1 0.6382 0.726 0.580 0.080 0.000 0.340
#> SRR1044443 1 0.6494 0.718 0.572 0.088 0.000 0.340
#> SRR1044444 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044445 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044446 3 0.2334 0.442 0.000 0.088 0.908 0.004
#> SRR1044447 2 0.4997 0.653 0.036 0.744 0.216 0.004
#> SRR1044449 3 0.0524 0.424 0.000 0.004 0.988 0.008
#> SRR1044448 3 0.1004 0.451 0.000 0.024 0.972 0.004
#> SRR1044450 3 0.1109 0.454 0.000 0.028 0.968 0.004
#> SRR1044451 2 0.4869 0.573 0.016 0.720 0.260 0.004
#> SRR1044452 3 0.4188 0.547 0.000 0.112 0.824 0.064
#> SRR1044453 3 0.4188 0.547 0.000 0.112 0.824 0.064
#> SRR1044454 3 0.4188 0.547 0.000 0.112 0.824 0.064
#> SRR1044455 2 0.2400 0.855 0.032 0.928 0.028 0.012
#> SRR1044456 2 0.1637 0.880 0.060 0.940 0.000 0.000
#> SRR1044457 2 0.3831 0.663 0.000 0.792 0.204 0.004
#> SRR1044458 2 0.2665 0.798 0.008 0.900 0.088 0.004
#> SRR1044459 3 0.5678 0.237 0.000 0.452 0.524 0.024
#> SRR1044460 2 0.1389 0.882 0.048 0.952 0.000 0.000
#> SRR1044461 2 0.2587 0.815 0.012 0.908 0.076 0.004
#> SRR1044462 1 0.3806 0.811 0.824 0.020 0.000 0.156
#> SRR1044463 1 0.1411 0.797 0.960 0.020 0.000 0.020
#> SRR1044464 1 0.4606 0.796 0.724 0.012 0.000 0.264
#> SRR1044466 1 0.1411 0.797 0.960 0.020 0.000 0.020
#> SRR1044465 1 0.0937 0.805 0.976 0.012 0.000 0.012
#> SRR1044467 1 0.0937 0.805 0.976 0.012 0.000 0.012
#> SRR1044468 2 0.1722 0.881 0.048 0.944 0.008 0.000
#> SRR1044469 3 0.6285 0.358 0.000 0.412 0.528 0.060
#> SRR1044470 1 0.1936 0.787 0.940 0.032 0.000 0.028
#> SRR1044471 1 0.1406 0.803 0.960 0.024 0.000 0.016
#> SRR1044472 1 0.1520 0.795 0.956 0.020 0.000 0.024
#> SRR1044473 1 0.1406 0.803 0.960 0.024 0.000 0.016
#> SRR1044474 2 0.1637 0.880 0.060 0.940 0.000 0.000
#> SRR1044475 3 0.6156 0.389 0.000 0.344 0.592 0.064
#> SRR1044476 2 0.2234 0.816 0.008 0.924 0.064 0.004
#> SRR1044477 2 0.1637 0.880 0.060 0.940 0.000 0.000
#> SRR1044478 2 0.2485 0.828 0.016 0.916 0.064 0.004
#> SRR1044479 2 0.1637 0.880 0.060 0.940 0.000 0.000
#> SRR1044480 1 0.4328 0.800 0.748 0.008 0.000 0.244
#> SRR1044481 1 0.2271 0.813 0.916 0.008 0.000 0.076
#> SRR1044482 2 0.1637 0.880 0.060 0.940 0.000 0.000
#> SRR1044483 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044484 1 0.1452 0.810 0.956 0.008 0.000 0.036
#> SRR1044486 1 0.1584 0.810 0.952 0.012 0.000 0.036
#> SRR1044485 2 0.1474 0.882 0.052 0.948 0.000 0.000
#> SRR1044487 2 0.1637 0.880 0.060 0.940 0.000 0.000
#> SRR1044488 2 0.1389 0.882 0.048 0.952 0.000 0.000
#> SRR1044489 2 0.1389 0.882 0.048 0.952 0.000 0.000
#> SRR1044490 1 0.1174 0.804 0.968 0.012 0.000 0.020
#> SRR1044491 1 0.1629 0.793 0.952 0.024 0.000 0.024
#> SRR1044492 1 0.1610 0.794 0.952 0.032 0.000 0.016
#> SRR1044493 1 0.1411 0.797 0.960 0.020 0.000 0.020
#> SRR1044494 2 0.1637 0.880 0.060 0.940 0.000 0.000
#> SRR1044496 2 0.1637 0.880 0.060 0.940 0.000 0.000
#> SRR1044495 2 0.1637 0.880 0.060 0.940 0.000 0.000
#> SRR1044497 1 0.4819 0.780 0.652 0.004 0.000 0.344
#> SRR1044499 2 0.6068 -0.142 0.000 0.508 0.448 0.044
#> SRR1044498 1 0.2546 0.814 0.900 0.008 0.000 0.092
#> SRR1044500 2 0.1389 0.882 0.048 0.952 0.000 0.000
#> SRR1044501 2 0.2528 0.806 0.008 0.908 0.080 0.004
#> SRR1044502 2 0.4836 0.465 0.008 0.672 0.320 0.000
#> SRR1044503 1 0.4819 0.780 0.652 0.004 0.000 0.344
#> SRR1044504 1 0.4819 0.780 0.652 0.004 0.000 0.344
#> SRR1044505 1 0.2443 0.813 0.916 0.024 0.000 0.060
#> SRR1044506 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044507 1 0.6275 0.737 0.596 0.076 0.000 0.328
#> SRR1044508 1 0.6494 0.718 0.572 0.088 0.000 0.340
#> SRR1044509 1 0.6494 0.718 0.572 0.088 0.000 0.340
#> SRR1044510 4 0.5060 0.931 0.000 0.004 0.412 0.584
#> SRR1044511 4 0.4977 0.966 0.000 0.000 0.460 0.540
#> SRR1044512 4 0.4977 0.966 0.000 0.000 0.460 0.540
#> SRR1044513 2 0.4810 0.693 0.036 0.764 0.196 0.004
#> SRR1044514 4 0.4977 0.966 0.000 0.000 0.460 0.540
#> SRR1044515 2 0.4810 0.693 0.036 0.764 0.196 0.004
#> SRR1044516 2 0.1302 0.880 0.044 0.956 0.000 0.000
#> SRR1044517 4 0.5060 0.931 0.000 0.004 0.412 0.584
#> SRR1044518 4 0.4977 0.966 0.000 0.000 0.460 0.540
#> SRR1044519 3 0.1004 0.451 0.000 0.024 0.972 0.004
#> SRR1044520 3 0.1004 0.451 0.000 0.024 0.972 0.004
#> SRR1044521 2 0.1389 0.882 0.048 0.952 0.000 0.000
#> SRR1044522 2 0.1637 0.880 0.060 0.940 0.000 0.000
#> SRR1044523 2 0.3245 0.850 0.056 0.880 0.064 0.000
#> SRR1044524 2 0.4866 0.243 0.000 0.596 0.404 0.000
#> SRR1044525 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044526 1 0.2623 0.812 0.908 0.028 0.000 0.064
#> SRR1044527 2 0.3009 0.858 0.056 0.892 0.052 0.000
#> SRR1044528 2 0.2101 0.874 0.060 0.928 0.000 0.012
#> SRR1044529 2 0.1637 0.880 0.060 0.940 0.000 0.000
#> SRR1044530 1 0.1411 0.797 0.960 0.020 0.000 0.020
#> SRR1044531 1 0.1284 0.799 0.964 0.024 0.000 0.012
#> SRR1044533 1 0.1042 0.802 0.972 0.020 0.000 0.008
#> SRR1044532 1 0.1411 0.797 0.960 0.020 0.000 0.020
#> SRR1044534 2 0.1389 0.882 0.048 0.952 0.000 0.000
#> SRR1044535 2 0.4898 0.206 0.000 0.584 0.416 0.000
#> SRR1044536 2 0.1389 0.882 0.048 0.952 0.000 0.000
#> SRR1044537 1 0.2124 0.805 0.932 0.028 0.000 0.040
#> SRR1044538 1 0.1520 0.795 0.956 0.020 0.000 0.024
#> SRR1044539 1 0.4781 0.782 0.660 0.004 0.000 0.336
#> SRR1044540 1 0.1174 0.806 0.968 0.012 0.000 0.020
#> SRR1044541 2 0.5695 -0.153 0.000 0.500 0.476 0.024
#> SRR1044542 1 0.1520 0.795 0.956 0.020 0.000 0.024
#> SRR1044543 1 0.1209 0.810 0.964 0.004 0.000 0.032
#> SRR1044544 2 0.3982 0.638 0.000 0.776 0.220 0.004
#> SRR1044545 1 0.4781 0.782 0.660 0.004 0.000 0.336
#> SRR1044546 1 0.1733 0.791 0.948 0.028 0.000 0.024
#> SRR1044547 1 0.5110 0.785 0.656 0.016 0.000 0.328
#> SRR1044548 1 0.1624 0.793 0.952 0.028 0.000 0.020
#> SRR1044549 2 0.3168 0.853 0.056 0.884 0.060 0.000
#> SRR1044550 2 0.1389 0.882 0.048 0.952 0.000 0.000
#> SRR1044551 2 0.1557 0.881 0.056 0.944 0.000 0.000
#> SRR1044552 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044553 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044554 1 0.1733 0.791 0.948 0.028 0.000 0.024
#> SRR1044555 2 0.4866 0.243 0.000 0.596 0.404 0.000
#> SRR1044556 1 0.4819 0.780 0.652 0.004 0.000 0.344
#> SRR1044557 1 0.1733 0.791 0.948 0.028 0.000 0.024
#> SRR1044558 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044559 1 0.1733 0.791 0.948 0.028 0.000 0.024
#> SRR1044561 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044560 2 0.2384 0.811 0.008 0.916 0.072 0.004
#> SRR1044562 1 0.1733 0.791 0.948 0.028 0.000 0.024
#> SRR1044563 1 0.4819 0.780 0.652 0.004 0.000 0.344
#> SRR1044564 1 0.2546 0.811 0.912 0.028 0.000 0.060
#> SRR1044565 2 0.1637 0.880 0.060 0.940 0.000 0.000
#> SRR1044566 2 0.2234 0.817 0.008 0.924 0.064 0.004
#> SRR1044567 1 0.1520 0.795 0.956 0.020 0.000 0.024
#> SRR1044568 1 0.4621 0.794 0.708 0.008 0.000 0.284
#> SRR1044569 1 0.1610 0.807 0.952 0.016 0.000 0.032
#> SRR1044570 1 0.1520 0.795 0.956 0.020 0.000 0.024
#> SRR1044571 1 0.1284 0.805 0.964 0.012 0.000 0.024
#> SRR1044572 1 0.1059 0.802 0.972 0.012 0.000 0.016
#> SRR1044573 1 0.1406 0.803 0.960 0.024 0.000 0.016
#> SRR1044574 1 0.1059 0.802 0.972 0.012 0.000 0.016
#> SRR1044575 1 0.1406 0.803 0.960 0.024 0.000 0.016
#> SRR1044576 2 0.1637 0.880 0.060 0.940 0.000 0.000
#> SRR1044577 2 0.1637 0.880 0.060 0.940 0.000 0.000
#> SRR1044578 2 0.1637 0.880 0.060 0.940 0.000 0.000
#> SRR1044579 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044580 1 0.2530 0.813 0.896 0.004 0.000 0.100
#> SRR1044581 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044582 1 0.1452 0.810 0.956 0.008 0.000 0.036
#> SRR1044583 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044584 1 0.3356 0.809 0.824 0.000 0.000 0.176
#> SRR1044585 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044586 1 0.1545 0.811 0.952 0.008 0.000 0.040
#> SRR1044587 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044588 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044589 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044590 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044591 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044592 1 0.6494 0.718 0.572 0.088 0.000 0.340
#> SRR1044593 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044594 1 0.4837 0.779 0.648 0.004 0.000 0.348
#> SRR1044595 1 0.6494 0.718 0.572 0.088 0.000 0.340
#> SRR1044596 1 0.6382 0.726 0.580 0.080 0.000 0.340
#> SRR1044597 1 0.4586 0.734 0.796 0.136 0.000 0.068
#> SRR1044598 1 0.1733 0.791 0.948 0.028 0.000 0.024
#> SRR1044599 1 0.1733 0.791 0.948 0.028 0.000 0.024
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.108 0.841 0.008 0.964 0.028 0.000 0.000
#> SRR1044416 2 0.141 0.879 0.060 0.940 0.000 0.000 0.000
#> SRR1044417 2 0.141 0.879 0.060 0.940 0.000 0.000 0.000
#> SRR1044418 2 0.141 0.879 0.060 0.940 0.000 0.000 0.000
#> SRR1044420 2 0.120 0.880 0.048 0.952 0.000 0.000 0.000
#> SRR1044419 2 0.192 0.820 0.008 0.924 0.064 0.000 0.004
#> SRR1044421 2 0.134 0.879 0.056 0.944 0.000 0.000 0.000
#> SRR1044422 2 0.120 0.875 0.040 0.956 0.004 0.000 0.000
#> SRR1044423 2 0.120 0.875 0.040 0.956 0.004 0.000 0.000
#> SRR1044424 2 0.112 0.878 0.044 0.956 0.000 0.000 0.000
#> SRR1044425 1 0.412 0.746 0.792 0.008 0.000 0.144 0.056
#> SRR1044426 1 0.619 0.444 0.540 0.008 0.000 0.328 0.124
#> SRR1044427 1 0.333 0.779 0.844 0.008 0.000 0.120 0.028
#> SRR1044428 1 0.602 0.504 0.612 0.008 0.000 0.176 0.204
#> SRR1044429 1 0.434 0.733 0.776 0.008 0.000 0.152 0.064
#> SRR1044430 1 0.657 0.235 0.500 0.000 0.004 0.276 0.220
#> SRR1044431 1 0.454 0.704 0.756 0.004 0.000 0.156 0.084
#> SRR1044433 4 0.650 0.791 0.316 0.048 0.000 0.552 0.084
#> SRR1044432 1 0.658 0.223 0.496 0.000 0.004 0.280 0.220
#> SRR1044434 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044435 4 0.405 0.909 0.356 0.000 0.000 0.644 0.000
#> SRR1044436 4 0.422 0.833 0.416 0.000 0.000 0.584 0.000
#> SRR1044437 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044439 4 0.422 0.833 0.416 0.000 0.000 0.584 0.000
#> SRR1044438 4 0.455 0.781 0.436 0.004 0.000 0.556 0.004
#> SRR1044440 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044441 4 0.417 0.912 0.348 0.000 0.000 0.648 0.004
#> SRR1044442 4 0.640 0.800 0.324 0.040 0.000 0.552 0.084
#> SRR1044443 4 0.650 0.791 0.316 0.048 0.000 0.552 0.084
#> SRR1044444 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044445 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044446 3 0.296 0.430 0.000 0.100 0.864 0.000 0.036
#> SRR1044447 2 0.488 0.628 0.036 0.724 0.216 0.004 0.020
#> SRR1044449 3 0.228 0.411 0.000 0.008 0.916 0.040 0.036
#> SRR1044448 3 0.192 0.445 0.000 0.036 0.928 0.000 0.036
#> SRR1044450 3 0.200 0.447 0.000 0.040 0.924 0.000 0.036
#> SRR1044451 2 0.464 0.547 0.012 0.708 0.256 0.004 0.020
#> SRR1044452 3 0.471 0.533 0.000 0.104 0.780 0.048 0.068
#> SRR1044453 3 0.471 0.533 0.000 0.104 0.780 0.048 0.068
#> SRR1044454 3 0.471 0.533 0.000 0.104 0.780 0.048 0.068
#> SRR1044455 2 0.229 0.848 0.028 0.924 0.024 0.012 0.012
#> SRR1044456 2 0.141 0.879 0.060 0.940 0.000 0.000 0.000
#> SRR1044457 2 0.339 0.656 0.000 0.792 0.200 0.000 0.008
#> SRR1044458 2 0.223 0.790 0.004 0.900 0.092 0.000 0.004
#> SRR1044459 3 0.523 0.233 0.000 0.452 0.504 0.000 0.044
#> SRR1044460 2 0.120 0.880 0.048 0.952 0.000 0.000 0.000
#> SRR1044461 2 0.218 0.808 0.008 0.908 0.080 0.000 0.004
#> SRR1044462 1 0.397 0.558 0.756 0.012 0.000 0.224 0.008
#> SRR1044463 1 0.215 0.811 0.924 0.012 0.000 0.028 0.036
#> SRR1044464 4 0.486 0.529 0.428 0.008 0.000 0.552 0.012
#> SRR1044466 1 0.215 0.811 0.924 0.012 0.000 0.028 0.036
#> SRR1044465 1 0.312 0.797 0.860 0.004 0.000 0.100 0.036
#> SRR1044467 1 0.322 0.794 0.852 0.004 0.000 0.108 0.036
#> SRR1044468 2 0.160 0.878 0.048 0.940 0.012 0.000 0.000
#> SRR1044469 3 0.597 0.365 0.000 0.412 0.508 0.024 0.056
#> SRR1044470 1 0.323 0.773 0.864 0.024 0.000 0.024 0.088
#> SRR1044471 1 0.292 0.805 0.880 0.016 0.000 0.080 0.024
#> SRR1044472 1 0.212 0.808 0.924 0.012 0.000 0.020 0.044
#> SRR1044473 1 0.286 0.806 0.884 0.016 0.000 0.076 0.024
#> SRR1044474 2 0.141 0.879 0.060 0.940 0.000 0.000 0.000
#> SRR1044475 3 0.620 0.391 0.000 0.336 0.560 0.048 0.056
#> SRR1044476 2 0.173 0.816 0.004 0.932 0.060 0.000 0.004
#> SRR1044477 2 0.141 0.879 0.060 0.940 0.000 0.000 0.000
#> SRR1044478 2 0.227 0.822 0.016 0.908 0.072 0.000 0.004
#> SRR1044479 2 0.141 0.879 0.060 0.940 0.000 0.000 0.000
#> SRR1044480 1 0.464 -0.359 0.568 0.004 0.000 0.420 0.008
#> SRR1044481 1 0.370 0.664 0.796 0.008 0.000 0.180 0.016
#> SRR1044482 2 0.141 0.879 0.060 0.940 0.000 0.000 0.000
#> SRR1044483 4 0.400 0.908 0.344 0.000 0.000 0.656 0.000
#> SRR1044484 1 0.303 0.739 0.848 0.008 0.000 0.136 0.008
#> SRR1044486 1 0.280 0.765 0.868 0.008 0.000 0.116 0.008
#> SRR1044485 2 0.127 0.880 0.052 0.948 0.000 0.000 0.000
#> SRR1044487 2 0.141 0.879 0.060 0.940 0.000 0.000 0.000
#> SRR1044488 2 0.120 0.880 0.048 0.952 0.000 0.000 0.000
#> SRR1044489 2 0.120 0.880 0.048 0.952 0.000 0.000 0.000
#> SRR1044490 1 0.333 0.795 0.852 0.004 0.000 0.084 0.060
#> SRR1044491 1 0.273 0.818 0.896 0.016 0.000 0.048 0.040
#> SRR1044492 1 0.171 0.809 0.944 0.024 0.000 0.012 0.020
#> SRR1044493 1 0.239 0.814 0.912 0.012 0.000 0.032 0.044
#> SRR1044494 2 0.141 0.879 0.060 0.940 0.000 0.000 0.000
#> SRR1044496 2 0.141 0.879 0.060 0.940 0.000 0.000 0.000
#> SRR1044495 2 0.141 0.879 0.060 0.940 0.000 0.000 0.000
#> SRR1044497 4 0.403 0.912 0.352 0.000 0.000 0.648 0.000
#> SRR1044499 2 0.569 -0.155 0.000 0.508 0.432 0.024 0.036
#> SRR1044498 1 0.367 0.629 0.784 0.008 0.000 0.200 0.008
#> SRR1044500 2 0.120 0.880 0.048 0.952 0.000 0.000 0.000
#> SRR1044501 2 0.205 0.801 0.004 0.912 0.080 0.000 0.004
#> SRR1044502 2 0.430 0.462 0.004 0.672 0.316 0.000 0.008
#> SRR1044503 4 0.403 0.912 0.352 0.000 0.000 0.648 0.000
#> SRR1044504 4 0.405 0.909 0.356 0.000 0.000 0.644 0.000
#> SRR1044505 1 0.341 0.785 0.844 0.016 0.000 0.116 0.024
#> SRR1044506 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044507 4 0.635 0.798 0.340 0.040 0.000 0.544 0.076
#> SRR1044508 4 0.650 0.791 0.316 0.048 0.000 0.552 0.084
#> SRR1044509 4 0.650 0.791 0.316 0.048 0.000 0.552 0.084
#> SRR1044510 5 0.485 0.909 0.000 0.004 0.340 0.028 0.628
#> SRR1044511 5 0.415 0.953 0.000 0.000 0.388 0.000 0.612
#> SRR1044512 5 0.415 0.953 0.000 0.000 0.388 0.000 0.612
#> SRR1044513 2 0.472 0.670 0.036 0.744 0.196 0.004 0.020
#> SRR1044514 5 0.416 0.955 0.000 0.000 0.392 0.000 0.608
#> SRR1044515 2 0.472 0.671 0.036 0.744 0.196 0.004 0.020
#> SRR1044516 2 0.112 0.878 0.044 0.956 0.000 0.000 0.000
#> SRR1044517 5 0.487 0.912 0.000 0.004 0.344 0.028 0.624
#> SRR1044518 5 0.416 0.955 0.000 0.000 0.392 0.000 0.608
#> SRR1044519 3 0.192 0.445 0.000 0.036 0.928 0.000 0.036
#> SRR1044520 3 0.192 0.445 0.000 0.036 0.928 0.000 0.036
#> SRR1044521 2 0.120 0.880 0.048 0.952 0.000 0.000 0.000
#> SRR1044522 2 0.141 0.879 0.060 0.940 0.000 0.000 0.000
#> SRR1044523 2 0.279 0.849 0.056 0.880 0.064 0.000 0.000
#> SRR1044524 2 0.453 0.243 0.000 0.596 0.392 0.000 0.012
#> SRR1044525 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044526 1 0.317 0.779 0.860 0.020 0.000 0.104 0.016
#> SRR1044527 2 0.259 0.857 0.056 0.892 0.052 0.000 0.000
#> SRR1044528 2 0.197 0.870 0.060 0.924 0.000 0.012 0.004
#> SRR1044529 2 0.141 0.879 0.060 0.940 0.000 0.000 0.000
#> SRR1044530 1 0.215 0.811 0.924 0.012 0.000 0.028 0.036
#> SRR1044531 1 0.313 0.813 0.872 0.016 0.000 0.072 0.040
#> SRR1044533 1 0.331 0.807 0.860 0.012 0.000 0.076 0.052
#> SRR1044532 1 0.215 0.811 0.924 0.012 0.000 0.028 0.036
#> SRR1044534 2 0.120 0.880 0.048 0.952 0.000 0.000 0.000
#> SRR1044535 2 0.456 0.208 0.000 0.584 0.404 0.000 0.012
#> SRR1044536 2 0.120 0.880 0.048 0.952 0.000 0.000 0.000
#> SRR1044537 1 0.249 0.802 0.908 0.020 0.000 0.048 0.024
#> SRR1044538 1 0.212 0.808 0.924 0.012 0.000 0.020 0.044
#> SRR1044539 4 0.423 0.820 0.424 0.000 0.000 0.576 0.000
#> SRR1044540 1 0.378 0.774 0.820 0.004 0.000 0.108 0.068
#> SRR1044541 2 0.523 -0.151 0.000 0.500 0.456 0.000 0.044
#> SRR1044542 1 0.212 0.808 0.924 0.012 0.000 0.020 0.044
#> SRR1044543 1 0.451 0.683 0.740 0.000 0.000 0.188 0.072
#> SRR1044544 2 0.352 0.632 0.000 0.776 0.216 0.000 0.008
#> SRR1044545 4 0.423 0.820 0.424 0.000 0.000 0.576 0.000
#> SRR1044546 1 0.172 0.805 0.944 0.020 0.000 0.016 0.020
#> SRR1044547 4 0.465 0.665 0.476 0.012 0.000 0.512 0.000
#> SRR1044548 1 0.191 0.806 0.936 0.020 0.000 0.024 0.020
#> SRR1044549 2 0.273 0.852 0.056 0.884 0.060 0.000 0.000
#> SRR1044550 2 0.120 0.880 0.048 0.952 0.000 0.000 0.000
#> SRR1044551 2 0.134 0.879 0.056 0.944 0.000 0.000 0.000
#> SRR1044552 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044553 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044554 1 0.172 0.806 0.944 0.020 0.000 0.016 0.020
#> SRR1044555 2 0.453 0.243 0.000 0.596 0.392 0.000 0.012
#> SRR1044556 4 0.422 0.833 0.416 0.000 0.000 0.584 0.000
#> SRR1044557 1 0.172 0.805 0.944 0.020 0.000 0.016 0.020
#> SRR1044558 4 0.403 0.912 0.352 0.000 0.000 0.648 0.000
#> SRR1044559 1 0.181 0.805 0.940 0.020 0.000 0.016 0.024
#> SRR1044561 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044560 2 0.186 0.810 0.004 0.924 0.068 0.000 0.004
#> SRR1044562 1 0.181 0.805 0.940 0.020 0.000 0.016 0.024
#> SRR1044563 4 0.422 0.833 0.416 0.000 0.000 0.584 0.000
#> SRR1044564 1 0.308 0.790 0.872 0.020 0.000 0.084 0.024
#> SRR1044565 2 0.141 0.879 0.060 0.940 0.000 0.000 0.000
#> SRR1044566 2 0.173 0.817 0.004 0.932 0.060 0.000 0.004
#> SRR1044567 1 0.212 0.808 0.924 0.012 0.000 0.020 0.044
#> SRR1044568 4 0.452 0.770 0.440 0.000 0.000 0.552 0.008
#> SRR1044569 1 0.348 0.793 0.844 0.008 0.000 0.096 0.052
#> SRR1044570 1 0.220 0.808 0.920 0.012 0.000 0.020 0.048
#> SRR1044571 1 0.368 0.777 0.824 0.004 0.000 0.116 0.056
#> SRR1044572 1 0.325 0.795 0.856 0.004 0.000 0.088 0.052
#> SRR1044573 1 0.292 0.805 0.880 0.016 0.000 0.080 0.024
#> SRR1044574 1 0.288 0.806 0.880 0.004 0.000 0.068 0.048
#> SRR1044575 1 0.301 0.805 0.876 0.016 0.000 0.080 0.028
#> SRR1044576 2 0.141 0.879 0.060 0.940 0.000 0.000 0.000
#> SRR1044577 2 0.141 0.879 0.060 0.940 0.000 0.000 0.000
#> SRR1044578 2 0.141 0.879 0.060 0.940 0.000 0.000 0.000
#> SRR1044579 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044580 1 0.409 0.520 0.736 0.004 0.000 0.244 0.016
#> SRR1044581 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044582 1 0.303 0.739 0.848 0.008 0.000 0.136 0.008
#> SRR1044583 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044584 1 0.438 0.172 0.660 0.000 0.000 0.324 0.016
#> SRR1044585 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044586 1 0.329 0.731 0.836 0.008 0.000 0.140 0.016
#> SRR1044587 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044588 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044589 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044590 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044591 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044592 4 0.650 0.791 0.316 0.048 0.000 0.552 0.084
#> SRR1044593 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044594 4 0.402 0.914 0.348 0.000 0.000 0.652 0.000
#> SRR1044595 4 0.650 0.791 0.316 0.048 0.000 0.552 0.084
#> SRR1044596 4 0.640 0.800 0.324 0.040 0.000 0.552 0.084
#> SRR1044597 1 0.539 0.600 0.720 0.108 0.000 0.136 0.036
#> SRR1044598 1 0.171 0.805 0.944 0.020 0.000 0.012 0.024
#> SRR1044599 1 0.171 0.805 0.944 0.020 0.000 0.012 0.024
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.1155 0.847 0.004 0.956 0.036 0.004 0.000 0.000
#> SRR1044416 2 0.1168 0.880 0.016 0.956 0.000 0.028 0.000 0.000
#> SRR1044417 2 0.1168 0.880 0.016 0.956 0.000 0.028 0.000 0.000
#> SRR1044418 2 0.1168 0.880 0.016 0.956 0.000 0.028 0.000 0.000
#> SRR1044420 2 0.0909 0.880 0.012 0.968 0.000 0.020 0.000 0.000
#> SRR1044419 2 0.1932 0.822 0.004 0.912 0.076 0.004 0.000 0.004
#> SRR1044421 2 0.1088 0.880 0.016 0.960 0.000 0.024 0.000 0.000
#> SRR1044422 2 0.0870 0.876 0.012 0.972 0.004 0.012 0.000 0.000
#> SRR1044423 2 0.0870 0.876 0.012 0.972 0.004 0.012 0.000 0.000
#> SRR1044424 2 0.0820 0.879 0.012 0.972 0.000 0.016 0.000 0.000
#> SRR1044425 1 0.5977 0.674 0.512 0.012 0.000 0.372 0.056 0.048
#> SRR1044426 6 0.7579 0.279 0.312 0.016 0.000 0.256 0.088 0.328
#> SRR1044427 1 0.5418 0.742 0.568 0.012 0.000 0.352 0.028 0.040
#> SRR1044428 6 0.7222 0.591 0.296 0.012 0.000 0.108 0.144 0.440
#> SRR1044429 1 0.6002 0.660 0.500 0.008 0.000 0.380 0.052 0.060
#> SRR1044430 6 0.5483 0.579 0.184 0.008 0.000 0.016 0.148 0.644
#> SRR1044431 1 0.6364 0.620 0.468 0.008 0.000 0.380 0.068 0.076
#> SRR1044433 4 0.3794 0.664 0.000 0.040 0.000 0.744 0.000 0.216
#> SRR1044432 6 0.5321 0.576 0.176 0.004 0.000 0.016 0.148 0.656
#> SRR1044434 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044435 4 0.0260 0.853 0.008 0.000 0.000 0.992 0.000 0.000
#> SRR1044436 4 0.1644 0.790 0.076 0.000 0.000 0.920 0.000 0.004
#> SRR1044437 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044439 4 0.1644 0.790 0.076 0.000 0.000 0.920 0.000 0.004
#> SRR1044438 4 0.2346 0.733 0.124 0.000 0.000 0.868 0.000 0.008
#> SRR1044440 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044441 4 0.0146 0.855 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1044442 4 0.3798 0.672 0.004 0.032 0.000 0.748 0.000 0.216
#> SRR1044443 4 0.3794 0.664 0.000 0.040 0.000 0.744 0.000 0.216
#> SRR1044444 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044445 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044446 3 0.3864 0.473 0.012 0.084 0.812 0.000 0.076 0.016
#> SRR1044447 2 0.4426 0.621 0.000 0.724 0.216 0.024 0.008 0.028
#> SRR1044449 3 0.3413 0.460 0.060 0.004 0.840 0.000 0.076 0.020
#> SRR1044448 3 0.2935 0.487 0.016 0.020 0.872 0.000 0.076 0.016
#> SRR1044450 3 0.3017 0.489 0.016 0.024 0.868 0.000 0.076 0.016
#> SRR1044451 2 0.4445 0.541 0.008 0.700 0.252 0.004 0.008 0.028
#> SRR1044452 3 0.4544 0.525 0.072 0.084 0.776 0.000 0.052 0.016
#> SRR1044453 3 0.4544 0.525 0.072 0.084 0.776 0.000 0.052 0.016
#> SRR1044454 3 0.4544 0.525 0.072 0.084 0.776 0.000 0.052 0.016
#> SRR1044455 2 0.1908 0.849 0.012 0.932 0.024 0.004 0.004 0.024
#> SRR1044456 2 0.1168 0.880 0.016 0.956 0.000 0.028 0.000 0.000
#> SRR1044457 2 0.3717 0.659 0.012 0.768 0.200 0.000 0.016 0.004
#> SRR1044458 2 0.2213 0.793 0.008 0.888 0.100 0.000 0.000 0.004
#> SRR1044459 3 0.5373 0.224 0.012 0.424 0.496 0.000 0.064 0.004
#> SRR1044460 2 0.0909 0.880 0.012 0.968 0.000 0.020 0.000 0.000
#> SRR1044461 2 0.1858 0.809 0.000 0.904 0.092 0.000 0.000 0.004
#> SRR1044462 1 0.5046 0.564 0.484 0.016 0.000 0.468 0.012 0.020
#> SRR1044463 1 0.5035 0.764 0.676 0.016 0.000 0.240 0.028 0.040
#> SRR1044464 4 0.5020 0.549 0.176 0.012 0.000 0.696 0.012 0.104
#> SRR1044466 1 0.5035 0.764 0.676 0.016 0.000 0.240 0.028 0.040
#> SRR1044465 1 0.5181 0.758 0.616 0.004 0.000 0.304 0.028 0.048
#> SRR1044467 1 0.5296 0.745 0.596 0.004 0.000 0.320 0.028 0.052
#> SRR1044468 2 0.1364 0.878 0.012 0.952 0.016 0.020 0.000 0.000
#> SRR1044469 3 0.4970 0.367 0.032 0.388 0.560 0.000 0.004 0.016
#> SRR1044470 1 0.6333 0.671 0.608 0.028 0.000 0.200 0.080 0.084
#> SRR1044471 1 0.4899 0.772 0.652 0.012 0.000 0.284 0.032 0.020
#> SRR1044472 1 0.5189 0.756 0.672 0.016 0.000 0.232 0.040 0.040
#> SRR1044473 1 0.4824 0.774 0.652 0.008 0.000 0.288 0.032 0.020
#> SRR1044474 2 0.1168 0.880 0.016 0.956 0.000 0.028 0.000 0.000
#> SRR1044475 3 0.5430 0.395 0.072 0.320 0.584 0.000 0.008 0.016
#> SRR1044476 2 0.1728 0.822 0.008 0.924 0.064 0.000 0.000 0.004
#> SRR1044477 2 0.1168 0.880 0.016 0.956 0.000 0.028 0.000 0.000
#> SRR1044478 2 0.1843 0.823 0.000 0.912 0.080 0.004 0.000 0.004
#> SRR1044479 2 0.1168 0.880 0.016 0.956 0.000 0.028 0.000 0.000
#> SRR1044480 4 0.4047 0.430 0.232 0.008 0.000 0.732 0.012 0.016
#> SRR1044481 1 0.5135 0.556 0.476 0.012 0.000 0.468 0.036 0.008
#> SRR1044482 2 0.1168 0.880 0.016 0.956 0.000 0.028 0.000 0.000
#> SRR1044483 4 0.0603 0.847 0.004 0.000 0.000 0.980 0.000 0.016
#> SRR1044484 1 0.4983 0.648 0.528 0.012 0.000 0.424 0.028 0.008
#> SRR1044486 1 0.5004 0.694 0.552 0.012 0.000 0.396 0.032 0.008
#> SRR1044485 2 0.1003 0.880 0.016 0.964 0.000 0.020 0.000 0.000
#> SRR1044487 2 0.1168 0.880 0.016 0.956 0.000 0.028 0.000 0.000
#> SRR1044488 2 0.0909 0.880 0.012 0.968 0.000 0.020 0.000 0.000
#> SRR1044489 2 0.0909 0.880 0.012 0.968 0.000 0.020 0.000 0.000
#> SRR1044490 1 0.5696 0.727 0.568 0.008 0.000 0.324 0.036 0.064
#> SRR1044491 1 0.5430 0.770 0.656 0.016 0.000 0.232 0.044 0.052
#> SRR1044492 1 0.4598 0.767 0.712 0.028 0.000 0.220 0.008 0.032
#> SRR1044493 1 0.5287 0.769 0.668 0.016 0.000 0.228 0.048 0.040
#> SRR1044494 2 0.1168 0.880 0.016 0.956 0.000 0.028 0.000 0.000
#> SRR1044496 2 0.1168 0.880 0.016 0.956 0.000 0.028 0.000 0.000
#> SRR1044495 2 0.1168 0.880 0.016 0.956 0.000 0.028 0.000 0.000
#> SRR1044497 4 0.0146 0.855 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044499 2 0.4985 -0.149 0.036 0.488 0.460 0.000 0.000 0.016
#> SRR1044498 4 0.5032 -0.506 0.456 0.012 0.000 0.496 0.024 0.012
#> SRR1044500 2 0.0909 0.880 0.012 0.968 0.000 0.020 0.000 0.000
#> SRR1044501 2 0.2062 0.804 0.008 0.900 0.088 0.000 0.000 0.004
#> SRR1044502 2 0.4459 0.458 0.004 0.648 0.312 0.004 0.032 0.000
#> SRR1044503 4 0.0146 0.855 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044504 4 0.0260 0.853 0.008 0.000 0.000 0.992 0.000 0.000
#> SRR1044505 1 0.5231 0.759 0.616 0.020 0.000 0.308 0.036 0.020
#> SRR1044506 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044507 4 0.4196 0.667 0.024 0.032 0.000 0.736 0.000 0.208
#> SRR1044508 4 0.3794 0.664 0.000 0.040 0.000 0.744 0.000 0.216
#> SRR1044509 4 0.3794 0.664 0.000 0.040 0.000 0.744 0.000 0.216
#> SRR1044510 5 0.5896 0.844 0.104 0.000 0.252 0.000 0.588 0.056
#> SRR1044511 5 0.3136 0.912 0.000 0.000 0.228 0.000 0.768 0.004
#> SRR1044512 5 0.3163 0.910 0.000 0.000 0.232 0.000 0.764 0.004
#> SRR1044513 2 0.4183 0.660 0.004 0.748 0.200 0.016 0.004 0.028
#> SRR1044514 5 0.2941 0.918 0.000 0.000 0.220 0.000 0.780 0.000
#> SRR1044515 2 0.4262 0.661 0.004 0.748 0.196 0.016 0.008 0.028
#> SRR1044516 2 0.0820 0.879 0.012 0.972 0.000 0.016 0.000 0.000
#> SRR1044517 5 0.5914 0.846 0.104 0.000 0.256 0.000 0.584 0.056
#> SRR1044518 5 0.2941 0.918 0.000 0.000 0.220 0.000 0.780 0.000
#> SRR1044519 3 0.2935 0.487 0.016 0.020 0.872 0.000 0.076 0.016
#> SRR1044520 3 0.2935 0.487 0.016 0.020 0.872 0.000 0.076 0.016
#> SRR1044521 2 0.0909 0.880 0.012 0.968 0.000 0.020 0.000 0.000
#> SRR1044522 2 0.1168 0.880 0.016 0.956 0.000 0.028 0.000 0.000
#> SRR1044523 2 0.2543 0.848 0.016 0.892 0.064 0.024 0.004 0.000
#> SRR1044524 2 0.4865 0.248 0.008 0.572 0.372 0.000 0.048 0.000
#> SRR1044525 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044526 1 0.4917 0.762 0.632 0.024 0.000 0.308 0.028 0.008
#> SRR1044527 2 0.2295 0.858 0.016 0.908 0.048 0.024 0.004 0.000
#> SRR1044528 2 0.1686 0.875 0.016 0.940 0.000 0.024 0.004 0.016
#> SRR1044529 2 0.1168 0.880 0.016 0.956 0.000 0.028 0.000 0.000
#> SRR1044530 1 0.5035 0.764 0.676 0.016 0.000 0.240 0.028 0.040
#> SRR1044531 1 0.5518 0.776 0.628 0.020 0.000 0.268 0.048 0.036
#> SRR1044533 1 0.5610 0.762 0.616 0.012 0.000 0.272 0.048 0.052
#> SRR1044532 1 0.5035 0.764 0.676 0.016 0.000 0.240 0.028 0.040
#> SRR1044534 2 0.0909 0.880 0.012 0.968 0.000 0.020 0.000 0.000
#> SRR1044535 2 0.4892 0.213 0.008 0.560 0.384 0.000 0.048 0.000
#> SRR1044536 2 0.0909 0.880 0.012 0.968 0.000 0.020 0.000 0.000
#> SRR1044537 1 0.4987 0.759 0.672 0.024 0.000 0.252 0.028 0.024
#> SRR1044538 1 0.5189 0.756 0.672 0.016 0.000 0.232 0.040 0.040
#> SRR1044539 4 0.1843 0.783 0.080 0.000 0.000 0.912 0.004 0.004
#> SRR1044540 1 0.5943 0.685 0.524 0.004 0.000 0.352 0.052 0.068
#> SRR1044541 2 0.5343 -0.147 0.012 0.472 0.452 0.000 0.060 0.004
#> SRR1044542 1 0.5189 0.756 0.672 0.016 0.000 0.232 0.040 0.040
#> SRR1044543 1 0.6212 0.528 0.444 0.000 0.000 0.404 0.056 0.096
#> SRR1044544 2 0.3832 0.635 0.012 0.752 0.216 0.000 0.016 0.004
#> SRR1044545 4 0.1843 0.783 0.080 0.000 0.000 0.912 0.004 0.004
#> SRR1044546 1 0.4896 0.751 0.700 0.024 0.000 0.216 0.040 0.020
#> SRR1044547 4 0.3194 0.620 0.172 0.012 0.000 0.808 0.004 0.004
#> SRR1044548 1 0.4947 0.754 0.692 0.024 0.000 0.224 0.040 0.020
#> SRR1044549 2 0.2483 0.851 0.016 0.896 0.060 0.024 0.004 0.000
#> SRR1044550 2 0.0909 0.880 0.012 0.968 0.000 0.020 0.000 0.000
#> SRR1044551 2 0.1088 0.880 0.016 0.960 0.000 0.024 0.000 0.000
#> SRR1044552 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044553 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044554 1 0.4866 0.757 0.700 0.024 0.000 0.220 0.032 0.024
#> SRR1044555 2 0.4865 0.248 0.008 0.572 0.372 0.000 0.048 0.000
#> SRR1044556 4 0.1644 0.790 0.076 0.000 0.000 0.920 0.000 0.004
#> SRR1044557 1 0.4896 0.751 0.700 0.024 0.000 0.216 0.040 0.020
#> SRR1044558 4 0.0146 0.855 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044559 1 0.4908 0.752 0.700 0.024 0.000 0.216 0.036 0.024
#> SRR1044561 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044560 2 0.1845 0.816 0.008 0.916 0.072 0.000 0.000 0.004
#> SRR1044562 1 0.4908 0.752 0.700 0.024 0.000 0.216 0.036 0.024
#> SRR1044563 4 0.1644 0.790 0.076 0.000 0.000 0.920 0.000 0.004
#> SRR1044564 1 0.5236 0.754 0.632 0.024 0.000 0.288 0.028 0.028
#> SRR1044565 2 0.1168 0.880 0.016 0.956 0.000 0.028 0.000 0.000
#> SRR1044566 2 0.1728 0.823 0.008 0.924 0.064 0.000 0.000 0.004
#> SRR1044567 1 0.5189 0.756 0.672 0.016 0.000 0.232 0.040 0.040
#> SRR1044568 4 0.2518 0.760 0.088 0.004 0.000 0.884 0.012 0.012
#> SRR1044569 1 0.5579 0.746 0.568 0.004 0.000 0.332 0.040 0.056
#> SRR1044570 1 0.5227 0.756 0.672 0.016 0.000 0.228 0.040 0.044
#> SRR1044571 1 0.5722 0.705 0.564 0.004 0.000 0.320 0.036 0.076
#> SRR1044572 1 0.5557 0.748 0.600 0.008 0.000 0.296 0.040 0.056
#> SRR1044573 1 0.4824 0.772 0.652 0.008 0.000 0.288 0.032 0.020
#> SRR1044574 1 0.5444 0.767 0.616 0.012 0.000 0.288 0.036 0.048
#> SRR1044575 1 0.4810 0.773 0.652 0.008 0.000 0.288 0.036 0.016
#> SRR1044576 2 0.1168 0.880 0.016 0.956 0.000 0.028 0.000 0.000
#> SRR1044577 2 0.1168 0.880 0.016 0.956 0.000 0.028 0.000 0.000
#> SRR1044578 2 0.1168 0.880 0.016 0.956 0.000 0.028 0.000 0.000
#> SRR1044579 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044580 4 0.4991 -0.359 0.404 0.008 0.000 0.544 0.036 0.008
#> SRR1044581 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044582 1 0.5059 0.655 0.528 0.016 0.000 0.420 0.028 0.008
#> SRR1044583 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044584 4 0.4478 0.116 0.308 0.004 0.000 0.652 0.028 0.008
#> SRR1044585 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044586 1 0.5204 0.628 0.508 0.012 0.000 0.432 0.036 0.012
#> SRR1044587 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044588 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044589 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044590 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044591 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044592 4 0.3794 0.664 0.000 0.040 0.000 0.744 0.000 0.216
#> SRR1044593 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044594 4 0.0000 0.857 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044595 4 0.3794 0.664 0.000 0.040 0.000 0.744 0.000 0.216
#> SRR1044596 4 0.3798 0.672 0.004 0.032 0.000 0.748 0.000 0.216
#> SRR1044597 1 0.6884 0.522 0.456 0.116 0.000 0.344 0.024 0.060
#> SRR1044598 1 0.4947 0.751 0.700 0.024 0.000 0.212 0.040 0.024
#> SRR1044599 1 0.4947 0.751 0.700 0.024 0.000 0.212 0.040 0.024
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.4925 0.508 0.508
#> 3 3 0.742 0.879 0.801 0.2513 0.827 0.662
#> 4 4 0.682 0.872 0.869 0.1392 0.921 0.774
#> 5 5 0.801 0.814 0.848 0.0714 0.995 0.983
#> 6 6 0.748 0.671 0.803 0.0393 0.943 0.795
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0.0000 1.000 0.000 1.000
#> SRR1044416 2 0.0000 1.000 0.000 1.000
#> SRR1044417 2 0.0000 1.000 0.000 1.000
#> SRR1044418 2 0.0000 1.000 0.000 1.000
#> SRR1044420 2 0.0000 1.000 0.000 1.000
#> SRR1044419 2 0.0000 1.000 0.000 1.000
#> SRR1044421 2 0.0000 1.000 0.000 1.000
#> SRR1044422 2 0.0000 1.000 0.000 1.000
#> SRR1044423 2 0.0000 1.000 0.000 1.000
#> SRR1044424 2 0.0000 1.000 0.000 1.000
#> SRR1044425 1 0.0000 1.000 1.000 0.000
#> SRR1044426 1 0.0000 1.000 1.000 0.000
#> SRR1044427 1 0.0000 1.000 1.000 0.000
#> SRR1044428 1 0.0000 1.000 1.000 0.000
#> SRR1044429 1 0.0000 1.000 1.000 0.000
#> SRR1044430 1 0.0000 1.000 1.000 0.000
#> SRR1044431 1 0.0000 1.000 1.000 0.000
#> SRR1044433 1 0.0000 1.000 1.000 0.000
#> SRR1044432 1 0.0000 1.000 1.000 0.000
#> SRR1044434 1 0.0000 1.000 1.000 0.000
#> SRR1044435 1 0.0000 1.000 1.000 0.000
#> SRR1044436 1 0.0000 1.000 1.000 0.000
#> SRR1044437 1 0.0000 1.000 1.000 0.000
#> SRR1044439 1 0.0000 1.000 1.000 0.000
#> SRR1044438 1 0.0000 1.000 1.000 0.000
#> SRR1044440 1 0.0000 1.000 1.000 0.000
#> SRR1044441 1 0.0000 1.000 1.000 0.000
#> SRR1044442 1 0.0000 1.000 1.000 0.000
#> SRR1044443 1 0.0938 0.988 0.988 0.012
#> SRR1044444 1 0.0000 1.000 1.000 0.000
#> SRR1044445 1 0.0000 1.000 1.000 0.000
#> SRR1044446 2 0.0000 1.000 0.000 1.000
#> SRR1044447 2 0.0000 1.000 0.000 1.000
#> SRR1044449 2 0.0000 1.000 0.000 1.000
#> SRR1044448 2 0.0000 1.000 0.000 1.000
#> SRR1044450 2 0.0000 1.000 0.000 1.000
#> SRR1044451 2 0.0000 1.000 0.000 1.000
#> SRR1044452 2 0.0000 1.000 0.000 1.000
#> SRR1044453 2 0.0000 1.000 0.000 1.000
#> SRR1044454 2 0.0000 1.000 0.000 1.000
#> SRR1044455 2 0.0000 1.000 0.000 1.000
#> SRR1044456 2 0.1843 0.971 0.028 0.972
#> SRR1044457 2 0.0000 1.000 0.000 1.000
#> SRR1044458 2 0.0000 1.000 0.000 1.000
#> SRR1044459 2 0.0000 1.000 0.000 1.000
#> SRR1044460 2 0.0000 1.000 0.000 1.000
#> SRR1044461 2 0.0000 1.000 0.000 1.000
#> SRR1044462 1 0.0000 1.000 1.000 0.000
#> SRR1044463 1 0.0000 1.000 1.000 0.000
#> SRR1044464 1 0.0000 1.000 1.000 0.000
#> SRR1044466 1 0.0000 1.000 1.000 0.000
#> SRR1044465 1 0.0000 1.000 1.000 0.000
#> SRR1044467 1 0.0000 1.000 1.000 0.000
#> SRR1044468 2 0.0000 1.000 0.000 1.000
#> SRR1044469 2 0.0000 1.000 0.000 1.000
#> SRR1044470 1 0.0000 1.000 1.000 0.000
#> SRR1044471 1 0.0000 1.000 1.000 0.000
#> SRR1044472 1 0.0000 1.000 1.000 0.000
#> SRR1044473 1 0.0000 1.000 1.000 0.000
#> SRR1044474 2 0.0000 1.000 0.000 1.000
#> SRR1044475 2 0.0000 1.000 0.000 1.000
#> SRR1044476 2 0.0000 1.000 0.000 1.000
#> SRR1044477 2 0.0000 1.000 0.000 1.000
#> SRR1044478 2 0.0000 1.000 0.000 1.000
#> SRR1044479 2 0.0000 1.000 0.000 1.000
#> SRR1044480 1 0.0000 1.000 1.000 0.000
#> SRR1044481 1 0.0000 1.000 1.000 0.000
#> SRR1044482 2 0.0000 1.000 0.000 1.000
#> SRR1044483 1 0.0000 1.000 1.000 0.000
#> SRR1044484 1 0.0000 1.000 1.000 0.000
#> SRR1044486 1 0.0000 1.000 1.000 0.000
#> SRR1044485 2 0.0000 1.000 0.000 1.000
#> SRR1044487 2 0.0000 1.000 0.000 1.000
#> SRR1044488 2 0.0000 1.000 0.000 1.000
#> SRR1044489 2 0.0000 1.000 0.000 1.000
#> SRR1044490 1 0.0000 1.000 1.000 0.000
#> SRR1044491 1 0.0000 1.000 1.000 0.000
#> SRR1044492 1 0.0000 1.000 1.000 0.000
#> SRR1044493 1 0.0000 1.000 1.000 0.000
#> SRR1044494 2 0.0000 1.000 0.000 1.000
#> SRR1044496 2 0.0000 1.000 0.000 1.000
#> SRR1044495 2 0.0000 1.000 0.000 1.000
#> SRR1044497 1 0.0000 1.000 1.000 0.000
#> SRR1044499 2 0.0000 1.000 0.000 1.000
#> SRR1044498 1 0.0000 1.000 1.000 0.000
#> SRR1044500 2 0.0000 1.000 0.000 1.000
#> SRR1044501 2 0.0000 1.000 0.000 1.000
#> SRR1044502 2 0.0000 1.000 0.000 1.000
#> SRR1044503 1 0.0000 1.000 1.000 0.000
#> SRR1044504 1 0.0000 1.000 1.000 0.000
#> SRR1044505 1 0.0000 1.000 1.000 0.000
#> SRR1044506 1 0.0000 1.000 1.000 0.000
#> SRR1044507 1 0.0000 1.000 1.000 0.000
#> SRR1044508 1 0.0000 1.000 1.000 0.000
#> SRR1044509 1 0.0000 1.000 1.000 0.000
#> SRR1044510 2 0.0000 1.000 0.000 1.000
#> SRR1044511 2 0.0000 1.000 0.000 1.000
#> SRR1044512 2 0.0000 1.000 0.000 1.000
#> SRR1044513 2 0.0000 1.000 0.000 1.000
#> SRR1044514 2 0.0000 1.000 0.000 1.000
#> SRR1044515 2 0.0000 1.000 0.000 1.000
#> SRR1044516 2 0.0000 1.000 0.000 1.000
#> SRR1044517 2 0.0000 1.000 0.000 1.000
#> SRR1044518 2 0.0000 1.000 0.000 1.000
#> SRR1044519 2 0.0000 1.000 0.000 1.000
#> SRR1044520 2 0.0000 1.000 0.000 1.000
#> SRR1044521 2 0.0000 1.000 0.000 1.000
#> SRR1044522 2 0.0000 1.000 0.000 1.000
#> SRR1044523 2 0.0000 1.000 0.000 1.000
#> SRR1044524 2 0.0000 1.000 0.000 1.000
#> SRR1044525 1 0.0000 1.000 1.000 0.000
#> SRR1044526 1 0.0000 1.000 1.000 0.000
#> SRR1044527 2 0.0000 1.000 0.000 1.000
#> SRR1044528 2 0.0000 1.000 0.000 1.000
#> SRR1044529 2 0.0000 1.000 0.000 1.000
#> SRR1044530 1 0.0000 1.000 1.000 0.000
#> SRR1044531 1 0.0000 1.000 1.000 0.000
#> SRR1044533 1 0.0000 1.000 1.000 0.000
#> SRR1044532 1 0.0000 1.000 1.000 0.000
#> SRR1044534 2 0.0000 1.000 0.000 1.000
#> SRR1044535 2 0.0000 1.000 0.000 1.000
#> SRR1044536 2 0.0000 1.000 0.000 1.000
#> SRR1044537 1 0.0000 1.000 1.000 0.000
#> SRR1044538 1 0.0000 1.000 1.000 0.000
#> SRR1044539 1 0.0000 1.000 1.000 0.000
#> SRR1044540 1 0.0000 1.000 1.000 0.000
#> SRR1044541 2 0.0000 1.000 0.000 1.000
#> SRR1044542 1 0.0000 1.000 1.000 0.000
#> SRR1044543 1 0.0000 1.000 1.000 0.000
#> SRR1044544 2 0.0000 1.000 0.000 1.000
#> SRR1044545 1 0.0000 1.000 1.000 0.000
#> SRR1044546 1 0.0000 1.000 1.000 0.000
#> SRR1044547 1 0.0000 1.000 1.000 0.000
#> SRR1044548 1 0.0000 1.000 1.000 0.000
#> SRR1044549 2 0.0000 1.000 0.000 1.000
#> SRR1044550 2 0.0000 1.000 0.000 1.000
#> SRR1044551 2 0.0000 1.000 0.000 1.000
#> SRR1044552 1 0.0000 1.000 1.000 0.000
#> SRR1044553 1 0.0000 1.000 1.000 0.000
#> SRR1044554 1 0.0000 1.000 1.000 0.000
#> SRR1044555 2 0.0000 1.000 0.000 1.000
#> SRR1044556 1 0.0000 1.000 1.000 0.000
#> SRR1044557 1 0.0000 1.000 1.000 0.000
#> SRR1044558 1 0.0000 1.000 1.000 0.000
#> SRR1044559 1 0.0000 1.000 1.000 0.000
#> SRR1044561 1 0.0000 1.000 1.000 0.000
#> SRR1044560 2 0.0000 1.000 0.000 1.000
#> SRR1044562 1 0.0000 1.000 1.000 0.000
#> SRR1044563 1 0.0000 1.000 1.000 0.000
#> SRR1044564 1 0.0000 1.000 1.000 0.000
#> SRR1044565 2 0.0000 1.000 0.000 1.000
#> SRR1044566 2 0.0000 1.000 0.000 1.000
#> SRR1044567 1 0.0000 1.000 1.000 0.000
#> SRR1044568 1 0.0000 1.000 1.000 0.000
#> SRR1044569 1 0.0000 1.000 1.000 0.000
#> SRR1044570 1 0.0000 1.000 1.000 0.000
#> SRR1044571 1 0.0000 1.000 1.000 0.000
#> SRR1044572 1 0.0000 1.000 1.000 0.000
#> SRR1044573 1 0.0000 1.000 1.000 0.000
#> SRR1044574 1 0.0000 1.000 1.000 0.000
#> SRR1044575 1 0.0000 1.000 1.000 0.000
#> SRR1044576 2 0.0000 1.000 0.000 1.000
#> SRR1044577 2 0.0000 1.000 0.000 1.000
#> SRR1044578 2 0.0000 1.000 0.000 1.000
#> SRR1044579 1 0.0000 1.000 1.000 0.000
#> SRR1044580 1 0.0000 1.000 1.000 0.000
#> SRR1044581 1 0.0000 1.000 1.000 0.000
#> SRR1044582 1 0.0000 1.000 1.000 0.000
#> SRR1044583 1 0.0000 1.000 1.000 0.000
#> SRR1044584 1 0.0000 1.000 1.000 0.000
#> SRR1044585 1 0.0000 1.000 1.000 0.000
#> SRR1044586 1 0.0000 1.000 1.000 0.000
#> SRR1044587 1 0.0000 1.000 1.000 0.000
#> SRR1044588 1 0.0000 1.000 1.000 0.000
#> SRR1044589 1 0.0000 1.000 1.000 0.000
#> SRR1044590 1 0.0000 1.000 1.000 0.000
#> SRR1044591 1 0.0000 1.000 1.000 0.000
#> SRR1044592 1 0.0000 1.000 1.000 0.000
#> SRR1044593 1 0.0000 1.000 1.000 0.000
#> SRR1044594 1 0.0000 1.000 1.000 0.000
#> SRR1044595 1 0.0000 1.000 1.000 0.000
#> SRR1044596 1 0.0000 1.000 1.000 0.000
#> SRR1044597 1 0.0000 1.000 1.000 0.000
#> SRR1044598 1 0.0000 1.000 1.000 0.000
#> SRR1044599 1 0.0000 1.000 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044416 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044417 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044418 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044420 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044419 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044421 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044422 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044423 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044424 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044425 3 0.4291 0.520 0.180 0.000 0.820
#> SRR1044426 1 0.6286 0.954 0.536 0.000 0.464
#> SRR1044427 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044428 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044429 1 0.6302 0.924 0.520 0.000 0.480
#> SRR1044430 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044431 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044433 3 0.0237 0.949 0.004 0.000 0.996
#> SRR1044432 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044434 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044435 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044436 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044437 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044439 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044438 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044440 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044441 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044442 3 0.0237 0.949 0.004 0.000 0.996
#> SRR1044443 3 0.1399 0.899 0.004 0.028 0.968
#> SRR1044444 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044445 3 0.0237 0.949 0.004 0.000 0.996
#> SRR1044446 2 0.0000 0.729 0.000 1.000 0.000
#> SRR1044447 2 0.5327 0.841 0.272 0.728 0.000
#> SRR1044449 2 0.0000 0.729 0.000 1.000 0.000
#> SRR1044448 2 0.0000 0.729 0.000 1.000 0.000
#> SRR1044450 2 0.0237 0.726 0.004 0.996 0.000
#> SRR1044451 2 0.4178 0.804 0.172 0.828 0.000
#> SRR1044452 2 0.0000 0.729 0.000 1.000 0.000
#> SRR1044453 2 0.0000 0.729 0.000 1.000 0.000
#> SRR1044454 2 0.0000 0.729 0.000 1.000 0.000
#> SRR1044455 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044456 1 0.6235 -0.814 0.564 0.436 0.000
#> SRR1044457 2 0.6267 0.895 0.452 0.548 0.000
#> SRR1044458 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044459 2 0.0000 0.729 0.000 1.000 0.000
#> SRR1044460 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044461 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044462 3 0.6225 -0.705 0.432 0.000 0.568
#> SRR1044463 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044464 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044466 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044465 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044467 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044468 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044469 2 0.4178 0.799 0.172 0.828 0.000
#> SRR1044470 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044471 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044472 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044473 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044474 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044475 2 0.4178 0.799 0.172 0.828 0.000
#> SRR1044476 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044477 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044478 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044479 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044480 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044481 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044482 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044483 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044484 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044486 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044485 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044487 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044488 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044489 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044490 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044491 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044492 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044493 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044494 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044496 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044495 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044497 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044499 2 0.5431 0.843 0.284 0.716 0.000
#> SRR1044498 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044500 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044501 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044502 2 0.5016 0.830 0.240 0.760 0.000
#> SRR1044503 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044504 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044505 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044506 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044507 3 0.0424 0.947 0.008 0.000 0.992
#> SRR1044508 3 0.0237 0.949 0.004 0.000 0.996
#> SRR1044509 3 0.0237 0.949 0.004 0.000 0.996
#> SRR1044510 2 0.0000 0.729 0.000 1.000 0.000
#> SRR1044511 2 0.0000 0.729 0.000 1.000 0.000
#> SRR1044512 2 0.0000 0.729 0.000 1.000 0.000
#> SRR1044513 2 0.5785 0.861 0.332 0.668 0.000
#> SRR1044514 2 0.0000 0.729 0.000 1.000 0.000
#> SRR1044515 2 0.5882 0.867 0.348 0.652 0.000
#> SRR1044516 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044517 2 0.0000 0.729 0.000 1.000 0.000
#> SRR1044518 2 0.0000 0.729 0.000 1.000 0.000
#> SRR1044519 2 0.0237 0.726 0.004 0.996 0.000
#> SRR1044520 2 0.0237 0.726 0.004 0.996 0.000
#> SRR1044521 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044522 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044523 2 0.6126 0.882 0.400 0.600 0.000
#> SRR1044524 2 0.1411 0.746 0.036 0.964 0.000
#> SRR1044525 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044526 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044527 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044528 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044529 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044530 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044531 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044533 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044532 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044534 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044535 2 0.1031 0.740 0.024 0.976 0.000
#> SRR1044536 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044537 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044538 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044539 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044540 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044541 2 0.6045 0.876 0.380 0.620 0.000
#> SRR1044542 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044543 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044544 2 0.5363 0.844 0.276 0.724 0.000
#> SRR1044545 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044546 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044547 3 0.1411 0.895 0.036 0.000 0.964
#> SRR1044548 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044549 2 0.6267 0.895 0.452 0.548 0.000
#> SRR1044550 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044551 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044552 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044553 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044554 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044555 2 0.0000 0.729 0.000 1.000 0.000
#> SRR1044556 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044557 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044558 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044559 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044561 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044560 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044562 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044563 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044564 1 0.6295 0.939 0.528 0.000 0.472
#> SRR1044565 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044566 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044567 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044568 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044569 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044570 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044571 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044572 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044573 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044574 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044575 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044576 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044577 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044578 2 0.6274 0.896 0.456 0.544 0.000
#> SRR1044579 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044580 3 0.5882 -0.383 0.348 0.000 0.652
#> SRR1044581 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044582 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044583 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044584 3 0.1964 0.857 0.056 0.000 0.944
#> SRR1044585 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044586 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044587 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044588 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044589 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044590 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044591 3 0.0237 0.949 0.004 0.000 0.996
#> SRR1044592 3 0.0237 0.949 0.004 0.000 0.996
#> SRR1044593 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044594 3 0.0000 0.953 0.000 0.000 1.000
#> SRR1044595 3 0.4399 0.505 0.188 0.000 0.812
#> SRR1044596 3 0.0237 0.949 0.004 0.000 0.996
#> SRR1044597 1 0.6307 0.906 0.512 0.000 0.488
#> SRR1044598 1 0.6280 0.962 0.540 0.000 0.460
#> SRR1044599 1 0.6280 0.962 0.540 0.000 0.460
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044416 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044417 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044418 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044420 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044419 2 0.0469 0.90576 0.012 0.988 0.000 0.000
#> SRR1044421 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044422 2 0.0469 0.90703 0.012 0.988 0.000 0.000
#> SRR1044423 2 0.0469 0.90703 0.012 0.988 0.000 0.000
#> SRR1044424 2 0.0469 0.90703 0.012 0.988 0.000 0.000
#> SRR1044425 4 0.5365 0.48864 0.264 0.000 0.044 0.692
#> SRR1044426 1 0.4775 0.91583 0.784 0.000 0.076 0.140
#> SRR1044427 1 0.5314 0.91380 0.748 0.000 0.108 0.144
#> SRR1044428 1 0.4724 0.91761 0.788 0.000 0.076 0.136
#> SRR1044429 1 0.4638 0.91593 0.788 0.000 0.060 0.152
#> SRR1044430 1 0.4724 0.91761 0.788 0.000 0.076 0.136
#> SRR1044431 1 0.4829 0.91010 0.776 0.000 0.068 0.156
#> SRR1044433 4 0.2546 0.91086 0.008 0.000 0.092 0.900
#> SRR1044432 1 0.4724 0.91761 0.788 0.000 0.076 0.136
#> SRR1044434 4 0.0000 0.95261 0.000 0.000 0.000 1.000
#> SRR1044435 4 0.0000 0.95261 0.000 0.000 0.000 1.000
#> SRR1044436 4 0.0336 0.95124 0.000 0.000 0.008 0.992
#> SRR1044437 4 0.0000 0.95261 0.000 0.000 0.000 1.000
#> SRR1044439 4 0.0188 0.95216 0.000 0.000 0.004 0.996
#> SRR1044438 4 0.0188 0.95170 0.000 0.000 0.004 0.996
#> SRR1044440 4 0.0000 0.95261 0.000 0.000 0.000 1.000
#> SRR1044441 4 0.0000 0.95261 0.000 0.000 0.000 1.000
#> SRR1044442 4 0.2216 0.91547 0.000 0.000 0.092 0.908
#> SRR1044443 4 0.2675 0.90482 0.008 0.000 0.100 0.892
#> SRR1044444 4 0.0000 0.95261 0.000 0.000 0.000 1.000
#> SRR1044445 4 0.0707 0.94893 0.000 0.000 0.020 0.980
#> SRR1044446 3 0.5113 0.95631 0.024 0.292 0.684 0.000
#> SRR1044447 2 0.5206 0.21239 0.024 0.668 0.308 0.000
#> SRR1044449 3 0.5623 0.95682 0.048 0.292 0.660 0.000
#> SRR1044448 3 0.5207 0.95659 0.028 0.292 0.680 0.000
#> SRR1044450 3 0.5207 0.95659 0.028 0.292 0.680 0.000
#> SRR1044451 2 0.5766 -0.27938 0.032 0.564 0.404 0.000
#> SRR1044452 3 0.5769 0.95094 0.056 0.292 0.652 0.000
#> SRR1044453 3 0.5839 0.95075 0.060 0.292 0.648 0.000
#> SRR1044454 3 0.5972 0.94747 0.068 0.292 0.640 0.000
#> SRR1044455 2 0.0592 0.90642 0.016 0.984 0.000 0.000
#> SRR1044456 2 0.2928 0.77652 0.052 0.896 0.052 0.000
#> SRR1044457 2 0.1510 0.87931 0.028 0.956 0.016 0.000
#> SRR1044458 2 0.0469 0.90576 0.012 0.988 0.000 0.000
#> SRR1044459 3 0.5769 0.95205 0.056 0.292 0.652 0.000
#> SRR1044460 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044461 2 0.0707 0.90472 0.020 0.980 0.000 0.000
#> SRR1044462 1 0.6627 0.70960 0.588 0.000 0.112 0.300
#> SRR1044463 1 0.3443 0.92888 0.848 0.000 0.016 0.136
#> SRR1044464 4 0.0188 0.95216 0.000 0.000 0.004 0.996
#> SRR1044466 1 0.3443 0.92826 0.848 0.000 0.016 0.136
#> SRR1044465 1 0.4586 0.91995 0.796 0.000 0.068 0.136
#> SRR1044467 1 0.4586 0.91995 0.796 0.000 0.068 0.136
#> SRR1044468 2 0.0188 0.90984 0.004 0.996 0.000 0.000
#> SRR1044469 2 0.6189 -0.27050 0.060 0.568 0.372 0.000
#> SRR1044470 1 0.2868 0.92896 0.864 0.000 0.000 0.136
#> SRR1044471 1 0.4656 0.92076 0.792 0.000 0.072 0.136
#> SRR1044472 1 0.3659 0.92833 0.840 0.000 0.024 0.136
#> SRR1044473 1 0.4656 0.92076 0.792 0.000 0.072 0.136
#> SRR1044474 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044475 2 0.6253 -0.28237 0.064 0.564 0.372 0.000
#> SRR1044476 2 0.0469 0.90576 0.012 0.988 0.000 0.000
#> SRR1044477 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044478 2 0.0336 0.90774 0.008 0.992 0.000 0.000
#> SRR1044479 2 0.0779 0.90034 0.016 0.980 0.004 0.000
#> SRR1044480 4 0.1022 0.93861 0.000 0.000 0.032 0.968
#> SRR1044481 1 0.5380 0.90993 0.744 0.000 0.120 0.136
#> SRR1044482 2 0.0336 0.90865 0.008 0.992 0.000 0.000
#> SRR1044483 4 0.0188 0.95216 0.000 0.000 0.004 0.996
#> SRR1044484 1 0.5432 0.90926 0.740 0.000 0.124 0.136
#> SRR1044486 1 0.5432 0.90926 0.740 0.000 0.124 0.136
#> SRR1044485 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044487 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044488 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044489 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044490 1 0.4586 0.91995 0.796 0.000 0.068 0.136
#> SRR1044491 1 0.4514 0.92372 0.800 0.000 0.064 0.136
#> SRR1044492 1 0.3856 0.92926 0.832 0.000 0.032 0.136
#> SRR1044493 1 0.3554 0.92821 0.844 0.000 0.020 0.136
#> SRR1044494 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044496 2 0.0469 0.90703 0.012 0.988 0.000 0.000
#> SRR1044495 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044497 4 0.0000 0.95261 0.000 0.000 0.000 1.000
#> SRR1044499 2 0.5608 0.26461 0.060 0.684 0.256 0.000
#> SRR1044498 1 0.5217 0.91146 0.756 0.000 0.108 0.136
#> SRR1044500 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044501 2 0.0469 0.90576 0.012 0.988 0.000 0.000
#> SRR1044502 2 0.5903 -0.00139 0.052 0.616 0.332 0.000
#> SRR1044503 4 0.0000 0.95261 0.000 0.000 0.000 1.000
#> SRR1044504 4 0.0000 0.95261 0.000 0.000 0.000 1.000
#> SRR1044505 1 0.5950 0.90815 0.696 0.000 0.156 0.148
#> SRR1044506 4 0.0707 0.94893 0.000 0.000 0.020 0.980
#> SRR1044507 4 0.2814 0.89004 0.000 0.000 0.132 0.868
#> SRR1044508 4 0.2546 0.91086 0.008 0.000 0.092 0.900
#> SRR1044509 4 0.2546 0.91086 0.008 0.000 0.092 0.900
#> SRR1044510 3 0.5769 0.95415 0.056 0.292 0.652 0.000
#> SRR1044511 3 0.5297 0.95581 0.032 0.292 0.676 0.000
#> SRR1044512 3 0.5297 0.95581 0.032 0.292 0.676 0.000
#> SRR1044513 2 0.3764 0.64985 0.012 0.816 0.172 0.000
#> SRR1044514 3 0.5297 0.95581 0.032 0.292 0.676 0.000
#> SRR1044515 2 0.3479 0.69946 0.012 0.840 0.148 0.000
#> SRR1044516 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044517 3 0.5839 0.95382 0.060 0.292 0.648 0.000
#> SRR1044518 3 0.5297 0.95581 0.032 0.292 0.676 0.000
#> SRR1044519 3 0.5207 0.95659 0.028 0.292 0.680 0.000
#> SRR1044520 3 0.5207 0.95659 0.028 0.292 0.680 0.000
#> SRR1044521 2 0.0469 0.90703 0.012 0.988 0.000 0.000
#> SRR1044522 2 0.1174 0.88604 0.020 0.968 0.012 0.000
#> SRR1044523 2 0.2450 0.81981 0.016 0.912 0.072 0.000
#> SRR1044524 3 0.5839 0.88437 0.044 0.352 0.604 0.000
#> SRR1044525 4 0.0000 0.95261 0.000 0.000 0.000 1.000
#> SRR1044526 1 0.5724 0.91154 0.716 0.000 0.140 0.144
#> SRR1044527 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044528 2 0.0336 0.90869 0.008 0.992 0.000 0.000
#> SRR1044529 2 0.0469 0.90703 0.012 0.988 0.000 0.000
#> SRR1044530 1 0.3443 0.92826 0.848 0.000 0.016 0.136
#> SRR1044531 1 0.4364 0.92259 0.808 0.000 0.056 0.136
#> SRR1044533 1 0.4586 0.91995 0.796 0.000 0.068 0.136
#> SRR1044532 1 0.3554 0.92821 0.844 0.000 0.020 0.136
#> SRR1044534 2 0.0188 0.90984 0.004 0.996 0.000 0.000
#> SRR1044535 3 0.5730 0.89565 0.040 0.344 0.616 0.000
#> SRR1044536 2 0.0469 0.90703 0.012 0.988 0.000 0.000
#> SRR1044537 1 0.5432 0.90926 0.740 0.000 0.124 0.136
#> SRR1044538 1 0.3443 0.92826 0.848 0.000 0.016 0.136
#> SRR1044539 4 0.0188 0.95216 0.000 0.000 0.004 0.996
#> SRR1044540 1 0.4586 0.91995 0.796 0.000 0.068 0.136
#> SRR1044541 2 0.3587 0.74686 0.040 0.856 0.104 0.000
#> SRR1044542 1 0.3659 0.92803 0.840 0.000 0.024 0.136
#> SRR1044543 1 0.4586 0.91995 0.796 0.000 0.068 0.136
#> SRR1044544 2 0.5549 0.22642 0.048 0.672 0.280 0.000
#> SRR1044545 4 0.1022 0.93855 0.000 0.000 0.032 0.968
#> SRR1044546 1 0.5432 0.90926 0.740 0.000 0.124 0.136
#> SRR1044547 4 0.3547 0.83342 0.072 0.000 0.064 0.864
#> SRR1044548 1 0.5432 0.90926 0.740 0.000 0.124 0.136
#> SRR1044549 2 0.0672 0.90111 0.008 0.984 0.008 0.000
#> SRR1044550 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044551 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044552 4 0.0000 0.95261 0.000 0.000 0.000 1.000
#> SRR1044553 4 0.0000 0.95261 0.000 0.000 0.000 1.000
#> SRR1044554 1 0.5432 0.90926 0.740 0.000 0.124 0.136
#> SRR1044555 3 0.5906 0.94994 0.064 0.292 0.644 0.000
#> SRR1044556 4 0.0188 0.95216 0.000 0.000 0.004 0.996
#> SRR1044557 1 0.5432 0.90926 0.740 0.000 0.124 0.136
#> SRR1044558 4 0.0000 0.95261 0.000 0.000 0.000 1.000
#> SRR1044559 1 0.5432 0.90926 0.740 0.000 0.124 0.136
#> SRR1044561 4 0.0000 0.95261 0.000 0.000 0.000 1.000
#> SRR1044560 2 0.0469 0.90576 0.012 0.988 0.000 0.000
#> SRR1044562 1 0.5432 0.90926 0.740 0.000 0.124 0.136
#> SRR1044563 4 0.0188 0.95216 0.000 0.000 0.004 0.996
#> SRR1044564 1 0.5657 0.89572 0.720 0.000 0.120 0.160
#> SRR1044565 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044566 2 0.0469 0.90576 0.012 0.988 0.000 0.000
#> SRR1044567 1 0.3554 0.92841 0.844 0.000 0.020 0.136
#> SRR1044568 4 0.0336 0.95143 0.000 0.000 0.008 0.992
#> SRR1044569 1 0.4656 0.92076 0.792 0.000 0.072 0.136
#> SRR1044570 1 0.3659 0.92803 0.840 0.000 0.024 0.136
#> SRR1044571 1 0.4586 0.91995 0.796 0.000 0.068 0.136
#> SRR1044572 1 0.4586 0.91995 0.796 0.000 0.068 0.136
#> SRR1044573 1 0.5102 0.92277 0.764 0.000 0.100 0.136
#> SRR1044574 1 0.4586 0.91995 0.796 0.000 0.068 0.136
#> SRR1044575 1 0.4586 0.91995 0.796 0.000 0.068 0.136
#> SRR1044576 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044577 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044578 2 0.0000 0.91072 0.000 1.000 0.000 0.000
#> SRR1044579 4 0.0000 0.95261 0.000 0.000 0.000 1.000
#> SRR1044580 4 0.6285 -0.12983 0.412 0.000 0.060 0.528
#> SRR1044581 4 0.0000 0.95261 0.000 0.000 0.000 1.000
#> SRR1044582 1 0.5432 0.90926 0.740 0.000 0.124 0.136
#> SRR1044583 4 0.0000 0.95261 0.000 0.000 0.000 1.000
#> SRR1044584 4 0.2222 0.89260 0.060 0.000 0.016 0.924
#> SRR1044585 4 0.0000 0.95261 0.000 0.000 0.000 1.000
#> SRR1044586 1 0.5432 0.90926 0.740 0.000 0.124 0.136
#> SRR1044587 4 0.0817 0.94842 0.000 0.000 0.024 0.976
#> SRR1044588 4 0.0707 0.94893 0.000 0.000 0.020 0.980
#> SRR1044589 4 0.0707 0.94893 0.000 0.000 0.020 0.980
#> SRR1044590 4 0.0707 0.94893 0.000 0.000 0.020 0.980
#> SRR1044591 4 0.0707 0.94893 0.000 0.000 0.020 0.980
#> SRR1044592 4 0.2480 0.91174 0.008 0.000 0.088 0.904
#> SRR1044593 4 0.0707 0.94893 0.000 0.000 0.020 0.980
#> SRR1044594 4 0.0707 0.94893 0.000 0.000 0.020 0.980
#> SRR1044595 4 0.6339 0.55238 0.196 0.000 0.148 0.656
#> SRR1044596 4 0.2216 0.91547 0.000 0.000 0.092 0.908
#> SRR1044597 1 0.5615 0.87903 0.716 0.000 0.096 0.188
#> SRR1044598 1 0.5432 0.90926 0.740 0.000 0.124 0.136
#> SRR1044599 1 0.5432 0.90926 0.740 0.000 0.124 0.136
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.0566 0.9035 0.004 0.984 0.000 0.000 NA
#> SRR1044416 2 0.0162 0.9064 0.004 0.996 0.000 0.000 NA
#> SRR1044417 2 0.0000 0.9069 0.000 1.000 0.000 0.000 NA
#> SRR1044418 2 0.0000 0.9069 0.000 1.000 0.000 0.000 NA
#> SRR1044420 2 0.0324 0.9056 0.004 0.992 0.000 0.000 NA
#> SRR1044419 2 0.1571 0.8794 0.004 0.936 0.000 0.000 NA
#> SRR1044421 2 0.0404 0.9046 0.000 0.988 0.000 0.000 NA
#> SRR1044422 2 0.0290 0.9064 0.008 0.992 0.000 0.000 NA
#> SRR1044423 2 0.0290 0.9064 0.008 0.992 0.000 0.000 NA
#> SRR1044424 2 0.0290 0.9064 0.008 0.992 0.000 0.000 NA
#> SRR1044425 4 0.4236 0.5201 0.328 0.000 0.004 0.664 NA
#> SRR1044426 1 0.2434 0.7736 0.912 0.000 0.024 0.040 NA
#> SRR1044427 1 0.5185 0.7928 0.580 0.000 0.004 0.040 NA
#> SRR1044428 1 0.2269 0.7792 0.920 0.000 0.028 0.032 NA
#> SRR1044429 1 0.2674 0.7909 0.896 0.000 0.012 0.060 NA
#> SRR1044430 1 0.2354 0.7793 0.916 0.000 0.032 0.032 NA
#> SRR1044431 1 0.1628 0.7831 0.936 0.000 0.008 0.056 NA
#> SRR1044433 4 0.4577 0.7893 0.000 0.000 0.084 0.740 NA
#> SRR1044432 1 0.2180 0.7799 0.924 0.000 0.024 0.032 NA
#> SRR1044434 4 0.0000 0.9155 0.000 0.000 0.000 1.000 NA
#> SRR1044435 4 0.0000 0.9155 0.000 0.000 0.000 1.000 NA
#> SRR1044436 4 0.0693 0.9126 0.000 0.000 0.008 0.980 NA
#> SRR1044437 4 0.0000 0.9155 0.000 0.000 0.000 1.000 NA
#> SRR1044439 4 0.0451 0.9141 0.000 0.000 0.004 0.988 NA
#> SRR1044438 4 0.0451 0.9143 0.000 0.000 0.004 0.988 NA
#> SRR1044440 4 0.0000 0.9155 0.000 0.000 0.000 1.000 NA
#> SRR1044441 4 0.0000 0.9155 0.000 0.000 0.000 1.000 NA
#> SRR1044442 4 0.4612 0.7869 0.000 0.000 0.084 0.736 NA
#> SRR1044443 4 0.4612 0.7869 0.000 0.000 0.084 0.736 NA
#> SRR1044444 4 0.0000 0.9155 0.000 0.000 0.000 1.000 NA
#> SRR1044445 4 0.1549 0.9038 0.000 0.000 0.016 0.944 NA
#> SRR1044446 3 0.3960 0.9019 0.004 0.140 0.800 0.000 NA
#> SRR1044447 2 0.5745 0.2181 0.004 0.592 0.304 0.000 NA
#> SRR1044449 3 0.4950 0.9022 0.008 0.140 0.732 0.000 NA
#> SRR1044448 3 0.3960 0.9019 0.004 0.140 0.800 0.000 NA
#> SRR1044450 3 0.3916 0.9012 0.004 0.136 0.804 0.000 NA
#> SRR1044451 3 0.6030 0.3985 0.004 0.424 0.472 0.000 NA
#> SRR1044452 3 0.5308 0.8844 0.004 0.140 0.688 0.000 NA
#> SRR1044453 3 0.5308 0.8844 0.004 0.140 0.688 0.000 NA
#> SRR1044454 3 0.5377 0.8817 0.004 0.140 0.680 0.000 NA
#> SRR1044455 2 0.1357 0.8865 0.004 0.948 0.000 0.000 NA
#> SRR1044456 2 0.1357 0.8610 0.004 0.948 0.000 0.000 NA
#> SRR1044457 2 0.3183 0.7830 0.000 0.828 0.016 0.000 NA
#> SRR1044458 2 0.1638 0.8769 0.004 0.932 0.000 0.000 NA
#> SRR1044459 3 0.4890 0.8910 0.000 0.140 0.720 0.000 NA
#> SRR1044460 2 0.0000 0.9069 0.000 1.000 0.000 0.000 NA
#> SRR1044461 2 0.1502 0.8818 0.004 0.940 0.000 0.000 NA
#> SRR1044462 1 0.6906 0.6335 0.400 0.000 0.012 0.204 NA
#> SRR1044463 1 0.4460 0.8203 0.748 0.000 0.016 0.032 NA
#> SRR1044464 4 0.0671 0.9134 0.000 0.000 0.004 0.980 NA
#> SRR1044466 1 0.4584 0.8189 0.732 0.000 0.016 0.032 NA
#> SRR1044465 1 0.1041 0.7939 0.964 0.000 0.000 0.032 NA
#> SRR1044467 1 0.1041 0.7924 0.964 0.000 0.004 0.032 NA
#> SRR1044468 2 0.0566 0.9035 0.004 0.984 0.000 0.000 NA
#> SRR1044469 2 0.6703 -0.3639 0.008 0.420 0.392 0.000 NA
#> SRR1044470 1 0.4328 0.8220 0.756 0.000 0.012 0.032 NA
#> SRR1044471 1 0.1202 0.7936 0.960 0.000 0.004 0.032 NA
#> SRR1044472 1 0.4384 0.8190 0.764 0.000 0.020 0.032 NA
#> SRR1044473 1 0.1442 0.7963 0.952 0.000 0.004 0.032 NA
#> SRR1044474 2 0.0000 0.9069 0.000 1.000 0.000 0.000 NA
#> SRR1044475 2 0.6642 -0.3984 0.008 0.412 0.412 0.000 NA
#> SRR1044476 2 0.1638 0.8769 0.004 0.932 0.000 0.000 NA
#> SRR1044477 2 0.0000 0.9069 0.000 1.000 0.000 0.000 NA
#> SRR1044478 2 0.0566 0.9035 0.004 0.984 0.000 0.000 NA
#> SRR1044479 2 0.0324 0.9043 0.004 0.992 0.000 0.000 NA
#> SRR1044480 4 0.2189 0.8743 0.000 0.000 0.012 0.904 NA
#> SRR1044481 1 0.5282 0.7799 0.520 0.000 0.008 0.032 NA
#> SRR1044482 2 0.0162 0.9062 0.004 0.996 0.000 0.000 NA
#> SRR1044483 4 0.0693 0.9128 0.000 0.000 0.008 0.980 NA
#> SRR1044484 1 0.5187 0.7761 0.504 0.000 0.004 0.032 NA
#> SRR1044486 1 0.5044 0.7758 0.504 0.000 0.000 0.032 NA
#> SRR1044485 2 0.0000 0.9069 0.000 1.000 0.000 0.000 NA
#> SRR1044487 2 0.0000 0.9069 0.000 1.000 0.000 0.000 NA
#> SRR1044488 2 0.0000 0.9069 0.000 1.000 0.000 0.000 NA
#> SRR1044489 2 0.0000 0.9069 0.000 1.000 0.000 0.000 NA
#> SRR1044490 1 0.0880 0.7925 0.968 0.000 0.000 0.032 NA
#> SRR1044491 1 0.5068 0.8096 0.636 0.000 0.012 0.032 NA
#> SRR1044492 1 0.4046 0.8219 0.780 0.000 0.008 0.032 NA
#> SRR1044493 1 0.4726 0.8179 0.712 0.000 0.016 0.032 NA
#> SRR1044494 2 0.0000 0.9069 0.000 1.000 0.000 0.000 NA
#> SRR1044496 2 0.0162 0.9062 0.004 0.996 0.000 0.000 NA
#> SRR1044495 2 0.0000 0.9069 0.000 1.000 0.000 0.000 NA
#> SRR1044497 4 0.0000 0.9155 0.000 0.000 0.000 1.000 NA
#> SRR1044499 2 0.6142 0.2434 0.004 0.580 0.232 0.000 NA
#> SRR1044498 1 0.5256 0.7819 0.540 0.000 0.008 0.032 NA
#> SRR1044500 2 0.0000 0.9069 0.000 1.000 0.000 0.000 NA
#> SRR1044501 2 0.1638 0.8769 0.004 0.932 0.000 0.000 NA
#> SRR1044502 2 0.6273 -0.0225 0.000 0.512 0.316 0.000 NA
#> SRR1044503 4 0.0000 0.9155 0.000 0.000 0.000 1.000 NA
#> SRR1044504 4 0.0000 0.9155 0.000 0.000 0.000 1.000 NA
#> SRR1044505 1 0.5148 0.7661 0.668 0.000 0.008 0.060 NA
#> SRR1044506 4 0.1549 0.9038 0.000 0.000 0.016 0.944 NA
#> SRR1044507 4 0.5140 0.7287 0.000 0.000 0.084 0.664 NA
#> SRR1044508 4 0.4612 0.7869 0.000 0.000 0.084 0.736 NA
#> SRR1044509 4 0.4612 0.7869 0.000 0.000 0.084 0.736 NA
#> SRR1044510 3 0.4869 0.8975 0.016 0.140 0.748 0.000 NA
#> SRR1044511 3 0.4155 0.9005 0.016 0.140 0.796 0.000 NA
#> SRR1044512 3 0.4155 0.9005 0.016 0.140 0.796 0.000 NA
#> SRR1044513 2 0.4642 0.6367 0.004 0.752 0.140 0.000 NA
#> SRR1044514 3 0.4155 0.9005 0.016 0.140 0.796 0.000 NA
#> SRR1044515 2 0.4447 0.6638 0.004 0.768 0.136 0.000 NA
#> SRR1044516 2 0.0324 0.9056 0.004 0.992 0.000 0.000 NA
#> SRR1044517 3 0.4919 0.8970 0.016 0.140 0.744 0.000 NA
#> SRR1044518 3 0.4155 0.9005 0.016 0.140 0.796 0.000 NA
#> SRR1044519 3 0.3916 0.9012 0.004 0.136 0.804 0.000 NA
#> SRR1044520 3 0.3849 0.9012 0.004 0.136 0.808 0.000 NA
#> SRR1044521 2 0.0162 0.9062 0.004 0.996 0.000 0.000 NA
#> SRR1044522 2 0.0771 0.8911 0.004 0.976 0.000 0.000 NA
#> SRR1044523 2 0.3281 0.7867 0.000 0.848 0.060 0.000 NA
#> SRR1044524 3 0.5653 0.8254 0.000 0.208 0.632 0.000 NA
#> SRR1044525 4 0.0000 0.9155 0.000 0.000 0.000 1.000 NA
#> SRR1044526 1 0.5735 0.7649 0.568 0.000 0.008 0.076 NA
#> SRR1044527 2 0.0510 0.9037 0.000 0.984 0.000 0.000 NA
#> SRR1044528 2 0.0162 0.9062 0.004 0.996 0.000 0.000 NA
#> SRR1044529 2 0.0162 0.9062 0.004 0.996 0.000 0.000 NA
#> SRR1044530 1 0.4614 0.8192 0.728 0.000 0.016 0.032 NA
#> SRR1044531 1 0.2299 0.8063 0.912 0.000 0.004 0.032 NA
#> SRR1044533 1 0.1041 0.7941 0.964 0.000 0.000 0.032 NA
#> SRR1044532 1 0.4643 0.8191 0.724 0.000 0.016 0.032 NA
#> SRR1044534 2 0.0000 0.9069 0.000 1.000 0.000 0.000 NA
#> SRR1044535 3 0.5761 0.8535 0.004 0.180 0.636 0.000 NA
#> SRR1044536 2 0.0162 0.9062 0.004 0.996 0.000 0.000 NA
#> SRR1044537 1 0.5189 0.7736 0.500 0.000 0.004 0.032 NA
#> SRR1044538 1 0.4671 0.8183 0.720 0.000 0.016 0.032 NA
#> SRR1044539 4 0.0579 0.9134 0.000 0.000 0.008 0.984 NA
#> SRR1044540 1 0.1168 0.7923 0.960 0.000 0.008 0.032 NA
#> SRR1044541 2 0.4373 0.6894 0.000 0.760 0.080 0.000 NA
#> SRR1044542 1 0.4726 0.8178 0.712 0.000 0.016 0.032 NA
#> SRR1044543 1 0.1168 0.7923 0.960 0.000 0.008 0.032 NA
#> SRR1044544 2 0.6158 0.1617 0.000 0.552 0.264 0.000 NA
#> SRR1044545 4 0.1764 0.8883 0.000 0.000 0.008 0.928 NA
#> SRR1044546 1 0.5187 0.7762 0.504 0.000 0.004 0.032 NA
#> SRR1044547 4 0.3934 0.7718 0.036 0.000 0.008 0.796 NA
#> SRR1044548 1 0.5044 0.7758 0.504 0.000 0.000 0.032 NA
#> SRR1044549 2 0.1638 0.8712 0.000 0.932 0.004 0.000 NA
#> SRR1044550 2 0.0000 0.9069 0.000 1.000 0.000 0.000 NA
#> SRR1044551 2 0.0000 0.9069 0.000 1.000 0.000 0.000 NA
#> SRR1044552 4 0.0000 0.9155 0.000 0.000 0.000 1.000 NA
#> SRR1044553 4 0.0000 0.9155 0.000 0.000 0.000 1.000 NA
#> SRR1044554 1 0.5187 0.7762 0.504 0.000 0.004 0.032 NA
#> SRR1044555 3 0.5354 0.8756 0.000 0.140 0.668 0.000 NA
#> SRR1044556 4 0.0451 0.9141 0.000 0.000 0.004 0.988 NA
#> SRR1044557 1 0.5187 0.7762 0.504 0.000 0.004 0.032 NA
#> SRR1044558 4 0.0000 0.9155 0.000 0.000 0.000 1.000 NA
#> SRR1044559 1 0.5044 0.7758 0.504 0.000 0.000 0.032 NA
#> SRR1044561 4 0.0000 0.9155 0.000 0.000 0.000 1.000 NA
#> SRR1044560 2 0.1638 0.8769 0.004 0.932 0.000 0.000 NA
#> SRR1044562 1 0.5044 0.7758 0.504 0.000 0.000 0.032 NA
#> SRR1044563 4 0.0451 0.9141 0.000 0.000 0.004 0.988 NA
#> SRR1044564 1 0.5495 0.7619 0.480 0.000 0.004 0.052 NA
#> SRR1044565 2 0.0000 0.9069 0.000 1.000 0.000 0.000 NA
#> SRR1044566 2 0.1571 0.8794 0.004 0.936 0.000 0.000 NA
#> SRR1044567 1 0.4614 0.8192 0.728 0.000 0.016 0.032 NA
#> SRR1044568 4 0.1483 0.9037 0.008 0.000 0.012 0.952 NA
#> SRR1044569 1 0.1329 0.7939 0.956 0.000 0.008 0.032 NA
#> SRR1044570 1 0.4753 0.8176 0.708 0.000 0.016 0.032 NA
#> SRR1044571 1 0.1168 0.7923 0.960 0.000 0.008 0.032 NA
#> SRR1044572 1 0.0880 0.7925 0.968 0.000 0.000 0.032 NA
#> SRR1044573 1 0.2040 0.7976 0.928 0.000 0.008 0.032 NA
#> SRR1044574 1 0.1041 0.7924 0.964 0.000 0.004 0.032 NA
#> SRR1044575 1 0.1041 0.7924 0.964 0.000 0.004 0.032 NA
#> SRR1044576 2 0.0000 0.9069 0.000 1.000 0.000 0.000 NA
#> SRR1044577 2 0.0000 0.9069 0.000 1.000 0.000 0.000 NA
#> SRR1044578 2 0.0000 0.9069 0.000 1.000 0.000 0.000 NA
#> SRR1044579 4 0.0000 0.9155 0.000 0.000 0.000 1.000 NA
#> SRR1044580 4 0.6442 0.0115 0.364 0.000 0.008 0.484 NA
#> SRR1044581 4 0.0000 0.9155 0.000 0.000 0.000 1.000 NA
#> SRR1044582 1 0.5187 0.7761 0.504 0.000 0.004 0.032 NA
#> SRR1044583 4 0.0000 0.9155 0.000 0.000 0.000 1.000 NA
#> SRR1044584 4 0.2661 0.8592 0.052 0.000 0.008 0.896 NA
#> SRR1044585 4 0.0000 0.9155 0.000 0.000 0.000 1.000 NA
#> SRR1044586 1 0.5044 0.7758 0.504 0.000 0.000 0.032 NA
#> SRR1044587 4 0.1648 0.9035 0.000 0.000 0.020 0.940 NA
#> SRR1044588 4 0.1549 0.9038 0.000 0.000 0.016 0.944 NA
#> SRR1044589 4 0.1549 0.9038 0.000 0.000 0.016 0.944 NA
#> SRR1044590 4 0.1549 0.9038 0.000 0.000 0.016 0.944 NA
#> SRR1044591 4 0.1549 0.9038 0.000 0.000 0.016 0.944 NA
#> SRR1044592 4 0.4522 0.7902 0.000 0.000 0.080 0.744 NA
#> SRR1044593 4 0.1549 0.9038 0.000 0.000 0.016 0.944 NA
#> SRR1044594 4 0.1469 0.9049 0.000 0.000 0.016 0.948 NA
#> SRR1044595 4 0.7343 0.4155 0.112 0.000 0.088 0.464 NA
#> SRR1044596 4 0.4577 0.7893 0.000 0.000 0.084 0.740 NA
#> SRR1044597 1 0.5920 0.7642 0.524 0.000 0.008 0.084 NA
#> SRR1044598 1 0.5392 0.7758 0.500 0.000 0.012 0.032 NA
#> SRR1044599 1 0.5392 0.7758 0.500 0.000 0.012 0.032 NA
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.0806 0.89511 0.000 0.972 0.000 0.000 0.020 0.008
#> SRR1044416 2 0.0146 0.90232 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044417 2 0.0146 0.90249 0.004 0.996 0.000 0.000 0.000 0.000
#> SRR1044418 2 0.0146 0.90249 0.004 0.996 0.000 0.000 0.000 0.000
#> SRR1044420 2 0.0146 0.90232 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044419 2 0.2537 0.83759 0.000 0.872 0.000 0.000 0.096 0.032
#> SRR1044421 2 0.0964 0.89505 0.004 0.968 0.000 0.000 0.012 0.016
#> SRR1044422 2 0.0146 0.90199 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1044423 2 0.0363 0.90186 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR1044424 2 0.0146 0.90199 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1044425 4 0.5863 -0.11532 0.076 0.000 0.012 0.556 0.032 0.324
#> SRR1044426 6 0.6423 0.71906 0.268 0.000 0.060 0.004 0.136 0.532
#> SRR1044427 1 0.3538 0.59270 0.828 0.000 0.016 0.016 0.028 0.112
#> SRR1044428 6 0.6544 0.70738 0.280 0.000 0.064 0.004 0.140 0.512
#> SRR1044429 6 0.5962 0.77740 0.316 0.000 0.028 0.036 0.056 0.564
#> SRR1044430 6 0.6600 0.70218 0.280 0.000 0.064 0.004 0.148 0.504
#> SRR1044431 6 0.4885 0.84888 0.284 0.000 0.008 0.028 0.028 0.652
#> SRR1044433 4 0.3797 -0.29898 0.000 0.000 0.000 0.580 0.420 0.000
#> SRR1044432 6 0.6530 0.70581 0.276 0.000 0.064 0.004 0.140 0.516
#> SRR1044434 4 0.0000 0.77644 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044435 4 0.0000 0.77644 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044436 4 0.1332 0.75070 0.008 0.000 0.012 0.952 0.028 0.000
#> SRR1044437 4 0.0000 0.77644 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044439 4 0.0993 0.75989 0.000 0.000 0.012 0.964 0.024 0.000
#> SRR1044438 4 0.1396 0.75152 0.012 0.000 0.008 0.952 0.024 0.004
#> SRR1044440 4 0.0000 0.77644 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044441 4 0.0000 0.77644 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044442 4 0.3930 -0.31275 0.004 0.000 0.000 0.576 0.420 0.000
#> SRR1044443 4 0.4196 -0.33861 0.004 0.000 0.004 0.568 0.420 0.004
#> SRR1044444 4 0.0000 0.77644 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044445 4 0.1812 0.71805 0.000 0.000 0.000 0.912 0.080 0.008
#> SRR1044446 3 0.3092 0.83302 0.000 0.120 0.840 0.000 0.028 0.012
#> SRR1044447 2 0.5590 0.08585 0.000 0.536 0.364 0.000 0.052 0.048
#> SRR1044449 3 0.4104 0.83657 0.000 0.120 0.784 0.000 0.056 0.040
#> SRR1044448 3 0.3192 0.83327 0.000 0.120 0.836 0.000 0.020 0.024
#> SRR1044450 3 0.3192 0.83316 0.000 0.120 0.836 0.000 0.024 0.020
#> SRR1044451 3 0.5721 0.49658 0.000 0.356 0.532 0.000 0.064 0.048
#> SRR1044452 3 0.5784 0.82078 0.000 0.120 0.644 0.000 0.144 0.092
#> SRR1044453 3 0.5827 0.81984 0.000 0.120 0.640 0.000 0.144 0.096
#> SRR1044454 3 0.6005 0.81344 0.000 0.120 0.620 0.000 0.156 0.104
#> SRR1044455 2 0.2485 0.85056 0.004 0.884 0.004 0.000 0.088 0.020
#> SRR1044456 2 0.1196 0.86620 0.040 0.952 0.000 0.000 0.008 0.000
#> SRR1044457 2 0.4436 0.70104 0.000 0.740 0.024 0.000 0.168 0.068
#> SRR1044458 2 0.2894 0.82190 0.000 0.852 0.004 0.000 0.108 0.036
#> SRR1044459 3 0.5431 0.82948 0.000 0.120 0.680 0.000 0.120 0.080
#> SRR1044460 2 0.0000 0.90248 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044461 2 0.2487 0.84045 0.000 0.876 0.000 0.000 0.092 0.032
#> SRR1044462 1 0.4539 0.45219 0.744 0.000 0.024 0.176 0.036 0.020
#> SRR1044463 1 0.5701 0.11102 0.536 0.000 0.020 0.004 0.092 0.348
#> SRR1044464 4 0.1232 0.76167 0.004 0.000 0.016 0.956 0.024 0.000
#> SRR1044466 1 0.5675 0.19772 0.556 0.000 0.020 0.004 0.096 0.324
#> SRR1044465 6 0.4225 0.88260 0.308 0.000 0.004 0.004 0.020 0.664
#> SRR1044467 6 0.4127 0.88422 0.304 0.000 0.004 0.004 0.016 0.672
#> SRR1044468 2 0.1092 0.89068 0.000 0.960 0.000 0.000 0.020 0.020
#> SRR1044469 3 0.7075 0.45413 0.000 0.356 0.356 0.000 0.204 0.084
#> SRR1044470 1 0.6038 0.11794 0.532 0.000 0.032 0.004 0.116 0.316
#> SRR1044471 6 0.4406 0.88094 0.308 0.000 0.008 0.004 0.024 0.656
#> SRR1044472 1 0.5959 0.10850 0.524 0.000 0.028 0.004 0.108 0.336
#> SRR1044473 6 0.4511 0.87336 0.316 0.000 0.008 0.004 0.028 0.644
#> SRR1044474 2 0.0000 0.90248 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044475 3 0.7097 0.48665 0.000 0.348 0.368 0.000 0.192 0.092
#> SRR1044476 2 0.2894 0.82190 0.000 0.852 0.004 0.000 0.108 0.036
#> SRR1044477 2 0.0000 0.90248 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044478 2 0.1049 0.89057 0.000 0.960 0.000 0.000 0.032 0.008
#> SRR1044479 2 0.0508 0.89509 0.012 0.984 0.000 0.000 0.004 0.000
#> SRR1044480 4 0.3843 0.50345 0.124 0.000 0.020 0.804 0.044 0.008
#> SRR1044481 1 0.1553 0.66950 0.944 0.000 0.012 0.004 0.008 0.032
#> SRR1044482 2 0.0146 0.90199 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1044483 4 0.1667 0.74179 0.008 0.000 0.008 0.936 0.044 0.004
#> SRR1044484 1 0.1210 0.67704 0.960 0.000 0.020 0.004 0.008 0.008
#> SRR1044486 1 0.0582 0.68562 0.984 0.000 0.004 0.004 0.004 0.004
#> SRR1044485 2 0.0000 0.90248 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044487 2 0.0000 0.90248 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044488 2 0.0146 0.90249 0.004 0.996 0.000 0.000 0.000 0.000
#> SRR1044489 2 0.0000 0.90248 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044490 6 0.3721 0.88375 0.308 0.000 0.000 0.004 0.004 0.684
#> SRR1044491 1 0.3835 0.54230 0.784 0.000 0.008 0.004 0.048 0.156
#> SRR1044492 1 0.5071 0.00719 0.552 0.000 0.004 0.004 0.060 0.380
#> SRR1044493 1 0.5042 0.37315 0.652 0.000 0.012 0.004 0.080 0.252
#> SRR1044494 2 0.0000 0.90248 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044496 2 0.0146 0.90199 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1044495 2 0.0000 0.90248 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044497 4 0.0000 0.77644 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044499 2 0.6777 -0.01995 0.000 0.488 0.216 0.000 0.216 0.080
#> SRR1044498 1 0.2602 0.64617 0.892 0.000 0.020 0.004 0.032 0.052
#> SRR1044500 2 0.0260 0.90203 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044501 2 0.2848 0.82520 0.000 0.856 0.004 0.000 0.104 0.036
#> SRR1044502 2 0.6492 -0.28248 0.000 0.416 0.380 0.000 0.160 0.044
#> SRR1044503 4 0.0000 0.77644 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044504 4 0.0146 0.77517 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1044505 1 0.5201 0.30364 0.676 0.000 0.028 0.020 0.052 0.224
#> SRR1044506 4 0.1812 0.71805 0.000 0.000 0.000 0.912 0.080 0.008
#> SRR1044507 5 0.5392 0.55147 0.112 0.000 0.000 0.444 0.444 0.000
#> SRR1044508 4 0.3930 -0.31275 0.004 0.000 0.000 0.576 0.420 0.000
#> SRR1044509 4 0.3930 -0.31275 0.004 0.000 0.000 0.576 0.420 0.000
#> SRR1044510 3 0.5560 0.81935 0.000 0.120 0.656 0.000 0.060 0.164
#> SRR1044511 3 0.4899 0.82298 0.000 0.120 0.712 0.000 0.032 0.136
#> SRR1044512 3 0.4899 0.82298 0.000 0.120 0.712 0.000 0.032 0.136
#> SRR1044513 2 0.4987 0.60733 0.000 0.712 0.152 0.000 0.072 0.064
#> SRR1044514 3 0.4899 0.82298 0.000 0.120 0.712 0.000 0.032 0.136
#> SRR1044515 2 0.4795 0.65377 0.000 0.736 0.112 0.000 0.092 0.060
#> SRR1044516 2 0.0291 0.90208 0.004 0.992 0.000 0.000 0.004 0.000
#> SRR1044517 3 0.5613 0.81890 0.000 0.120 0.652 0.000 0.064 0.164
#> SRR1044518 3 0.4899 0.82298 0.000 0.120 0.712 0.000 0.032 0.136
#> SRR1044519 3 0.3192 0.83327 0.000 0.120 0.836 0.000 0.020 0.024
#> SRR1044520 3 0.3269 0.83307 0.000 0.120 0.832 0.000 0.020 0.028
#> SRR1044521 2 0.0405 0.90086 0.004 0.988 0.000 0.000 0.008 0.000
#> SRR1044522 2 0.0717 0.89021 0.016 0.976 0.000 0.000 0.008 0.000
#> SRR1044523 2 0.3947 0.75747 0.000 0.804 0.052 0.000 0.080 0.064
#> SRR1044524 3 0.5807 0.79288 0.000 0.160 0.628 0.000 0.152 0.060
#> SRR1044525 4 0.0000 0.77644 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044526 1 0.4134 0.53773 0.796 0.000 0.028 0.024 0.036 0.116
#> SRR1044527 2 0.0603 0.89884 0.000 0.980 0.000 0.000 0.004 0.016
#> SRR1044528 2 0.0767 0.89694 0.004 0.976 0.000 0.000 0.012 0.008
#> SRR1044529 2 0.0146 0.90199 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1044530 1 0.5675 0.19772 0.556 0.000 0.020 0.004 0.096 0.324
#> SRR1044531 6 0.4237 0.80937 0.356 0.000 0.004 0.004 0.012 0.624
#> SRR1044533 6 0.4106 0.87534 0.312 0.000 0.000 0.004 0.020 0.664
#> SRR1044532 1 0.5637 0.23493 0.568 0.000 0.020 0.004 0.096 0.312
#> SRR1044534 2 0.0146 0.90249 0.004 0.996 0.000 0.000 0.000 0.000
#> SRR1044535 3 0.5579 0.80369 0.000 0.140 0.656 0.000 0.144 0.060
#> SRR1044536 2 0.0291 0.90194 0.004 0.992 0.000 0.000 0.004 0.000
#> SRR1044537 1 0.1406 0.67496 0.952 0.000 0.016 0.008 0.020 0.004
#> SRR1044538 1 0.5548 0.28664 0.592 0.000 0.020 0.004 0.096 0.288
#> SRR1044539 4 0.1313 0.75163 0.004 0.000 0.016 0.952 0.028 0.000
#> SRR1044540 6 0.3684 0.88460 0.300 0.000 0.000 0.004 0.004 0.692
#> SRR1044541 2 0.5459 0.57714 0.000 0.664 0.084 0.000 0.180 0.072
#> SRR1044542 1 0.5498 0.31332 0.604 0.000 0.020 0.004 0.096 0.276
#> SRR1044543 6 0.3791 0.88431 0.300 0.000 0.000 0.004 0.008 0.688
#> SRR1044544 2 0.7033 -0.21818 0.000 0.428 0.272 0.000 0.212 0.088
#> SRR1044545 4 0.3157 0.59301 0.088 0.000 0.016 0.848 0.048 0.000
#> SRR1044546 1 0.0665 0.68619 0.980 0.000 0.008 0.004 0.008 0.000
#> SRR1044547 4 0.4652 0.07180 0.252 0.000 0.020 0.680 0.048 0.000
#> SRR1044548 1 0.0436 0.68630 0.988 0.000 0.004 0.004 0.004 0.000
#> SRR1044549 2 0.2259 0.85413 0.000 0.904 0.008 0.000 0.044 0.044
#> SRR1044550 2 0.0000 0.90248 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044551 2 0.0146 0.90249 0.004 0.996 0.000 0.000 0.000 0.000
#> SRR1044552 4 0.0000 0.77644 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044553 4 0.0146 0.77531 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1044554 1 0.1007 0.68590 0.968 0.000 0.008 0.004 0.016 0.004
#> SRR1044555 3 0.5821 0.80844 0.000 0.120 0.632 0.000 0.172 0.076
#> SRR1044556 4 0.0993 0.75989 0.000 0.000 0.012 0.964 0.024 0.000
#> SRR1044557 1 0.0665 0.68619 0.980 0.000 0.008 0.004 0.008 0.000
#> SRR1044558 4 0.0291 0.77410 0.000 0.000 0.004 0.992 0.004 0.000
#> SRR1044559 1 0.0551 0.68634 0.984 0.000 0.004 0.004 0.008 0.000
#> SRR1044561 4 0.0000 0.77644 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044560 2 0.2894 0.82190 0.000 0.852 0.004 0.000 0.108 0.036
#> SRR1044562 1 0.0551 0.68634 0.984 0.000 0.004 0.004 0.008 0.000
#> SRR1044563 4 0.0993 0.75989 0.000 0.000 0.012 0.964 0.024 0.000
#> SRR1044564 1 0.2378 0.64514 0.908 0.000 0.024 0.032 0.028 0.008
#> SRR1044565 2 0.0000 0.90248 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044566 2 0.2586 0.83354 0.000 0.868 0.000 0.000 0.100 0.032
#> SRR1044567 1 0.5619 0.26918 0.580 0.000 0.020 0.004 0.100 0.296
#> SRR1044568 4 0.2776 0.68937 0.032 0.000 0.020 0.888 0.044 0.016
#> SRR1044569 6 0.4147 0.88575 0.304 0.000 0.000 0.004 0.024 0.668
#> SRR1044570 1 0.5498 0.31332 0.604 0.000 0.020 0.004 0.096 0.276
#> SRR1044571 6 0.3954 0.88458 0.296 0.000 0.000 0.004 0.016 0.684
#> SRR1044572 6 0.3721 0.88361 0.308 0.000 0.004 0.004 0.000 0.684
#> SRR1044573 6 0.4774 0.79893 0.368 0.000 0.012 0.004 0.028 0.588
#> SRR1044574 6 0.4088 0.88227 0.308 0.000 0.000 0.004 0.020 0.668
#> SRR1044575 6 0.4530 0.88258 0.304 0.000 0.008 0.004 0.032 0.652
#> SRR1044576 2 0.0146 0.90249 0.004 0.996 0.000 0.000 0.000 0.000
#> SRR1044577 2 0.0000 0.90248 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044578 2 0.0000 0.90248 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044579 4 0.0000 0.77644 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044580 4 0.6353 -0.27420 0.360 0.000 0.024 0.496 0.044 0.076
#> SRR1044581 4 0.0146 0.77517 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1044582 1 0.0405 0.68569 0.988 0.000 0.008 0.004 0.000 0.000
#> SRR1044583 4 0.0000 0.77644 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044584 4 0.2976 0.65219 0.056 0.000 0.016 0.876 0.024 0.028
#> SRR1044585 4 0.0000 0.77644 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044586 1 0.0551 0.68393 0.984 0.000 0.008 0.004 0.000 0.004
#> SRR1044587 4 0.1866 0.71482 0.000 0.000 0.000 0.908 0.084 0.008
#> SRR1044588 4 0.1812 0.71805 0.000 0.000 0.000 0.912 0.080 0.008
#> SRR1044589 4 0.1812 0.71805 0.000 0.000 0.000 0.912 0.080 0.008
#> SRR1044590 4 0.1812 0.71805 0.000 0.000 0.000 0.912 0.080 0.008
#> SRR1044591 4 0.1812 0.71805 0.000 0.000 0.000 0.912 0.080 0.008
#> SRR1044592 4 0.3797 -0.29898 0.000 0.000 0.000 0.580 0.420 0.000
#> SRR1044593 4 0.1812 0.71805 0.000 0.000 0.000 0.912 0.080 0.008
#> SRR1044594 4 0.1812 0.71805 0.000 0.000 0.000 0.912 0.080 0.008
#> SRR1044595 5 0.5944 0.65939 0.244 0.000 0.000 0.304 0.452 0.000
#> SRR1044596 4 0.3930 -0.31275 0.004 0.000 0.000 0.576 0.420 0.000
#> SRR1044597 1 0.3610 0.61413 0.840 0.000 0.020 0.036 0.036 0.068
#> SRR1044598 1 0.1406 0.68143 0.952 0.000 0.016 0.004 0.020 0.008
#> SRR1044599 1 0.1406 0.68143 0.952 0.000 0.016 0.004 0.020 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)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.4925 0.508 0.508
#> 3 3 1.000 0.979 0.990 0.3332 0.835 0.676
#> 4 4 0.955 0.930 0.970 0.1347 0.912 0.743
#> 5 5 0.873 0.836 0.894 0.0461 0.973 0.894
#> 6 6 0.839 0.816 0.888 0.0417 0.957 0.817
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0.000 1.000 0.000 1.000
#> SRR1044416 2 0.000 1.000 0.000 1.000
#> SRR1044417 2 0.000 1.000 0.000 1.000
#> SRR1044418 2 0.000 1.000 0.000 1.000
#> SRR1044420 2 0.000 1.000 0.000 1.000
#> SRR1044419 2 0.000 1.000 0.000 1.000
#> SRR1044421 2 0.000 1.000 0.000 1.000
#> SRR1044422 2 0.000 1.000 0.000 1.000
#> SRR1044423 2 0.000 1.000 0.000 1.000
#> SRR1044424 2 0.000 1.000 0.000 1.000
#> SRR1044425 1 0.000 1.000 1.000 0.000
#> SRR1044426 1 0.000 1.000 1.000 0.000
#> SRR1044427 1 0.000 1.000 1.000 0.000
#> SRR1044428 1 0.000 1.000 1.000 0.000
#> SRR1044429 1 0.000 1.000 1.000 0.000
#> SRR1044430 1 0.000 1.000 1.000 0.000
#> SRR1044431 1 0.000 1.000 1.000 0.000
#> SRR1044433 1 0.000 1.000 1.000 0.000
#> SRR1044432 1 0.000 1.000 1.000 0.000
#> SRR1044434 1 0.000 1.000 1.000 0.000
#> SRR1044435 1 0.000 1.000 1.000 0.000
#> SRR1044436 1 0.000 1.000 1.000 0.000
#> SRR1044437 1 0.000 1.000 1.000 0.000
#> SRR1044439 1 0.000 1.000 1.000 0.000
#> SRR1044438 1 0.000 1.000 1.000 0.000
#> SRR1044440 1 0.000 1.000 1.000 0.000
#> SRR1044441 1 0.000 1.000 1.000 0.000
#> SRR1044442 1 0.000 1.000 1.000 0.000
#> SRR1044443 1 0.118 0.984 0.984 0.016
#> SRR1044444 1 0.000 1.000 1.000 0.000
#> SRR1044445 1 0.000 1.000 1.000 0.000
#> SRR1044446 2 0.000 1.000 0.000 1.000
#> SRR1044447 2 0.000 1.000 0.000 1.000
#> SRR1044449 2 0.000 1.000 0.000 1.000
#> SRR1044448 2 0.000 1.000 0.000 1.000
#> SRR1044450 2 0.000 1.000 0.000 1.000
#> SRR1044451 2 0.000 1.000 0.000 1.000
#> SRR1044452 2 0.000 1.000 0.000 1.000
#> SRR1044453 2 0.000 1.000 0.000 1.000
#> SRR1044454 2 0.000 1.000 0.000 1.000
#> SRR1044455 2 0.000 1.000 0.000 1.000
#> SRR1044456 2 0.000 1.000 0.000 1.000
#> SRR1044457 2 0.000 1.000 0.000 1.000
#> SRR1044458 2 0.000 1.000 0.000 1.000
#> SRR1044459 2 0.000 1.000 0.000 1.000
#> SRR1044460 2 0.000 1.000 0.000 1.000
#> SRR1044461 2 0.000 1.000 0.000 1.000
#> SRR1044462 1 0.000 1.000 1.000 0.000
#> SRR1044463 1 0.000 1.000 1.000 0.000
#> SRR1044464 1 0.000 1.000 1.000 0.000
#> SRR1044466 1 0.000 1.000 1.000 0.000
#> SRR1044465 1 0.000 1.000 1.000 0.000
#> SRR1044467 1 0.000 1.000 1.000 0.000
#> SRR1044468 2 0.000 1.000 0.000 1.000
#> SRR1044469 2 0.000 1.000 0.000 1.000
#> SRR1044470 1 0.000 1.000 1.000 0.000
#> SRR1044471 1 0.000 1.000 1.000 0.000
#> SRR1044472 1 0.000 1.000 1.000 0.000
#> SRR1044473 1 0.000 1.000 1.000 0.000
#> SRR1044474 2 0.000 1.000 0.000 1.000
#> SRR1044475 2 0.000 1.000 0.000 1.000
#> SRR1044476 2 0.000 1.000 0.000 1.000
#> SRR1044477 2 0.000 1.000 0.000 1.000
#> SRR1044478 2 0.000 1.000 0.000 1.000
#> SRR1044479 2 0.000 1.000 0.000 1.000
#> SRR1044480 1 0.000 1.000 1.000 0.000
#> SRR1044481 1 0.000 1.000 1.000 0.000
#> SRR1044482 2 0.000 1.000 0.000 1.000
#> SRR1044483 1 0.000 1.000 1.000 0.000
#> SRR1044484 1 0.000 1.000 1.000 0.000
#> SRR1044486 1 0.000 1.000 1.000 0.000
#> SRR1044485 2 0.000 1.000 0.000 1.000
#> SRR1044487 2 0.000 1.000 0.000 1.000
#> SRR1044488 2 0.000 1.000 0.000 1.000
#> SRR1044489 2 0.000 1.000 0.000 1.000
#> SRR1044490 1 0.000 1.000 1.000 0.000
#> SRR1044491 1 0.000 1.000 1.000 0.000
#> SRR1044492 1 0.000 1.000 1.000 0.000
#> SRR1044493 1 0.000 1.000 1.000 0.000
#> SRR1044494 2 0.000 1.000 0.000 1.000
#> SRR1044496 2 0.000 1.000 0.000 1.000
#> SRR1044495 2 0.000 1.000 0.000 1.000
#> SRR1044497 1 0.000 1.000 1.000 0.000
#> SRR1044499 2 0.000 1.000 0.000 1.000
#> SRR1044498 1 0.000 1.000 1.000 0.000
#> SRR1044500 2 0.000 1.000 0.000 1.000
#> SRR1044501 2 0.000 1.000 0.000 1.000
#> SRR1044502 2 0.000 1.000 0.000 1.000
#> SRR1044503 1 0.000 1.000 1.000 0.000
#> SRR1044504 1 0.000 1.000 1.000 0.000
#> SRR1044505 1 0.000 1.000 1.000 0.000
#> SRR1044506 1 0.000 1.000 1.000 0.000
#> SRR1044507 1 0.000 1.000 1.000 0.000
#> SRR1044508 1 0.000 1.000 1.000 0.000
#> SRR1044509 1 0.000 1.000 1.000 0.000
#> SRR1044510 2 0.000 1.000 0.000 1.000
#> SRR1044511 2 0.000 1.000 0.000 1.000
#> SRR1044512 2 0.000 1.000 0.000 1.000
#> SRR1044513 2 0.000 1.000 0.000 1.000
#> SRR1044514 2 0.000 1.000 0.000 1.000
#> SRR1044515 2 0.000 1.000 0.000 1.000
#> SRR1044516 2 0.000 1.000 0.000 1.000
#> SRR1044517 2 0.000 1.000 0.000 1.000
#> SRR1044518 2 0.000 1.000 0.000 1.000
#> SRR1044519 2 0.000 1.000 0.000 1.000
#> SRR1044520 2 0.000 1.000 0.000 1.000
#> SRR1044521 2 0.000 1.000 0.000 1.000
#> SRR1044522 2 0.000 1.000 0.000 1.000
#> SRR1044523 2 0.000 1.000 0.000 1.000
#> SRR1044524 2 0.000 1.000 0.000 1.000
#> SRR1044525 1 0.000 1.000 1.000 0.000
#> SRR1044526 1 0.000 1.000 1.000 0.000
#> SRR1044527 2 0.000 1.000 0.000 1.000
#> SRR1044528 2 0.000 1.000 0.000 1.000
#> SRR1044529 2 0.000 1.000 0.000 1.000
#> SRR1044530 1 0.000 1.000 1.000 0.000
#> SRR1044531 1 0.000 1.000 1.000 0.000
#> SRR1044533 1 0.000 1.000 1.000 0.000
#> SRR1044532 1 0.000 1.000 1.000 0.000
#> SRR1044534 2 0.000 1.000 0.000 1.000
#> SRR1044535 2 0.000 1.000 0.000 1.000
#> SRR1044536 2 0.000 1.000 0.000 1.000
#> SRR1044537 1 0.000 1.000 1.000 0.000
#> SRR1044538 1 0.000 1.000 1.000 0.000
#> SRR1044539 1 0.000 1.000 1.000 0.000
#> SRR1044540 1 0.000 1.000 1.000 0.000
#> SRR1044541 2 0.000 1.000 0.000 1.000
#> SRR1044542 1 0.000 1.000 1.000 0.000
#> SRR1044543 1 0.000 1.000 1.000 0.000
#> SRR1044544 2 0.000 1.000 0.000 1.000
#> SRR1044545 1 0.000 1.000 1.000 0.000
#> SRR1044546 1 0.000 1.000 1.000 0.000
#> SRR1044547 1 0.000 1.000 1.000 0.000
#> SRR1044548 1 0.000 1.000 1.000 0.000
#> SRR1044549 2 0.000 1.000 0.000 1.000
#> SRR1044550 2 0.000 1.000 0.000 1.000
#> SRR1044551 2 0.000 1.000 0.000 1.000
#> SRR1044552 1 0.000 1.000 1.000 0.000
#> SRR1044553 1 0.000 1.000 1.000 0.000
#> SRR1044554 1 0.000 1.000 1.000 0.000
#> SRR1044555 2 0.000 1.000 0.000 1.000
#> SRR1044556 1 0.000 1.000 1.000 0.000
#> SRR1044557 1 0.000 1.000 1.000 0.000
#> SRR1044558 1 0.000 1.000 1.000 0.000
#> SRR1044559 1 0.000 1.000 1.000 0.000
#> SRR1044561 1 0.000 1.000 1.000 0.000
#> SRR1044560 2 0.000 1.000 0.000 1.000
#> SRR1044562 1 0.000 1.000 1.000 0.000
#> SRR1044563 1 0.000 1.000 1.000 0.000
#> SRR1044564 1 0.000 1.000 1.000 0.000
#> SRR1044565 2 0.000 1.000 0.000 1.000
#> SRR1044566 2 0.000 1.000 0.000 1.000
#> SRR1044567 1 0.000 1.000 1.000 0.000
#> SRR1044568 1 0.000 1.000 1.000 0.000
#> SRR1044569 1 0.000 1.000 1.000 0.000
#> SRR1044570 1 0.000 1.000 1.000 0.000
#> SRR1044571 1 0.000 1.000 1.000 0.000
#> SRR1044572 1 0.000 1.000 1.000 0.000
#> SRR1044573 1 0.000 1.000 1.000 0.000
#> SRR1044574 1 0.000 1.000 1.000 0.000
#> SRR1044575 1 0.000 1.000 1.000 0.000
#> SRR1044576 2 0.000 1.000 0.000 1.000
#> SRR1044577 2 0.000 1.000 0.000 1.000
#> SRR1044578 2 0.000 1.000 0.000 1.000
#> SRR1044579 1 0.000 1.000 1.000 0.000
#> SRR1044580 1 0.000 1.000 1.000 0.000
#> SRR1044581 1 0.000 1.000 1.000 0.000
#> SRR1044582 1 0.000 1.000 1.000 0.000
#> SRR1044583 1 0.000 1.000 1.000 0.000
#> SRR1044584 1 0.000 1.000 1.000 0.000
#> SRR1044585 1 0.000 1.000 1.000 0.000
#> SRR1044586 1 0.000 1.000 1.000 0.000
#> SRR1044587 1 0.000 1.000 1.000 0.000
#> SRR1044588 1 0.000 1.000 1.000 0.000
#> SRR1044589 1 0.000 1.000 1.000 0.000
#> SRR1044590 1 0.000 1.000 1.000 0.000
#> SRR1044591 1 0.000 1.000 1.000 0.000
#> SRR1044592 1 0.000 1.000 1.000 0.000
#> SRR1044593 1 0.000 1.000 1.000 0.000
#> SRR1044594 1 0.000 1.000 1.000 0.000
#> SRR1044595 1 0.000 1.000 1.000 0.000
#> SRR1044596 1 0.000 1.000 1.000 0.000
#> SRR1044597 1 0.000 1.000 1.000 0.000
#> SRR1044598 1 0.000 1.000 1.000 0.000
#> SRR1044599 1 0.000 1.000 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044416 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044417 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044418 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044420 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044419 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044421 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044422 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044423 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044424 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044425 3 0.5859 0.476 0.344 0.000 0.656
#> SRR1044426 1 0.2066 0.928 0.940 0.000 0.060
#> SRR1044427 1 0.0237 0.980 0.996 0.000 0.004
#> SRR1044428 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044429 1 0.1753 0.940 0.952 0.000 0.048
#> SRR1044430 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044431 1 0.0592 0.973 0.988 0.000 0.012
#> SRR1044433 3 0.0000 0.982 0.000 0.000 1.000
#> SRR1044432 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044434 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044435 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044436 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044437 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044439 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044438 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044440 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044441 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044442 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044443 3 0.0000 0.982 0.000 0.000 1.000
#> SRR1044444 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044445 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044446 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044447 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044449 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044448 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044450 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044451 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044452 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044453 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044454 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044455 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044456 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044457 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044458 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044459 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044460 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044461 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044462 1 0.4750 0.723 0.784 0.000 0.216
#> SRR1044463 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044464 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044466 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044465 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044467 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044468 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044469 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044470 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044471 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044472 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044473 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044474 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044475 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044476 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044477 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044478 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044479 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044480 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044481 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044482 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044483 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044484 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044486 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044485 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044487 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044488 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044489 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044490 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044491 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044492 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044493 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044494 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044496 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044495 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044497 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044499 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044498 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044500 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044501 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044502 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044503 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044504 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044505 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044506 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044507 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044508 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044509 3 0.0000 0.982 0.000 0.000 1.000
#> SRR1044510 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044511 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044512 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044513 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044514 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044515 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044516 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044517 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044518 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044519 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044520 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044521 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044522 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044523 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044524 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044525 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044526 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044527 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044528 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044529 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044530 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044531 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044533 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044532 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044534 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044535 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044536 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044537 1 0.0237 0.980 0.996 0.000 0.004
#> SRR1044538 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044539 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044540 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044541 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044542 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044543 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044544 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044545 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044546 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044547 3 0.1289 0.960 0.032 0.000 0.968
#> SRR1044548 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044549 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044550 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044551 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044552 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044553 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044554 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044555 2 0.0237 0.998 0.000 0.996 0.004
#> SRR1044556 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044557 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044558 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044559 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044561 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044560 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044562 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044563 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044564 1 0.0592 0.973 0.988 0.000 0.012
#> SRR1044565 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044566 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044567 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044568 3 0.0592 0.979 0.012 0.000 0.988
#> SRR1044569 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044570 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044571 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044572 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044573 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044574 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044575 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044576 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044577 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044578 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1044579 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044580 1 0.6154 0.298 0.592 0.000 0.408
#> SRR1044581 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044582 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044583 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044584 3 0.3619 0.843 0.136 0.000 0.864
#> SRR1044585 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044586 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044587 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044588 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044589 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044590 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044591 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044592 3 0.0000 0.982 0.000 0.000 1.000
#> SRR1044593 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044594 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044595 3 0.3941 0.817 0.156 0.000 0.844
#> SRR1044596 3 0.0237 0.986 0.004 0.000 0.996
#> SRR1044597 1 0.3816 0.823 0.852 0.000 0.148
#> SRR1044598 1 0.0000 0.983 1.000 0.000 0.000
#> SRR1044599 1 0.0000 0.983 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044416 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044417 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044418 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044420 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044419 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044421 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044422 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044423 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044424 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044425 4 0.4500 0.537 0.316 0.000 0.000 0.684
#> SRR1044426 1 0.1637 0.924 0.940 0.000 0.000 0.060
#> SRR1044427 1 0.0524 0.974 0.988 0.000 0.004 0.008
#> SRR1044428 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044429 1 0.1557 0.928 0.944 0.000 0.000 0.056
#> SRR1044430 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044431 1 0.0469 0.971 0.988 0.000 0.000 0.012
#> SRR1044433 4 0.0592 0.965 0.000 0.000 0.016 0.984
#> SRR1044432 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044434 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044435 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044436 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044437 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044439 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044438 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044440 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044441 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044442 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044443 4 0.4624 0.501 0.000 0.000 0.340 0.660
#> SRR1044444 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044445 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044446 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044447 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044449 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044448 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044450 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044451 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044452 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044453 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044454 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044455 3 0.4040 0.676 0.000 0.248 0.752 0.000
#> SRR1044456 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044457 3 0.0921 0.927 0.000 0.028 0.972 0.000
#> SRR1044458 2 0.4661 0.457 0.000 0.652 0.348 0.000
#> SRR1044459 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044460 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044461 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044462 1 0.3945 0.724 0.780 0.000 0.004 0.216
#> SRR1044463 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044464 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044466 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044465 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044467 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044468 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044469 3 0.3975 0.688 0.000 0.240 0.760 0.000
#> SRR1044470 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044471 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044472 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044473 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044474 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044475 3 0.4454 0.568 0.000 0.308 0.692 0.000
#> SRR1044476 2 0.4040 0.659 0.000 0.752 0.248 0.000
#> SRR1044477 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044478 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044479 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044480 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044481 1 0.0188 0.979 0.996 0.000 0.004 0.000
#> SRR1044482 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044483 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044484 1 0.0188 0.979 0.996 0.000 0.004 0.000
#> SRR1044486 1 0.0188 0.979 0.996 0.000 0.004 0.000
#> SRR1044485 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044487 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044488 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044489 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044490 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044491 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044492 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044493 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044494 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044496 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044495 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044497 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044499 3 0.4907 0.290 0.000 0.420 0.580 0.000
#> SRR1044498 1 0.0188 0.979 0.996 0.000 0.004 0.000
#> SRR1044500 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044501 2 0.4605 0.485 0.000 0.664 0.336 0.000
#> SRR1044502 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044503 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044504 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044505 1 0.0376 0.977 0.992 0.000 0.004 0.004
#> SRR1044506 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044507 4 0.0188 0.973 0.000 0.000 0.004 0.996
#> SRR1044508 4 0.0592 0.965 0.000 0.000 0.016 0.984
#> SRR1044509 4 0.0592 0.965 0.000 0.000 0.016 0.984
#> SRR1044510 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044511 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044512 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044513 3 0.0469 0.938 0.000 0.012 0.988 0.000
#> SRR1044514 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044515 3 0.0469 0.938 0.000 0.012 0.988 0.000
#> SRR1044516 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044517 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044518 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044519 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044520 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044521 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044522 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044523 3 0.4605 0.499 0.000 0.336 0.664 0.000
#> SRR1044524 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044525 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044526 1 0.0188 0.979 0.996 0.000 0.004 0.000
#> SRR1044527 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044528 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044529 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044530 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044531 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044533 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044532 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044534 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044535 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044536 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044537 1 0.0376 0.977 0.992 0.000 0.004 0.004
#> SRR1044538 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044539 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044540 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044541 3 0.1557 0.904 0.000 0.056 0.944 0.000
#> SRR1044542 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044543 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044544 3 0.0469 0.938 0.000 0.012 0.988 0.000
#> SRR1044545 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044546 1 0.0188 0.979 0.996 0.000 0.004 0.000
#> SRR1044547 4 0.1109 0.947 0.028 0.000 0.004 0.968
#> SRR1044548 1 0.0188 0.979 0.996 0.000 0.004 0.000
#> SRR1044549 2 0.4331 0.565 0.000 0.712 0.288 0.000
#> SRR1044550 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044551 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044552 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044553 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044554 1 0.0188 0.979 0.996 0.000 0.004 0.000
#> SRR1044555 3 0.0188 0.943 0.000 0.004 0.996 0.000
#> SRR1044556 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044557 1 0.0188 0.979 0.996 0.000 0.004 0.000
#> SRR1044558 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044559 1 0.0188 0.979 0.996 0.000 0.004 0.000
#> SRR1044561 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044560 2 0.4103 0.646 0.000 0.744 0.256 0.000
#> SRR1044562 1 0.0188 0.979 0.996 0.000 0.004 0.000
#> SRR1044563 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044564 1 0.0657 0.970 0.984 0.000 0.004 0.012
#> SRR1044565 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044566 2 0.3528 0.745 0.000 0.808 0.192 0.000
#> SRR1044567 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044568 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044569 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044570 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044571 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044572 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044573 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044574 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044575 1 0.0000 0.980 1.000 0.000 0.000 0.000
#> SRR1044576 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044577 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044578 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1044579 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044580 1 0.4898 0.276 0.584 0.000 0.000 0.416
#> SRR1044581 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044582 1 0.0188 0.979 0.996 0.000 0.004 0.000
#> SRR1044583 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044584 4 0.2704 0.843 0.124 0.000 0.000 0.876
#> SRR1044585 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044586 1 0.0188 0.979 0.996 0.000 0.004 0.000
#> SRR1044587 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044588 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044589 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044590 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044591 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044592 4 0.0592 0.965 0.000 0.000 0.016 0.984
#> SRR1044593 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044594 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044595 4 0.4035 0.764 0.176 0.000 0.020 0.804
#> SRR1044596 4 0.0000 0.976 0.000 0.000 0.000 1.000
#> SRR1044597 1 0.3074 0.818 0.848 0.000 0.000 0.152
#> SRR1044598 1 0.0188 0.979 0.996 0.000 0.004 0.000
#> SRR1044599 1 0.0188 0.979 0.996 0.000 0.004 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.0794 0.94082 0.000 0.972 0.000 0.000 0.028
#> SRR1044416 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044417 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044418 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044420 2 0.0290 0.95008 0.000 0.992 0.000 0.000 0.008
#> SRR1044419 2 0.0880 0.93856 0.000 0.968 0.000 0.000 0.032
#> SRR1044421 2 0.0609 0.94570 0.000 0.980 0.000 0.000 0.020
#> SRR1044422 2 0.0404 0.94906 0.000 0.988 0.000 0.000 0.012
#> SRR1044423 2 0.0609 0.94557 0.000 0.980 0.000 0.000 0.020
#> SRR1044424 2 0.0404 0.94906 0.000 0.988 0.000 0.000 0.012
#> SRR1044425 4 0.3534 0.36237 0.256 0.000 0.000 0.744 0.000
#> SRR1044426 1 0.1493 0.79814 0.948 0.000 0.000 0.028 0.024
#> SRR1044427 1 0.4592 0.74568 0.644 0.000 0.000 0.024 0.332
#> SRR1044428 1 0.0000 0.82771 1.000 0.000 0.000 0.000 0.000
#> SRR1044429 1 0.1908 0.76053 0.908 0.000 0.000 0.092 0.000
#> SRR1044430 1 0.0000 0.82771 1.000 0.000 0.000 0.000 0.000
#> SRR1044431 1 0.1908 0.75778 0.908 0.000 0.000 0.092 0.000
#> SRR1044433 5 0.4256 0.87590 0.000 0.000 0.000 0.436 0.564
#> SRR1044432 1 0.0000 0.82771 1.000 0.000 0.000 0.000 0.000
#> SRR1044434 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044435 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044436 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044437 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044439 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044438 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044440 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044441 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044442 5 0.4256 0.87590 0.000 0.000 0.000 0.436 0.564
#> SRR1044443 5 0.5294 0.81834 0.000 0.000 0.056 0.380 0.564
#> SRR1044444 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044445 4 0.2179 0.76528 0.000 0.000 0.000 0.888 0.112
#> SRR1044446 3 0.0000 0.93236 0.000 0.000 1.000 0.000 0.000
#> SRR1044447 3 0.0000 0.93236 0.000 0.000 1.000 0.000 0.000
#> SRR1044449 3 0.0000 0.93236 0.000 0.000 1.000 0.000 0.000
#> SRR1044448 3 0.0000 0.93236 0.000 0.000 1.000 0.000 0.000
#> SRR1044450 3 0.0000 0.93236 0.000 0.000 1.000 0.000 0.000
#> SRR1044451 3 0.0000 0.93236 0.000 0.000 1.000 0.000 0.000
#> SRR1044452 3 0.0404 0.92895 0.000 0.000 0.988 0.000 0.012
#> SRR1044453 3 0.0404 0.92895 0.000 0.000 0.988 0.000 0.012
#> SRR1044454 3 0.0510 0.92728 0.000 0.000 0.984 0.000 0.016
#> SRR1044455 3 0.3909 0.70108 0.000 0.216 0.760 0.000 0.024
#> SRR1044456 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044457 3 0.1168 0.91386 0.000 0.008 0.960 0.000 0.032
#> SRR1044458 2 0.4822 0.41493 0.000 0.616 0.352 0.000 0.032
#> SRR1044459 3 0.0162 0.93167 0.000 0.000 0.996 0.000 0.004
#> SRR1044460 2 0.0290 0.95008 0.000 0.992 0.000 0.000 0.008
#> SRR1044461 2 0.0880 0.93856 0.000 0.968 0.000 0.000 0.032
#> SRR1044462 1 0.6588 0.44726 0.436 0.000 0.000 0.216 0.348
#> SRR1044463 1 0.1608 0.83188 0.928 0.000 0.000 0.000 0.072
#> SRR1044464 4 0.0162 0.88435 0.000 0.000 0.000 0.996 0.004
#> SRR1044466 1 0.1671 0.83190 0.924 0.000 0.000 0.000 0.076
#> SRR1044465 1 0.0000 0.82771 1.000 0.000 0.000 0.000 0.000
#> SRR1044467 1 0.0000 0.82771 1.000 0.000 0.000 0.000 0.000
#> SRR1044468 2 0.0510 0.94765 0.000 0.984 0.000 0.000 0.016
#> SRR1044469 3 0.3877 0.70519 0.000 0.212 0.764 0.000 0.024
#> SRR1044470 1 0.1478 0.83244 0.936 0.000 0.000 0.000 0.064
#> SRR1044471 1 0.0000 0.82771 1.000 0.000 0.000 0.000 0.000
#> SRR1044472 1 0.1671 0.83190 0.924 0.000 0.000 0.000 0.076
#> SRR1044473 1 0.0000 0.82771 1.000 0.000 0.000 0.000 0.000
#> SRR1044474 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044475 3 0.4114 0.66099 0.000 0.244 0.732 0.000 0.024
#> SRR1044476 2 0.4248 0.64940 0.000 0.728 0.240 0.000 0.032
#> SRR1044477 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044478 2 0.0510 0.94744 0.000 0.984 0.000 0.000 0.016
#> SRR1044479 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044480 4 0.2813 0.60621 0.000 0.000 0.000 0.832 0.168
#> SRR1044481 1 0.4182 0.74479 0.600 0.000 0.000 0.000 0.400
#> SRR1044482 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044483 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044484 1 0.4192 0.74423 0.596 0.000 0.000 0.000 0.404
#> SRR1044486 1 0.4192 0.74423 0.596 0.000 0.000 0.000 0.404
#> SRR1044485 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044487 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044488 2 0.0162 0.95076 0.000 0.996 0.000 0.000 0.004
#> SRR1044489 2 0.0290 0.95008 0.000 0.992 0.000 0.000 0.008
#> SRR1044490 1 0.0000 0.82771 1.000 0.000 0.000 0.000 0.000
#> SRR1044491 1 0.3039 0.81143 0.808 0.000 0.000 0.000 0.192
#> SRR1044492 1 0.1121 0.83141 0.956 0.000 0.000 0.000 0.044
#> SRR1044493 1 0.1671 0.83190 0.924 0.000 0.000 0.000 0.076
#> SRR1044494 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044496 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044495 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044497 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044499 3 0.4958 0.28942 0.000 0.400 0.568 0.000 0.032
#> SRR1044498 1 0.4171 0.74512 0.604 0.000 0.000 0.000 0.396
#> SRR1044500 2 0.0404 0.94919 0.000 0.988 0.000 0.000 0.012
#> SRR1044501 2 0.4779 0.44495 0.000 0.628 0.340 0.000 0.032
#> SRR1044502 3 0.0000 0.93236 0.000 0.000 1.000 0.000 0.000
#> SRR1044503 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044504 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044505 1 0.4874 0.71805 0.632 0.000 0.000 0.040 0.328
#> SRR1044506 4 0.2179 0.76528 0.000 0.000 0.000 0.888 0.112
#> SRR1044507 5 0.3932 0.77179 0.000 0.000 0.000 0.328 0.672
#> SRR1044508 5 0.4256 0.87590 0.000 0.000 0.000 0.436 0.564
#> SRR1044509 5 0.4256 0.87590 0.000 0.000 0.000 0.436 0.564
#> SRR1044510 3 0.0162 0.93167 0.000 0.000 0.996 0.000 0.004
#> SRR1044511 3 0.0000 0.93236 0.000 0.000 1.000 0.000 0.000
#> SRR1044512 3 0.0000 0.93236 0.000 0.000 1.000 0.000 0.000
#> SRR1044513 3 0.0290 0.92777 0.000 0.008 0.992 0.000 0.000
#> SRR1044514 3 0.0000 0.93236 0.000 0.000 1.000 0.000 0.000
#> SRR1044515 3 0.0290 0.92777 0.000 0.008 0.992 0.000 0.000
#> SRR1044516 2 0.0404 0.94906 0.000 0.988 0.000 0.000 0.012
#> SRR1044517 3 0.0162 0.93167 0.000 0.000 0.996 0.000 0.004
#> SRR1044518 3 0.0000 0.93236 0.000 0.000 1.000 0.000 0.000
#> SRR1044519 3 0.0000 0.93236 0.000 0.000 1.000 0.000 0.000
#> SRR1044520 3 0.0000 0.93236 0.000 0.000 1.000 0.000 0.000
#> SRR1044521 2 0.0290 0.95008 0.000 0.992 0.000 0.000 0.008
#> SRR1044522 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044523 3 0.4183 0.50306 0.000 0.324 0.668 0.000 0.008
#> SRR1044524 3 0.0000 0.93236 0.000 0.000 1.000 0.000 0.000
#> SRR1044525 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044526 1 0.5043 0.71440 0.600 0.000 0.000 0.044 0.356
#> SRR1044527 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044528 2 0.0162 0.94931 0.000 0.996 0.004 0.000 0.000
#> SRR1044529 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044530 1 0.1671 0.83190 0.924 0.000 0.000 0.000 0.076
#> SRR1044531 1 0.0000 0.82771 1.000 0.000 0.000 0.000 0.000
#> SRR1044533 1 0.0000 0.82771 1.000 0.000 0.000 0.000 0.000
#> SRR1044532 1 0.1671 0.83190 0.924 0.000 0.000 0.000 0.076
#> SRR1044534 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044535 3 0.0000 0.93236 0.000 0.000 1.000 0.000 0.000
#> SRR1044536 2 0.0290 0.95008 0.000 0.992 0.000 0.000 0.008
#> SRR1044537 1 0.4341 0.74140 0.592 0.000 0.000 0.004 0.404
#> SRR1044538 1 0.1671 0.83190 0.924 0.000 0.000 0.000 0.076
#> SRR1044539 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044540 1 0.0000 0.82771 1.000 0.000 0.000 0.000 0.000
#> SRR1044541 3 0.1668 0.89663 0.000 0.032 0.940 0.000 0.028
#> SRR1044542 1 0.1732 0.83185 0.920 0.000 0.000 0.000 0.080
#> SRR1044543 1 0.0000 0.82771 1.000 0.000 0.000 0.000 0.000
#> SRR1044544 3 0.0794 0.92097 0.000 0.000 0.972 0.000 0.028
#> SRR1044545 4 0.2127 0.72287 0.000 0.000 0.000 0.892 0.108
#> SRR1044546 1 0.4192 0.74423 0.596 0.000 0.000 0.000 0.404
#> SRR1044547 4 0.3612 0.37899 0.000 0.000 0.000 0.732 0.268
#> SRR1044548 1 0.4192 0.74423 0.596 0.000 0.000 0.000 0.404
#> SRR1044549 2 0.4232 0.50983 0.000 0.676 0.312 0.000 0.012
#> SRR1044550 2 0.0290 0.95008 0.000 0.992 0.000 0.000 0.008
#> SRR1044551 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044552 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044553 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044554 1 0.4192 0.74423 0.596 0.000 0.000 0.000 0.404
#> SRR1044555 3 0.0290 0.93045 0.000 0.000 0.992 0.000 0.008
#> SRR1044556 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044557 1 0.4192 0.74423 0.596 0.000 0.000 0.000 0.404
#> SRR1044558 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044559 1 0.4192 0.74423 0.596 0.000 0.000 0.000 0.404
#> SRR1044561 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044560 2 0.4329 0.62852 0.000 0.716 0.252 0.000 0.032
#> SRR1044562 1 0.4192 0.74423 0.596 0.000 0.000 0.000 0.404
#> SRR1044563 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044564 1 0.4817 0.72593 0.572 0.000 0.000 0.024 0.404
#> SRR1044565 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044566 2 0.3841 0.72986 0.000 0.780 0.188 0.000 0.032
#> SRR1044567 1 0.1671 0.83190 0.924 0.000 0.000 0.000 0.076
#> SRR1044568 4 0.0693 0.86696 0.008 0.000 0.000 0.980 0.012
#> SRR1044569 1 0.0162 0.82815 0.996 0.000 0.000 0.000 0.004
#> SRR1044570 1 0.1732 0.83185 0.920 0.000 0.000 0.000 0.080
#> SRR1044571 1 0.0000 0.82771 1.000 0.000 0.000 0.000 0.000
#> SRR1044572 1 0.0000 0.82771 1.000 0.000 0.000 0.000 0.000
#> SRR1044573 1 0.0963 0.83038 0.964 0.000 0.000 0.000 0.036
#> SRR1044574 1 0.0000 0.82771 1.000 0.000 0.000 0.000 0.000
#> SRR1044575 1 0.0000 0.82771 1.000 0.000 0.000 0.000 0.000
#> SRR1044576 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044577 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044578 2 0.0000 0.95122 0.000 1.000 0.000 0.000 0.000
#> SRR1044579 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044580 4 0.6039 0.00202 0.300 0.000 0.000 0.552 0.148
#> SRR1044581 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044582 1 0.4192 0.74423 0.596 0.000 0.000 0.000 0.404
#> SRR1044583 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044584 4 0.1774 0.79180 0.052 0.000 0.000 0.932 0.016
#> SRR1044585 4 0.0000 0.88779 0.000 0.000 0.000 1.000 0.000
#> SRR1044586 1 0.4192 0.74423 0.596 0.000 0.000 0.000 0.404
#> SRR1044587 4 0.2179 0.76528 0.000 0.000 0.000 0.888 0.112
#> SRR1044588 4 0.2179 0.76528 0.000 0.000 0.000 0.888 0.112
#> SRR1044589 4 0.2179 0.76528 0.000 0.000 0.000 0.888 0.112
#> SRR1044590 4 0.2179 0.76528 0.000 0.000 0.000 0.888 0.112
#> SRR1044591 4 0.2179 0.76528 0.000 0.000 0.000 0.888 0.112
#> SRR1044592 5 0.4256 0.87590 0.000 0.000 0.000 0.436 0.564
#> SRR1044593 4 0.2179 0.76528 0.000 0.000 0.000 0.888 0.112
#> SRR1044594 4 0.2179 0.76528 0.000 0.000 0.000 0.888 0.112
#> SRR1044595 5 0.2970 0.58656 0.004 0.000 0.000 0.168 0.828
#> SRR1044596 5 0.4256 0.87590 0.000 0.000 0.000 0.436 0.564
#> SRR1044597 1 0.5559 0.67169 0.544 0.000 0.000 0.076 0.380
#> SRR1044598 1 0.4182 0.74599 0.600 0.000 0.000 0.000 0.400
#> SRR1044599 1 0.4182 0.74599 0.600 0.000 0.000 0.000 0.400
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.3112 0.850 0.000 0.836 0.000 0.000 0.068 0.096
#> SRR1044416 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044417 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044418 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044420 2 0.1245 0.910 0.000 0.952 0.000 0.000 0.016 0.032
#> SRR1044419 2 0.3514 0.826 0.000 0.804 0.000 0.000 0.088 0.108
#> SRR1044421 2 0.2201 0.891 0.000 0.900 0.000 0.000 0.052 0.048
#> SRR1044422 2 0.2164 0.890 0.000 0.900 0.000 0.000 0.032 0.068
#> SRR1044423 2 0.2685 0.873 0.000 0.868 0.000 0.000 0.060 0.072
#> SRR1044424 2 0.0806 0.914 0.000 0.972 0.000 0.000 0.008 0.020
#> SRR1044425 4 0.4032 0.299 0.420 0.000 0.000 0.572 0.000 0.008
#> SRR1044426 1 0.0508 0.806 0.984 0.000 0.000 0.004 0.000 0.012
#> SRR1044427 5 0.4090 0.577 0.384 0.000 0.000 0.004 0.604 0.008
#> SRR1044428 1 0.0260 0.816 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1044429 1 0.1477 0.767 0.940 0.000 0.000 0.048 0.004 0.008
#> SRR1044430 1 0.0000 0.817 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044431 1 0.0717 0.802 0.976 0.000 0.000 0.016 0.000 0.008
#> SRR1044433 6 0.2219 0.972 0.000 0.000 0.000 0.136 0.000 0.864
#> SRR1044432 1 0.0000 0.817 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044434 4 0.0000 0.910 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044435 4 0.0000 0.910 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044436 4 0.0260 0.908 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR1044437 4 0.0000 0.910 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044439 4 0.0260 0.908 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR1044438 4 0.0260 0.908 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR1044440 4 0.0000 0.910 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044441 4 0.0000 0.910 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044442 6 0.2219 0.972 0.000 0.000 0.000 0.136 0.000 0.864
#> SRR1044443 6 0.2536 0.960 0.000 0.000 0.020 0.116 0.000 0.864
#> SRR1044444 4 0.0000 0.910 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044445 4 0.2748 0.811 0.000 0.000 0.000 0.848 0.024 0.128
#> SRR1044446 3 0.0000 0.890 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044447 3 0.0000 0.890 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044449 3 0.0000 0.890 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044448 3 0.0000 0.890 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044450 3 0.0000 0.890 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044451 3 0.0000 0.890 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044452 3 0.1649 0.871 0.000 0.000 0.932 0.000 0.032 0.036
#> SRR1044453 3 0.1649 0.871 0.000 0.000 0.932 0.000 0.032 0.036
#> SRR1044454 3 0.2328 0.849 0.000 0.000 0.892 0.000 0.056 0.052
#> SRR1044455 3 0.6048 0.554 0.000 0.216 0.596 0.000 0.088 0.100
#> SRR1044456 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044457 3 0.3911 0.779 0.000 0.012 0.788 0.000 0.092 0.108
#> SRR1044458 2 0.6362 0.432 0.000 0.544 0.256 0.000 0.092 0.108
#> SRR1044459 3 0.1088 0.881 0.000 0.000 0.960 0.000 0.016 0.024
#> SRR1044460 2 0.1320 0.909 0.000 0.948 0.000 0.000 0.016 0.036
#> SRR1044461 2 0.3563 0.823 0.000 0.800 0.000 0.000 0.092 0.108
#> SRR1044462 5 0.5491 0.575 0.192 0.000 0.000 0.200 0.600 0.008
#> SRR1044463 1 0.3778 0.614 0.696 0.000 0.000 0.000 0.288 0.016
#> SRR1044464 4 0.0520 0.903 0.000 0.000 0.000 0.984 0.008 0.008
#> SRR1044466 1 0.3905 0.580 0.668 0.000 0.000 0.000 0.316 0.016
#> SRR1044465 1 0.0291 0.817 0.992 0.000 0.000 0.000 0.004 0.004
#> SRR1044467 1 0.0000 0.817 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044468 2 0.2003 0.897 0.000 0.912 0.000 0.000 0.044 0.044
#> SRR1044469 3 0.5767 0.583 0.000 0.212 0.624 0.000 0.080 0.084
#> SRR1044470 1 0.3674 0.626 0.716 0.000 0.000 0.000 0.268 0.016
#> SRR1044471 1 0.0405 0.816 0.988 0.000 0.000 0.000 0.008 0.004
#> SRR1044472 1 0.3835 0.599 0.684 0.000 0.000 0.000 0.300 0.016
#> SRR1044473 1 0.0508 0.815 0.984 0.000 0.000 0.000 0.012 0.004
#> SRR1044474 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044475 3 0.5857 0.555 0.000 0.236 0.604 0.000 0.080 0.080
#> SRR1044476 2 0.5814 0.620 0.000 0.636 0.168 0.000 0.088 0.108
#> SRR1044477 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044478 2 0.2801 0.868 0.000 0.860 0.000 0.000 0.068 0.072
#> SRR1044479 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044480 4 0.2848 0.752 0.008 0.000 0.000 0.828 0.160 0.004
#> SRR1044481 5 0.2520 0.860 0.152 0.000 0.000 0.000 0.844 0.004
#> SRR1044482 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044483 4 0.0260 0.908 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR1044484 5 0.2135 0.875 0.128 0.000 0.000 0.000 0.872 0.000
#> SRR1044486 5 0.2092 0.876 0.124 0.000 0.000 0.000 0.876 0.000
#> SRR1044485 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044487 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044488 2 0.1320 0.909 0.000 0.948 0.000 0.000 0.016 0.036
#> SRR1044489 2 0.1320 0.909 0.000 0.948 0.000 0.000 0.016 0.036
#> SRR1044490 1 0.0146 0.817 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1044491 5 0.4025 0.262 0.416 0.000 0.000 0.000 0.576 0.008
#> SRR1044492 1 0.3670 0.617 0.704 0.000 0.000 0.000 0.284 0.012
#> SRR1044493 1 0.4110 0.469 0.608 0.000 0.000 0.000 0.376 0.016
#> SRR1044494 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044496 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044495 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044497 4 0.0000 0.910 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044499 3 0.6640 0.144 0.000 0.364 0.436 0.000 0.092 0.108
#> SRR1044498 5 0.3043 0.819 0.196 0.000 0.000 0.004 0.796 0.004
#> SRR1044500 2 0.1168 0.911 0.000 0.956 0.000 0.000 0.016 0.028
#> SRR1044501 2 0.6327 0.451 0.000 0.552 0.248 0.000 0.092 0.108
#> SRR1044502 3 0.0146 0.890 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1044503 4 0.0000 0.910 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044504 4 0.0000 0.910 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044505 5 0.4656 0.467 0.420 0.000 0.000 0.028 0.544 0.008
#> SRR1044506 4 0.2748 0.811 0.000 0.000 0.000 0.848 0.024 0.128
#> SRR1044507 6 0.2573 0.955 0.000 0.000 0.000 0.112 0.024 0.864
#> SRR1044508 6 0.2320 0.973 0.000 0.000 0.004 0.132 0.000 0.864
#> SRR1044509 6 0.2320 0.973 0.000 0.000 0.004 0.132 0.000 0.864
#> SRR1044510 3 0.0508 0.888 0.000 0.000 0.984 0.000 0.004 0.012
#> SRR1044511 3 0.0000 0.890 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044512 3 0.0000 0.890 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044513 3 0.0260 0.887 0.000 0.008 0.992 0.000 0.000 0.000
#> SRR1044514 3 0.0000 0.890 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044515 3 0.0405 0.887 0.000 0.008 0.988 0.000 0.004 0.000
#> SRR1044516 2 0.1984 0.896 0.000 0.912 0.000 0.000 0.032 0.056
#> SRR1044517 3 0.0508 0.888 0.000 0.000 0.984 0.000 0.004 0.012
#> SRR1044518 3 0.0000 0.890 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044519 3 0.0000 0.890 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044520 3 0.0000 0.890 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044521 2 0.0806 0.915 0.000 0.972 0.000 0.000 0.008 0.020
#> SRR1044522 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044523 3 0.4135 0.533 0.000 0.292 0.680 0.000 0.016 0.012
#> SRR1044524 3 0.0520 0.888 0.000 0.000 0.984 0.000 0.008 0.008
#> SRR1044525 4 0.0000 0.910 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044526 5 0.4813 0.614 0.324 0.000 0.000 0.048 0.616 0.012
#> SRR1044527 2 0.0692 0.912 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1044528 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044529 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044530 1 0.3905 0.580 0.668 0.000 0.000 0.000 0.316 0.016
#> SRR1044531 1 0.1074 0.806 0.960 0.000 0.000 0.000 0.028 0.012
#> SRR1044533 1 0.0146 0.817 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1044532 1 0.3969 0.555 0.652 0.000 0.000 0.000 0.332 0.016
#> SRR1044534 2 0.0146 0.916 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1044535 3 0.0146 0.890 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1044536 2 0.1320 0.909 0.000 0.948 0.000 0.000 0.016 0.036
#> SRR1044537 5 0.2346 0.874 0.124 0.000 0.000 0.000 0.868 0.008
#> SRR1044538 1 0.4012 0.536 0.640 0.000 0.000 0.000 0.344 0.016
#> SRR1044539 4 0.0405 0.906 0.000 0.000 0.000 0.988 0.008 0.004
#> SRR1044540 1 0.0000 0.817 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044541 3 0.4001 0.776 0.000 0.016 0.784 0.000 0.092 0.108
#> SRR1044542 1 0.4088 0.489 0.616 0.000 0.000 0.000 0.368 0.016
#> SRR1044543 1 0.0146 0.816 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1044544 3 0.3325 0.802 0.000 0.000 0.820 0.000 0.084 0.096
#> SRR1044545 4 0.1700 0.848 0.000 0.000 0.000 0.916 0.080 0.004
#> SRR1044546 5 0.2092 0.876 0.124 0.000 0.000 0.000 0.876 0.000
#> SRR1044547 4 0.3426 0.567 0.000 0.000 0.000 0.720 0.276 0.004
#> SRR1044548 5 0.2092 0.876 0.124 0.000 0.000 0.000 0.876 0.000
#> SRR1044549 2 0.4519 0.479 0.000 0.656 0.296 0.000 0.036 0.012
#> SRR1044550 2 0.1480 0.907 0.000 0.940 0.000 0.000 0.020 0.040
#> SRR1044551 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044552 4 0.0000 0.910 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044553 4 0.0000 0.910 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044554 5 0.2092 0.876 0.124 0.000 0.000 0.000 0.876 0.000
#> SRR1044555 3 0.1418 0.876 0.000 0.000 0.944 0.000 0.024 0.032
#> SRR1044556 4 0.0260 0.908 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR1044557 5 0.2092 0.876 0.124 0.000 0.000 0.000 0.876 0.000
#> SRR1044558 4 0.0000 0.910 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044559 5 0.2092 0.876 0.124 0.000 0.000 0.000 0.876 0.000
#> SRR1044561 4 0.0000 0.910 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044560 2 0.5916 0.601 0.000 0.624 0.176 0.000 0.092 0.108
#> SRR1044562 5 0.2092 0.876 0.124 0.000 0.000 0.000 0.876 0.000
#> SRR1044563 4 0.0260 0.908 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR1044564 5 0.2588 0.865 0.124 0.000 0.000 0.012 0.860 0.004
#> SRR1044565 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044566 2 0.5657 0.653 0.000 0.656 0.148 0.000 0.088 0.108
#> SRR1044567 1 0.4026 0.529 0.636 0.000 0.000 0.000 0.348 0.016
#> SRR1044568 4 0.2257 0.848 0.040 0.000 0.000 0.904 0.048 0.008
#> SRR1044569 1 0.0291 0.815 0.992 0.000 0.000 0.000 0.004 0.004
#> SRR1044570 1 0.4088 0.489 0.616 0.000 0.000 0.000 0.368 0.016
#> SRR1044571 1 0.0000 0.817 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044572 1 0.0000 0.817 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044573 1 0.1700 0.755 0.916 0.000 0.000 0.000 0.080 0.004
#> SRR1044574 1 0.0146 0.817 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1044575 1 0.0146 0.816 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1044576 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044577 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044578 2 0.0000 0.917 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044579 4 0.0000 0.910 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044580 4 0.5652 0.340 0.224 0.000 0.000 0.572 0.196 0.008
#> SRR1044581 4 0.0000 0.910 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044582 5 0.2135 0.875 0.128 0.000 0.000 0.000 0.872 0.000
#> SRR1044583 4 0.0000 0.910 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044584 4 0.1989 0.856 0.028 0.000 0.000 0.916 0.052 0.004
#> SRR1044585 4 0.0000 0.910 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044586 5 0.2092 0.876 0.124 0.000 0.000 0.000 0.876 0.000
#> SRR1044587 4 0.2748 0.811 0.000 0.000 0.000 0.848 0.024 0.128
#> SRR1044588 4 0.2748 0.811 0.000 0.000 0.000 0.848 0.024 0.128
#> SRR1044589 4 0.2748 0.811 0.000 0.000 0.000 0.848 0.024 0.128
#> SRR1044590 4 0.2748 0.811 0.000 0.000 0.000 0.848 0.024 0.128
#> SRR1044591 4 0.2748 0.811 0.000 0.000 0.000 0.848 0.024 0.128
#> SRR1044592 6 0.2320 0.973 0.000 0.000 0.004 0.132 0.000 0.864
#> SRR1044593 4 0.2748 0.811 0.000 0.000 0.000 0.848 0.024 0.128
#> SRR1044594 4 0.2748 0.811 0.000 0.000 0.000 0.848 0.024 0.128
#> SRR1044595 6 0.2527 0.855 0.000 0.000 0.000 0.040 0.084 0.876
#> SRR1044596 6 0.2219 0.972 0.000 0.000 0.000 0.136 0.000 0.864
#> SRR1044597 5 0.4947 0.619 0.316 0.000 0.000 0.060 0.612 0.012
#> SRR1044598 5 0.2178 0.871 0.132 0.000 0.000 0.000 0.868 0.000
#> SRR1044599 5 0.2178 0.871 0.132 0.000 0.000 0.000 0.868 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)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.997 0.999 0.4929 0.508 0.508
#> 3 3 0.721 0.855 0.818 0.2881 0.835 0.675
#> 4 4 0.869 0.844 0.932 0.1620 0.888 0.687
#> 5 5 0.779 0.680 0.843 0.0517 0.952 0.820
#> 6 6 0.741 0.622 0.751 0.0373 0.901 0.625
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0.0000 1.000 0.000 1.000
#> SRR1044416 2 0.0000 1.000 0.000 1.000
#> SRR1044417 2 0.0000 1.000 0.000 1.000
#> SRR1044418 2 0.0000 1.000 0.000 1.000
#> SRR1044420 2 0.0000 1.000 0.000 1.000
#> SRR1044419 2 0.0000 1.000 0.000 1.000
#> SRR1044421 2 0.0000 1.000 0.000 1.000
#> SRR1044422 2 0.0000 1.000 0.000 1.000
#> SRR1044423 2 0.0000 1.000 0.000 1.000
#> SRR1044424 2 0.0000 1.000 0.000 1.000
#> SRR1044425 1 0.0000 0.998 1.000 0.000
#> SRR1044426 1 0.0000 0.998 1.000 0.000
#> SRR1044427 1 0.0000 0.998 1.000 0.000
#> SRR1044428 1 0.0000 0.998 1.000 0.000
#> SRR1044429 1 0.0000 0.998 1.000 0.000
#> SRR1044430 1 0.4431 0.901 0.908 0.092
#> SRR1044431 1 0.0000 0.998 1.000 0.000
#> SRR1044433 1 0.0000 0.998 1.000 0.000
#> SRR1044432 1 0.0000 0.998 1.000 0.000
#> SRR1044434 1 0.0000 0.998 1.000 0.000
#> SRR1044435 1 0.0000 0.998 1.000 0.000
#> SRR1044436 1 0.0000 0.998 1.000 0.000
#> SRR1044437 1 0.0000 0.998 1.000 0.000
#> SRR1044439 1 0.0000 0.998 1.000 0.000
#> SRR1044438 1 0.0000 0.998 1.000 0.000
#> SRR1044440 1 0.0000 0.998 1.000 0.000
#> SRR1044441 1 0.0000 0.998 1.000 0.000
#> SRR1044442 1 0.0000 0.998 1.000 0.000
#> SRR1044443 1 0.1184 0.983 0.984 0.016
#> SRR1044444 1 0.0000 0.998 1.000 0.000
#> SRR1044445 1 0.0000 0.998 1.000 0.000
#> SRR1044446 2 0.0000 1.000 0.000 1.000
#> SRR1044447 2 0.0000 1.000 0.000 1.000
#> SRR1044449 2 0.0000 1.000 0.000 1.000
#> SRR1044448 2 0.0000 1.000 0.000 1.000
#> SRR1044450 2 0.0000 1.000 0.000 1.000
#> SRR1044451 2 0.0000 1.000 0.000 1.000
#> SRR1044452 2 0.0000 1.000 0.000 1.000
#> SRR1044453 2 0.0000 1.000 0.000 1.000
#> SRR1044454 2 0.0000 1.000 0.000 1.000
#> SRR1044455 2 0.0000 1.000 0.000 1.000
#> SRR1044456 2 0.0000 1.000 0.000 1.000
#> SRR1044457 2 0.0000 1.000 0.000 1.000
#> SRR1044458 2 0.0000 1.000 0.000 1.000
#> SRR1044459 2 0.0000 1.000 0.000 1.000
#> SRR1044460 2 0.0000 1.000 0.000 1.000
#> SRR1044461 2 0.0000 1.000 0.000 1.000
#> SRR1044462 1 0.0000 0.998 1.000 0.000
#> SRR1044463 1 0.0000 0.998 1.000 0.000
#> SRR1044464 1 0.0000 0.998 1.000 0.000
#> SRR1044466 1 0.0376 0.995 0.996 0.004
#> SRR1044465 1 0.0000 0.998 1.000 0.000
#> SRR1044467 1 0.0000 0.998 1.000 0.000
#> SRR1044468 2 0.0000 1.000 0.000 1.000
#> SRR1044469 2 0.0000 1.000 0.000 1.000
#> SRR1044470 1 0.0672 0.991 0.992 0.008
#> SRR1044471 1 0.0000 0.998 1.000 0.000
#> SRR1044472 1 0.3879 0.919 0.924 0.076
#> SRR1044473 1 0.0000 0.998 1.000 0.000
#> SRR1044474 2 0.0000 1.000 0.000 1.000
#> SRR1044475 2 0.0000 1.000 0.000 1.000
#> SRR1044476 2 0.0000 1.000 0.000 1.000
#> SRR1044477 2 0.0000 1.000 0.000 1.000
#> SRR1044478 2 0.0000 1.000 0.000 1.000
#> SRR1044479 2 0.0000 1.000 0.000 1.000
#> SRR1044480 1 0.0000 0.998 1.000 0.000
#> SRR1044481 1 0.0000 0.998 1.000 0.000
#> SRR1044482 2 0.0000 1.000 0.000 1.000
#> SRR1044483 1 0.0000 0.998 1.000 0.000
#> SRR1044484 1 0.0000 0.998 1.000 0.000
#> SRR1044486 1 0.0000 0.998 1.000 0.000
#> SRR1044485 2 0.0000 1.000 0.000 1.000
#> SRR1044487 2 0.0000 1.000 0.000 1.000
#> SRR1044488 2 0.0000 1.000 0.000 1.000
#> SRR1044489 2 0.0000 1.000 0.000 1.000
#> SRR1044490 1 0.0000 0.998 1.000 0.000
#> SRR1044491 1 0.0376 0.995 0.996 0.004
#> SRR1044492 1 0.0376 0.994 0.996 0.004
#> SRR1044493 1 0.0000 0.998 1.000 0.000
#> SRR1044494 2 0.0000 1.000 0.000 1.000
#> SRR1044496 2 0.0000 1.000 0.000 1.000
#> SRR1044495 2 0.0000 1.000 0.000 1.000
#> SRR1044497 1 0.0000 0.998 1.000 0.000
#> SRR1044499 2 0.0000 1.000 0.000 1.000
#> SRR1044498 1 0.0000 0.998 1.000 0.000
#> SRR1044500 2 0.0000 1.000 0.000 1.000
#> SRR1044501 2 0.0000 1.000 0.000 1.000
#> SRR1044502 2 0.0000 1.000 0.000 1.000
#> SRR1044503 1 0.0000 0.998 1.000 0.000
#> SRR1044504 1 0.0000 0.998 1.000 0.000
#> SRR1044505 1 0.0000 0.998 1.000 0.000
#> SRR1044506 1 0.0000 0.998 1.000 0.000
#> SRR1044507 1 0.0000 0.998 1.000 0.000
#> SRR1044508 1 0.0000 0.998 1.000 0.000
#> SRR1044509 1 0.0000 0.998 1.000 0.000
#> SRR1044510 2 0.0000 1.000 0.000 1.000
#> SRR1044511 2 0.0000 1.000 0.000 1.000
#> SRR1044512 2 0.0000 1.000 0.000 1.000
#> SRR1044513 2 0.0000 1.000 0.000 1.000
#> SRR1044514 2 0.0000 1.000 0.000 1.000
#> SRR1044515 2 0.0000 1.000 0.000 1.000
#> SRR1044516 2 0.0000 1.000 0.000 1.000
#> SRR1044517 2 0.0000 1.000 0.000 1.000
#> SRR1044518 2 0.0000 1.000 0.000 1.000
#> SRR1044519 2 0.0000 1.000 0.000 1.000
#> SRR1044520 2 0.0000 1.000 0.000 1.000
#> SRR1044521 2 0.0000 1.000 0.000 1.000
#> SRR1044522 2 0.0000 1.000 0.000 1.000
#> SRR1044523 2 0.0000 1.000 0.000 1.000
#> SRR1044524 2 0.0000 1.000 0.000 1.000
#> SRR1044525 1 0.0000 0.998 1.000 0.000
#> SRR1044526 1 0.0000 0.998 1.000 0.000
#> SRR1044527 2 0.0000 1.000 0.000 1.000
#> SRR1044528 2 0.0000 1.000 0.000 1.000
#> SRR1044529 2 0.0000 1.000 0.000 1.000
#> SRR1044530 1 0.0000 0.998 1.000 0.000
#> SRR1044531 1 0.0000 0.998 1.000 0.000
#> SRR1044533 1 0.0000 0.998 1.000 0.000
#> SRR1044532 1 0.0000 0.998 1.000 0.000
#> SRR1044534 2 0.0000 1.000 0.000 1.000
#> SRR1044535 2 0.0000 1.000 0.000 1.000
#> SRR1044536 2 0.0000 1.000 0.000 1.000
#> SRR1044537 1 0.0000 0.998 1.000 0.000
#> SRR1044538 1 0.0000 0.998 1.000 0.000
#> SRR1044539 1 0.0000 0.998 1.000 0.000
#> SRR1044540 1 0.0000 0.998 1.000 0.000
#> SRR1044541 2 0.0000 1.000 0.000 1.000
#> SRR1044542 1 0.0000 0.998 1.000 0.000
#> SRR1044543 1 0.0000 0.998 1.000 0.000
#> SRR1044544 2 0.0000 1.000 0.000 1.000
#> SRR1044545 1 0.0000 0.998 1.000 0.000
#> SRR1044546 1 0.0000 0.998 1.000 0.000
#> SRR1044547 1 0.0000 0.998 1.000 0.000
#> SRR1044548 1 0.0376 0.995 0.996 0.004
#> SRR1044549 2 0.0000 1.000 0.000 1.000
#> SRR1044550 2 0.0000 1.000 0.000 1.000
#> SRR1044551 2 0.0000 1.000 0.000 1.000
#> SRR1044552 1 0.0000 0.998 1.000 0.000
#> SRR1044553 1 0.0000 0.998 1.000 0.000
#> SRR1044554 1 0.0376 0.995 0.996 0.004
#> SRR1044555 2 0.0000 1.000 0.000 1.000
#> SRR1044556 1 0.0000 0.998 1.000 0.000
#> SRR1044557 1 0.0376 0.995 0.996 0.004
#> SRR1044558 1 0.0000 0.998 1.000 0.000
#> SRR1044559 1 0.0376 0.995 0.996 0.004
#> SRR1044561 1 0.0000 0.998 1.000 0.000
#> SRR1044560 2 0.0000 1.000 0.000 1.000
#> SRR1044562 1 0.0000 0.998 1.000 0.000
#> SRR1044563 1 0.0000 0.998 1.000 0.000
#> SRR1044564 1 0.0000 0.998 1.000 0.000
#> SRR1044565 2 0.0000 1.000 0.000 1.000
#> SRR1044566 2 0.0000 1.000 0.000 1.000
#> SRR1044567 1 0.0000 0.998 1.000 0.000
#> SRR1044568 1 0.0000 0.998 1.000 0.000
#> SRR1044569 1 0.0000 0.998 1.000 0.000
#> SRR1044570 1 0.0000 0.998 1.000 0.000
#> SRR1044571 1 0.0000 0.998 1.000 0.000
#> SRR1044572 1 0.0000 0.998 1.000 0.000
#> SRR1044573 1 0.0000 0.998 1.000 0.000
#> SRR1044574 1 0.0000 0.998 1.000 0.000
#> SRR1044575 1 0.0000 0.998 1.000 0.000
#> SRR1044576 2 0.0000 1.000 0.000 1.000
#> SRR1044577 2 0.0000 1.000 0.000 1.000
#> SRR1044578 2 0.0000 1.000 0.000 1.000
#> SRR1044579 1 0.0000 0.998 1.000 0.000
#> SRR1044580 1 0.0000 0.998 1.000 0.000
#> SRR1044581 1 0.0000 0.998 1.000 0.000
#> SRR1044582 1 0.0000 0.998 1.000 0.000
#> SRR1044583 1 0.0000 0.998 1.000 0.000
#> SRR1044584 1 0.0000 0.998 1.000 0.000
#> SRR1044585 1 0.0000 0.998 1.000 0.000
#> SRR1044586 1 0.0000 0.998 1.000 0.000
#> SRR1044587 1 0.0000 0.998 1.000 0.000
#> SRR1044588 1 0.0000 0.998 1.000 0.000
#> SRR1044589 1 0.0000 0.998 1.000 0.000
#> SRR1044590 1 0.0000 0.998 1.000 0.000
#> SRR1044591 1 0.0000 0.998 1.000 0.000
#> SRR1044592 1 0.0000 0.998 1.000 0.000
#> SRR1044593 1 0.0000 0.998 1.000 0.000
#> SRR1044594 1 0.0000 0.998 1.000 0.000
#> SRR1044595 1 0.0000 0.998 1.000 0.000
#> SRR1044596 1 0.0000 0.998 1.000 0.000
#> SRR1044597 1 0.0376 0.994 0.996 0.004
#> SRR1044598 1 0.1184 0.984 0.984 0.016
#> SRR1044599 1 0.0938 0.987 0.988 0.012
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.0237 0.8833 0.004 0.996 0.000
#> SRR1044416 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044417 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044418 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044420 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044419 2 0.0000 0.8825 0.000 1.000 0.000
#> SRR1044421 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044422 2 0.5060 0.8990 0.156 0.816 0.028
#> SRR1044423 2 0.5180 0.8990 0.156 0.812 0.032
#> SRR1044424 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044425 1 0.5810 0.8979 0.664 0.000 0.336
#> SRR1044426 3 0.6095 -0.0845 0.392 0.000 0.608
#> SRR1044427 3 0.4842 0.5937 0.224 0.000 0.776
#> SRR1044428 3 0.1289 0.8746 0.032 0.000 0.968
#> SRR1044429 1 0.6305 0.5815 0.516 0.000 0.484
#> SRR1044430 3 0.2400 0.8029 0.064 0.004 0.932
#> SRR1044431 1 0.6192 0.7414 0.580 0.000 0.420
#> SRR1044433 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044432 3 0.1289 0.8746 0.032 0.000 0.968
#> SRR1044434 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044435 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044436 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044437 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044439 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044438 1 0.5529 0.9478 0.704 0.000 0.296
#> SRR1044440 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044441 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044442 1 0.5529 0.9481 0.704 0.000 0.296
#> SRR1044443 1 0.6262 0.9154 0.696 0.020 0.284
#> SRR1044444 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044445 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044446 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044447 2 0.5849 0.8915 0.216 0.756 0.028
#> SRR1044449 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044448 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044450 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044451 2 0.6056 0.8899 0.224 0.744 0.032
#> SRR1044452 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044453 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044454 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044455 2 0.0000 0.8825 0.000 1.000 0.000
#> SRR1044456 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044457 2 0.2356 0.8681 0.072 0.928 0.000
#> SRR1044458 2 0.0000 0.8825 0.000 1.000 0.000
#> SRR1044459 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044460 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044461 2 0.0000 0.8825 0.000 1.000 0.000
#> SRR1044462 1 0.6215 0.7294 0.572 0.000 0.428
#> SRR1044463 3 0.0424 0.8759 0.008 0.000 0.992
#> SRR1044464 1 0.5529 0.9476 0.704 0.000 0.296
#> SRR1044466 3 0.0424 0.8672 0.008 0.000 0.992
#> SRR1044465 3 0.1411 0.8738 0.036 0.000 0.964
#> SRR1044467 3 0.1860 0.8651 0.052 0.000 0.948
#> SRR1044468 2 0.5239 0.8989 0.160 0.808 0.032
#> SRR1044469 2 0.1964 0.8693 0.056 0.944 0.000
#> SRR1044470 3 0.0424 0.8671 0.008 0.000 0.992
#> SRR1044471 3 0.1411 0.8738 0.036 0.000 0.964
#> SRR1044472 3 0.1129 0.8730 0.020 0.004 0.976
#> SRR1044473 3 0.0592 0.8769 0.012 0.000 0.988
#> SRR1044474 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044475 2 0.1964 0.8693 0.056 0.944 0.000
#> SRR1044476 2 0.0000 0.8825 0.000 1.000 0.000
#> SRR1044477 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044478 2 0.0424 0.8839 0.008 0.992 0.000
#> SRR1044479 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044480 1 0.5835 0.8927 0.660 0.000 0.340
#> SRR1044481 3 0.2625 0.8344 0.084 0.000 0.916
#> SRR1044482 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044483 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044484 3 0.4974 0.5572 0.236 0.000 0.764
#> SRR1044486 3 0.1411 0.8744 0.036 0.000 0.964
#> SRR1044485 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044487 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044488 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044489 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044490 3 0.2066 0.8595 0.060 0.000 0.940
#> SRR1044491 3 0.0237 0.8705 0.004 0.000 0.996
#> SRR1044492 3 0.0237 0.8705 0.004 0.000 0.996
#> SRR1044493 3 0.0424 0.8759 0.008 0.000 0.992
#> SRR1044494 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044496 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044495 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044497 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044499 2 0.1860 0.8700 0.052 0.948 0.000
#> SRR1044498 3 0.6274 -0.3825 0.456 0.000 0.544
#> SRR1044500 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044501 2 0.0000 0.8825 0.000 1.000 0.000
#> SRR1044502 2 0.2448 0.8741 0.076 0.924 0.000
#> SRR1044503 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044504 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044505 3 0.6180 -0.2014 0.416 0.000 0.584
#> SRR1044506 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044507 1 0.5926 0.8673 0.644 0.000 0.356
#> SRR1044508 1 0.5621 0.9357 0.692 0.000 0.308
#> SRR1044509 1 0.5397 0.9619 0.720 0.000 0.280
#> SRR1044510 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044511 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044512 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044513 2 0.6056 0.8902 0.224 0.744 0.032
#> SRR1044514 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044515 2 0.5551 0.8924 0.212 0.768 0.020
#> SRR1044516 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044517 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044518 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044519 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044520 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044521 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044522 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044523 2 0.6056 0.8902 0.224 0.744 0.032
#> SRR1044524 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044525 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044526 3 0.5591 0.3773 0.304 0.000 0.696
#> SRR1044527 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044528 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044529 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044530 3 0.1031 0.8763 0.024 0.000 0.976
#> SRR1044531 3 0.1289 0.8746 0.032 0.000 0.968
#> SRR1044533 3 0.1289 0.8746 0.032 0.000 0.968
#> SRR1044532 3 0.0237 0.8705 0.004 0.000 0.996
#> SRR1044534 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044535 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044536 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044537 3 0.2356 0.8462 0.072 0.000 0.928
#> SRR1044538 3 0.0747 0.8770 0.016 0.000 0.984
#> SRR1044539 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044540 3 0.1289 0.8746 0.032 0.000 0.968
#> SRR1044541 2 0.2066 0.8716 0.060 0.940 0.000
#> SRR1044542 3 0.1031 0.8495 0.024 0.000 0.976
#> SRR1044543 3 0.2796 0.8296 0.092 0.000 0.908
#> SRR1044544 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044545 1 0.5397 0.9618 0.720 0.000 0.280
#> SRR1044546 3 0.0424 0.8741 0.008 0.000 0.992
#> SRR1044547 1 0.5560 0.9432 0.700 0.000 0.300
#> SRR1044548 3 0.0592 0.8725 0.012 0.000 0.988
#> SRR1044549 2 0.5467 0.8976 0.176 0.792 0.032
#> SRR1044550 2 0.5239 0.8989 0.160 0.808 0.032
#> SRR1044551 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044552 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044553 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044554 3 0.0237 0.8705 0.004 0.000 0.996
#> SRR1044555 2 0.3192 0.8550 0.112 0.888 0.000
#> SRR1044556 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044557 3 0.0237 0.8705 0.004 0.000 0.996
#> SRR1044558 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044559 3 0.1753 0.8600 0.048 0.000 0.952
#> SRR1044561 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044560 2 0.0000 0.8825 0.000 1.000 0.000
#> SRR1044562 3 0.0237 0.8705 0.004 0.000 0.996
#> SRR1044563 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044564 3 0.4974 0.5754 0.236 0.000 0.764
#> SRR1044565 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044566 2 0.0000 0.8825 0.000 1.000 0.000
#> SRR1044567 3 0.0747 0.8731 0.016 0.000 0.984
#> SRR1044568 1 0.5810 0.8996 0.664 0.000 0.336
#> SRR1044569 3 0.1964 0.8637 0.056 0.000 0.944
#> SRR1044570 3 0.0747 0.8763 0.016 0.000 0.984
#> SRR1044571 3 0.1289 0.8746 0.032 0.000 0.968
#> SRR1044572 3 0.1411 0.8735 0.036 0.000 0.964
#> SRR1044573 3 0.1411 0.8734 0.036 0.000 0.964
#> SRR1044574 3 0.2625 0.8371 0.084 0.000 0.916
#> SRR1044575 3 0.1289 0.8746 0.032 0.000 0.968
#> SRR1044576 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044577 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044578 2 0.5298 0.8986 0.164 0.804 0.032
#> SRR1044579 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044580 1 0.6192 0.7452 0.580 0.000 0.420
#> SRR1044581 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044582 3 0.0592 0.8768 0.012 0.000 0.988
#> SRR1044583 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044584 1 0.5948 0.8616 0.640 0.000 0.360
#> SRR1044585 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044586 3 0.1860 0.8620 0.052 0.000 0.948
#> SRR1044587 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044588 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044589 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044590 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044591 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044592 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044593 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044594 1 0.5363 0.9647 0.724 0.000 0.276
#> SRR1044595 3 0.6192 -0.2021 0.420 0.000 0.580
#> SRR1044596 1 0.5397 0.9619 0.720 0.000 0.280
#> SRR1044597 3 0.6836 -0.2463 0.412 0.016 0.572
#> SRR1044598 3 0.2066 0.8036 0.060 0.000 0.940
#> SRR1044599 3 0.2165 0.7980 0.064 0.000 0.936
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 2 0.4304 0.6035 0.000 0.716 0.284 0.000
#> SRR1044416 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044417 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044418 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044420 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044419 2 0.4356 0.5909 0.000 0.708 0.292 0.000
#> SRR1044421 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044422 2 0.0921 0.8857 0.000 0.972 0.028 0.000
#> SRR1044423 2 0.0592 0.8935 0.000 0.984 0.016 0.000
#> SRR1044424 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044425 4 0.1637 0.9040 0.060 0.000 0.000 0.940
#> SRR1044426 4 0.4877 0.3704 0.408 0.000 0.000 0.592
#> SRR1044427 1 0.4898 0.2583 0.584 0.000 0.000 0.416
#> SRR1044428 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044429 4 0.3801 0.7425 0.220 0.000 0.000 0.780
#> SRR1044430 1 0.0188 0.9493 0.996 0.000 0.000 0.004
#> SRR1044431 4 0.3311 0.7980 0.172 0.000 0.000 0.828
#> SRR1044433 4 0.0469 0.9332 0.000 0.000 0.012 0.988
#> SRR1044432 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044434 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044435 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044436 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044437 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044439 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044438 4 0.0707 0.9283 0.020 0.000 0.000 0.980
#> SRR1044440 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044441 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044442 4 0.1284 0.9255 0.024 0.000 0.012 0.964
#> SRR1044443 4 0.2983 0.8763 0.016 0.012 0.076 0.896
#> SRR1044444 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044445 4 0.0469 0.9332 0.000 0.000 0.012 0.988
#> SRR1044446 3 0.0469 0.8816 0.000 0.012 0.988 0.000
#> SRR1044447 2 0.4713 0.3705 0.000 0.640 0.360 0.000
#> SRR1044449 3 0.0469 0.8816 0.000 0.012 0.988 0.000
#> SRR1044448 3 0.0469 0.8816 0.000 0.012 0.988 0.000
#> SRR1044450 3 0.0469 0.8816 0.000 0.012 0.988 0.000
#> SRR1044451 3 0.4992 0.1305 0.000 0.476 0.524 0.000
#> SRR1044452 3 0.0469 0.8816 0.000 0.012 0.988 0.000
#> SRR1044453 3 0.0469 0.8816 0.000 0.012 0.988 0.000
#> SRR1044454 3 0.0469 0.8816 0.000 0.012 0.988 0.000
#> SRR1044455 2 0.4356 0.5909 0.000 0.708 0.292 0.000
#> SRR1044456 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044457 3 0.4431 0.5296 0.000 0.304 0.696 0.000
#> SRR1044458 2 0.4356 0.5909 0.000 0.708 0.292 0.000
#> SRR1044459 3 0.0469 0.8816 0.000 0.012 0.988 0.000
#> SRR1044460 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044461 2 0.4356 0.5909 0.000 0.708 0.292 0.000
#> SRR1044462 4 0.3356 0.7967 0.176 0.000 0.000 0.824
#> SRR1044463 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044464 4 0.0895 0.9283 0.020 0.000 0.004 0.976
#> SRR1044466 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044465 1 0.0188 0.9491 0.996 0.000 0.000 0.004
#> SRR1044467 1 0.0707 0.9404 0.980 0.000 0.000 0.020
#> SRR1044468 2 0.0817 0.8884 0.000 0.976 0.024 0.000
#> SRR1044469 3 0.3726 0.6847 0.000 0.212 0.788 0.000
#> SRR1044470 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044471 1 0.0469 0.9458 0.988 0.000 0.000 0.012
#> SRR1044472 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044473 1 0.0188 0.9491 0.996 0.000 0.000 0.004
#> SRR1044474 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044475 3 0.4564 0.5028 0.000 0.328 0.672 0.000
#> SRR1044476 2 0.4356 0.5909 0.000 0.708 0.292 0.000
#> SRR1044477 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044478 2 0.4250 0.6157 0.000 0.724 0.276 0.000
#> SRR1044479 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044480 4 0.1792 0.8983 0.068 0.000 0.000 0.932
#> SRR1044481 1 0.2011 0.8930 0.920 0.000 0.000 0.080
#> SRR1044482 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044483 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044484 1 0.4624 0.4617 0.660 0.000 0.000 0.340
#> SRR1044486 1 0.0469 0.9460 0.988 0.000 0.000 0.012
#> SRR1044485 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044487 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044488 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044489 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044490 1 0.0921 0.9356 0.972 0.000 0.000 0.028
#> SRR1044491 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044492 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044493 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044494 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044496 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044495 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044497 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044499 3 0.4941 0.2291 0.000 0.436 0.564 0.000
#> SRR1044498 4 0.4624 0.5332 0.340 0.000 0.000 0.660
#> SRR1044500 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044501 2 0.4356 0.5909 0.000 0.708 0.292 0.000
#> SRR1044502 3 0.4985 0.0707 0.000 0.468 0.532 0.000
#> SRR1044503 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044504 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044505 4 0.4713 0.4870 0.360 0.000 0.000 0.640
#> SRR1044506 4 0.0469 0.9332 0.000 0.000 0.012 0.988
#> SRR1044507 4 0.2676 0.8785 0.092 0.000 0.012 0.896
#> SRR1044508 4 0.1584 0.9189 0.036 0.000 0.012 0.952
#> SRR1044509 4 0.0657 0.9330 0.004 0.000 0.012 0.984
#> SRR1044510 3 0.0469 0.8816 0.000 0.012 0.988 0.000
#> SRR1044511 3 0.0469 0.8816 0.000 0.012 0.988 0.000
#> SRR1044512 3 0.0469 0.8816 0.000 0.012 0.988 0.000
#> SRR1044513 2 0.3610 0.6866 0.000 0.800 0.200 0.000
#> SRR1044514 3 0.0469 0.8816 0.000 0.012 0.988 0.000
#> SRR1044515 2 0.3907 0.6495 0.000 0.768 0.232 0.000
#> SRR1044516 2 0.0336 0.8978 0.000 0.992 0.008 0.000
#> SRR1044517 3 0.0469 0.8816 0.000 0.012 0.988 0.000
#> SRR1044518 3 0.0469 0.8816 0.000 0.012 0.988 0.000
#> SRR1044519 3 0.0469 0.8816 0.000 0.012 0.988 0.000
#> SRR1044520 3 0.0469 0.8816 0.000 0.012 0.988 0.000
#> SRR1044521 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044522 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044523 2 0.3528 0.6977 0.000 0.808 0.192 0.000
#> SRR1044524 3 0.0469 0.8816 0.000 0.012 0.988 0.000
#> SRR1044525 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044526 1 0.4830 0.3630 0.608 0.000 0.000 0.392
#> SRR1044527 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044528 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044529 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044530 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044531 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044533 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044532 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044534 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044535 3 0.0469 0.8816 0.000 0.012 0.988 0.000
#> SRR1044536 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044537 1 0.2011 0.8934 0.920 0.000 0.000 0.080
#> SRR1044538 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044539 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044540 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044541 3 0.4972 0.1182 0.000 0.456 0.544 0.000
#> SRR1044542 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044543 1 0.2408 0.8690 0.896 0.000 0.000 0.104
#> SRR1044544 3 0.1118 0.8645 0.000 0.036 0.964 0.000
#> SRR1044545 4 0.0376 0.9345 0.004 0.000 0.004 0.992
#> SRR1044546 1 0.0469 0.9463 0.988 0.000 0.000 0.012
#> SRR1044547 4 0.0817 0.9256 0.024 0.000 0.000 0.976
#> SRR1044548 1 0.0592 0.9438 0.984 0.000 0.000 0.016
#> SRR1044549 2 0.1389 0.8651 0.000 0.952 0.048 0.000
#> SRR1044550 2 0.0592 0.8933 0.000 0.984 0.016 0.000
#> SRR1044551 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044552 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044553 4 0.0469 0.9332 0.000 0.000 0.012 0.988
#> SRR1044554 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044555 3 0.0469 0.8816 0.000 0.012 0.988 0.000
#> SRR1044556 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044557 1 0.0188 0.9494 0.996 0.000 0.000 0.004
#> SRR1044558 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044559 1 0.1743 0.9137 0.940 0.004 0.000 0.056
#> SRR1044561 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044560 2 0.4356 0.5909 0.000 0.708 0.292 0.000
#> SRR1044562 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044563 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044564 1 0.4134 0.6601 0.740 0.000 0.000 0.260
#> SRR1044565 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044566 2 0.4356 0.5909 0.000 0.708 0.292 0.000
#> SRR1044567 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044568 4 0.1637 0.9048 0.060 0.000 0.000 0.940
#> SRR1044569 1 0.1022 0.9345 0.968 0.000 0.000 0.032
#> SRR1044570 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044571 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044572 1 0.0188 0.9494 0.996 0.000 0.000 0.004
#> SRR1044573 1 0.0469 0.9462 0.988 0.000 0.000 0.012
#> SRR1044574 1 0.1637 0.9100 0.940 0.000 0.000 0.060
#> SRR1044575 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044576 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044577 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044578 2 0.0000 0.9017 0.000 1.000 0.000 0.000
#> SRR1044579 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044580 4 0.3356 0.7949 0.176 0.000 0.000 0.824
#> SRR1044581 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044582 1 0.0188 0.9494 0.996 0.000 0.000 0.004
#> SRR1044583 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044584 4 0.2149 0.8834 0.088 0.000 0.000 0.912
#> SRR1044585 4 0.0000 0.9350 0.000 0.000 0.000 1.000
#> SRR1044586 1 0.1557 0.9145 0.944 0.000 0.000 0.056
#> SRR1044587 4 0.0469 0.9332 0.000 0.000 0.012 0.988
#> SRR1044588 4 0.0469 0.9332 0.000 0.000 0.012 0.988
#> SRR1044589 4 0.0469 0.9332 0.000 0.000 0.012 0.988
#> SRR1044590 4 0.0469 0.9332 0.000 0.000 0.012 0.988
#> SRR1044591 4 0.0469 0.9332 0.000 0.000 0.012 0.988
#> SRR1044592 4 0.0469 0.9332 0.000 0.000 0.012 0.988
#> SRR1044593 4 0.0469 0.9332 0.000 0.000 0.012 0.988
#> SRR1044594 4 0.0469 0.9332 0.000 0.000 0.012 0.988
#> SRR1044595 4 0.5402 0.1253 0.472 0.000 0.012 0.516
#> SRR1044596 4 0.0657 0.9330 0.004 0.000 0.012 0.984
#> SRR1044597 4 0.6425 0.4953 0.300 0.096 0.000 0.604
#> SRR1044598 1 0.0000 0.9503 1.000 0.000 0.000 0.000
#> SRR1044599 1 0.0000 0.9503 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.3928 0.6020 0.000 0.700 0.296 0.000 0.004
#> SRR1044416 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044417 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044418 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044420 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044419 2 0.3990 0.5845 0.000 0.688 0.308 0.000 0.004
#> SRR1044421 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044422 2 0.0880 0.8794 0.000 0.968 0.032 0.000 0.000
#> SRR1044423 2 0.0510 0.8896 0.000 0.984 0.016 0.000 0.000
#> SRR1044424 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044425 4 0.1117 0.5907 0.020 0.000 0.000 0.964 0.016
#> SRR1044426 4 0.6808 -0.1048 0.340 0.000 0.000 0.360 0.300
#> SRR1044427 4 0.5264 0.2203 0.392 0.000 0.000 0.556 0.052
#> SRR1044428 1 0.1270 0.9324 0.948 0.000 0.000 0.000 0.052
#> SRR1044429 4 0.4237 0.4267 0.200 0.000 0.000 0.752 0.048
#> SRR1044430 1 0.1168 0.9376 0.960 0.000 0.000 0.008 0.032
#> SRR1044431 4 0.3146 0.5398 0.092 0.000 0.000 0.856 0.052
#> SRR1044433 5 0.3752 0.8231 0.000 0.000 0.000 0.292 0.708
#> SRR1044432 1 0.0794 0.9390 0.972 0.000 0.000 0.000 0.028
#> SRR1044434 4 0.3561 0.3805 0.000 0.000 0.000 0.740 0.260
#> SRR1044435 4 0.3586 0.3880 0.000 0.000 0.000 0.736 0.264
#> SRR1044436 4 0.1197 0.5786 0.000 0.000 0.000 0.952 0.048
#> SRR1044437 4 0.3274 0.4498 0.000 0.000 0.000 0.780 0.220
#> SRR1044439 4 0.0963 0.5829 0.000 0.000 0.000 0.964 0.036
#> SRR1044438 4 0.2628 0.5436 0.028 0.000 0.000 0.884 0.088
#> SRR1044440 4 0.3636 0.3532 0.000 0.000 0.000 0.728 0.272
#> SRR1044441 4 0.3612 0.3611 0.000 0.000 0.000 0.732 0.268
#> SRR1044442 5 0.3752 0.8231 0.000 0.000 0.000 0.292 0.708
#> SRR1044443 5 0.3752 0.8231 0.000 0.000 0.000 0.292 0.708
#> SRR1044444 4 0.2891 0.4906 0.000 0.000 0.000 0.824 0.176
#> SRR1044445 5 0.4268 0.5690 0.000 0.000 0.000 0.444 0.556
#> SRR1044446 3 0.0609 0.8279 0.000 0.000 0.980 0.000 0.020
#> SRR1044447 2 0.4126 0.3056 0.000 0.620 0.380 0.000 0.000
#> SRR1044449 3 0.3210 0.7521 0.000 0.000 0.788 0.000 0.212
#> SRR1044448 3 0.0609 0.8279 0.000 0.000 0.980 0.000 0.020
#> SRR1044450 3 0.0609 0.8279 0.000 0.000 0.980 0.000 0.020
#> SRR1044451 3 0.4890 0.2125 0.000 0.452 0.524 0.000 0.024
#> SRR1044452 3 0.3039 0.7597 0.000 0.000 0.808 0.000 0.192
#> SRR1044453 3 0.3039 0.7597 0.000 0.000 0.808 0.000 0.192
#> SRR1044454 3 0.3039 0.7597 0.000 0.000 0.808 0.000 0.192
#> SRR1044455 2 0.3990 0.5845 0.000 0.688 0.308 0.000 0.004
#> SRR1044456 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044457 3 0.3790 0.5419 0.000 0.272 0.724 0.000 0.004
#> SRR1044458 2 0.3990 0.5845 0.000 0.688 0.308 0.000 0.004
#> SRR1044459 3 0.0000 0.8273 0.000 0.000 1.000 0.000 0.000
#> SRR1044460 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044461 2 0.3990 0.5845 0.000 0.688 0.308 0.000 0.004
#> SRR1044462 4 0.4025 0.4775 0.132 0.000 0.000 0.792 0.076
#> SRR1044463 1 0.0290 0.9394 0.992 0.000 0.000 0.000 0.008
#> SRR1044464 4 0.0865 0.5879 0.004 0.000 0.000 0.972 0.024
#> SRR1044466 1 0.0290 0.9394 0.992 0.000 0.000 0.000 0.008
#> SRR1044465 1 0.0807 0.9391 0.976 0.000 0.000 0.012 0.012
#> SRR1044467 1 0.1082 0.9260 0.964 0.000 0.000 0.028 0.008
#> SRR1044468 2 0.0865 0.8824 0.000 0.972 0.024 0.000 0.004
#> SRR1044469 3 0.3210 0.6476 0.000 0.212 0.788 0.000 0.000
#> SRR1044470 1 0.0404 0.9391 0.988 0.000 0.000 0.000 0.012
#> SRR1044471 1 0.0992 0.9339 0.968 0.000 0.000 0.024 0.008
#> SRR1044472 1 0.0162 0.9390 0.996 0.000 0.000 0.000 0.004
#> SRR1044473 1 0.0579 0.9367 0.984 0.000 0.000 0.008 0.008
#> SRR1044474 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044475 3 0.6452 0.4160 0.000 0.328 0.476 0.000 0.196
#> SRR1044476 2 0.3990 0.5845 0.000 0.688 0.308 0.000 0.004
#> SRR1044477 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044478 2 0.3906 0.6076 0.000 0.704 0.292 0.000 0.004
#> SRR1044479 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044480 4 0.1877 0.5649 0.012 0.000 0.000 0.924 0.064
#> SRR1044481 1 0.3767 0.8261 0.812 0.000 0.000 0.120 0.068
#> SRR1044482 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044483 4 0.0162 0.5896 0.000 0.000 0.000 0.996 0.004
#> SRR1044484 1 0.5649 0.1191 0.472 0.000 0.000 0.452 0.076
#> SRR1044486 1 0.1830 0.9223 0.924 0.000 0.000 0.008 0.068
#> SRR1044485 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044487 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044488 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044489 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044490 1 0.1907 0.9257 0.928 0.000 0.000 0.028 0.044
#> SRR1044491 1 0.0963 0.9367 0.964 0.000 0.000 0.000 0.036
#> SRR1044492 1 0.0404 0.9389 0.988 0.000 0.000 0.000 0.012
#> SRR1044493 1 0.0290 0.9394 0.992 0.000 0.000 0.000 0.008
#> SRR1044494 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044496 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044495 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044497 4 0.0794 0.5875 0.000 0.000 0.000 0.972 0.028
#> SRR1044499 3 0.4403 0.1503 0.000 0.436 0.560 0.000 0.004
#> SRR1044498 4 0.5064 0.3731 0.232 0.000 0.000 0.680 0.088
#> SRR1044500 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044501 2 0.3990 0.5845 0.000 0.688 0.308 0.000 0.004
#> SRR1044502 3 0.4397 0.1285 0.000 0.432 0.564 0.000 0.004
#> SRR1044503 4 0.1478 0.5727 0.000 0.000 0.000 0.936 0.064
#> SRR1044504 4 0.3274 0.4566 0.000 0.000 0.000 0.780 0.220
#> SRR1044505 4 0.5039 0.3661 0.244 0.000 0.000 0.676 0.080
#> SRR1044506 5 0.4060 0.7530 0.000 0.000 0.000 0.360 0.640
#> SRR1044507 4 0.4304 -0.3338 0.000 0.000 0.000 0.516 0.484
#> SRR1044508 5 0.3730 0.8172 0.000 0.000 0.000 0.288 0.712
#> SRR1044509 5 0.3752 0.8231 0.000 0.000 0.000 0.292 0.708
#> SRR1044510 3 0.0290 0.8277 0.000 0.000 0.992 0.000 0.008
#> SRR1044511 3 0.0000 0.8273 0.000 0.000 1.000 0.000 0.000
#> SRR1044512 3 0.2516 0.7885 0.000 0.000 0.860 0.000 0.140
#> SRR1044513 2 0.3210 0.6579 0.000 0.788 0.212 0.000 0.000
#> SRR1044514 3 0.0609 0.8279 0.000 0.000 0.980 0.000 0.020
#> SRR1044515 2 0.3534 0.6059 0.000 0.744 0.256 0.000 0.000
#> SRR1044516 2 0.0290 0.8941 0.000 0.992 0.008 0.000 0.000
#> SRR1044517 3 0.3039 0.7597 0.000 0.000 0.808 0.000 0.192
#> SRR1044518 3 0.0609 0.8279 0.000 0.000 0.980 0.000 0.020
#> SRR1044519 3 0.0609 0.8279 0.000 0.000 0.980 0.000 0.020
#> SRR1044520 3 0.0963 0.8252 0.000 0.000 0.964 0.000 0.036
#> SRR1044521 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044522 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044523 2 0.3143 0.6698 0.000 0.796 0.204 0.000 0.000
#> SRR1044524 3 0.0000 0.8273 0.000 0.000 1.000 0.000 0.000
#> SRR1044525 4 0.3366 0.4221 0.000 0.000 0.000 0.768 0.232
#> SRR1044526 4 0.4890 0.3524 0.256 0.000 0.000 0.680 0.064
#> SRR1044527 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044528 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044529 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044530 1 0.0290 0.9394 0.992 0.000 0.000 0.000 0.008
#> SRR1044531 1 0.0794 0.9391 0.972 0.000 0.000 0.000 0.028
#> SRR1044533 1 0.0290 0.9380 0.992 0.000 0.000 0.000 0.008
#> SRR1044532 1 0.0162 0.9390 0.996 0.000 0.000 0.000 0.004
#> SRR1044534 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044535 3 0.0162 0.8277 0.000 0.000 0.996 0.000 0.004
#> SRR1044536 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044537 1 0.4676 0.7130 0.720 0.000 0.000 0.208 0.072
#> SRR1044538 1 0.0404 0.9398 0.988 0.000 0.000 0.000 0.012
#> SRR1044539 4 0.0162 0.5890 0.000 0.000 0.000 0.996 0.004
#> SRR1044540 1 0.1121 0.9352 0.956 0.000 0.000 0.000 0.044
#> SRR1044541 3 0.4383 0.1528 0.000 0.424 0.572 0.000 0.004
#> SRR1044542 1 0.0290 0.9394 0.992 0.000 0.000 0.000 0.008
#> SRR1044543 1 0.2777 0.8297 0.864 0.000 0.000 0.120 0.016
#> SRR1044544 3 0.0865 0.8186 0.000 0.024 0.972 0.000 0.004
#> SRR1044545 4 0.1357 0.5794 0.004 0.000 0.000 0.948 0.048
#> SRR1044546 1 0.1704 0.9235 0.928 0.000 0.000 0.004 0.068
#> SRR1044547 4 0.1282 0.5850 0.004 0.000 0.000 0.952 0.044
#> SRR1044548 1 0.2144 0.9164 0.912 0.000 0.000 0.020 0.068
#> SRR1044549 2 0.1197 0.8602 0.000 0.952 0.048 0.000 0.000
#> SRR1044550 2 0.0510 0.8895 0.000 0.984 0.016 0.000 0.000
#> SRR1044551 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044552 4 0.3636 0.3554 0.000 0.000 0.000 0.728 0.272
#> SRR1044553 4 0.4235 -0.1740 0.000 0.000 0.000 0.576 0.424
#> SRR1044554 1 0.1704 0.9235 0.928 0.000 0.000 0.004 0.068
#> SRR1044555 3 0.0000 0.8273 0.000 0.000 1.000 0.000 0.000
#> SRR1044556 4 0.0703 0.5866 0.000 0.000 0.000 0.976 0.024
#> SRR1044557 1 0.2491 0.9068 0.896 0.000 0.000 0.036 0.068
#> SRR1044558 4 0.0609 0.5891 0.000 0.000 0.000 0.980 0.020
#> SRR1044559 1 0.4199 0.7837 0.772 0.000 0.000 0.160 0.068
#> SRR1044561 4 0.3612 0.3611 0.000 0.000 0.000 0.732 0.268
#> SRR1044560 2 0.3990 0.5845 0.000 0.688 0.308 0.000 0.004
#> SRR1044562 1 0.3464 0.8568 0.836 0.000 0.000 0.096 0.068
#> SRR1044563 4 0.0000 0.5887 0.000 0.000 0.000 1.000 0.000
#> SRR1044564 4 0.5553 -0.0874 0.448 0.000 0.000 0.484 0.068
#> SRR1044565 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044566 2 0.3990 0.5845 0.000 0.688 0.308 0.000 0.004
#> SRR1044567 1 0.0162 0.9390 0.996 0.000 0.000 0.000 0.004
#> SRR1044568 4 0.1965 0.5760 0.024 0.000 0.000 0.924 0.052
#> SRR1044569 1 0.1386 0.9297 0.952 0.000 0.000 0.032 0.016
#> SRR1044570 1 0.0290 0.9394 0.992 0.000 0.000 0.000 0.008
#> SRR1044571 1 0.0290 0.9380 0.992 0.000 0.000 0.000 0.008
#> SRR1044572 1 0.0703 0.9392 0.976 0.000 0.000 0.000 0.024
#> SRR1044573 1 0.0579 0.9404 0.984 0.000 0.000 0.008 0.008
#> SRR1044574 1 0.1894 0.8892 0.920 0.000 0.000 0.072 0.008
#> SRR1044575 1 0.0290 0.9394 0.992 0.000 0.000 0.000 0.008
#> SRR1044576 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044577 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044578 2 0.0000 0.8978 0.000 1.000 0.000 0.000 0.000
#> SRR1044579 4 0.3636 0.3532 0.000 0.000 0.000 0.728 0.272
#> SRR1044580 4 0.3416 0.5171 0.088 0.000 0.000 0.840 0.072
#> SRR1044581 4 0.3480 0.3973 0.000 0.000 0.000 0.752 0.248
#> SRR1044582 1 0.2144 0.9167 0.912 0.000 0.000 0.020 0.068
#> SRR1044583 4 0.3612 0.3611 0.000 0.000 0.000 0.732 0.268
#> SRR1044584 4 0.1740 0.5808 0.012 0.000 0.000 0.932 0.056
#> SRR1044585 4 0.2773 0.5024 0.000 0.000 0.000 0.836 0.164
#> SRR1044586 1 0.3994 0.8081 0.792 0.000 0.000 0.140 0.068
#> SRR1044587 5 0.4088 0.7412 0.000 0.000 0.000 0.368 0.632
#> SRR1044588 4 0.4307 -0.4128 0.000 0.000 0.000 0.504 0.496
#> SRR1044589 4 0.4307 -0.4128 0.000 0.000 0.000 0.504 0.496
#> SRR1044590 4 0.4307 -0.4380 0.000 0.000 0.000 0.504 0.496
#> SRR1044591 5 0.4235 0.6261 0.000 0.000 0.000 0.424 0.576
#> SRR1044592 5 0.3752 0.8231 0.000 0.000 0.000 0.292 0.708
#> SRR1044593 4 0.4307 -0.4128 0.000 0.000 0.000 0.504 0.496
#> SRR1044594 4 0.4307 -0.4249 0.000 0.000 0.000 0.500 0.500
#> SRR1044595 5 0.6384 0.1690 0.388 0.000 0.000 0.168 0.444
#> SRR1044596 5 0.3752 0.8231 0.000 0.000 0.000 0.292 0.708
#> SRR1044597 4 0.6447 0.3077 0.208 0.052 0.000 0.616 0.124
#> SRR1044598 1 0.0290 0.9394 0.992 0.000 0.000 0.000 0.008
#> SRR1044599 1 0.0510 0.9399 0.984 0.000 0.000 0.000 0.016
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 6 0.3864 0.66942 0.000 0.480 0.000 0.000 0.000 0.520
#> SRR1044416 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044417 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044418 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044420 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044419 6 0.3774 0.78475 0.000 0.408 0.000 0.000 0.000 0.592
#> SRR1044421 2 0.0363 0.91910 0.000 0.988 0.000 0.000 0.000 0.012
#> SRR1044422 2 0.1501 0.83638 0.000 0.924 0.000 0.000 0.000 0.076
#> SRR1044423 2 0.2219 0.73487 0.000 0.864 0.000 0.000 0.000 0.136
#> SRR1044424 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044425 4 0.4143 0.45715 0.016 0.000 0.000 0.692 0.276 0.016
#> SRR1044426 4 0.6587 -0.08683 0.316 0.000 0.000 0.452 0.184 0.048
#> SRR1044427 5 0.6245 0.54107 0.228 0.000 0.000 0.248 0.500 0.024
#> SRR1044428 1 0.2814 0.76768 0.820 0.000 0.000 0.000 0.172 0.008
#> SRR1044429 5 0.6400 0.19410 0.144 0.000 0.000 0.380 0.432 0.044
#> SRR1044430 1 0.3213 0.74594 0.784 0.000 0.000 0.008 0.204 0.004
#> SRR1044431 4 0.6112 0.08200 0.112 0.000 0.000 0.476 0.372 0.040
#> SRR1044433 4 0.5449 0.42163 0.000 0.000 0.000 0.504 0.128 0.368
#> SRR1044432 1 0.2320 0.79293 0.864 0.000 0.000 0.000 0.132 0.004
#> SRR1044434 4 0.0632 0.61650 0.000 0.000 0.000 0.976 0.024 0.000
#> SRR1044435 4 0.3167 0.61250 0.000 0.000 0.000 0.832 0.096 0.072
#> SRR1044436 4 0.4497 0.45553 0.000 0.000 0.000 0.624 0.328 0.048
#> SRR1044437 4 0.2331 0.61034 0.000 0.000 0.000 0.888 0.080 0.032
#> SRR1044439 4 0.4408 0.45046 0.000 0.000 0.000 0.636 0.320 0.044
#> SRR1044438 4 0.5254 0.39068 0.016 0.000 0.000 0.560 0.356 0.068
#> SRR1044440 4 0.0363 0.61544 0.000 0.000 0.000 0.988 0.000 0.012
#> SRR1044441 4 0.0603 0.61540 0.000 0.000 0.000 0.980 0.004 0.016
#> SRR1044442 4 0.5449 0.42163 0.000 0.000 0.000 0.504 0.128 0.368
#> SRR1044443 4 0.5449 0.42163 0.000 0.000 0.000 0.504 0.128 0.368
#> SRR1044444 4 0.1967 0.59105 0.000 0.000 0.000 0.904 0.084 0.012
#> SRR1044445 4 0.4614 0.54536 0.000 0.000 0.000 0.684 0.108 0.208
#> SRR1044446 3 0.3101 0.70566 0.000 0.000 0.756 0.000 0.000 0.244
#> SRR1044447 2 0.4378 0.19181 0.000 0.600 0.368 0.000 0.000 0.032
#> SRR1044449 3 0.0363 0.64889 0.000 0.000 0.988 0.000 0.012 0.000
#> SRR1044448 3 0.3101 0.70566 0.000 0.000 0.756 0.000 0.000 0.244
#> SRR1044450 3 0.3101 0.70566 0.000 0.000 0.756 0.000 0.000 0.244
#> SRR1044451 3 0.4101 0.29651 0.000 0.308 0.664 0.000 0.000 0.028
#> SRR1044452 3 0.3916 0.62185 0.000 0.000 0.752 0.000 0.064 0.184
#> SRR1044453 3 0.4122 0.60165 0.000 0.000 0.724 0.000 0.064 0.212
#> SRR1044454 3 0.4122 0.60165 0.000 0.000 0.724 0.000 0.064 0.212
#> SRR1044455 6 0.3774 0.78475 0.000 0.408 0.000 0.000 0.000 0.592
#> SRR1044456 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044457 6 0.4975 0.00739 0.000 0.092 0.312 0.000 0.000 0.596
#> SRR1044458 6 0.3774 0.78475 0.000 0.408 0.000 0.000 0.000 0.592
#> SRR1044459 3 0.3810 0.60413 0.000 0.000 0.572 0.000 0.000 0.428
#> SRR1044460 2 0.0146 0.92604 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044461 6 0.3774 0.78475 0.000 0.408 0.000 0.000 0.000 0.592
#> SRR1044462 5 0.4840 0.37854 0.056 0.000 0.000 0.360 0.580 0.004
#> SRR1044463 1 0.1387 0.81079 0.932 0.000 0.000 0.000 0.068 0.000
#> SRR1044464 4 0.3879 0.44543 0.000 0.000 0.000 0.688 0.292 0.020
#> SRR1044466 1 0.1387 0.80983 0.932 0.000 0.000 0.000 0.068 0.000
#> SRR1044465 1 0.1411 0.80427 0.936 0.000 0.000 0.004 0.060 0.000
#> SRR1044467 1 0.0717 0.79339 0.976 0.000 0.000 0.008 0.016 0.000
#> SRR1044468 2 0.2941 0.53909 0.000 0.780 0.000 0.000 0.000 0.220
#> SRR1044469 6 0.5802 0.35760 0.000 0.196 0.256 0.000 0.008 0.540
#> SRR1044470 1 0.1141 0.81169 0.948 0.000 0.000 0.000 0.052 0.000
#> SRR1044471 1 0.1462 0.79419 0.936 0.000 0.000 0.008 0.056 0.000
#> SRR1044472 1 0.1327 0.81043 0.936 0.000 0.000 0.000 0.064 0.000
#> SRR1044473 1 0.0717 0.79819 0.976 0.000 0.000 0.008 0.016 0.000
#> SRR1044474 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044475 3 0.7020 -0.34204 0.000 0.268 0.368 0.000 0.064 0.300
#> SRR1044476 6 0.3765 0.78238 0.000 0.404 0.000 0.000 0.000 0.596
#> SRR1044477 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044478 6 0.3867 0.63729 0.000 0.488 0.000 0.000 0.000 0.512
#> SRR1044479 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044480 4 0.4116 0.20848 0.000 0.000 0.000 0.572 0.416 0.012
#> SRR1044481 1 0.4683 0.45024 0.540 0.000 0.000 0.024 0.424 0.012
#> SRR1044482 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044483 4 0.3758 0.44222 0.000 0.000 0.000 0.700 0.284 0.016
#> SRR1044484 5 0.5017 0.54692 0.200 0.000 0.000 0.120 0.668 0.012
#> SRR1044486 1 0.4376 0.55877 0.592 0.000 0.000 0.012 0.384 0.012
#> SRR1044485 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044487 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044488 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044489 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044490 1 0.2346 0.79128 0.868 0.000 0.000 0.008 0.124 0.000
#> SRR1044491 1 0.3073 0.76555 0.788 0.000 0.000 0.000 0.204 0.008
#> SRR1044492 1 0.0458 0.80311 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1044493 1 0.1765 0.81095 0.904 0.000 0.000 0.000 0.096 0.000
#> SRR1044494 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044496 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044495 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044497 4 0.3342 0.49637 0.000 0.000 0.000 0.760 0.228 0.012
#> SRR1044499 6 0.4822 0.70450 0.000 0.332 0.072 0.000 0.000 0.596
#> SRR1044498 5 0.4875 0.57444 0.100 0.000 0.000 0.224 0.668 0.008
#> SRR1044500 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044501 6 0.3774 0.78475 0.000 0.408 0.000 0.000 0.000 0.592
#> SRR1044502 6 0.5454 0.31518 0.000 0.180 0.252 0.000 0.000 0.568
#> SRR1044503 4 0.3168 0.52704 0.000 0.000 0.000 0.792 0.192 0.016
#> SRR1044504 4 0.2726 0.60791 0.000 0.000 0.000 0.856 0.112 0.032
#> SRR1044505 5 0.4810 0.57846 0.120 0.000 0.000 0.220 0.660 0.000
#> SRR1044506 4 0.5305 0.47819 0.000 0.000 0.000 0.576 0.140 0.284
#> SRR1044507 5 0.6199 -0.28526 0.004 0.000 0.000 0.268 0.368 0.360
#> SRR1044508 4 0.5449 0.42163 0.000 0.000 0.000 0.504 0.128 0.368
#> SRR1044509 4 0.5449 0.42163 0.000 0.000 0.000 0.504 0.128 0.368
#> SRR1044510 3 0.4002 0.62732 0.000 0.000 0.588 0.000 0.008 0.404
#> SRR1044511 3 0.4645 0.69497 0.000 0.000 0.648 0.000 0.076 0.276
#> SRR1044512 3 0.2762 0.66768 0.000 0.000 0.860 0.000 0.092 0.048
#> SRR1044513 2 0.3103 0.57823 0.000 0.784 0.208 0.000 0.000 0.008
#> SRR1044514 3 0.3946 0.69871 0.000 0.000 0.756 0.000 0.076 0.168
#> SRR1044515 2 0.4871 0.32036 0.000 0.656 0.212 0.000 0.000 0.132
#> SRR1044516 2 0.0260 0.92218 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044517 3 0.3394 0.64588 0.000 0.000 0.804 0.000 0.052 0.144
#> SRR1044518 3 0.4012 0.70197 0.000 0.000 0.748 0.000 0.076 0.176
#> SRR1044519 3 0.3076 0.70692 0.000 0.000 0.760 0.000 0.000 0.240
#> SRR1044520 3 0.2340 0.70945 0.000 0.000 0.852 0.000 0.000 0.148
#> SRR1044521 2 0.1075 0.87911 0.000 0.952 0.000 0.000 0.000 0.048
#> SRR1044522 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044523 2 0.3649 0.55826 0.000 0.764 0.196 0.000 0.000 0.040
#> SRR1044524 3 0.3866 0.53244 0.000 0.000 0.516 0.000 0.000 0.484
#> SRR1044525 4 0.1082 0.61098 0.000 0.000 0.000 0.956 0.040 0.004
#> SRR1044526 5 0.5253 0.52820 0.128 0.000 0.000 0.296 0.576 0.000
#> SRR1044527 2 0.0146 0.92581 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044528 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044529 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044530 1 0.1387 0.81148 0.932 0.000 0.000 0.000 0.068 0.000
#> SRR1044531 1 0.2219 0.80195 0.864 0.000 0.000 0.000 0.136 0.000
#> SRR1044533 1 0.0547 0.79594 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1044532 1 0.1327 0.81043 0.936 0.000 0.000 0.000 0.064 0.000
#> SRR1044534 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044535 3 0.3810 0.60133 0.000 0.000 0.572 0.000 0.000 0.428
#> SRR1044536 2 0.0363 0.91910 0.000 0.988 0.000 0.000 0.000 0.012
#> SRR1044537 5 0.4541 -0.09821 0.428 0.000 0.000 0.016 0.544 0.012
#> SRR1044538 1 0.1765 0.81170 0.904 0.000 0.000 0.000 0.096 0.000
#> SRR1044539 4 0.3816 0.44081 0.000 0.000 0.000 0.688 0.296 0.016
#> SRR1044540 1 0.2632 0.77395 0.832 0.000 0.000 0.000 0.164 0.004
#> SRR1044541 6 0.5325 0.41697 0.000 0.192 0.212 0.000 0.000 0.596
#> SRR1044542 1 0.1444 0.80948 0.928 0.000 0.000 0.000 0.072 0.000
#> SRR1044543 1 0.2630 0.72035 0.872 0.000 0.000 0.064 0.064 0.000
#> SRR1044544 6 0.4066 -0.32806 0.000 0.012 0.392 0.000 0.000 0.596
#> SRR1044545 4 0.4538 0.45498 0.000 0.000 0.000 0.624 0.324 0.052
#> SRR1044546 1 0.3912 0.62804 0.648 0.000 0.000 0.000 0.340 0.012
#> SRR1044547 4 0.4092 0.39844 0.000 0.000 0.000 0.636 0.344 0.020
#> SRR1044548 1 0.4385 0.54459 0.588 0.000 0.000 0.012 0.388 0.012
#> SRR1044549 2 0.1219 0.86489 0.000 0.948 0.048 0.000 0.000 0.004
#> SRR1044550 2 0.1663 0.82417 0.000 0.912 0.000 0.000 0.000 0.088
#> SRR1044551 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044552 4 0.0820 0.61669 0.000 0.000 0.000 0.972 0.012 0.016
#> SRR1044553 4 0.3159 0.59315 0.000 0.000 0.000 0.832 0.068 0.100
#> SRR1044554 1 0.3927 0.62442 0.644 0.000 0.000 0.000 0.344 0.012
#> SRR1044555 3 0.3862 0.54491 0.000 0.000 0.524 0.000 0.000 0.476
#> SRR1044556 4 0.4316 0.44901 0.000 0.000 0.000 0.648 0.312 0.040
#> SRR1044557 1 0.4262 0.48416 0.560 0.000 0.000 0.004 0.424 0.012
#> SRR1044558 4 0.3541 0.46966 0.000 0.000 0.000 0.728 0.260 0.012
#> SRR1044559 5 0.4576 -0.26079 0.468 0.000 0.000 0.016 0.504 0.012
#> SRR1044561 4 0.0622 0.61563 0.000 0.000 0.000 0.980 0.008 0.012
#> SRR1044560 6 0.3774 0.78475 0.000 0.408 0.000 0.000 0.000 0.592
#> SRR1044562 1 0.4177 0.35238 0.520 0.000 0.000 0.000 0.468 0.012
#> SRR1044563 4 0.3690 0.43552 0.000 0.000 0.000 0.700 0.288 0.012
#> SRR1044564 5 0.5564 0.45875 0.292 0.000 0.000 0.128 0.568 0.012
#> SRR1044565 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044566 6 0.3774 0.78475 0.000 0.408 0.000 0.000 0.000 0.592
#> SRR1044567 1 0.1663 0.81189 0.912 0.000 0.000 0.000 0.088 0.000
#> SRR1044568 4 0.4432 0.17391 0.004 0.000 0.000 0.544 0.432 0.020
#> SRR1044569 1 0.2980 0.75909 0.800 0.000 0.000 0.008 0.192 0.000
#> SRR1044570 1 0.1501 0.80903 0.924 0.000 0.000 0.000 0.076 0.000
#> SRR1044571 1 0.0790 0.80008 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1044572 1 0.2730 0.76027 0.808 0.000 0.000 0.000 0.192 0.000
#> SRR1044573 1 0.2019 0.80743 0.900 0.000 0.000 0.012 0.088 0.000
#> SRR1044574 1 0.1498 0.77905 0.940 0.000 0.000 0.032 0.028 0.000
#> SRR1044575 1 0.1644 0.80663 0.920 0.000 0.000 0.004 0.076 0.000
#> SRR1044576 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044577 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044578 2 0.0000 0.92913 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044579 4 0.0508 0.61517 0.000 0.000 0.000 0.984 0.004 0.012
#> SRR1044580 5 0.4604 0.21880 0.024 0.000 0.000 0.432 0.536 0.008
#> SRR1044581 4 0.0972 0.61342 0.000 0.000 0.000 0.964 0.028 0.008
#> SRR1044582 1 0.4344 0.52253 0.568 0.000 0.000 0.008 0.412 0.012
#> SRR1044583 4 0.0508 0.61517 0.000 0.000 0.000 0.984 0.004 0.012
#> SRR1044584 4 0.3979 0.32354 0.000 0.000 0.000 0.628 0.360 0.012
#> SRR1044585 4 0.2020 0.58701 0.000 0.000 0.000 0.896 0.096 0.008
#> SRR1044586 5 0.4787 -0.24819 0.472 0.000 0.000 0.028 0.488 0.012
#> SRR1044587 4 0.5335 0.47860 0.000 0.000 0.000 0.576 0.148 0.276
#> SRR1044588 4 0.4191 0.56750 0.000 0.000 0.000 0.732 0.088 0.180
#> SRR1044589 4 0.4191 0.56750 0.000 0.000 0.000 0.732 0.088 0.180
#> SRR1044590 4 0.4624 0.55974 0.000 0.000 0.000 0.688 0.120 0.192
#> SRR1044591 4 0.4918 0.52285 0.000 0.000 0.000 0.644 0.124 0.232
#> SRR1044592 4 0.5449 0.42163 0.000 0.000 0.000 0.504 0.128 0.368
#> SRR1044593 4 0.4191 0.56750 0.000 0.000 0.000 0.732 0.088 0.180
#> SRR1044594 4 0.4238 0.56589 0.000 0.000 0.000 0.728 0.092 0.180
#> SRR1044595 1 0.7223 -0.12167 0.356 0.000 0.000 0.112 0.188 0.344
#> SRR1044596 4 0.5502 0.42238 0.000 0.000 0.000 0.500 0.136 0.364
#> SRR1044597 5 0.6510 0.50220 0.100 0.044 0.000 0.228 0.580 0.048
#> SRR1044598 1 0.2320 0.79724 0.864 0.000 0.000 0.000 0.132 0.004
#> SRR1044599 1 0.2743 0.78116 0.828 0.000 0.000 0.000 0.164 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)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.4925 0.508 0.508
#> 3 3 0.690 0.760 0.873 0.2390 0.856 0.724
#> 4 4 0.883 0.859 0.936 0.2185 0.793 0.515
#> 5 5 0.827 0.805 0.860 0.0415 0.967 0.874
#> 6 6 0.856 0.821 0.885 0.0277 0.968 0.866
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0 1 0 1
#> SRR1044416 2 0 1 0 1
#> SRR1044417 2 0 1 0 1
#> SRR1044418 2 0 1 0 1
#> SRR1044420 2 0 1 0 1
#> SRR1044419 2 0 1 0 1
#> SRR1044421 2 0 1 0 1
#> SRR1044422 2 0 1 0 1
#> SRR1044423 2 0 1 0 1
#> SRR1044424 2 0 1 0 1
#> SRR1044425 1 0 1 1 0
#> SRR1044426 1 0 1 1 0
#> SRR1044427 1 0 1 1 0
#> SRR1044428 1 0 1 1 0
#> SRR1044429 1 0 1 1 0
#> SRR1044430 1 0 1 1 0
#> SRR1044431 1 0 1 1 0
#> SRR1044433 1 0 1 1 0
#> SRR1044432 1 0 1 1 0
#> SRR1044434 1 0 1 1 0
#> SRR1044435 1 0 1 1 0
#> SRR1044436 1 0 1 1 0
#> SRR1044437 1 0 1 1 0
#> SRR1044439 1 0 1 1 0
#> SRR1044438 1 0 1 1 0
#> SRR1044440 1 0 1 1 0
#> SRR1044441 1 0 1 1 0
#> SRR1044442 1 0 1 1 0
#> SRR1044443 1 0 1 1 0
#> SRR1044444 1 0 1 1 0
#> SRR1044445 1 0 1 1 0
#> SRR1044446 2 0 1 0 1
#> SRR1044447 2 0 1 0 1
#> SRR1044449 2 0 1 0 1
#> SRR1044448 2 0 1 0 1
#> SRR1044450 2 0 1 0 1
#> SRR1044451 2 0 1 0 1
#> SRR1044452 2 0 1 0 1
#> SRR1044453 2 0 1 0 1
#> SRR1044454 2 0 1 0 1
#> SRR1044455 2 0 1 0 1
#> SRR1044456 2 0 1 0 1
#> SRR1044457 2 0 1 0 1
#> SRR1044458 2 0 1 0 1
#> SRR1044459 2 0 1 0 1
#> SRR1044460 2 0 1 0 1
#> SRR1044461 2 0 1 0 1
#> SRR1044462 1 0 1 1 0
#> SRR1044463 1 0 1 1 0
#> SRR1044464 1 0 1 1 0
#> SRR1044466 1 0 1 1 0
#> SRR1044465 1 0 1 1 0
#> SRR1044467 1 0 1 1 0
#> SRR1044468 2 0 1 0 1
#> SRR1044469 2 0 1 0 1
#> SRR1044470 1 0 1 1 0
#> SRR1044471 1 0 1 1 0
#> SRR1044472 1 0 1 1 0
#> SRR1044473 1 0 1 1 0
#> SRR1044474 2 0 1 0 1
#> SRR1044475 2 0 1 0 1
#> SRR1044476 2 0 1 0 1
#> SRR1044477 2 0 1 0 1
#> SRR1044478 2 0 1 0 1
#> SRR1044479 2 0 1 0 1
#> SRR1044480 1 0 1 1 0
#> SRR1044481 1 0 1 1 0
#> SRR1044482 2 0 1 0 1
#> SRR1044483 1 0 1 1 0
#> SRR1044484 1 0 1 1 0
#> SRR1044486 1 0 1 1 0
#> SRR1044485 2 0 1 0 1
#> SRR1044487 2 0 1 0 1
#> SRR1044488 2 0 1 0 1
#> SRR1044489 2 0 1 0 1
#> SRR1044490 1 0 1 1 0
#> SRR1044491 1 0 1 1 0
#> SRR1044492 1 0 1 1 0
#> SRR1044493 1 0 1 1 0
#> SRR1044494 2 0 1 0 1
#> SRR1044496 2 0 1 0 1
#> SRR1044495 2 0 1 0 1
#> SRR1044497 1 0 1 1 0
#> SRR1044499 2 0 1 0 1
#> SRR1044498 1 0 1 1 0
#> SRR1044500 2 0 1 0 1
#> SRR1044501 2 0 1 0 1
#> SRR1044502 2 0 1 0 1
#> SRR1044503 1 0 1 1 0
#> SRR1044504 1 0 1 1 0
#> SRR1044505 1 0 1 1 0
#> SRR1044506 1 0 1 1 0
#> SRR1044507 1 0 1 1 0
#> SRR1044508 1 0 1 1 0
#> SRR1044509 1 0 1 1 0
#> SRR1044510 2 0 1 0 1
#> SRR1044511 2 0 1 0 1
#> SRR1044512 2 0 1 0 1
#> SRR1044513 2 0 1 0 1
#> SRR1044514 2 0 1 0 1
#> SRR1044515 2 0 1 0 1
#> SRR1044516 2 0 1 0 1
#> SRR1044517 2 0 1 0 1
#> SRR1044518 2 0 1 0 1
#> SRR1044519 2 0 1 0 1
#> SRR1044520 2 0 1 0 1
#> SRR1044521 2 0 1 0 1
#> SRR1044522 2 0 1 0 1
#> SRR1044523 2 0 1 0 1
#> SRR1044524 2 0 1 0 1
#> SRR1044525 1 0 1 1 0
#> SRR1044526 1 0 1 1 0
#> SRR1044527 2 0 1 0 1
#> SRR1044528 2 0 1 0 1
#> SRR1044529 2 0 1 0 1
#> SRR1044530 1 0 1 1 0
#> SRR1044531 1 0 1 1 0
#> SRR1044533 1 0 1 1 0
#> SRR1044532 1 0 1 1 0
#> SRR1044534 2 0 1 0 1
#> SRR1044535 2 0 1 0 1
#> SRR1044536 2 0 1 0 1
#> SRR1044537 1 0 1 1 0
#> SRR1044538 1 0 1 1 0
#> SRR1044539 1 0 1 1 0
#> SRR1044540 1 0 1 1 0
#> SRR1044541 2 0 1 0 1
#> SRR1044542 1 0 1 1 0
#> SRR1044543 1 0 1 1 0
#> SRR1044544 2 0 1 0 1
#> SRR1044545 1 0 1 1 0
#> SRR1044546 1 0 1 1 0
#> SRR1044547 1 0 1 1 0
#> SRR1044548 1 0 1 1 0
#> SRR1044549 2 0 1 0 1
#> SRR1044550 2 0 1 0 1
#> SRR1044551 2 0 1 0 1
#> SRR1044552 1 0 1 1 0
#> SRR1044553 1 0 1 1 0
#> SRR1044554 1 0 1 1 0
#> SRR1044555 2 0 1 0 1
#> SRR1044556 1 0 1 1 0
#> SRR1044557 1 0 1 1 0
#> SRR1044558 1 0 1 1 0
#> SRR1044559 1 0 1 1 0
#> SRR1044561 1 0 1 1 0
#> SRR1044560 2 0 1 0 1
#> SRR1044562 1 0 1 1 0
#> SRR1044563 1 0 1 1 0
#> SRR1044564 1 0 1 1 0
#> SRR1044565 2 0 1 0 1
#> SRR1044566 2 0 1 0 1
#> SRR1044567 1 0 1 1 0
#> SRR1044568 1 0 1 1 0
#> SRR1044569 1 0 1 1 0
#> SRR1044570 1 0 1 1 0
#> SRR1044571 1 0 1 1 0
#> SRR1044572 1 0 1 1 0
#> SRR1044573 1 0 1 1 0
#> SRR1044574 1 0 1 1 0
#> SRR1044575 1 0 1 1 0
#> SRR1044576 2 0 1 0 1
#> SRR1044577 2 0 1 0 1
#> SRR1044578 2 0 1 0 1
#> SRR1044579 1 0 1 1 0
#> SRR1044580 1 0 1 1 0
#> SRR1044581 1 0 1 1 0
#> SRR1044582 1 0 1 1 0
#> SRR1044583 1 0 1 1 0
#> SRR1044584 1 0 1 1 0
#> SRR1044585 1 0 1 1 0
#> SRR1044586 1 0 1 1 0
#> SRR1044587 1 0 1 1 0
#> SRR1044588 1 0 1 1 0
#> SRR1044589 1 0 1 1 0
#> SRR1044590 1 0 1 1 0
#> SRR1044591 1 0 1 1 0
#> SRR1044592 1 0 1 1 0
#> SRR1044593 1 0 1 1 0
#> SRR1044594 1 0 1 1 0
#> SRR1044595 1 0 1 1 0
#> SRR1044596 1 0 1 1 0
#> SRR1044597 1 0 1 1 0
#> SRR1044598 1 0 1 1 0
#> SRR1044599 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044416 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044417 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044418 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044420 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044419 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044421 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044422 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044423 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044424 2 0.1529 0.8742 0.000 0.960 0.040
#> SRR1044425 1 0.0000 0.8989 1.000 0.000 0.000
#> SRR1044426 1 0.4842 0.7181 0.776 0.000 0.224
#> SRR1044427 1 0.0000 0.8989 1.000 0.000 0.000
#> SRR1044428 1 0.1289 0.8932 0.968 0.000 0.032
#> SRR1044429 1 0.0000 0.8989 1.000 0.000 0.000
#> SRR1044430 1 0.3267 0.8395 0.884 0.000 0.116
#> SRR1044431 1 0.0000 0.8989 1.000 0.000 0.000
#> SRR1044433 3 0.3340 0.5099 0.120 0.000 0.880
#> SRR1044432 1 0.3038 0.8471 0.896 0.000 0.104
#> SRR1044434 1 0.4002 0.8574 0.840 0.000 0.160
#> SRR1044435 1 0.3941 0.8593 0.844 0.000 0.156
#> SRR1044436 1 0.4002 0.8573 0.840 0.000 0.160
#> SRR1044437 1 0.3941 0.8593 0.844 0.000 0.156
#> SRR1044439 1 0.3941 0.8593 0.844 0.000 0.156
#> SRR1044438 1 0.3816 0.8625 0.852 0.000 0.148
#> SRR1044440 1 0.4121 0.8525 0.832 0.000 0.168
#> SRR1044441 1 0.5497 0.7348 0.708 0.000 0.292
#> SRR1044442 3 0.5497 0.2295 0.292 0.000 0.708
#> SRR1044443 3 0.3340 0.5099 0.120 0.000 0.880
#> SRR1044444 1 0.3941 0.8593 0.844 0.000 0.156
#> SRR1044445 1 0.5968 0.6455 0.636 0.000 0.364
#> SRR1044446 3 0.6079 0.5196 0.000 0.388 0.612
#> SRR1044447 3 0.6140 0.4967 0.000 0.404 0.596
#> SRR1044449 3 0.5785 0.5532 0.000 0.332 0.668
#> SRR1044448 3 0.6008 0.5383 0.000 0.372 0.628
#> SRR1044450 3 0.5785 0.5533 0.000 0.332 0.668
#> SRR1044451 3 0.6140 0.4967 0.000 0.404 0.596
#> SRR1044452 3 0.6235 0.4309 0.000 0.436 0.564
#> SRR1044453 3 0.6252 0.3999 0.000 0.444 0.556
#> SRR1044454 3 0.6286 0.3598 0.000 0.464 0.536
#> SRR1044455 2 0.6295 -0.1924 0.000 0.528 0.472
#> SRR1044456 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044457 2 0.0424 0.9042 0.000 0.992 0.008
#> SRR1044458 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044459 3 0.6095 0.5144 0.000 0.392 0.608
#> SRR1044460 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044461 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044462 1 0.0592 0.8986 0.988 0.000 0.012
#> SRR1044463 1 0.1163 0.8949 0.972 0.000 0.028
#> SRR1044464 3 0.6008 -0.0673 0.372 0.000 0.628
#> SRR1044466 1 0.1163 0.8949 0.972 0.000 0.028
#> SRR1044465 1 0.0424 0.8993 0.992 0.000 0.008
#> SRR1044467 1 0.0747 0.8988 0.984 0.000 0.016
#> SRR1044468 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044469 2 0.4399 0.6817 0.000 0.812 0.188
#> SRR1044470 1 0.1031 0.8965 0.976 0.000 0.024
#> SRR1044471 1 0.0424 0.8993 0.992 0.000 0.008
#> SRR1044472 1 0.2711 0.8620 0.912 0.000 0.088
#> SRR1044473 1 0.0424 0.8993 0.992 0.000 0.008
#> SRR1044474 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044475 2 0.4796 0.6271 0.000 0.780 0.220
#> SRR1044476 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044477 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044478 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044479 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044480 1 0.2625 0.8835 0.916 0.000 0.084
#> SRR1044481 1 0.0424 0.8993 0.992 0.000 0.008
#> SRR1044482 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044483 1 0.4002 0.8573 0.840 0.000 0.160
#> SRR1044484 1 0.0592 0.8991 0.988 0.000 0.012
#> SRR1044486 1 0.0424 0.8993 0.992 0.000 0.008
#> SRR1044485 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044487 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044488 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044489 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044490 1 0.0592 0.8992 0.988 0.000 0.012
#> SRR1044491 1 0.0892 0.8977 0.980 0.000 0.020
#> SRR1044492 1 0.0747 0.8986 0.984 0.000 0.016
#> SRR1044493 1 0.1163 0.8949 0.972 0.000 0.028
#> SRR1044494 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044496 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044495 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044497 1 0.3941 0.8593 0.844 0.000 0.156
#> SRR1044499 2 0.4062 0.7212 0.000 0.836 0.164
#> SRR1044498 1 0.0237 0.8993 0.996 0.000 0.004
#> SRR1044500 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044501 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044502 3 0.6302 0.3171 0.000 0.480 0.520
#> SRR1044503 1 0.3941 0.8593 0.844 0.000 0.156
#> SRR1044504 1 0.4002 0.8573 0.840 0.000 0.160
#> SRR1044505 1 0.0000 0.8989 1.000 0.000 0.000
#> SRR1044506 1 0.5968 0.6455 0.636 0.000 0.364
#> SRR1044507 3 0.5529 0.2194 0.296 0.000 0.704
#> SRR1044508 3 0.3340 0.5099 0.120 0.000 0.880
#> SRR1044509 3 0.3340 0.5099 0.120 0.000 0.880
#> SRR1044510 3 0.6008 0.5383 0.000 0.372 0.628
#> SRR1044511 3 0.6008 0.5383 0.000 0.372 0.628
#> SRR1044512 3 0.5835 0.5512 0.000 0.340 0.660
#> SRR1044513 2 0.6307 -0.2559 0.000 0.512 0.488
#> SRR1044514 3 0.6008 0.5383 0.000 0.372 0.628
#> SRR1044515 2 0.6192 0.0173 0.000 0.580 0.420
#> SRR1044516 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044517 3 0.6008 0.5383 0.000 0.372 0.628
#> SRR1044518 3 0.6008 0.5383 0.000 0.372 0.628
#> SRR1044519 3 0.5733 0.5535 0.000 0.324 0.676
#> SRR1044520 3 0.5706 0.5537 0.000 0.320 0.680
#> SRR1044521 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044522 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044523 2 0.2625 0.8175 0.000 0.916 0.084
#> SRR1044524 2 0.6280 -0.1443 0.000 0.540 0.460
#> SRR1044525 1 0.3941 0.8593 0.844 0.000 0.156
#> SRR1044526 1 0.0000 0.8989 1.000 0.000 0.000
#> SRR1044527 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044528 2 0.4605 0.6310 0.000 0.796 0.204
#> SRR1044529 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044530 1 0.1163 0.8949 0.972 0.000 0.028
#> SRR1044531 1 0.0592 0.8992 0.988 0.000 0.012
#> SRR1044533 1 0.0592 0.8992 0.988 0.000 0.012
#> SRR1044532 1 0.1163 0.8949 0.972 0.000 0.028
#> SRR1044534 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044535 3 0.6280 0.3739 0.000 0.460 0.540
#> SRR1044536 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044537 1 0.0424 0.8993 0.992 0.000 0.008
#> SRR1044538 1 0.1031 0.8963 0.976 0.000 0.024
#> SRR1044539 1 0.3941 0.8593 0.844 0.000 0.156
#> SRR1044540 1 0.0592 0.8987 0.988 0.000 0.012
#> SRR1044541 2 0.5905 0.2625 0.000 0.648 0.352
#> SRR1044542 1 0.1031 0.8963 0.976 0.000 0.024
#> SRR1044543 1 0.1964 0.8762 0.944 0.000 0.056
#> SRR1044544 2 0.3816 0.7469 0.000 0.852 0.148
#> SRR1044545 1 0.3941 0.8593 0.844 0.000 0.156
#> SRR1044546 1 0.0592 0.8991 0.988 0.000 0.012
#> SRR1044547 1 0.3482 0.8703 0.872 0.000 0.128
#> SRR1044548 1 0.0747 0.8986 0.984 0.000 0.016
#> SRR1044549 2 0.1289 0.8795 0.000 0.968 0.032
#> SRR1044550 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044551 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044552 1 0.3941 0.8593 0.844 0.000 0.156
#> SRR1044553 1 0.4178 0.8498 0.828 0.000 0.172
#> SRR1044554 1 0.0747 0.8985 0.984 0.000 0.016
#> SRR1044555 2 0.6299 -0.2028 0.000 0.524 0.476
#> SRR1044556 1 0.4002 0.8573 0.840 0.000 0.160
#> SRR1044557 1 0.0747 0.8985 0.984 0.000 0.016
#> SRR1044558 1 0.3941 0.8593 0.844 0.000 0.156
#> SRR1044559 1 0.1031 0.8963 0.976 0.000 0.024
#> SRR1044561 1 0.4062 0.8549 0.836 0.000 0.164
#> SRR1044560 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044562 1 0.0892 0.8975 0.980 0.000 0.020
#> SRR1044563 1 0.4062 0.8549 0.836 0.000 0.164
#> SRR1044564 1 0.0237 0.8993 0.996 0.000 0.004
#> SRR1044565 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044566 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044567 1 0.1031 0.8963 0.976 0.000 0.024
#> SRR1044568 1 0.2959 0.8790 0.900 0.000 0.100
#> SRR1044569 1 0.0424 0.8993 0.992 0.000 0.008
#> SRR1044570 1 0.1031 0.8963 0.976 0.000 0.024
#> SRR1044571 1 0.0424 0.8993 0.992 0.000 0.008
#> SRR1044572 1 0.0424 0.8996 0.992 0.000 0.008
#> SRR1044573 1 0.0000 0.8989 1.000 0.000 0.000
#> SRR1044574 1 0.0592 0.8996 0.988 0.000 0.012
#> SRR1044575 1 0.0424 0.8996 0.992 0.000 0.008
#> SRR1044576 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044577 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044578 2 0.0000 0.9109 0.000 1.000 0.000
#> SRR1044579 1 0.4121 0.8525 0.832 0.000 0.168
#> SRR1044580 1 0.0000 0.8989 1.000 0.000 0.000
#> SRR1044581 1 0.3941 0.8593 0.844 0.000 0.156
#> SRR1044582 1 0.0592 0.8991 0.988 0.000 0.012
#> SRR1044583 1 0.4002 0.8574 0.840 0.000 0.160
#> SRR1044584 1 0.3192 0.8752 0.888 0.000 0.112
#> SRR1044585 1 0.3941 0.8593 0.844 0.000 0.156
#> SRR1044586 1 0.0424 0.8993 0.992 0.000 0.008
#> SRR1044587 1 0.5968 0.6444 0.636 0.000 0.364
#> SRR1044588 1 0.5968 0.6455 0.636 0.000 0.364
#> SRR1044589 1 0.5968 0.6455 0.636 0.000 0.364
#> SRR1044590 1 0.5810 0.6801 0.664 0.000 0.336
#> SRR1044591 1 0.5968 0.6455 0.636 0.000 0.364
#> SRR1044592 3 0.3340 0.5099 0.120 0.000 0.880
#> SRR1044593 1 0.5859 0.6706 0.656 0.000 0.344
#> SRR1044594 1 0.5835 0.6754 0.660 0.000 0.340
#> SRR1044595 3 0.5291 0.2834 0.268 0.000 0.732
#> SRR1044596 3 0.6204 -0.2019 0.424 0.000 0.576
#> SRR1044597 3 0.6308 -0.2136 0.492 0.000 0.508
#> SRR1044598 1 0.1163 0.8951 0.972 0.000 0.028
#> SRR1044599 1 0.1163 0.8951 0.972 0.000 0.028
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044416 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044417 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044418 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044420 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044419 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044421 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044422 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044423 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044424 2 0.2760 0.836 0.000 0.872 0.128 0.000
#> SRR1044425 1 0.4250 0.635 0.724 0.000 0.000 0.276
#> SRR1044426 1 0.4992 0.748 0.772 0.000 0.132 0.096
#> SRR1044427 1 0.2149 0.895 0.912 0.000 0.000 0.088
#> SRR1044428 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044429 1 0.1389 0.932 0.952 0.000 0.000 0.048
#> SRR1044430 1 0.3301 0.871 0.876 0.000 0.048 0.076
#> SRR1044431 1 0.0469 0.956 0.988 0.000 0.000 0.012
#> SRR1044433 4 0.6074 0.316 0.044 0.000 0.456 0.500
#> SRR1044432 1 0.1109 0.944 0.968 0.000 0.004 0.028
#> SRR1044434 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044435 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044436 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044437 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044439 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044438 4 0.0469 0.850 0.012 0.000 0.000 0.988
#> SRR1044440 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044441 4 0.2760 0.767 0.000 0.000 0.128 0.872
#> SRR1044442 4 0.6071 0.325 0.044 0.000 0.452 0.504
#> SRR1044443 4 0.6074 0.316 0.044 0.000 0.456 0.500
#> SRR1044444 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044445 4 0.0188 0.852 0.004 0.000 0.000 0.996
#> SRR1044446 3 0.0188 0.920 0.000 0.004 0.996 0.000
#> SRR1044447 3 0.0188 0.920 0.000 0.004 0.996 0.000
#> SRR1044449 3 0.0188 0.920 0.000 0.004 0.996 0.000
#> SRR1044448 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> SRR1044450 3 0.0188 0.920 0.000 0.004 0.996 0.000
#> SRR1044451 3 0.0188 0.920 0.000 0.004 0.996 0.000
#> SRR1044452 3 0.0188 0.920 0.000 0.004 0.996 0.000
#> SRR1044453 3 0.0592 0.915 0.000 0.016 0.984 0.000
#> SRR1044454 3 0.0592 0.915 0.000 0.016 0.984 0.000
#> SRR1044455 3 0.0592 0.916 0.000 0.016 0.984 0.000
#> SRR1044456 2 0.0188 0.970 0.000 0.996 0.004 0.000
#> SRR1044457 2 0.3610 0.739 0.000 0.800 0.200 0.000
#> SRR1044458 2 0.0188 0.970 0.000 0.996 0.004 0.000
#> SRR1044459 3 0.0188 0.920 0.000 0.004 0.996 0.000
#> SRR1044460 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044461 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044462 1 0.3942 0.704 0.764 0.000 0.000 0.236
#> SRR1044463 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044464 4 0.6068 0.332 0.044 0.000 0.448 0.508
#> SRR1044466 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044465 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044467 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044468 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044469 3 0.4804 0.395 0.000 0.384 0.616 0.000
#> SRR1044470 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044471 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044472 1 0.1557 0.924 0.944 0.000 0.000 0.056
#> SRR1044473 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044474 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044475 3 0.4843 0.367 0.000 0.396 0.604 0.000
#> SRR1044476 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044477 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044478 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044479 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044480 4 0.4713 0.419 0.360 0.000 0.000 0.640
#> SRR1044481 1 0.1211 0.936 0.960 0.000 0.000 0.040
#> SRR1044482 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044483 4 0.0469 0.850 0.012 0.000 0.000 0.988
#> SRR1044484 1 0.3311 0.797 0.828 0.000 0.000 0.172
#> SRR1044486 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044485 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044487 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044488 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044489 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044490 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044491 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044492 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044493 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044494 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044496 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044495 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044497 4 0.0469 0.850 0.012 0.000 0.000 0.988
#> SRR1044499 3 0.4941 0.249 0.000 0.436 0.564 0.000
#> SRR1044498 1 0.3726 0.740 0.788 0.000 0.000 0.212
#> SRR1044500 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044501 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044502 3 0.0188 0.920 0.000 0.004 0.996 0.000
#> SRR1044503 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044504 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044505 1 0.1557 0.925 0.944 0.000 0.000 0.056
#> SRR1044506 4 0.0000 0.851 0.000 0.000 0.000 1.000
#> SRR1044507 4 0.6074 0.316 0.044 0.000 0.456 0.500
#> SRR1044508 4 0.6074 0.316 0.044 0.000 0.456 0.500
#> SRR1044509 4 0.6074 0.316 0.044 0.000 0.456 0.500
#> SRR1044510 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> SRR1044511 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> SRR1044512 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> SRR1044513 3 0.2011 0.866 0.000 0.080 0.920 0.000
#> SRR1044514 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> SRR1044515 3 0.2216 0.858 0.000 0.092 0.908 0.000
#> SRR1044516 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044517 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> SRR1044518 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> SRR1044519 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> SRR1044520 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> SRR1044521 2 0.0188 0.970 0.000 0.996 0.004 0.000
#> SRR1044522 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044523 2 0.4222 0.599 0.000 0.728 0.272 0.000
#> SRR1044524 3 0.0469 0.917 0.000 0.012 0.988 0.000
#> SRR1044525 4 0.1211 0.833 0.040 0.000 0.000 0.960
#> SRR1044526 1 0.2408 0.881 0.896 0.000 0.000 0.104
#> SRR1044527 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044528 2 0.4933 0.182 0.000 0.568 0.432 0.000
#> SRR1044529 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044530 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044531 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044533 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044532 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044534 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044535 3 0.0188 0.920 0.000 0.004 0.996 0.000
#> SRR1044536 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044537 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044538 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044539 4 0.0817 0.843 0.024 0.000 0.000 0.976
#> SRR1044540 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044541 3 0.2081 0.864 0.000 0.084 0.916 0.000
#> SRR1044542 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044543 1 0.0469 0.954 0.988 0.000 0.012 0.000
#> SRR1044544 3 0.4406 0.569 0.000 0.300 0.700 0.000
#> SRR1044545 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044546 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044547 4 0.1867 0.809 0.072 0.000 0.000 0.928
#> SRR1044548 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044549 2 0.2469 0.859 0.000 0.892 0.108 0.000
#> SRR1044550 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044551 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044552 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044553 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044554 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044555 3 0.0336 0.919 0.000 0.008 0.992 0.000
#> SRR1044556 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044557 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044558 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044559 1 0.0524 0.956 0.988 0.000 0.008 0.004
#> SRR1044561 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044560 2 0.0336 0.967 0.000 0.992 0.008 0.000
#> SRR1044562 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044563 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044564 1 0.0469 0.956 0.988 0.000 0.000 0.012
#> SRR1044565 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044566 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044567 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044568 4 0.4643 0.456 0.344 0.000 0.000 0.656
#> SRR1044569 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044570 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044571 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044572 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044573 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044574 1 0.0188 0.960 0.996 0.000 0.000 0.004
#> SRR1044575 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044576 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044577 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044578 2 0.0000 0.974 0.000 1.000 0.000 0.000
#> SRR1044579 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044580 1 0.4040 0.687 0.752 0.000 0.000 0.248
#> SRR1044581 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044582 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044583 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044584 4 0.3764 0.672 0.216 0.000 0.000 0.784
#> SRR1044585 4 0.0188 0.853 0.004 0.000 0.000 0.996
#> SRR1044586 1 0.0336 0.958 0.992 0.000 0.000 0.008
#> SRR1044587 4 0.0188 0.852 0.004 0.000 0.000 0.996
#> SRR1044588 4 0.0000 0.851 0.000 0.000 0.000 1.000
#> SRR1044589 4 0.0000 0.851 0.000 0.000 0.000 1.000
#> SRR1044590 4 0.0000 0.851 0.000 0.000 0.000 1.000
#> SRR1044591 4 0.0000 0.851 0.000 0.000 0.000 1.000
#> SRR1044592 4 0.6074 0.316 0.044 0.000 0.456 0.500
#> SRR1044593 4 0.0000 0.851 0.000 0.000 0.000 1.000
#> SRR1044594 4 0.0000 0.851 0.000 0.000 0.000 1.000
#> SRR1044595 4 0.6273 0.298 0.056 0.000 0.456 0.488
#> SRR1044596 4 0.6071 0.325 0.044 0.000 0.452 0.504
#> SRR1044597 4 0.6276 0.287 0.056 0.000 0.464 0.480
#> SRR1044598 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> SRR1044599 1 0.0000 0.962 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.2605 0.8026 0.000 0.852 0.000 0.148 0.000
#> SRR1044416 2 0.0609 0.8842 0.000 0.980 0.000 0.000 0.020
#> SRR1044417 2 0.0404 0.8843 0.000 0.988 0.000 0.000 0.012
#> SRR1044418 2 0.0609 0.8842 0.000 0.980 0.000 0.000 0.020
#> SRR1044420 2 0.0000 0.8837 0.000 1.000 0.000 0.000 0.000
#> SRR1044419 2 0.2690 0.7958 0.000 0.844 0.000 0.156 0.000
#> SRR1044421 2 0.1596 0.8684 0.000 0.948 0.012 0.012 0.028
#> SRR1044422 2 0.0000 0.8837 0.000 1.000 0.000 0.000 0.000
#> SRR1044423 2 0.0510 0.8807 0.000 0.984 0.000 0.016 0.000
#> SRR1044424 2 0.4709 0.7183 0.000 0.748 0.060 0.176 0.016
#> SRR1044425 1 0.5649 0.1098 0.472 0.000 0.000 0.076 0.452
#> SRR1044426 1 0.4769 0.6519 0.688 0.000 0.056 0.000 0.256
#> SRR1044427 1 0.4451 0.7165 0.712 0.000 0.000 0.040 0.248
#> SRR1044428 1 0.0880 0.9025 0.968 0.000 0.000 0.000 0.032
#> SRR1044429 1 0.3988 0.7851 0.768 0.000 0.000 0.036 0.196
#> SRR1044430 1 0.3476 0.7819 0.804 0.000 0.020 0.000 0.176
#> SRR1044431 1 0.3061 0.8514 0.844 0.000 0.000 0.020 0.136
#> SRR1044433 5 0.3107 0.8760 0.008 0.000 0.096 0.032 0.864
#> SRR1044432 1 0.2074 0.8658 0.896 0.000 0.000 0.000 0.104
#> SRR1044434 4 0.3816 0.9501 0.000 0.000 0.000 0.696 0.304
#> SRR1044435 4 0.3816 0.9501 0.000 0.000 0.000 0.696 0.304
#> SRR1044436 4 0.3816 0.9501 0.000 0.000 0.000 0.696 0.304
#> SRR1044437 4 0.3816 0.9501 0.000 0.000 0.000 0.696 0.304
#> SRR1044439 4 0.3816 0.9501 0.000 0.000 0.000 0.696 0.304
#> SRR1044438 4 0.4235 0.9061 0.008 0.000 0.000 0.656 0.336
#> SRR1044440 4 0.3816 0.9501 0.000 0.000 0.000 0.696 0.304
#> SRR1044441 4 0.5290 0.7598 0.004 0.000 0.044 0.560 0.392
#> SRR1044442 5 0.3107 0.8760 0.008 0.000 0.096 0.032 0.864
#> SRR1044443 5 0.3107 0.8760 0.008 0.000 0.096 0.032 0.864
#> SRR1044444 4 0.3816 0.9501 0.000 0.000 0.000 0.696 0.304
#> SRR1044445 4 0.4030 0.9182 0.000 0.000 0.000 0.648 0.352
#> SRR1044446 3 0.1992 0.7540 0.000 0.000 0.924 0.032 0.044
#> SRR1044447 3 0.6521 0.7021 0.000 0.072 0.564 0.300 0.064
#> SRR1044449 3 0.1270 0.7498 0.000 0.000 0.948 0.000 0.052
#> SRR1044448 3 0.1197 0.7513 0.000 0.000 0.952 0.000 0.048
#> SRR1044450 3 0.1270 0.7501 0.000 0.000 0.948 0.000 0.052
#> SRR1044451 3 0.6466 0.7032 0.000 0.072 0.568 0.300 0.060
#> SRR1044452 3 0.1043 0.7527 0.000 0.040 0.960 0.000 0.000
#> SRR1044453 3 0.1697 0.7485 0.000 0.060 0.932 0.000 0.008
#> SRR1044454 3 0.2476 0.7495 0.000 0.064 0.904 0.020 0.012
#> SRR1044455 3 0.6783 0.6630 0.000 0.136 0.524 0.304 0.036
#> SRR1044456 2 0.0703 0.8842 0.000 0.976 0.000 0.000 0.024
#> SRR1044457 2 0.7556 -0.1588 0.000 0.372 0.284 0.304 0.040
#> SRR1044458 2 0.4597 0.6212 0.000 0.672 0.004 0.300 0.024
#> SRR1044459 3 0.1282 0.7527 0.000 0.000 0.952 0.004 0.044
#> SRR1044460 2 0.0000 0.8837 0.000 1.000 0.000 0.000 0.000
#> SRR1044461 2 0.2516 0.8087 0.000 0.860 0.000 0.140 0.000
#> SRR1044462 1 0.5690 0.1823 0.492 0.000 0.004 0.068 0.436
#> SRR1044463 1 0.0290 0.9042 0.992 0.000 0.000 0.000 0.008
#> SRR1044464 5 0.3498 0.8660 0.016 0.000 0.092 0.044 0.848
#> SRR1044466 1 0.0609 0.9025 0.980 0.000 0.000 0.000 0.020
#> SRR1044465 1 0.0992 0.9065 0.968 0.000 0.000 0.008 0.024
#> SRR1044467 1 0.0955 0.9069 0.968 0.000 0.000 0.004 0.028
#> SRR1044468 2 0.0000 0.8837 0.000 1.000 0.000 0.000 0.000
#> SRR1044469 3 0.7521 0.4222 0.000 0.284 0.412 0.260 0.044
#> SRR1044470 1 0.0404 0.9061 0.988 0.000 0.000 0.000 0.012
#> SRR1044471 1 0.0865 0.9066 0.972 0.000 0.000 0.004 0.024
#> SRR1044472 1 0.1608 0.8786 0.928 0.000 0.000 0.000 0.072
#> SRR1044473 1 0.0955 0.9079 0.968 0.000 0.000 0.004 0.028
#> SRR1044474 2 0.0703 0.8842 0.000 0.976 0.000 0.000 0.024
#> SRR1044475 3 0.7239 0.4042 0.000 0.320 0.460 0.176 0.044
#> SRR1044476 2 0.3707 0.6658 0.000 0.716 0.000 0.284 0.000
#> SRR1044477 2 0.0703 0.8842 0.000 0.976 0.000 0.000 0.024
#> SRR1044478 2 0.1410 0.8616 0.000 0.940 0.000 0.060 0.000
#> SRR1044479 2 0.0703 0.8842 0.000 0.976 0.000 0.000 0.024
#> SRR1044480 5 0.6323 -0.0914 0.164 0.000 0.000 0.360 0.476
#> SRR1044481 1 0.2740 0.8701 0.876 0.000 0.000 0.028 0.096
#> SRR1044482 2 0.0703 0.8842 0.000 0.976 0.000 0.000 0.024
#> SRR1044483 4 0.3876 0.9417 0.000 0.000 0.000 0.684 0.316
#> SRR1044484 1 0.4428 0.6743 0.700 0.000 0.000 0.032 0.268
#> SRR1044486 1 0.2171 0.8881 0.912 0.000 0.000 0.024 0.064
#> SRR1044485 2 0.0703 0.8842 0.000 0.976 0.000 0.000 0.024
#> SRR1044487 2 0.0703 0.8842 0.000 0.976 0.000 0.000 0.024
#> SRR1044488 2 0.0000 0.8837 0.000 1.000 0.000 0.000 0.000
#> SRR1044489 2 0.0000 0.8837 0.000 1.000 0.000 0.000 0.000
#> SRR1044490 1 0.0865 0.9074 0.972 0.000 0.000 0.004 0.024
#> SRR1044491 1 0.0579 0.9070 0.984 0.000 0.000 0.008 0.008
#> SRR1044492 1 0.0566 0.9044 0.984 0.000 0.000 0.004 0.012
#> SRR1044493 1 0.0404 0.9032 0.988 0.000 0.000 0.000 0.012
#> SRR1044494 2 0.0703 0.8842 0.000 0.976 0.000 0.000 0.024
#> SRR1044496 2 0.0703 0.8842 0.000 0.976 0.000 0.000 0.024
#> SRR1044495 2 0.0703 0.8842 0.000 0.976 0.000 0.000 0.024
#> SRR1044497 4 0.4108 0.9394 0.008 0.000 0.000 0.684 0.308
#> SRR1044499 2 0.7579 -0.2766 0.000 0.348 0.324 0.288 0.040
#> SRR1044498 1 0.5056 0.4970 0.596 0.000 0.000 0.044 0.360
#> SRR1044500 2 0.0000 0.8837 0.000 1.000 0.000 0.000 0.000
#> SRR1044501 2 0.4577 0.6266 0.000 0.676 0.004 0.296 0.024
#> SRR1044502 3 0.6177 0.6923 0.000 0.096 0.576 0.304 0.024
#> SRR1044503 4 0.3816 0.9501 0.000 0.000 0.000 0.696 0.304
#> SRR1044504 4 0.3816 0.9501 0.000 0.000 0.000 0.696 0.304
#> SRR1044505 1 0.3951 0.7918 0.776 0.000 0.004 0.028 0.192
#> SRR1044506 4 0.4030 0.9182 0.000 0.000 0.000 0.648 0.352
#> SRR1044507 5 0.3187 0.8741 0.008 0.000 0.096 0.036 0.860
#> SRR1044508 5 0.3107 0.8760 0.008 0.000 0.096 0.032 0.864
#> SRR1044509 5 0.3107 0.8760 0.008 0.000 0.096 0.032 0.864
#> SRR1044510 3 0.1270 0.7496 0.000 0.000 0.948 0.000 0.052
#> SRR1044511 3 0.1197 0.7513 0.000 0.000 0.952 0.000 0.048
#> SRR1044512 3 0.1197 0.7513 0.000 0.000 0.952 0.000 0.048
#> SRR1044513 3 0.6382 0.6797 0.000 0.124 0.552 0.304 0.020
#> SRR1044514 3 0.1197 0.7513 0.000 0.000 0.952 0.000 0.048
#> SRR1044515 3 0.6503 0.6648 0.000 0.148 0.532 0.304 0.016
#> SRR1044516 2 0.2450 0.8509 0.000 0.912 0.028 0.032 0.028
#> SRR1044517 3 0.1270 0.7496 0.000 0.000 0.948 0.000 0.052
#> SRR1044518 3 0.1197 0.7513 0.000 0.000 0.952 0.000 0.048
#> SRR1044519 3 0.1341 0.7477 0.000 0.000 0.944 0.000 0.056
#> SRR1044520 3 0.1410 0.7466 0.000 0.000 0.940 0.000 0.060
#> SRR1044521 2 0.0963 0.8715 0.000 0.964 0.036 0.000 0.000
#> SRR1044522 2 0.0703 0.8842 0.000 0.976 0.000 0.000 0.024
#> SRR1044523 2 0.7220 -0.0263 0.000 0.452 0.328 0.180 0.040
#> SRR1044524 3 0.5822 0.7053 0.000 0.076 0.608 0.296 0.020
#> SRR1044525 4 0.4624 0.8783 0.024 0.000 0.000 0.636 0.340
#> SRR1044526 1 0.5257 0.6730 0.676 0.000 0.008 0.080 0.236
#> SRR1044527 2 0.1399 0.8675 0.000 0.952 0.020 0.000 0.028
#> SRR1044528 2 0.6173 0.1073 0.000 0.528 0.376 0.060 0.036
#> SRR1044529 2 0.0703 0.8842 0.000 0.976 0.000 0.000 0.024
#> SRR1044530 1 0.0404 0.9032 0.988 0.000 0.000 0.000 0.012
#> SRR1044531 1 0.0992 0.9065 0.968 0.000 0.000 0.008 0.024
#> SRR1044533 1 0.0992 0.9076 0.968 0.000 0.000 0.008 0.024
#> SRR1044532 1 0.0404 0.9032 0.988 0.000 0.000 0.000 0.012
#> SRR1044534 2 0.0000 0.8837 0.000 1.000 0.000 0.000 0.000
#> SRR1044535 3 0.5686 0.7116 0.000 0.064 0.628 0.284 0.024
#> SRR1044536 2 0.0000 0.8837 0.000 1.000 0.000 0.000 0.000
#> SRR1044537 1 0.2707 0.8705 0.876 0.000 0.000 0.024 0.100
#> SRR1044538 1 0.0566 0.9044 0.984 0.000 0.000 0.004 0.012
#> SRR1044539 4 0.4183 0.9239 0.008 0.000 0.000 0.668 0.324
#> SRR1044540 1 0.1522 0.9005 0.944 0.000 0.000 0.012 0.044
#> SRR1044541 3 0.6369 0.6743 0.000 0.132 0.548 0.304 0.016
#> SRR1044542 1 0.0451 0.9050 0.988 0.000 0.000 0.004 0.008
#> SRR1044543 1 0.1924 0.8947 0.924 0.000 0.004 0.008 0.064
#> SRR1044544 3 0.7147 0.6063 0.000 0.168 0.484 0.304 0.044
#> SRR1044545 4 0.3816 0.9501 0.000 0.000 0.000 0.696 0.304
#> SRR1044546 1 0.0912 0.9063 0.972 0.000 0.000 0.012 0.016
#> SRR1044547 4 0.4920 0.7659 0.032 0.000 0.000 0.584 0.384
#> SRR1044548 1 0.1012 0.9053 0.968 0.000 0.000 0.012 0.020
#> SRR1044549 2 0.4630 0.6153 0.000 0.732 0.216 0.016 0.036
#> SRR1044550 2 0.0000 0.8837 0.000 1.000 0.000 0.000 0.000
#> SRR1044551 2 0.1493 0.8655 0.000 0.948 0.024 0.000 0.028
#> SRR1044552 4 0.3816 0.9501 0.000 0.000 0.000 0.696 0.304
#> SRR1044553 4 0.3837 0.9476 0.000 0.000 0.000 0.692 0.308
#> SRR1044554 1 0.0671 0.9053 0.980 0.000 0.000 0.004 0.016
#> SRR1044555 3 0.5531 0.7180 0.000 0.068 0.652 0.260 0.020
#> SRR1044556 4 0.3816 0.9501 0.000 0.000 0.000 0.696 0.304
#> SRR1044557 1 0.0671 0.9053 0.980 0.000 0.000 0.004 0.016
#> SRR1044558 4 0.3816 0.9501 0.000 0.000 0.000 0.696 0.304
#> SRR1044559 1 0.2507 0.8765 0.900 0.000 0.016 0.012 0.072
#> SRR1044561 4 0.3816 0.9501 0.000 0.000 0.000 0.696 0.304
#> SRR1044560 2 0.3707 0.6658 0.000 0.716 0.000 0.284 0.000
#> SRR1044562 1 0.0290 0.9042 0.992 0.000 0.000 0.000 0.008
#> SRR1044563 4 0.3816 0.9501 0.000 0.000 0.000 0.696 0.304
#> SRR1044564 1 0.3134 0.8536 0.848 0.000 0.000 0.032 0.120
#> SRR1044565 2 0.0703 0.8842 0.000 0.976 0.000 0.000 0.024
#> SRR1044566 2 0.3336 0.7286 0.000 0.772 0.000 0.228 0.000
#> SRR1044567 1 0.0404 0.9053 0.988 0.000 0.000 0.000 0.012
#> SRR1044568 5 0.6006 0.1863 0.144 0.000 0.000 0.300 0.556
#> SRR1044569 1 0.1106 0.9068 0.964 0.000 0.000 0.012 0.024
#> SRR1044570 1 0.0404 0.9032 0.988 0.000 0.000 0.000 0.012
#> SRR1044571 1 0.0771 0.9076 0.976 0.000 0.000 0.004 0.020
#> SRR1044572 1 0.1168 0.9054 0.960 0.000 0.000 0.008 0.032
#> SRR1044573 1 0.1251 0.9069 0.956 0.000 0.000 0.008 0.036
#> SRR1044574 1 0.1251 0.9059 0.956 0.000 0.000 0.008 0.036
#> SRR1044575 1 0.1082 0.9057 0.964 0.000 0.000 0.008 0.028
#> SRR1044576 2 0.0703 0.8842 0.000 0.976 0.000 0.000 0.024
#> SRR1044577 2 0.0290 0.8843 0.000 0.992 0.000 0.000 0.008
#> SRR1044578 2 0.0703 0.8842 0.000 0.976 0.000 0.000 0.024
#> SRR1044579 4 0.3816 0.9501 0.000 0.000 0.000 0.696 0.304
#> SRR1044580 1 0.5855 0.3616 0.536 0.000 0.000 0.108 0.356
#> SRR1044581 4 0.3816 0.9501 0.000 0.000 0.000 0.696 0.304
#> SRR1044582 1 0.1386 0.9043 0.952 0.000 0.000 0.016 0.032
#> SRR1044583 4 0.3816 0.9501 0.000 0.000 0.000 0.696 0.304
#> SRR1044584 4 0.5555 0.4831 0.068 0.000 0.000 0.480 0.452
#> SRR1044585 4 0.3816 0.9501 0.000 0.000 0.000 0.696 0.304
#> SRR1044586 1 0.2172 0.8860 0.908 0.000 0.000 0.016 0.076
#> SRR1044587 4 0.4030 0.9182 0.000 0.000 0.000 0.648 0.352
#> SRR1044588 4 0.4030 0.9182 0.000 0.000 0.000 0.648 0.352
#> SRR1044589 4 0.4030 0.9182 0.000 0.000 0.000 0.648 0.352
#> SRR1044590 4 0.4030 0.9182 0.000 0.000 0.000 0.648 0.352
#> SRR1044591 4 0.4030 0.9182 0.000 0.000 0.000 0.648 0.352
#> SRR1044592 5 0.3107 0.8760 0.008 0.000 0.096 0.032 0.864
#> SRR1044593 4 0.4030 0.9182 0.000 0.000 0.000 0.648 0.352
#> SRR1044594 4 0.4030 0.9182 0.000 0.000 0.000 0.648 0.352
#> SRR1044595 5 0.3507 0.8554 0.024 0.000 0.096 0.032 0.848
#> SRR1044596 5 0.3265 0.8712 0.008 0.000 0.096 0.040 0.856
#> SRR1044597 5 0.5089 0.7856 0.060 0.000 0.096 0.088 0.756
#> SRR1044598 1 0.0290 0.9041 0.992 0.000 0.000 0.000 0.008
#> SRR1044599 1 0.0290 0.9041 0.992 0.000 0.000 0.000 0.008
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.1556 0.8747 0.000 0.920 0.000 0.000 0.000 0.080
#> SRR1044416 2 0.0458 0.9223 0.000 0.984 0.000 0.000 0.000 0.016
#> SRR1044417 2 0.0146 0.9220 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044418 2 0.0458 0.9228 0.000 0.984 0.000 0.000 0.000 0.016
#> SRR1044420 2 0.0260 0.9226 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044419 2 0.1814 0.8546 0.000 0.900 0.000 0.000 0.000 0.100
#> SRR1044421 2 0.1501 0.8835 0.000 0.924 0.000 0.000 0.000 0.076
#> SRR1044422 2 0.0146 0.9213 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044423 2 0.0458 0.9201 0.000 0.984 0.000 0.000 0.000 0.016
#> SRR1044424 2 0.3023 0.6945 0.000 0.784 0.004 0.000 0.000 0.212
#> SRR1044425 1 0.6730 0.0617 0.412 0.000 0.000 0.156 0.364 0.068
#> SRR1044426 1 0.5113 0.3726 0.572 0.000 0.040 0.000 0.360 0.028
#> SRR1044427 1 0.5329 0.6364 0.664 0.000 0.000 0.068 0.204 0.064
#> SRR1044428 1 0.1074 0.8839 0.960 0.000 0.000 0.000 0.028 0.012
#> SRR1044429 1 0.3975 0.7814 0.784 0.000 0.000 0.020 0.132 0.064
#> SRR1044430 1 0.4107 0.6725 0.728 0.000 0.020 0.000 0.228 0.024
#> SRR1044431 1 0.2979 0.8375 0.852 0.000 0.000 0.004 0.088 0.056
#> SRR1044433 5 0.2037 0.9444 0.008 0.000 0.060 0.008 0.916 0.008
#> SRR1044432 1 0.2869 0.7866 0.832 0.000 0.000 0.000 0.148 0.020
#> SRR1044434 4 0.0000 0.9341 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044435 4 0.0146 0.9338 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044436 4 0.0146 0.9338 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044437 4 0.0000 0.9341 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044439 4 0.0146 0.9338 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044438 4 0.0717 0.9273 0.008 0.000 0.000 0.976 0.016 0.000
#> SRR1044440 4 0.0000 0.9341 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044441 4 0.2357 0.8796 0.004 0.000 0.032 0.904 0.048 0.012
#> SRR1044442 5 0.2026 0.9434 0.008 0.000 0.060 0.012 0.916 0.004
#> SRR1044443 5 0.2037 0.9444 0.008 0.000 0.060 0.008 0.916 0.008
#> SRR1044444 4 0.0000 0.9341 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044445 4 0.1225 0.9196 0.000 0.000 0.000 0.952 0.036 0.012
#> SRR1044446 3 0.1075 0.8906 0.000 0.000 0.952 0.000 0.000 0.048
#> SRR1044447 6 0.3494 0.5251 0.000 0.012 0.252 0.000 0.000 0.736
#> SRR1044449 3 0.0937 0.8937 0.000 0.000 0.960 0.000 0.000 0.040
#> SRR1044448 3 0.0146 0.9075 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1044450 3 0.0363 0.9064 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1044451 6 0.3398 0.5192 0.000 0.008 0.252 0.000 0.000 0.740
#> SRR1044452 3 0.3690 0.6054 0.000 0.012 0.700 0.000 0.000 0.288
#> SRR1044453 3 0.4018 0.5405 0.000 0.020 0.656 0.000 0.000 0.324
#> SRR1044454 3 0.4237 0.3772 0.000 0.020 0.584 0.000 0.000 0.396
#> SRR1044455 6 0.5303 0.6992 0.000 0.260 0.136 0.000 0.004 0.600
#> SRR1044456 2 0.1267 0.9084 0.000 0.940 0.000 0.000 0.000 0.060
#> SRR1044457 6 0.4928 0.6106 0.000 0.352 0.076 0.000 0.000 0.572
#> SRR1044458 2 0.3221 0.6113 0.000 0.736 0.000 0.000 0.000 0.264
#> SRR1044459 3 0.1082 0.8934 0.000 0.004 0.956 0.000 0.000 0.040
#> SRR1044460 2 0.0000 0.9219 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044461 2 0.1556 0.8748 0.000 0.920 0.000 0.000 0.000 0.080
#> SRR1044462 1 0.6512 0.1909 0.452 0.000 0.000 0.144 0.348 0.056
#> SRR1044463 1 0.1003 0.8808 0.964 0.000 0.000 0.000 0.020 0.016
#> SRR1044464 5 0.2557 0.9312 0.008 0.000 0.060 0.032 0.892 0.008
#> SRR1044466 1 0.1168 0.8781 0.956 0.000 0.000 0.000 0.028 0.016
#> SRR1044465 1 0.0603 0.8859 0.980 0.000 0.000 0.000 0.016 0.004
#> SRR1044467 1 0.0260 0.8855 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1044468 2 0.0146 0.9213 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044469 6 0.4368 0.6726 0.000 0.272 0.056 0.000 0.000 0.672
#> SRR1044470 1 0.0458 0.8847 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1044471 1 0.0547 0.8866 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1044472 1 0.2581 0.8137 0.860 0.000 0.000 0.000 0.120 0.020
#> SRR1044473 1 0.0909 0.8854 0.968 0.000 0.000 0.000 0.012 0.020
#> SRR1044474 2 0.0547 0.9218 0.000 0.980 0.000 0.000 0.000 0.020
#> SRR1044475 6 0.5350 0.6153 0.000 0.296 0.140 0.000 0.000 0.564
#> SRR1044476 2 0.2941 0.6950 0.000 0.780 0.000 0.000 0.000 0.220
#> SRR1044477 2 0.0547 0.9218 0.000 0.980 0.000 0.000 0.000 0.020
#> SRR1044478 2 0.1007 0.9041 0.000 0.956 0.000 0.000 0.000 0.044
#> SRR1044479 2 0.0632 0.9216 0.000 0.976 0.000 0.000 0.000 0.024
#> SRR1044480 4 0.5986 0.3836 0.120 0.000 0.000 0.584 0.240 0.056
#> SRR1044481 1 0.2925 0.8443 0.864 0.000 0.000 0.012 0.064 0.060
#> SRR1044482 2 0.0547 0.9218 0.000 0.980 0.000 0.000 0.000 0.020
#> SRR1044483 4 0.1364 0.9083 0.004 0.000 0.000 0.944 0.048 0.004
#> SRR1044484 1 0.5530 0.5589 0.624 0.000 0.000 0.072 0.248 0.056
#> SRR1044486 1 0.2278 0.8650 0.904 0.000 0.000 0.012 0.032 0.052
#> SRR1044485 2 0.0547 0.9218 0.000 0.980 0.000 0.000 0.000 0.020
#> SRR1044487 2 0.0547 0.9218 0.000 0.980 0.000 0.000 0.000 0.020
#> SRR1044488 2 0.0146 0.9213 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044489 2 0.0146 0.9213 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044490 1 0.0717 0.8857 0.976 0.000 0.000 0.000 0.016 0.008
#> SRR1044491 1 0.0820 0.8830 0.972 0.000 0.000 0.000 0.016 0.012
#> SRR1044492 1 0.0717 0.8835 0.976 0.000 0.000 0.000 0.016 0.008
#> SRR1044493 1 0.1168 0.8781 0.956 0.000 0.000 0.000 0.028 0.016
#> SRR1044494 2 0.0547 0.9218 0.000 0.980 0.000 0.000 0.000 0.020
#> SRR1044496 2 0.0632 0.9216 0.000 0.976 0.000 0.000 0.000 0.024
#> SRR1044495 2 0.0547 0.9218 0.000 0.980 0.000 0.000 0.000 0.020
#> SRR1044497 4 0.0291 0.9321 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044499 6 0.4506 0.5821 0.000 0.348 0.044 0.000 0.000 0.608
#> SRR1044498 1 0.6044 0.4052 0.544 0.000 0.000 0.088 0.304 0.064
#> SRR1044500 2 0.0260 0.9211 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044501 2 0.3198 0.6155 0.000 0.740 0.000 0.000 0.000 0.260
#> SRR1044502 6 0.4062 0.6562 0.000 0.080 0.176 0.000 0.000 0.744
#> SRR1044503 4 0.0146 0.9338 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044504 4 0.0146 0.9338 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044505 1 0.4617 0.7361 0.740 0.000 0.000 0.048 0.148 0.064
#> SRR1044506 4 0.1297 0.9198 0.000 0.000 0.000 0.948 0.040 0.012
#> SRR1044507 5 0.2290 0.9380 0.008 0.000 0.060 0.024 0.904 0.004
#> SRR1044508 5 0.2037 0.9444 0.008 0.000 0.060 0.008 0.916 0.008
#> SRR1044509 5 0.2037 0.9444 0.008 0.000 0.060 0.008 0.916 0.008
#> SRR1044510 3 0.0146 0.9075 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1044511 3 0.0363 0.9058 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1044512 3 0.0260 0.9077 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1044513 6 0.4232 0.6642 0.000 0.100 0.168 0.000 0.000 0.732
#> SRR1044514 3 0.0146 0.9075 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1044515 6 0.4040 0.6795 0.000 0.112 0.132 0.000 0.000 0.756
#> SRR1044516 2 0.1863 0.8623 0.000 0.896 0.000 0.000 0.000 0.104
#> SRR1044517 3 0.0000 0.9069 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044518 3 0.0146 0.9075 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1044519 3 0.0603 0.9050 0.000 0.000 0.980 0.000 0.004 0.016
#> SRR1044520 3 0.0508 0.9058 0.000 0.000 0.984 0.000 0.004 0.012
#> SRR1044521 2 0.1500 0.8893 0.000 0.936 0.012 0.000 0.000 0.052
#> SRR1044522 2 0.0632 0.9216 0.000 0.976 0.000 0.000 0.000 0.024
#> SRR1044523 6 0.5140 0.5508 0.000 0.392 0.088 0.000 0.000 0.520
#> SRR1044524 6 0.3377 0.5907 0.000 0.028 0.188 0.000 0.000 0.784
#> SRR1044525 4 0.2326 0.8597 0.008 0.000 0.000 0.888 0.092 0.012
#> SRR1044526 1 0.5814 0.5659 0.620 0.000 0.000 0.112 0.204 0.064
#> SRR1044527 2 0.1663 0.8755 0.000 0.912 0.000 0.000 0.000 0.088
#> SRR1044528 6 0.5238 0.5227 0.000 0.408 0.096 0.000 0.000 0.496
#> SRR1044529 2 0.0547 0.9218 0.000 0.980 0.000 0.000 0.000 0.020
#> SRR1044530 1 0.1074 0.8798 0.960 0.000 0.000 0.000 0.028 0.012
#> SRR1044531 1 0.0405 0.8855 0.988 0.000 0.000 0.000 0.008 0.004
#> SRR1044533 1 0.0405 0.8862 0.988 0.000 0.000 0.000 0.008 0.004
#> SRR1044532 1 0.1074 0.8798 0.960 0.000 0.000 0.000 0.028 0.012
#> SRR1044534 2 0.0260 0.9211 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044535 6 0.3230 0.5663 0.000 0.012 0.212 0.000 0.000 0.776
#> SRR1044536 2 0.0260 0.9211 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044537 1 0.2556 0.8583 0.888 0.000 0.000 0.012 0.048 0.052
#> SRR1044538 1 0.0820 0.8827 0.972 0.000 0.000 0.000 0.016 0.012
#> SRR1044539 4 0.1477 0.9055 0.008 0.000 0.000 0.940 0.048 0.004
#> SRR1044540 1 0.0806 0.8852 0.972 0.000 0.000 0.000 0.020 0.008
#> SRR1044541 6 0.5523 0.6805 0.000 0.296 0.164 0.000 0.000 0.540
#> SRR1044542 1 0.1088 0.8797 0.960 0.000 0.000 0.000 0.024 0.016
#> SRR1044543 1 0.1483 0.8793 0.944 0.000 0.008 0.000 0.036 0.012
#> SRR1044544 6 0.4695 0.7087 0.000 0.208 0.116 0.000 0.000 0.676
#> SRR1044545 4 0.0363 0.9324 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR1044546 1 0.1829 0.8808 0.928 0.000 0.000 0.008 0.028 0.036
#> SRR1044547 4 0.4064 0.6259 0.040 0.000 0.000 0.720 0.236 0.004
#> SRR1044548 1 0.1749 0.8805 0.932 0.000 0.000 0.008 0.024 0.036
#> SRR1044549 2 0.4781 0.1353 0.000 0.608 0.072 0.000 0.000 0.320
#> SRR1044550 2 0.0146 0.9213 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044551 2 0.1501 0.8825 0.000 0.924 0.000 0.000 0.000 0.076
#> SRR1044552 4 0.0291 0.9328 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR1044553 4 0.0777 0.9241 0.000 0.000 0.000 0.972 0.024 0.004
#> SRR1044554 1 0.0725 0.8857 0.976 0.000 0.000 0.000 0.012 0.012
#> SRR1044555 6 0.3374 0.5622 0.000 0.020 0.208 0.000 0.000 0.772
#> SRR1044556 4 0.0146 0.9338 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044557 1 0.1321 0.8854 0.952 0.000 0.000 0.004 0.024 0.020
#> SRR1044558 4 0.0000 0.9341 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044559 1 0.2809 0.8638 0.880 0.000 0.016 0.008 0.064 0.032
#> SRR1044561 4 0.0000 0.9341 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044560 2 0.2823 0.7101 0.000 0.796 0.000 0.000 0.000 0.204
#> SRR1044562 1 0.1078 0.8864 0.964 0.000 0.000 0.008 0.016 0.012
#> SRR1044563 4 0.0000 0.9341 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044564 1 0.3338 0.8339 0.844 0.000 0.000 0.032 0.064 0.060
#> SRR1044565 2 0.0547 0.9218 0.000 0.980 0.000 0.000 0.000 0.020
#> SRR1044566 2 0.2340 0.7957 0.000 0.852 0.000 0.000 0.000 0.148
#> SRR1044567 1 0.1003 0.8807 0.964 0.000 0.000 0.000 0.020 0.016
#> SRR1044568 4 0.6383 0.0262 0.116 0.000 0.000 0.460 0.364 0.060
#> SRR1044569 1 0.0520 0.8861 0.984 0.000 0.000 0.000 0.008 0.008
#> SRR1044570 1 0.1168 0.8781 0.956 0.000 0.000 0.000 0.028 0.016
#> SRR1044571 1 0.0260 0.8855 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1044572 1 0.0717 0.8852 0.976 0.000 0.000 0.000 0.016 0.008
#> SRR1044573 1 0.1261 0.8828 0.952 0.000 0.000 0.000 0.024 0.024
#> SRR1044574 1 0.0777 0.8860 0.972 0.000 0.000 0.000 0.024 0.004
#> SRR1044575 1 0.0622 0.8853 0.980 0.000 0.000 0.000 0.012 0.008
#> SRR1044576 2 0.0458 0.9223 0.000 0.984 0.000 0.000 0.000 0.016
#> SRR1044577 2 0.0458 0.9228 0.000 0.984 0.000 0.000 0.000 0.016
#> SRR1044578 2 0.0547 0.9218 0.000 0.980 0.000 0.000 0.000 0.020
#> SRR1044579 4 0.0000 0.9341 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044580 1 0.6744 0.1403 0.432 0.000 0.000 0.164 0.336 0.068
#> SRR1044581 4 0.0000 0.9341 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044582 1 0.1755 0.8777 0.932 0.000 0.000 0.008 0.028 0.032
#> SRR1044583 4 0.0000 0.9341 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044584 4 0.5032 0.5811 0.052 0.000 0.000 0.684 0.208 0.056
#> SRR1044585 4 0.0000 0.9341 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044586 1 0.2485 0.8586 0.892 0.000 0.000 0.012 0.040 0.056
#> SRR1044587 4 0.1500 0.9152 0.000 0.000 0.000 0.936 0.052 0.012
#> SRR1044588 4 0.1297 0.9198 0.000 0.000 0.000 0.948 0.040 0.012
#> SRR1044589 4 0.1225 0.9196 0.000 0.000 0.000 0.952 0.036 0.012
#> SRR1044590 4 0.1297 0.9198 0.000 0.000 0.000 0.948 0.040 0.012
#> SRR1044591 4 0.1225 0.9196 0.000 0.000 0.000 0.952 0.036 0.012
#> SRR1044592 5 0.2037 0.9444 0.008 0.000 0.060 0.008 0.916 0.008
#> SRR1044593 4 0.1225 0.9196 0.000 0.000 0.000 0.952 0.036 0.012
#> SRR1044594 4 0.1225 0.9196 0.000 0.000 0.000 0.952 0.036 0.012
#> SRR1044595 5 0.2630 0.9148 0.036 0.000 0.060 0.008 0.888 0.008
#> SRR1044596 5 0.3241 0.8753 0.008 0.000 0.060 0.084 0.844 0.004
#> SRR1044597 5 0.6076 0.6844 0.104 0.000 0.052 0.164 0.644 0.036
#> SRR1044598 1 0.1647 0.8836 0.940 0.000 0.004 0.008 0.032 0.016
#> SRR1044599 1 0.1647 0.8836 0.940 0.000 0.004 0.008 0.032 0.016
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.995 0.998 0.4931 0.508 0.508
#> 3 3 0.732 0.828 0.793 0.2648 0.841 0.687
#> 4 4 0.904 0.885 0.947 0.1682 0.887 0.690
#> 5 5 0.801 0.707 0.855 0.0531 0.986 0.948
#> 6 6 0.788 0.692 0.825 0.0383 0.933 0.749
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0.0000 1.000 0.000 1.000
#> SRR1044416 2 0.0000 1.000 0.000 1.000
#> SRR1044417 2 0.0000 1.000 0.000 1.000
#> SRR1044418 2 0.0000 1.000 0.000 1.000
#> SRR1044420 2 0.0000 1.000 0.000 1.000
#> SRR1044419 2 0.0000 1.000 0.000 1.000
#> SRR1044421 2 0.0000 1.000 0.000 1.000
#> SRR1044422 2 0.0000 1.000 0.000 1.000
#> SRR1044423 2 0.0000 1.000 0.000 1.000
#> SRR1044424 2 0.0000 1.000 0.000 1.000
#> SRR1044425 1 0.0000 0.997 1.000 0.000
#> SRR1044426 1 0.0000 0.997 1.000 0.000
#> SRR1044427 1 0.0000 0.997 1.000 0.000
#> SRR1044428 1 0.0000 0.997 1.000 0.000
#> SRR1044429 1 0.0000 0.997 1.000 0.000
#> SRR1044430 1 0.0000 0.997 1.000 0.000
#> SRR1044431 1 0.0000 0.997 1.000 0.000
#> SRR1044433 1 0.0376 0.993 0.996 0.004
#> SRR1044432 1 0.0000 0.997 1.000 0.000
#> SRR1044434 1 0.0000 0.997 1.000 0.000
#> SRR1044435 1 0.0000 0.997 1.000 0.000
#> SRR1044436 1 0.0000 0.997 1.000 0.000
#> SRR1044437 1 0.0000 0.997 1.000 0.000
#> SRR1044439 1 0.0000 0.997 1.000 0.000
#> SRR1044438 1 0.0000 0.997 1.000 0.000
#> SRR1044440 1 0.0000 0.997 1.000 0.000
#> SRR1044441 1 0.0000 0.997 1.000 0.000
#> SRR1044442 1 0.0000 0.997 1.000 0.000
#> SRR1044443 1 0.8713 0.589 0.708 0.292
#> SRR1044444 1 0.0000 0.997 1.000 0.000
#> SRR1044445 1 0.0000 0.997 1.000 0.000
#> SRR1044446 2 0.0000 1.000 0.000 1.000
#> SRR1044447 2 0.0000 1.000 0.000 1.000
#> SRR1044449 2 0.0000 1.000 0.000 1.000
#> SRR1044448 2 0.0000 1.000 0.000 1.000
#> SRR1044450 2 0.0000 1.000 0.000 1.000
#> SRR1044451 2 0.0000 1.000 0.000 1.000
#> SRR1044452 2 0.0000 1.000 0.000 1.000
#> SRR1044453 2 0.0000 1.000 0.000 1.000
#> SRR1044454 2 0.0000 1.000 0.000 1.000
#> SRR1044455 2 0.0000 1.000 0.000 1.000
#> SRR1044456 2 0.0000 1.000 0.000 1.000
#> SRR1044457 2 0.0000 1.000 0.000 1.000
#> SRR1044458 2 0.0000 1.000 0.000 1.000
#> SRR1044459 2 0.0000 1.000 0.000 1.000
#> SRR1044460 2 0.0000 1.000 0.000 1.000
#> SRR1044461 2 0.0000 1.000 0.000 1.000
#> SRR1044462 1 0.0000 0.997 1.000 0.000
#> SRR1044463 1 0.0000 0.997 1.000 0.000
#> SRR1044464 1 0.0000 0.997 1.000 0.000
#> SRR1044466 1 0.0000 0.997 1.000 0.000
#> SRR1044465 1 0.0000 0.997 1.000 0.000
#> SRR1044467 1 0.0000 0.997 1.000 0.000
#> SRR1044468 2 0.0000 1.000 0.000 1.000
#> SRR1044469 2 0.0000 1.000 0.000 1.000
#> SRR1044470 1 0.0000 0.997 1.000 0.000
#> SRR1044471 1 0.0000 0.997 1.000 0.000
#> SRR1044472 1 0.0000 0.997 1.000 0.000
#> SRR1044473 1 0.0000 0.997 1.000 0.000
#> SRR1044474 2 0.0000 1.000 0.000 1.000
#> SRR1044475 2 0.0000 1.000 0.000 1.000
#> SRR1044476 2 0.0000 1.000 0.000 1.000
#> SRR1044477 2 0.0000 1.000 0.000 1.000
#> SRR1044478 2 0.0000 1.000 0.000 1.000
#> SRR1044479 2 0.0000 1.000 0.000 1.000
#> SRR1044480 1 0.0000 0.997 1.000 0.000
#> SRR1044481 1 0.0000 0.997 1.000 0.000
#> SRR1044482 2 0.0000 1.000 0.000 1.000
#> SRR1044483 1 0.0000 0.997 1.000 0.000
#> SRR1044484 1 0.0000 0.997 1.000 0.000
#> SRR1044486 1 0.0000 0.997 1.000 0.000
#> SRR1044485 2 0.0000 1.000 0.000 1.000
#> SRR1044487 2 0.0000 1.000 0.000 1.000
#> SRR1044488 2 0.0000 1.000 0.000 1.000
#> SRR1044489 2 0.0000 1.000 0.000 1.000
#> SRR1044490 1 0.0000 0.997 1.000 0.000
#> SRR1044491 1 0.0000 0.997 1.000 0.000
#> SRR1044492 1 0.0000 0.997 1.000 0.000
#> SRR1044493 1 0.0000 0.997 1.000 0.000
#> SRR1044494 2 0.0000 1.000 0.000 1.000
#> SRR1044496 2 0.0000 1.000 0.000 1.000
#> SRR1044495 2 0.0000 1.000 0.000 1.000
#> SRR1044497 1 0.0000 0.997 1.000 0.000
#> SRR1044499 2 0.0000 1.000 0.000 1.000
#> SRR1044498 1 0.0000 0.997 1.000 0.000
#> SRR1044500 2 0.0000 1.000 0.000 1.000
#> SRR1044501 2 0.0000 1.000 0.000 1.000
#> SRR1044502 2 0.0000 1.000 0.000 1.000
#> SRR1044503 1 0.0000 0.997 1.000 0.000
#> SRR1044504 1 0.0000 0.997 1.000 0.000
#> SRR1044505 1 0.0000 0.997 1.000 0.000
#> SRR1044506 1 0.0000 0.997 1.000 0.000
#> SRR1044507 1 0.0000 0.997 1.000 0.000
#> SRR1044508 1 0.0000 0.997 1.000 0.000
#> SRR1044509 1 0.0000 0.997 1.000 0.000
#> SRR1044510 2 0.0000 1.000 0.000 1.000
#> SRR1044511 2 0.0000 1.000 0.000 1.000
#> SRR1044512 2 0.0000 1.000 0.000 1.000
#> SRR1044513 2 0.0000 1.000 0.000 1.000
#> SRR1044514 2 0.0000 1.000 0.000 1.000
#> SRR1044515 2 0.0000 1.000 0.000 1.000
#> SRR1044516 2 0.0000 1.000 0.000 1.000
#> SRR1044517 2 0.0000 1.000 0.000 1.000
#> SRR1044518 2 0.0000 1.000 0.000 1.000
#> SRR1044519 2 0.0000 1.000 0.000 1.000
#> SRR1044520 2 0.0000 1.000 0.000 1.000
#> SRR1044521 2 0.0000 1.000 0.000 1.000
#> SRR1044522 2 0.0000 1.000 0.000 1.000
#> SRR1044523 2 0.0000 1.000 0.000 1.000
#> SRR1044524 2 0.0000 1.000 0.000 1.000
#> SRR1044525 1 0.0000 0.997 1.000 0.000
#> SRR1044526 1 0.0000 0.997 1.000 0.000
#> SRR1044527 2 0.0000 1.000 0.000 1.000
#> SRR1044528 2 0.0000 1.000 0.000 1.000
#> SRR1044529 2 0.0000 1.000 0.000 1.000
#> SRR1044530 1 0.0000 0.997 1.000 0.000
#> SRR1044531 1 0.0000 0.997 1.000 0.000
#> SRR1044533 1 0.0000 0.997 1.000 0.000
#> SRR1044532 1 0.0000 0.997 1.000 0.000
#> SRR1044534 2 0.0000 1.000 0.000 1.000
#> SRR1044535 2 0.0000 1.000 0.000 1.000
#> SRR1044536 2 0.0000 1.000 0.000 1.000
#> SRR1044537 1 0.0000 0.997 1.000 0.000
#> SRR1044538 1 0.0000 0.997 1.000 0.000
#> SRR1044539 1 0.0000 0.997 1.000 0.000
#> SRR1044540 1 0.0000 0.997 1.000 0.000
#> SRR1044541 2 0.0000 1.000 0.000 1.000
#> SRR1044542 1 0.0000 0.997 1.000 0.000
#> SRR1044543 1 0.0000 0.997 1.000 0.000
#> SRR1044544 2 0.0000 1.000 0.000 1.000
#> SRR1044545 1 0.0000 0.997 1.000 0.000
#> SRR1044546 1 0.0000 0.997 1.000 0.000
#> SRR1044547 1 0.0000 0.997 1.000 0.000
#> SRR1044548 1 0.0000 0.997 1.000 0.000
#> SRR1044549 2 0.0000 1.000 0.000 1.000
#> SRR1044550 2 0.0000 1.000 0.000 1.000
#> SRR1044551 2 0.0000 1.000 0.000 1.000
#> SRR1044552 1 0.0000 0.997 1.000 0.000
#> SRR1044553 1 0.0000 0.997 1.000 0.000
#> SRR1044554 1 0.0000 0.997 1.000 0.000
#> SRR1044555 2 0.0000 1.000 0.000 1.000
#> SRR1044556 1 0.0000 0.997 1.000 0.000
#> SRR1044557 1 0.0000 0.997 1.000 0.000
#> SRR1044558 1 0.0000 0.997 1.000 0.000
#> SRR1044559 1 0.0000 0.997 1.000 0.000
#> SRR1044561 1 0.0000 0.997 1.000 0.000
#> SRR1044560 2 0.0000 1.000 0.000 1.000
#> SRR1044562 1 0.0000 0.997 1.000 0.000
#> SRR1044563 1 0.0000 0.997 1.000 0.000
#> SRR1044564 1 0.0000 0.997 1.000 0.000
#> SRR1044565 2 0.0000 1.000 0.000 1.000
#> SRR1044566 2 0.0000 1.000 0.000 1.000
#> SRR1044567 1 0.0000 0.997 1.000 0.000
#> SRR1044568 1 0.0000 0.997 1.000 0.000
#> SRR1044569 1 0.0000 0.997 1.000 0.000
#> SRR1044570 1 0.0000 0.997 1.000 0.000
#> SRR1044571 1 0.0000 0.997 1.000 0.000
#> SRR1044572 1 0.0000 0.997 1.000 0.000
#> SRR1044573 1 0.0000 0.997 1.000 0.000
#> SRR1044574 1 0.0000 0.997 1.000 0.000
#> SRR1044575 1 0.0000 0.997 1.000 0.000
#> SRR1044576 2 0.0000 1.000 0.000 1.000
#> SRR1044577 2 0.0000 1.000 0.000 1.000
#> SRR1044578 2 0.0000 1.000 0.000 1.000
#> SRR1044579 1 0.0000 0.997 1.000 0.000
#> SRR1044580 1 0.0000 0.997 1.000 0.000
#> SRR1044581 1 0.0000 0.997 1.000 0.000
#> SRR1044582 1 0.0000 0.997 1.000 0.000
#> SRR1044583 1 0.0000 0.997 1.000 0.000
#> SRR1044584 1 0.0000 0.997 1.000 0.000
#> SRR1044585 1 0.0000 0.997 1.000 0.000
#> SRR1044586 1 0.0000 0.997 1.000 0.000
#> SRR1044587 1 0.0000 0.997 1.000 0.000
#> SRR1044588 1 0.0000 0.997 1.000 0.000
#> SRR1044589 1 0.0000 0.997 1.000 0.000
#> SRR1044590 1 0.0000 0.997 1.000 0.000
#> SRR1044591 1 0.0000 0.997 1.000 0.000
#> SRR1044592 1 0.0000 0.997 1.000 0.000
#> SRR1044593 1 0.0000 0.997 1.000 0.000
#> SRR1044594 1 0.0000 0.997 1.000 0.000
#> SRR1044595 1 0.0000 0.997 1.000 0.000
#> SRR1044596 1 0.0000 0.997 1.000 0.000
#> SRR1044597 1 0.3274 0.934 0.940 0.060
#> SRR1044598 1 0.0000 0.997 1.000 0.000
#> SRR1044599 1 0.0000 0.997 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044416 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044417 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044418 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044420 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044419 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044421 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044422 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044423 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044424 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044425 1 0.3116 0.7249 0.892 0.000 0.108
#> SRR1044426 3 0.6192 0.9828 0.420 0.000 0.580
#> SRR1044427 1 0.0747 0.8621 0.984 0.000 0.016
#> SRR1044428 3 0.6180 0.9810 0.416 0.000 0.584
#> SRR1044429 1 0.5465 0.0866 0.712 0.000 0.288
#> SRR1044430 3 0.6008 0.8992 0.372 0.000 0.628
#> SRR1044431 3 0.6215 0.9741 0.428 0.000 0.572
#> SRR1044433 1 0.1315 0.8511 0.972 0.008 0.020
#> SRR1044432 3 0.6154 0.9703 0.408 0.000 0.592
#> SRR1044434 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044435 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044436 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044437 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044439 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044438 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044440 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044441 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044442 1 0.0424 0.8703 0.992 0.000 0.008
#> SRR1044443 1 0.9002 0.2683 0.532 0.156 0.312
#> SRR1044444 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044445 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044446 2 0.6192 0.7572 0.000 0.580 0.420
#> SRR1044447 2 0.6126 0.7678 0.000 0.600 0.400
#> SRR1044449 2 0.6180 0.7597 0.000 0.584 0.416
#> SRR1044448 2 0.6180 0.7597 0.000 0.584 0.416
#> SRR1044450 2 0.6192 0.7572 0.000 0.580 0.420
#> SRR1044451 2 0.6180 0.7597 0.000 0.584 0.416
#> SRR1044452 2 0.6154 0.7639 0.000 0.592 0.408
#> SRR1044453 2 0.6045 0.7772 0.000 0.620 0.380
#> SRR1044454 2 0.6026 0.7790 0.000 0.624 0.376
#> SRR1044455 2 0.5785 0.7970 0.000 0.668 0.332
#> SRR1044456 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044457 2 0.1411 0.8884 0.000 0.964 0.036
#> SRR1044458 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044459 2 0.6180 0.7598 0.000 0.584 0.416
#> SRR1044460 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044461 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044462 1 0.1163 0.8470 0.972 0.000 0.028
#> SRR1044463 3 0.6180 0.9810 0.416 0.000 0.584
#> SRR1044464 1 0.0424 0.8701 0.992 0.000 0.008
#> SRR1044466 3 0.6168 0.9766 0.412 0.000 0.588
#> SRR1044465 3 0.6192 0.9828 0.420 0.000 0.580
#> SRR1044467 3 0.6192 0.9828 0.420 0.000 0.580
#> SRR1044468 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044469 2 0.3686 0.8610 0.000 0.860 0.140
#> SRR1044470 3 0.6180 0.9805 0.416 0.000 0.584
#> SRR1044471 3 0.6192 0.9828 0.420 0.000 0.580
#> SRR1044472 3 0.6154 0.9703 0.408 0.000 0.592
#> SRR1044473 3 0.6192 0.9828 0.420 0.000 0.580
#> SRR1044474 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044475 2 0.4178 0.8517 0.000 0.828 0.172
#> SRR1044476 2 0.0424 0.8935 0.000 0.992 0.008
#> SRR1044477 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044478 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044479 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044480 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044481 3 0.6204 0.9789 0.424 0.000 0.576
#> SRR1044482 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044483 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044484 1 0.3412 0.6922 0.876 0.000 0.124
#> SRR1044486 3 0.6280 0.9202 0.460 0.000 0.540
#> SRR1044485 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044487 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044488 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044489 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044490 3 0.6192 0.9828 0.420 0.000 0.580
#> SRR1044491 3 0.6168 0.9766 0.412 0.000 0.588
#> SRR1044492 3 0.6180 0.9805 0.416 0.000 0.584
#> SRR1044493 3 0.6180 0.9810 0.416 0.000 0.584
#> SRR1044494 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044496 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044495 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044497 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044499 2 0.0892 0.8914 0.000 0.980 0.020
#> SRR1044498 1 0.4399 0.5296 0.812 0.000 0.188
#> SRR1044500 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044501 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044502 2 0.6140 0.7658 0.000 0.596 0.404
#> SRR1044503 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044504 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044505 1 0.3879 0.6264 0.848 0.000 0.152
#> SRR1044506 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044507 1 0.0592 0.8685 0.988 0.000 0.012
#> SRR1044508 1 0.2625 0.7750 0.916 0.000 0.084
#> SRR1044509 1 0.3038 0.7274 0.896 0.000 0.104
#> SRR1044510 2 0.6180 0.7597 0.000 0.584 0.416
#> SRR1044511 2 0.6192 0.7572 0.000 0.580 0.420
#> SRR1044512 2 0.6180 0.7597 0.000 0.584 0.416
#> SRR1044513 2 0.5465 0.8125 0.000 0.712 0.288
#> SRR1044514 2 0.6180 0.7597 0.000 0.584 0.416
#> SRR1044515 2 0.2625 0.8764 0.000 0.916 0.084
#> SRR1044516 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044517 2 0.6168 0.7618 0.000 0.588 0.412
#> SRR1044518 2 0.6192 0.7572 0.000 0.580 0.420
#> SRR1044519 2 0.6180 0.7597 0.000 0.584 0.416
#> SRR1044520 2 0.6180 0.7597 0.000 0.584 0.416
#> SRR1044521 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044522 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044523 2 0.2878 0.8732 0.000 0.904 0.096
#> SRR1044524 2 0.5706 0.8018 0.000 0.680 0.320
#> SRR1044525 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044526 1 0.1411 0.8379 0.964 0.000 0.036
#> SRR1044527 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044528 2 0.0592 0.8928 0.000 0.988 0.012
#> SRR1044529 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044530 3 0.6180 0.9810 0.416 0.000 0.584
#> SRR1044531 3 0.6192 0.9828 0.420 0.000 0.580
#> SRR1044533 3 0.6192 0.9828 0.420 0.000 0.580
#> SRR1044532 3 0.6180 0.9810 0.416 0.000 0.584
#> SRR1044534 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044535 2 0.6154 0.7639 0.000 0.592 0.408
#> SRR1044536 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044537 3 0.6295 0.8962 0.472 0.000 0.528
#> SRR1044538 3 0.6180 0.9805 0.416 0.000 0.584
#> SRR1044539 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044540 3 0.6192 0.9828 0.420 0.000 0.580
#> SRR1044541 2 0.5621 0.8064 0.000 0.692 0.308
#> SRR1044542 3 0.6168 0.9766 0.412 0.000 0.588
#> SRR1044543 3 0.6192 0.9828 0.420 0.000 0.580
#> SRR1044544 2 0.3941 0.8576 0.000 0.844 0.156
#> SRR1044545 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044546 1 0.6225 -0.6441 0.568 0.000 0.432
#> SRR1044547 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044548 1 0.6309 -0.8279 0.504 0.000 0.496
#> SRR1044549 2 0.1643 0.8863 0.000 0.956 0.044
#> SRR1044550 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044551 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044552 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044553 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044554 3 0.6192 0.9828 0.420 0.000 0.580
#> SRR1044555 2 0.6045 0.7769 0.000 0.620 0.380
#> SRR1044556 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044557 3 0.6267 0.9361 0.452 0.000 0.548
#> SRR1044558 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044559 1 0.6267 -0.7080 0.548 0.000 0.452
#> SRR1044561 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044560 2 0.0237 0.8942 0.000 0.996 0.004
#> SRR1044562 3 0.6204 0.9754 0.424 0.000 0.576
#> SRR1044563 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044564 1 0.5785 -0.2423 0.668 0.000 0.332
#> SRR1044565 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044566 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044567 3 0.6180 0.9810 0.416 0.000 0.584
#> SRR1044568 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044569 3 0.6192 0.9828 0.420 0.000 0.580
#> SRR1044570 3 0.6180 0.9810 0.416 0.000 0.584
#> SRR1044571 3 0.6192 0.9828 0.420 0.000 0.580
#> SRR1044572 3 0.6192 0.9828 0.420 0.000 0.580
#> SRR1044573 3 0.6215 0.9738 0.428 0.000 0.572
#> SRR1044574 3 0.6192 0.9828 0.420 0.000 0.580
#> SRR1044575 3 0.6192 0.9828 0.420 0.000 0.580
#> SRR1044576 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044577 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044578 2 0.0000 0.8948 0.000 1.000 0.000
#> SRR1044579 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044580 1 0.6026 -0.4320 0.624 0.000 0.376
#> SRR1044581 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044582 3 0.6192 0.9828 0.420 0.000 0.580
#> SRR1044583 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044584 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044585 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044586 3 0.6305 0.8705 0.484 0.000 0.516
#> SRR1044587 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044588 1 0.0747 0.8564 0.984 0.016 0.000
#> SRR1044589 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044590 1 0.0237 0.8729 0.996 0.004 0.000
#> SRR1044591 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044592 1 0.1129 0.8498 0.976 0.004 0.020
#> SRR1044593 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044594 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044595 1 0.6513 -0.1523 0.592 0.008 0.400
#> SRR1044596 1 0.0000 0.8775 1.000 0.000 0.000
#> SRR1044597 1 0.5339 0.6401 0.824 0.080 0.096
#> SRR1044598 3 0.6192 0.9828 0.420 0.000 0.580
#> SRR1044599 3 0.6244 0.9558 0.440 0.000 0.560
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044416 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044417 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044418 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044420 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044419 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044421 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044422 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044423 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044424 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044425 4 0.4401 0.6286 0.272 0.000 0.004 0.724
#> SRR1044426 1 0.0188 0.9278 0.996 0.000 0.004 0.000
#> SRR1044427 4 0.1389 0.9110 0.048 0.000 0.000 0.952
#> SRR1044428 1 0.0336 0.9272 0.992 0.000 0.008 0.000
#> SRR1044429 1 0.5137 0.1523 0.544 0.000 0.004 0.452
#> SRR1044430 1 0.0592 0.9244 0.984 0.000 0.016 0.000
#> SRR1044431 1 0.0524 0.9267 0.988 0.000 0.008 0.004
#> SRR1044433 4 0.1211 0.9197 0.000 0.000 0.040 0.960
#> SRR1044432 1 0.0188 0.9278 0.996 0.000 0.004 0.000
#> SRR1044434 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044435 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044436 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044437 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044439 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044438 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044440 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044441 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044442 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044443 3 0.4978 0.3369 0.000 0.004 0.612 0.384
#> SRR1044444 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044445 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044446 3 0.1118 0.9086 0.000 0.036 0.964 0.000
#> SRR1044447 3 0.1389 0.9030 0.000 0.048 0.952 0.000
#> SRR1044449 3 0.1118 0.9086 0.000 0.036 0.964 0.000
#> SRR1044448 3 0.1118 0.9086 0.000 0.036 0.964 0.000
#> SRR1044450 3 0.1118 0.9086 0.000 0.036 0.964 0.000
#> SRR1044451 3 0.1118 0.9086 0.000 0.036 0.964 0.000
#> SRR1044452 3 0.2081 0.8797 0.000 0.084 0.916 0.000
#> SRR1044453 3 0.3311 0.7990 0.000 0.172 0.828 0.000
#> SRR1044454 3 0.4164 0.6762 0.000 0.264 0.736 0.000
#> SRR1044455 2 0.1940 0.8948 0.000 0.924 0.076 0.000
#> SRR1044456 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044457 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044458 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044459 3 0.1118 0.9086 0.000 0.036 0.964 0.000
#> SRR1044460 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044461 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044462 4 0.2797 0.8738 0.068 0.000 0.032 0.900
#> SRR1044463 1 0.0188 0.9271 0.996 0.000 0.004 0.000
#> SRR1044464 4 0.0592 0.9403 0.000 0.000 0.016 0.984
#> SRR1044466 1 0.0188 0.9271 0.996 0.000 0.004 0.000
#> SRR1044465 1 0.0188 0.9278 0.996 0.000 0.004 0.000
#> SRR1044467 1 0.0188 0.9278 0.996 0.000 0.004 0.000
#> SRR1044468 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044469 2 0.0707 0.9521 0.000 0.980 0.020 0.000
#> SRR1044470 1 0.0188 0.9271 0.996 0.000 0.004 0.000
#> SRR1044471 1 0.0336 0.9271 0.992 0.000 0.008 0.000
#> SRR1044472 1 0.0188 0.9271 0.996 0.000 0.004 0.000
#> SRR1044473 1 0.0188 0.9278 0.996 0.000 0.004 0.000
#> SRR1044474 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044475 2 0.3569 0.7365 0.000 0.804 0.196 0.000
#> SRR1044476 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044477 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044478 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044479 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044480 4 0.0921 0.9327 0.000 0.000 0.028 0.972
#> SRR1044481 1 0.0817 0.9186 0.976 0.000 0.024 0.000
#> SRR1044482 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044483 4 0.0707 0.9377 0.000 0.000 0.020 0.980
#> SRR1044484 4 0.5311 0.4986 0.328 0.000 0.024 0.648
#> SRR1044486 1 0.2593 0.8648 0.904 0.000 0.016 0.080
#> SRR1044485 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044487 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044488 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044489 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044490 1 0.0188 0.9278 0.996 0.000 0.004 0.000
#> SRR1044491 1 0.0000 0.9275 1.000 0.000 0.000 0.000
#> SRR1044492 1 0.0188 0.9278 0.996 0.000 0.004 0.000
#> SRR1044493 1 0.0000 0.9275 1.000 0.000 0.000 0.000
#> SRR1044494 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044496 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044495 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044497 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044499 2 0.0188 0.9656 0.000 0.996 0.004 0.000
#> SRR1044498 4 0.5168 0.0107 0.496 0.000 0.004 0.500
#> SRR1044500 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044501 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044502 3 0.4866 0.3842 0.000 0.404 0.596 0.000
#> SRR1044503 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044504 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044505 4 0.5321 0.5492 0.296 0.000 0.032 0.672
#> SRR1044506 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044507 4 0.0469 0.9425 0.000 0.000 0.012 0.988
#> SRR1044508 4 0.2281 0.8788 0.000 0.000 0.096 0.904
#> SRR1044509 4 0.2814 0.8278 0.000 0.000 0.132 0.868
#> SRR1044510 3 0.1118 0.9086 0.000 0.036 0.964 0.000
#> SRR1044511 3 0.1118 0.9086 0.000 0.036 0.964 0.000
#> SRR1044512 3 0.1118 0.9086 0.000 0.036 0.964 0.000
#> SRR1044513 2 0.4331 0.5654 0.000 0.712 0.288 0.000
#> SRR1044514 3 0.1118 0.9086 0.000 0.036 0.964 0.000
#> SRR1044515 2 0.0188 0.9656 0.000 0.996 0.004 0.000
#> SRR1044516 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044517 3 0.1118 0.9086 0.000 0.036 0.964 0.000
#> SRR1044518 3 0.1118 0.9086 0.000 0.036 0.964 0.000
#> SRR1044519 3 0.1118 0.9086 0.000 0.036 0.964 0.000
#> SRR1044520 3 0.1118 0.9086 0.000 0.036 0.964 0.000
#> SRR1044521 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044522 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044523 2 0.0817 0.9473 0.000 0.976 0.024 0.000
#> SRR1044524 2 0.4624 0.4435 0.000 0.660 0.340 0.000
#> SRR1044525 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044526 4 0.3547 0.8059 0.144 0.000 0.016 0.840
#> SRR1044527 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044528 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044529 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044530 1 0.0188 0.9271 0.996 0.000 0.004 0.000
#> SRR1044531 1 0.0188 0.9278 0.996 0.000 0.004 0.000
#> SRR1044533 1 0.0188 0.9278 0.996 0.000 0.004 0.000
#> SRR1044532 1 0.0188 0.9271 0.996 0.000 0.004 0.000
#> SRR1044534 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044535 3 0.3837 0.7361 0.000 0.224 0.776 0.000
#> SRR1044536 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044537 1 0.4323 0.7482 0.788 0.000 0.028 0.184
#> SRR1044538 1 0.0188 0.9271 0.996 0.000 0.004 0.000
#> SRR1044539 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044540 1 0.0188 0.9278 0.996 0.000 0.004 0.000
#> SRR1044541 2 0.4164 0.6191 0.000 0.736 0.264 0.000
#> SRR1044542 1 0.0188 0.9271 0.996 0.000 0.004 0.000
#> SRR1044543 1 0.0188 0.9278 0.996 0.000 0.004 0.000
#> SRR1044544 2 0.0592 0.9556 0.000 0.984 0.016 0.000
#> SRR1044545 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044546 1 0.5322 0.5563 0.660 0.000 0.028 0.312
#> SRR1044547 4 0.0469 0.9424 0.000 0.000 0.012 0.988
#> SRR1044548 1 0.4281 0.7555 0.792 0.000 0.028 0.180
#> SRR1044549 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044550 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044551 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044552 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044553 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044554 1 0.0817 0.9183 0.976 0.000 0.024 0.000
#> SRR1044555 2 0.4877 0.2484 0.000 0.592 0.408 0.000
#> SRR1044556 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044557 1 0.2466 0.8786 0.916 0.000 0.028 0.056
#> SRR1044558 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044559 1 0.5847 0.3319 0.560 0.000 0.036 0.404
#> SRR1044561 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044560 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044562 1 0.1388 0.9107 0.960 0.000 0.028 0.012
#> SRR1044563 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044564 1 0.5776 0.1514 0.504 0.000 0.028 0.468
#> SRR1044565 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044566 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044567 1 0.0188 0.9271 0.996 0.000 0.004 0.000
#> SRR1044568 4 0.2521 0.8840 0.064 0.000 0.024 0.912
#> SRR1044569 1 0.0188 0.9278 0.996 0.000 0.004 0.000
#> SRR1044570 1 0.0188 0.9271 0.996 0.000 0.004 0.000
#> SRR1044571 1 0.0188 0.9278 0.996 0.000 0.004 0.000
#> SRR1044572 1 0.0188 0.9278 0.996 0.000 0.004 0.000
#> SRR1044573 1 0.0524 0.9260 0.988 0.000 0.008 0.004
#> SRR1044574 1 0.0188 0.9278 0.996 0.000 0.004 0.000
#> SRR1044575 1 0.0188 0.9278 0.996 0.000 0.004 0.000
#> SRR1044576 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044577 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044578 2 0.0000 0.9688 0.000 1.000 0.000 0.000
#> SRR1044579 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044580 1 0.4122 0.7027 0.760 0.000 0.004 0.236
#> SRR1044581 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044582 1 0.0921 0.9164 0.972 0.000 0.028 0.000
#> SRR1044583 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044584 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044585 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044586 1 0.3958 0.7935 0.824 0.000 0.032 0.144
#> SRR1044587 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044588 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044589 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044590 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044591 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044592 4 0.0469 0.9411 0.000 0.000 0.012 0.988
#> SRR1044593 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044594 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044595 3 0.7095 0.4303 0.180 0.000 0.560 0.260
#> SRR1044596 4 0.0000 0.9486 0.000 0.000 0.000 1.000
#> SRR1044597 4 0.6172 0.6164 0.152 0.004 0.156 0.688
#> SRR1044598 1 0.0336 0.9264 0.992 0.000 0.008 0.000
#> SRR1044599 1 0.1743 0.8888 0.940 0.000 0.004 0.056
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.2280 0.8631 0.000 0.880 0.000 0.000 0.120
#> SRR1044416 2 0.0162 0.9203 0.000 0.996 0.000 0.000 0.004
#> SRR1044417 2 0.0162 0.9205 0.000 0.996 0.000 0.000 0.004
#> SRR1044418 2 0.0162 0.9205 0.000 0.996 0.000 0.000 0.004
#> SRR1044420 2 0.0162 0.9203 0.000 0.996 0.000 0.000 0.004
#> SRR1044419 2 0.1043 0.9106 0.000 0.960 0.000 0.000 0.040
#> SRR1044421 2 0.0162 0.9205 0.000 0.996 0.000 0.000 0.004
#> SRR1044422 2 0.0510 0.9182 0.000 0.984 0.000 0.000 0.016
#> SRR1044423 2 0.1197 0.9076 0.000 0.952 0.000 0.000 0.048
#> SRR1044424 2 0.0794 0.9156 0.000 0.972 0.000 0.000 0.028
#> SRR1044425 4 0.4548 0.4751 0.232 0.000 0.000 0.716 0.052
#> SRR1044426 1 0.0880 0.7453 0.968 0.000 0.000 0.000 0.032
#> SRR1044427 4 0.2221 0.8021 0.036 0.000 0.000 0.912 0.052
#> SRR1044428 1 0.3074 0.6196 0.804 0.000 0.000 0.000 0.196
#> SRR1044429 1 0.5385 -0.2405 0.512 0.000 0.000 0.432 0.056
#> SRR1044430 1 0.3305 0.5954 0.776 0.000 0.000 0.000 0.224
#> SRR1044431 1 0.1956 0.7373 0.916 0.000 0.000 0.008 0.076
#> SRR1044433 4 0.4326 0.5570 0.000 0.000 0.264 0.708 0.028
#> SRR1044432 1 0.2074 0.7236 0.896 0.000 0.000 0.000 0.104
#> SRR1044434 4 0.0703 0.8491 0.000 0.000 0.000 0.976 0.024
#> SRR1044435 4 0.0162 0.8537 0.000 0.000 0.000 0.996 0.004
#> SRR1044436 4 0.0000 0.8534 0.000 0.000 0.000 1.000 0.000
#> SRR1044437 4 0.0609 0.8509 0.000 0.000 0.000 0.980 0.020
#> SRR1044439 4 0.0000 0.8534 0.000 0.000 0.000 1.000 0.000
#> SRR1044438 4 0.0000 0.8534 0.000 0.000 0.000 1.000 0.000
#> SRR1044440 4 0.0963 0.8427 0.000 0.000 0.000 0.964 0.036
#> SRR1044441 4 0.0404 0.8524 0.000 0.000 0.000 0.988 0.012
#> SRR1044442 4 0.1668 0.8270 0.000 0.000 0.028 0.940 0.032
#> SRR1044443 3 0.3897 0.5879 0.000 0.000 0.768 0.204 0.028
#> SRR1044444 4 0.0609 0.8494 0.000 0.000 0.000 0.980 0.020
#> SRR1044445 4 0.0290 0.8535 0.000 0.000 0.000 0.992 0.008
#> SRR1044446 3 0.0162 0.8247 0.000 0.000 0.996 0.000 0.004
#> SRR1044447 3 0.0451 0.8247 0.000 0.004 0.988 0.000 0.008
#> SRR1044449 3 0.1608 0.8261 0.000 0.000 0.928 0.000 0.072
#> SRR1044448 3 0.0000 0.8249 0.000 0.000 1.000 0.000 0.000
#> SRR1044450 3 0.0703 0.8205 0.000 0.000 0.976 0.000 0.024
#> SRR1044451 3 0.0290 0.8241 0.000 0.000 0.992 0.000 0.008
#> SRR1044452 3 0.5128 0.7125 0.000 0.076 0.656 0.000 0.268
#> SRR1044453 3 0.5905 0.6461 0.000 0.144 0.580 0.000 0.276
#> SRR1044454 3 0.6557 0.5078 0.000 0.240 0.472 0.000 0.288
#> SRR1044455 2 0.3527 0.8036 0.000 0.804 0.024 0.000 0.172
#> SRR1044456 2 0.0162 0.9205 0.000 0.996 0.000 0.000 0.004
#> SRR1044457 2 0.2127 0.8752 0.000 0.892 0.000 0.000 0.108
#> SRR1044458 2 0.2377 0.8545 0.000 0.872 0.000 0.000 0.128
#> SRR1044459 3 0.3741 0.7591 0.000 0.004 0.732 0.000 0.264
#> SRR1044460 2 0.0290 0.9206 0.000 0.992 0.000 0.000 0.008
#> SRR1044461 2 0.1478 0.9001 0.000 0.936 0.000 0.000 0.064
#> SRR1044462 4 0.6162 -0.4277 0.132 0.000 0.000 0.436 0.432
#> SRR1044463 1 0.2280 0.7148 0.880 0.000 0.000 0.000 0.120
#> SRR1044464 4 0.2753 0.7299 0.008 0.000 0.000 0.856 0.136
#> SRR1044466 1 0.2377 0.7104 0.872 0.000 0.000 0.000 0.128
#> SRR1044465 1 0.1792 0.7294 0.916 0.000 0.000 0.000 0.084
#> SRR1044467 1 0.0963 0.7435 0.964 0.000 0.000 0.000 0.036
#> SRR1044468 2 0.0609 0.9171 0.000 0.980 0.000 0.000 0.020
#> SRR1044469 2 0.3661 0.7197 0.000 0.724 0.000 0.000 0.276
#> SRR1044470 1 0.2424 0.7164 0.868 0.000 0.000 0.000 0.132
#> SRR1044471 1 0.2471 0.6968 0.864 0.000 0.000 0.000 0.136
#> SRR1044472 1 0.2329 0.7127 0.876 0.000 0.000 0.000 0.124
#> SRR1044473 1 0.2516 0.6944 0.860 0.000 0.000 0.000 0.140
#> SRR1044474 2 0.0162 0.9205 0.000 0.996 0.000 0.000 0.004
#> SRR1044475 2 0.5245 0.5979 0.000 0.640 0.080 0.000 0.280
#> SRR1044476 2 0.3366 0.7714 0.000 0.768 0.000 0.000 0.232
#> SRR1044477 2 0.0290 0.9195 0.000 0.992 0.000 0.000 0.008
#> SRR1044478 2 0.0290 0.9195 0.000 0.992 0.000 0.000 0.008
#> SRR1044479 2 0.0290 0.9198 0.000 0.992 0.000 0.000 0.008
#> SRR1044480 4 0.4015 0.3592 0.000 0.000 0.000 0.652 0.348
#> SRR1044481 1 0.4193 0.3792 0.684 0.000 0.000 0.012 0.304
#> SRR1044482 2 0.0703 0.9161 0.000 0.976 0.000 0.000 0.024
#> SRR1044483 4 0.4009 0.4440 0.004 0.000 0.000 0.684 0.312
#> SRR1044484 4 0.6584 -0.3384 0.272 0.000 0.000 0.468 0.260
#> SRR1044486 1 0.4639 0.5317 0.708 0.000 0.000 0.056 0.236
#> SRR1044485 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> SRR1044487 2 0.0290 0.9198 0.000 0.992 0.000 0.000 0.008
#> SRR1044488 2 0.0162 0.9205 0.000 0.996 0.000 0.000 0.004
#> SRR1044489 2 0.0290 0.9198 0.000 0.992 0.000 0.000 0.008
#> SRR1044490 1 0.0880 0.7446 0.968 0.000 0.000 0.000 0.032
#> SRR1044491 1 0.1608 0.7340 0.928 0.000 0.000 0.000 0.072
#> SRR1044492 1 0.0880 0.7461 0.968 0.000 0.000 0.000 0.032
#> SRR1044493 1 0.0963 0.7430 0.964 0.000 0.000 0.000 0.036
#> SRR1044494 2 0.0162 0.9205 0.000 0.996 0.000 0.000 0.004
#> SRR1044496 2 0.0290 0.9198 0.000 0.992 0.000 0.000 0.008
#> SRR1044495 2 0.0290 0.9198 0.000 0.992 0.000 0.000 0.008
#> SRR1044497 4 0.0290 0.8532 0.000 0.000 0.000 0.992 0.008
#> SRR1044499 2 0.3366 0.7686 0.000 0.768 0.000 0.000 0.232
#> SRR1044498 4 0.6422 -0.2374 0.316 0.000 0.000 0.488 0.196
#> SRR1044500 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> SRR1044501 2 0.1043 0.9111 0.000 0.960 0.000 0.000 0.040
#> SRR1044502 3 0.4714 0.4758 0.000 0.324 0.644 0.000 0.032
#> SRR1044503 4 0.0404 0.8533 0.000 0.000 0.000 0.988 0.012
#> SRR1044504 4 0.0000 0.8534 0.000 0.000 0.000 1.000 0.000
#> SRR1044505 5 0.6576 0.5502 0.216 0.000 0.000 0.340 0.444
#> SRR1044506 4 0.0404 0.8530 0.000 0.000 0.000 0.988 0.012
#> SRR1044507 4 0.1485 0.8322 0.000 0.000 0.020 0.948 0.032
#> SRR1044508 4 0.6132 0.1607 0.000 0.000 0.388 0.480 0.132
#> SRR1044509 4 0.4520 0.5209 0.000 0.000 0.284 0.684 0.032
#> SRR1044510 3 0.3662 0.7650 0.000 0.004 0.744 0.000 0.252
#> SRR1044511 3 0.1965 0.8226 0.000 0.000 0.904 0.000 0.096
#> SRR1044512 3 0.1732 0.8256 0.000 0.000 0.920 0.000 0.080
#> SRR1044513 2 0.4300 0.0856 0.000 0.524 0.476 0.000 0.000
#> SRR1044514 3 0.1341 0.8269 0.000 0.000 0.944 0.000 0.056
#> SRR1044515 2 0.1168 0.9044 0.000 0.960 0.032 0.000 0.008
#> SRR1044516 2 0.0162 0.9201 0.000 0.996 0.000 0.000 0.004
#> SRR1044517 3 0.3561 0.7620 0.000 0.000 0.740 0.000 0.260
#> SRR1044518 3 0.1478 0.8271 0.000 0.000 0.936 0.000 0.064
#> SRR1044519 3 0.0162 0.8247 0.000 0.000 0.996 0.000 0.004
#> SRR1044520 3 0.0162 0.8247 0.000 0.000 0.996 0.000 0.004
#> SRR1044521 2 0.0162 0.9205 0.000 0.996 0.000 0.000 0.004
#> SRR1044522 2 0.0290 0.9198 0.000 0.992 0.000 0.000 0.008
#> SRR1044523 2 0.1740 0.8890 0.000 0.932 0.056 0.000 0.012
#> SRR1044524 2 0.5068 0.4780 0.000 0.640 0.300 0.000 0.060
#> SRR1044525 4 0.0000 0.8534 0.000 0.000 0.000 1.000 0.000
#> SRR1044526 4 0.6244 -0.1443 0.160 0.000 0.000 0.504 0.336
#> SRR1044527 2 0.0404 0.9196 0.000 0.988 0.000 0.000 0.012
#> SRR1044528 2 0.0290 0.9198 0.000 0.992 0.000 0.000 0.008
#> SRR1044529 2 0.0404 0.9196 0.000 0.988 0.000 0.000 0.012
#> SRR1044530 1 0.2377 0.7104 0.872 0.000 0.000 0.000 0.128
#> SRR1044531 1 0.1410 0.7430 0.940 0.000 0.000 0.000 0.060
#> SRR1044533 1 0.0880 0.7444 0.968 0.000 0.000 0.000 0.032
#> SRR1044532 1 0.1965 0.7248 0.904 0.000 0.000 0.000 0.096
#> SRR1044534 2 0.0290 0.9198 0.000 0.992 0.000 0.000 0.008
#> SRR1044535 3 0.3055 0.7434 0.000 0.144 0.840 0.000 0.016
#> SRR1044536 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> SRR1044537 5 0.5893 0.5300 0.436 0.000 0.000 0.100 0.464
#> SRR1044538 1 0.2377 0.7104 0.872 0.000 0.000 0.000 0.128
#> SRR1044539 4 0.1121 0.8303 0.000 0.000 0.000 0.956 0.044
#> SRR1044540 1 0.1671 0.7312 0.924 0.000 0.000 0.000 0.076
#> SRR1044541 2 0.6111 0.4252 0.000 0.560 0.180 0.000 0.260
#> SRR1044542 1 0.2377 0.7104 0.872 0.000 0.000 0.000 0.128
#> SRR1044543 1 0.2074 0.7145 0.896 0.000 0.000 0.000 0.104
#> SRR1044544 2 0.3814 0.7172 0.000 0.720 0.004 0.000 0.276
#> SRR1044545 4 0.1341 0.8183 0.000 0.000 0.000 0.944 0.056
#> SRR1044546 5 0.6356 0.6631 0.384 0.000 0.000 0.164 0.452
#> SRR1044547 4 0.3274 0.6126 0.000 0.000 0.000 0.780 0.220
#> SRR1044548 1 0.5687 -0.4711 0.484 0.000 0.000 0.080 0.436
#> SRR1044549 2 0.1281 0.9095 0.000 0.956 0.012 0.000 0.032
#> SRR1044550 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> SRR1044551 2 0.0162 0.9205 0.000 0.996 0.000 0.000 0.004
#> SRR1044552 4 0.0162 0.8537 0.000 0.000 0.000 0.996 0.004
#> SRR1044553 4 0.0162 0.8537 0.000 0.000 0.000 0.996 0.004
#> SRR1044554 1 0.4249 -0.0534 0.568 0.000 0.000 0.000 0.432
#> SRR1044555 2 0.6645 0.0437 0.000 0.440 0.316 0.000 0.244
#> SRR1044556 4 0.0000 0.8534 0.000 0.000 0.000 1.000 0.000
#> SRR1044557 1 0.5173 -0.3639 0.500 0.000 0.000 0.040 0.460
#> SRR1044558 4 0.0000 0.8534 0.000 0.000 0.000 1.000 0.000
#> SRR1044559 5 0.6535 0.7062 0.356 0.000 0.004 0.176 0.464
#> SRR1044561 4 0.0162 0.8536 0.000 0.000 0.000 0.996 0.004
#> SRR1044560 2 0.3395 0.7671 0.000 0.764 0.000 0.000 0.236
#> SRR1044562 1 0.4644 -0.2206 0.528 0.000 0.000 0.012 0.460
#> SRR1044563 4 0.0162 0.8536 0.000 0.000 0.000 0.996 0.004
#> SRR1044564 5 0.6678 0.6772 0.264 0.000 0.000 0.300 0.436
#> SRR1044565 2 0.0290 0.9198 0.000 0.992 0.000 0.000 0.008
#> SRR1044566 2 0.2929 0.8130 0.000 0.820 0.000 0.000 0.180
#> SRR1044567 1 0.2605 0.7056 0.852 0.000 0.000 0.000 0.148
#> SRR1044568 4 0.5589 -0.0410 0.080 0.000 0.000 0.548 0.372
#> SRR1044569 1 0.2074 0.7192 0.896 0.000 0.000 0.000 0.104
#> SRR1044570 1 0.2377 0.7104 0.872 0.000 0.000 0.000 0.128
#> SRR1044571 1 0.0609 0.7448 0.980 0.000 0.000 0.000 0.020
#> SRR1044572 1 0.0963 0.7445 0.964 0.000 0.000 0.000 0.036
#> SRR1044573 1 0.3455 0.6078 0.784 0.000 0.000 0.008 0.208
#> SRR1044574 1 0.1043 0.7430 0.960 0.000 0.000 0.000 0.040
#> SRR1044575 1 0.2424 0.6979 0.868 0.000 0.000 0.000 0.132
#> SRR1044576 2 0.0162 0.9205 0.000 0.996 0.000 0.000 0.004
#> SRR1044577 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> SRR1044578 2 0.0162 0.9205 0.000 0.996 0.000 0.000 0.004
#> SRR1044579 4 0.0290 0.8539 0.000 0.000 0.000 0.992 0.008
#> SRR1044580 1 0.5811 -0.0503 0.596 0.000 0.000 0.264 0.140
#> SRR1044581 4 0.0404 0.8524 0.000 0.000 0.000 0.988 0.012
#> SRR1044582 1 0.3752 0.3807 0.708 0.000 0.000 0.000 0.292
#> SRR1044583 4 0.0794 0.8456 0.000 0.000 0.000 0.972 0.028
#> SRR1044584 4 0.1082 0.8413 0.008 0.000 0.000 0.964 0.028
#> SRR1044585 4 0.0290 0.8532 0.000 0.000 0.000 0.992 0.008
#> SRR1044586 1 0.5927 -0.2349 0.468 0.000 0.000 0.104 0.428
#> SRR1044587 4 0.0290 0.8535 0.000 0.000 0.000 0.992 0.008
#> SRR1044588 4 0.0290 0.8535 0.000 0.000 0.000 0.992 0.008
#> SRR1044589 4 0.0290 0.8535 0.000 0.000 0.000 0.992 0.008
#> SRR1044590 4 0.0290 0.8535 0.000 0.000 0.000 0.992 0.008
#> SRR1044591 4 0.0290 0.8535 0.000 0.000 0.000 0.992 0.008
#> SRR1044592 4 0.2864 0.7542 0.000 0.000 0.112 0.864 0.024
#> SRR1044593 4 0.0290 0.8535 0.000 0.000 0.000 0.992 0.008
#> SRR1044594 4 0.0510 0.8532 0.000 0.000 0.000 0.984 0.016
#> SRR1044595 3 0.6136 0.4887 0.056 0.000 0.644 0.088 0.212
#> SRR1044596 4 0.0898 0.8449 0.000 0.000 0.008 0.972 0.020
#> SRR1044597 4 0.7945 0.2445 0.112 0.028 0.164 0.528 0.168
#> SRR1044598 1 0.3143 0.6615 0.796 0.000 0.000 0.000 0.204
#> SRR1044599 1 0.3264 0.6802 0.820 0.000 0.000 0.016 0.164
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.2941 0.6486 0.000 0.780 0.000 0.000 0.000 0.220
#> SRR1044416 2 0.0260 0.8932 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044417 2 0.0146 0.8944 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044418 2 0.0146 0.8944 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044420 2 0.0260 0.8932 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044419 2 0.1501 0.8510 0.000 0.924 0.000 0.000 0.000 0.076
#> SRR1044421 2 0.0260 0.8932 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044422 2 0.0632 0.8879 0.000 0.976 0.000 0.000 0.000 0.024
#> SRR1044423 2 0.1501 0.8524 0.000 0.924 0.000 0.000 0.000 0.076
#> SRR1044424 2 0.0790 0.8846 0.000 0.968 0.000 0.000 0.000 0.032
#> SRR1044425 4 0.4822 0.3943 0.304 0.000 0.000 0.632 0.048 0.016
#> SRR1044426 1 0.2852 0.7654 0.856 0.000 0.000 0.000 0.080 0.064
#> SRR1044427 4 0.3356 0.7492 0.092 0.000 0.000 0.836 0.052 0.020
#> SRR1044428 1 0.3720 0.5827 0.736 0.000 0.000 0.000 0.236 0.028
#> SRR1044429 1 0.5488 0.0379 0.484 0.000 0.000 0.428 0.060 0.028
#> SRR1044430 1 0.4866 0.3398 0.568 0.000 0.000 0.000 0.364 0.068
#> SRR1044431 1 0.3044 0.7446 0.860 0.000 0.000 0.036 0.076 0.028
#> SRR1044433 4 0.4611 0.3962 0.000 0.000 0.380 0.584 0.016 0.020
#> SRR1044432 1 0.3707 0.7375 0.784 0.000 0.000 0.000 0.136 0.080
#> SRR1044434 4 0.1116 0.8579 0.004 0.000 0.000 0.960 0.028 0.008
#> SRR1044435 4 0.0725 0.8660 0.000 0.000 0.000 0.976 0.012 0.012
#> SRR1044436 4 0.0692 0.8645 0.000 0.000 0.000 0.976 0.020 0.004
#> SRR1044437 4 0.0777 0.8614 0.000 0.000 0.000 0.972 0.024 0.004
#> SRR1044439 4 0.0713 0.8632 0.000 0.000 0.000 0.972 0.028 0.000
#> SRR1044438 4 0.0993 0.8668 0.000 0.000 0.000 0.964 0.024 0.012
#> SRR1044440 4 0.1080 0.8559 0.004 0.000 0.000 0.960 0.032 0.004
#> SRR1044441 4 0.0922 0.8642 0.004 0.000 0.000 0.968 0.024 0.004
#> SRR1044442 4 0.2685 0.8304 0.000 0.000 0.036 0.880 0.068 0.016
#> SRR1044443 3 0.2373 0.6993 0.000 0.000 0.888 0.084 0.004 0.024
#> SRR1044444 4 0.1194 0.8577 0.004 0.000 0.000 0.956 0.032 0.008
#> SRR1044445 4 0.1480 0.8596 0.000 0.000 0.000 0.940 0.040 0.020
#> SRR1044446 3 0.0260 0.7724 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1044447 3 0.0405 0.7730 0.000 0.008 0.988 0.000 0.004 0.000
#> SRR1044449 3 0.3094 0.6587 0.000 0.000 0.824 0.000 0.036 0.140
#> SRR1044448 3 0.0260 0.7731 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1044450 3 0.1088 0.7665 0.000 0.000 0.960 0.000 0.016 0.024
#> SRR1044451 3 0.0291 0.7729 0.000 0.004 0.992 0.000 0.000 0.004
#> SRR1044452 6 0.4732 0.5338 0.000 0.068 0.320 0.000 0.000 0.612
#> SRR1044453 6 0.4973 0.5971 0.000 0.112 0.264 0.000 0.000 0.624
#> SRR1044454 6 0.5027 0.6530 0.000 0.200 0.160 0.000 0.000 0.640
#> SRR1044455 2 0.4751 0.0825 0.000 0.580 0.040 0.000 0.008 0.372
#> SRR1044456 2 0.0547 0.8912 0.000 0.980 0.000 0.000 0.000 0.020
#> SRR1044457 2 0.2664 0.7188 0.000 0.816 0.000 0.000 0.000 0.184
#> SRR1044458 2 0.3288 0.5143 0.000 0.724 0.000 0.000 0.000 0.276
#> SRR1044459 6 0.4619 0.4346 0.000 0.044 0.392 0.000 0.000 0.564
#> SRR1044460 2 0.0260 0.8932 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044461 2 0.1957 0.8191 0.000 0.888 0.000 0.000 0.000 0.112
#> SRR1044462 5 0.4344 0.6913 0.096 0.000 0.000 0.188 0.716 0.000
#> SRR1044463 1 0.3792 0.7438 0.780 0.000 0.000 0.000 0.112 0.108
#> SRR1044464 4 0.3314 0.6185 0.004 0.000 0.000 0.740 0.256 0.000
#> SRR1044466 1 0.4455 0.7139 0.712 0.000 0.000 0.000 0.128 0.160
#> SRR1044465 1 0.1480 0.7559 0.940 0.000 0.000 0.000 0.040 0.020
#> SRR1044467 1 0.0820 0.7681 0.972 0.000 0.000 0.000 0.016 0.012
#> SRR1044468 2 0.0790 0.8847 0.000 0.968 0.000 0.000 0.000 0.032
#> SRR1044469 6 0.3782 0.4535 0.000 0.412 0.000 0.000 0.000 0.588
#> SRR1044470 1 0.4602 0.7184 0.696 0.000 0.000 0.000 0.144 0.160
#> SRR1044471 1 0.3230 0.6851 0.836 0.000 0.000 0.024 0.116 0.024
#> SRR1044472 1 0.4493 0.7135 0.708 0.000 0.000 0.000 0.132 0.160
#> SRR1044473 1 0.3292 0.6870 0.836 0.000 0.000 0.032 0.108 0.024
#> SRR1044474 2 0.0260 0.8943 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044475 6 0.4141 0.5162 0.000 0.388 0.016 0.000 0.000 0.596
#> SRR1044476 2 0.3854 -0.1021 0.000 0.536 0.000 0.000 0.000 0.464
#> SRR1044477 2 0.0363 0.8928 0.000 0.988 0.000 0.000 0.000 0.012
#> SRR1044478 2 0.0260 0.8936 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044479 2 0.0790 0.8849 0.000 0.968 0.000 0.000 0.000 0.032
#> SRR1044480 5 0.3795 0.4395 0.000 0.000 0.000 0.364 0.632 0.004
#> SRR1044481 5 0.4631 0.1297 0.464 0.000 0.000 0.008 0.504 0.024
#> SRR1044482 2 0.0632 0.8879 0.000 0.976 0.000 0.000 0.000 0.024
#> SRR1044483 5 0.4467 0.1662 0.004 0.000 0.000 0.480 0.496 0.020
#> SRR1044484 5 0.5894 0.3996 0.176 0.000 0.000 0.376 0.444 0.004
#> SRR1044486 1 0.6169 0.3689 0.508 0.000 0.000 0.048 0.328 0.116
#> SRR1044485 2 0.0146 0.8939 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044487 2 0.0632 0.8893 0.000 0.976 0.000 0.000 0.000 0.024
#> SRR1044488 2 0.0146 0.8944 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044489 2 0.0363 0.8934 0.000 0.988 0.000 0.000 0.000 0.012
#> SRR1044490 1 0.0820 0.7719 0.972 0.000 0.000 0.000 0.016 0.012
#> SRR1044491 1 0.1926 0.7707 0.912 0.000 0.000 0.000 0.068 0.020
#> SRR1044492 1 0.1921 0.7744 0.916 0.000 0.000 0.000 0.052 0.032
#> SRR1044493 1 0.3118 0.7617 0.836 0.000 0.000 0.000 0.092 0.072
#> SRR1044494 2 0.0000 0.8942 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044496 2 0.0458 0.8928 0.000 0.984 0.000 0.000 0.000 0.016
#> SRR1044495 2 0.0632 0.8893 0.000 0.976 0.000 0.000 0.000 0.024
#> SRR1044497 4 0.0458 0.8648 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1044499 2 0.3867 -0.1991 0.000 0.512 0.000 0.000 0.000 0.488
#> SRR1044498 4 0.6844 -0.2708 0.236 0.000 0.000 0.392 0.320 0.052
#> SRR1044500 2 0.0260 0.8932 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044501 2 0.1141 0.8712 0.000 0.948 0.000 0.000 0.000 0.052
#> SRR1044502 3 0.4836 0.2264 0.000 0.268 0.644 0.000 0.004 0.084
#> SRR1044503 4 0.0891 0.8602 0.000 0.000 0.000 0.968 0.024 0.008
#> SRR1044504 4 0.0858 0.8637 0.000 0.000 0.000 0.968 0.028 0.004
#> SRR1044505 5 0.5319 0.6197 0.228 0.000 0.000 0.116 0.636 0.020
#> SRR1044506 4 0.1492 0.8607 0.000 0.000 0.000 0.940 0.036 0.024
#> SRR1044507 4 0.3324 0.7982 0.000 0.000 0.060 0.840 0.080 0.020
#> SRR1044508 3 0.5690 0.3153 0.000 0.000 0.572 0.244 0.172 0.012
#> SRR1044509 4 0.5214 0.1671 0.000 0.000 0.440 0.492 0.048 0.020
#> SRR1044510 6 0.4624 0.3003 0.000 0.024 0.452 0.000 0.008 0.516
#> SRR1044511 3 0.2944 0.6715 0.000 0.012 0.832 0.000 0.008 0.148
#> SRR1044512 3 0.2257 0.7179 0.000 0.000 0.876 0.000 0.008 0.116
#> SRR1044513 3 0.4260 -0.0127 0.000 0.472 0.512 0.000 0.000 0.016
#> SRR1044514 3 0.2020 0.7346 0.000 0.000 0.896 0.000 0.008 0.096
#> SRR1044515 2 0.1605 0.8582 0.000 0.936 0.044 0.000 0.004 0.016
#> SRR1044516 2 0.0547 0.8947 0.000 0.980 0.000 0.000 0.000 0.020
#> SRR1044517 6 0.4546 0.3119 0.000 0.020 0.444 0.000 0.008 0.528
#> SRR1044518 3 0.2165 0.7253 0.000 0.000 0.884 0.000 0.008 0.108
#> SRR1044519 3 0.0260 0.7731 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1044520 3 0.0146 0.7733 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1044521 2 0.0363 0.8939 0.000 0.988 0.000 0.000 0.000 0.012
#> SRR1044522 2 0.0713 0.8871 0.000 0.972 0.000 0.000 0.000 0.028
#> SRR1044523 2 0.2282 0.8017 0.000 0.888 0.088 0.000 0.000 0.024
#> SRR1044524 2 0.4977 0.2967 0.000 0.636 0.236 0.000 0.000 0.128
#> SRR1044525 4 0.0692 0.8623 0.000 0.000 0.000 0.976 0.020 0.004
#> SRR1044526 4 0.6578 -0.3391 0.220 0.000 0.000 0.384 0.364 0.032
#> SRR1044527 2 0.0632 0.8919 0.000 0.976 0.000 0.000 0.000 0.024
#> SRR1044528 2 0.0937 0.8796 0.000 0.960 0.000 0.000 0.000 0.040
#> SRR1044529 2 0.0632 0.8932 0.000 0.976 0.000 0.000 0.000 0.024
#> SRR1044530 1 0.4162 0.7276 0.744 0.000 0.000 0.000 0.120 0.136
#> SRR1044531 1 0.0806 0.7709 0.972 0.000 0.000 0.000 0.008 0.020
#> SRR1044533 1 0.0909 0.7730 0.968 0.000 0.000 0.000 0.020 0.012
#> SRR1044532 1 0.3520 0.7513 0.804 0.000 0.000 0.000 0.096 0.100
#> SRR1044534 2 0.0547 0.8910 0.000 0.980 0.000 0.000 0.000 0.020
#> SRR1044535 3 0.3447 0.5867 0.000 0.148 0.804 0.000 0.004 0.044
#> SRR1044536 2 0.0146 0.8939 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044537 5 0.4087 0.7020 0.188 0.000 0.000 0.064 0.744 0.004
#> SRR1044538 1 0.4599 0.7041 0.696 0.000 0.000 0.000 0.140 0.164
#> SRR1044539 4 0.2300 0.7884 0.000 0.000 0.000 0.856 0.144 0.000
#> SRR1044540 1 0.0717 0.7678 0.976 0.000 0.000 0.000 0.016 0.008
#> SRR1044541 6 0.5181 0.6492 0.000 0.280 0.112 0.000 0.004 0.604
#> SRR1044542 1 0.4599 0.7041 0.696 0.000 0.000 0.000 0.140 0.164
#> SRR1044543 1 0.2058 0.7384 0.908 0.000 0.000 0.008 0.072 0.012
#> SRR1044544 6 0.3899 0.4730 0.000 0.404 0.004 0.000 0.000 0.592
#> SRR1044545 4 0.2416 0.7623 0.000 0.000 0.000 0.844 0.156 0.000
#> SRR1044546 5 0.3834 0.7108 0.144 0.000 0.000 0.084 0.772 0.000
#> SRR1044547 4 0.3833 0.1003 0.000 0.000 0.000 0.556 0.444 0.000
#> SRR1044548 5 0.4239 0.6973 0.180 0.000 0.000 0.072 0.740 0.008
#> SRR1044549 2 0.1285 0.8714 0.000 0.944 0.004 0.000 0.000 0.052
#> SRR1044550 2 0.0146 0.8944 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044551 2 0.0458 0.8929 0.000 0.984 0.000 0.000 0.000 0.016
#> SRR1044552 4 0.0508 0.8645 0.000 0.000 0.000 0.984 0.012 0.004
#> SRR1044553 4 0.0717 0.8657 0.000 0.000 0.000 0.976 0.016 0.008
#> SRR1044554 5 0.3608 0.5719 0.248 0.000 0.000 0.004 0.736 0.012
#> SRR1044555 6 0.5764 0.6269 0.000 0.216 0.224 0.000 0.008 0.552
#> SRR1044556 4 0.0865 0.8624 0.000 0.000 0.000 0.964 0.036 0.000
#> SRR1044557 5 0.3800 0.6919 0.168 0.000 0.000 0.048 0.776 0.008
#> SRR1044558 4 0.0937 0.8628 0.000 0.000 0.000 0.960 0.040 0.000
#> SRR1044559 5 0.4334 0.7126 0.132 0.000 0.000 0.092 0.756 0.020
#> SRR1044561 4 0.0692 0.8643 0.000 0.000 0.000 0.976 0.020 0.004
#> SRR1044560 2 0.3860 -0.1341 0.000 0.528 0.000 0.000 0.000 0.472
#> SRR1044562 5 0.3626 0.5963 0.288 0.000 0.000 0.004 0.704 0.004
#> SRR1044563 4 0.0937 0.8627 0.000 0.000 0.000 0.960 0.040 0.000
#> SRR1044564 5 0.4111 0.7022 0.084 0.000 0.000 0.176 0.740 0.000
#> SRR1044565 2 0.0547 0.8910 0.000 0.980 0.000 0.000 0.000 0.020
#> SRR1044566 2 0.3684 0.2386 0.000 0.628 0.000 0.000 0.000 0.372
#> SRR1044567 1 0.4526 0.7088 0.704 0.000 0.000 0.000 0.132 0.164
#> SRR1044568 5 0.4633 0.5473 0.044 0.000 0.000 0.316 0.632 0.008
#> SRR1044569 1 0.1951 0.7390 0.908 0.000 0.000 0.000 0.076 0.016
#> SRR1044570 1 0.4563 0.7063 0.700 0.000 0.000 0.000 0.136 0.164
#> SRR1044571 1 0.0520 0.7707 0.984 0.000 0.000 0.000 0.008 0.008
#> SRR1044572 1 0.0692 0.7731 0.976 0.000 0.000 0.000 0.004 0.020
#> SRR1044573 1 0.3872 0.6357 0.788 0.000 0.000 0.044 0.144 0.024
#> SRR1044574 1 0.1313 0.7677 0.952 0.000 0.000 0.004 0.028 0.016
#> SRR1044575 1 0.3170 0.6970 0.840 0.000 0.000 0.016 0.112 0.032
#> SRR1044576 2 0.0146 0.8939 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044577 2 0.0458 0.8923 0.000 0.984 0.000 0.000 0.000 0.016
#> SRR1044578 2 0.0547 0.8910 0.000 0.980 0.000 0.000 0.000 0.020
#> SRR1044579 4 0.0291 0.8655 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR1044580 1 0.6592 0.1274 0.468 0.000 0.000 0.240 0.248 0.044
#> SRR1044581 4 0.0837 0.8649 0.004 0.000 0.000 0.972 0.020 0.004
#> SRR1044582 5 0.4550 0.2369 0.420 0.000 0.000 0.000 0.544 0.036
#> SRR1044583 4 0.1003 0.8577 0.004 0.000 0.000 0.964 0.028 0.004
#> SRR1044584 4 0.1605 0.8470 0.016 0.000 0.000 0.940 0.032 0.012
#> SRR1044585 4 0.0603 0.8641 0.000 0.000 0.000 0.980 0.016 0.004
#> SRR1044586 5 0.5580 0.5094 0.216 0.000 0.000 0.056 0.636 0.092
#> SRR1044587 4 0.1245 0.8632 0.000 0.000 0.000 0.952 0.032 0.016
#> SRR1044588 4 0.1480 0.8589 0.000 0.000 0.000 0.940 0.020 0.040
#> SRR1044589 4 0.1492 0.8600 0.000 0.000 0.000 0.940 0.036 0.024
#> SRR1044590 4 0.1575 0.8587 0.000 0.000 0.000 0.936 0.032 0.032
#> SRR1044591 4 0.1633 0.8585 0.000 0.000 0.000 0.932 0.044 0.024
#> SRR1044592 4 0.3300 0.7774 0.000 0.000 0.116 0.832 0.032 0.020
#> SRR1044593 4 0.1575 0.8587 0.000 0.000 0.000 0.936 0.032 0.032
#> SRR1044594 4 0.1257 0.8609 0.000 0.000 0.000 0.952 0.020 0.028
#> SRR1044595 3 0.5098 0.5820 0.016 0.000 0.716 0.036 0.152 0.080
#> SRR1044596 4 0.1976 0.8515 0.000 0.000 0.008 0.916 0.060 0.016
#> SRR1044597 4 0.7440 0.3518 0.068 0.016 0.172 0.544 0.068 0.132
#> SRR1044598 1 0.5093 0.6425 0.632 0.000 0.000 0.000 0.192 0.176
#> SRR1044599 1 0.5059 0.6733 0.652 0.000 0.000 0.004 0.168 0.176
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.752 0.847 0.938 0.2125 0.815 0.815
#> 3 3 0.588 0.724 0.881 0.9651 0.685 0.622
#> 4 4 0.591 0.706 0.874 0.0433 0.978 0.960
#> 5 5 0.639 0.714 0.866 0.0932 0.931 0.874
#> 6 6 0.555 0.765 0.863 0.0672 0.893 0.798
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 1 0.8763 0.5216 0.704 0.296
#> SRR1044416 1 0.2043 0.9196 0.968 0.032
#> SRR1044417 1 0.1843 0.9225 0.972 0.028
#> SRR1044418 1 0.1843 0.9225 0.972 0.028
#> SRR1044420 1 0.3733 0.8869 0.928 0.072
#> SRR1044419 1 0.8443 0.5769 0.728 0.272
#> SRR1044421 1 0.3879 0.8834 0.924 0.076
#> SRR1044422 1 0.4690 0.8592 0.900 0.100
#> SRR1044423 1 0.5059 0.8457 0.888 0.112
#> SRR1044424 1 0.3733 0.8869 0.928 0.072
#> SRR1044425 1 0.0000 0.9396 1.000 0.000
#> SRR1044426 1 0.0000 0.9396 1.000 0.000
#> SRR1044427 1 0.0000 0.9396 1.000 0.000
#> SRR1044428 1 0.0000 0.9396 1.000 0.000
#> SRR1044429 1 0.0000 0.9396 1.000 0.000
#> SRR1044430 1 0.0000 0.9396 1.000 0.000
#> SRR1044431 1 0.0000 0.9396 1.000 0.000
#> SRR1044433 1 0.0376 0.9378 0.996 0.004
#> SRR1044432 1 0.0000 0.9396 1.000 0.000
#> SRR1044434 1 0.0000 0.9396 1.000 0.000
#> SRR1044435 1 0.0000 0.9396 1.000 0.000
#> SRR1044436 1 0.0000 0.9396 1.000 0.000
#> SRR1044437 1 0.0000 0.9396 1.000 0.000
#> SRR1044439 1 0.0000 0.9396 1.000 0.000
#> SRR1044438 1 0.0000 0.9396 1.000 0.000
#> SRR1044440 1 0.0000 0.9396 1.000 0.000
#> SRR1044441 1 0.0000 0.9396 1.000 0.000
#> SRR1044442 1 0.0000 0.9396 1.000 0.000
#> SRR1044443 1 0.0376 0.9378 0.996 0.004
#> SRR1044444 1 0.0000 0.9396 1.000 0.000
#> SRR1044445 1 0.0000 0.9396 1.000 0.000
#> SRR1044446 1 0.9983 -0.1435 0.524 0.476
#> SRR1044447 1 0.7056 0.7346 0.808 0.192
#> SRR1044449 2 0.1414 0.7812 0.020 0.980
#> SRR1044448 2 0.9881 0.4127 0.436 0.564
#> SRR1044450 2 0.9909 0.3913 0.444 0.556
#> SRR1044451 1 0.8443 0.5798 0.728 0.272
#> SRR1044452 2 0.0000 0.7875 0.000 1.000
#> SRR1044453 2 0.0000 0.7875 0.000 1.000
#> SRR1044454 2 0.0000 0.7875 0.000 1.000
#> SRR1044455 1 0.7376 0.7031 0.792 0.208
#> SRR1044456 1 0.0000 0.9396 1.000 0.000
#> SRR1044457 1 0.9209 0.4156 0.664 0.336
#> SRR1044458 1 0.8861 0.5019 0.696 0.304
#> SRR1044459 2 0.9933 0.3621 0.452 0.548
#> SRR1044460 1 0.3733 0.8869 0.928 0.072
#> SRR1044461 1 0.8016 0.6359 0.756 0.244
#> SRR1044462 1 0.0000 0.9396 1.000 0.000
#> SRR1044463 1 0.0000 0.9396 1.000 0.000
#> SRR1044464 1 0.0000 0.9396 1.000 0.000
#> SRR1044466 1 0.0000 0.9396 1.000 0.000
#> SRR1044465 1 0.0000 0.9396 1.000 0.000
#> SRR1044467 1 0.0000 0.9396 1.000 0.000
#> SRR1044468 1 0.4298 0.8724 0.912 0.088
#> SRR1044469 2 0.9209 0.5704 0.336 0.664
#> SRR1044470 1 0.0000 0.9396 1.000 0.000
#> SRR1044471 1 0.0000 0.9396 1.000 0.000
#> SRR1044472 1 0.0000 0.9396 1.000 0.000
#> SRR1044473 1 0.0000 0.9396 1.000 0.000
#> SRR1044474 1 0.0672 0.9357 0.992 0.008
#> SRR1044475 2 0.0000 0.7875 0.000 1.000
#> SRR1044476 1 0.9248 0.4034 0.660 0.340
#> SRR1044477 1 0.0376 0.9378 0.996 0.004
#> SRR1044478 1 0.5519 0.8251 0.872 0.128
#> SRR1044479 1 0.0672 0.9357 0.992 0.008
#> SRR1044480 1 0.0000 0.9396 1.000 0.000
#> SRR1044481 1 0.0000 0.9396 1.000 0.000
#> SRR1044482 1 0.0938 0.9334 0.988 0.012
#> SRR1044483 1 0.0000 0.9396 1.000 0.000
#> SRR1044484 1 0.0000 0.9396 1.000 0.000
#> SRR1044486 1 0.0000 0.9396 1.000 0.000
#> SRR1044485 1 0.3431 0.8944 0.936 0.064
#> SRR1044487 1 0.0672 0.9357 0.992 0.008
#> SRR1044488 1 0.3733 0.8869 0.928 0.072
#> SRR1044489 1 0.3733 0.8869 0.928 0.072
#> SRR1044490 1 0.0000 0.9396 1.000 0.000
#> SRR1044491 1 0.0000 0.9396 1.000 0.000
#> SRR1044492 1 0.0000 0.9396 1.000 0.000
#> SRR1044493 1 0.0000 0.9396 1.000 0.000
#> SRR1044494 1 0.0672 0.9357 0.992 0.008
#> SRR1044496 1 0.0672 0.9357 0.992 0.008
#> SRR1044495 1 0.0672 0.9357 0.992 0.008
#> SRR1044497 1 0.0000 0.9396 1.000 0.000
#> SRR1044499 2 0.9427 0.5404 0.360 0.640
#> SRR1044498 1 0.0000 0.9396 1.000 0.000
#> SRR1044500 1 0.3733 0.8869 0.928 0.072
#> SRR1044501 1 0.8713 0.5305 0.708 0.292
#> SRR1044502 1 0.8081 0.6288 0.752 0.248
#> SRR1044503 1 0.0000 0.9396 1.000 0.000
#> SRR1044504 1 0.0000 0.9396 1.000 0.000
#> SRR1044505 1 0.0000 0.9396 1.000 0.000
#> SRR1044506 1 0.0000 0.9396 1.000 0.000
#> SRR1044507 1 0.0000 0.9396 1.000 0.000
#> SRR1044508 1 0.0376 0.9378 0.996 0.004
#> SRR1044509 1 0.0376 0.9378 0.996 0.004
#> SRR1044510 2 0.0000 0.7875 0.000 1.000
#> SRR1044511 2 0.0000 0.7875 0.000 1.000
#> SRR1044512 2 0.0000 0.7875 0.000 1.000
#> SRR1044513 1 0.5294 0.8375 0.880 0.120
#> SRR1044514 2 0.0000 0.7875 0.000 1.000
#> SRR1044515 1 0.5294 0.8375 0.880 0.120
#> SRR1044516 1 0.4815 0.8544 0.896 0.104
#> SRR1044517 2 0.0000 0.7875 0.000 1.000
#> SRR1044518 2 0.0000 0.7875 0.000 1.000
#> SRR1044519 2 0.9881 0.4127 0.436 0.564
#> SRR1044520 2 0.9881 0.4127 0.436 0.564
#> SRR1044521 1 0.3274 0.8973 0.940 0.060
#> SRR1044522 1 0.0000 0.9396 1.000 0.000
#> SRR1044523 1 0.5178 0.8431 0.884 0.116
#> SRR1044524 1 0.9944 -0.0524 0.544 0.456
#> SRR1044525 1 0.0000 0.9396 1.000 0.000
#> SRR1044526 1 0.0000 0.9396 1.000 0.000
#> SRR1044527 1 0.2778 0.9072 0.952 0.048
#> SRR1044528 1 0.2948 0.9040 0.948 0.052
#> SRR1044529 1 0.0938 0.9334 0.988 0.012
#> SRR1044530 1 0.0000 0.9396 1.000 0.000
#> SRR1044531 1 0.0000 0.9396 1.000 0.000
#> SRR1044533 1 0.0000 0.9396 1.000 0.000
#> SRR1044532 1 0.0000 0.9396 1.000 0.000
#> SRR1044534 1 0.3431 0.8939 0.936 0.064
#> SRR1044535 1 0.9393 0.3532 0.644 0.356
#> SRR1044536 1 0.3879 0.8836 0.924 0.076
#> SRR1044537 1 0.0000 0.9396 1.000 0.000
#> SRR1044538 1 0.0000 0.9396 1.000 0.000
#> SRR1044539 1 0.0000 0.9396 1.000 0.000
#> SRR1044540 1 0.0000 0.9396 1.000 0.000
#> SRR1044541 2 0.9963 0.3259 0.464 0.536
#> SRR1044542 1 0.0000 0.9396 1.000 0.000
#> SRR1044543 1 0.0000 0.9396 1.000 0.000
#> SRR1044544 1 0.9896 0.0224 0.560 0.440
#> SRR1044545 1 0.0000 0.9396 1.000 0.000
#> SRR1044546 1 0.0000 0.9396 1.000 0.000
#> SRR1044547 1 0.0000 0.9396 1.000 0.000
#> SRR1044548 1 0.0000 0.9396 1.000 0.000
#> SRR1044549 1 0.3584 0.8913 0.932 0.068
#> SRR1044550 1 0.3733 0.8869 0.928 0.072
#> SRR1044551 1 0.3274 0.8974 0.940 0.060
#> SRR1044552 1 0.0000 0.9396 1.000 0.000
#> SRR1044553 1 0.0000 0.9396 1.000 0.000
#> SRR1044554 1 0.0000 0.9396 1.000 0.000
#> SRR1044555 1 0.9944 -0.0524 0.544 0.456
#> SRR1044556 1 0.0000 0.9396 1.000 0.000
#> SRR1044557 1 0.0000 0.9396 1.000 0.000
#> SRR1044558 1 0.0000 0.9396 1.000 0.000
#> SRR1044559 1 0.0000 0.9396 1.000 0.000
#> SRR1044561 1 0.0000 0.9396 1.000 0.000
#> SRR1044560 1 0.9248 0.4034 0.660 0.340
#> SRR1044562 1 0.0000 0.9396 1.000 0.000
#> SRR1044563 1 0.0000 0.9396 1.000 0.000
#> SRR1044564 1 0.0000 0.9396 1.000 0.000
#> SRR1044565 1 0.0672 0.9357 0.992 0.008
#> SRR1044566 1 0.9248 0.4034 0.660 0.340
#> SRR1044567 1 0.0000 0.9396 1.000 0.000
#> SRR1044568 1 0.0000 0.9396 1.000 0.000
#> SRR1044569 1 0.0000 0.9396 1.000 0.000
#> SRR1044570 1 0.0000 0.9396 1.000 0.000
#> SRR1044571 1 0.0000 0.9396 1.000 0.000
#> SRR1044572 1 0.0000 0.9396 1.000 0.000
#> SRR1044573 1 0.0000 0.9396 1.000 0.000
#> SRR1044574 1 0.0000 0.9396 1.000 0.000
#> SRR1044575 1 0.0000 0.9396 1.000 0.000
#> SRR1044576 1 0.2043 0.9196 0.968 0.032
#> SRR1044577 1 0.1184 0.9308 0.984 0.016
#> SRR1044578 1 0.0672 0.9357 0.992 0.008
#> SRR1044579 1 0.0000 0.9396 1.000 0.000
#> SRR1044580 1 0.0000 0.9396 1.000 0.000
#> SRR1044581 1 0.0000 0.9396 1.000 0.000
#> SRR1044582 1 0.0000 0.9396 1.000 0.000
#> SRR1044583 1 0.0000 0.9396 1.000 0.000
#> SRR1044584 1 0.0000 0.9396 1.000 0.000
#> SRR1044585 1 0.0000 0.9396 1.000 0.000
#> SRR1044586 1 0.0000 0.9396 1.000 0.000
#> SRR1044587 1 0.0000 0.9396 1.000 0.000
#> SRR1044588 1 0.0000 0.9396 1.000 0.000
#> SRR1044589 1 0.0000 0.9396 1.000 0.000
#> SRR1044590 1 0.0000 0.9396 1.000 0.000
#> SRR1044591 1 0.0000 0.9396 1.000 0.000
#> SRR1044592 1 0.0376 0.9378 0.996 0.004
#> SRR1044593 1 0.0000 0.9396 1.000 0.000
#> SRR1044594 1 0.0000 0.9396 1.000 0.000
#> SRR1044595 1 0.0376 0.9378 0.996 0.004
#> SRR1044596 1 0.0000 0.9396 1.000 0.000
#> SRR1044597 1 0.0000 0.9396 1.000 0.000
#> SRR1044598 1 0.0000 0.9396 1.000 0.000
#> SRR1044599 1 0.0000 0.9396 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.5220 0.6854 0.208 0.780 0.012
#> SRR1044416 1 0.6168 -0.1092 0.588 0.412 0.000
#> SRR1044417 1 0.6192 -0.1450 0.580 0.420 0.000
#> SRR1044418 1 0.6154 -0.0908 0.592 0.408 0.000
#> SRR1044420 2 0.6225 0.6185 0.432 0.568 0.000
#> SRR1044419 2 0.5070 0.6965 0.224 0.772 0.004
#> SRR1044421 2 0.6225 0.6181 0.432 0.568 0.000
#> SRR1044422 2 0.6140 0.6546 0.404 0.596 0.000
#> SRR1044423 2 0.6095 0.6659 0.392 0.608 0.000
#> SRR1044424 2 0.6225 0.6185 0.432 0.568 0.000
#> SRR1044425 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044426 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044427 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044428 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044429 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044430 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044431 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044433 1 0.1163 0.8789 0.972 0.028 0.000
#> SRR1044432 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044434 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044435 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044436 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044437 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044439 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044438 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044440 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044441 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044442 1 0.0424 0.9006 0.992 0.008 0.000
#> SRR1044443 1 0.1163 0.8789 0.972 0.028 0.000
#> SRR1044444 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044445 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044446 2 0.0983 0.4329 0.016 0.980 0.004
#> SRR1044447 2 0.5650 0.7099 0.312 0.688 0.000
#> SRR1044449 3 0.3752 0.9221 0.000 0.144 0.856
#> SRR1044448 2 0.2448 0.3017 0.000 0.924 0.076
#> SRR1044450 2 0.2261 0.3146 0.000 0.932 0.068
#> SRR1044451 2 0.4750 0.6842 0.216 0.784 0.000
#> SRR1044452 3 0.1753 0.9678 0.000 0.048 0.952
#> SRR1044453 3 0.1753 0.9678 0.000 0.048 0.952
#> SRR1044454 3 0.1753 0.9678 0.000 0.048 0.952
#> SRR1044455 2 0.5431 0.7177 0.284 0.716 0.000
#> SRR1044456 1 0.0237 0.9045 0.996 0.004 0.000
#> SRR1044457 2 0.4782 0.6494 0.164 0.820 0.016
#> SRR1044458 2 0.5122 0.6802 0.200 0.788 0.012
#> SRR1044459 2 0.4475 0.3177 0.016 0.840 0.144
#> SRR1044460 2 0.6225 0.6185 0.432 0.568 0.000
#> SRR1044461 2 0.5365 0.7080 0.252 0.744 0.004
#> SRR1044462 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044463 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044464 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044466 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044465 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044467 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044468 2 0.6410 0.6359 0.420 0.576 0.004
#> SRR1044469 2 0.6701 -0.2241 0.012 0.576 0.412
#> SRR1044470 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044471 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044472 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044473 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044474 1 0.6026 0.0602 0.624 0.376 0.000
#> SRR1044475 3 0.2165 0.9640 0.000 0.064 0.936
#> SRR1044476 2 0.4782 0.6496 0.164 0.820 0.016
#> SRR1044477 1 0.5926 0.1396 0.644 0.356 0.000
#> SRR1044478 2 0.6026 0.6780 0.376 0.624 0.000
#> SRR1044479 1 0.5988 0.0954 0.632 0.368 0.000
#> SRR1044480 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044481 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044482 1 0.6062 0.0235 0.616 0.384 0.000
#> SRR1044483 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044484 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044486 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044485 1 0.6308 -0.4208 0.508 0.492 0.000
#> SRR1044487 1 0.5988 0.0954 0.632 0.368 0.000
#> SRR1044488 2 0.6225 0.6185 0.432 0.568 0.000
#> SRR1044489 2 0.6225 0.6185 0.432 0.568 0.000
#> SRR1044490 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044491 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044492 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044493 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044494 1 0.5988 0.0954 0.632 0.368 0.000
#> SRR1044496 1 0.5988 0.0954 0.632 0.368 0.000
#> SRR1044495 1 0.5988 0.0954 0.632 0.368 0.000
#> SRR1044497 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044499 2 0.6255 -0.0400 0.012 0.668 0.320
#> SRR1044498 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044500 2 0.6225 0.6185 0.432 0.568 0.000
#> SRR1044501 2 0.4834 0.6854 0.204 0.792 0.004
#> SRR1044502 2 0.5016 0.7018 0.240 0.760 0.000
#> SRR1044503 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044504 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044505 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044506 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044507 1 0.0424 0.9006 0.992 0.008 0.000
#> SRR1044508 1 0.1163 0.8789 0.972 0.028 0.000
#> SRR1044509 1 0.1163 0.8789 0.972 0.028 0.000
#> SRR1044510 3 0.1031 0.9679 0.000 0.024 0.976
#> SRR1044511 3 0.2066 0.9661 0.000 0.060 0.940
#> SRR1044512 3 0.1860 0.9672 0.000 0.052 0.948
#> SRR1044513 2 0.6079 0.6667 0.388 0.612 0.000
#> SRR1044514 3 0.2261 0.9643 0.000 0.068 0.932
#> SRR1044515 2 0.6079 0.6667 0.388 0.612 0.000
#> SRR1044516 2 0.6140 0.6546 0.404 0.596 0.000
#> SRR1044517 3 0.0892 0.9674 0.000 0.020 0.980
#> SRR1044518 3 0.2356 0.9624 0.000 0.072 0.928
#> SRR1044519 2 0.2448 0.3017 0.000 0.924 0.076
#> SRR1044520 2 0.2448 0.3017 0.000 0.924 0.076
#> SRR1044521 2 0.6260 0.5838 0.448 0.552 0.000
#> SRR1044522 1 0.0424 0.9005 0.992 0.008 0.000
#> SRR1044523 2 0.6111 0.6548 0.396 0.604 0.000
#> SRR1044524 2 0.2903 0.4839 0.048 0.924 0.028
#> SRR1044525 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044526 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044527 1 0.6274 -0.2954 0.544 0.456 0.000
#> SRR1044528 2 0.6286 0.5442 0.464 0.536 0.000
#> SRR1044529 1 0.6026 0.0603 0.624 0.376 0.000
#> SRR1044530 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044531 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044533 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044532 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044534 2 0.6252 0.5931 0.444 0.556 0.000
#> SRR1044535 2 0.3851 0.6180 0.136 0.860 0.004
#> SRR1044536 2 0.6215 0.6244 0.428 0.572 0.000
#> SRR1044537 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044538 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044539 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044540 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044541 2 0.4485 0.3405 0.020 0.844 0.136
#> SRR1044542 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044543 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044544 2 0.3310 0.5088 0.064 0.908 0.028
#> SRR1044545 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044546 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044547 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044548 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044549 1 0.6309 -0.4474 0.500 0.500 0.000
#> SRR1044550 2 0.6225 0.6185 0.432 0.568 0.000
#> SRR1044551 2 0.6274 0.5640 0.456 0.544 0.000
#> SRR1044552 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044553 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044554 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044555 2 0.2903 0.4839 0.048 0.924 0.028
#> SRR1044556 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044557 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044558 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044559 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044561 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044560 2 0.4782 0.6496 0.164 0.820 0.016
#> SRR1044562 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044563 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044564 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044565 1 0.5988 0.0954 0.632 0.368 0.000
#> SRR1044566 2 0.4782 0.6496 0.164 0.820 0.016
#> SRR1044567 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044568 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044569 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044570 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044571 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044572 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044573 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044574 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044575 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044576 1 0.6204 -0.1630 0.576 0.424 0.000
#> SRR1044577 1 0.6095 -0.0151 0.608 0.392 0.000
#> SRR1044578 1 0.6008 0.0781 0.628 0.372 0.000
#> SRR1044579 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044580 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044581 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044582 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044583 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044584 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044585 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044586 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044587 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044588 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044589 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044590 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044591 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044592 1 0.1163 0.8789 0.972 0.028 0.000
#> SRR1044593 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044594 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044595 1 0.1163 0.8789 0.972 0.028 0.000
#> SRR1044596 1 0.0424 0.9006 0.992 0.008 0.000
#> SRR1044597 1 0.0237 0.9045 0.996 0.004 0.000
#> SRR1044598 1 0.0000 0.9083 1.000 0.000 0.000
#> SRR1044599 1 0.0000 0.9083 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 2 0.3990 0.65990 0.176 0.808 0.012 0.004
#> SRR1044416 1 0.4948 -0.19866 0.560 0.440 0.000 0.000
#> SRR1044417 1 0.4961 -0.23142 0.552 0.448 0.000 0.000
#> SRR1044418 1 0.4941 -0.18265 0.564 0.436 0.000 0.000
#> SRR1044420 2 0.4855 0.65561 0.400 0.600 0.000 0.000
#> SRR1044419 2 0.3892 0.67291 0.192 0.800 0.004 0.004
#> SRR1044421 2 0.4855 0.65534 0.400 0.600 0.000 0.000
#> SRR1044422 2 0.4761 0.68481 0.372 0.628 0.000 0.000
#> SRR1044423 2 0.4713 0.69359 0.360 0.640 0.000 0.000
#> SRR1044424 2 0.4855 0.65561 0.400 0.600 0.000 0.000
#> SRR1044425 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044426 1 0.0188 0.90884 0.996 0.000 0.000 0.004
#> SRR1044427 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044428 1 0.0188 0.90915 0.996 0.000 0.000 0.004
#> SRR1044429 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044430 1 0.1488 0.87993 0.956 0.012 0.000 0.032
#> SRR1044431 1 0.0188 0.90915 0.996 0.000 0.000 0.004
#> SRR1044433 1 0.1022 0.88089 0.968 0.032 0.000 0.000
#> SRR1044432 1 0.0921 0.89306 0.972 0.000 0.000 0.028
#> SRR1044434 1 0.0188 0.90920 0.996 0.000 0.000 0.004
#> SRR1044435 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044436 1 0.0188 0.90908 0.996 0.000 0.000 0.004
#> SRR1044437 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044439 1 0.0188 0.90908 0.996 0.000 0.000 0.004
#> SRR1044438 1 0.0188 0.90920 0.996 0.000 0.000 0.004
#> SRR1044440 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044441 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044442 1 0.0336 0.90455 0.992 0.008 0.000 0.000
#> SRR1044443 1 0.1022 0.88089 0.968 0.032 0.000 0.000
#> SRR1044444 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044445 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044446 2 0.2011 0.35371 0.000 0.920 0.000 0.080
#> SRR1044447 2 0.4883 0.70302 0.288 0.696 0.000 0.016
#> SRR1044449 3 0.3840 0.63946 0.000 0.052 0.844 0.104
#> SRR1044448 2 0.4236 0.20540 0.000 0.824 0.088 0.088
#> SRR1044450 2 0.4039 0.22809 0.000 0.836 0.080 0.084
#> SRR1044451 2 0.4095 0.66184 0.192 0.792 0.000 0.016
#> SRR1044452 3 0.0000 0.76226 0.000 0.000 1.000 0.000
#> SRR1044453 3 0.0000 0.76226 0.000 0.000 1.000 0.000
#> SRR1044454 3 0.0000 0.76226 0.000 0.000 1.000 0.000
#> SRR1044455 2 0.4252 0.70047 0.252 0.744 0.000 0.004
#> SRR1044456 1 0.0188 0.90782 0.996 0.004 0.000 0.000
#> SRR1044457 2 0.3573 0.61928 0.132 0.848 0.016 0.004
#> SRR1044458 2 0.3901 0.65370 0.168 0.816 0.012 0.004
#> SRR1044459 2 0.3377 0.28922 0.000 0.848 0.140 0.012
#> SRR1044460 2 0.4855 0.65561 0.400 0.600 0.000 0.000
#> SRR1044461 2 0.4163 0.68770 0.220 0.772 0.004 0.004
#> SRR1044462 1 0.0469 0.90543 0.988 0.000 0.000 0.012
#> SRR1044463 1 0.0188 0.90915 0.996 0.000 0.000 0.004
#> SRR1044464 1 0.0188 0.90908 0.996 0.000 0.000 0.004
#> SRR1044466 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044465 1 0.0188 0.90915 0.996 0.000 0.000 0.004
#> SRR1044467 1 0.0188 0.90915 0.996 0.000 0.000 0.004
#> SRR1044468 2 0.4991 0.66879 0.388 0.608 0.004 0.000
#> SRR1044469 2 0.5088 -0.22100 0.000 0.572 0.424 0.004
#> SRR1044470 1 0.0188 0.90908 0.996 0.000 0.000 0.004
#> SRR1044471 1 0.0188 0.90915 0.996 0.000 0.000 0.004
#> SRR1044472 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044473 1 0.0336 0.90818 0.992 0.000 0.000 0.008
#> SRR1044474 1 0.4866 -0.04384 0.596 0.404 0.000 0.000
#> SRR1044475 3 0.0779 0.75063 0.000 0.016 0.980 0.004
#> SRR1044476 2 0.3684 0.61843 0.132 0.844 0.020 0.004
#> SRR1044477 1 0.4790 0.05685 0.620 0.380 0.000 0.000
#> SRR1044478 2 0.4643 0.70285 0.344 0.656 0.000 0.000
#> SRR1044479 1 0.4843 -0.00678 0.604 0.396 0.000 0.000
#> SRR1044480 1 0.0336 0.90740 0.992 0.000 0.000 0.008
#> SRR1044481 1 0.0336 0.90740 0.992 0.000 0.000 0.008
#> SRR1044482 1 0.4888 -0.07956 0.588 0.412 0.000 0.000
#> SRR1044483 1 0.0469 0.90543 0.988 0.000 0.000 0.012
#> SRR1044484 1 0.0188 0.90920 0.996 0.000 0.000 0.004
#> SRR1044486 1 0.0336 0.90740 0.992 0.000 0.000 0.008
#> SRR1044485 2 0.4992 0.47579 0.476 0.524 0.000 0.000
#> SRR1044487 1 0.4843 -0.00678 0.604 0.396 0.000 0.000
#> SRR1044488 2 0.4855 0.65561 0.400 0.600 0.000 0.000
#> SRR1044489 2 0.4855 0.65561 0.400 0.600 0.000 0.000
#> SRR1044490 1 0.0336 0.90776 0.992 0.000 0.000 0.008
#> SRR1044491 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044492 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044493 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044494 1 0.4843 -0.00678 0.604 0.396 0.000 0.000
#> SRR1044496 1 0.4843 -0.00678 0.604 0.396 0.000 0.000
#> SRR1044495 1 0.4843 -0.00678 0.604 0.396 0.000 0.000
#> SRR1044497 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044499 2 0.4897 -0.05840 0.000 0.660 0.332 0.008
#> SRR1044498 1 0.0336 0.90740 0.992 0.000 0.000 0.008
#> SRR1044500 2 0.4855 0.65561 0.400 0.600 0.000 0.000
#> SRR1044501 2 0.3676 0.65954 0.172 0.820 0.004 0.004
#> SRR1044502 2 0.3688 0.67993 0.208 0.792 0.000 0.000
#> SRR1044503 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044504 1 0.0336 0.90776 0.992 0.000 0.000 0.008
#> SRR1044505 1 0.0188 0.90915 0.996 0.000 0.000 0.004
#> SRR1044506 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044507 1 0.0336 0.90455 0.992 0.008 0.000 0.000
#> SRR1044508 1 0.1022 0.88089 0.968 0.032 0.000 0.000
#> SRR1044509 1 0.1022 0.88089 0.968 0.032 0.000 0.000
#> SRR1044510 3 0.4996 -0.03523 0.000 0.000 0.516 0.484
#> SRR1044511 4 0.3048 0.95201 0.000 0.016 0.108 0.876
#> SRR1044512 4 0.3743 0.90460 0.000 0.016 0.160 0.824
#> SRR1044513 2 0.5159 0.68894 0.364 0.624 0.000 0.012
#> SRR1044514 4 0.2973 0.95642 0.000 0.020 0.096 0.884
#> SRR1044515 2 0.5159 0.68894 0.364 0.624 0.000 0.012
#> SRR1044516 2 0.4761 0.68450 0.372 0.628 0.000 0.000
#> SRR1044517 3 0.4961 0.09161 0.000 0.000 0.552 0.448
#> SRR1044518 4 0.3015 0.95104 0.000 0.024 0.092 0.884
#> SRR1044519 2 0.4236 0.20540 0.000 0.824 0.088 0.088
#> SRR1044520 2 0.4236 0.20540 0.000 0.824 0.088 0.088
#> SRR1044521 2 0.4898 0.62687 0.416 0.584 0.000 0.000
#> SRR1044522 1 0.0336 0.90466 0.992 0.008 0.000 0.000
#> SRR1044523 2 0.5189 0.67719 0.372 0.616 0.000 0.012
#> SRR1044524 2 0.1958 0.44323 0.020 0.944 0.028 0.008
#> SRR1044525 1 0.0336 0.90776 0.992 0.000 0.000 0.008
#> SRR1044526 1 0.0336 0.90776 0.992 0.000 0.000 0.008
#> SRR1044527 1 0.4996 -0.36693 0.516 0.484 0.000 0.000
#> SRR1044528 2 0.4941 0.58603 0.436 0.564 0.000 0.000
#> SRR1044529 1 0.4866 -0.04372 0.596 0.404 0.000 0.000
#> SRR1044530 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044531 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044533 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044532 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044534 2 0.4898 0.62811 0.416 0.584 0.000 0.000
#> SRR1044535 2 0.2839 0.58927 0.108 0.884 0.004 0.004
#> SRR1044536 2 0.4843 0.65913 0.396 0.604 0.000 0.000
#> SRR1044537 1 0.0469 0.90543 0.988 0.000 0.000 0.012
#> SRR1044538 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044539 1 0.0469 0.90543 0.988 0.000 0.000 0.012
#> SRR1044540 1 0.0336 0.90818 0.992 0.000 0.000 0.008
#> SRR1044541 2 0.3455 0.31150 0.004 0.852 0.132 0.012
#> SRR1044542 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044543 1 0.0336 0.90702 0.992 0.000 0.000 0.008
#> SRR1044544 2 0.2269 0.46379 0.032 0.932 0.028 0.008
#> SRR1044545 1 0.0469 0.90543 0.988 0.000 0.000 0.012
#> SRR1044546 1 0.0469 0.90543 0.988 0.000 0.000 0.012
#> SRR1044547 1 0.0469 0.90543 0.988 0.000 0.000 0.012
#> SRR1044548 1 0.0469 0.90543 0.988 0.000 0.000 0.012
#> SRR1044549 2 0.4989 0.48899 0.472 0.528 0.000 0.000
#> SRR1044550 2 0.4855 0.65561 0.400 0.600 0.000 0.000
#> SRR1044551 2 0.4916 0.61034 0.424 0.576 0.000 0.000
#> SRR1044552 1 0.0336 0.90776 0.992 0.000 0.000 0.008
#> SRR1044553 1 0.0336 0.90776 0.992 0.000 0.000 0.008
#> SRR1044554 1 0.0469 0.90543 0.988 0.000 0.000 0.012
#> SRR1044555 2 0.1958 0.44323 0.020 0.944 0.028 0.008
#> SRR1044556 1 0.0188 0.90908 0.996 0.000 0.000 0.004
#> SRR1044557 1 0.0469 0.90543 0.988 0.000 0.000 0.012
#> SRR1044558 1 0.0188 0.90908 0.996 0.000 0.000 0.004
#> SRR1044559 1 0.0469 0.90543 0.988 0.000 0.000 0.012
#> SRR1044561 1 0.0188 0.90908 0.996 0.000 0.000 0.004
#> SRR1044560 2 0.3684 0.61843 0.132 0.844 0.020 0.004
#> SRR1044562 1 0.0469 0.90543 0.988 0.000 0.000 0.012
#> SRR1044563 1 0.0469 0.90543 0.988 0.000 0.000 0.012
#> SRR1044564 1 0.0469 0.90543 0.988 0.000 0.000 0.012
#> SRR1044565 1 0.4843 -0.00678 0.604 0.396 0.000 0.000
#> SRR1044566 2 0.3684 0.61843 0.132 0.844 0.020 0.004
#> SRR1044567 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044568 1 0.0469 0.90543 0.988 0.000 0.000 0.012
#> SRR1044569 1 0.0188 0.90884 0.996 0.000 0.000 0.004
#> SRR1044570 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044571 1 0.0336 0.90818 0.992 0.000 0.000 0.008
#> SRR1044572 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044573 1 0.0336 0.90818 0.992 0.000 0.000 0.008
#> SRR1044574 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044575 1 0.0336 0.90818 0.992 0.000 0.000 0.008
#> SRR1044576 1 0.4967 -0.24715 0.548 0.452 0.000 0.000
#> SRR1044577 1 0.4907 -0.11463 0.580 0.420 0.000 0.000
#> SRR1044578 1 0.4855 -0.02532 0.600 0.400 0.000 0.000
#> SRR1044579 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044580 1 0.0336 0.90740 0.992 0.000 0.000 0.008
#> SRR1044581 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044582 1 0.0188 0.90920 0.996 0.000 0.000 0.004
#> SRR1044583 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044584 1 0.0188 0.90920 0.996 0.000 0.000 0.004
#> SRR1044585 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044586 1 0.0336 0.90740 0.992 0.000 0.000 0.008
#> SRR1044587 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044588 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044589 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044590 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044591 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044592 1 0.1022 0.88089 0.968 0.032 0.000 0.000
#> SRR1044593 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044594 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044595 1 0.1022 0.88089 0.968 0.032 0.000 0.000
#> SRR1044596 1 0.0336 0.90455 0.992 0.008 0.000 0.000
#> SRR1044597 1 0.0188 0.90788 0.996 0.004 0.000 0.000
#> SRR1044598 1 0.0000 0.90974 1.000 0.000 0.000 0.000
#> SRR1044599 1 0.0000 0.90974 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.2789 0.6007 0.092 0.880 0.008 0.000 NA
#> SRR1044416 2 0.4294 0.4333 0.468 0.532 0.000 0.000 NA
#> SRR1044417 2 0.4287 0.4545 0.460 0.540 0.000 0.000 NA
#> SRR1044418 2 0.4297 0.4224 0.472 0.528 0.000 0.000 NA
#> SRR1044420 2 0.3837 0.7143 0.308 0.692 0.000 0.000 NA
#> SRR1044419 2 0.2722 0.6185 0.108 0.872 0.000 0.000 NA
#> SRR1044421 2 0.3837 0.7141 0.308 0.692 0.000 0.000 NA
#> SRR1044422 2 0.3861 0.7147 0.284 0.712 0.000 0.000 NA
#> SRR1044423 2 0.3934 0.7128 0.276 0.716 0.000 0.000 NA
#> SRR1044424 2 0.3837 0.7143 0.308 0.692 0.000 0.000 NA
#> SRR1044425 1 0.0000 0.9215 1.000 0.000 0.000 0.000 NA
#> SRR1044426 1 0.1557 0.8827 0.940 0.008 0.000 0.000 NA
#> SRR1044427 1 0.0162 0.9212 0.996 0.004 0.000 0.000 NA
#> SRR1044428 1 0.1124 0.9054 0.960 0.004 0.000 0.000 NA
#> SRR1044429 1 0.0000 0.9215 1.000 0.000 0.000 0.000 NA
#> SRR1044430 1 0.4215 0.6829 0.772 0.052 0.004 0.000 NA
#> SRR1044431 1 0.0671 0.9190 0.980 0.004 0.000 0.000 NA
#> SRR1044433 1 0.1768 0.8574 0.924 0.072 0.000 0.000 NA
#> SRR1044432 1 0.3381 0.7274 0.808 0.016 0.000 0.000 NA
#> SRR1044434 1 0.0404 0.9205 0.988 0.000 0.000 0.000 NA
#> SRR1044435 1 0.0290 0.9214 0.992 0.000 0.000 0.000 NA
#> SRR1044436 1 0.0162 0.9214 0.996 0.000 0.000 0.000 NA
#> SRR1044437 1 0.0290 0.9214 0.992 0.000 0.000 0.000 NA
#> SRR1044439 1 0.0162 0.9214 0.996 0.000 0.000 0.000 NA
#> SRR1044438 1 0.0404 0.9205 0.988 0.000 0.000 0.000 NA
#> SRR1044440 1 0.0290 0.9214 0.992 0.000 0.000 0.000 NA
#> SRR1044441 1 0.0000 0.9215 1.000 0.000 0.000 0.000 NA
#> SRR1044442 1 0.0880 0.9034 0.968 0.032 0.000 0.000 NA
#> SRR1044443 1 0.1768 0.8574 0.924 0.072 0.000 0.000 NA
#> SRR1044444 1 0.0000 0.9215 1.000 0.000 0.000 0.000 NA
#> SRR1044445 1 0.0162 0.9212 0.996 0.004 0.000 0.000 NA
#> SRR1044446 2 0.3961 0.2174 0.000 0.736 0.000 0.016 NA
#> SRR1044447 2 0.5037 0.6752 0.228 0.696 0.000 0.008 NA
#> SRR1044449 3 0.3915 0.6520 0.000 0.004 0.812 0.096 NA
#> SRR1044448 2 0.5737 -0.1572 0.000 0.552 0.056 0.016 NA
#> SRR1044450 2 0.5539 -0.0814 0.000 0.588 0.048 0.016 NA
#> SRR1044451 2 0.4404 0.6062 0.136 0.776 0.000 0.008 NA
#> SRR1044452 3 0.0162 0.7791 0.000 0.004 0.996 0.000 NA
#> SRR1044453 3 0.0162 0.7791 0.000 0.004 0.996 0.000 NA
#> SRR1044454 3 0.0162 0.7791 0.000 0.004 0.996 0.000 NA
#> SRR1044455 2 0.3053 0.6615 0.164 0.828 0.000 0.000 NA
#> SRR1044456 1 0.0510 0.9176 0.984 0.016 0.000 0.000 NA
#> SRR1044457 2 0.2886 0.5626 0.068 0.884 0.012 0.000 NA
#> SRR1044458 2 0.2674 0.5924 0.084 0.888 0.008 0.000 NA
#> SRR1044459 2 0.4062 0.2732 0.000 0.796 0.132 0.004 NA
#> SRR1044460 2 0.3837 0.7143 0.308 0.692 0.000 0.000 NA
#> SRR1044461 2 0.3061 0.6410 0.136 0.844 0.000 0.000 NA
#> SRR1044462 1 0.0510 0.9171 0.984 0.000 0.000 0.000 NA
#> SRR1044463 1 0.0798 0.9182 0.976 0.008 0.000 0.000 NA
#> SRR1044464 1 0.1124 0.8998 0.960 0.004 0.000 0.000 NA
#> SRR1044466 1 0.0290 0.9207 0.992 0.008 0.000 0.000 NA
#> SRR1044465 1 0.0671 0.9190 0.980 0.004 0.000 0.000 NA
#> SRR1044467 1 0.0671 0.9190 0.980 0.004 0.000 0.000 NA
#> SRR1044468 2 0.4046 0.7151 0.296 0.696 0.000 0.000 NA
#> SRR1044469 2 0.4996 -0.2123 0.000 0.548 0.420 0.000 NA
#> SRR1044470 1 0.0566 0.9196 0.984 0.012 0.000 0.000 NA
#> SRR1044471 1 0.0671 0.9190 0.980 0.004 0.000 0.000 NA
#> SRR1044472 1 0.0290 0.9207 0.992 0.008 0.000 0.000 NA
#> SRR1044473 1 0.0771 0.9173 0.976 0.004 0.000 0.000 NA
#> SRR1044474 1 0.4307 -0.3421 0.504 0.496 0.000 0.000 NA
#> SRR1044475 3 0.0807 0.7683 0.000 0.012 0.976 0.000 NA
#> SRR1044476 2 0.2741 0.5587 0.064 0.892 0.012 0.000 NA
#> SRR1044477 1 0.4297 -0.2689 0.528 0.472 0.000 0.000 NA
#> SRR1044478 2 0.3508 0.7054 0.252 0.748 0.000 0.000 NA
#> SRR1044479 1 0.4305 -0.3156 0.512 0.488 0.000 0.000 NA
#> SRR1044480 1 0.0290 0.9202 0.992 0.000 0.000 0.000 NA
#> SRR1044481 1 0.0290 0.9202 0.992 0.000 0.000 0.000 NA
#> SRR1044482 2 0.4307 0.3503 0.496 0.504 0.000 0.000 NA
#> SRR1044483 1 0.0794 0.9084 0.972 0.000 0.000 0.000 NA
#> SRR1044484 1 0.0324 0.9220 0.992 0.004 0.000 0.000 NA
#> SRR1044486 1 0.0451 0.9215 0.988 0.004 0.000 0.000 NA
#> SRR1044485 2 0.4138 0.6129 0.384 0.616 0.000 0.000 NA
#> SRR1044487 1 0.4305 -0.3156 0.512 0.488 0.000 0.000 NA
#> SRR1044488 2 0.3837 0.7143 0.308 0.692 0.000 0.000 NA
#> SRR1044489 2 0.3837 0.7143 0.308 0.692 0.000 0.000 NA
#> SRR1044490 1 0.0609 0.9180 0.980 0.000 0.000 0.000 NA
#> SRR1044491 1 0.0290 0.9206 0.992 0.008 0.000 0.000 NA
#> SRR1044492 1 0.0290 0.9207 0.992 0.008 0.000 0.000 NA
#> SRR1044493 1 0.0290 0.9206 0.992 0.008 0.000 0.000 NA
#> SRR1044494 1 0.4305 -0.3156 0.512 0.488 0.000 0.000 NA
#> SRR1044496 1 0.4305 -0.3156 0.512 0.488 0.000 0.000 NA
#> SRR1044495 1 0.4305 -0.3156 0.512 0.488 0.000 0.000 NA
#> SRR1044497 1 0.0000 0.9215 1.000 0.000 0.000 0.000 NA
#> SRR1044499 2 0.5006 -0.0565 0.000 0.624 0.328 0.000 NA
#> SRR1044498 1 0.0290 0.9202 0.992 0.000 0.000 0.000 NA
#> SRR1044500 2 0.3837 0.7143 0.308 0.692 0.000 0.000 NA
#> SRR1044501 2 0.2448 0.5998 0.088 0.892 0.000 0.000 NA
#> SRR1044502 2 0.3012 0.6246 0.124 0.852 0.000 0.000 NA
#> SRR1044503 1 0.0290 0.9214 0.992 0.000 0.000 0.000 NA
#> SRR1044504 1 0.0510 0.9188 0.984 0.000 0.000 0.000 NA
#> SRR1044505 1 0.0671 0.9190 0.980 0.004 0.000 0.000 NA
#> SRR1044506 1 0.0162 0.9212 0.996 0.004 0.000 0.000 NA
#> SRR1044507 1 0.0794 0.9059 0.972 0.028 0.000 0.000 NA
#> SRR1044508 1 0.1768 0.8574 0.924 0.072 0.000 0.000 NA
#> SRR1044509 1 0.1768 0.8574 0.924 0.072 0.000 0.000 NA
#> SRR1044510 3 0.6726 0.3296 0.000 0.004 0.400 0.208 NA
#> SRR1044511 4 0.0609 0.9517 0.000 0.000 0.020 0.980 NA
#> SRR1044512 4 0.2069 0.9018 0.000 0.000 0.076 0.912 NA
#> SRR1044513 2 0.4360 0.7116 0.284 0.692 0.000 0.000 NA
#> SRR1044514 4 0.0451 0.9553 0.000 0.000 0.008 0.988 NA
#> SRR1044515 2 0.4360 0.7116 0.284 0.692 0.000 0.000 NA
#> SRR1044516 2 0.3684 0.7140 0.280 0.720 0.000 0.000 NA
#> SRR1044517 3 0.6531 0.3874 0.000 0.004 0.432 0.168 NA
#> SRR1044518 4 0.0162 0.9516 0.000 0.004 0.000 0.996 NA
#> SRR1044519 2 0.5737 -0.1572 0.000 0.552 0.056 0.016 NA
#> SRR1044520 2 0.5737 -0.1572 0.000 0.552 0.056 0.016 NA
#> SRR1044521 2 0.3913 0.7029 0.324 0.676 0.000 0.000 NA
#> SRR1044522 1 0.0609 0.9150 0.980 0.020 0.000 0.000 NA
#> SRR1044523 2 0.4968 0.7028 0.300 0.652 0.000 0.004 NA
#> SRR1044524 2 0.2833 0.4048 0.004 0.884 0.020 0.008 NA
#> SRR1044525 1 0.0510 0.9188 0.984 0.000 0.000 0.000 NA
#> SRR1044526 1 0.0609 0.9165 0.980 0.000 0.000 0.000 NA
#> SRR1044527 2 0.4235 0.5378 0.424 0.576 0.000 0.000 NA
#> SRR1044528 2 0.3999 0.6791 0.344 0.656 0.000 0.000 NA
#> SRR1044529 1 0.4307 -0.3418 0.504 0.496 0.000 0.000 NA
#> SRR1044530 1 0.0290 0.9207 0.992 0.008 0.000 0.000 NA
#> SRR1044531 1 0.0324 0.9218 0.992 0.004 0.000 0.000 NA
#> SRR1044533 1 0.0290 0.9206 0.992 0.008 0.000 0.000 NA
#> SRR1044532 1 0.0290 0.9207 0.992 0.008 0.000 0.000 NA
#> SRR1044534 2 0.3913 0.7036 0.324 0.676 0.000 0.000 NA
#> SRR1044535 2 0.2820 0.5139 0.044 0.892 0.004 0.008 NA
#> SRR1044536 2 0.3816 0.7147 0.304 0.696 0.000 0.000 NA
#> SRR1044537 1 0.0865 0.9126 0.972 0.004 0.000 0.000 NA
#> SRR1044538 1 0.0290 0.9207 0.992 0.008 0.000 0.000 NA
#> SRR1044539 1 0.0404 0.9188 0.988 0.000 0.000 0.000 NA
#> SRR1044540 1 0.0771 0.9173 0.976 0.004 0.000 0.000 NA
#> SRR1044541 2 0.4128 0.2958 0.004 0.800 0.124 0.004 NA
#> SRR1044542 1 0.0404 0.9194 0.988 0.012 0.000 0.000 NA
#> SRR1044543 1 0.1484 0.8910 0.944 0.008 0.000 0.000 NA
#> SRR1044544 2 0.2304 0.4234 0.004 0.908 0.020 0.000 NA
#> SRR1044545 1 0.0404 0.9188 0.988 0.000 0.000 0.000 NA
#> SRR1044546 1 0.0693 0.9196 0.980 0.008 0.000 0.000 NA
#> SRR1044547 1 0.0566 0.9197 0.984 0.004 0.000 0.000 NA
#> SRR1044548 1 0.0693 0.9196 0.980 0.008 0.000 0.000 NA
#> SRR1044549 2 0.4126 0.6208 0.380 0.620 0.000 0.000 NA
#> SRR1044550 2 0.3837 0.7143 0.308 0.692 0.000 0.000 NA
#> SRR1044551 2 0.3949 0.6933 0.332 0.668 0.000 0.000 NA
#> SRR1044552 1 0.0510 0.9188 0.984 0.000 0.000 0.000 NA
#> SRR1044553 1 0.0510 0.9188 0.984 0.000 0.000 0.000 NA
#> SRR1044554 1 0.0703 0.9115 0.976 0.000 0.000 0.000 NA
#> SRR1044555 2 0.2833 0.4048 0.004 0.884 0.020 0.008 NA
#> SRR1044556 1 0.0162 0.9214 0.996 0.000 0.000 0.000 NA
#> SRR1044557 1 0.0671 0.9180 0.980 0.004 0.000 0.000 NA
#> SRR1044558 1 0.0162 0.9214 0.996 0.000 0.000 0.000 NA
#> SRR1044559 1 0.0693 0.9196 0.980 0.008 0.000 0.000 NA
#> SRR1044561 1 0.0162 0.9214 0.996 0.000 0.000 0.000 NA
#> SRR1044560 2 0.2741 0.5587 0.064 0.892 0.012 0.000 NA
#> SRR1044562 1 0.0671 0.9179 0.980 0.004 0.000 0.000 NA
#> SRR1044563 1 0.0404 0.9188 0.988 0.000 0.000 0.000 NA
#> SRR1044564 1 0.0865 0.9126 0.972 0.004 0.000 0.000 NA
#> SRR1044565 1 0.4305 -0.3156 0.512 0.488 0.000 0.000 NA
#> SRR1044566 2 0.2741 0.5587 0.064 0.892 0.012 0.000 NA
#> SRR1044567 1 0.0290 0.9207 0.992 0.008 0.000 0.000 NA
#> SRR1044568 1 0.0703 0.9115 0.976 0.000 0.000 0.000 NA
#> SRR1044569 1 0.0671 0.9182 0.980 0.004 0.000 0.000 NA
#> SRR1044570 1 0.0290 0.9207 0.992 0.008 0.000 0.000 NA
#> SRR1044571 1 0.0771 0.9173 0.976 0.004 0.000 0.000 NA
#> SRR1044572 1 0.0162 0.9214 0.996 0.004 0.000 0.000 NA
#> SRR1044573 1 0.0771 0.9173 0.976 0.004 0.000 0.000 NA
#> SRR1044574 1 0.0162 0.9214 0.996 0.004 0.000 0.000 NA
#> SRR1044575 1 0.0771 0.9173 0.976 0.004 0.000 0.000 NA
#> SRR1044576 2 0.4283 0.4648 0.456 0.544 0.000 0.000 NA
#> SRR1044577 2 0.4305 0.3754 0.488 0.512 0.000 0.000 NA
#> SRR1044578 1 0.4306 -0.3287 0.508 0.492 0.000 0.000 NA
#> SRR1044579 1 0.0000 0.9215 1.000 0.000 0.000 0.000 NA
#> SRR1044580 1 0.0290 0.9202 0.992 0.000 0.000 0.000 NA
#> SRR1044581 1 0.0000 0.9215 1.000 0.000 0.000 0.000 NA
#> SRR1044582 1 0.0324 0.9220 0.992 0.004 0.000 0.000 NA
#> SRR1044583 1 0.0000 0.9215 1.000 0.000 0.000 0.000 NA
#> SRR1044584 1 0.0162 0.9213 0.996 0.000 0.000 0.000 NA
#> SRR1044585 1 0.0000 0.9215 1.000 0.000 0.000 0.000 NA
#> SRR1044586 1 0.0290 0.9202 0.992 0.000 0.000 0.000 NA
#> SRR1044587 1 0.0162 0.9212 0.996 0.004 0.000 0.000 NA
#> SRR1044588 1 0.0162 0.9212 0.996 0.004 0.000 0.000 NA
#> SRR1044589 1 0.0162 0.9212 0.996 0.004 0.000 0.000 NA
#> SRR1044590 1 0.0162 0.9212 0.996 0.004 0.000 0.000 NA
#> SRR1044591 1 0.0162 0.9212 0.996 0.004 0.000 0.000 NA
#> SRR1044592 1 0.1768 0.8574 0.924 0.072 0.000 0.000 NA
#> SRR1044593 1 0.0162 0.9212 0.996 0.004 0.000 0.000 NA
#> SRR1044594 1 0.0162 0.9212 0.996 0.004 0.000 0.000 NA
#> SRR1044595 1 0.1768 0.8574 0.924 0.072 0.000 0.000 NA
#> SRR1044596 1 0.0880 0.9034 0.968 0.032 0.000 0.000 NA
#> SRR1044597 1 0.0510 0.9177 0.984 0.016 0.000 0.000 NA
#> SRR1044598 1 0.0404 0.9194 0.988 0.012 0.000 0.000 NA
#> SRR1044599 1 0.0404 0.9194 0.988 0.012 0.000 0.000 NA
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.3026 0.399339 0.000 0.868 0.008 0.068 0.020 0.036
#> SRR1044416 2 0.3789 0.620689 0.000 0.584 0.000 0.416 0.000 0.000
#> SRR1044417 2 0.3774 0.631146 0.000 0.592 0.000 0.408 0.000 0.000
#> SRR1044418 2 0.3797 0.614531 0.000 0.580 0.000 0.420 0.000 0.000
#> SRR1044420 2 0.3151 0.684990 0.000 0.748 0.000 0.252 0.000 0.000
#> SRR1044419 2 0.2865 0.435331 0.000 0.868 0.000 0.080 0.020 0.032
#> SRR1044421 2 0.3151 0.684915 0.000 0.748 0.000 0.252 0.000 0.000
#> SRR1044422 2 0.3136 0.670937 0.000 0.768 0.000 0.228 0.004 0.000
#> SRR1044423 2 0.3357 0.665565 0.000 0.764 0.000 0.224 0.004 0.008
#> SRR1044424 2 0.3151 0.684990 0.000 0.748 0.000 0.252 0.000 0.000
#> SRR1044425 4 0.0146 0.953984 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1044426 4 0.4171 0.700136 0.000 0.020 0.000 0.772 0.092 0.116
#> SRR1044427 4 0.0363 0.952985 0.000 0.012 0.000 0.988 0.000 0.000
#> SRR1044428 4 0.2932 0.841662 0.000 0.012 0.000 0.860 0.040 0.088
#> SRR1044429 4 0.0146 0.954389 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044430 4 0.6787 -0.010375 0.000 0.068 0.000 0.440 0.312 0.180
#> SRR1044431 4 0.1251 0.945069 0.000 0.008 0.000 0.956 0.024 0.012
#> SRR1044433 4 0.2149 0.850192 0.000 0.104 0.000 0.888 0.004 0.004
#> SRR1044432 4 0.6326 0.031074 0.000 0.020 0.000 0.464 0.252 0.264
#> SRR1044434 4 0.0508 0.952817 0.000 0.000 0.000 0.984 0.012 0.004
#> SRR1044435 4 0.0291 0.954383 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR1044436 4 0.0146 0.954349 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044437 4 0.0291 0.954383 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR1044439 4 0.0146 0.954349 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044438 4 0.0653 0.954181 0.000 0.004 0.000 0.980 0.012 0.004
#> SRR1044440 4 0.0291 0.954383 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR1044441 4 0.0000 0.953586 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044442 4 0.1349 0.917021 0.000 0.056 0.000 0.940 0.004 0.000
#> SRR1044443 4 0.2149 0.850192 0.000 0.104 0.000 0.888 0.004 0.004
#> SRR1044444 4 0.0000 0.953586 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044445 4 0.0363 0.953256 0.000 0.012 0.000 0.988 0.000 0.000
#> SRR1044446 2 0.3881 -0.547962 0.004 0.600 0.000 0.000 0.000 0.396
#> SRR1044447 2 0.4536 0.558138 0.000 0.700 0.000 0.180 0.000 0.120
#> SRR1044449 3 0.3714 0.646864 0.080 0.000 0.808 0.000 0.016 0.096
#> SRR1044448 6 0.3515 0.959950 0.000 0.324 0.000 0.000 0.000 0.676
#> SRR1044450 6 0.3695 0.885726 0.000 0.376 0.000 0.000 0.000 0.624
#> SRR1044451 2 0.3985 0.365451 0.000 0.760 0.000 0.100 0.000 0.140
#> SRR1044452 3 0.0000 0.905378 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044453 3 0.0000 0.905378 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044454 3 0.0000 0.905378 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044455 2 0.2766 0.534286 0.000 0.852 0.000 0.124 0.004 0.020
#> SRR1044456 4 0.0632 0.948413 0.000 0.024 0.000 0.976 0.000 0.000
#> SRR1044457 2 0.3007 0.313664 0.000 0.872 0.008 0.044 0.024 0.052
#> SRR1044458 2 0.2992 0.380081 0.000 0.872 0.008 0.060 0.024 0.036
#> SRR1044459 2 0.4980 -0.258587 0.004 0.724 0.128 0.000 0.052 0.092
#> SRR1044460 2 0.3151 0.684990 0.000 0.748 0.000 0.252 0.000 0.000
#> SRR1044461 2 0.2605 0.476232 0.000 0.876 0.000 0.092 0.012 0.020
#> SRR1044462 4 0.0790 0.947457 0.000 0.000 0.000 0.968 0.032 0.000
#> SRR1044463 4 0.1275 0.947684 0.000 0.016 0.000 0.956 0.016 0.012
#> SRR1044464 4 0.3544 0.777131 0.000 0.016 0.000 0.820 0.064 0.100
#> SRR1044466 4 0.0603 0.952509 0.000 0.016 0.000 0.980 0.000 0.004
#> SRR1044465 4 0.1138 0.945453 0.000 0.004 0.000 0.960 0.024 0.012
#> SRR1044467 4 0.1138 0.945453 0.000 0.004 0.000 0.960 0.024 0.012
#> SRR1044468 2 0.3354 0.679283 0.000 0.752 0.000 0.240 0.004 0.004
#> SRR1044469 2 0.5482 -0.508046 0.000 0.492 0.420 0.000 0.028 0.060
#> SRR1044470 4 0.0806 0.948958 0.000 0.020 0.000 0.972 0.008 0.000
#> SRR1044471 4 0.0964 0.948374 0.000 0.004 0.000 0.968 0.016 0.012
#> SRR1044472 4 0.0458 0.951741 0.000 0.016 0.000 0.984 0.000 0.000
#> SRR1044473 4 0.1218 0.943231 0.000 0.004 0.000 0.956 0.028 0.012
#> SRR1044474 2 0.3843 0.560523 0.000 0.548 0.000 0.452 0.000 0.000
#> SRR1044475 3 0.0692 0.877190 0.000 0.004 0.976 0.000 0.020 0.000
#> SRR1044476 2 0.3260 0.299982 0.000 0.860 0.012 0.044 0.032 0.052
#> SRR1044477 2 0.3862 0.507320 0.000 0.524 0.000 0.476 0.000 0.000
#> SRR1044478 2 0.3073 0.645201 0.000 0.788 0.000 0.204 0.000 0.008
#> SRR1044479 2 0.3851 0.543939 0.000 0.540 0.000 0.460 0.000 0.000
#> SRR1044480 4 0.0458 0.952774 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1044481 4 0.0603 0.953651 0.000 0.004 0.000 0.980 0.016 0.000
#> SRR1044482 2 0.3833 0.575140 0.000 0.556 0.000 0.444 0.000 0.000
#> SRR1044483 4 0.1265 0.932300 0.000 0.000 0.000 0.948 0.044 0.008
#> SRR1044484 4 0.0520 0.954956 0.000 0.008 0.000 0.984 0.008 0.000
#> SRR1044486 4 0.0717 0.954580 0.000 0.008 0.000 0.976 0.016 0.000
#> SRR1044485 2 0.3531 0.666204 0.000 0.672 0.000 0.328 0.000 0.000
#> SRR1044487 2 0.3851 0.543939 0.000 0.540 0.000 0.460 0.000 0.000
#> SRR1044488 2 0.3151 0.684990 0.000 0.748 0.000 0.252 0.000 0.000
#> SRR1044489 2 0.3151 0.684990 0.000 0.748 0.000 0.252 0.000 0.000
#> SRR1044490 4 0.0725 0.952254 0.000 0.000 0.000 0.976 0.012 0.012
#> SRR1044491 4 0.0458 0.951972 0.000 0.016 0.000 0.984 0.000 0.000
#> SRR1044492 4 0.0458 0.951741 0.000 0.016 0.000 0.984 0.000 0.000
#> SRR1044493 4 0.0603 0.952110 0.000 0.016 0.000 0.980 0.004 0.000
#> SRR1044494 2 0.3851 0.543939 0.000 0.540 0.000 0.460 0.000 0.000
#> SRR1044496 2 0.3851 0.543939 0.000 0.540 0.000 0.460 0.000 0.000
#> SRR1044495 2 0.3851 0.543939 0.000 0.540 0.000 0.460 0.000 0.000
#> SRR1044497 4 0.0000 0.953586 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044499 2 0.5628 -0.465861 0.000 0.564 0.324 0.000 0.044 0.068
#> SRR1044498 4 0.0603 0.953651 0.000 0.004 0.000 0.980 0.016 0.000
#> SRR1044500 2 0.3151 0.684990 0.000 0.748 0.000 0.252 0.000 0.000
#> SRR1044501 2 0.2797 0.392800 0.000 0.876 0.000 0.064 0.024 0.036
#> SRR1044502 2 0.2956 0.426102 0.000 0.848 0.000 0.088 0.000 0.064
#> SRR1044503 4 0.0291 0.954383 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR1044504 4 0.0603 0.951359 0.000 0.000 0.000 0.980 0.016 0.004
#> SRR1044505 4 0.0870 0.950391 0.000 0.004 0.000 0.972 0.012 0.012
#> SRR1044506 4 0.0363 0.953256 0.000 0.012 0.000 0.988 0.000 0.000
#> SRR1044507 4 0.1141 0.918576 0.000 0.052 0.000 0.948 0.000 0.000
#> SRR1044508 4 0.2149 0.850192 0.000 0.104 0.000 0.888 0.004 0.004
#> SRR1044509 4 0.2149 0.850192 0.000 0.104 0.000 0.888 0.004 0.004
#> SRR1044510 5 0.5042 0.921073 0.100 0.000 0.308 0.000 0.592 0.000
#> SRR1044511 1 0.0665 0.939580 0.980 0.000 0.008 0.000 0.008 0.004
#> SRR1044512 1 0.2527 0.859083 0.884 0.000 0.064 0.000 0.048 0.004
#> SRR1044513 2 0.3740 0.664818 0.000 0.740 0.000 0.228 0.000 0.032
#> SRR1044514 1 0.0405 0.943656 0.988 0.000 0.008 0.000 0.000 0.004
#> SRR1044515 2 0.3740 0.664818 0.000 0.740 0.000 0.228 0.000 0.032
#> SRR1044516 2 0.2969 0.670238 0.000 0.776 0.000 0.224 0.000 0.000
#> SRR1044517 5 0.5592 0.918437 0.072 0.000 0.336 0.000 0.556 0.036
#> SRR1044518 1 0.0146 0.941942 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1044519 6 0.3515 0.959950 0.000 0.324 0.000 0.000 0.000 0.676
#> SRR1044520 6 0.3515 0.959950 0.000 0.324 0.000 0.000 0.000 0.676
#> SRR1044521 2 0.3244 0.684523 0.000 0.732 0.000 0.268 0.000 0.000
#> SRR1044522 4 0.0713 0.945621 0.000 0.028 0.000 0.972 0.000 0.000
#> SRR1044523 2 0.4215 0.660091 0.000 0.700 0.000 0.244 0.000 0.056
#> SRR1044524 2 0.3690 -0.072289 0.004 0.808 0.016 0.000 0.044 0.128
#> SRR1044525 4 0.0603 0.951359 0.000 0.000 0.000 0.980 0.016 0.004
#> SRR1044526 4 0.0717 0.949750 0.000 0.000 0.000 0.976 0.016 0.008
#> SRR1044527 2 0.3672 0.649834 0.000 0.632 0.000 0.368 0.000 0.000
#> SRR1044528 2 0.3371 0.679941 0.000 0.708 0.000 0.292 0.000 0.000
#> SRR1044529 2 0.3843 0.560156 0.000 0.548 0.000 0.452 0.000 0.000
#> SRR1044530 4 0.0458 0.951741 0.000 0.016 0.000 0.984 0.000 0.000
#> SRR1044531 4 0.0767 0.952704 0.000 0.012 0.000 0.976 0.008 0.004
#> SRR1044533 4 0.0717 0.952147 0.000 0.016 0.000 0.976 0.008 0.000
#> SRR1044532 4 0.0458 0.951741 0.000 0.016 0.000 0.984 0.000 0.000
#> SRR1044534 2 0.3244 0.684785 0.000 0.732 0.000 0.268 0.000 0.000
#> SRR1044535 2 0.2872 0.166830 0.004 0.860 0.004 0.020 0.004 0.108
#> SRR1044536 2 0.3126 0.683867 0.000 0.752 0.000 0.248 0.000 0.000
#> SRR1044537 4 0.1226 0.939858 0.000 0.004 0.000 0.952 0.040 0.004
#> SRR1044538 4 0.0458 0.951741 0.000 0.016 0.000 0.984 0.000 0.000
#> SRR1044539 4 0.0632 0.950476 0.000 0.000 0.000 0.976 0.024 0.000
#> SRR1044540 4 0.1218 0.943231 0.000 0.004 0.000 0.956 0.028 0.012
#> SRR1044541 2 0.5040 -0.227102 0.004 0.728 0.120 0.004 0.052 0.092
#> SRR1044542 4 0.0547 0.950325 0.000 0.020 0.000 0.980 0.000 0.000
#> SRR1044543 4 0.2649 0.874525 0.000 0.016 0.000 0.884 0.052 0.048
#> SRR1044544 2 0.3270 0.000979 0.000 0.840 0.016 0.000 0.052 0.092
#> SRR1044545 4 0.0632 0.950476 0.000 0.000 0.000 0.976 0.024 0.000
#> SRR1044546 4 0.0891 0.951216 0.000 0.008 0.000 0.968 0.024 0.000
#> SRR1044547 4 0.0777 0.951209 0.000 0.004 0.000 0.972 0.024 0.000
#> SRR1044548 4 0.0891 0.951216 0.000 0.008 0.000 0.968 0.024 0.000
#> SRR1044549 2 0.3515 0.668099 0.000 0.676 0.000 0.324 0.000 0.000
#> SRR1044550 2 0.3151 0.684990 0.000 0.748 0.000 0.252 0.000 0.000
#> SRR1044551 2 0.3309 0.682930 0.000 0.720 0.000 0.280 0.000 0.000
#> SRR1044552 4 0.0603 0.951359 0.000 0.000 0.000 0.980 0.016 0.004
#> SRR1044553 4 0.0603 0.951359 0.000 0.000 0.000 0.980 0.016 0.004
#> SRR1044554 4 0.1010 0.941798 0.000 0.000 0.000 0.960 0.036 0.004
#> SRR1044555 2 0.3648 -0.061227 0.004 0.812 0.016 0.000 0.044 0.124
#> SRR1044556 4 0.0146 0.954349 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044557 4 0.0935 0.947896 0.000 0.004 0.000 0.964 0.032 0.000
#> SRR1044558 4 0.0458 0.953774 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1044559 4 0.0891 0.951216 0.000 0.008 0.000 0.968 0.024 0.000
#> SRR1044561 4 0.0146 0.954349 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044560 2 0.3260 0.299982 0.000 0.860 0.012 0.044 0.032 0.052
#> SRR1044562 4 0.1003 0.947891 0.000 0.004 0.000 0.964 0.028 0.004
#> SRR1044563 4 0.0632 0.950476 0.000 0.000 0.000 0.976 0.024 0.000
#> SRR1044564 4 0.1226 0.939858 0.000 0.004 0.000 0.952 0.040 0.004
#> SRR1044565 2 0.3851 0.543939 0.000 0.540 0.000 0.460 0.000 0.000
#> SRR1044566 2 0.3260 0.299982 0.000 0.860 0.012 0.044 0.032 0.052
#> SRR1044567 4 0.0458 0.951741 0.000 0.016 0.000 0.984 0.000 0.000
#> SRR1044568 4 0.1082 0.939342 0.000 0.000 0.000 0.956 0.040 0.004
#> SRR1044569 4 0.1138 0.945008 0.000 0.004 0.000 0.960 0.024 0.012
#> SRR1044570 4 0.0458 0.951741 0.000 0.016 0.000 0.984 0.000 0.000
#> SRR1044571 4 0.1332 0.941689 0.000 0.008 0.000 0.952 0.028 0.012
#> SRR1044572 4 0.0405 0.954930 0.000 0.008 0.000 0.988 0.004 0.000
#> SRR1044573 4 0.1218 0.943231 0.000 0.004 0.000 0.956 0.028 0.012
#> SRR1044574 4 0.0520 0.954721 0.000 0.008 0.000 0.984 0.008 0.000
#> SRR1044575 4 0.1218 0.943231 0.000 0.004 0.000 0.956 0.028 0.012
#> SRR1044576 2 0.3765 0.633205 0.000 0.596 0.000 0.404 0.000 0.000
#> SRR1044577 2 0.3823 0.588924 0.000 0.564 0.000 0.436 0.000 0.000
#> SRR1044578 2 0.3847 0.552406 0.000 0.544 0.000 0.456 0.000 0.000
#> SRR1044579 4 0.0000 0.953586 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044580 4 0.0458 0.952774 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1044581 4 0.0000 0.953586 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044582 4 0.0725 0.955154 0.000 0.012 0.000 0.976 0.012 0.000
#> SRR1044583 4 0.0000 0.953586 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044584 4 0.0508 0.954392 0.000 0.004 0.000 0.984 0.012 0.000
#> SRR1044585 4 0.0000 0.953586 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044586 4 0.0603 0.953651 0.000 0.004 0.000 0.980 0.016 0.000
#> SRR1044587 4 0.0363 0.953256 0.000 0.012 0.000 0.988 0.000 0.000
#> SRR1044588 4 0.0363 0.953256 0.000 0.012 0.000 0.988 0.000 0.000
#> SRR1044589 4 0.0363 0.953256 0.000 0.012 0.000 0.988 0.000 0.000
#> SRR1044590 4 0.0363 0.953256 0.000 0.012 0.000 0.988 0.000 0.000
#> SRR1044591 4 0.0363 0.953256 0.000 0.012 0.000 0.988 0.000 0.000
#> SRR1044592 4 0.2149 0.850192 0.000 0.104 0.000 0.888 0.004 0.004
#> SRR1044593 4 0.0363 0.953256 0.000 0.012 0.000 0.988 0.000 0.000
#> SRR1044594 4 0.0363 0.953256 0.000 0.012 0.000 0.988 0.000 0.000
#> SRR1044595 4 0.2149 0.850192 0.000 0.104 0.000 0.888 0.004 0.004
#> SRR1044596 4 0.1349 0.917021 0.000 0.056 0.000 0.940 0.004 0.000
#> SRR1044597 4 0.0632 0.948579 0.000 0.024 0.000 0.976 0.000 0.000
#> SRR1044598 4 0.0547 0.950325 0.000 0.020 0.000 0.980 0.000 0.000
#> SRR1044599 4 0.0547 0.950325 0.000 0.020 0.000 0.980 0.000 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)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.881 0.928 0.970 0.3279 0.685 0.685
#> 3 3 1.000 0.967 0.979 0.6988 0.673 0.549
#> 4 4 0.755 0.903 0.880 0.2455 0.829 0.613
#> 5 5 0.677 0.816 0.837 0.0757 0.994 0.978
#> 6 6 0.707 0.583 0.750 0.0464 0.952 0.824
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0.8267 0.639 0.260 0.740
#> SRR1044416 1 0.0376 0.968 0.996 0.004
#> SRR1044417 1 0.0000 0.971 1.000 0.000
#> SRR1044418 1 0.0000 0.971 1.000 0.000
#> SRR1044420 1 0.6623 0.791 0.828 0.172
#> SRR1044419 2 0.5059 0.844 0.112 0.888
#> SRR1044421 1 0.7745 0.712 0.772 0.228
#> SRR1044422 1 0.7299 0.748 0.796 0.204
#> SRR1044423 1 0.7602 0.725 0.780 0.220
#> SRR1044424 1 0.2043 0.943 0.968 0.032
#> SRR1044425 1 0.0000 0.971 1.000 0.000
#> SRR1044426 1 0.0000 0.971 1.000 0.000
#> SRR1044427 1 0.0000 0.971 1.000 0.000
#> SRR1044428 1 0.0000 0.971 1.000 0.000
#> SRR1044429 1 0.0000 0.971 1.000 0.000
#> SRR1044430 1 0.0000 0.971 1.000 0.000
#> SRR1044431 1 0.0000 0.971 1.000 0.000
#> SRR1044433 1 0.0000 0.971 1.000 0.000
#> SRR1044432 1 0.0000 0.971 1.000 0.000
#> SRR1044434 1 0.0000 0.971 1.000 0.000
#> SRR1044435 1 0.0000 0.971 1.000 0.000
#> SRR1044436 1 0.0000 0.971 1.000 0.000
#> SRR1044437 1 0.0000 0.971 1.000 0.000
#> SRR1044439 1 0.0000 0.971 1.000 0.000
#> SRR1044438 1 0.0000 0.971 1.000 0.000
#> SRR1044440 1 0.0000 0.971 1.000 0.000
#> SRR1044441 1 0.0000 0.971 1.000 0.000
#> SRR1044442 1 0.0000 0.971 1.000 0.000
#> SRR1044443 1 0.0000 0.971 1.000 0.000
#> SRR1044444 1 0.0000 0.971 1.000 0.000
#> SRR1044445 1 0.0000 0.971 1.000 0.000
#> SRR1044446 2 0.0000 0.951 0.000 1.000
#> SRR1044447 1 0.9661 0.366 0.608 0.392
#> SRR1044449 2 0.0000 0.951 0.000 1.000
#> SRR1044448 2 0.0000 0.951 0.000 1.000
#> SRR1044450 2 0.0000 0.951 0.000 1.000
#> SRR1044451 2 0.9661 0.353 0.392 0.608
#> SRR1044452 2 0.0000 0.951 0.000 1.000
#> SRR1044453 2 0.0000 0.951 0.000 1.000
#> SRR1044454 2 0.0000 0.951 0.000 1.000
#> SRR1044455 2 0.0000 0.951 0.000 1.000
#> SRR1044456 1 0.0000 0.971 1.000 0.000
#> SRR1044457 2 0.0000 0.951 0.000 1.000
#> SRR1044458 2 0.0000 0.951 0.000 1.000
#> SRR1044459 2 0.0000 0.951 0.000 1.000
#> SRR1044460 1 0.7883 0.700 0.764 0.236
#> SRR1044461 2 0.9815 0.275 0.420 0.580
#> SRR1044462 1 0.0000 0.971 1.000 0.000
#> SRR1044463 1 0.0000 0.971 1.000 0.000
#> SRR1044464 1 0.0000 0.971 1.000 0.000
#> SRR1044466 1 0.0000 0.971 1.000 0.000
#> SRR1044465 1 0.0000 0.971 1.000 0.000
#> SRR1044467 1 0.0000 0.971 1.000 0.000
#> SRR1044468 1 0.7528 0.731 0.784 0.216
#> SRR1044469 2 0.0000 0.951 0.000 1.000
#> SRR1044470 1 0.0000 0.971 1.000 0.000
#> SRR1044471 1 0.0000 0.971 1.000 0.000
#> SRR1044472 1 0.0000 0.971 1.000 0.000
#> SRR1044473 1 0.0000 0.971 1.000 0.000
#> SRR1044474 1 0.0000 0.971 1.000 0.000
#> SRR1044475 2 0.0000 0.951 0.000 1.000
#> SRR1044476 2 0.0000 0.951 0.000 1.000
#> SRR1044477 1 0.0000 0.971 1.000 0.000
#> SRR1044478 1 0.7139 0.760 0.804 0.196
#> SRR1044479 1 0.0000 0.971 1.000 0.000
#> SRR1044480 1 0.0000 0.971 1.000 0.000
#> SRR1044481 1 0.0000 0.971 1.000 0.000
#> SRR1044482 1 0.0000 0.971 1.000 0.000
#> SRR1044483 1 0.0000 0.971 1.000 0.000
#> SRR1044484 1 0.0000 0.971 1.000 0.000
#> SRR1044486 1 0.0000 0.971 1.000 0.000
#> SRR1044485 1 0.0376 0.968 0.996 0.004
#> SRR1044487 1 0.0000 0.971 1.000 0.000
#> SRR1044488 1 0.5629 0.840 0.868 0.132
#> SRR1044489 1 0.7056 0.765 0.808 0.192
#> SRR1044490 1 0.0000 0.971 1.000 0.000
#> SRR1044491 1 0.0000 0.971 1.000 0.000
#> SRR1044492 1 0.0000 0.971 1.000 0.000
#> SRR1044493 1 0.0000 0.971 1.000 0.000
#> SRR1044494 1 0.0000 0.971 1.000 0.000
#> SRR1044496 1 0.0000 0.971 1.000 0.000
#> SRR1044495 1 0.0000 0.971 1.000 0.000
#> SRR1044497 1 0.0000 0.971 1.000 0.000
#> SRR1044499 2 0.0000 0.951 0.000 1.000
#> SRR1044498 1 0.0000 0.971 1.000 0.000
#> SRR1044500 1 0.4298 0.889 0.912 0.088
#> SRR1044501 2 0.0000 0.951 0.000 1.000
#> SRR1044502 2 0.9881 0.225 0.436 0.564
#> SRR1044503 1 0.0000 0.971 1.000 0.000
#> SRR1044504 1 0.0000 0.971 1.000 0.000
#> SRR1044505 1 0.0000 0.971 1.000 0.000
#> SRR1044506 1 0.0000 0.971 1.000 0.000
#> SRR1044507 1 0.0000 0.971 1.000 0.000
#> SRR1044508 1 0.0000 0.971 1.000 0.000
#> SRR1044509 1 0.0000 0.971 1.000 0.000
#> SRR1044510 2 0.0000 0.951 0.000 1.000
#> SRR1044511 2 0.0000 0.951 0.000 1.000
#> SRR1044512 2 0.0000 0.951 0.000 1.000
#> SRR1044513 1 0.9552 0.409 0.624 0.376
#> SRR1044514 2 0.0000 0.951 0.000 1.000
#> SRR1044515 1 0.9044 0.542 0.680 0.320
#> SRR1044516 1 0.9286 0.489 0.656 0.344
#> SRR1044517 2 0.0000 0.951 0.000 1.000
#> SRR1044518 2 0.0000 0.951 0.000 1.000
#> SRR1044519 2 0.0000 0.951 0.000 1.000
#> SRR1044520 2 0.0000 0.951 0.000 1.000
#> SRR1044521 1 0.1843 0.947 0.972 0.028
#> SRR1044522 1 0.0000 0.971 1.000 0.000
#> SRR1044523 1 0.7674 0.719 0.776 0.224
#> SRR1044524 2 0.0000 0.951 0.000 1.000
#> SRR1044525 1 0.0000 0.971 1.000 0.000
#> SRR1044526 1 0.0000 0.971 1.000 0.000
#> SRR1044527 1 0.0000 0.971 1.000 0.000
#> SRR1044528 1 0.0000 0.971 1.000 0.000
#> SRR1044529 1 0.0000 0.971 1.000 0.000
#> SRR1044530 1 0.0000 0.971 1.000 0.000
#> SRR1044531 1 0.0000 0.971 1.000 0.000
#> SRR1044533 1 0.0000 0.971 1.000 0.000
#> SRR1044532 1 0.0000 0.971 1.000 0.000
#> SRR1044534 1 0.0000 0.971 1.000 0.000
#> SRR1044535 2 0.0000 0.951 0.000 1.000
#> SRR1044536 1 0.6801 0.781 0.820 0.180
#> SRR1044537 1 0.0000 0.971 1.000 0.000
#> SRR1044538 1 0.0000 0.971 1.000 0.000
#> SRR1044539 1 0.0000 0.971 1.000 0.000
#> SRR1044540 1 0.0000 0.971 1.000 0.000
#> SRR1044541 2 0.0000 0.951 0.000 1.000
#> SRR1044542 1 0.0000 0.971 1.000 0.000
#> SRR1044543 1 0.0000 0.971 1.000 0.000
#> SRR1044544 2 0.0000 0.951 0.000 1.000
#> SRR1044545 1 0.0000 0.971 1.000 0.000
#> SRR1044546 1 0.0000 0.971 1.000 0.000
#> SRR1044547 1 0.0000 0.971 1.000 0.000
#> SRR1044548 1 0.0000 0.971 1.000 0.000
#> SRR1044549 1 0.0000 0.971 1.000 0.000
#> SRR1044550 1 0.6973 0.770 0.812 0.188
#> SRR1044551 1 0.0000 0.971 1.000 0.000
#> SRR1044552 1 0.0000 0.971 1.000 0.000
#> SRR1044553 1 0.0000 0.971 1.000 0.000
#> SRR1044554 1 0.0000 0.971 1.000 0.000
#> SRR1044555 2 0.0000 0.951 0.000 1.000
#> SRR1044556 1 0.0000 0.971 1.000 0.000
#> SRR1044557 1 0.0000 0.971 1.000 0.000
#> SRR1044558 1 0.0000 0.971 1.000 0.000
#> SRR1044559 1 0.0000 0.971 1.000 0.000
#> SRR1044561 1 0.0000 0.971 1.000 0.000
#> SRR1044560 2 0.0000 0.951 0.000 1.000
#> SRR1044562 1 0.0000 0.971 1.000 0.000
#> SRR1044563 1 0.0000 0.971 1.000 0.000
#> SRR1044564 1 0.0000 0.971 1.000 0.000
#> SRR1044565 1 0.0000 0.971 1.000 0.000
#> SRR1044566 2 0.0000 0.951 0.000 1.000
#> SRR1044567 1 0.0000 0.971 1.000 0.000
#> SRR1044568 1 0.0000 0.971 1.000 0.000
#> SRR1044569 1 0.0000 0.971 1.000 0.000
#> SRR1044570 1 0.0000 0.971 1.000 0.000
#> SRR1044571 1 0.0000 0.971 1.000 0.000
#> SRR1044572 1 0.0000 0.971 1.000 0.000
#> SRR1044573 1 0.0000 0.971 1.000 0.000
#> SRR1044574 1 0.0000 0.971 1.000 0.000
#> SRR1044575 1 0.0000 0.971 1.000 0.000
#> SRR1044576 1 0.0000 0.971 1.000 0.000
#> SRR1044577 1 0.0000 0.971 1.000 0.000
#> SRR1044578 1 0.0000 0.971 1.000 0.000
#> SRR1044579 1 0.0000 0.971 1.000 0.000
#> SRR1044580 1 0.0000 0.971 1.000 0.000
#> SRR1044581 1 0.0000 0.971 1.000 0.000
#> SRR1044582 1 0.0000 0.971 1.000 0.000
#> SRR1044583 1 0.0000 0.971 1.000 0.000
#> SRR1044584 1 0.0000 0.971 1.000 0.000
#> SRR1044585 1 0.0000 0.971 1.000 0.000
#> SRR1044586 1 0.0000 0.971 1.000 0.000
#> SRR1044587 1 0.0000 0.971 1.000 0.000
#> SRR1044588 1 0.0000 0.971 1.000 0.000
#> SRR1044589 1 0.0000 0.971 1.000 0.000
#> SRR1044590 1 0.0000 0.971 1.000 0.000
#> SRR1044591 1 0.0000 0.971 1.000 0.000
#> SRR1044592 1 0.0000 0.971 1.000 0.000
#> SRR1044593 1 0.0000 0.971 1.000 0.000
#> SRR1044594 1 0.0000 0.971 1.000 0.000
#> SRR1044595 1 0.0000 0.971 1.000 0.000
#> SRR1044596 1 0.0000 0.971 1.000 0.000
#> SRR1044597 1 0.0000 0.971 1.000 0.000
#> SRR1044598 1 0.0000 0.971 1.000 0.000
#> SRR1044599 1 0.0000 0.971 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.0237 0.949 0.000 0.996 0.004
#> SRR1044416 2 0.1163 0.962 0.028 0.972 0.000
#> SRR1044417 2 0.1163 0.962 0.028 0.972 0.000
#> SRR1044418 2 0.1163 0.962 0.028 0.972 0.000
#> SRR1044420 2 0.0747 0.962 0.016 0.984 0.000
#> SRR1044419 2 0.0237 0.949 0.000 0.996 0.004
#> SRR1044421 2 0.0747 0.962 0.016 0.984 0.000
#> SRR1044422 2 0.0747 0.962 0.016 0.984 0.000
#> SRR1044423 2 0.0592 0.960 0.012 0.988 0.000
#> SRR1044424 2 0.1163 0.962 0.028 0.972 0.000
#> SRR1044425 1 0.0237 0.990 0.996 0.000 0.004
#> SRR1044426 1 0.0424 0.988 0.992 0.000 0.008
#> SRR1044427 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044428 1 0.0592 0.987 0.988 0.000 0.012
#> SRR1044429 1 0.0237 0.990 0.996 0.000 0.004
#> SRR1044430 1 0.0592 0.987 0.988 0.000 0.012
#> SRR1044431 1 0.0237 0.990 0.996 0.000 0.004
#> SRR1044433 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044432 1 0.0592 0.987 0.988 0.000 0.012
#> SRR1044434 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044435 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044436 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044437 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044439 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044438 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044440 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044441 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044442 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044443 1 0.0592 0.988 0.988 0.012 0.000
#> SRR1044444 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044445 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044446 3 0.6026 0.413 0.000 0.376 0.624
#> SRR1044447 2 0.0848 0.958 0.008 0.984 0.008
#> SRR1044449 3 0.0747 0.970 0.000 0.016 0.984
#> SRR1044448 3 0.1031 0.969 0.000 0.024 0.976
#> SRR1044450 3 0.1643 0.956 0.000 0.044 0.956
#> SRR1044451 2 0.1129 0.951 0.004 0.976 0.020
#> SRR1044452 3 0.1163 0.972 0.000 0.028 0.972
#> SRR1044453 3 0.1163 0.972 0.000 0.028 0.972
#> SRR1044454 3 0.1163 0.972 0.000 0.028 0.972
#> SRR1044455 2 0.0237 0.949 0.000 0.996 0.004
#> SRR1044456 2 0.6111 0.368 0.396 0.604 0.000
#> SRR1044457 2 0.0237 0.949 0.000 0.996 0.004
#> SRR1044458 2 0.0237 0.949 0.000 0.996 0.004
#> SRR1044459 3 0.1163 0.972 0.000 0.028 0.972
#> SRR1044460 2 0.0592 0.960 0.012 0.988 0.000
#> SRR1044461 2 0.0237 0.949 0.000 0.996 0.004
#> SRR1044462 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044463 1 0.1129 0.977 0.976 0.020 0.004
#> SRR1044464 1 0.0661 0.990 0.988 0.004 0.008
#> SRR1044466 1 0.1399 0.970 0.968 0.028 0.004
#> SRR1044465 1 0.0237 0.990 0.996 0.000 0.004
#> SRR1044467 1 0.0237 0.990 0.996 0.000 0.004
#> SRR1044468 2 0.0747 0.962 0.016 0.984 0.000
#> SRR1044469 3 0.1163 0.972 0.000 0.028 0.972
#> SRR1044470 1 0.1585 0.969 0.964 0.028 0.008
#> SRR1044471 1 0.0237 0.990 0.996 0.000 0.004
#> SRR1044472 1 0.1399 0.970 0.968 0.028 0.004
#> SRR1044473 1 0.0237 0.990 0.996 0.000 0.004
#> SRR1044474 2 0.1163 0.962 0.028 0.972 0.000
#> SRR1044475 3 0.1163 0.972 0.000 0.028 0.972
#> SRR1044476 2 0.0237 0.949 0.000 0.996 0.004
#> SRR1044477 2 0.1411 0.955 0.036 0.964 0.000
#> SRR1044478 2 0.0892 0.962 0.020 0.980 0.000
#> SRR1044479 2 0.1964 0.930 0.056 0.944 0.000
#> SRR1044480 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044481 1 0.0237 0.991 0.996 0.000 0.004
#> SRR1044482 2 0.1163 0.962 0.028 0.972 0.000
#> SRR1044483 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044484 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044486 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044485 2 0.1163 0.962 0.028 0.972 0.000
#> SRR1044487 2 0.1643 0.945 0.044 0.956 0.000
#> SRR1044488 2 0.0892 0.962 0.020 0.980 0.000
#> SRR1044489 2 0.0892 0.962 0.020 0.980 0.000
#> SRR1044490 1 0.0237 0.990 0.996 0.000 0.004
#> SRR1044491 1 0.0829 0.984 0.984 0.012 0.004
#> SRR1044492 1 0.1525 0.966 0.964 0.032 0.004
#> SRR1044493 1 0.0237 0.990 0.996 0.000 0.004
#> SRR1044494 2 0.1289 0.959 0.032 0.968 0.000
#> SRR1044496 2 0.1411 0.955 0.036 0.964 0.000
#> SRR1044495 2 0.1411 0.955 0.036 0.964 0.000
#> SRR1044497 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044499 3 0.1753 0.960 0.000 0.048 0.952
#> SRR1044498 1 0.0237 0.991 0.996 0.000 0.004
#> SRR1044500 2 0.1163 0.962 0.028 0.972 0.000
#> SRR1044501 2 0.0237 0.949 0.000 0.996 0.004
#> SRR1044502 2 0.0848 0.956 0.008 0.984 0.008
#> SRR1044503 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044504 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044505 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044506 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044507 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044508 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044509 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044510 3 0.1031 0.971 0.000 0.024 0.976
#> SRR1044511 3 0.0592 0.970 0.000 0.012 0.988
#> SRR1044512 3 0.0592 0.970 0.000 0.012 0.988
#> SRR1044513 2 0.0848 0.958 0.008 0.984 0.008
#> SRR1044514 3 0.0592 0.970 0.000 0.012 0.988
#> SRR1044515 2 0.0848 0.958 0.008 0.984 0.008
#> SRR1044516 2 0.0592 0.960 0.012 0.988 0.000
#> SRR1044517 3 0.1031 0.971 0.000 0.024 0.976
#> SRR1044518 3 0.0592 0.970 0.000 0.012 0.988
#> SRR1044519 3 0.1643 0.956 0.000 0.044 0.956
#> SRR1044520 3 0.1031 0.969 0.000 0.024 0.976
#> SRR1044521 2 0.1163 0.962 0.028 0.972 0.000
#> SRR1044522 2 0.3686 0.803 0.140 0.860 0.000
#> SRR1044523 2 0.0829 0.960 0.012 0.984 0.004
#> SRR1044524 2 0.4842 0.692 0.000 0.776 0.224
#> SRR1044525 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044526 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044527 2 0.1163 0.962 0.028 0.972 0.000
#> SRR1044528 2 0.1163 0.962 0.028 0.972 0.000
#> SRR1044529 2 0.1289 0.958 0.032 0.968 0.000
#> SRR1044530 1 0.1399 0.970 0.968 0.028 0.004
#> SRR1044531 1 0.0237 0.990 0.996 0.000 0.004
#> SRR1044533 1 0.0237 0.990 0.996 0.000 0.004
#> SRR1044532 1 0.1399 0.970 0.968 0.028 0.004
#> SRR1044534 2 0.1163 0.962 0.028 0.972 0.000
#> SRR1044535 2 0.1964 0.916 0.000 0.944 0.056
#> SRR1044536 2 0.0892 0.962 0.020 0.980 0.000
#> SRR1044537 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044538 1 0.1399 0.970 0.968 0.028 0.004
#> SRR1044539 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044540 1 0.0237 0.990 0.996 0.000 0.004
#> SRR1044541 2 0.1289 0.932 0.000 0.968 0.032
#> SRR1044542 1 0.1399 0.970 0.968 0.028 0.004
#> SRR1044543 1 0.0237 0.990 0.996 0.000 0.004
#> SRR1044544 2 0.3482 0.824 0.000 0.872 0.128
#> SRR1044545 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044546 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044547 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044548 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044549 2 0.1163 0.962 0.028 0.972 0.000
#> SRR1044550 2 0.0747 0.962 0.016 0.984 0.000
#> SRR1044551 2 0.1163 0.962 0.028 0.972 0.000
#> SRR1044552 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044553 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044554 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044555 3 0.1411 0.969 0.000 0.036 0.964
#> SRR1044556 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044557 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044558 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044559 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044561 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044560 2 0.0237 0.949 0.000 0.996 0.004
#> SRR1044562 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044563 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044564 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044565 2 0.1411 0.955 0.036 0.964 0.000
#> SRR1044566 2 0.0237 0.949 0.000 0.996 0.004
#> SRR1044567 1 0.0661 0.987 0.988 0.008 0.004
#> SRR1044568 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044569 1 0.0237 0.990 0.996 0.000 0.004
#> SRR1044570 1 0.1399 0.970 0.968 0.028 0.004
#> SRR1044571 1 0.0237 0.990 0.996 0.000 0.004
#> SRR1044572 1 0.0237 0.990 0.996 0.000 0.004
#> SRR1044573 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044574 1 0.0237 0.990 0.996 0.000 0.004
#> SRR1044575 1 0.0237 0.990 0.996 0.000 0.004
#> SRR1044576 2 0.1163 0.962 0.028 0.972 0.000
#> SRR1044577 2 0.1163 0.962 0.028 0.972 0.000
#> SRR1044578 2 0.1163 0.962 0.028 0.972 0.000
#> SRR1044579 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044580 1 0.0237 0.991 0.996 0.000 0.004
#> SRR1044581 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044582 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044583 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044584 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044585 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044586 1 0.0475 0.992 0.992 0.004 0.004
#> SRR1044587 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044588 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044589 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044590 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044591 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044592 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044593 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044594 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044595 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044596 1 0.0237 0.993 0.996 0.004 0.000
#> SRR1044597 1 0.0747 0.985 0.984 0.016 0.000
#> SRR1044598 1 0.1289 0.970 0.968 0.032 0.000
#> SRR1044599 1 0.1289 0.970 0.968 0.032 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 2 0.0921 0.948 0.000 0.972 0.000 0.028
#> SRR1044416 2 0.0188 0.954 0.004 0.996 0.000 0.000
#> SRR1044417 2 0.0188 0.954 0.004 0.996 0.000 0.000
#> SRR1044418 2 0.0188 0.954 0.004 0.996 0.000 0.000
#> SRR1044420 2 0.0000 0.954 0.000 1.000 0.000 0.000
#> SRR1044419 2 0.1022 0.946 0.000 0.968 0.000 0.032
#> SRR1044421 2 0.0188 0.953 0.000 0.996 0.000 0.004
#> SRR1044422 2 0.0000 0.954 0.000 1.000 0.000 0.000
#> SRR1044423 2 0.0336 0.953 0.000 0.992 0.000 0.008
#> SRR1044424 2 0.0188 0.954 0.004 0.996 0.000 0.000
#> SRR1044425 4 0.4605 0.878 0.336 0.000 0.000 0.664
#> SRR1044426 1 0.3444 0.800 0.816 0.000 0.000 0.184
#> SRR1044427 1 0.1557 0.897 0.944 0.000 0.000 0.056
#> SRR1044428 1 0.1867 0.860 0.928 0.000 0.000 0.072
#> SRR1044429 1 0.4933 -0.201 0.568 0.000 0.000 0.432
#> SRR1044430 1 0.2760 0.839 0.872 0.000 0.000 0.128
#> SRR1044431 1 0.0592 0.901 0.984 0.000 0.000 0.016
#> SRR1044433 4 0.3764 0.924 0.216 0.000 0.000 0.784
#> SRR1044432 1 0.2345 0.840 0.900 0.000 0.000 0.100
#> SRR1044434 4 0.4103 0.955 0.256 0.000 0.000 0.744
#> SRR1044435 4 0.4103 0.955 0.256 0.000 0.000 0.744
#> SRR1044436 4 0.4193 0.948 0.268 0.000 0.000 0.732
#> SRR1044437 4 0.4103 0.955 0.256 0.000 0.000 0.744
#> SRR1044439 4 0.4134 0.953 0.260 0.000 0.000 0.740
#> SRR1044438 4 0.4103 0.955 0.256 0.000 0.000 0.744
#> SRR1044440 4 0.4103 0.955 0.256 0.000 0.000 0.744
#> SRR1044441 4 0.4072 0.954 0.252 0.000 0.000 0.748
#> SRR1044442 4 0.3942 0.942 0.236 0.000 0.000 0.764
#> SRR1044443 4 0.3751 0.897 0.196 0.004 0.000 0.800
#> SRR1044444 4 0.4103 0.955 0.256 0.000 0.000 0.744
#> SRR1044445 4 0.4103 0.949 0.256 0.000 0.000 0.744
#> SRR1044446 3 0.6859 0.300 0.000 0.380 0.512 0.108
#> SRR1044447 2 0.1474 0.937 0.000 0.948 0.000 0.052
#> SRR1044449 3 0.0817 0.949 0.000 0.000 0.976 0.024
#> SRR1044448 3 0.2530 0.935 0.000 0.004 0.896 0.100
#> SRR1044450 3 0.3205 0.925 0.000 0.024 0.872 0.104
#> SRR1044451 2 0.2197 0.915 0.000 0.916 0.004 0.080
#> SRR1044452 3 0.0000 0.949 0.000 0.000 1.000 0.000
#> SRR1044453 3 0.0000 0.949 0.000 0.000 1.000 0.000
#> SRR1044454 3 0.0000 0.949 0.000 0.000 1.000 0.000
#> SRR1044455 2 0.1305 0.943 0.000 0.960 0.004 0.036
#> SRR1044456 1 0.4405 0.744 0.800 0.152 0.000 0.048
#> SRR1044457 2 0.1305 0.943 0.000 0.960 0.004 0.036
#> SRR1044458 2 0.1305 0.943 0.000 0.960 0.004 0.036
#> SRR1044459 3 0.1474 0.945 0.000 0.000 0.948 0.052
#> SRR1044460 2 0.0000 0.954 0.000 1.000 0.000 0.000
#> SRR1044461 2 0.0921 0.948 0.000 0.972 0.000 0.028
#> SRR1044462 1 0.4431 0.590 0.696 0.000 0.000 0.304
#> SRR1044463 1 0.1767 0.904 0.944 0.012 0.000 0.044
#> SRR1044464 4 0.3726 0.881 0.212 0.000 0.000 0.788
#> SRR1044466 1 0.2002 0.902 0.936 0.020 0.000 0.044
#> SRR1044465 1 0.0336 0.900 0.992 0.000 0.000 0.008
#> SRR1044467 1 0.0188 0.900 0.996 0.000 0.000 0.004
#> SRR1044468 2 0.0336 0.953 0.000 0.992 0.000 0.008
#> SRR1044469 3 0.1211 0.946 0.000 0.000 0.960 0.040
#> SRR1044470 1 0.2928 0.892 0.880 0.012 0.000 0.108
#> SRR1044471 1 0.0336 0.900 0.992 0.000 0.000 0.008
#> SRR1044472 1 0.2413 0.897 0.916 0.020 0.000 0.064
#> SRR1044473 1 0.0188 0.900 0.996 0.000 0.000 0.004
#> SRR1044474 2 0.1474 0.925 0.052 0.948 0.000 0.000
#> SRR1044475 3 0.0000 0.949 0.000 0.000 1.000 0.000
#> SRR1044476 2 0.1452 0.941 0.000 0.956 0.008 0.036
#> SRR1044477 2 0.2266 0.893 0.084 0.912 0.000 0.004
#> SRR1044478 2 0.0188 0.954 0.000 0.996 0.000 0.004
#> SRR1044479 2 0.4453 0.662 0.244 0.744 0.000 0.012
#> SRR1044480 4 0.3907 0.905 0.232 0.000 0.000 0.768
#> SRR1044481 1 0.2814 0.873 0.868 0.000 0.000 0.132
#> SRR1044482 2 0.0336 0.953 0.008 0.992 0.000 0.000
#> SRR1044483 4 0.3942 0.902 0.236 0.000 0.000 0.764
#> SRR1044484 1 0.2345 0.873 0.900 0.000 0.000 0.100
#> SRR1044486 1 0.2281 0.876 0.904 0.000 0.000 0.096
#> SRR1044485 2 0.0188 0.954 0.004 0.996 0.000 0.000
#> SRR1044487 2 0.2266 0.893 0.084 0.912 0.000 0.004
#> SRR1044488 2 0.0000 0.954 0.000 1.000 0.000 0.000
#> SRR1044489 2 0.0000 0.954 0.000 1.000 0.000 0.000
#> SRR1044490 1 0.1474 0.900 0.948 0.000 0.000 0.052
#> SRR1044491 1 0.1722 0.906 0.944 0.008 0.000 0.048
#> SRR1044492 1 0.2174 0.902 0.928 0.020 0.000 0.052
#> SRR1044493 1 0.1576 0.902 0.948 0.004 0.000 0.048
#> SRR1044494 2 0.1940 0.904 0.076 0.924 0.000 0.000
#> SRR1044496 2 0.2266 0.893 0.084 0.912 0.000 0.004
#> SRR1044495 2 0.2266 0.893 0.084 0.912 0.000 0.004
#> SRR1044497 4 0.4103 0.955 0.256 0.000 0.000 0.744
#> SRR1044499 3 0.2759 0.915 0.000 0.052 0.904 0.044
#> SRR1044498 1 0.2647 0.873 0.880 0.000 0.000 0.120
#> SRR1044500 2 0.0000 0.954 0.000 1.000 0.000 0.000
#> SRR1044501 2 0.1305 0.943 0.000 0.960 0.004 0.036
#> SRR1044502 2 0.1118 0.946 0.000 0.964 0.000 0.036
#> SRR1044503 4 0.4103 0.955 0.256 0.000 0.000 0.744
#> SRR1044504 4 0.4072 0.951 0.252 0.000 0.000 0.748
#> SRR1044505 1 0.1022 0.893 0.968 0.000 0.000 0.032
#> SRR1044506 4 0.4134 0.950 0.260 0.000 0.000 0.740
#> SRR1044507 4 0.4040 0.949 0.248 0.000 0.000 0.752
#> SRR1044508 4 0.3764 0.912 0.216 0.000 0.000 0.784
#> SRR1044509 4 0.3801 0.928 0.220 0.000 0.000 0.780
#> SRR1044510 3 0.1022 0.946 0.000 0.000 0.968 0.032
#> SRR1044511 3 0.1302 0.947 0.000 0.000 0.956 0.044
#> SRR1044512 3 0.1211 0.946 0.000 0.000 0.960 0.040
#> SRR1044513 2 0.1022 0.947 0.000 0.968 0.000 0.032
#> SRR1044514 3 0.1389 0.947 0.000 0.000 0.952 0.048
#> SRR1044515 2 0.0817 0.950 0.000 0.976 0.000 0.024
#> SRR1044516 2 0.0336 0.953 0.000 0.992 0.000 0.008
#> SRR1044517 3 0.1022 0.946 0.000 0.000 0.968 0.032
#> SRR1044518 3 0.1474 0.947 0.000 0.000 0.948 0.052
#> SRR1044519 3 0.3143 0.926 0.000 0.024 0.876 0.100
#> SRR1044520 3 0.2530 0.935 0.000 0.004 0.896 0.100
#> SRR1044521 2 0.0000 0.954 0.000 1.000 0.000 0.000
#> SRR1044522 2 0.5420 0.569 0.272 0.684 0.000 0.044
#> SRR1044523 2 0.0592 0.952 0.000 0.984 0.000 0.016
#> SRR1044524 2 0.5128 0.728 0.000 0.760 0.148 0.092
#> SRR1044525 4 0.4134 0.948 0.260 0.000 0.000 0.740
#> SRR1044526 1 0.4072 0.676 0.748 0.000 0.000 0.252
#> SRR1044527 2 0.0336 0.952 0.008 0.992 0.000 0.000
#> SRR1044528 2 0.0188 0.954 0.004 0.996 0.000 0.000
#> SRR1044529 2 0.1557 0.922 0.056 0.944 0.000 0.000
#> SRR1044530 1 0.2089 0.902 0.932 0.020 0.000 0.048
#> SRR1044531 1 0.1661 0.901 0.944 0.004 0.000 0.052
#> SRR1044533 1 0.1256 0.903 0.964 0.008 0.000 0.028
#> SRR1044532 1 0.2089 0.902 0.932 0.020 0.000 0.048
#> SRR1044534 2 0.0188 0.954 0.004 0.996 0.000 0.000
#> SRR1044535 2 0.2662 0.904 0.000 0.900 0.016 0.084
#> SRR1044536 2 0.0000 0.954 0.000 1.000 0.000 0.000
#> SRR1044537 1 0.2921 0.868 0.860 0.000 0.000 0.140
#> SRR1044538 1 0.2089 0.902 0.932 0.020 0.000 0.048
#> SRR1044539 4 0.3907 0.904 0.232 0.000 0.000 0.768
#> SRR1044540 1 0.0336 0.899 0.992 0.000 0.000 0.008
#> SRR1044541 2 0.2032 0.931 0.000 0.936 0.028 0.036
#> SRR1044542 1 0.2089 0.902 0.932 0.020 0.000 0.048
#> SRR1044543 1 0.1637 0.876 0.940 0.000 0.000 0.060
#> SRR1044544 2 0.3245 0.880 0.000 0.880 0.056 0.064
#> SRR1044545 4 0.3837 0.909 0.224 0.000 0.000 0.776
#> SRR1044546 1 0.3024 0.868 0.852 0.000 0.000 0.148
#> SRR1044547 4 0.4585 0.755 0.332 0.000 0.000 0.668
#> SRR1044548 1 0.3024 0.868 0.852 0.000 0.000 0.148
#> SRR1044549 2 0.0000 0.954 0.000 1.000 0.000 0.000
#> SRR1044550 2 0.0000 0.954 0.000 1.000 0.000 0.000
#> SRR1044551 2 0.0188 0.954 0.004 0.996 0.000 0.000
#> SRR1044552 4 0.4072 0.951 0.252 0.000 0.000 0.748
#> SRR1044553 4 0.4134 0.948 0.260 0.000 0.000 0.740
#> SRR1044554 1 0.2973 0.867 0.856 0.000 0.000 0.144
#> SRR1044555 3 0.2522 0.935 0.000 0.016 0.908 0.076
#> SRR1044556 4 0.4134 0.953 0.260 0.000 0.000 0.740
#> SRR1044557 1 0.2921 0.868 0.860 0.000 0.000 0.140
#> SRR1044558 4 0.3975 0.946 0.240 0.000 0.000 0.760
#> SRR1044559 1 0.3024 0.868 0.852 0.000 0.000 0.148
#> SRR1044561 4 0.4103 0.955 0.256 0.000 0.000 0.744
#> SRR1044560 2 0.1452 0.941 0.000 0.956 0.008 0.036
#> SRR1044562 1 0.3024 0.868 0.852 0.000 0.000 0.148
#> SRR1044563 4 0.3764 0.912 0.216 0.000 0.000 0.784
#> SRR1044564 1 0.2973 0.867 0.856 0.000 0.000 0.144
#> SRR1044565 2 0.2081 0.897 0.084 0.916 0.000 0.000
#> SRR1044566 2 0.1452 0.941 0.000 0.956 0.008 0.036
#> SRR1044567 1 0.1975 0.903 0.936 0.016 0.000 0.048
#> SRR1044568 4 0.4277 0.856 0.280 0.000 0.000 0.720
#> SRR1044569 1 0.0336 0.900 0.992 0.000 0.000 0.008
#> SRR1044570 1 0.2089 0.902 0.932 0.020 0.000 0.048
#> SRR1044571 1 0.1302 0.883 0.956 0.000 0.000 0.044
#> SRR1044572 1 0.1474 0.902 0.948 0.000 0.000 0.052
#> SRR1044573 1 0.0779 0.899 0.980 0.004 0.000 0.016
#> SRR1044574 1 0.1576 0.902 0.948 0.004 0.000 0.048
#> SRR1044575 1 0.0188 0.900 0.996 0.000 0.000 0.004
#> SRR1044576 2 0.0188 0.954 0.004 0.996 0.000 0.000
#> SRR1044577 2 0.0188 0.954 0.004 0.996 0.000 0.000
#> SRR1044578 2 0.1118 0.937 0.036 0.964 0.000 0.000
#> SRR1044579 4 0.4103 0.955 0.256 0.000 0.000 0.744
#> SRR1044580 1 0.4164 0.676 0.736 0.000 0.000 0.264
#> SRR1044581 4 0.4103 0.955 0.256 0.000 0.000 0.744
#> SRR1044582 1 0.2921 0.871 0.860 0.000 0.000 0.140
#> SRR1044583 4 0.4103 0.955 0.256 0.000 0.000 0.744
#> SRR1044584 4 0.4382 0.920 0.296 0.000 0.000 0.704
#> SRR1044585 4 0.4103 0.955 0.256 0.000 0.000 0.744
#> SRR1044586 1 0.2868 0.875 0.864 0.000 0.000 0.136
#> SRR1044587 4 0.4331 0.924 0.288 0.000 0.000 0.712
#> SRR1044588 4 0.4134 0.950 0.260 0.000 0.000 0.740
#> SRR1044589 4 0.4134 0.950 0.260 0.000 0.000 0.740
#> SRR1044590 4 0.4304 0.933 0.284 0.000 0.000 0.716
#> SRR1044591 4 0.4072 0.951 0.252 0.000 0.000 0.748
#> SRR1044592 4 0.3764 0.924 0.216 0.000 0.000 0.784
#> SRR1044593 4 0.4134 0.950 0.260 0.000 0.000 0.740
#> SRR1044594 4 0.4134 0.950 0.260 0.000 0.000 0.740
#> SRR1044595 4 0.4356 0.853 0.292 0.000 0.000 0.708
#> SRR1044596 4 0.4008 0.947 0.244 0.000 0.000 0.756
#> SRR1044597 1 0.2578 0.894 0.912 0.036 0.000 0.052
#> SRR1044598 1 0.2578 0.894 0.912 0.036 0.000 0.052
#> SRR1044599 1 0.2578 0.894 0.912 0.036 0.000 0.052
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.1270 0.885 0.000 0.948 0.000 0.000 NA
#> SRR1044416 2 0.1211 0.892 0.024 0.960 0.000 0.000 NA
#> SRR1044417 2 0.1701 0.884 0.048 0.936 0.000 0.000 NA
#> SRR1044418 2 0.2568 0.859 0.092 0.888 0.000 0.004 NA
#> SRR1044420 2 0.0162 0.897 0.000 0.996 0.000 0.000 NA
#> SRR1044419 2 0.1544 0.879 0.000 0.932 0.000 0.000 NA
#> SRR1044421 2 0.0290 0.896 0.000 0.992 0.000 0.000 NA
#> SRR1044422 2 0.0290 0.896 0.000 0.992 0.000 0.000 NA
#> SRR1044423 2 0.0510 0.895 0.000 0.984 0.000 0.000 NA
#> SRR1044424 2 0.0693 0.896 0.008 0.980 0.000 0.000 NA
#> SRR1044425 4 0.2563 0.832 0.120 0.000 0.000 0.872 NA
#> SRR1044426 1 0.6281 0.627 0.488 0.000 0.000 0.160 NA
#> SRR1044427 1 0.2890 0.805 0.836 0.000 0.000 0.160 NA
#> SRR1044428 1 0.5338 0.632 0.544 0.000 0.000 0.056 NA
#> SRR1044429 4 0.4805 0.410 0.312 0.000 0.000 0.648 NA
#> SRR1044430 1 0.4877 0.550 0.524 0.004 0.000 0.016 NA
#> SRR1044431 1 0.4647 0.785 0.736 0.000 0.000 0.092 NA
#> SRR1044433 4 0.2722 0.847 0.020 0.000 0.000 0.872 NA
#> SRR1044432 1 0.4867 0.586 0.544 0.000 0.000 0.024 NA
#> SRR1044434 4 0.0794 0.905 0.028 0.000 0.000 0.972 NA
#> SRR1044435 4 0.0609 0.906 0.020 0.000 0.000 0.980 NA
#> SRR1044436 4 0.1041 0.902 0.032 0.000 0.000 0.964 NA
#> SRR1044437 4 0.0609 0.906 0.020 0.000 0.000 0.980 NA
#> SRR1044439 4 0.0703 0.905 0.024 0.000 0.000 0.976 NA
#> SRR1044438 4 0.0794 0.906 0.028 0.000 0.000 0.972 NA
#> SRR1044440 4 0.0609 0.906 0.020 0.000 0.000 0.980 NA
#> SRR1044441 4 0.0510 0.906 0.016 0.000 0.000 0.984 NA
#> SRR1044442 4 0.2448 0.857 0.020 0.000 0.000 0.892 NA
#> SRR1044443 4 0.2873 0.839 0.020 0.000 0.000 0.860 NA
#> SRR1044444 4 0.0609 0.906 0.020 0.000 0.000 0.980 NA
#> SRR1044445 4 0.0771 0.897 0.020 0.000 0.000 0.976 NA
#> SRR1044446 3 0.6931 0.342 0.004 0.332 0.372 0.000 NA
#> SRR1044447 2 0.2179 0.858 0.000 0.888 0.000 0.000 NA
#> SRR1044449 3 0.1851 0.895 0.000 0.000 0.912 0.000 NA
#> SRR1044448 3 0.4262 0.856 0.004 0.012 0.696 0.000 NA
#> SRR1044450 3 0.4616 0.849 0.004 0.028 0.680 0.000 NA
#> SRR1044451 2 0.3088 0.810 0.004 0.828 0.004 0.000 NA
#> SRR1044452 3 0.0404 0.891 0.000 0.000 0.988 0.000 NA
#> SRR1044453 3 0.0404 0.891 0.000 0.000 0.988 0.000 NA
#> SRR1044454 3 0.0404 0.891 0.000 0.000 0.988 0.000 NA
#> SRR1044455 2 0.2127 0.858 0.000 0.892 0.000 0.000 NA
#> SRR1044456 1 0.5057 0.710 0.732 0.144 0.000 0.108 NA
#> SRR1044457 2 0.2127 0.858 0.000 0.892 0.000 0.000 NA
#> SRR1044458 2 0.2411 0.854 0.000 0.884 0.008 0.000 NA
#> SRR1044459 3 0.2605 0.887 0.000 0.000 0.852 0.000 NA
#> SRR1044460 2 0.0162 0.896 0.000 0.996 0.000 0.000 NA
#> SRR1044461 2 0.1197 0.887 0.000 0.952 0.000 0.000 NA
#> SRR1044462 1 0.5868 0.456 0.576 0.000 0.000 0.292 NA
#> SRR1044463 1 0.3170 0.810 0.852 0.016 0.000 0.120 NA
#> SRR1044464 4 0.5526 0.673 0.152 0.000 0.000 0.648 NA
#> SRR1044466 1 0.2984 0.808 0.856 0.016 0.000 0.124 NA
#> SRR1044465 1 0.4818 0.769 0.708 0.000 0.000 0.080 NA
#> SRR1044467 1 0.4987 0.758 0.684 0.000 0.000 0.080 NA
#> SRR1044468 2 0.0290 0.897 0.000 0.992 0.000 0.000 NA
#> SRR1044469 3 0.2230 0.883 0.000 0.000 0.884 0.000 NA
#> SRR1044470 1 0.2672 0.795 0.896 0.016 0.000 0.064 NA
#> SRR1044471 1 0.4757 0.773 0.716 0.000 0.000 0.080 NA
#> SRR1044472 1 0.3458 0.809 0.840 0.016 0.000 0.120 NA
#> SRR1044473 1 0.4605 0.778 0.732 0.000 0.000 0.076 NA
#> SRR1044474 2 0.3312 0.825 0.132 0.840 0.000 0.012 NA
#> SRR1044475 3 0.0703 0.890 0.000 0.000 0.976 0.000 NA
#> SRR1044476 2 0.2813 0.844 0.000 0.868 0.024 0.000 NA
#> SRR1044477 2 0.3774 0.804 0.140 0.816 0.000 0.028 NA
#> SRR1044478 2 0.0404 0.896 0.000 0.988 0.000 0.000 NA
#> SRR1044479 2 0.5610 0.298 0.400 0.540 0.000 0.044 NA
#> SRR1044480 4 0.4845 0.733 0.148 0.000 0.000 0.724 NA
#> SRR1044481 1 0.4300 0.768 0.772 0.000 0.000 0.132 NA
#> SRR1044482 2 0.2802 0.852 0.100 0.876 0.000 0.008 NA
#> SRR1044483 4 0.4723 0.747 0.136 0.000 0.000 0.736 NA
#> SRR1044484 1 0.4693 0.771 0.724 0.000 0.000 0.196 NA
#> SRR1044486 1 0.4407 0.789 0.768 0.012 0.000 0.168 NA
#> SRR1044485 2 0.0912 0.895 0.012 0.972 0.000 0.000 NA
#> SRR1044487 2 0.3856 0.800 0.140 0.812 0.000 0.032 NA
#> SRR1044488 2 0.0162 0.896 0.000 0.996 0.000 0.000 NA
#> SRR1044489 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA
#> SRR1044490 1 0.5610 0.757 0.640 0.000 0.000 0.176 NA
#> SRR1044491 1 0.2783 0.811 0.868 0.012 0.000 0.116 NA
#> SRR1044492 1 0.3073 0.807 0.856 0.024 0.000 0.116 NA
#> SRR1044493 1 0.2536 0.811 0.868 0.004 0.000 0.128 NA
#> SRR1044494 2 0.3644 0.812 0.136 0.824 0.000 0.024 NA
#> SRR1044496 2 0.3774 0.804 0.140 0.816 0.000 0.028 NA
#> SRR1044495 2 0.3774 0.804 0.140 0.816 0.000 0.028 NA
#> SRR1044497 4 0.0609 0.906 0.020 0.000 0.000 0.980 NA
#> SRR1044499 3 0.4351 0.819 0.000 0.100 0.768 0.000 NA
#> SRR1044498 1 0.4944 0.741 0.700 0.000 0.000 0.208 NA
#> SRR1044500 2 0.0290 0.897 0.000 0.992 0.000 0.000 NA
#> SRR1044501 2 0.2127 0.858 0.000 0.892 0.000 0.000 NA
#> SRR1044502 2 0.1270 0.887 0.000 0.948 0.000 0.000 NA
#> SRR1044503 4 0.0609 0.906 0.020 0.000 0.000 0.980 NA
#> SRR1044504 4 0.1197 0.897 0.048 0.000 0.000 0.952 NA
#> SRR1044505 1 0.4958 0.783 0.692 0.000 0.000 0.084 NA
#> SRR1044506 4 0.0955 0.903 0.028 0.000 0.000 0.968 NA
#> SRR1044507 4 0.2769 0.859 0.032 0.000 0.000 0.876 NA
#> SRR1044508 4 0.3064 0.845 0.036 0.000 0.000 0.856 NA
#> SRR1044509 4 0.2722 0.847 0.020 0.000 0.000 0.872 NA
#> SRR1044510 3 0.1502 0.888 0.004 0.000 0.940 0.000 NA
#> SRR1044511 3 0.2536 0.889 0.004 0.000 0.868 0.000 NA
#> SRR1044512 3 0.2439 0.889 0.004 0.000 0.876 0.000 NA
#> SRR1044513 2 0.1341 0.889 0.000 0.944 0.000 0.000 NA
#> SRR1044514 3 0.2629 0.889 0.004 0.000 0.860 0.000 NA
#> SRR1044515 2 0.1121 0.893 0.000 0.956 0.000 0.000 NA
#> SRR1044516 2 0.0510 0.895 0.000 0.984 0.000 0.000 NA
#> SRR1044517 3 0.1121 0.887 0.000 0.000 0.956 0.000 NA
#> SRR1044518 3 0.2674 0.888 0.004 0.000 0.856 0.000 NA
#> SRR1044519 3 0.4535 0.851 0.004 0.024 0.684 0.000 NA
#> SRR1044520 3 0.3790 0.864 0.004 0.000 0.724 0.000 NA
#> SRR1044521 2 0.0290 0.897 0.000 0.992 0.000 0.000 NA
#> SRR1044522 2 0.6046 0.330 0.356 0.544 0.000 0.084 NA
#> SRR1044523 2 0.0703 0.897 0.000 0.976 0.000 0.000 NA
#> SRR1044524 2 0.4707 0.672 0.000 0.708 0.064 0.000 NA
#> SRR1044525 4 0.1478 0.891 0.064 0.000 0.000 0.936 NA
#> SRR1044526 1 0.5785 0.555 0.560 0.000 0.000 0.332 NA
#> SRR1044527 2 0.2199 0.876 0.060 0.916 0.000 0.008 NA
#> SRR1044528 2 0.1386 0.891 0.032 0.952 0.000 0.000 NA
#> SRR1044529 2 0.3357 0.822 0.136 0.836 0.000 0.012 NA
#> SRR1044530 1 0.3155 0.808 0.848 0.016 0.000 0.128 NA
#> SRR1044531 1 0.4930 0.793 0.716 0.000 0.000 0.140 NA
#> SRR1044533 1 0.5068 0.785 0.708 0.004 0.000 0.108 NA
#> SRR1044532 1 0.3031 0.808 0.852 0.016 0.000 0.128 NA
#> SRR1044534 2 0.0798 0.895 0.008 0.976 0.000 0.000 NA
#> SRR1044535 2 0.3462 0.780 0.000 0.792 0.012 0.000 NA
#> SRR1044536 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA
#> SRR1044537 1 0.4017 0.734 0.800 0.004 0.000 0.068 NA
#> SRR1044538 1 0.3127 0.807 0.848 0.020 0.000 0.128 NA
#> SRR1044539 4 0.4591 0.757 0.132 0.000 0.000 0.748 NA
#> SRR1044540 1 0.5136 0.746 0.660 0.000 0.000 0.080 NA
#> SRR1044541 2 0.3141 0.834 0.000 0.852 0.040 0.000 NA
#> SRR1044542 1 0.3127 0.807 0.848 0.020 0.000 0.128 NA
#> SRR1044543 1 0.5781 0.670 0.552 0.000 0.000 0.104 NA
#> SRR1044544 2 0.4035 0.767 0.000 0.784 0.060 0.000 NA
#> SRR1044545 4 0.4723 0.745 0.136 0.000 0.000 0.736 NA
#> SRR1044546 1 0.4205 0.736 0.788 0.004 0.000 0.084 NA
#> SRR1044547 4 0.5796 0.507 0.284 0.000 0.000 0.588 NA
#> SRR1044548 1 0.4149 0.736 0.792 0.004 0.000 0.080 NA
#> SRR1044549 2 0.0798 0.895 0.008 0.976 0.000 0.000 NA
#> SRR1044550 2 0.0162 0.896 0.000 0.996 0.000 0.000 NA
#> SRR1044551 2 0.1018 0.894 0.016 0.968 0.000 0.000 NA
#> SRR1044552 4 0.1197 0.897 0.048 0.000 0.000 0.952 NA
#> SRR1044553 4 0.1270 0.896 0.052 0.000 0.000 0.948 NA
#> SRR1044554 1 0.4123 0.732 0.792 0.004 0.000 0.072 NA
#> SRR1044555 3 0.3977 0.861 0.000 0.032 0.764 0.000 NA
#> SRR1044556 4 0.0794 0.904 0.028 0.000 0.000 0.972 NA
#> SRR1044557 1 0.4137 0.733 0.792 0.004 0.000 0.076 NA
#> SRR1044558 4 0.2248 0.869 0.088 0.000 0.000 0.900 NA
#> SRR1044559 1 0.4194 0.734 0.788 0.004 0.000 0.080 NA
#> SRR1044561 4 0.0703 0.905 0.024 0.000 0.000 0.976 NA
#> SRR1044560 2 0.2813 0.844 0.000 0.868 0.024 0.000 NA
#> SRR1044562 1 0.4091 0.737 0.796 0.004 0.000 0.076 NA
#> SRR1044563 4 0.4164 0.786 0.120 0.000 0.000 0.784 NA
#> SRR1044564 1 0.4139 0.733 0.784 0.000 0.000 0.084 NA
#> SRR1044565 2 0.3730 0.808 0.136 0.820 0.000 0.028 NA
#> SRR1044566 2 0.2761 0.847 0.000 0.872 0.024 0.000 NA
#> SRR1044567 1 0.3031 0.808 0.852 0.016 0.000 0.128 NA
#> SRR1044568 4 0.5184 0.694 0.176 0.000 0.000 0.688 NA
#> SRR1044569 1 0.5211 0.757 0.668 0.000 0.000 0.100 NA
#> SRR1044570 1 0.3031 0.808 0.852 0.016 0.000 0.128 NA
#> SRR1044571 1 0.5368 0.689 0.596 0.000 0.000 0.072 NA
#> SRR1044572 1 0.5115 0.786 0.696 0.000 0.000 0.136 NA
#> SRR1044573 1 0.4800 0.776 0.716 0.000 0.000 0.088 NA
#> SRR1044574 1 0.4583 0.803 0.748 0.000 0.000 0.140 NA
#> SRR1044575 1 0.5013 0.756 0.680 0.000 0.000 0.080 NA
#> SRR1044576 2 0.1469 0.889 0.036 0.948 0.000 0.000 NA
#> SRR1044577 2 0.1774 0.883 0.052 0.932 0.000 0.000 NA
#> SRR1044578 2 0.3265 0.828 0.128 0.844 0.000 0.012 NA
#> SRR1044579 4 0.0609 0.906 0.020 0.000 0.000 0.980 NA
#> SRR1044580 1 0.5996 0.542 0.548 0.000 0.000 0.316 NA
#> SRR1044581 4 0.0609 0.906 0.020 0.000 0.000 0.980 NA
#> SRR1044582 1 0.3906 0.751 0.812 0.004 0.000 0.080 NA
#> SRR1044583 4 0.0609 0.906 0.020 0.000 0.000 0.980 NA
#> SRR1044584 4 0.1638 0.881 0.064 0.000 0.000 0.932 NA
#> SRR1044585 4 0.0609 0.906 0.020 0.000 0.000 0.980 NA
#> SRR1044586 1 0.4541 0.768 0.760 0.004 0.000 0.140 NA
#> SRR1044587 4 0.1357 0.894 0.048 0.000 0.000 0.948 NA
#> SRR1044588 4 0.0955 0.903 0.028 0.000 0.000 0.968 NA
#> SRR1044589 4 0.0771 0.903 0.020 0.000 0.000 0.976 NA
#> SRR1044590 4 0.1205 0.900 0.040 0.000 0.000 0.956 NA
#> SRR1044591 4 0.0566 0.901 0.012 0.000 0.000 0.984 NA
#> SRR1044592 4 0.2722 0.847 0.020 0.000 0.000 0.872 NA
#> SRR1044593 4 0.0955 0.903 0.028 0.000 0.000 0.968 NA
#> SRR1044594 4 0.0955 0.903 0.028 0.000 0.000 0.968 NA
#> SRR1044595 4 0.4679 0.716 0.136 0.000 0.000 0.740 NA
#> SRR1044596 4 0.2448 0.857 0.020 0.000 0.000 0.892 NA
#> SRR1044597 1 0.4139 0.790 0.804 0.052 0.000 0.124 NA
#> SRR1044598 1 0.3925 0.796 0.816 0.040 0.000 0.124 NA
#> SRR1044599 1 0.3925 0.796 0.816 0.040 0.000 0.124 NA
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.1970 0.6566 0.000 0.900 0.000 0.000 0.092 0.008
#> SRR1044416 2 0.2432 0.7104 0.024 0.876 0.000 0.000 0.100 0.000
#> SRR1044417 2 0.3720 0.6768 0.064 0.804 0.000 0.004 0.120 0.008
#> SRR1044418 2 0.4554 0.6317 0.116 0.744 0.000 0.012 0.120 0.008
#> SRR1044420 2 0.0000 0.7207 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044419 2 0.2257 0.6314 0.000 0.876 0.000 0.000 0.116 0.008
#> SRR1044421 2 0.0000 0.7207 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044422 2 0.0000 0.7207 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044423 2 0.0405 0.7175 0.000 0.988 0.000 0.000 0.004 0.008
#> SRR1044424 2 0.2255 0.7164 0.016 0.892 0.000 0.000 0.088 0.004
#> SRR1044425 4 0.3855 0.7246 0.048 0.004 0.000 0.812 0.040 0.096
#> SRR1044426 6 0.5918 0.4419 0.092 0.000 0.000 0.100 0.188 0.620
#> SRR1044427 1 0.6215 0.2816 0.544 0.004 0.000 0.108 0.056 0.288
#> SRR1044428 6 0.4706 0.4851 0.124 0.000 0.000 0.016 0.144 0.716
#> SRR1044429 4 0.5761 0.2644 0.196 0.000 0.000 0.576 0.016 0.212
#> SRR1044430 6 0.5945 0.2910 0.276 0.000 0.000 0.012 0.192 0.520
#> SRR1044431 6 0.4446 0.6342 0.348 0.000 0.000 0.040 0.000 0.612
#> SRR1044433 4 0.4200 0.7325 0.020 0.000 0.000 0.744 0.192 0.044
#> SRR1044432 6 0.5025 0.4328 0.128 0.000 0.000 0.008 0.204 0.660
#> SRR1044434 4 0.0717 0.8585 0.016 0.000 0.000 0.976 0.008 0.000
#> SRR1044435 4 0.0520 0.8614 0.008 0.000 0.000 0.984 0.008 0.000
#> SRR1044436 4 0.1411 0.8406 0.060 0.000 0.000 0.936 0.000 0.004
#> SRR1044437 4 0.0405 0.8612 0.004 0.000 0.000 0.988 0.008 0.000
#> SRR1044439 4 0.0363 0.8612 0.012 0.000 0.000 0.988 0.000 0.000
#> SRR1044438 4 0.0622 0.8601 0.012 0.000 0.000 0.980 0.008 0.000
#> SRR1044440 4 0.0405 0.8612 0.004 0.000 0.000 0.988 0.008 0.000
#> SRR1044441 4 0.0000 0.8610 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044442 4 0.3806 0.7685 0.024 0.000 0.000 0.792 0.144 0.040
#> SRR1044443 4 0.4234 0.7227 0.016 0.000 0.000 0.732 0.208 0.044
#> SRR1044444 4 0.0458 0.8602 0.016 0.000 0.000 0.984 0.000 0.000
#> SRR1044445 4 0.0767 0.8574 0.012 0.000 0.000 0.976 0.008 0.004
#> SRR1044446 5 0.6448 0.0000 0.000 0.304 0.260 0.000 0.416 0.020
#> SRR1044447 2 0.2697 0.5545 0.000 0.812 0.000 0.000 0.188 0.000
#> SRR1044449 3 0.2701 0.7290 0.004 0.000 0.864 0.000 0.104 0.028
#> SRR1044448 3 0.4879 0.4054 0.000 0.028 0.548 0.000 0.404 0.020
#> SRR1044450 3 0.5071 0.3582 0.000 0.040 0.532 0.000 0.408 0.020
#> SRR1044451 2 0.3429 0.3981 0.000 0.740 0.004 0.000 0.252 0.004
#> SRR1044452 3 0.0862 0.7416 0.004 0.000 0.972 0.000 0.008 0.016
#> SRR1044453 3 0.0862 0.7416 0.004 0.000 0.972 0.000 0.008 0.016
#> SRR1044454 3 0.0862 0.7416 0.004 0.000 0.972 0.000 0.008 0.016
#> SRR1044455 2 0.2980 0.5274 0.000 0.800 0.000 0.000 0.192 0.008
#> SRR1044456 1 0.8073 0.2339 0.424 0.180 0.000 0.076 0.124 0.196
#> SRR1044457 2 0.2980 0.5274 0.000 0.800 0.000 0.000 0.192 0.008
#> SRR1044458 2 0.3121 0.5211 0.000 0.796 0.004 0.000 0.192 0.008
#> SRR1044459 3 0.3429 0.6118 0.000 0.004 0.740 0.000 0.252 0.004
#> SRR1044460 2 0.0260 0.7201 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1044461 2 0.1918 0.6606 0.000 0.904 0.000 0.000 0.088 0.008
#> SRR1044462 1 0.3281 0.2997 0.784 0.000 0.000 0.200 0.004 0.012
#> SRR1044463 1 0.6306 0.3317 0.544 0.012 0.000 0.072 0.076 0.296
#> SRR1044464 4 0.6631 0.4377 0.252 0.000 0.000 0.504 0.076 0.168
#> SRR1044466 1 0.6472 0.3667 0.548 0.016 0.000 0.076 0.088 0.272
#> SRR1044465 6 0.4181 0.6545 0.328 0.000 0.000 0.028 0.000 0.644
#> SRR1044467 6 0.4170 0.6650 0.308 0.000 0.000 0.032 0.000 0.660
#> SRR1044468 2 0.0146 0.7189 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1044469 3 0.3329 0.6164 0.004 0.000 0.768 0.000 0.220 0.008
#> SRR1044470 1 0.5728 0.3666 0.624 0.008 0.000 0.072 0.056 0.240
#> SRR1044471 6 0.4249 0.6535 0.328 0.000 0.000 0.032 0.000 0.640
#> SRR1044472 1 0.6557 0.3233 0.524 0.016 0.000 0.076 0.088 0.296
#> SRR1044473 6 0.4292 0.6427 0.340 0.000 0.000 0.032 0.000 0.628
#> SRR1044474 2 0.5381 0.5810 0.140 0.688 0.000 0.036 0.124 0.012
#> SRR1044475 3 0.1148 0.7384 0.004 0.000 0.960 0.000 0.020 0.016
#> SRR1044476 2 0.3328 0.5081 0.000 0.788 0.012 0.000 0.192 0.008
#> SRR1044477 2 0.5481 0.5713 0.144 0.680 0.000 0.040 0.124 0.012
#> SRR1044478 2 0.0291 0.7180 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1044479 2 0.7141 0.2151 0.316 0.460 0.000 0.052 0.124 0.048
#> SRR1044480 4 0.4103 0.4393 0.448 0.000 0.000 0.544 0.004 0.004
#> SRR1044481 1 0.3274 0.4517 0.824 0.000 0.000 0.096 0.000 0.080
#> SRR1044482 2 0.4649 0.6297 0.112 0.740 0.000 0.012 0.124 0.012
#> SRR1044483 4 0.4285 0.4558 0.432 0.000 0.000 0.552 0.008 0.008
#> SRR1044484 1 0.4271 0.4555 0.768 0.000 0.000 0.120 0.028 0.084
#> SRR1044486 1 0.5105 0.4364 0.700 0.000 0.000 0.096 0.052 0.152
#> SRR1044485 2 0.2070 0.7145 0.008 0.892 0.000 0.000 0.100 0.000
#> SRR1044487 2 0.5446 0.5767 0.140 0.684 0.000 0.040 0.124 0.012
#> SRR1044488 2 0.0363 0.7235 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR1044489 2 0.0146 0.7220 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1044490 6 0.5876 0.5114 0.320 0.000 0.000 0.136 0.020 0.524
#> SRR1044491 1 0.6319 0.3332 0.544 0.008 0.000 0.084 0.076 0.288
#> SRR1044492 1 0.6617 0.3835 0.552 0.024 0.000 0.076 0.096 0.252
#> SRR1044493 1 0.6365 0.3582 0.552 0.012 0.000 0.080 0.080 0.276
#> SRR1044494 2 0.5446 0.5767 0.140 0.684 0.000 0.040 0.124 0.012
#> SRR1044496 2 0.5446 0.5767 0.140 0.684 0.000 0.040 0.124 0.012
#> SRR1044495 2 0.5446 0.5767 0.140 0.684 0.000 0.040 0.124 0.012
#> SRR1044497 4 0.0146 0.8608 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044499 3 0.5242 0.2203 0.000 0.136 0.628 0.000 0.228 0.008
#> SRR1044498 1 0.4234 0.3993 0.744 0.000 0.000 0.152 0.004 0.100
#> SRR1044500 2 0.0547 0.7236 0.000 0.980 0.000 0.000 0.020 0.000
#> SRR1044501 2 0.2980 0.5274 0.000 0.800 0.000 0.000 0.192 0.008
#> SRR1044502 2 0.1644 0.6807 0.004 0.920 0.000 0.000 0.076 0.000
#> SRR1044503 4 0.0405 0.8612 0.004 0.000 0.000 0.988 0.008 0.000
#> SRR1044504 4 0.1049 0.8530 0.032 0.000 0.000 0.960 0.008 0.000
#> SRR1044505 1 0.4814 -0.4145 0.504 0.000 0.000 0.036 0.008 0.452
#> SRR1044506 4 0.0717 0.8561 0.016 0.000 0.000 0.976 0.008 0.000
#> SRR1044507 4 0.3811 0.7801 0.036 0.000 0.000 0.796 0.136 0.032
#> SRR1044508 4 0.4493 0.7276 0.036 0.000 0.000 0.728 0.192 0.044
#> SRR1044509 4 0.4200 0.7325 0.020 0.000 0.000 0.744 0.192 0.044
#> SRR1044510 3 0.1552 0.7352 0.004 0.000 0.940 0.000 0.036 0.020
#> SRR1044511 3 0.2182 0.7347 0.004 0.000 0.900 0.000 0.076 0.020
#> SRR1044512 3 0.2126 0.7346 0.004 0.000 0.904 0.000 0.072 0.020
#> SRR1044513 2 0.1387 0.6909 0.000 0.932 0.000 0.000 0.068 0.000
#> SRR1044514 3 0.2540 0.7288 0.004 0.000 0.872 0.000 0.104 0.020
#> SRR1044515 2 0.1267 0.6964 0.000 0.940 0.000 0.000 0.060 0.000
#> SRR1044516 2 0.0146 0.7189 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1044517 3 0.1320 0.7356 0.000 0.000 0.948 0.000 0.036 0.016
#> SRR1044518 3 0.2730 0.7264 0.004 0.004 0.864 0.000 0.108 0.020
#> SRR1044519 3 0.4984 0.4019 0.000 0.036 0.552 0.000 0.392 0.020
#> SRR1044520 3 0.4698 0.4563 0.000 0.020 0.576 0.000 0.384 0.020
#> SRR1044521 2 0.1010 0.7245 0.004 0.960 0.000 0.000 0.036 0.000
#> SRR1044522 2 0.7174 0.2843 0.260 0.500 0.000 0.064 0.124 0.052
#> SRR1044523 2 0.0458 0.7183 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1044524 2 0.4289 -0.0542 0.000 0.612 0.028 0.000 0.360 0.000
#> SRR1044525 4 0.1268 0.8496 0.036 0.000 0.000 0.952 0.008 0.004
#> SRR1044526 1 0.4235 0.2654 0.672 0.000 0.000 0.296 0.012 0.020
#> SRR1044527 2 0.4187 0.6613 0.076 0.780 0.000 0.012 0.120 0.012
#> SRR1044528 2 0.3501 0.6899 0.036 0.828 0.000 0.012 0.112 0.012
#> SRR1044529 2 0.5314 0.5853 0.140 0.692 0.000 0.032 0.124 0.012
#> SRR1044530 1 0.6500 0.3698 0.548 0.016 0.000 0.080 0.088 0.268
#> SRR1044531 6 0.6155 0.3052 0.400 0.004 0.000 0.092 0.044 0.460
#> SRR1044533 6 0.5556 0.5196 0.324 0.000 0.000 0.072 0.036 0.568
#> SRR1044532 1 0.6507 0.3795 0.552 0.016 0.000 0.080 0.092 0.260
#> SRR1044534 2 0.2699 0.7061 0.020 0.864 0.000 0.000 0.108 0.008
#> SRR1044535 2 0.3819 0.1072 0.000 0.652 0.008 0.000 0.340 0.000
#> SRR1044536 2 0.0146 0.7220 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1044537 1 0.1692 0.4375 0.932 0.000 0.000 0.048 0.008 0.012
#> SRR1044538 1 0.6507 0.3795 0.552 0.016 0.000 0.080 0.092 0.260
#> SRR1044539 4 0.4070 0.4787 0.424 0.000 0.000 0.568 0.004 0.004
#> SRR1044540 6 0.4525 0.6581 0.276 0.000 0.000 0.032 0.020 0.672
#> SRR1044541 2 0.3230 0.5148 0.000 0.792 0.008 0.000 0.192 0.008
#> SRR1044542 1 0.6540 0.3777 0.552 0.020 0.000 0.076 0.092 0.260
#> SRR1044543 6 0.4171 0.5677 0.132 0.000 0.000 0.044 0.048 0.776
#> SRR1044544 2 0.4374 0.2169 0.000 0.680 0.040 0.000 0.272 0.008
#> SRR1044545 4 0.3966 0.4535 0.444 0.000 0.000 0.552 0.004 0.000
#> SRR1044546 1 0.1219 0.4483 0.948 0.000 0.000 0.048 0.000 0.004
#> SRR1044547 1 0.4098 -0.2272 0.548 0.000 0.000 0.444 0.004 0.004
#> SRR1044548 1 0.1434 0.4499 0.940 0.000 0.000 0.048 0.000 0.012
#> SRR1044549 2 0.1707 0.7222 0.012 0.928 0.000 0.000 0.056 0.004
#> SRR1044550 2 0.0000 0.7207 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044551 2 0.2812 0.7049 0.028 0.860 0.000 0.000 0.104 0.008
#> SRR1044552 4 0.1049 0.8530 0.032 0.000 0.000 0.960 0.008 0.000
#> SRR1044553 4 0.1049 0.8530 0.032 0.000 0.000 0.960 0.008 0.000
#> SRR1044554 1 0.1692 0.4369 0.932 0.000 0.000 0.048 0.008 0.012
#> SRR1044555 3 0.5144 0.1978 0.000 0.100 0.560 0.000 0.340 0.000
#> SRR1044556 4 0.0260 0.8610 0.008 0.000 0.000 0.992 0.000 0.000
#> SRR1044557 1 0.1477 0.4418 0.940 0.000 0.000 0.048 0.008 0.004
#> SRR1044558 4 0.1327 0.8407 0.064 0.000 0.000 0.936 0.000 0.000
#> SRR1044559 1 0.1219 0.4443 0.948 0.000 0.000 0.048 0.004 0.000
#> SRR1044561 4 0.0260 0.8614 0.008 0.000 0.000 0.992 0.000 0.000
#> SRR1044560 2 0.3328 0.5081 0.000 0.788 0.012 0.000 0.192 0.008
#> SRR1044562 1 0.1219 0.4483 0.948 0.000 0.000 0.048 0.000 0.004
#> SRR1044563 4 0.3728 0.5891 0.344 0.000 0.000 0.652 0.004 0.000
#> SRR1044564 1 0.2036 0.4250 0.912 0.000 0.000 0.064 0.008 0.016
#> SRR1044565 2 0.5446 0.5767 0.140 0.684 0.000 0.040 0.124 0.012
#> SRR1044566 2 0.3264 0.5226 0.000 0.796 0.012 0.000 0.184 0.008
#> SRR1044567 1 0.6408 0.3827 0.560 0.012 0.000 0.080 0.092 0.256
#> SRR1044568 4 0.4488 0.3658 0.468 0.000 0.000 0.508 0.008 0.016
#> SRR1044569 6 0.4601 0.6644 0.308 0.000 0.000 0.044 0.008 0.640
#> SRR1044570 1 0.6507 0.3795 0.552 0.016 0.000 0.080 0.092 0.260
#> SRR1044571 6 0.4130 0.6050 0.180 0.000 0.000 0.028 0.036 0.756
#> SRR1044572 6 0.5489 0.5000 0.340 0.000 0.000 0.124 0.004 0.532
#> SRR1044573 6 0.4344 0.6464 0.336 0.000 0.000 0.036 0.000 0.628
#> SRR1044574 6 0.6066 0.3145 0.404 0.004 0.000 0.108 0.028 0.456
#> SRR1044575 6 0.4323 0.6648 0.312 0.000 0.000 0.032 0.004 0.652
#> SRR1044576 2 0.3339 0.6881 0.048 0.824 0.000 0.000 0.120 0.008
#> SRR1044577 2 0.3870 0.6749 0.060 0.800 0.000 0.008 0.120 0.012
#> SRR1044578 2 0.5314 0.5853 0.140 0.692 0.000 0.032 0.124 0.012
#> SRR1044579 4 0.0291 0.8613 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044580 1 0.4368 0.2554 0.672 0.000 0.000 0.272 0.000 0.056
#> SRR1044581 4 0.0146 0.8608 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044582 1 0.2278 0.4535 0.900 0.000 0.000 0.052 0.004 0.044
#> SRR1044583 4 0.0146 0.8608 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044584 4 0.1500 0.8365 0.052 0.000 0.000 0.936 0.000 0.012
#> SRR1044585 4 0.0146 0.8608 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044586 1 0.3189 0.4656 0.840 0.000 0.000 0.096 0.008 0.056
#> SRR1044587 4 0.1116 0.8491 0.028 0.000 0.000 0.960 0.008 0.004
#> SRR1044588 4 0.0717 0.8561 0.016 0.000 0.000 0.976 0.008 0.000
#> SRR1044589 4 0.0717 0.8561 0.016 0.000 0.000 0.976 0.008 0.000
#> SRR1044590 4 0.1370 0.8388 0.036 0.004 0.000 0.948 0.012 0.000
#> SRR1044591 4 0.0622 0.8576 0.012 0.000 0.000 0.980 0.008 0.000
#> SRR1044592 4 0.4200 0.7325 0.020 0.000 0.000 0.744 0.192 0.044
#> SRR1044593 4 0.0717 0.8561 0.016 0.000 0.000 0.976 0.008 0.000
#> SRR1044594 4 0.0717 0.8561 0.016 0.000 0.000 0.976 0.008 0.000
#> SRR1044595 4 0.5903 0.6063 0.160 0.000 0.000 0.604 0.188 0.048
#> SRR1044596 4 0.3806 0.7685 0.024 0.000 0.000 0.792 0.144 0.040
#> SRR1044597 1 0.7188 0.3608 0.524 0.056 0.000 0.076 0.124 0.220
#> SRR1044598 1 0.7011 0.3703 0.532 0.040 0.000 0.076 0.124 0.228
#> SRR1044599 1 0.7011 0.3703 0.532 0.040 0.000 0.076 0.124 0.228
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.980 0.992 0.4881 0.510 0.510
#> 3 3 0.807 0.875 0.937 0.3193 0.766 0.570
#> 4 4 0.831 0.884 0.933 0.1566 0.783 0.467
#> 5 5 0.756 0.693 0.789 0.0581 0.954 0.825
#> 6 6 0.788 0.773 0.803 0.0449 0.906 0.615
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0.000 0.9809 0.000 1.000
#> SRR1044416 2 0.000 0.9809 0.000 1.000
#> SRR1044417 2 0.000 0.9809 0.000 1.000
#> SRR1044418 2 0.000 0.9809 0.000 1.000
#> SRR1044420 2 0.000 0.9809 0.000 1.000
#> SRR1044419 2 0.000 0.9809 0.000 1.000
#> SRR1044421 2 0.000 0.9809 0.000 1.000
#> SRR1044422 2 0.000 0.9809 0.000 1.000
#> SRR1044423 2 0.000 0.9809 0.000 1.000
#> SRR1044424 2 0.000 0.9809 0.000 1.000
#> SRR1044425 1 0.000 0.9992 1.000 0.000
#> SRR1044426 1 0.000 0.9992 1.000 0.000
#> SRR1044427 1 0.000 0.9992 1.000 0.000
#> SRR1044428 1 0.000 0.9992 1.000 0.000
#> SRR1044429 1 0.000 0.9992 1.000 0.000
#> SRR1044430 1 0.000 0.9992 1.000 0.000
#> SRR1044431 1 0.000 0.9992 1.000 0.000
#> SRR1044433 1 0.000 0.9992 1.000 0.000
#> SRR1044432 1 0.000 0.9992 1.000 0.000
#> SRR1044434 1 0.000 0.9992 1.000 0.000
#> SRR1044435 1 0.000 0.9992 1.000 0.000
#> SRR1044436 1 0.000 0.9992 1.000 0.000
#> SRR1044437 1 0.000 0.9992 1.000 0.000
#> SRR1044439 1 0.000 0.9992 1.000 0.000
#> SRR1044438 1 0.000 0.9992 1.000 0.000
#> SRR1044440 1 0.000 0.9992 1.000 0.000
#> SRR1044441 1 0.000 0.9992 1.000 0.000
#> SRR1044442 1 0.000 0.9992 1.000 0.000
#> SRR1044443 1 0.184 0.9707 0.972 0.028
#> SRR1044444 1 0.000 0.9992 1.000 0.000
#> SRR1044445 1 0.000 0.9992 1.000 0.000
#> SRR1044446 2 0.000 0.9809 0.000 1.000
#> SRR1044447 2 0.000 0.9809 0.000 1.000
#> SRR1044449 2 0.000 0.9809 0.000 1.000
#> SRR1044448 2 0.000 0.9809 0.000 1.000
#> SRR1044450 2 0.000 0.9809 0.000 1.000
#> SRR1044451 2 0.000 0.9809 0.000 1.000
#> SRR1044452 2 0.000 0.9809 0.000 1.000
#> SRR1044453 2 0.000 0.9809 0.000 1.000
#> SRR1044454 2 0.000 0.9809 0.000 1.000
#> SRR1044455 2 0.000 0.9809 0.000 1.000
#> SRR1044456 1 0.311 0.9390 0.944 0.056
#> SRR1044457 2 0.000 0.9809 0.000 1.000
#> SRR1044458 2 0.000 0.9809 0.000 1.000
#> SRR1044459 2 0.000 0.9809 0.000 1.000
#> SRR1044460 2 0.000 0.9809 0.000 1.000
#> SRR1044461 2 0.000 0.9809 0.000 1.000
#> SRR1044462 1 0.000 0.9992 1.000 0.000
#> SRR1044463 1 0.000 0.9992 1.000 0.000
#> SRR1044464 1 0.000 0.9992 1.000 0.000
#> SRR1044466 1 0.000 0.9992 1.000 0.000
#> SRR1044465 1 0.000 0.9992 1.000 0.000
#> SRR1044467 1 0.000 0.9992 1.000 0.000
#> SRR1044468 2 0.000 0.9809 0.000 1.000
#> SRR1044469 2 0.000 0.9809 0.000 1.000
#> SRR1044470 1 0.000 0.9992 1.000 0.000
#> SRR1044471 1 0.000 0.9992 1.000 0.000
#> SRR1044472 1 0.000 0.9992 1.000 0.000
#> SRR1044473 1 0.000 0.9992 1.000 0.000
#> SRR1044474 2 0.260 0.9455 0.044 0.956
#> SRR1044475 2 0.000 0.9809 0.000 1.000
#> SRR1044476 2 0.000 0.9809 0.000 1.000
#> SRR1044477 2 0.443 0.8993 0.092 0.908
#> SRR1044478 2 0.000 0.9809 0.000 1.000
#> SRR1044479 2 1.000 0.0663 0.492 0.508
#> SRR1044480 1 0.000 0.9992 1.000 0.000
#> SRR1044481 1 0.000 0.9992 1.000 0.000
#> SRR1044482 2 0.000 0.9809 0.000 1.000
#> SRR1044483 1 0.000 0.9992 1.000 0.000
#> SRR1044484 1 0.000 0.9992 1.000 0.000
#> SRR1044486 1 0.000 0.9992 1.000 0.000
#> SRR1044485 2 0.000 0.9809 0.000 1.000
#> SRR1044487 2 0.529 0.8674 0.120 0.880
#> SRR1044488 2 0.000 0.9809 0.000 1.000
#> SRR1044489 2 0.000 0.9809 0.000 1.000
#> SRR1044490 1 0.000 0.9992 1.000 0.000
#> SRR1044491 1 0.000 0.9992 1.000 0.000
#> SRR1044492 1 0.000 0.9992 1.000 0.000
#> SRR1044493 1 0.000 0.9992 1.000 0.000
#> SRR1044494 2 0.343 0.9272 0.064 0.936
#> SRR1044496 2 0.443 0.8994 0.092 0.908
#> SRR1044495 2 0.456 0.8950 0.096 0.904
#> SRR1044497 1 0.000 0.9992 1.000 0.000
#> SRR1044499 2 0.000 0.9809 0.000 1.000
#> SRR1044498 1 0.000 0.9992 1.000 0.000
#> SRR1044500 2 0.000 0.9809 0.000 1.000
#> SRR1044501 2 0.000 0.9809 0.000 1.000
#> SRR1044502 2 0.000 0.9809 0.000 1.000
#> SRR1044503 1 0.000 0.9992 1.000 0.000
#> SRR1044504 1 0.000 0.9992 1.000 0.000
#> SRR1044505 1 0.000 0.9992 1.000 0.000
#> SRR1044506 1 0.000 0.9992 1.000 0.000
#> SRR1044507 1 0.000 0.9992 1.000 0.000
#> SRR1044508 1 0.000 0.9992 1.000 0.000
#> SRR1044509 1 0.000 0.9992 1.000 0.000
#> SRR1044510 2 0.000 0.9809 0.000 1.000
#> SRR1044511 2 0.000 0.9809 0.000 1.000
#> SRR1044512 2 0.000 0.9809 0.000 1.000
#> SRR1044513 2 0.000 0.9809 0.000 1.000
#> SRR1044514 2 0.000 0.9809 0.000 1.000
#> SRR1044515 2 0.000 0.9809 0.000 1.000
#> SRR1044516 2 0.000 0.9809 0.000 1.000
#> SRR1044517 2 0.000 0.9809 0.000 1.000
#> SRR1044518 2 0.000 0.9809 0.000 1.000
#> SRR1044519 2 0.000 0.9809 0.000 1.000
#> SRR1044520 2 0.000 0.9809 0.000 1.000
#> SRR1044521 2 0.000 0.9809 0.000 1.000
#> SRR1044522 2 0.932 0.4890 0.348 0.652
#> SRR1044523 2 0.000 0.9809 0.000 1.000
#> SRR1044524 2 0.000 0.9809 0.000 1.000
#> SRR1044525 1 0.000 0.9992 1.000 0.000
#> SRR1044526 1 0.000 0.9992 1.000 0.000
#> SRR1044527 2 0.000 0.9809 0.000 1.000
#> SRR1044528 2 0.000 0.9809 0.000 1.000
#> SRR1044529 2 0.224 0.9524 0.036 0.964
#> SRR1044530 1 0.000 0.9992 1.000 0.000
#> SRR1044531 1 0.000 0.9992 1.000 0.000
#> SRR1044533 1 0.000 0.9992 1.000 0.000
#> SRR1044532 1 0.000 0.9992 1.000 0.000
#> SRR1044534 2 0.000 0.9809 0.000 1.000
#> SRR1044535 2 0.000 0.9809 0.000 1.000
#> SRR1044536 2 0.000 0.9809 0.000 1.000
#> SRR1044537 1 0.000 0.9992 1.000 0.000
#> SRR1044538 1 0.000 0.9992 1.000 0.000
#> SRR1044539 1 0.000 0.9992 1.000 0.000
#> SRR1044540 1 0.000 0.9992 1.000 0.000
#> SRR1044541 2 0.000 0.9809 0.000 1.000
#> SRR1044542 1 0.000 0.9992 1.000 0.000
#> SRR1044543 1 0.000 0.9992 1.000 0.000
#> SRR1044544 2 0.000 0.9809 0.000 1.000
#> SRR1044545 1 0.000 0.9992 1.000 0.000
#> SRR1044546 1 0.000 0.9992 1.000 0.000
#> SRR1044547 1 0.000 0.9992 1.000 0.000
#> SRR1044548 1 0.000 0.9992 1.000 0.000
#> SRR1044549 2 0.000 0.9809 0.000 1.000
#> SRR1044550 2 0.000 0.9809 0.000 1.000
#> SRR1044551 2 0.000 0.9809 0.000 1.000
#> SRR1044552 1 0.000 0.9992 1.000 0.000
#> SRR1044553 1 0.000 0.9992 1.000 0.000
#> SRR1044554 1 0.000 0.9992 1.000 0.000
#> SRR1044555 2 0.000 0.9809 0.000 1.000
#> SRR1044556 1 0.000 0.9992 1.000 0.000
#> SRR1044557 1 0.000 0.9992 1.000 0.000
#> SRR1044558 1 0.000 0.9992 1.000 0.000
#> SRR1044559 1 0.000 0.9992 1.000 0.000
#> SRR1044561 1 0.000 0.9992 1.000 0.000
#> SRR1044560 2 0.000 0.9809 0.000 1.000
#> SRR1044562 1 0.000 0.9992 1.000 0.000
#> SRR1044563 1 0.000 0.9992 1.000 0.000
#> SRR1044564 1 0.000 0.9992 1.000 0.000
#> SRR1044565 2 0.373 0.9196 0.072 0.928
#> SRR1044566 2 0.000 0.9809 0.000 1.000
#> SRR1044567 1 0.000 0.9992 1.000 0.000
#> SRR1044568 1 0.000 0.9992 1.000 0.000
#> SRR1044569 1 0.000 0.9992 1.000 0.000
#> SRR1044570 1 0.000 0.9992 1.000 0.000
#> SRR1044571 1 0.000 0.9992 1.000 0.000
#> SRR1044572 1 0.000 0.9992 1.000 0.000
#> SRR1044573 1 0.000 0.9992 1.000 0.000
#> SRR1044574 1 0.000 0.9992 1.000 0.000
#> SRR1044575 1 0.000 0.9992 1.000 0.000
#> SRR1044576 2 0.000 0.9809 0.000 1.000
#> SRR1044577 2 0.000 0.9809 0.000 1.000
#> SRR1044578 2 0.118 0.9686 0.016 0.984
#> SRR1044579 1 0.000 0.9992 1.000 0.000
#> SRR1044580 1 0.000 0.9992 1.000 0.000
#> SRR1044581 1 0.000 0.9992 1.000 0.000
#> SRR1044582 1 0.000 0.9992 1.000 0.000
#> SRR1044583 1 0.000 0.9992 1.000 0.000
#> SRR1044584 1 0.000 0.9992 1.000 0.000
#> SRR1044585 1 0.000 0.9992 1.000 0.000
#> SRR1044586 1 0.000 0.9992 1.000 0.000
#> SRR1044587 1 0.000 0.9992 1.000 0.000
#> SRR1044588 1 0.000 0.9992 1.000 0.000
#> SRR1044589 1 0.000 0.9992 1.000 0.000
#> SRR1044590 1 0.000 0.9992 1.000 0.000
#> SRR1044591 1 0.000 0.9992 1.000 0.000
#> SRR1044592 1 0.000 0.9992 1.000 0.000
#> SRR1044593 1 0.000 0.9992 1.000 0.000
#> SRR1044594 1 0.000 0.9992 1.000 0.000
#> SRR1044595 1 0.000 0.9992 1.000 0.000
#> SRR1044596 1 0.000 0.9992 1.000 0.000
#> SRR1044597 1 0.000 0.9992 1.000 0.000
#> SRR1044598 1 0.000 0.9992 1.000 0.000
#> SRR1044599 1 0.000 0.9992 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044416 3 0.1964 0.794 0.000 0.056 0.944
#> SRR1044417 3 0.0424 0.820 0.000 0.008 0.992
#> SRR1044418 3 0.0000 0.825 0.000 0.000 1.000
#> SRR1044420 2 0.2796 0.917 0.000 0.908 0.092
#> SRR1044419 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044421 2 0.1163 0.957 0.000 0.972 0.028
#> SRR1044422 2 0.1411 0.953 0.000 0.964 0.036
#> SRR1044423 2 0.2448 0.930 0.000 0.924 0.076
#> SRR1044424 3 0.6307 -0.151 0.000 0.488 0.512
#> SRR1044425 1 0.2066 0.914 0.940 0.000 0.060
#> SRR1044426 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044427 1 0.4452 0.770 0.808 0.000 0.192
#> SRR1044428 1 0.3686 0.829 0.860 0.000 0.140
#> SRR1044429 1 0.0237 0.960 0.996 0.000 0.004
#> SRR1044430 1 0.5109 0.705 0.780 0.008 0.212
#> SRR1044431 1 0.1643 0.934 0.956 0.000 0.044
#> SRR1044433 1 0.0592 0.952 0.988 0.012 0.000
#> SRR1044432 1 0.2448 0.905 0.924 0.000 0.076
#> SRR1044434 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044435 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044436 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044437 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044439 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044438 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044440 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044441 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044442 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044443 1 0.1860 0.910 0.948 0.052 0.000
#> SRR1044444 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044445 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044446 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044447 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044449 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044448 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044450 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044451 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044452 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044453 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044454 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044455 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044456 3 0.0424 0.827 0.008 0.000 0.992
#> SRR1044457 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044458 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044459 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044460 2 0.2448 0.929 0.000 0.924 0.076
#> SRR1044461 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044462 1 0.0237 0.960 0.996 0.000 0.004
#> SRR1044463 3 0.4555 0.767 0.200 0.000 0.800
#> SRR1044464 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044466 3 0.3619 0.810 0.136 0.000 0.864
#> SRR1044465 1 0.1643 0.936 0.956 0.000 0.044
#> SRR1044467 1 0.1753 0.932 0.952 0.000 0.048
#> SRR1044468 2 0.2356 0.932 0.000 0.928 0.072
#> SRR1044469 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044470 3 0.5058 0.727 0.244 0.000 0.756
#> SRR1044471 1 0.1031 0.950 0.976 0.000 0.024
#> SRR1044472 3 0.3686 0.808 0.140 0.000 0.860
#> SRR1044473 1 0.5988 0.326 0.632 0.000 0.368
#> SRR1044474 3 0.0000 0.825 0.000 0.000 1.000
#> SRR1044475 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044476 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044477 3 0.0000 0.825 0.000 0.000 1.000
#> SRR1044478 2 0.1529 0.951 0.000 0.960 0.040
#> SRR1044479 3 0.0000 0.825 0.000 0.000 1.000
#> SRR1044480 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044481 1 0.2878 0.886 0.904 0.000 0.096
#> SRR1044482 3 0.0000 0.825 0.000 0.000 1.000
#> SRR1044483 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044484 1 0.3340 0.857 0.880 0.000 0.120
#> SRR1044486 3 0.5363 0.691 0.276 0.000 0.724
#> SRR1044485 3 0.2796 0.759 0.000 0.092 0.908
#> SRR1044487 3 0.0000 0.825 0.000 0.000 1.000
#> SRR1044488 2 0.3116 0.903 0.000 0.892 0.108
#> SRR1044489 2 0.2537 0.926 0.000 0.920 0.080
#> SRR1044490 1 0.0592 0.957 0.988 0.000 0.012
#> SRR1044491 3 0.4702 0.756 0.212 0.000 0.788
#> SRR1044492 3 0.2356 0.828 0.072 0.000 0.928
#> SRR1044493 3 0.4452 0.772 0.192 0.000 0.808
#> SRR1044494 3 0.0000 0.825 0.000 0.000 1.000
#> SRR1044496 3 0.0000 0.825 0.000 0.000 1.000
#> SRR1044495 3 0.0000 0.825 0.000 0.000 1.000
#> SRR1044497 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044499 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044498 1 0.0237 0.960 0.996 0.000 0.004
#> SRR1044500 2 0.2537 0.926 0.000 0.920 0.080
#> SRR1044501 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044502 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044503 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044504 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044505 1 0.3116 0.871 0.892 0.000 0.108
#> SRR1044506 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044507 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044508 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044509 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044510 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044511 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044512 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044513 2 0.0424 0.966 0.000 0.992 0.008
#> SRR1044514 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044515 2 0.0424 0.966 0.000 0.992 0.008
#> SRR1044516 2 0.0592 0.965 0.000 0.988 0.012
#> SRR1044517 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044518 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044519 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044520 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044521 2 0.3412 0.887 0.000 0.876 0.124
#> SRR1044522 3 0.0237 0.826 0.004 0.000 0.996
#> SRR1044523 2 0.1529 0.951 0.000 0.960 0.040
#> SRR1044524 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044525 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044526 1 0.0892 0.952 0.980 0.000 0.020
#> SRR1044527 3 0.0237 0.823 0.000 0.004 0.996
#> SRR1044528 3 0.5397 0.474 0.000 0.280 0.720
#> SRR1044529 3 0.0000 0.825 0.000 0.000 1.000
#> SRR1044530 3 0.3482 0.814 0.128 0.000 0.872
#> SRR1044531 1 0.4452 0.768 0.808 0.000 0.192
#> SRR1044533 1 0.5363 0.614 0.724 0.000 0.276
#> SRR1044532 3 0.3551 0.812 0.132 0.000 0.868
#> SRR1044534 2 0.6291 0.262 0.000 0.532 0.468
#> SRR1044535 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044536 2 0.2537 0.926 0.000 0.920 0.080
#> SRR1044537 3 0.6280 0.327 0.460 0.000 0.540
#> SRR1044538 3 0.3619 0.810 0.136 0.000 0.864
#> SRR1044539 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044540 1 0.0237 0.960 0.996 0.000 0.004
#> SRR1044541 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044542 3 0.3551 0.812 0.132 0.000 0.868
#> SRR1044543 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044544 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044545 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044546 3 0.5926 0.573 0.356 0.000 0.644
#> SRR1044547 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044548 3 0.5926 0.573 0.356 0.000 0.644
#> SRR1044549 2 0.5254 0.672 0.000 0.736 0.264
#> SRR1044550 2 0.2448 0.929 0.000 0.924 0.076
#> SRR1044551 3 0.5363 0.484 0.000 0.276 0.724
#> SRR1044552 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044553 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044554 3 0.6267 0.350 0.452 0.000 0.548
#> SRR1044555 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044556 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044557 3 0.6225 0.406 0.432 0.000 0.568
#> SRR1044558 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044559 3 0.5835 0.600 0.340 0.000 0.660
#> SRR1044561 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044560 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044562 3 0.5835 0.600 0.340 0.000 0.660
#> SRR1044563 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044564 1 0.2796 0.889 0.908 0.000 0.092
#> SRR1044565 3 0.0000 0.825 0.000 0.000 1.000
#> SRR1044566 2 0.0000 0.969 0.000 1.000 0.000
#> SRR1044567 3 0.3686 0.808 0.140 0.000 0.860
#> SRR1044568 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044569 1 0.3941 0.806 0.844 0.000 0.156
#> SRR1044570 3 0.3619 0.810 0.136 0.000 0.864
#> SRR1044571 1 0.1289 0.945 0.968 0.000 0.032
#> SRR1044572 1 0.1411 0.942 0.964 0.000 0.036
#> SRR1044573 1 0.3340 0.863 0.880 0.000 0.120
#> SRR1044574 1 0.1643 0.934 0.956 0.000 0.044
#> SRR1044575 1 0.0592 0.957 0.988 0.000 0.012
#> SRR1044576 3 0.1753 0.791 0.000 0.048 0.952
#> SRR1044577 3 0.0424 0.820 0.000 0.008 0.992
#> SRR1044578 3 0.0000 0.825 0.000 0.000 1.000
#> SRR1044579 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044580 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044581 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044582 3 0.6168 0.456 0.412 0.000 0.588
#> SRR1044583 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044584 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044585 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044586 3 0.6204 0.427 0.424 0.000 0.576
#> SRR1044587 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044588 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044589 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044590 1 0.0747 0.953 0.984 0.000 0.016
#> SRR1044591 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044592 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044593 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044594 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044595 1 0.0237 0.960 0.996 0.000 0.004
#> SRR1044596 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1044597 3 0.1860 0.829 0.052 0.000 0.948
#> SRR1044598 3 0.0424 0.827 0.008 0.000 0.992
#> SRR1044599 3 0.0424 0.827 0.008 0.000 0.992
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 3 0.0592 0.9473 0.000 0.016 0.984 0.000
#> SRR1044416 2 0.0336 0.9171 0.000 0.992 0.008 0.000
#> SRR1044417 2 0.0188 0.9193 0.004 0.996 0.000 0.000
#> SRR1044418 2 0.0336 0.9192 0.008 0.992 0.000 0.000
#> SRR1044420 2 0.2814 0.8534 0.000 0.868 0.132 0.000
#> SRR1044419 3 0.0469 0.9496 0.000 0.012 0.988 0.000
#> SRR1044421 3 0.4643 0.4551 0.000 0.344 0.656 0.000
#> SRR1044422 2 0.5000 0.0735 0.000 0.504 0.496 0.000
#> SRR1044423 2 0.3837 0.7517 0.000 0.776 0.224 0.000
#> SRR1044424 2 0.0469 0.9162 0.000 0.988 0.012 0.000
#> SRR1044425 4 0.3725 0.7924 0.180 0.008 0.000 0.812
#> SRR1044426 1 0.4916 0.2370 0.576 0.000 0.000 0.424
#> SRR1044427 1 0.1174 0.9016 0.968 0.020 0.000 0.012
#> SRR1044428 1 0.0592 0.9018 0.984 0.000 0.000 0.016
#> SRR1044429 4 0.4406 0.6015 0.300 0.000 0.000 0.700
#> SRR1044430 1 0.1576 0.8996 0.948 0.000 0.004 0.048
#> SRR1044431 1 0.0592 0.9018 0.984 0.000 0.000 0.016
#> SRR1044433 4 0.1059 0.9480 0.016 0.000 0.012 0.972
#> SRR1044432 1 0.0592 0.9009 0.984 0.000 0.000 0.016
#> SRR1044434 4 0.0469 0.9634 0.012 0.000 0.000 0.988
#> SRR1044435 4 0.0469 0.9634 0.012 0.000 0.000 0.988
#> SRR1044436 4 0.0592 0.9599 0.016 0.000 0.000 0.984
#> SRR1044437 4 0.0469 0.9634 0.012 0.000 0.000 0.988
#> SRR1044439 4 0.0336 0.9620 0.008 0.000 0.000 0.992
#> SRR1044438 4 0.0592 0.9626 0.016 0.000 0.000 0.984
#> SRR1044440 4 0.0469 0.9634 0.012 0.000 0.000 0.988
#> SRR1044441 4 0.0469 0.9634 0.012 0.000 0.000 0.988
#> SRR1044442 4 0.0707 0.9587 0.020 0.000 0.000 0.980
#> SRR1044443 4 0.1584 0.9280 0.012 0.000 0.036 0.952
#> SRR1044444 4 0.0469 0.9634 0.012 0.000 0.000 0.988
#> SRR1044445 4 0.0707 0.9617 0.020 0.000 0.000 0.980
#> SRR1044446 3 0.0524 0.9476 0.004 0.000 0.988 0.008
#> SRR1044447 3 0.0524 0.9476 0.004 0.000 0.988 0.008
#> SRR1044449 3 0.0524 0.9476 0.004 0.000 0.988 0.008
#> SRR1044448 3 0.0524 0.9476 0.004 0.000 0.988 0.008
#> SRR1044450 3 0.0524 0.9476 0.004 0.000 0.988 0.008
#> SRR1044451 3 0.0524 0.9476 0.004 0.000 0.988 0.008
#> SRR1044452 3 0.0188 0.9503 0.000 0.004 0.996 0.000
#> SRR1044453 3 0.0188 0.9503 0.000 0.004 0.996 0.000
#> SRR1044454 3 0.0188 0.9503 0.000 0.004 0.996 0.000
#> SRR1044455 3 0.0469 0.9496 0.000 0.012 0.988 0.000
#> SRR1044456 2 0.1302 0.8985 0.044 0.956 0.000 0.000
#> SRR1044457 3 0.0469 0.9496 0.000 0.012 0.988 0.000
#> SRR1044458 3 0.0469 0.9496 0.000 0.012 0.988 0.000
#> SRR1044459 3 0.0188 0.9503 0.000 0.004 0.996 0.000
#> SRR1044460 2 0.3172 0.8299 0.000 0.840 0.160 0.000
#> SRR1044461 3 0.0469 0.9496 0.000 0.012 0.988 0.000
#> SRR1044462 4 0.4992 -0.0661 0.476 0.000 0.000 0.524
#> SRR1044463 1 0.0657 0.9012 0.984 0.004 0.000 0.012
#> SRR1044464 4 0.1389 0.9445 0.048 0.000 0.000 0.952
#> SRR1044466 1 0.0817 0.8943 0.976 0.024 0.000 0.000
#> SRR1044465 1 0.0592 0.9019 0.984 0.000 0.000 0.016
#> SRR1044467 1 0.0707 0.9022 0.980 0.000 0.000 0.020
#> SRR1044468 2 0.3444 0.8054 0.000 0.816 0.184 0.000
#> SRR1044469 3 0.0469 0.9496 0.000 0.012 0.988 0.000
#> SRR1044470 1 0.1474 0.8995 0.948 0.000 0.000 0.052
#> SRR1044471 1 0.0817 0.9021 0.976 0.000 0.000 0.024
#> SRR1044472 1 0.0707 0.8953 0.980 0.020 0.000 0.000
#> SRR1044473 1 0.0469 0.9010 0.988 0.000 0.000 0.012
#> SRR1044474 2 0.0469 0.9187 0.012 0.988 0.000 0.000
#> SRR1044475 3 0.0469 0.9496 0.000 0.012 0.988 0.000
#> SRR1044476 3 0.0469 0.9496 0.000 0.012 0.988 0.000
#> SRR1044477 2 0.0469 0.9187 0.012 0.988 0.000 0.000
#> SRR1044478 3 0.4522 0.5152 0.000 0.320 0.680 0.000
#> SRR1044479 2 0.0469 0.9187 0.012 0.988 0.000 0.000
#> SRR1044480 4 0.1557 0.9334 0.056 0.000 0.000 0.944
#> SRR1044481 1 0.3266 0.8491 0.832 0.000 0.000 0.168
#> SRR1044482 2 0.0188 0.9193 0.004 0.996 0.000 0.000
#> SRR1044483 4 0.1389 0.9400 0.048 0.000 0.000 0.952
#> SRR1044484 1 0.3311 0.8457 0.828 0.000 0.000 0.172
#> SRR1044486 1 0.3123 0.8565 0.844 0.000 0.000 0.156
#> SRR1044485 2 0.0469 0.9162 0.000 0.988 0.012 0.000
#> SRR1044487 2 0.0469 0.9187 0.012 0.988 0.000 0.000
#> SRR1044488 2 0.2408 0.8729 0.000 0.896 0.104 0.000
#> SRR1044489 2 0.3123 0.8336 0.000 0.844 0.156 0.000
#> SRR1044490 1 0.3024 0.8268 0.852 0.000 0.000 0.148
#> SRR1044491 1 0.0336 0.9007 0.992 0.000 0.000 0.008
#> SRR1044492 1 0.2589 0.8480 0.884 0.116 0.000 0.000
#> SRR1044493 1 0.0524 0.9004 0.988 0.004 0.000 0.008
#> SRR1044494 2 0.0469 0.9187 0.012 0.988 0.000 0.000
#> SRR1044496 2 0.0469 0.9187 0.012 0.988 0.000 0.000
#> SRR1044495 2 0.0469 0.9187 0.012 0.988 0.000 0.000
#> SRR1044497 4 0.0469 0.9634 0.012 0.000 0.000 0.988
#> SRR1044499 3 0.0469 0.9496 0.000 0.012 0.988 0.000
#> SRR1044498 1 0.3172 0.8524 0.840 0.000 0.000 0.160
#> SRR1044500 2 0.2973 0.8439 0.000 0.856 0.144 0.000
#> SRR1044501 3 0.0469 0.9496 0.000 0.012 0.988 0.000
#> SRR1044502 3 0.0524 0.9476 0.004 0.000 0.988 0.008
#> SRR1044503 4 0.0469 0.9634 0.012 0.000 0.000 0.988
#> SRR1044504 4 0.0469 0.9634 0.012 0.000 0.000 0.988
#> SRR1044505 1 0.1211 0.9025 0.960 0.000 0.000 0.040
#> SRR1044506 4 0.0707 0.9617 0.020 0.000 0.000 0.980
#> SRR1044507 4 0.0817 0.9593 0.024 0.000 0.000 0.976
#> SRR1044508 4 0.0672 0.9511 0.008 0.000 0.008 0.984
#> SRR1044509 4 0.0927 0.9506 0.016 0.000 0.008 0.976
#> SRR1044510 3 0.0000 0.9499 0.000 0.000 1.000 0.000
#> SRR1044511 3 0.0524 0.9476 0.004 0.000 0.988 0.008
#> SRR1044512 3 0.0524 0.9476 0.004 0.000 0.988 0.008
#> SRR1044513 3 0.4074 0.7280 0.004 0.196 0.792 0.008
#> SRR1044514 3 0.0524 0.9476 0.004 0.000 0.988 0.008
#> SRR1044515 3 0.4946 0.5219 0.004 0.308 0.680 0.008
#> SRR1044516 3 0.4624 0.4576 0.000 0.340 0.660 0.000
#> SRR1044517 3 0.0188 0.9503 0.000 0.004 0.996 0.000
#> SRR1044518 3 0.0524 0.9476 0.004 0.000 0.988 0.008
#> SRR1044519 3 0.0524 0.9476 0.004 0.000 0.988 0.008
#> SRR1044520 3 0.0524 0.9476 0.004 0.000 0.988 0.008
#> SRR1044521 2 0.1867 0.8909 0.000 0.928 0.072 0.000
#> SRR1044522 2 0.0469 0.9187 0.012 0.988 0.000 0.000
#> SRR1044523 2 0.5054 0.5643 0.004 0.660 0.328 0.008
#> SRR1044524 3 0.0336 0.9486 0.000 0.000 0.992 0.008
#> SRR1044525 4 0.0469 0.9634 0.012 0.000 0.000 0.988
#> SRR1044526 1 0.4866 0.4688 0.596 0.000 0.000 0.404
#> SRR1044527 2 0.0188 0.9193 0.004 0.996 0.000 0.000
#> SRR1044528 2 0.0336 0.9192 0.008 0.992 0.000 0.000
#> SRR1044529 2 0.0469 0.9187 0.012 0.988 0.000 0.000
#> SRR1044530 1 0.0921 0.8941 0.972 0.028 0.000 0.000
#> SRR1044531 1 0.0804 0.8993 0.980 0.012 0.000 0.008
#> SRR1044533 1 0.0469 0.8976 0.988 0.012 0.000 0.000
#> SRR1044532 1 0.1022 0.8928 0.968 0.032 0.000 0.000
#> SRR1044534 2 0.0188 0.9179 0.000 0.996 0.004 0.000
#> SRR1044535 3 0.0188 0.9493 0.000 0.000 0.996 0.004
#> SRR1044536 2 0.3311 0.8185 0.000 0.828 0.172 0.000
#> SRR1044537 1 0.3266 0.8491 0.832 0.000 0.000 0.168
#> SRR1044538 1 0.1022 0.8928 0.968 0.032 0.000 0.000
#> SRR1044539 4 0.1022 0.9513 0.032 0.000 0.000 0.968
#> SRR1044540 1 0.0921 0.9026 0.972 0.000 0.000 0.028
#> SRR1044541 3 0.0469 0.9496 0.000 0.012 0.988 0.000
#> SRR1044542 1 0.1022 0.8928 0.968 0.032 0.000 0.000
#> SRR1044543 1 0.2921 0.8395 0.860 0.000 0.000 0.140
#> SRR1044544 3 0.0469 0.9496 0.000 0.012 0.988 0.000
#> SRR1044545 4 0.1211 0.9466 0.040 0.000 0.000 0.960
#> SRR1044546 1 0.3266 0.8491 0.832 0.000 0.000 0.168
#> SRR1044547 4 0.2868 0.8397 0.136 0.000 0.000 0.864
#> SRR1044548 1 0.3266 0.8491 0.832 0.000 0.000 0.168
#> SRR1044549 2 0.3024 0.8442 0.000 0.852 0.148 0.000
#> SRR1044550 2 0.3172 0.8299 0.000 0.840 0.160 0.000
#> SRR1044551 2 0.0188 0.9193 0.004 0.996 0.000 0.000
#> SRR1044552 4 0.0469 0.9634 0.012 0.000 0.000 0.988
#> SRR1044553 4 0.0469 0.9634 0.012 0.000 0.000 0.988
#> SRR1044554 1 0.3219 0.8520 0.836 0.000 0.000 0.164
#> SRR1044555 3 0.0188 0.9503 0.000 0.004 0.996 0.000
#> SRR1044556 4 0.0469 0.9606 0.012 0.000 0.000 0.988
#> SRR1044557 1 0.3266 0.8491 0.832 0.000 0.000 0.168
#> SRR1044558 4 0.0469 0.9606 0.012 0.000 0.000 0.988
#> SRR1044559 1 0.3266 0.8491 0.832 0.000 0.000 0.168
#> SRR1044561 4 0.0336 0.9620 0.008 0.000 0.000 0.992
#> SRR1044560 3 0.0469 0.9496 0.000 0.012 0.988 0.000
#> SRR1044562 1 0.3266 0.8491 0.832 0.000 0.000 0.168
#> SRR1044563 4 0.0469 0.9606 0.012 0.000 0.000 0.988
#> SRR1044564 1 0.3266 0.8491 0.832 0.000 0.000 0.168
#> SRR1044565 2 0.0469 0.9187 0.012 0.988 0.000 0.000
#> SRR1044566 3 0.0469 0.9496 0.000 0.012 0.988 0.000
#> SRR1044567 1 0.1022 0.8928 0.968 0.032 0.000 0.000
#> SRR1044568 4 0.1792 0.9214 0.068 0.000 0.000 0.932
#> SRR1044569 1 0.1211 0.9025 0.960 0.000 0.000 0.040
#> SRR1044570 1 0.1022 0.8928 0.968 0.032 0.000 0.000
#> SRR1044571 1 0.0592 0.9019 0.984 0.000 0.000 0.016
#> SRR1044572 1 0.0817 0.9024 0.976 0.000 0.000 0.024
#> SRR1044573 1 0.1940 0.8828 0.924 0.000 0.000 0.076
#> SRR1044574 1 0.1356 0.8979 0.960 0.008 0.000 0.032
#> SRR1044575 1 0.0707 0.9025 0.980 0.000 0.000 0.020
#> SRR1044576 2 0.0188 0.9193 0.004 0.996 0.000 0.000
#> SRR1044577 2 0.0188 0.9193 0.004 0.996 0.000 0.000
#> SRR1044578 2 0.0469 0.9187 0.012 0.988 0.000 0.000
#> SRR1044579 4 0.0469 0.9634 0.012 0.000 0.000 0.988
#> SRR1044580 1 0.4304 0.7038 0.716 0.000 0.000 0.284
#> SRR1044581 4 0.0469 0.9634 0.012 0.000 0.000 0.988
#> SRR1044582 1 0.3172 0.8543 0.840 0.000 0.000 0.160
#> SRR1044583 4 0.0469 0.9634 0.012 0.000 0.000 0.988
#> SRR1044584 4 0.0707 0.9586 0.020 0.000 0.000 0.980
#> SRR1044585 4 0.0469 0.9634 0.012 0.000 0.000 0.988
#> SRR1044586 1 0.3266 0.8491 0.832 0.000 0.000 0.168
#> SRR1044587 4 0.1302 0.9462 0.044 0.000 0.000 0.956
#> SRR1044588 4 0.0707 0.9617 0.020 0.000 0.000 0.980
#> SRR1044589 4 0.0707 0.9617 0.020 0.000 0.000 0.980
#> SRR1044590 4 0.1305 0.9504 0.036 0.004 0.000 0.960
#> SRR1044591 4 0.0707 0.9617 0.020 0.000 0.000 0.980
#> SRR1044592 4 0.1059 0.9480 0.016 0.000 0.012 0.972
#> SRR1044593 4 0.0707 0.9617 0.020 0.000 0.000 0.980
#> SRR1044594 4 0.0707 0.9617 0.020 0.000 0.000 0.980
#> SRR1044595 4 0.1545 0.9393 0.040 0.000 0.008 0.952
#> SRR1044596 4 0.0707 0.9617 0.020 0.000 0.000 0.980
#> SRR1044597 1 0.4781 0.7431 0.752 0.212 0.000 0.036
#> SRR1044598 1 0.3907 0.7339 0.768 0.232 0.000 0.000
#> SRR1044599 1 0.3907 0.7339 0.768 0.232 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 3 0.4450 0.2879 0.000 0.004 0.508 0.000 0.488
#> SRR1044416 2 0.0880 0.8189 0.000 0.968 0.000 0.000 0.032
#> SRR1044417 2 0.0162 0.8442 0.000 0.996 0.000 0.000 0.004
#> SRR1044418 2 0.0000 0.8456 0.000 1.000 0.000 0.000 0.000
#> SRR1044420 5 0.5551 0.5983 0.000 0.444 0.068 0.000 0.488
#> SRR1044419 3 0.4305 0.3003 0.000 0.000 0.512 0.000 0.488
#> SRR1044421 5 0.6094 0.1758 0.000 0.128 0.384 0.000 0.488
#> SRR1044422 5 0.6496 0.4883 0.000 0.232 0.280 0.000 0.488
#> SRR1044423 5 0.6218 0.6704 0.000 0.364 0.148 0.000 0.488
#> SRR1044424 2 0.4403 -0.2804 0.000 0.560 0.004 0.000 0.436
#> SRR1044425 4 0.3670 0.7312 0.188 0.012 0.000 0.792 0.008
#> SRR1044426 1 0.4960 0.6356 0.708 0.000 0.000 0.180 0.112
#> SRR1044427 1 0.3042 0.7726 0.880 0.020 0.000 0.044 0.056
#> SRR1044428 1 0.2471 0.7754 0.864 0.000 0.000 0.000 0.136
#> SRR1044429 4 0.5385 0.4655 0.288 0.000 0.000 0.624 0.088
#> SRR1044430 1 0.4759 0.7193 0.636 0.000 0.004 0.024 0.336
#> SRR1044431 1 0.2286 0.7724 0.888 0.000 0.000 0.004 0.108
#> SRR1044433 4 0.3390 0.8148 0.000 0.000 0.100 0.840 0.060
#> SRR1044432 1 0.2561 0.7754 0.856 0.000 0.000 0.000 0.144
#> SRR1044434 4 0.0000 0.9036 0.000 0.000 0.000 1.000 0.000
#> SRR1044435 4 0.0000 0.9036 0.000 0.000 0.000 1.000 0.000
#> SRR1044436 4 0.1608 0.8729 0.000 0.000 0.000 0.928 0.072
#> SRR1044437 4 0.0000 0.9036 0.000 0.000 0.000 1.000 0.000
#> SRR1044439 4 0.0510 0.8999 0.000 0.000 0.000 0.984 0.016
#> SRR1044438 4 0.0290 0.9021 0.000 0.000 0.000 0.992 0.008
#> SRR1044440 4 0.0000 0.9036 0.000 0.000 0.000 1.000 0.000
#> SRR1044441 4 0.0000 0.9036 0.000 0.000 0.000 1.000 0.000
#> SRR1044442 4 0.1983 0.8797 0.008 0.000 0.008 0.924 0.060
#> SRR1044443 4 0.3734 0.7903 0.000 0.000 0.128 0.812 0.060
#> SRR1044444 4 0.0000 0.9036 0.000 0.000 0.000 1.000 0.000
#> SRR1044445 4 0.0807 0.8984 0.012 0.000 0.000 0.976 0.012
#> SRR1044446 3 0.0000 0.7418 0.000 0.000 1.000 0.000 0.000
#> SRR1044447 3 0.0000 0.7418 0.000 0.000 1.000 0.000 0.000
#> SRR1044449 3 0.0000 0.7418 0.000 0.000 1.000 0.000 0.000
#> SRR1044448 3 0.0000 0.7418 0.000 0.000 1.000 0.000 0.000
#> SRR1044450 3 0.0000 0.7418 0.000 0.000 1.000 0.000 0.000
#> SRR1044451 3 0.0290 0.7397 0.000 0.000 0.992 0.000 0.008
#> SRR1044452 3 0.1851 0.7351 0.000 0.000 0.912 0.000 0.088
#> SRR1044453 3 0.1851 0.7351 0.000 0.000 0.912 0.000 0.088
#> SRR1044454 3 0.1965 0.7317 0.000 0.000 0.904 0.000 0.096
#> SRR1044455 3 0.4273 0.3762 0.000 0.000 0.552 0.000 0.448
#> SRR1044456 2 0.1341 0.7929 0.056 0.944 0.000 0.000 0.000
#> SRR1044457 3 0.4291 0.3497 0.000 0.000 0.536 0.000 0.464
#> SRR1044458 3 0.4300 0.3263 0.000 0.000 0.524 0.000 0.476
#> SRR1044459 3 0.1544 0.7403 0.000 0.000 0.932 0.000 0.068
#> SRR1044460 5 0.5840 0.6550 0.000 0.416 0.096 0.000 0.488
#> SRR1044461 3 0.4305 0.3003 0.000 0.000 0.512 0.000 0.488
#> SRR1044462 5 0.6821 -0.4565 0.328 0.000 0.000 0.320 0.352
#> SRR1044463 1 0.0404 0.7784 0.988 0.012 0.000 0.000 0.000
#> SRR1044464 4 0.4119 0.7446 0.036 0.000 0.000 0.752 0.212
#> SRR1044466 1 0.0609 0.7765 0.980 0.020 0.000 0.000 0.000
#> SRR1044465 1 0.2497 0.7704 0.880 0.004 0.000 0.004 0.112
#> SRR1044467 1 0.2462 0.7705 0.880 0.000 0.000 0.008 0.112
#> SRR1044468 5 0.6037 0.6713 0.000 0.392 0.120 0.000 0.488
#> SRR1044469 3 0.2891 0.6867 0.000 0.000 0.824 0.000 0.176
#> SRR1044470 1 0.2953 0.7605 0.868 0.004 0.000 0.028 0.100
#> SRR1044471 1 0.2497 0.7704 0.880 0.004 0.000 0.004 0.112
#> SRR1044472 1 0.0771 0.7770 0.976 0.020 0.000 0.000 0.004
#> SRR1044473 1 0.2389 0.7723 0.880 0.000 0.000 0.004 0.116
#> SRR1044474 2 0.0000 0.8456 0.000 1.000 0.000 0.000 0.000
#> SRR1044475 3 0.2813 0.6922 0.000 0.000 0.832 0.000 0.168
#> SRR1044476 3 0.4300 0.3263 0.000 0.000 0.524 0.000 0.476
#> SRR1044477 2 0.0000 0.8456 0.000 1.000 0.000 0.000 0.000
#> SRR1044478 5 0.6037 0.1399 0.000 0.120 0.392 0.000 0.488
#> SRR1044479 2 0.0000 0.8456 0.000 1.000 0.000 0.000 0.000
#> SRR1044480 4 0.4575 0.6155 0.024 0.000 0.000 0.648 0.328
#> SRR1044481 1 0.5838 0.6326 0.552 0.000 0.000 0.112 0.336
#> SRR1044482 2 0.0162 0.8442 0.000 0.996 0.000 0.000 0.004
#> SRR1044483 4 0.4473 0.6272 0.020 0.000 0.000 0.656 0.324
#> SRR1044484 1 0.5865 0.6322 0.552 0.000 0.000 0.116 0.332
#> SRR1044486 1 0.5960 0.6357 0.556 0.004 0.000 0.112 0.328
#> SRR1044485 2 0.1851 0.7452 0.000 0.912 0.000 0.000 0.088
#> SRR1044487 2 0.0000 0.8456 0.000 1.000 0.000 0.000 0.000
#> SRR1044488 5 0.5505 0.5763 0.000 0.452 0.064 0.000 0.484
#> SRR1044489 5 0.5876 0.6602 0.000 0.412 0.100 0.000 0.488
#> SRR1044490 1 0.4126 0.7445 0.796 0.004 0.000 0.096 0.104
#> SRR1044491 1 0.0451 0.7793 0.988 0.008 0.000 0.000 0.004
#> SRR1044492 1 0.3656 0.6758 0.800 0.168 0.000 0.000 0.032
#> SRR1044493 1 0.0510 0.7776 0.984 0.016 0.000 0.000 0.000
#> SRR1044494 2 0.0000 0.8456 0.000 1.000 0.000 0.000 0.000
#> SRR1044496 2 0.0000 0.8456 0.000 1.000 0.000 0.000 0.000
#> SRR1044495 2 0.0000 0.8456 0.000 1.000 0.000 0.000 0.000
#> SRR1044497 4 0.0000 0.9036 0.000 0.000 0.000 1.000 0.000
#> SRR1044499 3 0.4249 0.3971 0.000 0.000 0.568 0.000 0.432
#> SRR1044498 1 0.5862 0.6349 0.544 0.000 0.000 0.112 0.344
#> SRR1044500 5 0.5684 0.6265 0.000 0.432 0.080 0.000 0.488
#> SRR1044501 3 0.4300 0.3263 0.000 0.000 0.524 0.000 0.476
#> SRR1044502 3 0.0404 0.7414 0.000 0.000 0.988 0.000 0.012
#> SRR1044503 4 0.0000 0.9036 0.000 0.000 0.000 1.000 0.000
#> SRR1044504 4 0.0000 0.9036 0.000 0.000 0.000 1.000 0.000
#> SRR1044505 1 0.4550 0.7455 0.688 0.000 0.000 0.036 0.276
#> SRR1044506 4 0.0807 0.8984 0.012 0.000 0.000 0.976 0.012
#> SRR1044507 4 0.2574 0.8666 0.012 0.000 0.000 0.876 0.112
#> SRR1044508 4 0.3336 0.8429 0.000 0.000 0.060 0.844 0.096
#> SRR1044509 4 0.3384 0.8236 0.004 0.000 0.088 0.848 0.060
#> SRR1044510 3 0.1270 0.7425 0.000 0.000 0.948 0.000 0.052
#> SRR1044511 3 0.0000 0.7418 0.000 0.000 1.000 0.000 0.000
#> SRR1044512 3 0.0000 0.7418 0.000 0.000 1.000 0.000 0.000
#> SRR1044513 3 0.2905 0.6447 0.000 0.096 0.868 0.000 0.036
#> SRR1044514 3 0.0000 0.7418 0.000 0.000 1.000 0.000 0.000
#> SRR1044515 3 0.3953 0.5447 0.000 0.148 0.792 0.000 0.060
#> SRR1044516 5 0.6299 0.2501 0.000 0.156 0.380 0.000 0.464
#> SRR1044517 3 0.1671 0.7387 0.000 0.000 0.924 0.000 0.076
#> SRR1044518 3 0.0000 0.7418 0.000 0.000 1.000 0.000 0.000
#> SRR1044519 3 0.0000 0.7418 0.000 0.000 1.000 0.000 0.000
#> SRR1044520 3 0.0000 0.7418 0.000 0.000 1.000 0.000 0.000
#> SRR1044521 2 0.4968 -0.4368 0.000 0.516 0.028 0.000 0.456
#> SRR1044522 2 0.0290 0.8393 0.008 0.992 0.000 0.000 0.000
#> SRR1044523 3 0.6342 -0.2143 0.000 0.372 0.464 0.000 0.164
#> SRR1044524 3 0.0510 0.7437 0.000 0.000 0.984 0.000 0.016
#> SRR1044525 4 0.0000 0.9036 0.000 0.000 0.000 1.000 0.000
#> SRR1044526 1 0.6748 0.3754 0.404 0.000 0.000 0.320 0.276
#> SRR1044527 2 0.0162 0.8442 0.000 0.996 0.000 0.000 0.004
#> SRR1044528 2 0.0510 0.8367 0.000 0.984 0.000 0.000 0.016
#> SRR1044529 2 0.0000 0.8456 0.000 1.000 0.000 0.000 0.000
#> SRR1044530 1 0.0703 0.7756 0.976 0.024 0.000 0.000 0.000
#> SRR1044531 1 0.2783 0.7740 0.868 0.012 0.000 0.004 0.116
#> SRR1044533 1 0.2573 0.7687 0.880 0.016 0.000 0.000 0.104
#> SRR1044532 1 0.0703 0.7756 0.976 0.024 0.000 0.000 0.000
#> SRR1044534 2 0.4045 0.0636 0.000 0.644 0.000 0.000 0.356
#> SRR1044535 3 0.0703 0.7440 0.000 0.000 0.976 0.000 0.024
#> SRR1044536 5 0.5944 0.6676 0.000 0.404 0.108 0.000 0.488
#> SRR1044537 1 0.5862 0.6304 0.544 0.000 0.000 0.112 0.344
#> SRR1044538 1 0.0794 0.7747 0.972 0.028 0.000 0.000 0.000
#> SRR1044539 4 0.4288 0.6364 0.012 0.000 0.000 0.664 0.324
#> SRR1044540 1 0.2574 0.7720 0.876 0.000 0.000 0.012 0.112
#> SRR1044541 3 0.4291 0.3480 0.000 0.000 0.536 0.000 0.464
#> SRR1044542 1 0.0963 0.7721 0.964 0.036 0.000 0.000 0.000
#> SRR1044543 1 0.3791 0.7489 0.812 0.000 0.000 0.076 0.112
#> SRR1044544 3 0.3242 0.6567 0.000 0.000 0.784 0.000 0.216
#> SRR1044545 4 0.4467 0.6065 0.016 0.000 0.000 0.640 0.344
#> SRR1044546 1 0.5851 0.6305 0.548 0.000 0.000 0.112 0.340
#> SRR1044547 4 0.5652 0.4718 0.092 0.000 0.000 0.564 0.344
#> SRR1044548 1 0.5851 0.6305 0.548 0.000 0.000 0.112 0.340
#> SRR1044549 2 0.3307 0.6489 0.000 0.844 0.104 0.000 0.052
#> SRR1044550 5 0.5944 0.6678 0.000 0.404 0.108 0.000 0.488
#> SRR1044551 2 0.0794 0.8264 0.000 0.972 0.000 0.000 0.028
#> SRR1044552 4 0.0000 0.9036 0.000 0.000 0.000 1.000 0.000
#> SRR1044553 4 0.0000 0.9036 0.000 0.000 0.000 1.000 0.000
#> SRR1044554 1 0.5884 0.6302 0.536 0.000 0.000 0.112 0.352
#> SRR1044555 3 0.1671 0.7387 0.000 0.000 0.924 0.000 0.076
#> SRR1044556 4 0.0703 0.8972 0.000 0.000 0.000 0.976 0.024
#> SRR1044557 1 0.5851 0.6305 0.548 0.000 0.000 0.112 0.340
#> SRR1044558 4 0.0794 0.8955 0.000 0.000 0.000 0.972 0.028
#> SRR1044559 1 0.5851 0.6305 0.548 0.000 0.000 0.112 0.340
#> SRR1044561 4 0.0000 0.9036 0.000 0.000 0.000 1.000 0.000
#> SRR1044560 3 0.4300 0.3263 0.000 0.000 0.524 0.000 0.476
#> SRR1044562 1 0.5851 0.6305 0.548 0.000 0.000 0.112 0.340
#> SRR1044563 4 0.3491 0.7467 0.004 0.000 0.000 0.768 0.228
#> SRR1044564 1 0.5862 0.6304 0.544 0.000 0.000 0.112 0.344
#> SRR1044565 2 0.0000 0.8456 0.000 1.000 0.000 0.000 0.000
#> SRR1044566 3 0.4300 0.3263 0.000 0.000 0.524 0.000 0.476
#> SRR1044567 1 0.0865 0.7758 0.972 0.024 0.000 0.004 0.000
#> SRR1044568 4 0.5016 0.5572 0.044 0.000 0.000 0.608 0.348
#> SRR1044569 1 0.3035 0.7724 0.856 0.000 0.000 0.032 0.112
#> SRR1044570 1 0.0794 0.7747 0.972 0.028 0.000 0.000 0.000
#> SRR1044571 1 0.2338 0.7704 0.884 0.004 0.000 0.000 0.112
#> SRR1044572 1 0.2864 0.7677 0.864 0.000 0.000 0.024 0.112
#> SRR1044573 1 0.3758 0.7627 0.816 0.004 0.000 0.052 0.128
#> SRR1044574 1 0.3237 0.7696 0.860 0.016 0.000 0.028 0.096
#> SRR1044575 1 0.2574 0.7701 0.876 0.000 0.000 0.012 0.112
#> SRR1044576 2 0.0290 0.8414 0.000 0.992 0.000 0.000 0.008
#> SRR1044577 2 0.0162 0.8442 0.000 0.996 0.000 0.000 0.004
#> SRR1044578 2 0.0000 0.8456 0.000 1.000 0.000 0.000 0.000
#> SRR1044579 4 0.0000 0.9036 0.000 0.000 0.000 1.000 0.000
#> SRR1044580 1 0.6539 0.5333 0.432 0.000 0.000 0.200 0.368
#> SRR1044581 4 0.0000 0.9036 0.000 0.000 0.000 1.000 0.000
#> SRR1044582 1 0.5851 0.6305 0.548 0.000 0.000 0.112 0.340
#> SRR1044583 4 0.0000 0.9036 0.000 0.000 0.000 1.000 0.000
#> SRR1044584 4 0.1124 0.8908 0.004 0.000 0.000 0.960 0.036
#> SRR1044585 4 0.0000 0.9036 0.000 0.000 0.000 1.000 0.000
#> SRR1044586 1 0.5851 0.6305 0.548 0.000 0.000 0.112 0.340
#> SRR1044587 4 0.1195 0.8920 0.028 0.000 0.000 0.960 0.012
#> SRR1044588 4 0.0807 0.8984 0.012 0.000 0.000 0.976 0.012
#> SRR1044589 4 0.0807 0.8984 0.012 0.000 0.000 0.976 0.012
#> SRR1044590 4 0.0854 0.8986 0.008 0.004 0.000 0.976 0.012
#> SRR1044591 4 0.0693 0.8994 0.008 0.000 0.000 0.980 0.012
#> SRR1044592 4 0.3547 0.8124 0.004 0.000 0.100 0.836 0.060
#> SRR1044593 4 0.0807 0.8984 0.012 0.000 0.000 0.976 0.012
#> SRR1044594 4 0.0807 0.8984 0.012 0.000 0.000 0.976 0.012
#> SRR1044595 4 0.4784 0.7954 0.032 0.000 0.068 0.764 0.136
#> SRR1044596 4 0.1697 0.8837 0.008 0.000 0.000 0.932 0.060
#> SRR1044597 2 0.6021 0.2865 0.364 0.548 0.000 0.032 0.056
#> SRR1044598 2 0.4638 0.4474 0.324 0.648 0.000 0.000 0.028
#> SRR1044599 2 0.4506 0.4801 0.296 0.676 0.000 0.000 0.028
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.2597 0.8135 0.000 0.824 0.176 0.000 0.000 0.000
#> SRR1044416 6 0.1075 0.8918 0.000 0.048 0.000 0.000 0.000 0.952
#> SRR1044417 6 0.0000 0.9304 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044418 6 0.0000 0.9304 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044420 2 0.2738 0.8144 0.000 0.820 0.004 0.000 0.000 0.176
#> SRR1044419 2 0.2597 0.8135 0.000 0.824 0.176 0.000 0.000 0.000
#> SRR1044421 2 0.3227 0.8350 0.000 0.824 0.116 0.000 0.000 0.060
#> SRR1044422 2 0.3274 0.8370 0.000 0.824 0.080 0.000 0.000 0.096
#> SRR1044423 2 0.3123 0.8332 0.000 0.824 0.040 0.000 0.000 0.136
#> SRR1044424 2 0.3499 0.6222 0.000 0.680 0.000 0.000 0.000 0.320
#> SRR1044425 4 0.3135 0.7269 0.152 0.008 0.000 0.824 0.008 0.008
#> SRR1044426 1 0.1866 0.7519 0.908 0.000 0.000 0.084 0.008 0.000
#> SRR1044427 1 0.5460 0.6548 0.648 0.024 0.000 0.092 0.224 0.012
#> SRR1044428 1 0.0937 0.8089 0.960 0.000 0.000 0.000 0.040 0.000
#> SRR1044429 4 0.5209 0.3321 0.324 0.000 0.000 0.564 0.112 0.000
#> SRR1044430 1 0.3684 0.2192 0.628 0.000 0.000 0.000 0.372 0.000
#> SRR1044431 1 0.0547 0.8207 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1044433 4 0.6062 0.6069 0.000 0.132 0.112 0.616 0.140 0.000
#> SRR1044432 1 0.0547 0.8161 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1044434 4 0.0363 0.8699 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR1044435 4 0.0363 0.8699 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR1044436 4 0.1957 0.7932 0.000 0.000 0.000 0.888 0.112 0.000
#> SRR1044437 4 0.0363 0.8699 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR1044439 4 0.0790 0.8609 0.000 0.000 0.000 0.968 0.032 0.000
#> SRR1044438 4 0.0713 0.8643 0.000 0.000 0.000 0.972 0.028 0.000
#> SRR1044440 4 0.0363 0.8699 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR1044441 4 0.0363 0.8699 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR1044442 4 0.4934 0.6740 0.000 0.132 0.020 0.696 0.152 0.000
#> SRR1044443 4 0.6807 0.4808 0.000 0.132 0.220 0.508 0.140 0.000
#> SRR1044444 4 0.0458 0.8688 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1044445 4 0.0405 0.8656 0.000 0.008 0.000 0.988 0.004 0.000
#> SRR1044446 3 0.0000 0.8801 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044447 3 0.0000 0.8801 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044449 3 0.0146 0.8813 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1044448 3 0.0000 0.8801 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044450 3 0.0000 0.8801 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044451 3 0.0363 0.8762 0.000 0.012 0.988 0.000 0.000 0.000
#> SRR1044452 3 0.1910 0.8394 0.000 0.108 0.892 0.000 0.000 0.000
#> SRR1044453 3 0.1910 0.8394 0.000 0.108 0.892 0.000 0.000 0.000
#> SRR1044454 3 0.2092 0.8240 0.000 0.124 0.876 0.000 0.000 0.000
#> SRR1044455 2 0.3151 0.7570 0.000 0.748 0.252 0.000 0.000 0.000
#> SRR1044456 6 0.0858 0.9101 0.000 0.028 0.000 0.000 0.004 0.968
#> SRR1044457 2 0.3198 0.7461 0.000 0.740 0.260 0.000 0.000 0.000
#> SRR1044458 2 0.2941 0.7910 0.000 0.780 0.220 0.000 0.000 0.000
#> SRR1044459 3 0.1714 0.8505 0.000 0.092 0.908 0.000 0.000 0.000
#> SRR1044460 2 0.2896 0.8278 0.000 0.824 0.016 0.000 0.000 0.160
#> SRR1044461 2 0.2597 0.8135 0.000 0.824 0.176 0.000 0.000 0.000
#> SRR1044462 5 0.4302 0.7269 0.116 0.000 0.000 0.156 0.728 0.000
#> SRR1044463 1 0.3714 0.7696 0.760 0.044 0.000 0.000 0.196 0.000
#> SRR1044464 4 0.4378 0.3878 0.040 0.000 0.000 0.632 0.328 0.000
#> SRR1044466 1 0.3714 0.7696 0.760 0.044 0.000 0.000 0.196 0.000
#> SRR1044465 1 0.0000 0.8183 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044467 1 0.0000 0.8183 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044468 2 0.2896 0.8278 0.000 0.824 0.016 0.000 0.000 0.160
#> SRR1044469 3 0.3607 0.4303 0.000 0.348 0.652 0.000 0.000 0.000
#> SRR1044470 1 0.4649 0.4516 0.560 0.036 0.000 0.004 0.400 0.000
#> SRR1044471 1 0.0405 0.8192 0.988 0.000 0.000 0.004 0.008 0.000
#> SRR1044472 1 0.3453 0.7831 0.792 0.044 0.000 0.000 0.164 0.000
#> SRR1044473 1 0.0790 0.8221 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1044474 6 0.0000 0.9304 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044475 3 0.3446 0.5289 0.000 0.308 0.692 0.000 0.000 0.000
#> SRR1044476 2 0.2941 0.7910 0.000 0.780 0.220 0.000 0.000 0.000
#> SRR1044477 6 0.0000 0.9304 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044478 2 0.3227 0.8353 0.000 0.824 0.116 0.000 0.000 0.060
#> SRR1044479 6 0.0000 0.9304 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044480 5 0.3819 0.4683 0.004 0.000 0.000 0.372 0.624 0.000
#> SRR1044481 5 0.2734 0.7780 0.148 0.004 0.000 0.008 0.840 0.000
#> SRR1044482 6 0.0000 0.9304 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044483 5 0.3945 0.4507 0.008 0.000 0.000 0.380 0.612 0.000
#> SRR1044484 5 0.3054 0.7765 0.136 0.000 0.000 0.036 0.828 0.000
#> SRR1044486 5 0.3421 0.7375 0.160 0.020 0.000 0.016 0.804 0.000
#> SRR1044485 6 0.2378 0.7608 0.000 0.152 0.000 0.000 0.000 0.848
#> SRR1044487 6 0.0000 0.9304 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044488 2 0.2896 0.8278 0.000 0.824 0.016 0.000 0.000 0.160
#> SRR1044489 2 0.2896 0.8278 0.000 0.824 0.016 0.000 0.000 0.160
#> SRR1044490 1 0.1908 0.7617 0.900 0.000 0.000 0.096 0.004 0.000
#> SRR1044491 1 0.3587 0.7759 0.772 0.040 0.000 0.000 0.188 0.000
#> SRR1044492 1 0.6240 0.5226 0.532 0.044 0.000 0.000 0.264 0.160
#> SRR1044493 1 0.3823 0.7712 0.760 0.044 0.000 0.004 0.192 0.000
#> SRR1044494 6 0.0000 0.9304 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044496 6 0.0000 0.9304 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044495 6 0.0000 0.9304 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044497 4 0.0363 0.8699 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR1044499 2 0.3175 0.7517 0.000 0.744 0.256 0.000 0.000 0.000
#> SRR1044498 5 0.3144 0.7584 0.172 0.004 0.000 0.016 0.808 0.000
#> SRR1044500 2 0.2703 0.8174 0.000 0.824 0.004 0.000 0.000 0.172
#> SRR1044501 2 0.2941 0.7910 0.000 0.780 0.220 0.000 0.000 0.000
#> SRR1044502 3 0.0865 0.8760 0.000 0.036 0.964 0.000 0.000 0.000
#> SRR1044503 4 0.0363 0.8699 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR1044504 4 0.0458 0.8692 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1044505 1 0.4099 0.2848 0.612 0.000 0.000 0.016 0.372 0.000
#> SRR1044506 4 0.0291 0.8668 0.000 0.004 0.000 0.992 0.004 0.000
#> SRR1044507 4 0.5324 0.5626 0.000 0.132 0.004 0.592 0.272 0.000
#> SRR1044508 4 0.6091 0.5803 0.000 0.132 0.072 0.592 0.204 0.000
#> SRR1044509 4 0.5725 0.6359 0.000 0.132 0.080 0.648 0.140 0.000
#> SRR1044510 3 0.1501 0.8589 0.000 0.076 0.924 0.000 0.000 0.000
#> SRR1044511 3 0.0146 0.8813 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1044512 3 0.0146 0.8813 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1044513 3 0.2688 0.7911 0.000 0.068 0.868 0.000 0.000 0.064
#> SRR1044514 3 0.0146 0.8813 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1044515 3 0.3321 0.7458 0.000 0.100 0.820 0.000 0.000 0.080
#> SRR1044516 2 0.3772 0.8143 0.000 0.772 0.160 0.000 0.000 0.068
#> SRR1044517 3 0.1814 0.8453 0.000 0.100 0.900 0.000 0.000 0.000
#> SRR1044518 3 0.0146 0.8813 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1044519 3 0.0000 0.8801 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044520 3 0.0000 0.8801 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044521 2 0.3136 0.7599 0.000 0.768 0.004 0.000 0.000 0.228
#> SRR1044522 6 0.0458 0.9206 0.000 0.016 0.000 0.000 0.000 0.984
#> SRR1044523 3 0.5617 0.2943 0.000 0.188 0.532 0.000 0.000 0.280
#> SRR1044524 3 0.0632 0.8793 0.000 0.024 0.976 0.000 0.000 0.000
#> SRR1044525 4 0.0547 0.8679 0.000 0.000 0.000 0.980 0.020 0.000
#> SRR1044526 5 0.5255 0.6186 0.140 0.000 0.000 0.272 0.588 0.000
#> SRR1044527 6 0.0000 0.9304 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044528 6 0.1007 0.9003 0.000 0.044 0.000 0.000 0.000 0.956
#> SRR1044529 6 0.0000 0.9304 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044530 1 0.4286 0.7624 0.740 0.044 0.000 0.004 0.196 0.016
#> SRR1044531 1 0.1900 0.8214 0.916 0.008 0.000 0.000 0.068 0.008
#> SRR1044533 1 0.1390 0.8243 0.948 0.016 0.000 0.000 0.032 0.004
#> SRR1044532 1 0.4286 0.7624 0.740 0.044 0.000 0.004 0.196 0.016
#> SRR1044534 2 0.3823 0.3564 0.000 0.564 0.000 0.000 0.000 0.436
#> SRR1044535 3 0.0632 0.8793 0.000 0.024 0.976 0.000 0.000 0.000
#> SRR1044536 2 0.2896 0.8278 0.000 0.824 0.016 0.000 0.000 0.160
#> SRR1044537 5 0.2553 0.7829 0.144 0.000 0.000 0.008 0.848 0.000
#> SRR1044538 1 0.4286 0.7624 0.740 0.044 0.000 0.004 0.196 0.016
#> SRR1044539 5 0.3797 0.3542 0.000 0.000 0.000 0.420 0.580 0.000
#> SRR1044540 1 0.0146 0.8186 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1044541 2 0.3126 0.7652 0.000 0.752 0.248 0.000 0.000 0.000
#> SRR1044542 1 0.4992 0.7394 0.704 0.044 0.000 0.012 0.196 0.044
#> SRR1044543 1 0.1462 0.7904 0.936 0.000 0.000 0.056 0.008 0.000
#> SRR1044544 3 0.3838 0.0933 0.000 0.448 0.552 0.000 0.000 0.000
#> SRR1044545 5 0.3578 0.5280 0.000 0.000 0.000 0.340 0.660 0.000
#> SRR1044546 5 0.2513 0.7835 0.140 0.000 0.000 0.008 0.852 0.000
#> SRR1044547 5 0.3541 0.6486 0.012 0.000 0.000 0.260 0.728 0.000
#> SRR1044548 5 0.2553 0.7821 0.144 0.000 0.000 0.008 0.848 0.000
#> SRR1044549 6 0.3225 0.7768 0.000 0.092 0.080 0.000 0.000 0.828
#> SRR1044550 2 0.2896 0.8278 0.000 0.824 0.016 0.000 0.000 0.160
#> SRR1044551 6 0.1267 0.8871 0.000 0.060 0.000 0.000 0.000 0.940
#> SRR1044552 4 0.0458 0.8692 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1044553 4 0.0458 0.8692 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1044554 5 0.2593 0.7812 0.148 0.000 0.000 0.008 0.844 0.000
#> SRR1044555 3 0.1814 0.8453 0.000 0.100 0.900 0.000 0.000 0.000
#> SRR1044556 4 0.0865 0.8591 0.000 0.000 0.000 0.964 0.036 0.000
#> SRR1044557 5 0.2513 0.7835 0.140 0.000 0.000 0.008 0.852 0.000
#> SRR1044558 4 0.1765 0.8132 0.000 0.000 0.000 0.904 0.096 0.000
#> SRR1044559 5 0.2513 0.7835 0.140 0.000 0.000 0.008 0.852 0.000
#> SRR1044561 4 0.0363 0.8699 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR1044560 2 0.2941 0.7910 0.000 0.780 0.220 0.000 0.000 0.000
#> SRR1044562 5 0.2513 0.7835 0.140 0.000 0.000 0.008 0.852 0.000
#> SRR1044563 4 0.3747 0.2451 0.000 0.000 0.000 0.604 0.396 0.000
#> SRR1044564 5 0.2553 0.7829 0.144 0.000 0.000 0.008 0.848 0.000
#> SRR1044565 6 0.0000 0.9304 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044566 2 0.2883 0.7964 0.000 0.788 0.212 0.000 0.000 0.000
#> SRR1044567 1 0.4578 0.7561 0.728 0.044 0.000 0.016 0.196 0.016
#> SRR1044568 5 0.4153 0.5243 0.024 0.000 0.000 0.340 0.636 0.000
#> SRR1044569 1 0.1049 0.8122 0.960 0.000 0.000 0.032 0.008 0.000
#> SRR1044570 1 0.4286 0.7624 0.740 0.044 0.000 0.004 0.196 0.016
#> SRR1044571 1 0.0000 0.8183 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044572 1 0.0405 0.8207 0.988 0.004 0.000 0.000 0.008 0.000
#> SRR1044573 1 0.2499 0.7825 0.880 0.000 0.000 0.072 0.048 0.000
#> SRR1044574 1 0.2454 0.8165 0.904 0.032 0.000 0.032 0.024 0.008
#> SRR1044575 1 0.0405 0.8174 0.988 0.000 0.000 0.008 0.004 0.000
#> SRR1044576 6 0.0000 0.9304 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044577 6 0.0000 0.9304 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044578 6 0.0000 0.9304 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044579 4 0.0363 0.8699 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR1044580 5 0.4374 0.7273 0.192 0.000 0.000 0.096 0.712 0.000
#> SRR1044581 4 0.0363 0.8699 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR1044582 5 0.2482 0.7761 0.148 0.000 0.000 0.004 0.848 0.000
#> SRR1044583 4 0.0363 0.8699 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR1044584 4 0.1444 0.8329 0.000 0.000 0.000 0.928 0.072 0.000
#> SRR1044585 4 0.0363 0.8699 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR1044586 5 0.2734 0.7780 0.148 0.004 0.000 0.008 0.840 0.000
#> SRR1044587 4 0.0551 0.8649 0.004 0.008 0.000 0.984 0.004 0.000
#> SRR1044588 4 0.0291 0.8668 0.000 0.004 0.000 0.992 0.004 0.000
#> SRR1044589 4 0.0291 0.8668 0.000 0.004 0.000 0.992 0.004 0.000
#> SRR1044590 4 0.0260 0.8664 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR1044591 4 0.0405 0.8656 0.000 0.008 0.000 0.988 0.004 0.000
#> SRR1044592 4 0.5725 0.6359 0.000 0.132 0.080 0.648 0.140 0.000
#> SRR1044593 4 0.0291 0.8668 0.000 0.004 0.000 0.992 0.004 0.000
#> SRR1044594 4 0.0291 0.8668 0.000 0.004 0.000 0.992 0.004 0.000
#> SRR1044595 4 0.6468 0.5036 0.004 0.132 0.072 0.540 0.252 0.000
#> SRR1044596 4 0.4493 0.6899 0.000 0.132 0.004 0.720 0.144 0.000
#> SRR1044597 6 0.5825 0.5275 0.076 0.044 0.000 0.024 0.220 0.636
#> SRR1044598 6 0.5126 0.5705 0.068 0.044 0.000 0.000 0.216 0.672
#> SRR1044599 6 0.5099 0.5730 0.064 0.044 0.000 0.000 0.220 0.672
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.702 0.876 0.934 0.4868 0.504 0.504
#> 3 3 0.728 0.857 0.929 0.3017 0.809 0.639
#> 4 4 0.647 0.765 0.852 0.0659 0.987 0.965
#> 5 5 0.682 0.800 0.867 0.0925 0.852 0.603
#> 6 6 0.743 0.776 0.879 0.0317 0.989 0.957
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0.0376 0.9084 0.004 0.996
#> SRR1044416 2 0.1414 0.9084 0.020 0.980
#> SRR1044417 2 0.4022 0.8931 0.080 0.920
#> SRR1044418 2 0.4161 0.8914 0.084 0.916
#> SRR1044420 2 0.0672 0.9092 0.008 0.992
#> SRR1044419 2 0.0376 0.9084 0.004 0.996
#> SRR1044421 2 0.0672 0.9092 0.008 0.992
#> SRR1044422 2 0.0672 0.9092 0.008 0.992
#> SRR1044423 2 0.0672 0.9092 0.008 0.992
#> SRR1044424 2 0.2423 0.9045 0.040 0.960
#> SRR1044425 1 0.0000 0.9562 1.000 0.000
#> SRR1044426 1 0.0376 0.9543 0.996 0.004
#> SRR1044427 1 0.2423 0.9319 0.960 0.040
#> SRR1044428 2 0.9522 0.5503 0.372 0.628
#> SRR1044429 1 0.0376 0.9545 0.996 0.004
#> SRR1044430 2 0.5519 0.8642 0.128 0.872
#> SRR1044431 1 0.0376 0.9546 0.996 0.004
#> SRR1044433 1 0.0938 0.9500 0.988 0.012
#> SRR1044432 2 0.8267 0.7350 0.260 0.740
#> SRR1044434 1 0.0000 0.9562 1.000 0.000
#> SRR1044435 1 0.0000 0.9562 1.000 0.000
#> SRR1044436 1 0.0000 0.9562 1.000 0.000
#> SRR1044437 1 0.0000 0.9562 1.000 0.000
#> SRR1044439 1 0.0000 0.9562 1.000 0.000
#> SRR1044438 1 0.0000 0.9562 1.000 0.000
#> SRR1044440 1 0.0000 0.9562 1.000 0.000
#> SRR1044441 1 0.0000 0.9562 1.000 0.000
#> SRR1044442 1 0.0672 0.9528 0.992 0.008
#> SRR1044443 1 0.8386 0.6286 0.732 0.268
#> SRR1044444 1 0.0000 0.9562 1.000 0.000
#> SRR1044445 1 0.0000 0.9562 1.000 0.000
#> SRR1044446 2 0.0000 0.9072 0.000 1.000
#> SRR1044447 2 0.2236 0.9055 0.036 0.964
#> SRR1044449 2 0.0000 0.9072 0.000 1.000
#> SRR1044448 2 0.0000 0.9072 0.000 1.000
#> SRR1044450 2 0.0376 0.9084 0.004 0.996
#> SRR1044451 2 0.0938 0.9092 0.012 0.988
#> SRR1044452 2 0.0000 0.9072 0.000 1.000
#> SRR1044453 2 0.0000 0.9072 0.000 1.000
#> SRR1044454 2 0.0000 0.9072 0.000 1.000
#> SRR1044455 2 0.0376 0.9084 0.004 0.996
#> SRR1044456 2 0.6247 0.8407 0.156 0.844
#> SRR1044457 2 0.0000 0.9072 0.000 1.000
#> SRR1044458 2 0.0000 0.9072 0.000 1.000
#> SRR1044459 2 0.0000 0.9072 0.000 1.000
#> SRR1044460 2 0.0376 0.9084 0.004 0.996
#> SRR1044461 2 0.0376 0.9084 0.004 0.996
#> SRR1044462 1 0.0938 0.9505 0.988 0.012
#> SRR1044463 1 0.9881 0.1071 0.564 0.436
#> SRR1044464 1 0.0000 0.9562 1.000 0.000
#> SRR1044466 2 0.7139 0.8040 0.196 0.804
#> SRR1044465 1 0.4431 0.8832 0.908 0.092
#> SRR1044467 1 0.0938 0.9502 0.988 0.012
#> SRR1044468 2 0.0672 0.9092 0.008 0.992
#> SRR1044469 2 0.0000 0.9072 0.000 1.000
#> SRR1044470 2 0.8016 0.7549 0.244 0.756
#> SRR1044471 1 0.2236 0.9341 0.964 0.036
#> SRR1044472 2 0.6148 0.8450 0.152 0.848
#> SRR1044473 1 0.5629 0.8365 0.868 0.132
#> SRR1044474 2 0.4161 0.8914 0.084 0.916
#> SRR1044475 2 0.0000 0.9072 0.000 1.000
#> SRR1044476 2 0.0000 0.9072 0.000 1.000
#> SRR1044477 2 0.4298 0.8895 0.088 0.912
#> SRR1044478 2 0.0672 0.9092 0.008 0.992
#> SRR1044479 2 0.5178 0.8721 0.116 0.884
#> SRR1044480 1 0.0000 0.9562 1.000 0.000
#> SRR1044481 1 0.4690 0.8725 0.900 0.100
#> SRR1044482 2 0.4161 0.8914 0.084 0.916
#> SRR1044483 1 0.0000 0.9562 1.000 0.000
#> SRR1044484 1 0.0000 0.9562 1.000 0.000
#> SRR1044486 1 0.7299 0.7288 0.796 0.204
#> SRR1044485 2 0.0938 0.9093 0.012 0.988
#> SRR1044487 2 0.4298 0.8895 0.088 0.912
#> SRR1044488 2 0.0672 0.9092 0.008 0.992
#> SRR1044489 2 0.0672 0.9092 0.008 0.992
#> SRR1044490 1 0.0672 0.9529 0.992 0.008
#> SRR1044491 2 0.7674 0.7753 0.224 0.776
#> SRR1044492 2 0.9170 0.6125 0.332 0.668
#> SRR1044493 2 0.8555 0.7037 0.280 0.720
#> SRR1044494 2 0.4298 0.8895 0.088 0.912
#> SRR1044496 2 0.4298 0.8895 0.088 0.912
#> SRR1044495 2 0.4298 0.8895 0.088 0.912
#> SRR1044497 1 0.0000 0.9562 1.000 0.000
#> SRR1044499 2 0.0000 0.9072 0.000 1.000
#> SRR1044498 1 0.0000 0.9562 1.000 0.000
#> SRR1044500 2 0.0672 0.9092 0.008 0.992
#> SRR1044501 2 0.0376 0.9084 0.004 0.996
#> SRR1044502 2 0.0938 0.9092 0.012 0.988
#> SRR1044503 1 0.0000 0.9562 1.000 0.000
#> SRR1044504 1 0.0000 0.9562 1.000 0.000
#> SRR1044505 1 0.5629 0.8317 0.868 0.132
#> SRR1044506 1 0.0000 0.9562 1.000 0.000
#> SRR1044507 1 0.0938 0.9505 0.988 0.012
#> SRR1044508 1 0.1633 0.9426 0.976 0.024
#> SRR1044509 1 0.0000 0.9562 1.000 0.000
#> SRR1044510 2 0.0000 0.9072 0.000 1.000
#> SRR1044511 2 0.0000 0.9072 0.000 1.000
#> SRR1044512 2 0.0000 0.9072 0.000 1.000
#> SRR1044513 2 0.0938 0.9092 0.012 0.988
#> SRR1044514 2 0.0000 0.9072 0.000 1.000
#> SRR1044515 2 0.1184 0.9089 0.016 0.984
#> SRR1044516 2 0.0672 0.9092 0.008 0.992
#> SRR1044517 2 0.0000 0.9072 0.000 1.000
#> SRR1044518 2 0.0000 0.9072 0.000 1.000
#> SRR1044519 2 0.0672 0.9092 0.008 0.992
#> SRR1044520 2 0.0000 0.9072 0.000 1.000
#> SRR1044521 2 0.1414 0.9084 0.020 0.980
#> SRR1044522 2 0.5059 0.8746 0.112 0.888
#> SRR1044523 2 0.1184 0.9089 0.016 0.984
#> SRR1044524 2 0.0000 0.9072 0.000 1.000
#> SRR1044525 1 0.0000 0.9562 1.000 0.000
#> SRR1044526 1 0.0000 0.9562 1.000 0.000
#> SRR1044527 2 0.4022 0.8931 0.080 0.920
#> SRR1044528 2 0.3879 0.8945 0.076 0.924
#> SRR1044529 2 0.4161 0.8914 0.084 0.916
#> SRR1044530 1 0.9922 0.0645 0.552 0.448
#> SRR1044531 1 0.6712 0.7812 0.824 0.176
#> SRR1044533 1 0.7453 0.7234 0.788 0.212
#> SRR1044532 2 0.8207 0.7366 0.256 0.744
#> SRR1044534 2 0.3431 0.8984 0.064 0.936
#> SRR1044535 2 0.0000 0.9072 0.000 1.000
#> SRR1044536 2 0.0672 0.9092 0.008 0.992
#> SRR1044537 2 0.8555 0.7068 0.280 0.720
#> SRR1044538 2 0.8144 0.7429 0.252 0.748
#> SRR1044539 1 0.0000 0.9562 1.000 0.000
#> SRR1044540 1 0.0000 0.9562 1.000 0.000
#> SRR1044541 2 0.0000 0.9072 0.000 1.000
#> SRR1044542 2 0.9850 0.3918 0.428 0.572
#> SRR1044543 1 0.0376 0.9546 0.996 0.004
#> SRR1044544 2 0.0000 0.9072 0.000 1.000
#> SRR1044545 1 0.0000 0.9562 1.000 0.000
#> SRR1044546 1 0.7219 0.7346 0.800 0.200
#> SRR1044547 1 0.0000 0.9562 1.000 0.000
#> SRR1044548 2 0.9427 0.5687 0.360 0.640
#> SRR1044549 2 0.3584 0.8972 0.068 0.932
#> SRR1044550 2 0.0672 0.9092 0.008 0.992
#> SRR1044551 2 0.3274 0.8995 0.060 0.940
#> SRR1044552 1 0.0000 0.9562 1.000 0.000
#> SRR1044553 1 0.0000 0.9562 1.000 0.000
#> SRR1044554 2 0.9686 0.4902 0.396 0.604
#> SRR1044555 2 0.0000 0.9072 0.000 1.000
#> SRR1044556 1 0.0000 0.9562 1.000 0.000
#> SRR1044557 2 0.9358 0.5890 0.352 0.648
#> SRR1044558 1 0.0000 0.9562 1.000 0.000
#> SRR1044559 2 0.8555 0.7065 0.280 0.720
#> SRR1044561 1 0.0000 0.9562 1.000 0.000
#> SRR1044560 2 0.0000 0.9072 0.000 1.000
#> SRR1044562 2 0.8661 0.6951 0.288 0.712
#> SRR1044563 1 0.0000 0.9562 1.000 0.000
#> SRR1044564 1 0.4298 0.8863 0.912 0.088
#> SRR1044565 2 0.4298 0.8895 0.088 0.912
#> SRR1044566 2 0.0000 0.9072 0.000 1.000
#> SRR1044567 2 0.9944 0.3142 0.456 0.544
#> SRR1044568 1 0.0000 0.9562 1.000 0.000
#> SRR1044569 1 0.1843 0.9396 0.972 0.028
#> SRR1044570 2 0.9170 0.6148 0.332 0.668
#> SRR1044571 1 0.3114 0.9169 0.944 0.056
#> SRR1044572 1 0.0000 0.9562 1.000 0.000
#> SRR1044573 1 0.3733 0.9007 0.928 0.072
#> SRR1044574 1 0.1843 0.9404 0.972 0.028
#> SRR1044575 1 0.0376 0.9546 0.996 0.004
#> SRR1044576 2 0.4022 0.8931 0.080 0.920
#> SRR1044577 2 0.4022 0.8931 0.080 0.920
#> SRR1044578 2 0.4161 0.8914 0.084 0.916
#> SRR1044579 1 0.0000 0.9562 1.000 0.000
#> SRR1044580 1 0.0000 0.9562 1.000 0.000
#> SRR1044581 1 0.0000 0.9562 1.000 0.000
#> SRR1044582 2 0.9427 0.5715 0.360 0.640
#> SRR1044583 1 0.0000 0.9562 1.000 0.000
#> SRR1044584 1 0.0000 0.9562 1.000 0.000
#> SRR1044585 1 0.0000 0.9562 1.000 0.000
#> SRR1044586 1 0.6712 0.7631 0.824 0.176
#> SRR1044587 1 0.0000 0.9562 1.000 0.000
#> SRR1044588 1 0.0000 0.9562 1.000 0.000
#> SRR1044589 1 0.0000 0.9562 1.000 0.000
#> SRR1044590 1 0.0000 0.9562 1.000 0.000
#> SRR1044591 1 0.0000 0.9562 1.000 0.000
#> SRR1044592 1 0.0000 0.9562 1.000 0.000
#> SRR1044593 1 0.0000 0.9562 1.000 0.000
#> SRR1044594 1 0.0000 0.9562 1.000 0.000
#> SRR1044595 1 0.4161 0.8922 0.916 0.084
#> SRR1044596 1 0.0000 0.9562 1.000 0.000
#> SRR1044597 2 0.6712 0.8237 0.176 0.824
#> SRR1044598 2 0.7376 0.7917 0.208 0.792
#> SRR1044599 2 0.7299 0.7956 0.204 0.796
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 3 0.3412 0.891 0.000 0.124 0.876
#> SRR1044416 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044417 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044418 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044420 2 0.0237 0.888 0.000 0.996 0.004
#> SRR1044419 3 0.3340 0.895 0.000 0.120 0.880
#> SRR1044421 2 0.1860 0.860 0.000 0.948 0.052
#> SRR1044422 2 0.3941 0.761 0.000 0.844 0.156
#> SRR1044423 2 0.5948 0.370 0.000 0.640 0.360
#> SRR1044424 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044425 1 0.0892 0.925 0.980 0.020 0.000
#> SRR1044426 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044427 1 0.5138 0.687 0.748 0.252 0.000
#> SRR1044428 2 0.5178 0.720 0.256 0.744 0.000
#> SRR1044429 1 0.0747 0.927 0.984 0.016 0.000
#> SRR1044430 2 0.2537 0.871 0.080 0.920 0.000
#> SRR1044431 1 0.2165 0.896 0.936 0.064 0.000
#> SRR1044433 1 0.1529 0.910 0.960 0.040 0.000
#> SRR1044432 2 0.5070 0.762 0.224 0.772 0.004
#> SRR1044434 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044435 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044436 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044437 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044439 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044438 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044440 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044441 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044442 1 0.1289 0.918 0.968 0.032 0.000
#> SRR1044443 1 0.5397 0.648 0.720 0.280 0.000
#> SRR1044444 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044445 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044446 3 0.2959 0.899 0.000 0.100 0.900
#> SRR1044447 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044449 3 0.0000 0.944 0.000 0.000 1.000
#> SRR1044448 3 0.1163 0.939 0.000 0.028 0.972
#> SRR1044450 3 0.3619 0.866 0.000 0.136 0.864
#> SRR1044451 2 0.1529 0.874 0.000 0.960 0.040
#> SRR1044452 3 0.0000 0.944 0.000 0.000 1.000
#> SRR1044453 3 0.0000 0.944 0.000 0.000 1.000
#> SRR1044454 3 0.0000 0.944 0.000 0.000 1.000
#> SRR1044455 3 0.3340 0.895 0.000 0.120 0.880
#> SRR1044456 2 0.0237 0.889 0.004 0.996 0.000
#> SRR1044457 3 0.1753 0.935 0.000 0.048 0.952
#> SRR1044458 3 0.2537 0.921 0.000 0.080 0.920
#> SRR1044459 3 0.0000 0.944 0.000 0.000 1.000
#> SRR1044460 2 0.5497 0.579 0.000 0.708 0.292
#> SRR1044461 3 0.3340 0.895 0.000 0.120 0.880
#> SRR1044462 1 0.2261 0.896 0.932 0.068 0.000
#> SRR1044463 2 0.4842 0.760 0.224 0.776 0.000
#> SRR1044464 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044466 2 0.2261 0.874 0.068 0.932 0.000
#> SRR1044465 1 0.5138 0.684 0.748 0.252 0.000
#> SRR1044467 1 0.2448 0.883 0.924 0.076 0.000
#> SRR1044468 2 0.2878 0.833 0.000 0.904 0.096
#> SRR1044469 3 0.0000 0.944 0.000 0.000 1.000
#> SRR1044470 2 0.4399 0.798 0.188 0.812 0.000
#> SRR1044471 1 0.2878 0.871 0.904 0.096 0.000
#> SRR1044472 2 0.2448 0.871 0.076 0.924 0.000
#> SRR1044473 2 0.6260 0.255 0.448 0.552 0.000
#> SRR1044474 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044475 3 0.0000 0.944 0.000 0.000 1.000
#> SRR1044476 3 0.2537 0.921 0.000 0.080 0.920
#> SRR1044477 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044478 3 0.6026 0.522 0.000 0.376 0.624
#> SRR1044479 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044480 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044481 1 0.6204 0.197 0.576 0.424 0.000
#> SRR1044482 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044483 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044484 1 0.2356 0.887 0.928 0.072 0.000
#> SRR1044486 2 0.6140 0.418 0.404 0.596 0.000
#> SRR1044485 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044487 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044488 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044489 2 0.1031 0.879 0.000 0.976 0.024
#> SRR1044490 1 0.1643 0.913 0.956 0.044 0.000
#> SRR1044491 2 0.3038 0.857 0.104 0.896 0.000
#> SRR1044492 2 0.2165 0.876 0.064 0.936 0.000
#> SRR1044493 2 0.3192 0.853 0.112 0.888 0.000
#> SRR1044494 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044496 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044495 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044497 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044499 3 0.0000 0.944 0.000 0.000 1.000
#> SRR1044498 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044500 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044501 3 0.3340 0.895 0.000 0.120 0.880
#> SRR1044502 2 0.5835 0.395 0.000 0.660 0.340
#> SRR1044503 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044504 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044505 1 0.5363 0.597 0.724 0.276 0.000
#> SRR1044506 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044507 1 0.1643 0.915 0.956 0.044 0.000
#> SRR1044508 1 0.0747 0.928 0.984 0.016 0.000
#> SRR1044509 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044510 3 0.0000 0.944 0.000 0.000 1.000
#> SRR1044511 3 0.0000 0.944 0.000 0.000 1.000
#> SRR1044512 3 0.0000 0.944 0.000 0.000 1.000
#> SRR1044513 2 0.0237 0.888 0.000 0.996 0.004
#> SRR1044514 3 0.0000 0.944 0.000 0.000 1.000
#> SRR1044515 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044516 2 0.1529 0.871 0.000 0.960 0.040
#> SRR1044517 3 0.0000 0.944 0.000 0.000 1.000
#> SRR1044518 3 0.0000 0.944 0.000 0.000 1.000
#> SRR1044519 3 0.3941 0.845 0.000 0.156 0.844
#> SRR1044520 3 0.1411 0.936 0.000 0.036 0.964
#> SRR1044521 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044522 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044523 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044524 3 0.0000 0.944 0.000 0.000 1.000
#> SRR1044525 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044526 1 0.1163 0.922 0.972 0.028 0.000
#> SRR1044527 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044528 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044529 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044530 2 0.3816 0.829 0.148 0.852 0.000
#> SRR1044531 1 0.6095 0.398 0.608 0.392 0.000
#> SRR1044533 1 0.5810 0.535 0.664 0.336 0.000
#> SRR1044532 2 0.2448 0.870 0.076 0.924 0.000
#> SRR1044534 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044535 3 0.1411 0.936 0.000 0.036 0.964
#> SRR1044536 2 0.1289 0.876 0.000 0.968 0.032
#> SRR1044537 2 0.4750 0.770 0.216 0.784 0.000
#> SRR1044538 2 0.2537 0.870 0.080 0.920 0.000
#> SRR1044539 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044540 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044541 3 0.2066 0.931 0.000 0.060 0.940
#> SRR1044542 2 0.3340 0.848 0.120 0.880 0.000
#> SRR1044543 1 0.1411 0.917 0.964 0.036 0.000
#> SRR1044544 3 0.0000 0.944 0.000 0.000 1.000
#> SRR1044545 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044546 2 0.5497 0.664 0.292 0.708 0.000
#> SRR1044547 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044548 2 0.4605 0.782 0.204 0.796 0.000
#> SRR1044549 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044550 2 0.2066 0.854 0.000 0.940 0.060
#> SRR1044551 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044552 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044553 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044554 2 0.5058 0.737 0.244 0.756 0.000
#> SRR1044555 3 0.0000 0.944 0.000 0.000 1.000
#> SRR1044556 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044557 2 0.5138 0.726 0.252 0.748 0.000
#> SRR1044558 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044559 2 0.4887 0.756 0.228 0.772 0.000
#> SRR1044561 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044560 3 0.2165 0.929 0.000 0.064 0.936
#> SRR1044562 2 0.4974 0.746 0.236 0.764 0.000
#> SRR1044563 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044564 1 0.5882 0.442 0.652 0.348 0.000
#> SRR1044565 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044566 3 0.2625 0.918 0.000 0.084 0.916
#> SRR1044567 2 0.4002 0.822 0.160 0.840 0.000
#> SRR1044568 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044569 1 0.6154 0.245 0.592 0.408 0.000
#> SRR1044570 2 0.2625 0.867 0.084 0.916 0.000
#> SRR1044571 1 0.5098 0.679 0.752 0.248 0.000
#> SRR1044572 1 0.0592 0.929 0.988 0.012 0.000
#> SRR1044573 1 0.4931 0.719 0.768 0.232 0.000
#> SRR1044574 1 0.3619 0.834 0.864 0.136 0.000
#> SRR1044575 1 0.1411 0.917 0.964 0.036 0.000
#> SRR1044576 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044577 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044578 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044579 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044580 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044581 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044582 2 0.5098 0.731 0.248 0.752 0.000
#> SRR1044583 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044584 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044585 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044586 2 0.5810 0.585 0.336 0.664 0.000
#> SRR1044587 1 0.0592 0.929 0.988 0.012 0.000
#> SRR1044588 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044589 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044590 1 0.0237 0.932 0.996 0.004 0.000
#> SRR1044591 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044592 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044593 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044594 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044595 1 0.3879 0.816 0.848 0.152 0.000
#> SRR1044596 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1044597 2 0.0000 0.890 0.000 1.000 0.000
#> SRR1044598 2 0.2165 0.875 0.064 0.936 0.000
#> SRR1044599 2 0.2261 0.874 0.068 0.932 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 3 0.2589 0.789 0.000 0.116 0.884 0.000
#> SRR1044416 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044417 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044418 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044420 2 0.0469 0.804 0.000 0.988 0.012 0.000
#> SRR1044419 3 0.2530 0.794 0.000 0.112 0.888 0.000
#> SRR1044421 2 0.3569 0.625 0.000 0.804 0.196 0.000
#> SRR1044422 2 0.3688 0.623 0.000 0.792 0.208 0.000
#> SRR1044423 2 0.4843 0.200 0.000 0.604 0.396 0.000
#> SRR1044424 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044425 4 0.2256 0.859 0.056 0.020 0.000 0.924
#> SRR1044426 4 0.2647 0.842 0.120 0.000 0.000 0.880
#> SRR1044427 4 0.6576 0.610 0.168 0.200 0.000 0.632
#> SRR1044428 2 0.6675 0.663 0.228 0.616 0.000 0.156
#> SRR1044429 4 0.2563 0.859 0.072 0.020 0.000 0.908
#> SRR1044430 2 0.5530 0.746 0.192 0.732 0.008 0.068
#> SRR1044431 4 0.4553 0.786 0.180 0.040 0.000 0.780
#> SRR1044433 4 0.0921 0.870 0.000 0.028 0.000 0.972
#> SRR1044432 2 0.7090 0.658 0.232 0.604 0.012 0.152
#> SRR1044434 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044435 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044436 4 0.0592 0.883 0.016 0.000 0.000 0.984
#> SRR1044437 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044439 4 0.0592 0.883 0.016 0.000 0.000 0.984
#> SRR1044438 4 0.0188 0.884 0.004 0.000 0.000 0.996
#> SRR1044440 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044441 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044442 4 0.1256 0.872 0.008 0.028 0.000 0.964
#> SRR1044443 4 0.4647 0.608 0.008 0.288 0.000 0.704
#> SRR1044444 4 0.0336 0.884 0.008 0.000 0.000 0.992
#> SRR1044445 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044446 3 0.3820 0.752 0.088 0.064 0.848 0.000
#> SRR1044447 2 0.1510 0.794 0.028 0.956 0.016 0.000
#> SRR1044449 1 0.3942 0.896 0.764 0.000 0.236 0.000
#> SRR1044448 3 0.2909 0.767 0.092 0.020 0.888 0.000
#> SRR1044450 3 0.4171 0.735 0.088 0.084 0.828 0.000
#> SRR1044451 2 0.4114 0.694 0.060 0.828 0.112 0.000
#> SRR1044452 1 0.4500 0.949 0.684 0.000 0.316 0.000
#> SRR1044453 1 0.4500 0.949 0.684 0.000 0.316 0.000
#> SRR1044454 1 0.4500 0.949 0.684 0.000 0.316 0.000
#> SRR1044455 3 0.2530 0.794 0.000 0.112 0.888 0.000
#> SRR1044456 2 0.2266 0.793 0.084 0.912 0.000 0.004
#> SRR1044457 3 0.1716 0.814 0.000 0.064 0.936 0.000
#> SRR1044458 3 0.2216 0.809 0.000 0.092 0.908 0.000
#> SRR1044459 3 0.1474 0.761 0.052 0.000 0.948 0.000
#> SRR1044460 2 0.4697 0.407 0.000 0.644 0.356 0.000
#> SRR1044461 3 0.2530 0.794 0.000 0.112 0.888 0.000
#> SRR1044462 4 0.3156 0.846 0.048 0.068 0.000 0.884
#> SRR1044463 2 0.6623 0.662 0.232 0.620 0.000 0.148
#> SRR1044464 4 0.1637 0.875 0.060 0.000 0.000 0.940
#> SRR1044466 2 0.5008 0.737 0.228 0.732 0.000 0.040
#> SRR1044465 4 0.6781 0.588 0.212 0.180 0.000 0.608
#> SRR1044467 4 0.5363 0.731 0.216 0.064 0.000 0.720
#> SRR1044468 2 0.4164 0.550 0.000 0.736 0.264 0.000
#> SRR1044469 3 0.2921 0.620 0.140 0.000 0.860 0.000
#> SRR1044470 2 0.6327 0.693 0.216 0.652 0.000 0.132
#> SRR1044471 4 0.5220 0.756 0.156 0.092 0.000 0.752
#> SRR1044472 2 0.5067 0.740 0.216 0.736 0.000 0.048
#> SRR1044473 2 0.7669 0.293 0.228 0.444 0.000 0.328
#> SRR1044474 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044475 1 0.4522 0.946 0.680 0.000 0.320 0.000
#> SRR1044476 3 0.2216 0.809 0.000 0.092 0.908 0.000
#> SRR1044477 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044478 3 0.4955 0.336 0.000 0.444 0.556 0.000
#> SRR1044479 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044480 4 0.0921 0.882 0.028 0.000 0.000 0.972
#> SRR1044481 4 0.7442 0.126 0.184 0.340 0.000 0.476
#> SRR1044482 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044483 4 0.0817 0.883 0.024 0.000 0.000 0.976
#> SRR1044484 4 0.3168 0.841 0.060 0.056 0.000 0.884
#> SRR1044486 2 0.7432 0.373 0.184 0.480 0.000 0.336
#> SRR1044485 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044487 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044488 2 0.0469 0.803 0.000 0.988 0.012 0.000
#> SRR1044489 2 0.2011 0.761 0.000 0.920 0.080 0.000
#> SRR1044490 4 0.4194 0.793 0.172 0.028 0.000 0.800
#> SRR1044491 2 0.5599 0.722 0.228 0.700 0.000 0.072
#> SRR1044492 2 0.4956 0.737 0.232 0.732 0.000 0.036
#> SRR1044493 2 0.5464 0.726 0.228 0.708 0.000 0.064
#> SRR1044494 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044496 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044495 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044497 4 0.0336 0.884 0.008 0.000 0.000 0.992
#> SRR1044499 3 0.0000 0.786 0.000 0.000 1.000 0.000
#> SRR1044498 4 0.2081 0.862 0.084 0.000 0.000 0.916
#> SRR1044500 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044501 3 0.2530 0.794 0.000 0.112 0.888 0.000
#> SRR1044502 2 0.5376 0.103 0.016 0.588 0.396 0.000
#> SRR1044503 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044504 4 0.0188 0.884 0.004 0.000 0.000 0.996
#> SRR1044505 4 0.6140 0.556 0.096 0.252 0.000 0.652
#> SRR1044506 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044507 4 0.2363 0.859 0.024 0.056 0.000 0.920
#> SRR1044508 4 0.0927 0.881 0.008 0.016 0.000 0.976
#> SRR1044509 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044510 1 0.4500 0.935 0.684 0.000 0.316 0.000
#> SRR1044511 3 0.3726 0.590 0.212 0.000 0.788 0.000
#> SRR1044512 1 0.4008 0.901 0.756 0.000 0.244 0.000
#> SRR1044513 2 0.0895 0.802 0.020 0.976 0.004 0.000
#> SRR1044514 3 0.4040 0.548 0.248 0.000 0.752 0.000
#> SRR1044515 2 0.0707 0.803 0.020 0.980 0.000 0.000
#> SRR1044516 2 0.2081 0.762 0.000 0.916 0.084 0.000
#> SRR1044517 1 0.4713 0.905 0.640 0.000 0.360 0.000
#> SRR1044518 3 0.2149 0.764 0.088 0.000 0.912 0.000
#> SRR1044519 3 0.4424 0.715 0.088 0.100 0.812 0.000
#> SRR1044520 3 0.3863 0.719 0.144 0.028 0.828 0.000
#> SRR1044521 2 0.0188 0.807 0.000 0.996 0.004 0.000
#> SRR1044522 2 0.0336 0.808 0.008 0.992 0.000 0.000
#> SRR1044523 2 0.0336 0.806 0.008 0.992 0.000 0.000
#> SRR1044524 3 0.0469 0.785 0.012 0.000 0.988 0.000
#> SRR1044525 4 0.0188 0.884 0.004 0.000 0.000 0.996
#> SRR1044526 4 0.2489 0.862 0.068 0.020 0.000 0.912
#> SRR1044527 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044528 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044529 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044530 2 0.5880 0.708 0.232 0.680 0.000 0.088
#> SRR1044531 4 0.7396 0.394 0.216 0.268 0.000 0.516
#> SRR1044533 4 0.7227 0.493 0.228 0.224 0.000 0.548
#> SRR1044532 2 0.5123 0.732 0.232 0.724 0.000 0.044
#> SRR1044534 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044535 3 0.2060 0.799 0.016 0.052 0.932 0.000
#> SRR1044536 2 0.2081 0.758 0.000 0.916 0.084 0.000
#> SRR1044537 2 0.6362 0.684 0.168 0.656 0.000 0.176
#> SRR1044538 2 0.5102 0.738 0.220 0.732 0.000 0.048
#> SRR1044539 4 0.0592 0.883 0.016 0.000 0.000 0.984
#> SRR1044540 4 0.3266 0.815 0.168 0.000 0.000 0.832
#> SRR1044541 3 0.1867 0.814 0.000 0.072 0.928 0.000
#> SRR1044542 2 0.5496 0.724 0.232 0.704 0.000 0.064
#> SRR1044543 4 0.4035 0.800 0.176 0.020 0.000 0.804
#> SRR1044544 3 0.0188 0.784 0.004 0.000 0.996 0.000
#> SRR1044545 4 0.0817 0.883 0.024 0.000 0.000 0.976
#> SRR1044546 2 0.7001 0.590 0.180 0.576 0.000 0.244
#> SRR1044547 4 0.1211 0.879 0.040 0.000 0.000 0.960
#> SRR1044548 2 0.6363 0.685 0.172 0.656 0.000 0.172
#> SRR1044549 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044550 2 0.3024 0.688 0.000 0.852 0.148 0.000
#> SRR1044551 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044552 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044553 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044554 2 0.6617 0.667 0.196 0.628 0.000 0.176
#> SRR1044555 3 0.0469 0.785 0.012 0.000 0.988 0.000
#> SRR1044556 4 0.0592 0.883 0.016 0.000 0.000 0.984
#> SRR1044557 2 0.6313 0.662 0.128 0.652 0.000 0.220
#> SRR1044558 4 0.0469 0.884 0.012 0.000 0.000 0.988
#> SRR1044559 2 0.5572 0.699 0.088 0.716 0.000 0.196
#> SRR1044561 4 0.0469 0.884 0.012 0.000 0.000 0.988
#> SRR1044560 3 0.1940 0.814 0.000 0.076 0.924 0.000
#> SRR1044562 2 0.6449 0.665 0.152 0.644 0.000 0.204
#> SRR1044563 4 0.0707 0.883 0.020 0.000 0.000 0.980
#> SRR1044564 4 0.7346 0.311 0.200 0.280 0.000 0.520
#> SRR1044565 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044566 3 0.2216 0.809 0.000 0.092 0.908 0.000
#> SRR1044567 2 0.5988 0.709 0.224 0.676 0.000 0.100
#> SRR1044568 4 0.0921 0.883 0.028 0.000 0.000 0.972
#> SRR1044569 4 0.7345 0.143 0.172 0.336 0.000 0.492
#> SRR1044570 2 0.5327 0.732 0.220 0.720 0.000 0.060
#> SRR1044571 4 0.7114 0.506 0.232 0.204 0.000 0.564
#> SRR1044572 4 0.3908 0.781 0.212 0.004 0.000 0.784
#> SRR1044573 4 0.6204 0.676 0.164 0.164 0.000 0.672
#> SRR1044574 4 0.5803 0.707 0.196 0.104 0.000 0.700
#> SRR1044575 4 0.4867 0.747 0.232 0.032 0.000 0.736
#> SRR1044576 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044577 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044578 2 0.0000 0.808 0.000 1.000 0.000 0.000
#> SRR1044579 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044580 4 0.1474 0.875 0.052 0.000 0.000 0.948
#> SRR1044581 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044582 2 0.6686 0.659 0.200 0.620 0.000 0.180
#> SRR1044583 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044584 4 0.0469 0.884 0.012 0.000 0.000 0.988
#> SRR1044585 4 0.0336 0.884 0.008 0.000 0.000 0.992
#> SRR1044586 2 0.7117 0.561 0.180 0.556 0.000 0.264
#> SRR1044587 4 0.1807 0.867 0.052 0.008 0.000 0.940
#> SRR1044588 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044589 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044590 4 0.1488 0.873 0.032 0.012 0.000 0.956
#> SRR1044591 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044592 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044593 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044594 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044595 4 0.4898 0.771 0.116 0.104 0.000 0.780
#> SRR1044596 4 0.0000 0.884 0.000 0.000 0.000 1.000
#> SRR1044597 2 0.2011 0.795 0.080 0.920 0.000 0.000
#> SRR1044598 2 0.4833 0.740 0.228 0.740 0.000 0.032
#> SRR1044599 2 0.4951 0.743 0.212 0.744 0.000 0.044
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 3 0.0404 0.881 0.000 0.012 0.988 0.000 0.000
#> SRR1044416 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044417 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044418 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044420 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044419 3 0.0290 0.884 0.000 0.008 0.992 0.000 0.000
#> SRR1044421 2 0.1792 0.873 0.000 0.916 0.084 0.000 0.000
#> SRR1044422 2 0.1608 0.885 0.000 0.928 0.072 0.000 0.000
#> SRR1044423 2 0.3534 0.668 0.000 0.744 0.256 0.000 0.000
#> SRR1044424 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044425 4 0.2669 0.803 0.104 0.020 0.000 0.876 0.000
#> SRR1044426 4 0.4126 0.352 0.380 0.000 0.000 0.620 0.000
#> SRR1044427 4 0.5796 0.267 0.312 0.116 0.000 0.572 0.000
#> SRR1044428 1 0.4593 0.798 0.736 0.184 0.000 0.080 0.000
#> SRR1044429 4 0.3278 0.770 0.156 0.020 0.000 0.824 0.000
#> SRR1044430 1 0.4818 0.753 0.688 0.260 0.000 0.048 0.004
#> SRR1044431 4 0.4567 0.435 0.356 0.012 0.000 0.628 0.004
#> SRR1044433 4 0.0955 0.871 0.000 0.028 0.000 0.968 0.004
#> SRR1044432 1 0.4166 0.798 0.792 0.116 0.000 0.088 0.004
#> SRR1044434 4 0.0000 0.888 0.000 0.000 0.000 1.000 0.000
#> SRR1044435 4 0.0000 0.888 0.000 0.000 0.000 1.000 0.000
#> SRR1044436 4 0.1041 0.881 0.032 0.000 0.000 0.964 0.004
#> SRR1044437 4 0.0000 0.888 0.000 0.000 0.000 1.000 0.000
#> SRR1044439 4 0.0955 0.882 0.028 0.000 0.000 0.968 0.004
#> SRR1044438 4 0.0510 0.887 0.016 0.000 0.000 0.984 0.000
#> SRR1044440 4 0.0000 0.888 0.000 0.000 0.000 1.000 0.000
#> SRR1044441 4 0.0000 0.888 0.000 0.000 0.000 1.000 0.000
#> SRR1044442 4 0.1278 0.873 0.016 0.020 0.000 0.960 0.004
#> SRR1044443 4 0.4536 0.469 0.016 0.324 0.000 0.656 0.004
#> SRR1044444 4 0.0404 0.887 0.012 0.000 0.000 0.988 0.000
#> SRR1044445 4 0.0000 0.888 0.000 0.000 0.000 1.000 0.000
#> SRR1044446 3 0.5126 0.767 0.140 0.052 0.744 0.000 0.064
#> SRR1044447 2 0.1757 0.894 0.048 0.936 0.004 0.000 0.012
#> SRR1044449 5 0.1877 0.906 0.064 0.000 0.012 0.000 0.924
#> SRR1044448 3 0.4891 0.776 0.140 0.024 0.752 0.000 0.084
#> SRR1044450 3 0.5702 0.725 0.140 0.092 0.704 0.000 0.064
#> SRR1044451 2 0.3997 0.759 0.136 0.808 0.032 0.000 0.024
#> SRR1044452 5 0.1410 0.956 0.000 0.000 0.060 0.000 0.940
#> SRR1044453 5 0.1410 0.956 0.000 0.000 0.060 0.000 0.940
#> SRR1044454 5 0.1410 0.956 0.000 0.000 0.060 0.000 0.940
#> SRR1044455 3 0.0290 0.884 0.000 0.008 0.992 0.000 0.000
#> SRR1044456 2 0.2930 0.721 0.164 0.832 0.000 0.004 0.000
#> SRR1044457 3 0.0162 0.885 0.000 0.004 0.996 0.000 0.000
#> SRR1044458 3 0.0162 0.885 0.000 0.004 0.996 0.000 0.000
#> SRR1044459 3 0.2280 0.828 0.000 0.000 0.880 0.000 0.120
#> SRR1044460 2 0.3452 0.697 0.000 0.756 0.244 0.000 0.000
#> SRR1044461 3 0.0290 0.884 0.000 0.008 0.992 0.000 0.000
#> SRR1044462 4 0.3693 0.799 0.124 0.044 0.000 0.824 0.008
#> SRR1044463 1 0.3953 0.798 0.784 0.168 0.000 0.048 0.000
#> SRR1044464 4 0.2513 0.837 0.116 0.000 0.000 0.876 0.008
#> SRR1044466 1 0.3663 0.779 0.776 0.208 0.000 0.016 0.000
#> SRR1044465 1 0.5687 0.598 0.580 0.104 0.000 0.316 0.000
#> SRR1044467 1 0.3878 0.713 0.748 0.016 0.000 0.236 0.000
#> SRR1044468 2 0.2471 0.830 0.000 0.864 0.136 0.000 0.000
#> SRR1044469 3 0.2280 0.811 0.000 0.000 0.880 0.000 0.120
#> SRR1044470 1 0.4829 0.801 0.732 0.164 0.000 0.100 0.004
#> SRR1044471 4 0.5144 0.422 0.304 0.064 0.000 0.632 0.000
#> SRR1044472 1 0.3882 0.770 0.756 0.224 0.000 0.020 0.000
#> SRR1044473 1 0.4909 0.784 0.716 0.120 0.000 0.164 0.000
#> SRR1044474 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044475 5 0.1544 0.951 0.000 0.000 0.068 0.000 0.932
#> SRR1044476 3 0.0162 0.885 0.000 0.004 0.996 0.000 0.000
#> SRR1044477 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044478 2 0.3109 0.730 0.000 0.800 0.200 0.000 0.000
#> SRR1044479 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044480 4 0.1831 0.861 0.076 0.000 0.000 0.920 0.004
#> SRR1044481 1 0.5165 0.736 0.676 0.080 0.000 0.240 0.004
#> SRR1044482 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044483 4 0.1628 0.871 0.056 0.000 0.000 0.936 0.008
#> SRR1044484 4 0.3812 0.714 0.196 0.020 0.000 0.780 0.004
#> SRR1044486 1 0.5180 0.769 0.684 0.120 0.000 0.196 0.000
#> SRR1044485 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044487 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044488 2 0.0162 0.925 0.000 0.996 0.004 0.000 0.000
#> SRR1044489 2 0.0510 0.921 0.000 0.984 0.016 0.000 0.000
#> SRR1044490 1 0.4731 0.284 0.528 0.016 0.000 0.456 0.000
#> SRR1044491 1 0.4054 0.793 0.760 0.204 0.000 0.036 0.000
#> SRR1044492 1 0.3612 0.770 0.764 0.228 0.000 0.008 0.000
#> SRR1044493 1 0.3876 0.790 0.776 0.192 0.000 0.032 0.000
#> SRR1044494 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044496 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044495 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044497 4 0.0404 0.887 0.012 0.000 0.000 0.988 0.000
#> SRR1044499 3 0.0000 0.883 0.000 0.000 1.000 0.000 0.000
#> SRR1044498 4 0.3491 0.689 0.228 0.000 0.000 0.768 0.004
#> SRR1044500 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044501 3 0.0290 0.884 0.000 0.008 0.992 0.000 0.000
#> SRR1044502 2 0.3437 0.756 0.012 0.808 0.176 0.000 0.004
#> SRR1044503 4 0.0000 0.888 0.000 0.000 0.000 1.000 0.000
#> SRR1044504 4 0.0162 0.888 0.004 0.000 0.000 0.996 0.000
#> SRR1044505 4 0.5753 0.465 0.216 0.148 0.000 0.632 0.004
#> SRR1044506 4 0.0162 0.888 0.004 0.000 0.000 0.996 0.000
#> SRR1044507 4 0.2659 0.832 0.060 0.052 0.000 0.888 0.000
#> SRR1044508 4 0.1471 0.875 0.020 0.024 0.000 0.952 0.004
#> SRR1044509 4 0.0162 0.887 0.000 0.000 0.000 0.996 0.004
#> SRR1044510 5 0.1764 0.944 0.008 0.000 0.064 0.000 0.928
#> SRR1044511 3 0.5426 0.534 0.084 0.000 0.608 0.000 0.308
#> SRR1044512 5 0.1914 0.918 0.060 0.000 0.016 0.000 0.924
#> SRR1044513 2 0.0955 0.912 0.028 0.968 0.000 0.000 0.004
#> SRR1044514 3 0.6092 0.518 0.180 0.000 0.564 0.000 0.256
#> SRR1044515 2 0.0955 0.912 0.028 0.968 0.000 0.000 0.004
#> SRR1044516 2 0.1270 0.901 0.000 0.948 0.052 0.000 0.000
#> SRR1044517 5 0.2230 0.915 0.000 0.000 0.116 0.000 0.884
#> SRR1044518 3 0.4444 0.769 0.180 0.000 0.748 0.000 0.072
#> SRR1044519 3 0.5752 0.719 0.140 0.096 0.700 0.000 0.064
#> SRR1044520 3 0.5420 0.741 0.140 0.024 0.708 0.000 0.128
#> SRR1044521 2 0.0162 0.925 0.000 0.996 0.004 0.000 0.000
#> SRR1044522 2 0.0609 0.913 0.020 0.980 0.000 0.000 0.000
#> SRR1044523 2 0.0290 0.924 0.008 0.992 0.000 0.000 0.000
#> SRR1044524 3 0.0566 0.880 0.004 0.000 0.984 0.000 0.012
#> SRR1044525 4 0.0290 0.888 0.008 0.000 0.000 0.992 0.000
#> SRR1044526 4 0.3352 0.740 0.192 0.004 0.000 0.800 0.004
#> SRR1044527 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044528 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044529 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044530 1 0.3586 0.788 0.792 0.188 0.000 0.020 0.000
#> SRR1044531 1 0.5116 0.758 0.692 0.120 0.000 0.188 0.000
#> SRR1044533 1 0.4394 0.792 0.764 0.136 0.000 0.100 0.000
#> SRR1044532 1 0.3630 0.782 0.780 0.204 0.000 0.016 0.000
#> SRR1044534 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044535 3 0.2444 0.838 0.016 0.068 0.904 0.000 0.012
#> SRR1044536 2 0.0703 0.917 0.000 0.976 0.024 0.000 0.000
#> SRR1044537 1 0.6251 0.662 0.552 0.296 0.000 0.144 0.008
#> SRR1044538 1 0.3789 0.777 0.768 0.212 0.000 0.020 0.000
#> SRR1044539 4 0.1251 0.879 0.036 0.000 0.000 0.956 0.008
#> SRR1044540 1 0.4287 0.273 0.540 0.000 0.000 0.460 0.000
#> SRR1044541 3 0.0162 0.885 0.000 0.004 0.996 0.000 0.000
#> SRR1044542 1 0.3779 0.787 0.776 0.200 0.000 0.024 0.000
#> SRR1044543 4 0.4649 0.242 0.404 0.016 0.000 0.580 0.000
#> SRR1044544 3 0.0162 0.882 0.000 0.000 0.996 0.000 0.004
#> SRR1044545 4 0.1628 0.871 0.056 0.000 0.000 0.936 0.008
#> SRR1044546 1 0.5728 0.756 0.648 0.148 0.000 0.196 0.008
#> SRR1044547 4 0.2660 0.818 0.128 0.000 0.000 0.864 0.008
#> SRR1044548 1 0.5641 0.770 0.660 0.180 0.000 0.152 0.008
#> SRR1044549 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044550 2 0.0963 0.908 0.000 0.964 0.036 0.000 0.000
#> SRR1044551 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044552 4 0.0000 0.888 0.000 0.000 0.000 1.000 0.000
#> SRR1044553 4 0.0000 0.888 0.000 0.000 0.000 1.000 0.000
#> SRR1044554 1 0.5448 0.781 0.680 0.180 0.000 0.132 0.008
#> SRR1044555 3 0.0912 0.879 0.016 0.000 0.972 0.000 0.012
#> SRR1044556 4 0.1041 0.881 0.032 0.000 0.000 0.964 0.004
#> SRR1044557 2 0.6749 -0.270 0.340 0.452 0.000 0.200 0.008
#> SRR1044558 4 0.0771 0.885 0.020 0.000 0.000 0.976 0.004
#> SRR1044559 2 0.6131 0.223 0.216 0.596 0.000 0.180 0.008
#> SRR1044561 4 0.0671 0.885 0.016 0.000 0.000 0.980 0.004
#> SRR1044560 3 0.0162 0.885 0.000 0.004 0.996 0.000 0.000
#> SRR1044562 1 0.6691 0.564 0.468 0.332 0.000 0.192 0.008
#> SRR1044563 4 0.1168 0.881 0.032 0.000 0.000 0.960 0.008
#> SRR1044564 1 0.4455 0.737 0.736 0.036 0.000 0.220 0.008
#> SRR1044565 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044566 3 0.0162 0.885 0.000 0.004 0.996 0.000 0.000
#> SRR1044567 1 0.3995 0.793 0.776 0.180 0.000 0.044 0.000
#> SRR1044568 4 0.1894 0.864 0.072 0.000 0.000 0.920 0.008
#> SRR1044569 1 0.4840 0.716 0.676 0.056 0.000 0.268 0.000
#> SRR1044570 1 0.3845 0.780 0.768 0.208 0.000 0.024 0.000
#> SRR1044571 1 0.4010 0.787 0.796 0.088 0.000 0.116 0.000
#> SRR1044572 1 0.3730 0.651 0.712 0.000 0.000 0.288 0.000
#> SRR1044573 4 0.5766 0.106 0.392 0.092 0.000 0.516 0.000
#> SRR1044574 1 0.5519 0.384 0.520 0.068 0.000 0.412 0.000
#> SRR1044575 1 0.3690 0.719 0.764 0.012 0.000 0.224 0.000
#> SRR1044576 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044577 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044578 2 0.0000 0.927 0.000 1.000 0.000 0.000 0.000
#> SRR1044579 4 0.0000 0.888 0.000 0.000 0.000 1.000 0.000
#> SRR1044580 4 0.2970 0.774 0.168 0.000 0.000 0.828 0.004
#> SRR1044581 4 0.0000 0.888 0.000 0.000 0.000 1.000 0.000
#> SRR1044582 1 0.4887 0.788 0.720 0.132 0.000 0.148 0.000
#> SRR1044583 4 0.0000 0.888 0.000 0.000 0.000 1.000 0.000
#> SRR1044584 4 0.0963 0.883 0.036 0.000 0.000 0.964 0.000
#> SRR1044585 4 0.0404 0.887 0.012 0.000 0.000 0.988 0.000
#> SRR1044586 1 0.5481 0.737 0.652 0.108 0.000 0.236 0.004
#> SRR1044587 4 0.2233 0.820 0.104 0.004 0.000 0.892 0.000
#> SRR1044588 4 0.0000 0.888 0.000 0.000 0.000 1.000 0.000
#> SRR1044589 4 0.0000 0.888 0.000 0.000 0.000 1.000 0.000
#> SRR1044590 4 0.1809 0.853 0.060 0.012 0.000 0.928 0.000
#> SRR1044591 4 0.0000 0.888 0.000 0.000 0.000 1.000 0.000
#> SRR1044592 4 0.0162 0.887 0.000 0.000 0.000 0.996 0.004
#> SRR1044593 4 0.0000 0.888 0.000 0.000 0.000 1.000 0.000
#> SRR1044594 4 0.0000 0.888 0.000 0.000 0.000 1.000 0.000
#> SRR1044595 4 0.5422 0.385 0.308 0.072 0.000 0.616 0.004
#> SRR1044596 4 0.0162 0.888 0.004 0.000 0.000 0.996 0.000
#> SRR1044597 2 0.3132 0.705 0.172 0.820 0.000 0.008 0.000
#> SRR1044598 1 0.3890 0.757 0.736 0.252 0.000 0.012 0.000
#> SRR1044599 1 0.4551 0.614 0.616 0.368 0.000 0.016 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 3 0.0146 0.8810 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1044416 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044417 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044418 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044420 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044419 3 0.0000 0.8844 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044421 2 0.1501 0.8699 0.000 0.924 0.076 0.000 0.000 0.000
#> SRR1044422 2 0.0790 0.9070 0.000 0.968 0.032 0.000 0.000 0.000
#> SRR1044423 2 0.2730 0.7400 0.000 0.808 0.192 0.000 0.000 0.000
#> SRR1044424 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044425 4 0.2955 0.7353 0.172 0.008 0.000 0.816 0.004 0.000
#> SRR1044426 4 0.3998 0.0610 0.492 0.000 0.000 0.504 0.004 0.000
#> SRR1044427 4 0.4537 0.2553 0.412 0.036 0.000 0.552 0.000 0.000
#> SRR1044428 1 0.2895 0.7727 0.852 0.116 0.000 0.016 0.016 0.000
#> SRR1044429 4 0.3163 0.7108 0.212 0.004 0.000 0.780 0.004 0.000
#> SRR1044430 1 0.3379 0.7317 0.804 0.168 0.000 0.012 0.008 0.008
#> SRR1044431 4 0.4546 0.2435 0.444 0.008 0.000 0.528 0.020 0.000
#> SRR1044433 4 0.1364 0.8595 0.016 0.012 0.000 0.952 0.020 0.000
#> SRR1044432 1 0.1528 0.7908 0.936 0.048 0.000 0.016 0.000 0.000
#> SRR1044434 4 0.0146 0.8705 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044435 4 0.0291 0.8699 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044436 4 0.1480 0.8599 0.040 0.000 0.000 0.940 0.020 0.000
#> SRR1044437 4 0.0291 0.8699 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044439 4 0.1320 0.8617 0.036 0.000 0.000 0.948 0.016 0.000
#> SRR1044438 4 0.0858 0.8705 0.028 0.000 0.000 0.968 0.004 0.000
#> SRR1044440 4 0.0146 0.8702 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044441 4 0.0146 0.8705 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044442 4 0.1793 0.8519 0.048 0.012 0.000 0.928 0.012 0.000
#> SRR1044443 4 0.4798 0.4474 0.020 0.308 0.000 0.632 0.040 0.000
#> SRR1044444 4 0.0603 0.8697 0.016 0.000 0.000 0.980 0.004 0.000
#> SRR1044445 4 0.0603 0.8686 0.016 0.000 0.000 0.980 0.004 0.000
#> SRR1044446 3 0.4238 0.5827 0.016 0.000 0.636 0.000 0.340 0.008
#> SRR1044447 2 0.1471 0.8848 0.000 0.932 0.004 0.000 0.064 0.000
#> SRR1044449 6 0.2994 0.6176 0.004 0.000 0.000 0.000 0.208 0.788
#> SRR1044448 3 0.4411 0.5730 0.020 0.000 0.628 0.000 0.340 0.012
#> SRR1044450 3 0.4650 0.5638 0.020 0.012 0.620 0.000 0.340 0.008
#> SRR1044451 2 0.4483 0.5465 0.016 0.668 0.032 0.000 0.284 0.000
#> SRR1044452 6 0.0260 0.8887 0.000 0.000 0.008 0.000 0.000 0.992
#> SRR1044453 6 0.0260 0.8887 0.000 0.000 0.008 0.000 0.000 0.992
#> SRR1044454 6 0.0260 0.8887 0.000 0.000 0.008 0.000 0.000 0.992
#> SRR1044455 3 0.0000 0.8844 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044456 2 0.3076 0.6393 0.240 0.760 0.000 0.000 0.000 0.000
#> SRR1044457 3 0.0000 0.8844 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044458 3 0.0000 0.8844 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044459 3 0.2340 0.7782 0.000 0.000 0.852 0.000 0.000 0.148
#> SRR1044460 2 0.2969 0.7096 0.000 0.776 0.224 0.000 0.000 0.000
#> SRR1044461 3 0.0000 0.8844 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044462 4 0.3913 0.7766 0.152 0.020 0.000 0.788 0.032 0.008
#> SRR1044463 1 0.1643 0.7917 0.924 0.068 0.000 0.008 0.000 0.000
#> SRR1044464 4 0.2983 0.8108 0.136 0.000 0.000 0.832 0.032 0.000
#> SRR1044466 1 0.1753 0.7869 0.912 0.084 0.000 0.004 0.000 0.000
#> SRR1044465 1 0.4061 0.6508 0.708 0.044 0.000 0.248 0.000 0.000
#> SRR1044467 1 0.1958 0.7651 0.896 0.004 0.000 0.100 0.000 0.000
#> SRR1044468 2 0.1910 0.8455 0.000 0.892 0.108 0.000 0.000 0.000
#> SRR1044469 3 0.1957 0.8022 0.000 0.000 0.888 0.000 0.000 0.112
#> SRR1044470 1 0.3472 0.7823 0.820 0.096 0.000 0.076 0.000 0.008
#> SRR1044471 4 0.4176 0.3167 0.404 0.016 0.000 0.580 0.000 0.000
#> SRR1044472 1 0.2070 0.7802 0.892 0.100 0.000 0.008 0.000 0.000
#> SRR1044473 1 0.3284 0.7764 0.832 0.056 0.000 0.104 0.008 0.000
#> SRR1044474 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044475 6 0.0363 0.8854 0.000 0.000 0.012 0.000 0.000 0.988
#> SRR1044476 3 0.0000 0.8844 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044477 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044478 2 0.2454 0.7724 0.000 0.840 0.160 0.000 0.000 0.000
#> SRR1044479 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044480 4 0.2456 0.8381 0.076 0.000 0.000 0.888 0.028 0.008
#> SRR1044481 1 0.3978 0.6913 0.748 0.024 0.000 0.212 0.008 0.008
#> SRR1044482 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044483 4 0.2420 0.8445 0.068 0.000 0.000 0.892 0.032 0.008
#> SRR1044484 4 0.3748 0.6876 0.224 0.012 0.000 0.748 0.016 0.000
#> SRR1044486 1 0.3712 0.7267 0.768 0.052 0.000 0.180 0.000 0.000
#> SRR1044485 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044487 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044488 2 0.0146 0.9199 0.000 0.996 0.004 0.000 0.000 0.000
#> SRR1044489 2 0.0363 0.9171 0.000 0.988 0.012 0.000 0.000 0.000
#> SRR1044490 1 0.3795 0.4819 0.632 0.004 0.000 0.364 0.000 0.000
#> SRR1044491 1 0.2070 0.7884 0.892 0.100 0.000 0.008 0.000 0.000
#> SRR1044492 1 0.1910 0.7838 0.892 0.108 0.000 0.000 0.000 0.000
#> SRR1044493 1 0.1838 0.7921 0.916 0.068 0.000 0.016 0.000 0.000
#> SRR1044494 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044496 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044495 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044497 4 0.0547 0.8708 0.020 0.000 0.000 0.980 0.000 0.000
#> SRR1044499 3 0.0000 0.8844 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044498 4 0.3445 0.6484 0.260 0.000 0.000 0.732 0.008 0.000
#> SRR1044500 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044501 3 0.0000 0.8844 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044502 2 0.2968 0.7514 0.000 0.816 0.168 0.000 0.016 0.000
#> SRR1044503 4 0.0000 0.8704 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044504 4 0.0146 0.8707 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044505 4 0.5498 0.4529 0.272 0.120 0.000 0.592 0.016 0.000
#> SRR1044506 4 0.0692 0.8695 0.020 0.000 0.000 0.976 0.004 0.000
#> SRR1044507 4 0.2776 0.8197 0.104 0.032 0.000 0.860 0.004 0.000
#> SRR1044508 4 0.2257 0.8523 0.060 0.016 0.000 0.904 0.020 0.000
#> SRR1044509 4 0.0914 0.8658 0.016 0.000 0.000 0.968 0.016 0.000
#> SRR1044510 6 0.2950 0.7306 0.000 0.000 0.024 0.000 0.148 0.828
#> SRR1044511 5 0.3888 0.6564 0.000 0.000 0.032 0.000 0.716 0.252
#> SRR1044512 5 0.3592 0.5106 0.000 0.000 0.000 0.000 0.656 0.344
#> SRR1044513 2 0.0937 0.9018 0.000 0.960 0.000 0.000 0.040 0.000
#> SRR1044514 5 0.1713 0.7248 0.000 0.000 0.044 0.000 0.928 0.028
#> SRR1044515 2 0.0937 0.9018 0.000 0.960 0.000 0.000 0.040 0.000
#> SRR1044516 2 0.0713 0.9089 0.000 0.972 0.028 0.000 0.000 0.000
#> SRR1044517 6 0.1686 0.8274 0.000 0.000 0.064 0.000 0.012 0.924
#> SRR1044518 5 0.1531 0.7141 0.000 0.000 0.068 0.000 0.928 0.004
#> SRR1044519 3 0.4887 0.5455 0.020 0.024 0.608 0.000 0.340 0.008
#> SRR1044520 3 0.4575 0.5627 0.020 0.000 0.620 0.000 0.340 0.020
#> SRR1044521 2 0.0146 0.9199 0.000 0.996 0.004 0.000 0.000 0.000
#> SRR1044522 2 0.1141 0.8818 0.052 0.948 0.000 0.000 0.000 0.000
#> SRR1044523 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044524 3 0.0405 0.8804 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1044525 4 0.0622 0.8717 0.012 0.000 0.000 0.980 0.008 0.000
#> SRR1044526 4 0.3650 0.7011 0.216 0.004 0.000 0.756 0.024 0.000
#> SRR1044527 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044528 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044529 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044530 1 0.1643 0.7914 0.924 0.068 0.000 0.008 0.000 0.000
#> SRR1044531 1 0.2972 0.7675 0.836 0.036 0.000 0.128 0.000 0.000
#> SRR1044533 1 0.2213 0.7944 0.904 0.044 0.000 0.048 0.004 0.000
#> SRR1044532 1 0.1700 0.7891 0.916 0.080 0.000 0.004 0.000 0.000
#> SRR1044534 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044535 3 0.2781 0.7983 0.004 0.064 0.876 0.000 0.048 0.008
#> SRR1044536 2 0.0458 0.9156 0.000 0.984 0.016 0.000 0.000 0.000
#> SRR1044537 1 0.5956 0.5691 0.592 0.236 0.000 0.132 0.032 0.008
#> SRR1044538 1 0.1918 0.7855 0.904 0.088 0.000 0.008 0.000 0.000
#> SRR1044539 4 0.2000 0.8524 0.048 0.000 0.000 0.916 0.032 0.004
#> SRR1044540 1 0.3636 0.5338 0.676 0.000 0.000 0.320 0.004 0.000
#> SRR1044541 3 0.0000 0.8844 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044542 1 0.1806 0.7869 0.908 0.088 0.000 0.004 0.000 0.000
#> SRR1044543 4 0.4493 0.0517 0.484 0.008 0.000 0.492 0.016 0.000
#> SRR1044544 3 0.0146 0.8827 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1044545 4 0.2361 0.8440 0.064 0.000 0.000 0.896 0.032 0.008
#> SRR1044546 1 0.5170 0.6641 0.684 0.076 0.000 0.200 0.032 0.008
#> SRR1044547 4 0.3427 0.7738 0.156 0.000 0.000 0.804 0.032 0.008
#> SRR1044548 1 0.5127 0.6946 0.700 0.108 0.000 0.156 0.028 0.008
#> SRR1044549 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044550 2 0.0865 0.9003 0.000 0.964 0.036 0.000 0.000 0.000
#> SRR1044551 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044552 4 0.0146 0.8705 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044553 4 0.0291 0.8702 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044554 1 0.4852 0.7233 0.732 0.132 0.000 0.096 0.032 0.008
#> SRR1044555 3 0.0806 0.8743 0.000 0.000 0.972 0.000 0.020 0.008
#> SRR1044556 4 0.1408 0.8607 0.036 0.000 0.000 0.944 0.020 0.000
#> SRR1044557 2 0.6716 -0.2441 0.376 0.388 0.000 0.196 0.032 0.008
#> SRR1044558 4 0.1245 0.8678 0.032 0.000 0.000 0.952 0.016 0.000
#> SRR1044559 2 0.6242 0.2378 0.248 0.544 0.000 0.172 0.028 0.008
#> SRR1044561 4 0.1074 0.8650 0.028 0.000 0.000 0.960 0.012 0.000
#> SRR1044560 3 0.0000 0.8844 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044562 1 0.6380 0.4710 0.516 0.264 0.000 0.184 0.028 0.008
#> SRR1044563 4 0.1933 0.8540 0.044 0.000 0.000 0.920 0.032 0.004
#> SRR1044564 1 0.3701 0.7254 0.800 0.012 0.000 0.148 0.032 0.008
#> SRR1044565 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044566 3 0.0000 0.8844 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044567 1 0.1983 0.7895 0.908 0.072 0.000 0.020 0.000 0.000
#> SRR1044568 4 0.2691 0.8329 0.088 0.000 0.000 0.872 0.032 0.008
#> SRR1044569 1 0.3290 0.7146 0.776 0.016 0.000 0.208 0.000 0.000
#> SRR1044570 1 0.2019 0.7855 0.900 0.088 0.000 0.012 0.000 0.000
#> SRR1044571 1 0.1088 0.7837 0.960 0.024 0.000 0.016 0.000 0.000
#> SRR1044572 1 0.2340 0.7431 0.852 0.000 0.000 0.148 0.000 0.000
#> SRR1044573 1 0.4654 -0.0107 0.504 0.016 0.000 0.464 0.016 0.000
#> SRR1044574 1 0.4181 0.5314 0.644 0.028 0.000 0.328 0.000 0.000
#> SRR1044575 1 0.1471 0.7771 0.932 0.004 0.000 0.064 0.000 0.000
#> SRR1044576 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044577 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044578 2 0.0000 0.9216 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044579 4 0.0146 0.8702 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044580 4 0.3253 0.7385 0.192 0.000 0.000 0.788 0.020 0.000
#> SRR1044581 4 0.0000 0.8704 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044582 1 0.3885 0.7597 0.796 0.068 0.000 0.120 0.008 0.008
#> SRR1044583 4 0.0000 0.8704 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044584 4 0.1333 0.8656 0.048 0.000 0.000 0.944 0.008 0.000
#> SRR1044585 4 0.0692 0.8691 0.020 0.000 0.000 0.976 0.004 0.000
#> SRR1044586 1 0.4410 0.6730 0.720 0.040 0.000 0.220 0.012 0.008
#> SRR1044587 4 0.2871 0.7350 0.192 0.000 0.000 0.804 0.004 0.000
#> SRR1044588 4 0.0603 0.8686 0.016 0.000 0.000 0.980 0.004 0.000
#> SRR1044589 4 0.0603 0.8686 0.016 0.000 0.000 0.980 0.004 0.000
#> SRR1044590 4 0.2333 0.8059 0.120 0.004 0.000 0.872 0.004 0.000
#> SRR1044591 4 0.0603 0.8686 0.016 0.000 0.000 0.980 0.004 0.000
#> SRR1044592 4 0.1003 0.8645 0.016 0.000 0.000 0.964 0.020 0.000
#> SRR1044593 4 0.0603 0.8686 0.016 0.000 0.000 0.980 0.004 0.000
#> SRR1044594 4 0.0508 0.8693 0.012 0.000 0.000 0.984 0.004 0.000
#> SRR1044595 4 0.4796 0.3159 0.396 0.024 0.000 0.560 0.020 0.000
#> SRR1044596 4 0.0806 0.8689 0.020 0.000 0.000 0.972 0.008 0.000
#> SRR1044597 2 0.3398 0.6062 0.252 0.740 0.000 0.008 0.000 0.000
#> SRR1044598 1 0.2178 0.7674 0.868 0.132 0.000 0.000 0.000 0.000
#> SRR1044599 1 0.3521 0.6425 0.724 0.268 0.000 0.004 0.004 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)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.827 0.905 0.955 0.4913 0.510 0.510
#> 3 3 0.862 0.879 0.936 0.2409 0.810 0.646
#> 4 4 0.627 0.606 0.786 0.1426 0.948 0.861
#> 5 5 0.565 0.502 0.701 0.0637 0.888 0.685
#> 6 6 0.585 0.436 0.690 0.0339 0.941 0.796
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0.0376 0.971 0.004 0.996
#> SRR1044416 2 0.1633 0.965 0.024 0.976
#> SRR1044417 2 0.2043 0.960 0.032 0.968
#> SRR1044418 2 0.2423 0.954 0.040 0.960
#> SRR1044420 2 0.0938 0.971 0.012 0.988
#> SRR1044419 2 0.0376 0.971 0.004 0.996
#> SRR1044421 2 0.0672 0.972 0.008 0.992
#> SRR1044422 2 0.0938 0.971 0.012 0.988
#> SRR1044423 2 0.0376 0.971 0.004 0.996
#> SRR1044424 2 0.0938 0.971 0.012 0.988
#> SRR1044425 1 0.0000 0.940 1.000 0.000
#> SRR1044426 1 0.8608 0.636 0.716 0.284
#> SRR1044427 1 0.0000 0.940 1.000 0.000
#> SRR1044428 1 0.2043 0.921 0.968 0.032
#> SRR1044429 1 0.0000 0.940 1.000 0.000
#> SRR1044430 1 0.8955 0.586 0.688 0.312
#> SRR1044431 1 0.0000 0.940 1.000 0.000
#> SRR1044433 1 0.9754 0.381 0.592 0.408
#> SRR1044432 1 0.9170 0.559 0.668 0.332
#> SRR1044434 1 0.0000 0.940 1.000 0.000
#> SRR1044435 1 0.0000 0.940 1.000 0.000
#> SRR1044436 1 0.0000 0.940 1.000 0.000
#> SRR1044437 1 0.0000 0.940 1.000 0.000
#> SRR1044439 1 0.0000 0.940 1.000 0.000
#> SRR1044438 1 0.0000 0.940 1.000 0.000
#> SRR1044440 1 0.0000 0.940 1.000 0.000
#> SRR1044441 1 0.0000 0.940 1.000 0.000
#> SRR1044442 1 0.9608 0.439 0.616 0.384
#> SRR1044443 1 0.9754 0.381 0.592 0.408
#> SRR1044444 1 0.0000 0.940 1.000 0.000
#> SRR1044445 1 0.0938 0.934 0.988 0.012
#> SRR1044446 2 0.0376 0.971 0.004 0.996
#> SRR1044447 2 0.0376 0.971 0.004 0.996
#> SRR1044449 2 0.0000 0.969 0.000 1.000
#> SRR1044448 2 0.0000 0.969 0.000 1.000
#> SRR1044450 2 0.0000 0.969 0.000 1.000
#> SRR1044451 2 0.0376 0.971 0.004 0.996
#> SRR1044452 2 0.0000 0.969 0.000 1.000
#> SRR1044453 2 0.0000 0.969 0.000 1.000
#> SRR1044454 2 0.0000 0.969 0.000 1.000
#> SRR1044455 2 0.0376 0.971 0.004 0.996
#> SRR1044456 1 0.9686 0.369 0.604 0.396
#> SRR1044457 2 0.0376 0.971 0.004 0.996
#> SRR1044458 2 0.0376 0.971 0.004 0.996
#> SRR1044459 2 0.0000 0.969 0.000 1.000
#> SRR1044460 2 0.0938 0.971 0.012 0.988
#> SRR1044461 2 0.0376 0.971 0.004 0.996
#> SRR1044462 1 0.0000 0.940 1.000 0.000
#> SRR1044463 1 0.0376 0.939 0.996 0.004
#> SRR1044464 1 0.8267 0.673 0.740 0.260
#> SRR1044466 1 0.0672 0.937 0.992 0.008
#> SRR1044465 1 0.0000 0.940 1.000 0.000
#> SRR1044467 1 0.0000 0.940 1.000 0.000
#> SRR1044468 2 0.0376 0.971 0.004 0.996
#> SRR1044469 2 0.0000 0.969 0.000 1.000
#> SRR1044470 1 0.4690 0.865 0.900 0.100
#> SRR1044471 1 0.0672 0.937 0.992 0.008
#> SRR1044472 1 0.7883 0.705 0.764 0.236
#> SRR1044473 1 0.0376 0.939 0.996 0.004
#> SRR1044474 2 0.3584 0.931 0.068 0.932
#> SRR1044475 2 0.0000 0.969 0.000 1.000
#> SRR1044476 2 0.0376 0.971 0.004 0.996
#> SRR1044477 2 0.5178 0.881 0.116 0.884
#> SRR1044478 2 0.0376 0.971 0.004 0.996
#> SRR1044479 2 0.7950 0.700 0.240 0.760
#> SRR1044480 1 0.0000 0.940 1.000 0.000
#> SRR1044481 1 0.0000 0.940 1.000 0.000
#> SRR1044482 2 0.2236 0.957 0.036 0.964
#> SRR1044483 1 0.1184 0.932 0.984 0.016
#> SRR1044484 1 0.0000 0.940 1.000 0.000
#> SRR1044486 1 0.0000 0.940 1.000 0.000
#> SRR1044485 2 0.0938 0.971 0.012 0.988
#> SRR1044487 2 0.6531 0.816 0.168 0.832
#> SRR1044488 2 0.0938 0.971 0.012 0.988
#> SRR1044489 2 0.0938 0.971 0.012 0.988
#> SRR1044490 1 0.0376 0.939 0.996 0.004
#> SRR1044491 1 0.4022 0.883 0.920 0.080
#> SRR1044492 1 0.1414 0.930 0.980 0.020
#> SRR1044493 1 0.0376 0.939 0.996 0.004
#> SRR1044494 2 0.5178 0.881 0.116 0.884
#> SRR1044496 2 0.6247 0.832 0.156 0.844
#> SRR1044495 2 0.6048 0.843 0.148 0.852
#> SRR1044497 1 0.0000 0.940 1.000 0.000
#> SRR1044499 2 0.0000 0.969 0.000 1.000
#> SRR1044498 1 0.0000 0.940 1.000 0.000
#> SRR1044500 2 0.0938 0.971 0.012 0.988
#> SRR1044501 2 0.0376 0.971 0.004 0.996
#> SRR1044502 2 0.0376 0.971 0.004 0.996
#> SRR1044503 1 0.0000 0.940 1.000 0.000
#> SRR1044504 1 0.0000 0.940 1.000 0.000
#> SRR1044505 1 0.0000 0.940 1.000 0.000
#> SRR1044506 1 0.0000 0.940 1.000 0.000
#> SRR1044507 1 0.7950 0.703 0.760 0.240
#> SRR1044508 1 0.9754 0.381 0.592 0.408
#> SRR1044509 1 0.9754 0.381 0.592 0.408
#> SRR1044510 2 0.1414 0.963 0.020 0.980
#> SRR1044511 2 0.1414 0.963 0.020 0.980
#> SRR1044512 2 0.1414 0.963 0.020 0.980
#> SRR1044513 2 0.0672 0.972 0.008 0.992
#> SRR1044514 2 0.1414 0.963 0.020 0.980
#> SRR1044515 2 0.0938 0.971 0.012 0.988
#> SRR1044516 2 0.0672 0.972 0.008 0.992
#> SRR1044517 2 0.1414 0.963 0.020 0.980
#> SRR1044518 2 0.1414 0.963 0.020 0.980
#> SRR1044519 2 0.0000 0.969 0.000 1.000
#> SRR1044520 2 0.0376 0.970 0.004 0.996
#> SRR1044521 2 0.1184 0.969 0.016 0.984
#> SRR1044522 2 0.8443 0.642 0.272 0.728
#> SRR1044523 2 0.0938 0.971 0.012 0.988
#> SRR1044524 2 0.0376 0.971 0.004 0.996
#> SRR1044525 1 0.0000 0.940 1.000 0.000
#> SRR1044526 1 0.0000 0.940 1.000 0.000
#> SRR1044527 2 0.2043 0.960 0.032 0.968
#> SRR1044528 2 0.1184 0.969 0.016 0.984
#> SRR1044529 2 0.4298 0.911 0.088 0.912
#> SRR1044530 1 0.0376 0.939 0.996 0.004
#> SRR1044531 1 0.0000 0.940 1.000 0.000
#> SRR1044533 1 0.0376 0.939 0.996 0.004
#> SRR1044532 1 0.0376 0.939 0.996 0.004
#> SRR1044534 2 0.0938 0.971 0.012 0.988
#> SRR1044535 2 0.0376 0.971 0.004 0.996
#> SRR1044536 2 0.0938 0.971 0.012 0.988
#> SRR1044537 1 0.1184 0.933 0.984 0.016
#> SRR1044538 1 0.0376 0.939 0.996 0.004
#> SRR1044539 1 0.0000 0.940 1.000 0.000
#> SRR1044540 1 0.0000 0.940 1.000 0.000
#> SRR1044541 2 0.0376 0.971 0.004 0.996
#> SRR1044542 1 0.0376 0.939 0.996 0.004
#> SRR1044543 1 0.1843 0.924 0.972 0.028
#> SRR1044544 2 0.0376 0.971 0.004 0.996
#> SRR1044545 1 0.0000 0.940 1.000 0.000
#> SRR1044546 1 0.0376 0.939 0.996 0.004
#> SRR1044547 1 0.0000 0.940 1.000 0.000
#> SRR1044548 1 0.0376 0.939 0.996 0.004
#> SRR1044549 2 0.0938 0.971 0.012 0.988
#> SRR1044550 2 0.0672 0.972 0.008 0.992
#> SRR1044551 2 0.1184 0.969 0.016 0.984
#> SRR1044552 1 0.0000 0.940 1.000 0.000
#> SRR1044553 1 0.0000 0.940 1.000 0.000
#> SRR1044554 1 0.1184 0.933 0.984 0.016
#> SRR1044555 2 0.0000 0.969 0.000 1.000
#> SRR1044556 1 0.0000 0.940 1.000 0.000
#> SRR1044557 1 0.0376 0.939 0.996 0.004
#> SRR1044558 1 0.0000 0.940 1.000 0.000
#> SRR1044559 1 0.0376 0.939 0.996 0.004
#> SRR1044561 1 0.0000 0.940 1.000 0.000
#> SRR1044560 2 0.0376 0.971 0.004 0.996
#> SRR1044562 1 0.0938 0.934 0.988 0.012
#> SRR1044563 1 0.0000 0.940 1.000 0.000
#> SRR1044564 1 0.0376 0.939 0.996 0.004
#> SRR1044565 2 0.6531 0.815 0.168 0.832
#> SRR1044566 2 0.0376 0.971 0.004 0.996
#> SRR1044567 1 0.3114 0.904 0.944 0.056
#> SRR1044568 1 0.0000 0.940 1.000 0.000
#> SRR1044569 1 0.0672 0.937 0.992 0.008
#> SRR1044570 1 0.0672 0.937 0.992 0.008
#> SRR1044571 1 0.0672 0.937 0.992 0.008
#> SRR1044572 1 0.1414 0.929 0.980 0.020
#> SRR1044573 1 0.0000 0.940 1.000 0.000
#> SRR1044574 1 0.0000 0.940 1.000 0.000
#> SRR1044575 1 0.0000 0.940 1.000 0.000
#> SRR1044576 2 0.1414 0.967 0.020 0.980
#> SRR1044577 2 0.2043 0.960 0.032 0.968
#> SRR1044578 2 0.3431 0.934 0.064 0.936
#> SRR1044579 1 0.0000 0.940 1.000 0.000
#> SRR1044580 1 0.0000 0.940 1.000 0.000
#> SRR1044581 1 0.0000 0.940 1.000 0.000
#> SRR1044582 1 0.0376 0.939 0.996 0.004
#> SRR1044583 1 0.0000 0.940 1.000 0.000
#> SRR1044584 1 0.0000 0.940 1.000 0.000
#> SRR1044585 1 0.0000 0.940 1.000 0.000
#> SRR1044586 1 0.0376 0.939 0.996 0.004
#> SRR1044587 1 0.0000 0.940 1.000 0.000
#> SRR1044588 1 0.0000 0.940 1.000 0.000
#> SRR1044589 1 0.0000 0.940 1.000 0.000
#> SRR1044590 1 0.0000 0.940 1.000 0.000
#> SRR1044591 1 0.0000 0.940 1.000 0.000
#> SRR1044592 1 0.9754 0.381 0.592 0.408
#> SRR1044593 1 0.0000 0.940 1.000 0.000
#> SRR1044594 1 0.0000 0.940 1.000 0.000
#> SRR1044595 1 0.9754 0.381 0.592 0.408
#> SRR1044596 1 0.9209 0.540 0.664 0.336
#> SRR1044597 1 0.4161 0.881 0.916 0.084
#> SRR1044598 1 0.6247 0.809 0.844 0.156
#> SRR1044599 1 0.5408 0.843 0.876 0.124
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.0424 0.946 0.000 0.992 0.008
#> SRR1044416 2 0.0237 0.944 0.000 0.996 0.004
#> SRR1044417 2 0.0000 0.945 0.000 1.000 0.000
#> SRR1044418 2 0.0000 0.945 0.000 1.000 0.000
#> SRR1044420 2 0.0424 0.946 0.000 0.992 0.008
#> SRR1044419 2 0.0424 0.946 0.000 0.992 0.008
#> SRR1044421 2 0.0424 0.946 0.000 0.992 0.008
#> SRR1044422 2 0.0424 0.946 0.000 0.992 0.008
#> SRR1044423 2 0.0424 0.946 0.000 0.992 0.008
#> SRR1044424 2 0.0237 0.945 0.000 0.996 0.004
#> SRR1044425 1 0.0592 0.974 0.988 0.000 0.012
#> SRR1044426 3 0.6264 0.506 0.380 0.004 0.616
#> SRR1044427 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044428 1 0.2096 0.932 0.944 0.004 0.052
#> SRR1044429 1 0.0747 0.973 0.984 0.000 0.016
#> SRR1044430 3 0.5956 0.617 0.324 0.004 0.672
#> SRR1044431 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044433 3 0.5754 0.651 0.296 0.004 0.700
#> SRR1044432 3 0.6081 0.576 0.344 0.004 0.652
#> SRR1044434 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044435 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044436 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044437 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044439 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044438 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044440 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044441 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044442 3 0.5929 0.618 0.320 0.004 0.676
#> SRR1044443 3 0.5754 0.651 0.296 0.004 0.700
#> SRR1044444 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044445 1 0.2448 0.924 0.924 0.000 0.076
#> SRR1044446 3 0.4504 0.703 0.000 0.196 0.804
#> SRR1044447 3 0.4178 0.720 0.000 0.172 0.828
#> SRR1044449 3 0.1289 0.785 0.000 0.032 0.968
#> SRR1044448 3 0.1753 0.782 0.000 0.048 0.952
#> SRR1044450 3 0.1753 0.782 0.000 0.048 0.952
#> SRR1044451 3 0.4702 0.689 0.000 0.212 0.788
#> SRR1044452 3 0.1411 0.785 0.000 0.036 0.964
#> SRR1044453 3 0.1289 0.785 0.000 0.032 0.968
#> SRR1044454 3 0.1411 0.785 0.000 0.036 0.964
#> SRR1044455 2 0.1289 0.930 0.000 0.968 0.032
#> SRR1044456 2 0.5291 0.548 0.268 0.732 0.000
#> SRR1044457 2 0.0424 0.946 0.000 0.992 0.008
#> SRR1044458 2 0.0592 0.944 0.000 0.988 0.012
#> SRR1044459 3 0.2796 0.767 0.000 0.092 0.908
#> SRR1044460 2 0.0424 0.946 0.000 0.992 0.008
#> SRR1044461 2 0.0424 0.946 0.000 0.992 0.008
#> SRR1044462 1 0.0747 0.970 0.984 0.000 0.016
#> SRR1044463 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044464 3 0.6460 0.357 0.440 0.004 0.556
#> SRR1044466 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044465 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044467 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044468 2 0.0424 0.946 0.000 0.992 0.008
#> SRR1044469 3 0.2878 0.765 0.000 0.096 0.904
#> SRR1044470 1 0.2269 0.934 0.944 0.040 0.016
#> SRR1044471 1 0.1860 0.944 0.948 0.000 0.052
#> SRR1044472 1 0.5365 0.605 0.744 0.004 0.252
#> SRR1044473 1 0.0592 0.971 0.988 0.000 0.012
#> SRR1044474 2 0.0000 0.945 0.000 1.000 0.000
#> SRR1044475 3 0.1411 0.785 0.000 0.036 0.964
#> SRR1044476 2 0.0592 0.944 0.000 0.988 0.012
#> SRR1044477 2 0.0000 0.945 0.000 1.000 0.000
#> SRR1044478 2 0.0424 0.946 0.000 0.992 0.008
#> SRR1044479 2 0.0424 0.940 0.008 0.992 0.000
#> SRR1044480 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044481 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044482 2 0.0000 0.945 0.000 1.000 0.000
#> SRR1044483 1 0.2261 0.914 0.932 0.000 0.068
#> SRR1044484 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044486 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044485 2 0.0424 0.946 0.000 0.992 0.008
#> SRR1044487 2 0.0000 0.945 0.000 1.000 0.000
#> SRR1044488 2 0.0424 0.946 0.000 0.992 0.008
#> SRR1044489 2 0.0424 0.946 0.000 0.992 0.008
#> SRR1044490 1 0.0829 0.969 0.984 0.004 0.012
#> SRR1044491 1 0.1399 0.957 0.968 0.004 0.028
#> SRR1044492 1 0.1525 0.950 0.964 0.032 0.004
#> SRR1044493 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044494 2 0.0000 0.945 0.000 1.000 0.000
#> SRR1044496 2 0.0000 0.945 0.000 1.000 0.000
#> SRR1044495 2 0.0000 0.945 0.000 1.000 0.000
#> SRR1044497 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044499 2 0.5291 0.607 0.000 0.732 0.268
#> SRR1044498 1 0.0000 0.974 1.000 0.000 0.000
#> SRR1044500 2 0.0424 0.946 0.000 0.992 0.008
#> SRR1044501 2 0.0592 0.944 0.000 0.988 0.012
#> SRR1044502 3 0.6008 0.442 0.000 0.372 0.628
#> SRR1044503 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044504 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044505 1 0.0747 0.971 0.984 0.000 0.016
#> SRR1044506 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044507 1 0.6314 0.221 0.604 0.004 0.392
#> SRR1044508 3 0.5785 0.646 0.300 0.004 0.696
#> SRR1044509 3 0.5754 0.651 0.296 0.004 0.700
#> SRR1044510 3 0.1163 0.784 0.000 0.028 0.972
#> SRR1044511 3 0.1163 0.784 0.000 0.028 0.972
#> SRR1044512 3 0.1163 0.784 0.000 0.028 0.972
#> SRR1044513 3 0.5760 0.528 0.000 0.328 0.672
#> SRR1044514 3 0.1163 0.784 0.000 0.028 0.972
#> SRR1044515 3 0.6079 0.402 0.000 0.388 0.612
#> SRR1044516 2 0.3619 0.813 0.000 0.864 0.136
#> SRR1044517 3 0.1289 0.785 0.000 0.032 0.968
#> SRR1044518 3 0.1163 0.784 0.000 0.028 0.972
#> SRR1044519 3 0.1411 0.785 0.000 0.036 0.964
#> SRR1044520 3 0.1163 0.784 0.000 0.028 0.972
#> SRR1044521 2 0.2625 0.876 0.000 0.916 0.084
#> SRR1044522 2 0.0592 0.935 0.012 0.988 0.000
#> SRR1044523 2 0.6192 0.196 0.000 0.580 0.420
#> SRR1044524 3 0.5138 0.646 0.000 0.252 0.748
#> SRR1044525 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044526 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044527 2 0.0000 0.945 0.000 1.000 0.000
#> SRR1044528 2 0.1163 0.931 0.000 0.972 0.028
#> SRR1044529 2 0.0000 0.945 0.000 1.000 0.000
#> SRR1044530 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044531 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044533 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044532 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044534 2 0.0237 0.945 0.000 0.996 0.004
#> SRR1044535 3 0.4931 0.669 0.000 0.232 0.768
#> SRR1044536 2 0.0424 0.946 0.000 0.992 0.008
#> SRR1044537 1 0.1643 0.946 0.956 0.000 0.044
#> SRR1044538 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044539 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044540 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044541 2 0.2356 0.893 0.000 0.928 0.072
#> SRR1044542 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044543 1 0.4178 0.768 0.828 0.000 0.172
#> SRR1044544 2 0.2066 0.906 0.000 0.940 0.060
#> SRR1044545 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044546 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044547 1 0.0424 0.974 0.992 0.000 0.008
#> SRR1044548 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044549 2 0.2711 0.871 0.000 0.912 0.088
#> SRR1044550 2 0.0424 0.946 0.000 0.992 0.008
#> SRR1044551 2 0.0000 0.945 0.000 1.000 0.000
#> SRR1044552 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044553 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044554 1 0.1163 0.959 0.972 0.000 0.028
#> SRR1044555 3 0.4887 0.674 0.000 0.228 0.772
#> SRR1044556 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044557 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044558 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044559 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044561 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044560 2 0.0592 0.944 0.000 0.988 0.012
#> SRR1044562 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044563 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044564 1 0.1031 0.964 0.976 0.000 0.024
#> SRR1044565 2 0.0000 0.945 0.000 1.000 0.000
#> SRR1044566 2 0.0424 0.946 0.000 0.992 0.008
#> SRR1044567 1 0.0424 0.972 0.992 0.000 0.008
#> SRR1044568 1 0.0424 0.974 0.992 0.000 0.008
#> SRR1044569 1 0.0592 0.971 0.988 0.000 0.012
#> SRR1044570 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044571 1 0.1411 0.954 0.964 0.000 0.036
#> SRR1044572 1 0.1411 0.956 0.964 0.000 0.036
#> SRR1044573 1 0.0747 0.969 0.984 0.000 0.016
#> SRR1044574 1 0.0424 0.972 0.992 0.000 0.008
#> SRR1044575 1 0.0424 0.974 0.992 0.000 0.008
#> SRR1044576 2 0.0000 0.945 0.000 1.000 0.000
#> SRR1044577 2 0.0000 0.945 0.000 1.000 0.000
#> SRR1044578 2 0.0000 0.945 0.000 1.000 0.000
#> SRR1044579 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044580 1 0.0000 0.974 1.000 0.000 0.000
#> SRR1044581 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044582 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044583 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044584 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044585 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044586 1 0.0237 0.973 0.996 0.000 0.004
#> SRR1044587 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044588 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044589 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044590 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044591 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044592 3 0.5754 0.651 0.296 0.004 0.700
#> SRR1044593 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044594 1 0.0747 0.974 0.984 0.000 0.016
#> SRR1044595 3 0.5845 0.641 0.308 0.004 0.688
#> SRR1044596 3 0.6410 0.417 0.420 0.004 0.576
#> SRR1044597 1 0.2793 0.919 0.928 0.044 0.028
#> SRR1044598 2 0.6148 0.397 0.356 0.640 0.004
#> SRR1044599 2 0.6126 0.405 0.352 0.644 0.004
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 2 0.1356 0.9019 0.008 0.960 0.032 0.000
#> SRR1044416 2 0.1576 0.9044 0.048 0.948 0.004 0.000
#> SRR1044417 2 0.0592 0.9121 0.016 0.984 0.000 0.000
#> SRR1044418 2 0.0592 0.9119 0.016 0.984 0.000 0.000
#> SRR1044420 2 0.0188 0.9120 0.000 0.996 0.004 0.000
#> SRR1044419 2 0.0779 0.9099 0.004 0.980 0.016 0.000
#> SRR1044421 2 0.0895 0.9084 0.004 0.976 0.020 0.000
#> SRR1044422 2 0.0336 0.9120 0.000 0.992 0.008 0.000
#> SRR1044423 2 0.0469 0.9116 0.000 0.988 0.012 0.000
#> SRR1044424 2 0.0524 0.9129 0.008 0.988 0.004 0.000
#> SRR1044425 4 0.1211 0.6516 0.040 0.000 0.000 0.960
#> SRR1044426 1 0.7685 0.4164 0.456 0.000 0.288 0.256
#> SRR1044427 4 0.4382 0.6134 0.296 0.000 0.000 0.704
#> SRR1044428 4 0.5695 0.3187 0.476 0.000 0.024 0.500
#> SRR1044429 4 0.3024 0.6401 0.148 0.000 0.000 0.852
#> SRR1044430 1 0.7198 0.4067 0.520 0.000 0.320 0.160
#> SRR1044431 4 0.4605 0.5979 0.336 0.000 0.000 0.664
#> SRR1044433 3 0.7608 -0.1825 0.392 0.000 0.408 0.200
#> SRR1044432 1 0.7261 0.3871 0.500 0.000 0.340 0.160
#> SRR1044434 4 0.0921 0.6371 0.028 0.000 0.000 0.972
#> SRR1044435 4 0.0592 0.6300 0.016 0.000 0.000 0.984
#> SRR1044436 4 0.0707 0.6467 0.020 0.000 0.000 0.980
#> SRR1044437 4 0.0188 0.6376 0.004 0.000 0.000 0.996
#> SRR1044439 4 0.0469 0.6442 0.012 0.000 0.000 0.988
#> SRR1044438 4 0.0921 0.6495 0.028 0.000 0.000 0.972
#> SRR1044440 4 0.0469 0.6329 0.012 0.000 0.000 0.988
#> SRR1044441 4 0.2589 0.5852 0.116 0.000 0.000 0.884
#> SRR1044442 1 0.7647 0.2898 0.444 0.000 0.336 0.220
#> SRR1044443 3 0.7546 -0.1979 0.404 0.000 0.408 0.188
#> SRR1044444 4 0.0592 0.6300 0.016 0.000 0.000 0.984
#> SRR1044445 4 0.4567 0.2940 0.276 0.000 0.008 0.716
#> SRR1044446 3 0.4123 0.6558 0.008 0.220 0.772 0.000
#> SRR1044447 3 0.5168 0.6357 0.040 0.248 0.712 0.000
#> SRR1044449 3 0.0000 0.7278 0.000 0.000 1.000 0.000
#> SRR1044448 3 0.0376 0.7273 0.004 0.004 0.992 0.000
#> SRR1044450 3 0.0937 0.7254 0.012 0.012 0.976 0.000
#> SRR1044451 3 0.5013 0.6081 0.020 0.292 0.688 0.000
#> SRR1044452 3 0.0000 0.7278 0.000 0.000 1.000 0.000
#> SRR1044453 3 0.0000 0.7278 0.000 0.000 1.000 0.000
#> SRR1044454 3 0.0000 0.7278 0.000 0.000 1.000 0.000
#> SRR1044455 2 0.1890 0.8861 0.008 0.936 0.056 0.000
#> SRR1044456 2 0.5867 0.5533 0.096 0.688 0.000 0.216
#> SRR1044457 2 0.1256 0.9039 0.008 0.964 0.028 0.000
#> SRR1044458 2 0.1356 0.9019 0.008 0.960 0.032 0.000
#> SRR1044459 3 0.2334 0.7077 0.004 0.088 0.908 0.000
#> SRR1044460 2 0.0336 0.9122 0.000 0.992 0.008 0.000
#> SRR1044461 2 0.0524 0.9118 0.004 0.988 0.008 0.000
#> SRR1044462 4 0.4776 0.4991 0.376 0.000 0.000 0.624
#> SRR1044463 4 0.4972 0.4919 0.456 0.000 0.000 0.544
#> SRR1044464 1 0.7661 0.4565 0.464 0.000 0.264 0.272
#> SRR1044466 4 0.5132 0.4994 0.448 0.004 0.000 0.548
#> SRR1044465 4 0.4679 0.5890 0.352 0.000 0.000 0.648
#> SRR1044467 4 0.4889 0.5806 0.360 0.000 0.004 0.636
#> SRR1044468 2 0.0376 0.9125 0.004 0.992 0.004 0.000
#> SRR1044469 3 0.3450 0.6835 0.008 0.156 0.836 0.000
#> SRR1044470 1 0.5979 -0.1745 0.588 0.032 0.008 0.372
#> SRR1044471 4 0.5402 0.3264 0.472 0.000 0.012 0.516
#> SRR1044472 1 0.5717 0.0384 0.632 0.000 0.044 0.324
#> SRR1044473 4 0.4996 0.4680 0.484 0.000 0.000 0.516
#> SRR1044474 2 0.1637 0.8989 0.060 0.940 0.000 0.000
#> SRR1044475 3 0.0000 0.7278 0.000 0.000 1.000 0.000
#> SRR1044476 2 0.1356 0.9019 0.008 0.960 0.032 0.000
#> SRR1044477 2 0.2048 0.8943 0.064 0.928 0.000 0.008
#> SRR1044478 2 0.0376 0.9125 0.004 0.992 0.004 0.000
#> SRR1044479 2 0.3398 0.8406 0.068 0.872 0.000 0.060
#> SRR1044480 4 0.1867 0.6532 0.072 0.000 0.000 0.928
#> SRR1044481 4 0.4643 0.5859 0.344 0.000 0.000 0.656
#> SRR1044482 2 0.1118 0.9077 0.036 0.964 0.000 0.000
#> SRR1044483 4 0.6314 0.3493 0.372 0.000 0.068 0.560
#> SRR1044484 4 0.4382 0.6145 0.296 0.000 0.000 0.704
#> SRR1044486 4 0.4830 0.5524 0.392 0.000 0.000 0.608
#> SRR1044485 2 0.0524 0.9130 0.008 0.988 0.004 0.000
#> SRR1044487 2 0.3071 0.8597 0.068 0.888 0.000 0.044
#> SRR1044488 2 0.0524 0.9127 0.008 0.988 0.004 0.000
#> SRR1044489 2 0.0376 0.9125 0.004 0.992 0.004 0.000
#> SRR1044490 4 0.4920 0.5586 0.368 0.000 0.004 0.628
#> SRR1044491 1 0.5288 -0.4026 0.520 0.000 0.008 0.472
#> SRR1044492 4 0.6003 0.4309 0.456 0.040 0.000 0.504
#> SRR1044493 4 0.4961 0.4998 0.448 0.000 0.000 0.552
#> SRR1044494 2 0.1824 0.8984 0.060 0.936 0.000 0.004
#> SRR1044496 2 0.2908 0.8654 0.064 0.896 0.000 0.040
#> SRR1044495 2 0.2335 0.8877 0.060 0.920 0.000 0.020
#> SRR1044497 4 0.0336 0.6394 0.008 0.000 0.000 0.992
#> SRR1044499 2 0.5085 0.2862 0.008 0.616 0.376 0.000
#> SRR1044498 4 0.4304 0.6211 0.284 0.000 0.000 0.716
#> SRR1044500 2 0.0524 0.9127 0.008 0.988 0.004 0.000
#> SRR1044501 2 0.1151 0.9056 0.008 0.968 0.024 0.000
#> SRR1044502 3 0.6005 0.2372 0.040 0.460 0.500 0.000
#> SRR1044503 4 0.0336 0.6352 0.008 0.000 0.000 0.992
#> SRR1044504 4 0.0921 0.6323 0.028 0.000 0.000 0.972
#> SRR1044505 4 0.4925 0.4930 0.428 0.000 0.000 0.572
#> SRR1044506 4 0.2216 0.6335 0.092 0.000 0.000 0.908
#> SRR1044507 1 0.7205 0.3750 0.504 0.000 0.152 0.344
#> SRR1044508 1 0.7424 0.1413 0.424 0.000 0.408 0.168
#> SRR1044509 3 0.7608 -0.1825 0.392 0.000 0.408 0.200
#> SRR1044510 3 0.0000 0.7278 0.000 0.000 1.000 0.000
#> SRR1044511 3 0.0000 0.7278 0.000 0.000 1.000 0.000
#> SRR1044512 3 0.0000 0.7278 0.000 0.000 1.000 0.000
#> SRR1044513 3 0.6031 0.3459 0.044 0.420 0.536 0.000
#> SRR1044514 3 0.0000 0.7278 0.000 0.000 1.000 0.000
#> SRR1044515 3 0.6074 0.2487 0.044 0.456 0.500 0.000
#> SRR1044516 2 0.4163 0.7070 0.020 0.792 0.188 0.000
#> SRR1044517 3 0.0000 0.7278 0.000 0.000 1.000 0.000
#> SRR1044518 3 0.0000 0.7278 0.000 0.000 1.000 0.000
#> SRR1044519 3 0.0469 0.7256 0.012 0.000 0.988 0.000
#> SRR1044520 3 0.0000 0.7278 0.000 0.000 1.000 0.000
#> SRR1044521 2 0.1256 0.9072 0.008 0.964 0.028 0.000
#> SRR1044522 2 0.3245 0.8491 0.064 0.880 0.000 0.056
#> SRR1044523 2 0.5989 0.0945 0.044 0.556 0.400 0.000
#> SRR1044524 3 0.5110 0.5533 0.016 0.328 0.656 0.000
#> SRR1044525 4 0.2868 0.6082 0.136 0.000 0.000 0.864
#> SRR1044526 4 0.4454 0.6116 0.308 0.000 0.000 0.692
#> SRR1044527 2 0.0707 0.9118 0.020 0.980 0.000 0.000
#> SRR1044528 2 0.1929 0.8947 0.024 0.940 0.036 0.000
#> SRR1044529 2 0.1854 0.8998 0.048 0.940 0.000 0.012
#> SRR1044530 4 0.4972 0.4882 0.456 0.000 0.000 0.544
#> SRR1044531 4 0.5039 0.5482 0.404 0.000 0.004 0.592
#> SRR1044533 4 0.4679 0.5887 0.352 0.000 0.000 0.648
#> SRR1044532 4 0.5143 0.4826 0.456 0.004 0.000 0.540
#> SRR1044534 2 0.0524 0.9127 0.008 0.988 0.004 0.000
#> SRR1044535 3 0.5130 0.5541 0.016 0.332 0.652 0.000
#> SRR1044536 2 0.0376 0.9125 0.004 0.992 0.004 0.000
#> SRR1044537 1 0.5039 -0.2745 0.592 0.000 0.004 0.404
#> SRR1044538 4 0.5143 0.4826 0.456 0.004 0.000 0.540
#> SRR1044539 4 0.2081 0.6180 0.084 0.000 0.000 0.916
#> SRR1044540 4 0.4790 0.5528 0.380 0.000 0.000 0.620
#> SRR1044541 2 0.2737 0.8421 0.008 0.888 0.104 0.000
#> SRR1044542 4 0.5112 0.5100 0.436 0.004 0.000 0.560
#> SRR1044543 1 0.5837 0.0780 0.564 0.000 0.036 0.400
#> SRR1044544 2 0.2412 0.8627 0.008 0.908 0.084 0.000
#> SRR1044545 4 0.1637 0.6440 0.060 0.000 0.000 0.940
#> SRR1044546 4 0.4907 0.5253 0.420 0.000 0.000 0.580
#> SRR1044547 4 0.4103 0.6196 0.256 0.000 0.000 0.744
#> SRR1044548 4 0.4992 0.4734 0.476 0.000 0.000 0.524
#> SRR1044549 2 0.1938 0.8854 0.012 0.936 0.052 0.000
#> SRR1044550 2 0.0188 0.9120 0.000 0.996 0.004 0.000
#> SRR1044551 2 0.0707 0.9113 0.020 0.980 0.000 0.000
#> SRR1044552 4 0.0592 0.6300 0.016 0.000 0.000 0.984
#> SRR1044553 4 0.2011 0.6270 0.080 0.000 0.000 0.920
#> SRR1044554 4 0.5295 0.4415 0.488 0.000 0.008 0.504
#> SRR1044555 3 0.4844 0.5993 0.012 0.300 0.688 0.000
#> SRR1044556 4 0.0469 0.6442 0.012 0.000 0.000 0.988
#> SRR1044557 4 0.4996 0.4684 0.484 0.000 0.000 0.516
#> SRR1044558 4 0.1302 0.6452 0.044 0.000 0.000 0.956
#> SRR1044559 4 0.4907 0.5293 0.420 0.000 0.000 0.580
#> SRR1044561 4 0.0592 0.6300 0.016 0.000 0.000 0.984
#> SRR1044560 2 0.1356 0.9019 0.008 0.960 0.032 0.000
#> SRR1044562 4 0.4981 0.4838 0.464 0.000 0.000 0.536
#> SRR1044563 4 0.1302 0.6261 0.044 0.000 0.000 0.956
#> SRR1044564 4 0.5168 0.3646 0.496 0.000 0.004 0.500
#> SRR1044565 2 0.2908 0.8655 0.064 0.896 0.000 0.040
#> SRR1044566 2 0.1356 0.9019 0.008 0.960 0.032 0.000
#> SRR1044567 4 0.5303 0.4922 0.448 0.004 0.004 0.544
#> SRR1044568 4 0.3975 0.5902 0.240 0.000 0.000 0.760
#> SRR1044569 4 0.4977 0.4856 0.460 0.000 0.000 0.540
#> SRR1044570 4 0.5119 0.5040 0.440 0.004 0.000 0.556
#> SRR1044571 1 0.4999 -0.3016 0.508 0.000 0.000 0.492
#> SRR1044572 4 0.5228 0.5773 0.312 0.000 0.024 0.664
#> SRR1044573 4 0.4843 0.5255 0.396 0.000 0.000 0.604
#> SRR1044574 4 0.4817 0.5456 0.388 0.000 0.000 0.612
#> SRR1044575 4 0.3837 0.6224 0.224 0.000 0.000 0.776
#> SRR1044576 2 0.1211 0.9060 0.040 0.960 0.000 0.000
#> SRR1044577 2 0.1389 0.9035 0.048 0.952 0.000 0.000
#> SRR1044578 2 0.1716 0.8973 0.064 0.936 0.000 0.000
#> SRR1044579 4 0.0469 0.6329 0.012 0.000 0.000 0.988
#> SRR1044580 4 0.3837 0.6396 0.224 0.000 0.000 0.776
#> SRR1044581 4 0.0188 0.6374 0.004 0.000 0.000 0.996
#> SRR1044582 4 0.4925 0.5270 0.428 0.000 0.000 0.572
#> SRR1044583 4 0.0592 0.6300 0.016 0.000 0.000 0.984
#> SRR1044584 4 0.1716 0.6543 0.064 0.000 0.000 0.936
#> SRR1044585 4 0.0592 0.6300 0.016 0.000 0.000 0.984
#> SRR1044586 4 0.4830 0.5506 0.392 0.000 0.000 0.608
#> SRR1044587 4 0.2408 0.6427 0.104 0.000 0.000 0.896
#> SRR1044588 4 0.1792 0.6239 0.068 0.000 0.000 0.932
#> SRR1044589 4 0.2530 0.5748 0.112 0.000 0.000 0.888
#> SRR1044590 4 0.1211 0.6507 0.040 0.000 0.000 0.960
#> SRR1044591 4 0.3123 0.5365 0.156 0.000 0.000 0.844
#> SRR1044592 3 0.7608 -0.1825 0.392 0.000 0.408 0.200
#> SRR1044593 4 0.2281 0.5941 0.096 0.000 0.000 0.904
#> SRR1044594 4 0.2469 0.5868 0.108 0.000 0.000 0.892
#> SRR1044595 1 0.6901 0.1914 0.488 0.000 0.404 0.108
#> SRR1044596 1 0.7790 0.4431 0.424 0.000 0.272 0.304
#> SRR1044597 4 0.7206 0.3231 0.432 0.088 0.016 0.464
#> SRR1044598 2 0.6672 0.4117 0.168 0.620 0.000 0.212
#> SRR1044599 2 0.7072 0.2395 0.172 0.560 0.000 0.268
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.2470 0.7694 0.000 0.884 0.012 0.000 0.104
#> SRR1044416 2 0.3906 0.7640 0.004 0.704 0.000 0.000 0.292
#> SRR1044417 2 0.3274 0.7746 0.000 0.780 0.000 0.000 0.220
#> SRR1044418 2 0.3177 0.7788 0.000 0.792 0.000 0.000 0.208
#> SRR1044420 2 0.0609 0.7988 0.000 0.980 0.000 0.000 0.020
#> SRR1044419 2 0.2286 0.7725 0.000 0.888 0.004 0.000 0.108
#> SRR1044421 2 0.2522 0.7885 0.000 0.880 0.012 0.000 0.108
#> SRR1044422 2 0.1121 0.7920 0.000 0.956 0.000 0.000 0.044
#> SRR1044423 2 0.1410 0.7884 0.000 0.940 0.000 0.000 0.060
#> SRR1044424 2 0.1197 0.7992 0.000 0.952 0.000 0.000 0.048
#> SRR1044425 4 0.2260 0.6495 0.064 0.000 0.000 0.908 0.028
#> SRR1044426 1 0.8151 0.0616 0.420 0.000 0.172 0.176 0.232
#> SRR1044427 4 0.4679 0.2696 0.316 0.000 0.000 0.652 0.032
#> SRR1044428 1 0.7050 0.2410 0.400 0.000 0.024 0.392 0.184
#> SRR1044429 4 0.3771 0.5783 0.164 0.000 0.000 0.796 0.040
#> SRR1044430 1 0.7947 0.0674 0.452 0.004 0.212 0.100 0.232
#> SRR1044431 4 0.5484 0.1535 0.336 0.000 0.000 0.584 0.080
#> SRR1044433 3 0.8241 0.3003 0.284 0.000 0.332 0.116 0.268
#> SRR1044432 1 0.8112 0.0158 0.416 0.004 0.240 0.104 0.236
#> SRR1044434 4 0.1668 0.6509 0.028 0.000 0.000 0.940 0.032
#> SRR1044435 4 0.1168 0.6480 0.008 0.000 0.000 0.960 0.032
#> SRR1044436 4 0.1915 0.6516 0.040 0.000 0.000 0.928 0.032
#> SRR1044437 4 0.1041 0.6482 0.004 0.000 0.000 0.964 0.032
#> SRR1044439 4 0.1399 0.6538 0.020 0.000 0.000 0.952 0.028
#> SRR1044438 4 0.1399 0.6533 0.028 0.000 0.000 0.952 0.020
#> SRR1044440 4 0.1041 0.6490 0.004 0.000 0.000 0.964 0.032
#> SRR1044441 4 0.3798 0.5889 0.128 0.000 0.000 0.808 0.064
#> SRR1044442 1 0.8428 -0.1452 0.328 0.000 0.252 0.160 0.260
#> SRR1044443 3 0.8199 0.2945 0.292 0.000 0.328 0.108 0.272
#> SRR1044444 4 0.1168 0.6480 0.008 0.000 0.000 0.960 0.032
#> SRR1044445 4 0.5060 0.3957 0.224 0.000 0.000 0.684 0.092
#> SRR1044446 3 0.5159 0.6612 0.000 0.124 0.688 0.000 0.188
#> SRR1044447 3 0.5849 0.5790 0.000 0.196 0.608 0.000 0.196
#> SRR1044449 3 0.0290 0.7716 0.000 0.000 0.992 0.000 0.008
#> SRR1044448 3 0.0794 0.7728 0.000 0.000 0.972 0.000 0.028
#> SRR1044450 3 0.1282 0.7722 0.000 0.004 0.952 0.000 0.044
#> SRR1044451 3 0.6008 0.5589 0.000 0.200 0.584 0.000 0.216
#> SRR1044452 3 0.0703 0.7716 0.000 0.000 0.976 0.000 0.024
#> SRR1044453 3 0.0609 0.7715 0.000 0.000 0.980 0.000 0.020
#> SRR1044454 3 0.0703 0.7716 0.000 0.000 0.976 0.000 0.024
#> SRR1044455 2 0.3752 0.7312 0.000 0.804 0.048 0.000 0.148
#> SRR1044456 2 0.7000 0.5498 0.056 0.544 0.000 0.156 0.244
#> SRR1044457 2 0.3241 0.7523 0.000 0.832 0.024 0.000 0.144
#> SRR1044458 2 0.2723 0.7612 0.000 0.864 0.012 0.000 0.124
#> SRR1044459 3 0.4254 0.7141 0.000 0.080 0.772 0.000 0.148
#> SRR1044460 2 0.1197 0.7950 0.000 0.952 0.000 0.000 0.048
#> SRR1044461 2 0.2124 0.7766 0.000 0.900 0.004 0.000 0.096
#> SRR1044462 4 0.5284 0.2257 0.376 0.000 0.000 0.568 0.056
#> SRR1044463 1 0.5741 0.3210 0.484 0.004 0.000 0.440 0.072
#> SRR1044464 1 0.8129 0.1024 0.424 0.000 0.160 0.188 0.228
#> SRR1044466 1 0.5683 0.3363 0.500 0.004 0.000 0.428 0.068
#> SRR1044465 4 0.5684 0.1198 0.340 0.000 0.000 0.564 0.096
#> SRR1044467 4 0.5672 0.0960 0.368 0.000 0.000 0.544 0.088
#> SRR1044468 2 0.0404 0.7964 0.000 0.988 0.000 0.000 0.012
#> SRR1044469 3 0.5404 0.6222 0.000 0.184 0.664 0.000 0.152
#> SRR1044470 1 0.5932 0.4056 0.608 0.012 0.004 0.284 0.092
#> SRR1044471 1 0.5953 0.1031 0.476 0.000 0.004 0.428 0.092
#> SRR1044472 1 0.7219 0.3910 0.496 0.004 0.040 0.284 0.176
#> SRR1044473 1 0.4815 0.2195 0.524 0.000 0.000 0.456 0.020
#> SRR1044474 2 0.4046 0.7325 0.008 0.696 0.000 0.000 0.296
#> SRR1044475 3 0.1568 0.7718 0.000 0.020 0.944 0.000 0.036
#> SRR1044476 2 0.2777 0.7617 0.000 0.864 0.016 0.000 0.120
#> SRR1044477 2 0.4305 0.7295 0.012 0.688 0.000 0.004 0.296
#> SRR1044478 2 0.0510 0.7956 0.000 0.984 0.000 0.000 0.016
#> SRR1044479 2 0.5503 0.6889 0.024 0.632 0.000 0.048 0.296
#> SRR1044480 4 0.2927 0.6369 0.092 0.000 0.000 0.868 0.040
#> SRR1044481 4 0.4963 0.1481 0.352 0.000 0.000 0.608 0.040
#> SRR1044482 2 0.2852 0.7836 0.000 0.828 0.000 0.000 0.172
#> SRR1044483 4 0.7214 -0.0640 0.328 0.000 0.052 0.468 0.152
#> SRR1044484 4 0.4464 0.3172 0.288 0.000 0.000 0.684 0.028
#> SRR1044486 4 0.4824 -0.1708 0.468 0.000 0.000 0.512 0.020
#> SRR1044485 2 0.1410 0.7981 0.000 0.940 0.000 0.000 0.060
#> SRR1044487 2 0.4859 0.7229 0.020 0.672 0.000 0.020 0.288
#> SRR1044488 2 0.0880 0.7995 0.000 0.968 0.000 0.000 0.032
#> SRR1044489 2 0.0404 0.7977 0.000 0.988 0.000 0.000 0.012
#> SRR1044490 4 0.6394 -0.0431 0.344 0.000 0.000 0.476 0.180
#> SRR1044491 1 0.5390 0.3654 0.536 0.000 0.004 0.412 0.048
#> SRR1044492 1 0.6221 0.3864 0.532 0.020 0.000 0.356 0.092
#> SRR1044493 1 0.5143 0.3482 0.532 0.000 0.000 0.428 0.040
#> SRR1044494 2 0.4199 0.7307 0.008 0.692 0.000 0.004 0.296
#> SRR1044496 2 0.4681 0.7315 0.020 0.692 0.000 0.016 0.272
#> SRR1044495 2 0.4217 0.7394 0.004 0.704 0.000 0.012 0.280
#> SRR1044497 4 0.0992 0.6515 0.008 0.000 0.000 0.968 0.024
#> SRR1044499 2 0.6253 0.1382 0.000 0.492 0.352 0.000 0.156
#> SRR1044498 4 0.4645 0.3724 0.268 0.000 0.000 0.688 0.044
#> SRR1044500 2 0.1121 0.8007 0.000 0.956 0.000 0.000 0.044
#> SRR1044501 2 0.2358 0.7722 0.000 0.888 0.008 0.000 0.104
#> SRR1044502 2 0.6934 -0.0628 0.004 0.372 0.328 0.000 0.296
#> SRR1044503 4 0.1082 0.6485 0.008 0.000 0.000 0.964 0.028
#> SRR1044504 4 0.1915 0.6451 0.040 0.000 0.000 0.928 0.032
#> SRR1044505 4 0.5348 -0.0202 0.456 0.000 0.000 0.492 0.052
#> SRR1044506 4 0.3339 0.6212 0.124 0.000 0.000 0.836 0.040
#> SRR1044507 1 0.8084 0.2679 0.404 0.000 0.116 0.236 0.244
#> SRR1044508 3 0.8094 0.2782 0.308 0.000 0.324 0.092 0.276
#> SRR1044509 3 0.8241 0.3003 0.284 0.000 0.332 0.116 0.268
#> SRR1044510 3 0.1197 0.7710 0.000 0.000 0.952 0.000 0.048
#> SRR1044511 3 0.1043 0.7719 0.000 0.000 0.960 0.000 0.040
#> SRR1044512 3 0.0963 0.7714 0.000 0.000 0.964 0.000 0.036
#> SRR1044513 3 0.6891 0.2163 0.004 0.316 0.400 0.000 0.280
#> SRR1044514 3 0.0963 0.7720 0.000 0.000 0.964 0.000 0.036
#> SRR1044515 2 0.6927 -0.1064 0.004 0.360 0.352 0.000 0.284
#> SRR1044516 2 0.5475 0.6126 0.000 0.644 0.124 0.000 0.232
#> SRR1044517 3 0.1410 0.7722 0.000 0.000 0.940 0.000 0.060
#> SRR1044518 3 0.0880 0.7720 0.000 0.000 0.968 0.000 0.032
#> SRR1044519 3 0.0703 0.7724 0.000 0.000 0.976 0.000 0.024
#> SRR1044520 3 0.0609 0.7719 0.000 0.000 0.980 0.000 0.020
#> SRR1044521 2 0.1569 0.8018 0.008 0.944 0.004 0.000 0.044
#> SRR1044522 2 0.5246 0.7106 0.024 0.664 0.000 0.040 0.272
#> SRR1044523 2 0.6740 0.2258 0.004 0.460 0.260 0.000 0.276
#> SRR1044524 3 0.6084 0.5271 0.000 0.220 0.572 0.000 0.208
#> SRR1044525 4 0.4058 0.5824 0.152 0.000 0.000 0.784 0.064
#> SRR1044526 4 0.5831 0.1921 0.304 0.000 0.004 0.584 0.108
#> SRR1044527 2 0.3010 0.7870 0.004 0.824 0.000 0.000 0.172
#> SRR1044528 2 0.4019 0.7540 0.004 0.768 0.028 0.000 0.200
#> SRR1044529 2 0.3855 0.7589 0.008 0.748 0.000 0.004 0.240
#> SRR1044530 1 0.5414 0.3567 0.528 0.000 0.000 0.412 0.060
#> SRR1044531 4 0.5747 -0.0339 0.408 0.000 0.000 0.504 0.088
#> SRR1044533 4 0.5951 -0.0324 0.364 0.000 0.000 0.520 0.116
#> SRR1044532 1 0.5586 0.3688 0.536 0.004 0.000 0.396 0.064
#> SRR1044534 2 0.1205 0.8013 0.004 0.956 0.000 0.000 0.040
#> SRR1044535 3 0.6202 0.5136 0.000 0.220 0.552 0.000 0.228
#> SRR1044536 2 0.0703 0.7943 0.000 0.976 0.000 0.000 0.024
#> SRR1044537 1 0.4608 0.4036 0.700 0.000 0.004 0.260 0.036
#> SRR1044538 1 0.5658 0.3560 0.520 0.004 0.000 0.408 0.068
#> SRR1044539 4 0.2871 0.6171 0.088 0.000 0.000 0.872 0.040
#> SRR1044540 4 0.6076 0.0704 0.320 0.000 0.000 0.536 0.144
#> SRR1044541 2 0.3950 0.7251 0.000 0.796 0.068 0.000 0.136
#> SRR1044542 1 0.5532 0.3247 0.508 0.008 0.000 0.436 0.048
#> SRR1044543 1 0.6982 0.2788 0.496 0.000 0.028 0.280 0.196
#> SRR1044544 2 0.4686 0.6705 0.000 0.736 0.104 0.000 0.160
#> SRR1044545 4 0.3035 0.6274 0.112 0.000 0.000 0.856 0.032
#> SRR1044546 4 0.4744 -0.2298 0.476 0.000 0.000 0.508 0.016
#> SRR1044547 4 0.4901 0.4359 0.268 0.000 0.000 0.672 0.060
#> SRR1044548 1 0.4604 0.3138 0.560 0.000 0.000 0.428 0.012
#> SRR1044549 2 0.3276 0.7892 0.000 0.836 0.032 0.000 0.132
#> SRR1044550 2 0.0404 0.7979 0.000 0.988 0.000 0.000 0.012
#> SRR1044551 2 0.2891 0.7869 0.000 0.824 0.000 0.000 0.176
#> SRR1044552 4 0.1211 0.6495 0.016 0.000 0.000 0.960 0.024
#> SRR1044553 4 0.2770 0.6368 0.076 0.000 0.000 0.880 0.044
#> SRR1044554 1 0.5658 0.2998 0.520 0.000 0.004 0.408 0.068
#> SRR1044555 3 0.5956 0.5551 0.000 0.212 0.592 0.000 0.196
#> SRR1044556 4 0.1310 0.6540 0.020 0.000 0.000 0.956 0.024
#> SRR1044557 1 0.4900 0.2037 0.512 0.000 0.000 0.464 0.024
#> SRR1044558 4 0.2228 0.6520 0.048 0.000 0.000 0.912 0.040
#> SRR1044559 1 0.5115 0.2531 0.484 0.000 0.000 0.480 0.036
#> SRR1044561 4 0.1124 0.6476 0.004 0.000 0.000 0.960 0.036
#> SRR1044560 2 0.2674 0.7636 0.000 0.868 0.012 0.000 0.120
#> SRR1044562 1 0.4965 0.2988 0.520 0.000 0.000 0.452 0.028
#> SRR1044563 4 0.2124 0.6395 0.056 0.000 0.000 0.916 0.028
#> SRR1044564 1 0.6092 0.1701 0.464 0.000 0.000 0.412 0.124
#> SRR1044565 2 0.4754 0.7150 0.020 0.664 0.000 0.012 0.304
#> SRR1044566 2 0.2727 0.7642 0.000 0.868 0.016 0.000 0.116
#> SRR1044567 1 0.5775 0.3430 0.496 0.004 0.000 0.424 0.076
#> SRR1044568 4 0.5037 0.4751 0.228 0.000 0.000 0.684 0.088
#> SRR1044569 1 0.5353 0.1047 0.476 0.000 0.000 0.472 0.052
#> SRR1044570 1 0.5687 0.3294 0.496 0.004 0.000 0.432 0.068
#> SRR1044571 1 0.6620 0.2432 0.464 0.000 0.008 0.356 0.172
#> SRR1044572 4 0.6078 0.1846 0.280 0.000 0.008 0.580 0.132
#> SRR1044573 4 0.5019 0.1834 0.396 0.000 0.000 0.568 0.036
#> SRR1044574 4 0.6178 -0.0881 0.376 0.000 0.000 0.484 0.140
#> SRR1044575 4 0.4665 0.4527 0.260 0.000 0.000 0.692 0.048
#> SRR1044576 2 0.3607 0.7657 0.004 0.752 0.000 0.000 0.244
#> SRR1044577 2 0.3534 0.7585 0.000 0.744 0.000 0.000 0.256
#> SRR1044578 2 0.4003 0.7386 0.008 0.704 0.000 0.000 0.288
#> SRR1044579 4 0.1251 0.6460 0.008 0.000 0.000 0.956 0.036
#> SRR1044580 4 0.4779 0.4563 0.200 0.000 0.000 0.716 0.084
#> SRR1044581 4 0.1082 0.6503 0.008 0.000 0.000 0.964 0.028
#> SRR1044582 1 0.4740 0.2671 0.516 0.000 0.000 0.468 0.016
#> SRR1044583 4 0.1168 0.6463 0.008 0.000 0.000 0.960 0.032
#> SRR1044584 4 0.2654 0.6299 0.084 0.000 0.000 0.884 0.032
#> SRR1044585 4 0.1041 0.6477 0.004 0.000 0.000 0.964 0.032
#> SRR1044586 4 0.4627 -0.1336 0.444 0.000 0.000 0.544 0.012
#> SRR1044587 4 0.3555 0.6144 0.124 0.000 0.000 0.824 0.052
#> SRR1044588 4 0.2903 0.6249 0.080 0.000 0.000 0.872 0.048
#> SRR1044589 4 0.3267 0.6027 0.112 0.000 0.000 0.844 0.044
#> SRR1044590 4 0.2616 0.6452 0.076 0.000 0.000 0.888 0.036
#> SRR1044591 4 0.3846 0.5622 0.144 0.000 0.000 0.800 0.056
#> SRR1044592 3 0.8241 0.3003 0.284 0.000 0.332 0.116 0.268
#> SRR1044593 4 0.3216 0.6027 0.108 0.000 0.000 0.848 0.044
#> SRR1044594 4 0.3164 0.6051 0.104 0.000 0.000 0.852 0.044
#> SRR1044595 1 0.7496 -0.2790 0.364 0.000 0.332 0.036 0.268
#> SRR1044596 1 0.8497 0.1183 0.320 0.000 0.192 0.268 0.220
#> SRR1044597 1 0.7550 0.3374 0.432 0.088 0.032 0.392 0.056
#> SRR1044598 2 0.7622 0.1708 0.224 0.472 0.000 0.224 0.080
#> SRR1044599 2 0.7821 0.0437 0.228 0.436 0.000 0.248 0.088
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.2704 0.4403 0.000 0.844 0.016 0.000 0.000 0.140
#> SRR1044416 2 0.4933 0.4661 0.004 0.616 0.000 0.000 0.300 0.080
#> SRR1044417 2 0.4019 0.5118 0.004 0.652 0.000 0.000 0.332 0.012
#> SRR1044418 2 0.4090 0.5112 0.004 0.652 0.000 0.000 0.328 0.016
#> SRR1044420 2 0.0993 0.5718 0.000 0.964 0.000 0.000 0.024 0.012
#> SRR1044419 2 0.2783 0.4289 0.000 0.836 0.016 0.000 0.000 0.148
#> SRR1044421 2 0.2781 0.5215 0.004 0.880 0.016 0.000 0.040 0.060
#> SRR1044422 2 0.0972 0.5562 0.000 0.964 0.000 0.000 0.008 0.028
#> SRR1044423 2 0.1901 0.5218 0.000 0.912 0.004 0.000 0.008 0.076
#> SRR1044424 2 0.1219 0.5775 0.000 0.948 0.000 0.000 0.048 0.004
#> SRR1044425 4 0.2677 0.6158 0.056 0.000 0.000 0.884 0.024 0.036
#> SRR1044426 5 0.8161 0.6796 0.280 0.000 0.076 0.076 0.300 0.268
#> SRR1044427 4 0.4456 0.2240 0.276 0.000 0.000 0.676 0.020 0.028
#> SRR1044428 4 0.7530 -0.2361 0.284 0.000 0.008 0.384 0.188 0.136
#> SRR1044429 4 0.4232 0.5431 0.152 0.000 0.000 0.764 0.044 0.040
#> SRR1044430 1 0.8224 -0.6630 0.300 0.000 0.104 0.064 0.296 0.236
#> SRR1044431 4 0.5668 0.0981 0.316 0.000 0.000 0.568 0.056 0.060
#> SRR1044433 5 0.7219 0.7613 0.056 0.000 0.180 0.048 0.500 0.216
#> SRR1044432 5 0.8135 0.6434 0.296 0.000 0.124 0.044 0.304 0.232
#> SRR1044434 4 0.2015 0.6187 0.016 0.000 0.000 0.916 0.012 0.056
#> SRR1044435 4 0.1590 0.6157 0.008 0.000 0.000 0.936 0.008 0.048
#> SRR1044436 4 0.2119 0.6156 0.044 0.000 0.000 0.912 0.008 0.036
#> SRR1044437 4 0.1116 0.6184 0.004 0.000 0.000 0.960 0.008 0.028
#> SRR1044439 4 0.1679 0.6227 0.016 0.000 0.000 0.936 0.012 0.036
#> SRR1044438 4 0.2152 0.6216 0.040 0.000 0.000 0.912 0.012 0.036
#> SRR1044440 4 0.1542 0.6146 0.004 0.000 0.000 0.936 0.008 0.052
#> SRR1044441 4 0.3610 0.5925 0.052 0.000 0.000 0.824 0.036 0.088
#> SRR1044442 5 0.7903 0.7544 0.088 0.000 0.132 0.104 0.444 0.232
#> SRR1044443 5 0.7141 0.7557 0.052 0.000 0.188 0.044 0.504 0.212
#> SRR1044444 4 0.1524 0.6148 0.000 0.000 0.000 0.932 0.008 0.060
#> SRR1044445 4 0.5523 0.4155 0.100 0.000 0.000 0.672 0.096 0.132
#> SRR1044446 3 0.5518 0.3085 0.008 0.120 0.616 0.000 0.012 0.244
#> SRR1044447 3 0.6947 -0.3675 0.008 0.196 0.432 0.000 0.056 0.308
#> SRR1044449 3 0.0363 0.7165 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1044448 3 0.1528 0.7128 0.012 0.000 0.944 0.000 0.016 0.028
#> SRR1044450 3 0.1777 0.7116 0.012 0.000 0.932 0.000 0.024 0.032
#> SRR1044451 3 0.6627 -0.2828 0.008 0.196 0.460 0.000 0.032 0.304
#> SRR1044452 3 0.3099 0.6951 0.060 0.000 0.848 0.000 0.008 0.084
#> SRR1044453 3 0.3090 0.6964 0.056 0.000 0.848 0.000 0.008 0.088
#> SRR1044454 3 0.3150 0.6938 0.060 0.000 0.844 0.000 0.008 0.088
#> SRR1044455 2 0.4282 0.1870 0.000 0.724 0.072 0.000 0.004 0.200
#> SRR1044456 2 0.7481 0.1625 0.116 0.380 0.000 0.176 0.316 0.012
#> SRR1044457 2 0.3806 0.3198 0.000 0.768 0.068 0.000 0.000 0.164
#> SRR1044458 2 0.2968 0.3998 0.000 0.816 0.016 0.000 0.000 0.168
#> SRR1044459 3 0.4915 0.4985 0.024 0.076 0.680 0.000 0.000 0.220
#> SRR1044460 2 0.1787 0.5298 0.000 0.920 0.004 0.000 0.008 0.068
#> SRR1044461 2 0.2165 0.4822 0.000 0.884 0.008 0.000 0.000 0.108
#> SRR1044462 4 0.5467 0.2725 0.304 0.000 0.000 0.592 0.048 0.056
#> SRR1044463 1 0.5387 0.6175 0.508 0.000 0.000 0.412 0.048 0.032
#> SRR1044464 5 0.7992 0.6699 0.280 0.000 0.052 0.080 0.300 0.288
#> SRR1044466 1 0.5123 0.6587 0.540 0.000 0.000 0.396 0.040 0.024
#> SRR1044465 4 0.5737 0.0589 0.312 0.000 0.000 0.564 0.076 0.048
#> SRR1044467 4 0.5609 0.2345 0.264 0.000 0.000 0.608 0.056 0.072
#> SRR1044468 2 0.0458 0.5607 0.000 0.984 0.000 0.000 0.000 0.016
#> SRR1044469 3 0.6256 0.1637 0.032 0.180 0.536 0.000 0.004 0.248
#> SRR1044470 1 0.6251 0.5499 0.580 0.020 0.004 0.268 0.072 0.056
#> SRR1044471 4 0.6428 -0.0216 0.380 0.000 0.004 0.456 0.076 0.084
#> SRR1044472 1 0.6831 0.4769 0.516 0.000 0.016 0.264 0.112 0.092
#> SRR1044473 1 0.4528 0.4763 0.544 0.000 0.000 0.428 0.008 0.020
#> SRR1044474 2 0.4379 0.4772 0.028 0.576 0.000 0.000 0.396 0.000
#> SRR1044475 3 0.3448 0.6921 0.064 0.004 0.828 0.000 0.008 0.096
#> SRR1044476 2 0.2968 0.4033 0.000 0.816 0.016 0.000 0.000 0.168
#> SRR1044477 2 0.4586 0.4690 0.032 0.564 0.000 0.004 0.400 0.000
#> SRR1044478 2 0.0914 0.5674 0.000 0.968 0.000 0.000 0.016 0.016
#> SRR1044479 2 0.5549 0.4220 0.052 0.516 0.000 0.032 0.396 0.004
#> SRR1044480 4 0.2797 0.6177 0.064 0.000 0.000 0.876 0.024 0.036
#> SRR1044481 4 0.5027 -0.0150 0.312 0.000 0.000 0.616 0.032 0.040
#> SRR1044482 2 0.3499 0.5307 0.000 0.680 0.000 0.000 0.320 0.000
#> SRR1044483 4 0.7511 0.0389 0.208 0.000 0.020 0.456 0.152 0.164
#> SRR1044484 4 0.4149 0.2920 0.248 0.000 0.000 0.712 0.016 0.024
#> SRR1044486 4 0.4786 -0.4402 0.444 0.000 0.000 0.516 0.016 0.024
#> SRR1044485 2 0.1327 0.5772 0.000 0.936 0.000 0.000 0.064 0.000
#> SRR1044487 2 0.4946 0.4598 0.052 0.556 0.000 0.008 0.384 0.000
#> SRR1044488 2 0.0632 0.5732 0.000 0.976 0.000 0.000 0.024 0.000
#> SRR1044489 2 0.0777 0.5729 0.000 0.972 0.000 0.000 0.024 0.004
#> SRR1044490 4 0.7089 -0.0668 0.212 0.000 0.000 0.468 0.168 0.152
#> SRR1044491 1 0.5398 0.6363 0.548 0.000 0.004 0.372 0.032 0.044
#> SRR1044492 1 0.5941 0.6552 0.548 0.020 0.000 0.336 0.056 0.040
#> SRR1044493 1 0.4746 0.6343 0.540 0.000 0.000 0.420 0.012 0.028
#> SRR1044494 2 0.4395 0.4712 0.028 0.568 0.000 0.000 0.404 0.000
#> SRR1044496 2 0.4685 0.4725 0.040 0.568 0.000 0.004 0.388 0.000
#> SRR1044495 2 0.4560 0.4817 0.024 0.580 0.000 0.004 0.388 0.004
#> SRR1044497 4 0.1477 0.6209 0.004 0.000 0.000 0.940 0.008 0.048
#> SRR1044499 2 0.6464 -0.5335 0.012 0.388 0.340 0.000 0.004 0.256
#> SRR1044498 4 0.4227 0.3991 0.212 0.000 0.000 0.732 0.028 0.028
#> SRR1044500 2 0.1049 0.5742 0.000 0.960 0.000 0.000 0.032 0.008
#> SRR1044501 2 0.3101 0.4082 0.000 0.820 0.032 0.000 0.000 0.148
#> SRR1044502 6 0.7397 0.9157 0.000 0.320 0.208 0.000 0.132 0.340
#> SRR1044503 4 0.1442 0.6175 0.004 0.000 0.000 0.944 0.012 0.040
#> SRR1044504 4 0.2071 0.6230 0.028 0.000 0.000 0.916 0.012 0.044
#> SRR1044505 4 0.5447 -0.0561 0.420 0.000 0.000 0.496 0.032 0.052
#> SRR1044506 4 0.3095 0.5969 0.072 0.000 0.000 0.856 0.020 0.052
#> SRR1044507 5 0.8454 0.4188 0.188 0.000 0.080 0.196 0.352 0.184
#> SRR1044508 5 0.7241 0.7601 0.064 0.000 0.180 0.040 0.492 0.224
#> SRR1044509 5 0.7219 0.7613 0.056 0.000 0.180 0.048 0.500 0.216
#> SRR1044510 3 0.3220 0.7063 0.052 0.000 0.844 0.000 0.016 0.088
#> SRR1044511 3 0.1989 0.7111 0.004 0.000 0.916 0.000 0.028 0.052
#> SRR1044512 3 0.1777 0.7130 0.004 0.000 0.928 0.000 0.024 0.044
#> SRR1044513 6 0.7460 0.8867 0.000 0.276 0.252 0.000 0.132 0.340
#> SRR1044514 3 0.2302 0.7093 0.008 0.000 0.900 0.000 0.032 0.060
#> SRR1044515 6 0.7438 0.9235 0.000 0.304 0.204 0.000 0.144 0.348
#> SRR1044516 2 0.6455 -0.2108 0.000 0.552 0.100 0.000 0.132 0.216
#> SRR1044517 3 0.3721 0.6989 0.064 0.000 0.808 0.000 0.020 0.108
#> SRR1044518 3 0.2240 0.7094 0.008 0.000 0.904 0.000 0.032 0.056
#> SRR1044519 3 0.1700 0.7103 0.012 0.000 0.936 0.000 0.024 0.028
#> SRR1044520 3 0.1176 0.7113 0.000 0.000 0.956 0.000 0.024 0.020
#> SRR1044521 2 0.1261 0.5727 0.004 0.956 0.004 0.000 0.028 0.008
#> SRR1044522 2 0.5490 0.4304 0.048 0.524 0.000 0.032 0.392 0.004
#> SRR1044523 2 0.7265 -0.7587 0.000 0.392 0.148 0.000 0.156 0.304
#> SRR1044524 3 0.6307 -0.2233 0.016 0.220 0.480 0.000 0.004 0.280
#> SRR1044525 4 0.4562 0.5552 0.104 0.000 0.000 0.752 0.044 0.100
#> SRR1044526 4 0.5671 0.2431 0.236 0.000 0.000 0.620 0.072 0.072
#> SRR1044527 2 0.3809 0.5251 0.004 0.684 0.000 0.000 0.304 0.008
#> SRR1044528 2 0.5621 0.2906 0.000 0.612 0.028 0.000 0.224 0.136
#> SRR1044529 2 0.4446 0.4922 0.028 0.600 0.000 0.000 0.368 0.004
#> SRR1044530 1 0.5100 0.6621 0.556 0.000 0.000 0.380 0.036 0.028
#> SRR1044531 4 0.5975 -0.0616 0.344 0.000 0.000 0.520 0.056 0.080
#> SRR1044533 4 0.6135 -0.1752 0.332 0.000 0.000 0.516 0.076 0.076
#> SRR1044532 1 0.5055 0.6642 0.572 0.000 0.000 0.364 0.040 0.024
#> SRR1044534 2 0.1411 0.5769 0.000 0.936 0.000 0.000 0.060 0.004
#> SRR1044535 3 0.6014 -0.3026 0.004 0.236 0.468 0.000 0.000 0.292
#> SRR1044536 2 0.0291 0.5663 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1044537 1 0.4981 0.5390 0.664 0.000 0.000 0.248 0.044 0.044
#> SRR1044538 1 0.5073 0.6653 0.568 0.000 0.000 0.368 0.036 0.028
#> SRR1044539 4 0.3210 0.5979 0.096 0.000 0.000 0.844 0.020 0.040
#> SRR1044540 4 0.6293 0.1720 0.232 0.000 0.000 0.564 0.104 0.100
#> SRR1044541 2 0.4199 0.2416 0.000 0.736 0.100 0.000 0.000 0.164
#> SRR1044542 1 0.5030 0.6403 0.532 0.000 0.000 0.412 0.028 0.028
#> SRR1044543 1 0.7931 -0.0286 0.304 0.000 0.012 0.260 0.232 0.192
#> SRR1044544 2 0.5007 -0.0206 0.004 0.648 0.124 0.000 0.000 0.224
#> SRR1044545 4 0.3054 0.6025 0.088 0.000 0.000 0.856 0.028 0.028
#> SRR1044546 1 0.4529 0.5683 0.508 0.000 0.000 0.460 0.000 0.032
#> SRR1044547 4 0.4714 0.4773 0.188 0.000 0.000 0.716 0.044 0.052
#> SRR1044548 1 0.4950 0.5994 0.540 0.000 0.000 0.408 0.020 0.032
#> SRR1044549 2 0.4256 0.4985 0.004 0.736 0.012 0.000 0.204 0.044
#> SRR1044550 2 0.1003 0.5665 0.000 0.964 0.000 0.000 0.016 0.020
#> SRR1044551 2 0.3448 0.5395 0.004 0.716 0.000 0.000 0.280 0.000
#> SRR1044552 4 0.1921 0.6192 0.012 0.000 0.000 0.920 0.012 0.056
#> SRR1044553 4 0.2798 0.6188 0.048 0.000 0.000 0.876 0.020 0.056
#> SRR1044554 1 0.5738 0.5015 0.524 0.000 0.000 0.364 0.064 0.048
#> SRR1044555 3 0.6032 0.0556 0.020 0.180 0.524 0.000 0.000 0.276
#> SRR1044556 4 0.1692 0.6212 0.012 0.000 0.000 0.932 0.008 0.048
#> SRR1044557 1 0.4957 0.5206 0.544 0.000 0.000 0.400 0.012 0.044
#> SRR1044558 4 0.2973 0.6186 0.040 0.000 0.000 0.868 0.036 0.056
#> SRR1044559 1 0.4832 0.6369 0.532 0.000 0.000 0.424 0.016 0.028
#> SRR1044561 4 0.1528 0.6171 0.000 0.000 0.000 0.936 0.016 0.048
#> SRR1044560 2 0.3098 0.4022 0.000 0.812 0.024 0.000 0.000 0.164
#> SRR1044562 1 0.4824 0.6376 0.544 0.000 0.000 0.412 0.020 0.024
#> SRR1044563 4 0.2520 0.6180 0.052 0.000 0.000 0.888 0.008 0.052
#> SRR1044564 4 0.6749 -0.1356 0.380 0.000 0.004 0.420 0.100 0.096
#> SRR1044565 2 0.4810 0.4585 0.040 0.552 0.000 0.008 0.400 0.000
#> SRR1044566 2 0.2981 0.4111 0.000 0.820 0.020 0.000 0.000 0.160
#> SRR1044567 1 0.5511 0.6490 0.544 0.000 0.000 0.360 0.060 0.036
#> SRR1044568 4 0.5758 0.4378 0.160 0.000 0.004 0.652 0.080 0.104
#> SRR1044569 4 0.5414 -0.2045 0.448 0.000 0.000 0.472 0.032 0.048
#> SRR1044570 1 0.5083 0.6599 0.560 0.000 0.000 0.376 0.040 0.024
#> SRR1044571 4 0.7535 -0.2259 0.328 0.000 0.004 0.336 0.160 0.172
#> SRR1044572 4 0.6671 0.0349 0.228 0.000 0.012 0.548 0.100 0.112
#> SRR1044573 4 0.5292 0.1953 0.344 0.000 0.000 0.572 0.028 0.056
#> SRR1044574 4 0.6282 -0.0195 0.288 0.000 0.000 0.532 0.104 0.076
#> SRR1044575 4 0.4633 0.4530 0.232 0.000 0.000 0.696 0.032 0.040
#> SRR1044576 2 0.4167 0.5075 0.008 0.636 0.000 0.000 0.344 0.012
#> SRR1044577 2 0.3647 0.5122 0.000 0.640 0.000 0.000 0.360 0.000
#> SRR1044578 2 0.4301 0.4817 0.024 0.584 0.000 0.000 0.392 0.000
#> SRR1044579 4 0.1464 0.6177 0.004 0.000 0.000 0.944 0.016 0.036
#> SRR1044580 4 0.4498 0.4632 0.136 0.000 0.000 0.752 0.068 0.044
#> SRR1044581 4 0.1511 0.6165 0.004 0.000 0.000 0.940 0.012 0.044
#> SRR1044582 1 0.4381 0.5691 0.524 0.000 0.000 0.456 0.004 0.016
#> SRR1044583 4 0.1707 0.6123 0.004 0.000 0.000 0.928 0.012 0.056
#> SRR1044584 4 0.2401 0.6089 0.048 0.000 0.000 0.900 0.024 0.028
#> SRR1044585 4 0.1644 0.6141 0.004 0.000 0.000 0.932 0.012 0.052
#> SRR1044586 4 0.4600 -0.4838 0.468 0.000 0.000 0.500 0.004 0.028
#> SRR1044587 4 0.3473 0.5877 0.088 0.000 0.000 0.824 0.012 0.076
#> SRR1044588 4 0.3002 0.5976 0.040 0.000 0.000 0.864 0.028 0.068
#> SRR1044589 4 0.3266 0.5887 0.048 0.000 0.000 0.848 0.032 0.072
#> SRR1044590 4 0.2672 0.6109 0.048 0.000 0.000 0.884 0.020 0.048
#> SRR1044591 4 0.4013 0.5530 0.056 0.000 0.000 0.796 0.048 0.100
#> SRR1044592 5 0.7239 0.7606 0.052 0.000 0.180 0.052 0.496 0.220
#> SRR1044593 4 0.2941 0.5964 0.048 0.000 0.000 0.868 0.024 0.060
#> SRR1044594 4 0.2941 0.5964 0.048 0.000 0.000 0.868 0.024 0.060
#> SRR1044595 5 0.7133 0.7486 0.076 0.000 0.176 0.028 0.504 0.216
#> SRR1044596 5 0.8257 0.6044 0.088 0.000 0.100 0.236 0.368 0.208
#> SRR1044597 1 0.7181 0.5768 0.420 0.032 0.016 0.388 0.076 0.068
#> SRR1044598 2 0.8315 -0.2035 0.236 0.324 0.004 0.256 0.132 0.048
#> SRR1044599 2 0.8291 -0.3107 0.240 0.292 0.004 0.284 0.140 0.040
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.991 0.996 0.4936 0.508 0.508
#> 3 3 0.675 0.705 0.837 0.2824 0.854 0.713
#> 4 4 0.746 0.796 0.890 0.1389 0.849 0.617
#> 5 5 0.761 0.721 0.846 0.0550 0.946 0.808
#> 6 6 0.786 0.748 0.850 0.0379 0.957 0.826
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0.0000 1.000 0.000 1.000
#> SRR1044416 2 0.0000 1.000 0.000 1.000
#> SRR1044417 2 0.0000 1.000 0.000 1.000
#> SRR1044418 2 0.0000 1.000 0.000 1.000
#> SRR1044420 2 0.0000 1.000 0.000 1.000
#> SRR1044419 2 0.0000 1.000 0.000 1.000
#> SRR1044421 2 0.0000 1.000 0.000 1.000
#> SRR1044422 2 0.0000 1.000 0.000 1.000
#> SRR1044423 2 0.0000 1.000 0.000 1.000
#> SRR1044424 2 0.0000 1.000 0.000 1.000
#> SRR1044425 1 0.0000 0.993 1.000 0.000
#> SRR1044426 1 0.0000 0.993 1.000 0.000
#> SRR1044427 1 0.0000 0.993 1.000 0.000
#> SRR1044428 1 0.0000 0.993 1.000 0.000
#> SRR1044429 1 0.0000 0.993 1.000 0.000
#> SRR1044430 1 0.0938 0.983 0.988 0.012
#> SRR1044431 1 0.0000 0.993 1.000 0.000
#> SRR1044433 1 0.1633 0.972 0.976 0.024
#> SRR1044432 1 0.0000 0.993 1.000 0.000
#> SRR1044434 1 0.0000 0.993 1.000 0.000
#> SRR1044435 1 0.0000 0.993 1.000 0.000
#> SRR1044436 1 0.0000 0.993 1.000 0.000
#> SRR1044437 1 0.0000 0.993 1.000 0.000
#> SRR1044439 1 0.0000 0.993 1.000 0.000
#> SRR1044438 1 0.0000 0.993 1.000 0.000
#> SRR1044440 1 0.0000 0.993 1.000 0.000
#> SRR1044441 1 0.0000 0.993 1.000 0.000
#> SRR1044442 1 0.0000 0.993 1.000 0.000
#> SRR1044443 1 0.5629 0.852 0.868 0.132
#> SRR1044444 1 0.0000 0.993 1.000 0.000
#> SRR1044445 1 0.0000 0.993 1.000 0.000
#> SRR1044446 2 0.0000 1.000 0.000 1.000
#> SRR1044447 2 0.0000 1.000 0.000 1.000
#> SRR1044449 2 0.0000 1.000 0.000 1.000
#> SRR1044448 2 0.0000 1.000 0.000 1.000
#> SRR1044450 2 0.0000 1.000 0.000 1.000
#> SRR1044451 2 0.0000 1.000 0.000 1.000
#> SRR1044452 2 0.0000 1.000 0.000 1.000
#> SRR1044453 2 0.0000 1.000 0.000 1.000
#> SRR1044454 2 0.0000 1.000 0.000 1.000
#> SRR1044455 2 0.0000 1.000 0.000 1.000
#> SRR1044456 2 0.0000 1.000 0.000 1.000
#> SRR1044457 2 0.0000 1.000 0.000 1.000
#> SRR1044458 2 0.0000 1.000 0.000 1.000
#> SRR1044459 2 0.0000 1.000 0.000 1.000
#> SRR1044460 2 0.0000 1.000 0.000 1.000
#> SRR1044461 2 0.0000 1.000 0.000 1.000
#> SRR1044462 1 0.0000 0.993 1.000 0.000
#> SRR1044463 1 0.0000 0.993 1.000 0.000
#> SRR1044464 1 0.0000 0.993 1.000 0.000
#> SRR1044466 1 0.0376 0.989 0.996 0.004
#> SRR1044465 1 0.0000 0.993 1.000 0.000
#> SRR1044467 1 0.0000 0.993 1.000 0.000
#> SRR1044468 2 0.0000 1.000 0.000 1.000
#> SRR1044469 2 0.0000 1.000 0.000 1.000
#> SRR1044470 1 0.2778 0.948 0.952 0.048
#> SRR1044471 1 0.0000 0.993 1.000 0.000
#> SRR1044472 1 0.4161 0.909 0.916 0.084
#> SRR1044473 1 0.0000 0.993 1.000 0.000
#> SRR1044474 2 0.0000 1.000 0.000 1.000
#> SRR1044475 2 0.0000 1.000 0.000 1.000
#> SRR1044476 2 0.0000 1.000 0.000 1.000
#> SRR1044477 2 0.0000 1.000 0.000 1.000
#> SRR1044478 2 0.0000 1.000 0.000 1.000
#> SRR1044479 2 0.0000 1.000 0.000 1.000
#> SRR1044480 1 0.0000 0.993 1.000 0.000
#> SRR1044481 1 0.0000 0.993 1.000 0.000
#> SRR1044482 2 0.0000 1.000 0.000 1.000
#> SRR1044483 1 0.0000 0.993 1.000 0.000
#> SRR1044484 1 0.0000 0.993 1.000 0.000
#> SRR1044486 1 0.0000 0.993 1.000 0.000
#> SRR1044485 2 0.0000 1.000 0.000 1.000
#> SRR1044487 2 0.0000 1.000 0.000 1.000
#> SRR1044488 2 0.0000 1.000 0.000 1.000
#> SRR1044489 2 0.0000 1.000 0.000 1.000
#> SRR1044490 1 0.0000 0.993 1.000 0.000
#> SRR1044491 1 0.0376 0.989 0.996 0.004
#> SRR1044492 1 0.6048 0.832 0.852 0.148
#> SRR1044493 1 0.0000 0.993 1.000 0.000
#> SRR1044494 2 0.0000 1.000 0.000 1.000
#> SRR1044496 2 0.0000 1.000 0.000 1.000
#> SRR1044495 2 0.0000 1.000 0.000 1.000
#> SRR1044497 1 0.0000 0.993 1.000 0.000
#> SRR1044499 2 0.0000 1.000 0.000 1.000
#> SRR1044498 1 0.0000 0.993 1.000 0.000
#> SRR1044500 2 0.0000 1.000 0.000 1.000
#> SRR1044501 2 0.0000 1.000 0.000 1.000
#> SRR1044502 2 0.0000 1.000 0.000 1.000
#> SRR1044503 1 0.0000 0.993 1.000 0.000
#> SRR1044504 1 0.0000 0.993 1.000 0.000
#> SRR1044505 1 0.0000 0.993 1.000 0.000
#> SRR1044506 1 0.0000 0.993 1.000 0.000
#> SRR1044507 1 0.0000 0.993 1.000 0.000
#> SRR1044508 1 0.0000 0.993 1.000 0.000
#> SRR1044509 1 0.0672 0.986 0.992 0.008
#> SRR1044510 2 0.0000 1.000 0.000 1.000
#> SRR1044511 2 0.0000 1.000 0.000 1.000
#> SRR1044512 2 0.0000 1.000 0.000 1.000
#> SRR1044513 2 0.0000 1.000 0.000 1.000
#> SRR1044514 2 0.0000 1.000 0.000 1.000
#> SRR1044515 2 0.0000 1.000 0.000 1.000
#> SRR1044516 2 0.0000 1.000 0.000 1.000
#> SRR1044517 2 0.0000 1.000 0.000 1.000
#> SRR1044518 2 0.0000 1.000 0.000 1.000
#> SRR1044519 2 0.0000 1.000 0.000 1.000
#> SRR1044520 2 0.0000 1.000 0.000 1.000
#> SRR1044521 2 0.0000 1.000 0.000 1.000
#> SRR1044522 2 0.0000 1.000 0.000 1.000
#> SRR1044523 2 0.0000 1.000 0.000 1.000
#> SRR1044524 2 0.0000 1.000 0.000 1.000
#> SRR1044525 1 0.0000 0.993 1.000 0.000
#> SRR1044526 1 0.0000 0.993 1.000 0.000
#> SRR1044527 2 0.0000 1.000 0.000 1.000
#> SRR1044528 2 0.0000 1.000 0.000 1.000
#> SRR1044529 2 0.0000 1.000 0.000 1.000
#> SRR1044530 1 0.0000 0.993 1.000 0.000
#> SRR1044531 1 0.0000 0.993 1.000 0.000
#> SRR1044533 1 0.0000 0.993 1.000 0.000
#> SRR1044532 1 0.0000 0.993 1.000 0.000
#> SRR1044534 2 0.0000 1.000 0.000 1.000
#> SRR1044535 2 0.0000 1.000 0.000 1.000
#> SRR1044536 2 0.0000 1.000 0.000 1.000
#> SRR1044537 1 0.0000 0.993 1.000 0.000
#> SRR1044538 1 0.0000 0.993 1.000 0.000
#> SRR1044539 1 0.0000 0.993 1.000 0.000
#> SRR1044540 1 0.0000 0.993 1.000 0.000
#> SRR1044541 2 0.0000 1.000 0.000 1.000
#> SRR1044542 1 0.0376 0.989 0.996 0.004
#> SRR1044543 1 0.0000 0.993 1.000 0.000
#> SRR1044544 2 0.0000 1.000 0.000 1.000
#> SRR1044545 1 0.0000 0.993 1.000 0.000
#> SRR1044546 1 0.0000 0.993 1.000 0.000
#> SRR1044547 1 0.0000 0.993 1.000 0.000
#> SRR1044548 1 0.0000 0.993 1.000 0.000
#> SRR1044549 2 0.0000 1.000 0.000 1.000
#> SRR1044550 2 0.0000 1.000 0.000 1.000
#> SRR1044551 2 0.0000 1.000 0.000 1.000
#> SRR1044552 1 0.0000 0.993 1.000 0.000
#> SRR1044553 1 0.0000 0.993 1.000 0.000
#> SRR1044554 1 0.0000 0.993 1.000 0.000
#> SRR1044555 2 0.0000 1.000 0.000 1.000
#> SRR1044556 1 0.0000 0.993 1.000 0.000
#> SRR1044557 1 0.0000 0.993 1.000 0.000
#> SRR1044558 1 0.0000 0.993 1.000 0.000
#> SRR1044559 1 0.0000 0.993 1.000 0.000
#> SRR1044561 1 0.0000 0.993 1.000 0.000
#> SRR1044560 2 0.0000 1.000 0.000 1.000
#> SRR1044562 1 0.0000 0.993 1.000 0.000
#> SRR1044563 1 0.0000 0.993 1.000 0.000
#> SRR1044564 1 0.0000 0.993 1.000 0.000
#> SRR1044565 2 0.0000 1.000 0.000 1.000
#> SRR1044566 2 0.0000 1.000 0.000 1.000
#> SRR1044567 1 0.0000 0.993 1.000 0.000
#> SRR1044568 1 0.0000 0.993 1.000 0.000
#> SRR1044569 1 0.0000 0.993 1.000 0.000
#> SRR1044570 1 0.0000 0.993 1.000 0.000
#> SRR1044571 1 0.0000 0.993 1.000 0.000
#> SRR1044572 1 0.0000 0.993 1.000 0.000
#> SRR1044573 1 0.0000 0.993 1.000 0.000
#> SRR1044574 1 0.0000 0.993 1.000 0.000
#> SRR1044575 1 0.0000 0.993 1.000 0.000
#> SRR1044576 2 0.0000 1.000 0.000 1.000
#> SRR1044577 2 0.0000 1.000 0.000 1.000
#> SRR1044578 2 0.0000 1.000 0.000 1.000
#> SRR1044579 1 0.0000 0.993 1.000 0.000
#> SRR1044580 1 0.0000 0.993 1.000 0.000
#> SRR1044581 1 0.0000 0.993 1.000 0.000
#> SRR1044582 1 0.0000 0.993 1.000 0.000
#> SRR1044583 1 0.0000 0.993 1.000 0.000
#> SRR1044584 1 0.0000 0.993 1.000 0.000
#> SRR1044585 1 0.0000 0.993 1.000 0.000
#> SRR1044586 1 0.0000 0.993 1.000 0.000
#> SRR1044587 1 0.0000 0.993 1.000 0.000
#> SRR1044588 1 0.0000 0.993 1.000 0.000
#> SRR1044589 1 0.0000 0.993 1.000 0.000
#> SRR1044590 1 0.0000 0.993 1.000 0.000
#> SRR1044591 1 0.0000 0.993 1.000 0.000
#> SRR1044592 1 0.0000 0.993 1.000 0.000
#> SRR1044593 1 0.0000 0.993 1.000 0.000
#> SRR1044594 1 0.0000 0.993 1.000 0.000
#> SRR1044595 1 0.1184 0.979 0.984 0.016
#> SRR1044596 1 0.0000 0.993 1.000 0.000
#> SRR1044597 1 0.8386 0.642 0.732 0.268
#> SRR1044598 1 0.0376 0.989 0.996 0.004
#> SRR1044599 1 0.1843 0.968 0.972 0.028
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.0592 0.91646 0.000 0.988 0.012
#> SRR1044416 2 0.0424 0.91712 0.000 0.992 0.008
#> SRR1044417 2 0.2711 0.88556 0.000 0.912 0.088
#> SRR1044418 2 0.5138 0.79131 0.000 0.748 0.252
#> SRR1044420 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044419 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044421 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044422 2 0.0592 0.91646 0.000 0.988 0.012
#> SRR1044423 2 0.0592 0.91646 0.000 0.988 0.012
#> SRR1044424 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044425 1 0.1964 0.73905 0.944 0.000 0.056
#> SRR1044426 3 0.6168 0.80526 0.412 0.000 0.588
#> SRR1044427 1 0.1529 0.75551 0.960 0.000 0.040
#> SRR1044428 3 0.6126 0.81355 0.400 0.000 0.600
#> SRR1044429 1 0.0237 0.76828 0.996 0.000 0.004
#> SRR1044430 3 0.6448 0.78581 0.328 0.016 0.656
#> SRR1044431 1 0.5678 0.10184 0.684 0.000 0.316
#> SRR1044433 1 0.6448 0.36913 0.636 0.012 0.352
#> SRR1044432 3 0.5882 0.81819 0.348 0.000 0.652
#> SRR1044434 1 0.0747 0.77039 0.984 0.000 0.016
#> SRR1044435 1 0.0424 0.77069 0.992 0.000 0.008
#> SRR1044436 1 0.0237 0.76828 0.996 0.000 0.004
#> SRR1044437 1 0.0747 0.77039 0.984 0.000 0.016
#> SRR1044439 1 0.0000 0.76962 1.000 0.000 0.000
#> SRR1044438 1 0.0000 0.76962 1.000 0.000 0.000
#> SRR1044440 1 0.0747 0.77039 0.984 0.000 0.016
#> SRR1044441 1 0.0892 0.76927 0.980 0.000 0.020
#> SRR1044442 1 0.4291 0.60134 0.820 0.000 0.180
#> SRR1044443 1 0.7030 0.30862 0.580 0.024 0.396
#> SRR1044444 1 0.0000 0.76962 1.000 0.000 0.000
#> SRR1044445 1 0.1031 0.76754 0.976 0.000 0.024
#> SRR1044446 2 0.5810 0.73221 0.000 0.664 0.336
#> SRR1044447 2 0.6111 0.69044 0.000 0.604 0.396
#> SRR1044449 2 0.5733 0.74356 0.000 0.676 0.324
#> SRR1044448 2 0.6095 0.69381 0.000 0.608 0.392
#> SRR1044450 2 0.5948 0.71671 0.000 0.640 0.360
#> SRR1044451 2 0.6095 0.69351 0.000 0.608 0.392
#> SRR1044452 2 0.0592 0.91646 0.000 0.988 0.012
#> SRR1044453 2 0.0747 0.91577 0.000 0.984 0.016
#> SRR1044454 2 0.0592 0.91646 0.000 0.988 0.012
#> SRR1044455 2 0.0237 0.91762 0.000 0.996 0.004
#> SRR1044456 2 0.2448 0.89061 0.000 0.924 0.076
#> SRR1044457 2 0.0592 0.91646 0.000 0.988 0.012
#> SRR1044458 2 0.0592 0.91646 0.000 0.988 0.012
#> SRR1044459 2 0.1411 0.91043 0.000 0.964 0.036
#> SRR1044460 2 0.0592 0.91646 0.000 0.988 0.012
#> SRR1044461 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044462 1 0.2165 0.71314 0.936 0.000 0.064
#> SRR1044463 3 0.5560 0.79327 0.300 0.000 0.700
#> SRR1044464 1 0.5905 -0.21137 0.648 0.000 0.352
#> SRR1044466 3 0.5115 0.72235 0.228 0.004 0.768
#> SRR1044465 1 0.6309 -0.66797 0.500 0.000 0.500
#> SRR1044467 3 0.6215 0.79340 0.428 0.000 0.572
#> SRR1044468 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044469 2 0.0592 0.91646 0.000 0.988 0.012
#> SRR1044470 3 0.6313 0.77789 0.308 0.016 0.676
#> SRR1044471 1 0.6215 -0.42463 0.572 0.000 0.428
#> SRR1044472 3 0.5355 0.64966 0.168 0.032 0.800
#> SRR1044473 3 0.6180 0.80133 0.416 0.000 0.584
#> SRR1044474 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044475 2 0.0592 0.91646 0.000 0.988 0.012
#> SRR1044476 2 0.0592 0.91646 0.000 0.988 0.012
#> SRR1044477 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044478 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044479 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044480 1 0.0237 0.76828 0.996 0.000 0.004
#> SRR1044481 3 0.6308 0.71515 0.492 0.000 0.508
#> SRR1044482 2 0.0237 0.91763 0.000 0.996 0.004
#> SRR1044483 1 0.0424 0.76686 0.992 0.000 0.008
#> SRR1044484 1 0.0237 0.76828 0.996 0.000 0.004
#> SRR1044486 1 0.6295 -0.64507 0.528 0.000 0.472
#> SRR1044485 2 0.0237 0.91762 0.000 0.996 0.004
#> SRR1044487 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044488 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044489 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044490 3 0.6204 0.79985 0.424 0.000 0.576
#> SRR1044491 3 0.6129 0.80667 0.324 0.008 0.668
#> SRR1044492 3 0.4979 0.61095 0.168 0.020 0.812
#> SRR1044493 3 0.6026 0.81966 0.376 0.000 0.624
#> SRR1044494 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044496 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044495 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044497 1 0.0592 0.77079 0.988 0.000 0.012
#> SRR1044499 2 0.0592 0.91646 0.000 0.988 0.012
#> SRR1044498 1 0.1860 0.73053 0.948 0.000 0.052
#> SRR1044500 2 0.0424 0.91712 0.000 0.992 0.008
#> SRR1044501 2 0.0424 0.91712 0.000 0.992 0.008
#> SRR1044502 2 0.5678 0.74666 0.000 0.684 0.316
#> SRR1044503 1 0.0747 0.77039 0.984 0.000 0.016
#> SRR1044504 1 0.0237 0.77050 0.996 0.000 0.004
#> SRR1044505 1 0.5810 -0.07346 0.664 0.000 0.336
#> SRR1044506 1 0.0892 0.76927 0.980 0.000 0.020
#> SRR1044507 1 0.1529 0.75706 0.960 0.000 0.040
#> SRR1044508 1 0.4002 0.61505 0.840 0.000 0.160
#> SRR1044509 1 0.6252 0.38494 0.648 0.008 0.344
#> SRR1044510 2 0.4121 0.85280 0.000 0.832 0.168
#> SRR1044511 2 0.6168 0.68626 0.000 0.588 0.412
#> SRR1044512 2 0.6095 0.70550 0.000 0.608 0.392
#> SRR1044513 2 0.6045 0.70259 0.000 0.620 0.380
#> SRR1044514 2 0.6180 0.68191 0.000 0.584 0.416
#> SRR1044515 2 0.5621 0.75633 0.000 0.692 0.308
#> SRR1044516 2 0.1163 0.91417 0.000 0.972 0.028
#> SRR1044517 2 0.2711 0.88584 0.000 0.912 0.088
#> SRR1044518 2 0.6168 0.68626 0.000 0.588 0.412
#> SRR1044519 2 0.6140 0.68363 0.000 0.596 0.404
#> SRR1044520 2 0.6140 0.68363 0.000 0.596 0.404
#> SRR1044521 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044522 2 0.1529 0.90630 0.000 0.960 0.040
#> SRR1044523 2 0.5529 0.76264 0.000 0.704 0.296
#> SRR1044524 2 0.2625 0.88844 0.000 0.916 0.084
#> SRR1044525 1 0.0000 0.76962 1.000 0.000 0.000
#> SRR1044526 1 0.0747 0.76253 0.984 0.000 0.016
#> SRR1044527 2 0.1289 0.90959 0.000 0.968 0.032
#> SRR1044528 2 0.5650 0.74985 0.000 0.688 0.312
#> SRR1044529 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044530 3 0.5363 0.77549 0.276 0.000 0.724
#> SRR1044531 3 0.6302 0.71624 0.480 0.000 0.520
#> SRR1044533 3 0.6045 0.81938 0.380 0.000 0.620
#> SRR1044532 3 0.5397 0.77871 0.280 0.000 0.720
#> SRR1044534 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044535 2 0.4235 0.83650 0.000 0.824 0.176
#> SRR1044536 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044537 1 0.6291 -0.63121 0.532 0.000 0.468
#> SRR1044538 3 0.5517 0.76866 0.268 0.004 0.728
#> SRR1044539 1 0.0237 0.76828 0.996 0.000 0.004
#> SRR1044540 3 0.6192 0.79805 0.420 0.000 0.580
#> SRR1044541 2 0.0592 0.91646 0.000 0.988 0.012
#> SRR1044542 3 0.6079 0.81582 0.388 0.000 0.612
#> SRR1044543 3 0.6215 0.79305 0.428 0.000 0.572
#> SRR1044544 2 0.0592 0.91646 0.000 0.988 0.012
#> SRR1044545 1 0.0237 0.76828 0.996 0.000 0.004
#> SRR1044546 1 0.6026 -0.31461 0.624 0.000 0.376
#> SRR1044547 1 0.1860 0.72824 0.948 0.000 0.052
#> SRR1044548 3 0.6521 0.71165 0.492 0.004 0.504
#> SRR1044549 2 0.1289 0.90933 0.000 0.968 0.032
#> SRR1044550 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044551 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044552 1 0.0000 0.76962 1.000 0.000 0.000
#> SRR1044553 1 0.0000 0.76962 1.000 0.000 0.000
#> SRR1044554 3 0.6307 0.72288 0.488 0.000 0.512
#> SRR1044555 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044556 1 0.0237 0.76828 0.996 0.000 0.004
#> SRR1044557 1 0.6140 -0.42588 0.596 0.000 0.404
#> SRR1044558 1 0.0237 0.77049 0.996 0.000 0.004
#> SRR1044559 1 0.5650 -0.00841 0.688 0.000 0.312
#> SRR1044561 1 0.0592 0.77079 0.988 0.000 0.012
#> SRR1044560 2 0.0592 0.91646 0.000 0.988 0.012
#> SRR1044562 3 0.6308 0.71556 0.492 0.000 0.508
#> SRR1044563 1 0.0237 0.76828 0.996 0.000 0.004
#> SRR1044564 1 0.6309 -0.70069 0.504 0.000 0.496
#> SRR1044565 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044566 2 0.0592 0.91646 0.000 0.988 0.012
#> SRR1044567 3 0.6033 0.81286 0.336 0.004 0.660
#> SRR1044568 1 0.1860 0.72872 0.948 0.000 0.052
#> SRR1044569 3 0.6192 0.79761 0.420 0.000 0.580
#> SRR1044570 3 0.4974 0.73050 0.236 0.000 0.764
#> SRR1044571 3 0.6168 0.80523 0.412 0.000 0.588
#> SRR1044572 3 0.6291 0.73895 0.468 0.000 0.532
#> SRR1044573 1 0.4172 0.59982 0.840 0.004 0.156
#> SRR1044574 3 0.6140 0.81103 0.404 0.000 0.596
#> SRR1044575 1 0.6235 -0.46325 0.564 0.000 0.436
#> SRR1044576 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044577 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044578 2 0.0000 0.91792 0.000 1.000 0.000
#> SRR1044579 1 0.0892 0.76927 0.980 0.000 0.020
#> SRR1044580 1 0.5988 -0.29084 0.632 0.000 0.368
#> SRR1044581 1 0.0747 0.77043 0.984 0.000 0.016
#> SRR1044582 3 0.6299 0.74202 0.476 0.000 0.524
#> SRR1044583 1 0.0892 0.76927 0.980 0.000 0.020
#> SRR1044584 1 0.0237 0.76828 0.996 0.000 0.004
#> SRR1044585 1 0.0892 0.76927 0.980 0.000 0.020
#> SRR1044586 1 0.6204 -0.50890 0.576 0.000 0.424
#> SRR1044587 1 0.1289 0.76227 0.968 0.000 0.032
#> SRR1044588 1 0.1031 0.76754 0.976 0.000 0.024
#> SRR1044589 1 0.1031 0.76754 0.976 0.000 0.024
#> SRR1044590 1 0.1031 0.76754 0.976 0.000 0.024
#> SRR1044591 1 0.0892 0.76927 0.980 0.000 0.020
#> SRR1044592 1 0.5845 0.43456 0.688 0.004 0.308
#> SRR1044593 1 0.1031 0.76754 0.976 0.000 0.024
#> SRR1044594 1 0.1031 0.76754 0.976 0.000 0.024
#> SRR1044595 1 0.6745 0.28270 0.560 0.012 0.428
#> SRR1044596 1 0.3116 0.68135 0.892 0.000 0.108
#> SRR1044597 1 0.8475 0.26878 0.568 0.112 0.320
#> SRR1044598 3 0.6326 0.78220 0.292 0.020 0.688
#> SRR1044599 3 0.6025 0.54263 0.232 0.028 0.740
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 2 0.0817 0.9230 0.000 0.976 0.024 0.000
#> SRR1044416 2 0.0000 0.9311 0.000 1.000 0.000 0.000
#> SRR1044417 2 0.3791 0.6734 0.004 0.796 0.200 0.000
#> SRR1044418 2 0.5099 0.1933 0.008 0.612 0.380 0.000
#> SRR1044420 2 0.0000 0.9311 0.000 1.000 0.000 0.000
#> SRR1044419 2 0.0336 0.9299 0.000 0.992 0.008 0.000
#> SRR1044421 2 0.0336 0.9294 0.000 0.992 0.008 0.000
#> SRR1044422 2 0.0592 0.9267 0.000 0.984 0.016 0.000
#> SRR1044423 2 0.0469 0.9286 0.000 0.988 0.012 0.000
#> SRR1044424 2 0.0000 0.9311 0.000 1.000 0.000 0.000
#> SRR1044425 4 0.2868 0.8087 0.136 0.000 0.000 0.864
#> SRR1044426 1 0.0921 0.8314 0.972 0.000 0.000 0.028
#> SRR1044427 4 0.2011 0.8766 0.080 0.000 0.000 0.920
#> SRR1044428 1 0.1820 0.8257 0.944 0.000 0.036 0.020
#> SRR1044429 4 0.1767 0.9034 0.044 0.000 0.012 0.944
#> SRR1044430 1 0.2111 0.8240 0.932 0.000 0.024 0.044
#> SRR1044431 1 0.4643 0.5475 0.656 0.000 0.000 0.344
#> SRR1044433 3 0.5451 0.0656 0.008 0.004 0.524 0.464
#> SRR1044432 1 0.0376 0.8266 0.992 0.000 0.004 0.004
#> SRR1044434 4 0.0592 0.9155 0.016 0.000 0.000 0.984
#> SRR1044435 4 0.0657 0.9158 0.012 0.000 0.004 0.984
#> SRR1044436 4 0.0672 0.9113 0.008 0.000 0.008 0.984
#> SRR1044437 4 0.0592 0.9155 0.016 0.000 0.000 0.984
#> SRR1044439 4 0.0672 0.9113 0.008 0.000 0.008 0.984
#> SRR1044438 4 0.0672 0.9124 0.008 0.000 0.008 0.984
#> SRR1044440 4 0.0707 0.9151 0.020 0.000 0.000 0.980
#> SRR1044441 4 0.0707 0.9151 0.020 0.000 0.000 0.980
#> SRR1044442 4 0.3852 0.7223 0.008 0.000 0.192 0.800
#> SRR1044443 3 0.3992 0.6317 0.008 0.004 0.800 0.188
#> SRR1044444 4 0.0188 0.9142 0.000 0.000 0.004 0.996
#> SRR1044445 4 0.0817 0.9138 0.024 0.000 0.000 0.976
#> SRR1044446 3 0.5161 0.4628 0.008 0.400 0.592 0.000
#> SRR1044447 3 0.3142 0.7788 0.008 0.132 0.860 0.000
#> SRR1044449 3 0.4996 0.2363 0.000 0.484 0.516 0.000
#> SRR1044448 3 0.2737 0.7804 0.008 0.104 0.888 0.000
#> SRR1044450 3 0.3636 0.7562 0.008 0.172 0.820 0.000
#> SRR1044451 3 0.3196 0.7773 0.008 0.136 0.856 0.000
#> SRR1044452 2 0.0921 0.9205 0.000 0.972 0.028 0.000
#> SRR1044453 2 0.0921 0.9205 0.000 0.972 0.028 0.000
#> SRR1044454 2 0.0921 0.9205 0.000 0.972 0.028 0.000
#> SRR1044455 2 0.0336 0.9299 0.000 0.992 0.008 0.000
#> SRR1044456 2 0.3157 0.7770 0.004 0.852 0.144 0.000
#> SRR1044457 2 0.0592 0.9275 0.000 0.984 0.016 0.000
#> SRR1044458 2 0.0469 0.9286 0.000 0.988 0.012 0.000
#> SRR1044459 2 0.2868 0.8116 0.000 0.864 0.136 0.000
#> SRR1044460 2 0.0469 0.9286 0.000 0.988 0.012 0.000
#> SRR1044461 2 0.0188 0.9307 0.000 0.996 0.004 0.000
#> SRR1044462 4 0.5035 0.6807 0.196 0.000 0.056 0.748
#> SRR1044463 1 0.1302 0.8319 0.956 0.000 0.000 0.044
#> SRR1044464 1 0.5626 0.5057 0.588 0.000 0.028 0.384
#> SRR1044466 1 0.2002 0.8250 0.936 0.000 0.020 0.044
#> SRR1044465 1 0.2868 0.8033 0.864 0.000 0.000 0.136
#> SRR1044467 1 0.1118 0.8342 0.964 0.000 0.000 0.036
#> SRR1044468 2 0.0000 0.9311 0.000 1.000 0.000 0.000
#> SRR1044469 2 0.0469 0.9286 0.000 0.988 0.012 0.000
#> SRR1044470 1 0.2546 0.8259 0.900 0.000 0.008 0.092
#> SRR1044471 1 0.4134 0.6710 0.740 0.000 0.000 0.260
#> SRR1044472 1 0.1820 0.8255 0.944 0.000 0.020 0.036
#> SRR1044473 1 0.0707 0.8296 0.980 0.000 0.000 0.020
#> SRR1044474 2 0.0188 0.9305 0.000 0.996 0.004 0.000
#> SRR1044475 2 0.0921 0.9205 0.000 0.972 0.028 0.000
#> SRR1044476 2 0.0817 0.9230 0.000 0.976 0.024 0.000
#> SRR1044477 2 0.0336 0.9294 0.000 0.992 0.008 0.000
#> SRR1044478 2 0.0000 0.9311 0.000 1.000 0.000 0.000
#> SRR1044479 2 0.0336 0.9294 0.000 0.992 0.008 0.000
#> SRR1044480 4 0.3245 0.8553 0.064 0.000 0.056 0.880
#> SRR1044481 1 0.4182 0.7865 0.796 0.000 0.024 0.180
#> SRR1044482 2 0.0000 0.9311 0.000 1.000 0.000 0.000
#> SRR1044483 4 0.2844 0.8709 0.048 0.000 0.052 0.900
#> SRR1044484 4 0.1837 0.8966 0.028 0.000 0.028 0.944
#> SRR1044486 1 0.4855 0.7284 0.712 0.000 0.020 0.268
#> SRR1044485 2 0.0188 0.9307 0.000 0.996 0.004 0.000
#> SRR1044487 2 0.0336 0.9294 0.000 0.992 0.008 0.000
#> SRR1044488 2 0.0188 0.9305 0.000 0.996 0.004 0.000
#> SRR1044489 2 0.0188 0.9305 0.000 0.996 0.004 0.000
#> SRR1044490 1 0.2589 0.8269 0.884 0.000 0.000 0.116
#> SRR1044491 1 0.0657 0.8276 0.984 0.000 0.004 0.012
#> SRR1044492 1 0.2796 0.7894 0.892 0.000 0.092 0.016
#> SRR1044493 1 0.0707 0.8305 0.980 0.000 0.000 0.020
#> SRR1044494 2 0.0336 0.9294 0.000 0.992 0.008 0.000
#> SRR1044496 2 0.0336 0.9294 0.000 0.992 0.008 0.000
#> SRR1044495 2 0.0592 0.9258 0.000 0.984 0.016 0.000
#> SRR1044497 4 0.0469 0.9157 0.012 0.000 0.000 0.988
#> SRR1044499 2 0.0817 0.9230 0.000 0.976 0.024 0.000
#> SRR1044498 4 0.3266 0.8253 0.108 0.000 0.024 0.868
#> SRR1044500 2 0.0336 0.9299 0.000 0.992 0.008 0.000
#> SRR1044501 2 0.0188 0.9307 0.000 0.996 0.004 0.000
#> SRR1044502 2 0.5263 -0.0801 0.008 0.544 0.448 0.000
#> SRR1044503 4 0.0707 0.9151 0.020 0.000 0.000 0.980
#> SRR1044504 4 0.0524 0.9124 0.004 0.000 0.008 0.988
#> SRR1044505 1 0.5847 0.5576 0.628 0.000 0.052 0.320
#> SRR1044506 4 0.0817 0.9138 0.024 0.000 0.000 0.976
#> SRR1044507 4 0.1406 0.9051 0.016 0.000 0.024 0.960
#> SRR1044508 4 0.5400 0.4086 0.020 0.000 0.372 0.608
#> SRR1044509 4 0.5229 0.2185 0.008 0.000 0.428 0.564
#> SRR1044510 3 0.4817 0.3743 0.000 0.388 0.612 0.000
#> SRR1044511 3 0.1792 0.7691 0.000 0.068 0.932 0.000
#> SRR1044512 3 0.1792 0.7691 0.000 0.068 0.932 0.000
#> SRR1044513 3 0.3450 0.7671 0.008 0.156 0.836 0.000
#> SRR1044514 3 0.1792 0.7691 0.000 0.068 0.932 0.000
#> SRR1044515 3 0.5203 0.4273 0.008 0.416 0.576 0.000
#> SRR1044516 2 0.0707 0.9253 0.000 0.980 0.020 0.000
#> SRR1044517 2 0.4941 0.1326 0.000 0.564 0.436 0.000
#> SRR1044518 3 0.1792 0.7691 0.000 0.068 0.932 0.000
#> SRR1044519 3 0.2342 0.7738 0.008 0.080 0.912 0.000
#> SRR1044520 3 0.2342 0.7738 0.008 0.080 0.912 0.000
#> SRR1044521 2 0.0336 0.9294 0.000 0.992 0.008 0.000
#> SRR1044522 2 0.1211 0.9067 0.000 0.960 0.040 0.000
#> SRR1044523 3 0.5294 0.2481 0.008 0.484 0.508 0.000
#> SRR1044524 2 0.2973 0.7779 0.000 0.856 0.144 0.000
#> SRR1044525 4 0.0672 0.9113 0.008 0.000 0.008 0.984
#> SRR1044526 4 0.2675 0.8747 0.044 0.000 0.048 0.908
#> SRR1044527 2 0.2714 0.8237 0.004 0.884 0.112 0.000
#> SRR1044528 2 0.5263 -0.0778 0.008 0.544 0.448 0.000
#> SRR1044529 2 0.0188 0.9306 0.000 0.996 0.004 0.000
#> SRR1044530 1 0.1488 0.8300 0.956 0.000 0.012 0.032
#> SRR1044531 1 0.1716 0.8333 0.936 0.000 0.000 0.064
#> SRR1044533 1 0.0779 0.8283 0.980 0.000 0.004 0.016
#> SRR1044532 1 0.1174 0.8228 0.968 0.000 0.020 0.012
#> SRR1044534 2 0.0000 0.9311 0.000 1.000 0.000 0.000
#> SRR1044535 2 0.4647 0.4786 0.008 0.704 0.288 0.000
#> SRR1044536 2 0.0000 0.9311 0.000 1.000 0.000 0.000
#> SRR1044537 1 0.5386 0.7196 0.708 0.000 0.056 0.236
#> SRR1044538 1 0.1938 0.8286 0.936 0.000 0.012 0.052
#> SRR1044539 4 0.2761 0.8731 0.048 0.000 0.048 0.904
#> SRR1044540 1 0.0592 0.8290 0.984 0.000 0.000 0.016
#> SRR1044541 2 0.0336 0.9300 0.000 0.992 0.008 0.000
#> SRR1044542 1 0.2480 0.8245 0.904 0.000 0.008 0.088
#> SRR1044543 1 0.1743 0.8358 0.940 0.000 0.004 0.056
#> SRR1044544 2 0.0469 0.9286 0.000 0.988 0.012 0.000
#> SRR1044545 4 0.2926 0.8676 0.048 0.000 0.056 0.896
#> SRR1044546 1 0.6083 0.5213 0.584 0.000 0.056 0.360
#> SRR1044547 4 0.4656 0.7411 0.160 0.000 0.056 0.784
#> SRR1044548 1 0.5109 0.7430 0.736 0.000 0.052 0.212
#> SRR1044549 2 0.2469 0.8325 0.000 0.892 0.108 0.000
#> SRR1044550 2 0.0000 0.9311 0.000 1.000 0.000 0.000
#> SRR1044551 2 0.0469 0.9277 0.000 0.988 0.012 0.000
#> SRR1044552 4 0.0376 0.9129 0.004 0.000 0.004 0.992
#> SRR1044553 4 0.0336 0.9135 0.000 0.000 0.008 0.992
#> SRR1044554 1 0.5148 0.7443 0.736 0.000 0.056 0.208
#> SRR1044555 2 0.0188 0.9305 0.000 0.996 0.004 0.000
#> SRR1044556 4 0.0804 0.9100 0.012 0.000 0.008 0.980
#> SRR1044557 1 0.5936 0.5917 0.620 0.000 0.056 0.324
#> SRR1044558 4 0.0707 0.9161 0.020 0.000 0.000 0.980
#> SRR1044559 1 0.6265 0.2935 0.500 0.000 0.056 0.444
#> SRR1044561 4 0.0469 0.9158 0.012 0.000 0.000 0.988
#> SRR1044560 2 0.0817 0.9230 0.000 0.976 0.024 0.000
#> SRR1044562 1 0.5035 0.7545 0.748 0.000 0.056 0.196
#> SRR1044563 4 0.1520 0.9023 0.024 0.000 0.020 0.956
#> SRR1044564 1 0.5386 0.7169 0.708 0.000 0.056 0.236
#> SRR1044565 2 0.0336 0.9294 0.000 0.992 0.008 0.000
#> SRR1044566 2 0.0707 0.9245 0.000 0.980 0.020 0.000
#> SRR1044567 1 0.1975 0.8286 0.936 0.000 0.016 0.048
#> SRR1044568 4 0.4701 0.7357 0.164 0.000 0.056 0.780
#> SRR1044569 1 0.1118 0.8336 0.964 0.000 0.000 0.036
#> SRR1044570 1 0.1975 0.8276 0.936 0.000 0.016 0.048
#> SRR1044571 1 0.0707 0.8296 0.980 0.000 0.000 0.020
#> SRR1044572 1 0.2921 0.8066 0.860 0.000 0.000 0.140
#> SRR1044573 4 0.5040 0.4342 0.364 0.000 0.008 0.628
#> SRR1044574 1 0.2342 0.8310 0.912 0.000 0.008 0.080
#> SRR1044575 1 0.3610 0.7414 0.800 0.000 0.000 0.200
#> SRR1044576 2 0.0000 0.9311 0.000 1.000 0.000 0.000
#> SRR1044577 2 0.0336 0.9294 0.000 0.992 0.008 0.000
#> SRR1044578 2 0.0336 0.9294 0.000 0.992 0.008 0.000
#> SRR1044579 4 0.0707 0.9151 0.020 0.000 0.000 0.980
#> SRR1044580 1 0.5467 0.5782 0.612 0.000 0.024 0.364
#> SRR1044581 4 0.0188 0.9150 0.004 0.000 0.000 0.996
#> SRR1044582 1 0.4499 0.7795 0.792 0.000 0.048 0.160
#> SRR1044583 4 0.0707 0.9151 0.020 0.000 0.000 0.980
#> SRR1044584 4 0.0937 0.9092 0.012 0.000 0.012 0.976
#> SRR1044585 4 0.0707 0.9151 0.020 0.000 0.000 0.980
#> SRR1044586 1 0.5884 0.6153 0.620 0.000 0.052 0.328
#> SRR1044587 4 0.2469 0.8474 0.108 0.000 0.000 0.892
#> SRR1044588 4 0.0817 0.9138 0.024 0.000 0.000 0.976
#> SRR1044589 4 0.0921 0.9119 0.028 0.000 0.000 0.972
#> SRR1044590 4 0.0817 0.9138 0.024 0.000 0.000 0.976
#> SRR1044591 4 0.0707 0.9151 0.020 0.000 0.000 0.980
#> SRR1044592 4 0.4826 0.5978 0.020 0.000 0.264 0.716
#> SRR1044593 4 0.0921 0.9119 0.028 0.000 0.000 0.972
#> SRR1044594 4 0.0817 0.9138 0.024 0.000 0.000 0.976
#> SRR1044595 3 0.4791 0.6306 0.100 0.004 0.796 0.100
#> SRR1044596 4 0.2125 0.8708 0.004 0.000 0.076 0.920
#> SRR1044597 3 0.6561 0.1814 0.016 0.044 0.512 0.428
#> SRR1044598 1 0.1398 0.8141 0.956 0.004 0.040 0.000
#> SRR1044599 1 0.6718 0.6003 0.656 0.020 0.208 0.116
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.1408 0.9116 0.000 0.948 0.008 0.000 0.044
#> SRR1044416 2 0.0290 0.9255 0.000 0.992 0.008 0.000 0.000
#> SRR1044417 2 0.3353 0.7216 0.000 0.796 0.196 0.000 0.008
#> SRR1044418 2 0.4650 -0.0224 0.000 0.520 0.468 0.000 0.012
#> SRR1044420 2 0.0162 0.9261 0.000 0.996 0.000 0.000 0.004
#> SRR1044419 2 0.0579 0.9241 0.000 0.984 0.008 0.000 0.008
#> SRR1044421 2 0.1117 0.9168 0.000 0.964 0.016 0.000 0.020
#> SRR1044422 2 0.1251 0.9153 0.000 0.956 0.008 0.000 0.036
#> SRR1044423 2 0.1082 0.9187 0.000 0.964 0.008 0.000 0.028
#> SRR1044424 2 0.0324 0.9263 0.000 0.992 0.004 0.000 0.004
#> SRR1044425 4 0.2983 0.7693 0.096 0.000 0.000 0.864 0.040
#> SRR1044426 1 0.0898 0.7632 0.972 0.000 0.000 0.008 0.020
#> SRR1044427 4 0.1908 0.8115 0.092 0.000 0.000 0.908 0.000
#> SRR1044428 1 0.4451 0.4464 0.644 0.000 0.000 0.016 0.340
#> SRR1044429 4 0.2473 0.8285 0.032 0.000 0.000 0.896 0.072
#> SRR1044430 1 0.4371 0.4548 0.644 0.000 0.000 0.012 0.344
#> SRR1044431 1 0.5515 0.4179 0.628 0.000 0.000 0.260 0.112
#> SRR1044433 3 0.3752 0.5331 0.000 0.000 0.708 0.292 0.000
#> SRR1044432 1 0.3318 0.6998 0.808 0.000 0.000 0.012 0.180
#> SRR1044434 4 0.0162 0.8748 0.004 0.000 0.000 0.996 0.000
#> SRR1044435 4 0.0162 0.8748 0.004 0.000 0.000 0.996 0.000
#> SRR1044436 4 0.0794 0.8631 0.000 0.000 0.000 0.972 0.028
#> SRR1044437 4 0.0162 0.8748 0.004 0.000 0.000 0.996 0.000
#> SRR1044439 4 0.0609 0.8668 0.000 0.000 0.000 0.980 0.020
#> SRR1044438 4 0.0703 0.8663 0.000 0.000 0.000 0.976 0.024
#> SRR1044440 4 0.0290 0.8751 0.008 0.000 0.000 0.992 0.000
#> SRR1044441 4 0.0510 0.8737 0.016 0.000 0.000 0.984 0.000
#> SRR1044442 4 0.3480 0.6137 0.000 0.000 0.248 0.752 0.000
#> SRR1044443 3 0.1430 0.7286 0.000 0.004 0.944 0.052 0.000
#> SRR1044444 4 0.0162 0.8726 0.000 0.000 0.000 0.996 0.004
#> SRR1044445 4 0.0703 0.8697 0.024 0.000 0.000 0.976 0.000
#> SRR1044446 3 0.3663 0.6923 0.000 0.208 0.776 0.000 0.016
#> SRR1044447 3 0.1121 0.7498 0.000 0.044 0.956 0.000 0.000
#> SRR1044449 3 0.5018 0.6256 0.000 0.268 0.664 0.000 0.068
#> SRR1044448 3 0.0703 0.7457 0.000 0.024 0.976 0.000 0.000
#> SRR1044450 3 0.1205 0.7496 0.004 0.040 0.956 0.000 0.000
#> SRR1044451 3 0.1205 0.7490 0.000 0.040 0.956 0.000 0.004
#> SRR1044452 2 0.1484 0.9096 0.000 0.944 0.008 0.000 0.048
#> SRR1044453 2 0.1830 0.8984 0.000 0.924 0.008 0.000 0.068
#> SRR1044454 2 0.1484 0.9096 0.000 0.944 0.008 0.000 0.048
#> SRR1044455 2 0.0404 0.9262 0.000 0.988 0.012 0.000 0.000
#> SRR1044456 2 0.4635 0.7135 0.024 0.772 0.132 0.000 0.072
#> SRR1044457 2 0.0798 0.9225 0.000 0.976 0.008 0.000 0.016
#> SRR1044458 2 0.1168 0.9172 0.000 0.960 0.008 0.000 0.032
#> SRR1044459 2 0.2520 0.8762 0.000 0.896 0.056 0.000 0.048
#> SRR1044460 2 0.1168 0.9172 0.000 0.960 0.008 0.000 0.032
#> SRR1044461 2 0.0000 0.9262 0.000 1.000 0.000 0.000 0.000
#> SRR1044462 5 0.5369 0.5300 0.060 0.000 0.000 0.388 0.552
#> SRR1044463 1 0.1502 0.7585 0.940 0.000 0.000 0.004 0.056
#> SRR1044464 1 0.6544 -0.2322 0.468 0.000 0.000 0.308 0.224
#> SRR1044466 1 0.1484 0.7554 0.944 0.000 0.000 0.008 0.048
#> SRR1044465 1 0.4072 0.6987 0.792 0.000 0.000 0.108 0.100
#> SRR1044467 1 0.2149 0.7635 0.916 0.000 0.000 0.036 0.048
#> SRR1044468 2 0.0324 0.9255 0.000 0.992 0.004 0.000 0.004
#> SRR1044469 2 0.1251 0.9153 0.000 0.956 0.008 0.000 0.036
#> SRR1044470 1 0.3577 0.6818 0.808 0.000 0.000 0.032 0.160
#> SRR1044471 1 0.5927 0.3595 0.592 0.000 0.000 0.236 0.172
#> SRR1044472 1 0.1282 0.7555 0.952 0.000 0.000 0.004 0.044
#> SRR1044473 1 0.3163 0.7182 0.824 0.000 0.000 0.012 0.164
#> SRR1044474 2 0.0162 0.9260 0.000 0.996 0.004 0.000 0.000
#> SRR1044475 2 0.1484 0.9096 0.000 0.944 0.008 0.000 0.048
#> SRR1044476 2 0.1484 0.9096 0.000 0.944 0.008 0.000 0.048
#> SRR1044477 2 0.0566 0.9235 0.000 0.984 0.012 0.000 0.004
#> SRR1044478 2 0.0162 0.9260 0.000 0.996 0.004 0.000 0.000
#> SRR1044479 2 0.0566 0.9235 0.000 0.984 0.012 0.000 0.004
#> SRR1044480 5 0.4560 0.2748 0.008 0.000 0.000 0.484 0.508
#> SRR1044481 1 0.5666 0.1792 0.592 0.000 0.000 0.108 0.300
#> SRR1044482 2 0.0162 0.9260 0.000 0.996 0.004 0.000 0.000
#> SRR1044483 4 0.4449 -0.2318 0.004 0.000 0.000 0.512 0.484
#> SRR1044484 4 0.2377 0.7715 0.000 0.000 0.000 0.872 0.128
#> SRR1044486 1 0.5590 0.3207 0.640 0.000 0.000 0.156 0.204
#> SRR1044485 2 0.0324 0.9256 0.000 0.992 0.004 0.000 0.004
#> SRR1044487 2 0.0566 0.9235 0.000 0.984 0.012 0.000 0.004
#> SRR1044488 2 0.0162 0.9260 0.000 0.996 0.004 0.000 0.000
#> SRR1044489 2 0.0162 0.9260 0.000 0.996 0.004 0.000 0.000
#> SRR1044490 1 0.3421 0.7388 0.840 0.000 0.000 0.080 0.080
#> SRR1044491 1 0.2179 0.7577 0.896 0.000 0.000 0.004 0.100
#> SRR1044492 1 0.3798 0.6974 0.836 0.004 0.052 0.016 0.092
#> SRR1044493 1 0.1502 0.7652 0.940 0.000 0.000 0.004 0.056
#> SRR1044494 2 0.0898 0.9193 0.000 0.972 0.020 0.000 0.008
#> SRR1044496 2 0.0807 0.9224 0.000 0.976 0.012 0.000 0.012
#> SRR1044495 2 0.1484 0.9010 0.000 0.944 0.048 0.000 0.008
#> SRR1044497 4 0.0162 0.8748 0.004 0.000 0.000 0.996 0.000
#> SRR1044499 2 0.1408 0.9116 0.000 0.948 0.008 0.000 0.044
#> SRR1044498 4 0.4121 0.6444 0.112 0.000 0.000 0.788 0.100
#> SRR1044500 2 0.0324 0.9260 0.000 0.992 0.004 0.000 0.004
#> SRR1044501 2 0.0451 0.9248 0.000 0.988 0.008 0.000 0.004
#> SRR1044502 3 0.6350 0.4506 0.068 0.352 0.536 0.000 0.044
#> SRR1044503 4 0.0404 0.8748 0.012 0.000 0.000 0.988 0.000
#> SRR1044504 4 0.0162 0.8733 0.000 0.000 0.000 0.996 0.004
#> SRR1044505 5 0.6420 0.4687 0.324 0.000 0.000 0.192 0.484
#> SRR1044506 4 0.0609 0.8723 0.020 0.000 0.000 0.980 0.000
#> SRR1044507 4 0.3301 0.7768 0.000 0.000 0.072 0.848 0.080
#> SRR1044508 3 0.6405 0.2231 0.000 0.000 0.512 0.252 0.236
#> SRR1044509 3 0.4138 0.3579 0.000 0.000 0.616 0.384 0.000
#> SRR1044510 3 0.6778 0.3497 0.000 0.312 0.392 0.000 0.296
#> SRR1044511 3 0.3861 0.6567 0.000 0.008 0.728 0.000 0.264
#> SRR1044512 3 0.3992 0.6553 0.000 0.012 0.720 0.000 0.268
#> SRR1044513 3 0.1914 0.7486 0.000 0.060 0.924 0.000 0.016
#> SRR1044514 3 0.3861 0.6567 0.000 0.008 0.728 0.000 0.264
#> SRR1044515 3 0.4301 0.6476 0.000 0.260 0.712 0.000 0.028
#> SRR1044516 2 0.1469 0.9141 0.000 0.948 0.016 0.000 0.036
#> SRR1044517 2 0.6562 0.0738 0.000 0.464 0.228 0.000 0.308
#> SRR1044518 3 0.3861 0.6567 0.000 0.008 0.728 0.000 0.264
#> SRR1044519 3 0.0290 0.7390 0.000 0.008 0.992 0.000 0.000
#> SRR1044520 3 0.0290 0.7390 0.000 0.008 0.992 0.000 0.000
#> SRR1044521 2 0.0566 0.9235 0.000 0.984 0.012 0.000 0.004
#> SRR1044522 2 0.3738 0.7833 0.024 0.824 0.128 0.000 0.024
#> SRR1044523 3 0.3741 0.6422 0.000 0.264 0.732 0.000 0.004
#> SRR1044524 2 0.3282 0.7433 0.000 0.804 0.188 0.000 0.008
#> SRR1044525 4 0.0609 0.8677 0.000 0.000 0.000 0.980 0.020
#> SRR1044526 4 0.4604 -0.0758 0.012 0.000 0.000 0.560 0.428
#> SRR1044527 2 0.4218 0.6870 0.004 0.760 0.196 0.000 0.040
#> SRR1044528 3 0.5576 0.5271 0.032 0.324 0.608 0.000 0.036
#> SRR1044529 2 0.0451 0.9246 0.000 0.988 0.008 0.000 0.004
#> SRR1044530 1 0.1357 0.7559 0.948 0.000 0.000 0.004 0.048
#> SRR1044531 1 0.4256 0.6928 0.764 0.004 0.000 0.048 0.184
#> SRR1044533 1 0.1942 0.7618 0.920 0.000 0.000 0.012 0.068
#> SRR1044532 1 0.0451 0.7599 0.988 0.000 0.000 0.004 0.008
#> SRR1044534 2 0.0162 0.9260 0.000 0.996 0.004 0.000 0.000
#> SRR1044535 2 0.4825 0.1895 0.000 0.568 0.408 0.000 0.024
#> SRR1044536 2 0.0162 0.9260 0.000 0.996 0.004 0.000 0.000
#> SRR1044537 5 0.6024 0.6793 0.288 0.000 0.000 0.152 0.560
#> SRR1044538 1 0.1670 0.7545 0.936 0.000 0.000 0.012 0.052
#> SRR1044539 4 0.4045 0.2809 0.000 0.000 0.000 0.644 0.356
#> SRR1044540 1 0.2879 0.7530 0.868 0.000 0.000 0.032 0.100
#> SRR1044541 2 0.1168 0.9173 0.000 0.960 0.008 0.000 0.032
#> SRR1044542 1 0.2278 0.7519 0.908 0.000 0.000 0.032 0.060
#> SRR1044543 1 0.3615 0.7254 0.808 0.000 0.000 0.036 0.156
#> SRR1044544 2 0.0693 0.9234 0.000 0.980 0.008 0.000 0.012
#> SRR1044545 4 0.4192 0.1076 0.000 0.000 0.000 0.596 0.404
#> SRR1044546 5 0.6109 0.6895 0.272 0.000 0.000 0.172 0.556
#> SRR1044547 5 0.5092 0.4162 0.036 0.000 0.000 0.440 0.524
#> SRR1044548 5 0.6002 0.5089 0.392 0.000 0.000 0.116 0.492
#> SRR1044549 2 0.3521 0.6758 0.000 0.764 0.232 0.000 0.004
#> SRR1044550 2 0.0162 0.9260 0.000 0.996 0.004 0.000 0.000
#> SRR1044551 2 0.1469 0.9058 0.000 0.948 0.036 0.000 0.016
#> SRR1044552 4 0.0510 0.8689 0.000 0.000 0.000 0.984 0.016
#> SRR1044553 4 0.0404 0.8710 0.000 0.000 0.000 0.988 0.012
#> SRR1044554 5 0.5799 0.6228 0.324 0.000 0.000 0.112 0.564
#> SRR1044555 2 0.0566 0.9235 0.000 0.984 0.012 0.000 0.004
#> SRR1044556 4 0.1043 0.8556 0.000 0.000 0.000 0.960 0.040
#> SRR1044557 5 0.6022 0.6831 0.280 0.000 0.000 0.156 0.564
#> SRR1044558 4 0.0451 0.8744 0.004 0.000 0.000 0.988 0.008
#> SRR1044559 5 0.6150 0.6891 0.236 0.000 0.000 0.204 0.560
#> SRR1044561 4 0.0324 0.8745 0.004 0.000 0.000 0.992 0.004
#> SRR1044560 2 0.1408 0.9116 0.000 0.948 0.008 0.000 0.044
#> SRR1044562 5 0.5799 0.6219 0.324 0.000 0.000 0.112 0.564
#> SRR1044563 4 0.2516 0.7528 0.000 0.000 0.000 0.860 0.140
#> SRR1044564 5 0.5744 0.6052 0.332 0.000 0.000 0.104 0.564
#> SRR1044565 2 0.0798 0.9217 0.000 0.976 0.016 0.000 0.008
#> SRR1044566 2 0.1408 0.9116 0.000 0.948 0.008 0.000 0.044
#> SRR1044567 1 0.2032 0.7523 0.924 0.000 0.004 0.020 0.052
#> SRR1044568 5 0.5393 0.4285 0.056 0.000 0.000 0.440 0.504
#> SRR1044569 1 0.3691 0.7222 0.804 0.000 0.000 0.040 0.156
#> SRR1044570 1 0.1670 0.7545 0.936 0.000 0.000 0.012 0.052
#> SRR1044571 1 0.2470 0.7488 0.884 0.000 0.000 0.012 0.104
#> SRR1044572 1 0.2771 0.7062 0.860 0.000 0.000 0.128 0.012
#> SRR1044573 4 0.6192 0.0943 0.300 0.000 0.000 0.532 0.168
#> SRR1044574 1 0.2426 0.7531 0.900 0.000 0.000 0.064 0.036
#> SRR1044575 1 0.4840 0.6214 0.724 0.000 0.000 0.124 0.152
#> SRR1044576 2 0.0162 0.9260 0.000 0.996 0.004 0.000 0.000
#> SRR1044577 2 0.0693 0.9225 0.000 0.980 0.012 0.000 0.008
#> SRR1044578 2 0.0671 0.9223 0.000 0.980 0.016 0.000 0.004
#> SRR1044579 4 0.0404 0.8748 0.012 0.000 0.000 0.988 0.000
#> SRR1044580 1 0.6557 -0.2398 0.472 0.000 0.000 0.240 0.288
#> SRR1044581 4 0.0290 0.8751 0.008 0.000 0.000 0.992 0.000
#> SRR1044582 1 0.5819 -0.3581 0.456 0.000 0.000 0.092 0.452
#> SRR1044583 4 0.0404 0.8748 0.012 0.000 0.000 0.988 0.000
#> SRR1044584 4 0.1410 0.8404 0.000 0.000 0.000 0.940 0.060
#> SRR1044585 4 0.0404 0.8748 0.012 0.000 0.000 0.988 0.000
#> SRR1044586 5 0.6342 0.6061 0.356 0.000 0.000 0.168 0.476
#> SRR1044587 4 0.2136 0.8077 0.088 0.000 0.000 0.904 0.008
#> SRR1044588 4 0.0703 0.8697 0.024 0.000 0.000 0.976 0.000
#> SRR1044589 4 0.0794 0.8669 0.028 0.000 0.000 0.972 0.000
#> SRR1044590 4 0.0609 0.8720 0.020 0.000 0.000 0.980 0.000
#> SRR1044591 4 0.0510 0.8737 0.016 0.000 0.000 0.984 0.000
#> SRR1044592 4 0.4211 0.3825 0.004 0.000 0.360 0.636 0.000
#> SRR1044593 4 0.0794 0.8669 0.028 0.000 0.000 0.972 0.000
#> SRR1044594 4 0.0609 0.8720 0.020 0.000 0.000 0.980 0.000
#> SRR1044595 3 0.2361 0.7169 0.032 0.004 0.916 0.008 0.040
#> SRR1044596 4 0.1571 0.8357 0.004 0.000 0.060 0.936 0.000
#> SRR1044597 3 0.5665 0.5419 0.044 0.024 0.652 0.268 0.012
#> SRR1044598 1 0.2424 0.7518 0.908 0.004 0.024 0.004 0.060
#> SRR1044599 1 0.6118 0.5330 0.696 0.028 0.148 0.052 0.076
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.1926 0.8934 0.000 0.912 0.000 0.000 0.020 0.068
#> SRR1044416 2 0.0146 0.9185 0.000 0.996 0.004 0.000 0.000 0.000
#> SRR1044417 2 0.2883 0.6906 0.000 0.788 0.212 0.000 0.000 0.000
#> SRR1044418 3 0.4093 0.2633 0.000 0.404 0.584 0.000 0.000 0.012
#> SRR1044420 2 0.0458 0.9196 0.000 0.984 0.000 0.000 0.000 0.016
#> SRR1044419 2 0.1010 0.9149 0.000 0.960 0.000 0.000 0.004 0.036
#> SRR1044421 2 0.1434 0.8960 0.000 0.940 0.012 0.000 0.000 0.048
#> SRR1044422 2 0.1779 0.8980 0.000 0.920 0.000 0.000 0.016 0.064
#> SRR1044423 2 0.1152 0.9130 0.000 0.952 0.000 0.000 0.004 0.044
#> SRR1044424 2 0.0603 0.9202 0.000 0.980 0.004 0.000 0.000 0.016
#> SRR1044425 4 0.2806 0.8230 0.060 0.000 0.000 0.872 0.012 0.056
#> SRR1044426 1 0.3089 0.7772 0.844 0.000 0.000 0.004 0.060 0.092
#> SRR1044427 4 0.2706 0.7719 0.160 0.000 0.000 0.832 0.008 0.000
#> SRR1044428 1 0.4397 0.4324 0.596 0.000 0.000 0.004 0.376 0.024
#> SRR1044429 4 0.3926 0.7654 0.080 0.000 0.000 0.796 0.100 0.024
#> SRR1044430 1 0.5853 0.3833 0.492 0.000 0.008 0.004 0.360 0.136
#> SRR1044431 1 0.4513 0.6460 0.732 0.000 0.000 0.180 0.056 0.032
#> SRR1044433 3 0.2879 0.5063 0.000 0.000 0.816 0.176 0.004 0.004
#> SRR1044432 1 0.3857 0.7169 0.772 0.000 0.000 0.004 0.160 0.064
#> SRR1044434 4 0.0000 0.9151 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044435 4 0.0000 0.9151 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044436 4 0.0865 0.9020 0.000 0.000 0.000 0.964 0.036 0.000
#> SRR1044437 4 0.0000 0.9151 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044439 4 0.0458 0.9108 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1044438 4 0.1285 0.8904 0.000 0.000 0.000 0.944 0.052 0.004
#> SRR1044440 4 0.0146 0.9153 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044441 4 0.0146 0.9153 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044442 4 0.3606 0.6035 0.000 0.000 0.284 0.708 0.004 0.004
#> SRR1044443 3 0.0653 0.6154 0.000 0.000 0.980 0.004 0.004 0.012
#> SRR1044444 4 0.0547 0.9099 0.000 0.000 0.000 0.980 0.020 0.000
#> SRR1044445 4 0.0436 0.9139 0.004 0.000 0.000 0.988 0.004 0.004
#> SRR1044446 3 0.2212 0.6343 0.000 0.112 0.880 0.000 0.000 0.008
#> SRR1044447 3 0.0603 0.6330 0.000 0.016 0.980 0.000 0.000 0.004
#> SRR1044449 3 0.5262 0.3131 0.000 0.204 0.632 0.000 0.008 0.156
#> SRR1044448 3 0.0520 0.6278 0.000 0.008 0.984 0.000 0.000 0.008
#> SRR1044450 3 0.1082 0.6445 0.000 0.040 0.956 0.000 0.000 0.004
#> SRR1044451 3 0.1285 0.6443 0.000 0.052 0.944 0.000 0.000 0.004
#> SRR1044452 2 0.1926 0.8934 0.000 0.912 0.000 0.000 0.020 0.068
#> SRR1044453 2 0.2748 0.8433 0.000 0.848 0.000 0.000 0.024 0.128
#> SRR1044454 2 0.2066 0.8888 0.000 0.904 0.000 0.000 0.024 0.072
#> SRR1044455 2 0.0837 0.9155 0.000 0.972 0.004 0.000 0.004 0.020
#> SRR1044456 2 0.5123 0.5625 0.036 0.696 0.076 0.000 0.008 0.184
#> SRR1044457 2 0.1082 0.9136 0.000 0.956 0.000 0.000 0.004 0.040
#> SRR1044458 2 0.1500 0.9060 0.000 0.936 0.000 0.000 0.012 0.052
#> SRR1044459 2 0.3497 0.8174 0.000 0.824 0.064 0.000 0.016 0.096
#> SRR1044460 2 0.1349 0.9077 0.000 0.940 0.000 0.000 0.004 0.056
#> SRR1044461 2 0.0790 0.9198 0.000 0.968 0.000 0.000 0.000 0.032
#> SRR1044462 5 0.2685 0.7843 0.008 0.000 0.000 0.132 0.852 0.008
#> SRR1044463 1 0.2863 0.7744 0.860 0.000 0.000 0.008 0.036 0.096
#> SRR1044464 5 0.6838 0.1069 0.348 0.000 0.000 0.212 0.384 0.056
#> SRR1044466 1 0.3733 0.7564 0.792 0.000 0.000 0.020 0.036 0.152
#> SRR1044465 1 0.2515 0.7688 0.892 0.000 0.000 0.052 0.040 0.016
#> SRR1044467 1 0.1262 0.7783 0.956 0.000 0.000 0.008 0.016 0.020
#> SRR1044468 2 0.0146 0.9198 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044469 2 0.1594 0.9042 0.000 0.932 0.000 0.000 0.016 0.052
#> SRR1044470 1 0.5221 0.6702 0.648 0.000 0.000 0.012 0.184 0.156
#> SRR1044471 1 0.5248 0.5639 0.672 0.000 0.000 0.196 0.084 0.048
#> SRR1044472 1 0.3909 0.7502 0.772 0.000 0.000 0.020 0.036 0.172
#> SRR1044473 1 0.2653 0.7538 0.868 0.000 0.000 0.004 0.100 0.028
#> SRR1044474 2 0.0260 0.9175 0.000 0.992 0.008 0.000 0.000 0.000
#> SRR1044475 2 0.2066 0.8888 0.000 0.904 0.000 0.000 0.024 0.072
#> SRR1044476 2 0.1926 0.8934 0.000 0.912 0.000 0.000 0.020 0.068
#> SRR1044477 2 0.0260 0.9175 0.000 0.992 0.008 0.000 0.000 0.000
#> SRR1044478 2 0.0260 0.9205 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044479 2 0.0363 0.9165 0.000 0.988 0.012 0.000 0.000 0.000
#> SRR1044480 5 0.2703 0.7765 0.004 0.000 0.000 0.172 0.824 0.000
#> SRR1044481 1 0.5670 0.0771 0.460 0.000 0.000 0.060 0.440 0.040
#> SRR1044482 2 0.0291 0.9194 0.000 0.992 0.004 0.000 0.000 0.004
#> SRR1044483 5 0.3121 0.7673 0.004 0.000 0.000 0.192 0.796 0.008
#> SRR1044484 4 0.3163 0.6651 0.004 0.000 0.000 0.764 0.232 0.000
#> SRR1044486 1 0.6014 0.3298 0.536 0.000 0.000 0.068 0.320 0.076
#> SRR1044485 2 0.0713 0.9177 0.000 0.972 0.000 0.000 0.000 0.028
#> SRR1044487 2 0.0405 0.9174 0.000 0.988 0.008 0.000 0.000 0.004
#> SRR1044488 2 0.0146 0.9185 0.000 0.996 0.004 0.000 0.000 0.000
#> SRR1044489 2 0.0146 0.9185 0.000 0.996 0.004 0.000 0.000 0.000
#> SRR1044490 1 0.3434 0.7748 0.836 0.000 0.000 0.028 0.072 0.064
#> SRR1044491 1 0.2420 0.7795 0.892 0.000 0.000 0.008 0.068 0.032
#> SRR1044492 1 0.5701 0.6855 0.628 0.004 0.024 0.004 0.136 0.204
#> SRR1044493 1 0.2591 0.7812 0.880 0.000 0.000 0.004 0.064 0.052
#> SRR1044494 2 0.0692 0.9136 0.000 0.976 0.020 0.000 0.000 0.004
#> SRR1044496 2 0.0806 0.9133 0.000 0.972 0.008 0.000 0.000 0.020
#> SRR1044495 2 0.1807 0.8746 0.000 0.920 0.060 0.000 0.000 0.020
#> SRR1044497 4 0.0000 0.9151 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044499 2 0.1926 0.8934 0.000 0.912 0.000 0.000 0.020 0.068
#> SRR1044498 4 0.4552 0.5698 0.092 0.000 0.000 0.700 0.204 0.004
#> SRR1044500 2 0.0363 0.9202 0.000 0.988 0.000 0.000 0.000 0.012
#> SRR1044501 2 0.0713 0.9177 0.000 0.972 0.000 0.000 0.000 0.028
#> SRR1044502 3 0.5528 0.4107 0.004 0.244 0.600 0.000 0.008 0.144
#> SRR1044503 4 0.0146 0.9153 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044504 4 0.0547 0.9103 0.000 0.000 0.000 0.980 0.020 0.000
#> SRR1044505 5 0.4743 0.4098 0.292 0.000 0.000 0.024 0.648 0.036
#> SRR1044506 4 0.0146 0.9153 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044507 4 0.4907 0.5315 0.000 0.000 0.256 0.644 0.096 0.004
#> SRR1044508 3 0.4980 0.2914 0.000 0.000 0.624 0.092 0.280 0.004
#> SRR1044509 3 0.3583 0.3900 0.000 0.000 0.728 0.260 0.004 0.008
#> SRR1044510 6 0.5408 0.5058 0.000 0.212 0.184 0.000 0.004 0.600
#> SRR1044511 6 0.4051 0.6497 0.000 0.008 0.432 0.000 0.000 0.560
#> SRR1044512 6 0.3937 0.6516 0.000 0.004 0.424 0.000 0.000 0.572
#> SRR1044513 3 0.2568 0.6075 0.000 0.056 0.876 0.000 0.000 0.068
#> SRR1044514 6 0.3823 0.6456 0.000 0.000 0.436 0.000 0.000 0.564
#> SRR1044515 3 0.3681 0.5706 0.000 0.156 0.780 0.000 0.000 0.064
#> SRR1044516 2 0.2558 0.8439 0.000 0.868 0.028 0.000 0.000 0.104
#> SRR1044517 6 0.4901 0.3854 0.000 0.316 0.072 0.000 0.004 0.608
#> SRR1044518 6 0.3823 0.6456 0.000 0.000 0.436 0.000 0.000 0.564
#> SRR1044519 3 0.0260 0.6154 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1044520 3 0.0363 0.6122 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1044521 2 0.0909 0.9113 0.000 0.968 0.012 0.000 0.000 0.020
#> SRR1044522 2 0.4442 0.6357 0.008 0.732 0.144 0.000 0.000 0.116
#> SRR1044523 3 0.2562 0.5947 0.000 0.172 0.828 0.000 0.000 0.000
#> SRR1044524 2 0.4255 0.5942 0.000 0.712 0.228 0.000 0.004 0.056
#> SRR1044525 4 0.1471 0.8808 0.000 0.000 0.000 0.932 0.064 0.004
#> SRR1044526 5 0.4787 0.5570 0.040 0.000 0.000 0.352 0.596 0.012
#> SRR1044527 2 0.5229 0.2867 0.000 0.596 0.320 0.000 0.032 0.052
#> SRR1044528 3 0.4530 0.5089 0.000 0.208 0.692 0.000 0.000 0.100
#> SRR1044529 2 0.0146 0.9185 0.000 0.996 0.004 0.000 0.000 0.000
#> SRR1044530 1 0.3301 0.7671 0.828 0.000 0.000 0.016 0.032 0.124
#> SRR1044531 1 0.3752 0.7428 0.804 0.000 0.000 0.020 0.116 0.060
#> SRR1044533 1 0.2146 0.7774 0.908 0.000 0.000 0.004 0.044 0.044
#> SRR1044532 1 0.2540 0.7738 0.872 0.000 0.000 0.004 0.020 0.104
#> SRR1044534 2 0.0291 0.9194 0.000 0.992 0.004 0.000 0.000 0.004
#> SRR1044535 3 0.5063 0.1870 0.000 0.432 0.500 0.000 0.004 0.064
#> SRR1044536 2 0.0363 0.9198 0.000 0.988 0.000 0.000 0.000 0.012
#> SRR1044537 5 0.2340 0.7818 0.044 0.000 0.000 0.056 0.896 0.004
#> SRR1044538 1 0.3988 0.7505 0.772 0.000 0.000 0.024 0.040 0.164
#> SRR1044539 5 0.3950 0.3803 0.004 0.000 0.000 0.432 0.564 0.000
#> SRR1044540 1 0.1889 0.7727 0.920 0.000 0.000 0.004 0.056 0.020
#> SRR1044541 2 0.2094 0.8918 0.000 0.900 0.000 0.000 0.020 0.080
#> SRR1044542 1 0.4436 0.7381 0.740 0.000 0.000 0.040 0.044 0.176
#> SRR1044543 1 0.3207 0.7560 0.848 0.000 0.004 0.012 0.088 0.048
#> SRR1044544 2 0.1088 0.9159 0.000 0.960 0.000 0.000 0.016 0.024
#> SRR1044545 5 0.3684 0.6081 0.004 0.000 0.000 0.332 0.664 0.000
#> SRR1044546 5 0.2608 0.7940 0.048 0.000 0.000 0.080 0.872 0.000
#> SRR1044547 5 0.2879 0.7741 0.004 0.000 0.000 0.176 0.816 0.004
#> SRR1044548 5 0.4447 0.6884 0.176 0.000 0.000 0.064 0.736 0.024
#> SRR1044549 2 0.4192 0.1469 0.000 0.572 0.412 0.000 0.000 0.016
#> SRR1044550 2 0.0146 0.9199 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044551 2 0.1088 0.9067 0.000 0.960 0.024 0.000 0.000 0.016
#> SRR1044552 4 0.1082 0.8981 0.000 0.000 0.000 0.956 0.040 0.004
#> SRR1044553 4 0.1010 0.9013 0.000 0.000 0.000 0.960 0.036 0.004
#> SRR1044554 5 0.2639 0.7855 0.048 0.000 0.000 0.064 0.880 0.008
#> SRR1044555 2 0.0976 0.9166 0.000 0.968 0.008 0.000 0.008 0.016
#> SRR1044556 4 0.1007 0.8979 0.000 0.000 0.000 0.956 0.044 0.000
#> SRR1044557 5 0.2365 0.7912 0.040 0.000 0.000 0.072 0.888 0.000
#> SRR1044558 4 0.0632 0.9090 0.000 0.000 0.000 0.976 0.024 0.000
#> SRR1044559 5 0.2457 0.7938 0.036 0.000 0.000 0.084 0.880 0.000
#> SRR1044561 4 0.0000 0.9151 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044560 2 0.1926 0.8934 0.000 0.912 0.000 0.000 0.020 0.068
#> SRR1044562 5 0.2519 0.7735 0.056 0.000 0.000 0.048 0.888 0.008
#> SRR1044563 4 0.2854 0.7055 0.000 0.000 0.000 0.792 0.208 0.000
#> SRR1044564 5 0.2876 0.7717 0.080 0.000 0.000 0.056 0.860 0.004
#> SRR1044565 2 0.0820 0.9130 0.000 0.972 0.012 0.000 0.000 0.016
#> SRR1044566 2 0.1983 0.8909 0.000 0.908 0.000 0.000 0.020 0.072
#> SRR1044567 1 0.4332 0.7462 0.752 0.000 0.000 0.036 0.048 0.164
#> SRR1044568 5 0.2871 0.7678 0.004 0.000 0.000 0.192 0.804 0.000
#> SRR1044569 1 0.3069 0.7621 0.852 0.000 0.000 0.032 0.096 0.020
#> SRR1044570 1 0.3988 0.7505 0.772 0.000 0.000 0.024 0.040 0.164
#> SRR1044571 1 0.2000 0.7673 0.916 0.000 0.000 0.004 0.048 0.032
#> SRR1044572 1 0.2743 0.7774 0.880 0.000 0.000 0.060 0.032 0.028
#> SRR1044573 1 0.5848 0.0942 0.452 0.000 0.000 0.424 0.096 0.028
#> SRR1044574 1 0.3982 0.7704 0.808 0.000 0.004 0.064 0.052 0.072
#> SRR1044575 1 0.4210 0.7122 0.784 0.000 0.000 0.076 0.088 0.052
#> SRR1044576 2 0.0146 0.9185 0.000 0.996 0.004 0.000 0.000 0.000
#> SRR1044577 2 0.0146 0.9185 0.000 0.996 0.004 0.000 0.000 0.000
#> SRR1044578 2 0.0405 0.9174 0.000 0.988 0.008 0.000 0.000 0.004
#> SRR1044579 4 0.0146 0.9153 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044580 1 0.6295 0.1029 0.448 0.000 0.000 0.204 0.328 0.020
#> SRR1044581 4 0.0291 0.9154 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044582 5 0.4555 0.5094 0.284 0.000 0.000 0.048 0.660 0.008
#> SRR1044583 4 0.0146 0.9153 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044584 4 0.1863 0.8472 0.000 0.000 0.000 0.896 0.104 0.000
#> SRR1044585 4 0.0146 0.9153 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044586 5 0.4340 0.7194 0.168 0.000 0.000 0.080 0.740 0.012
#> SRR1044587 4 0.1956 0.8573 0.080 0.000 0.000 0.908 0.008 0.004
#> SRR1044588 4 0.0146 0.9153 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044589 4 0.0260 0.9135 0.008 0.000 0.000 0.992 0.000 0.000
#> SRR1044590 4 0.0146 0.9153 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044591 4 0.0146 0.9153 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044592 4 0.4158 0.3198 0.004 0.000 0.400 0.588 0.004 0.004
#> SRR1044593 4 0.0291 0.9135 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044594 4 0.0146 0.9153 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044595 3 0.1686 0.6094 0.016 0.000 0.940 0.004 0.024 0.016
#> SRR1044596 4 0.1429 0.8815 0.000 0.000 0.052 0.940 0.004 0.004
#> SRR1044597 3 0.4440 0.5189 0.036 0.020 0.768 0.140 0.000 0.036
#> SRR1044598 1 0.3946 0.7501 0.752 0.000 0.000 0.004 0.052 0.192
#> SRR1044599 1 0.6779 0.5896 0.568 0.016 0.124 0.024 0.048 0.220
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.523 0.581 0.847 0.3425 0.727 0.727
#> 3 3 0.345 0.830 0.826 0.4866 0.638 0.530
#> 4 4 0.358 0.449 0.761 0.1747 0.983 0.963
#> 5 5 0.351 0.648 0.736 0.0787 0.849 0.654
#> 6 6 0.390 0.685 0.767 0.0444 0.896 0.686
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 1 0.9983 0.09506 0.524 0.476
#> SRR1044416 1 0.9970 0.12198 0.532 0.468
#> SRR1044417 1 0.9970 0.12198 0.532 0.468
#> SRR1044418 1 0.9970 0.12198 0.532 0.468
#> SRR1044420 1 0.9977 0.10950 0.528 0.472
#> SRR1044419 1 0.9998 0.03332 0.508 0.492
#> SRR1044421 1 0.9970 0.12198 0.532 0.468
#> SRR1044422 1 0.9970 0.12198 0.532 0.468
#> SRR1044423 1 0.9977 0.10950 0.528 0.472
#> SRR1044424 1 0.9970 0.12198 0.532 0.468
#> SRR1044425 1 0.0000 0.78596 1.000 0.000
#> SRR1044426 1 0.0000 0.78596 1.000 0.000
#> SRR1044427 1 0.0000 0.78596 1.000 0.000
#> SRR1044428 1 0.0000 0.78596 1.000 0.000
#> SRR1044429 1 0.0000 0.78596 1.000 0.000
#> SRR1044430 1 0.0000 0.78596 1.000 0.000
#> SRR1044431 1 0.0000 0.78596 1.000 0.000
#> SRR1044433 1 0.2423 0.76015 0.960 0.040
#> SRR1044432 1 0.0000 0.78596 1.000 0.000
#> SRR1044434 1 0.0000 0.78596 1.000 0.000
#> SRR1044435 1 0.0000 0.78596 1.000 0.000
#> SRR1044436 1 0.0000 0.78596 1.000 0.000
#> SRR1044437 1 0.0000 0.78596 1.000 0.000
#> SRR1044439 1 0.0000 0.78596 1.000 0.000
#> SRR1044438 1 0.0000 0.78596 1.000 0.000
#> SRR1044440 1 0.0000 0.78596 1.000 0.000
#> SRR1044441 1 0.0000 0.78596 1.000 0.000
#> SRR1044442 1 0.2423 0.76015 0.960 0.040
#> SRR1044443 1 0.2423 0.76015 0.960 0.040
#> SRR1044444 1 0.0000 0.78596 1.000 0.000
#> SRR1044445 1 0.0000 0.78596 1.000 0.000
#> SRR1044446 2 0.6712 0.73484 0.176 0.824
#> SRR1044447 2 0.9944 0.17358 0.456 0.544
#> SRR1044449 2 0.0000 0.78325 0.000 1.000
#> SRR1044448 2 0.0376 0.78292 0.004 0.996
#> SRR1044450 2 0.0000 0.78325 0.000 1.000
#> SRR1044451 2 0.9491 0.45745 0.368 0.632
#> SRR1044452 2 0.0000 0.78325 0.000 1.000
#> SRR1044453 2 0.0000 0.78325 0.000 1.000
#> SRR1044454 2 0.0000 0.78325 0.000 1.000
#> SRR1044455 1 0.9909 0.14903 0.556 0.444
#> SRR1044456 1 0.9970 0.12198 0.532 0.468
#> SRR1044457 2 0.9833 0.27406 0.424 0.576
#> SRR1044458 1 1.0000 0.01645 0.504 0.496
#> SRR1044459 2 0.7745 0.69962 0.228 0.772
#> SRR1044460 1 0.9977 0.10950 0.528 0.472
#> SRR1044461 1 1.0000 0.01645 0.504 0.496
#> SRR1044462 1 0.0000 0.78596 1.000 0.000
#> SRR1044463 1 0.0000 0.78596 1.000 0.000
#> SRR1044464 1 0.0000 0.78596 1.000 0.000
#> SRR1044466 1 0.0000 0.78596 1.000 0.000
#> SRR1044465 1 0.0000 0.78596 1.000 0.000
#> SRR1044467 1 0.0000 0.78596 1.000 0.000
#> SRR1044468 1 0.9983 0.09506 0.524 0.476
#> SRR1044469 2 0.7219 0.71701 0.200 0.800
#> SRR1044470 1 0.0000 0.78596 1.000 0.000
#> SRR1044471 1 0.0000 0.78596 1.000 0.000
#> SRR1044472 1 0.0000 0.78596 1.000 0.000
#> SRR1044473 1 0.0000 0.78596 1.000 0.000
#> SRR1044474 1 0.9970 0.12198 0.532 0.468
#> SRR1044475 2 0.4161 0.76250 0.084 0.916
#> SRR1044476 1 0.9998 0.03332 0.508 0.492
#> SRR1044477 1 0.9970 0.12198 0.532 0.468
#> SRR1044478 1 1.0000 0.01645 0.504 0.496
#> SRR1044479 1 0.9970 0.12198 0.532 0.468
#> SRR1044480 1 0.0000 0.78596 1.000 0.000
#> SRR1044481 1 0.0000 0.78596 1.000 0.000
#> SRR1044482 1 0.9970 0.12198 0.532 0.468
#> SRR1044483 1 0.0000 0.78596 1.000 0.000
#> SRR1044484 1 0.0000 0.78596 1.000 0.000
#> SRR1044486 1 0.0000 0.78596 1.000 0.000
#> SRR1044485 1 0.9970 0.12198 0.532 0.468
#> SRR1044487 1 0.9970 0.12198 0.532 0.468
#> SRR1044488 1 0.9977 0.10950 0.528 0.472
#> SRR1044489 1 0.9977 0.10950 0.528 0.472
#> SRR1044490 1 0.0000 0.78596 1.000 0.000
#> SRR1044491 1 0.0000 0.78596 1.000 0.000
#> SRR1044492 1 0.0000 0.78596 1.000 0.000
#> SRR1044493 1 0.0000 0.78596 1.000 0.000
#> SRR1044494 1 0.9970 0.12198 0.532 0.468
#> SRR1044496 1 0.9970 0.12198 0.532 0.468
#> SRR1044495 1 0.9970 0.12198 0.532 0.468
#> SRR1044497 1 0.0000 0.78596 1.000 0.000
#> SRR1044499 2 0.8608 0.61181 0.284 0.716
#> SRR1044498 1 0.0000 0.78596 1.000 0.000
#> SRR1044500 1 0.9977 0.10950 0.528 0.472
#> SRR1044501 1 1.0000 -0.00167 0.500 0.500
#> SRR1044502 2 0.7602 0.70843 0.220 0.780
#> SRR1044503 1 0.0000 0.78596 1.000 0.000
#> SRR1044504 1 0.0000 0.78596 1.000 0.000
#> SRR1044505 1 0.0000 0.78596 1.000 0.000
#> SRR1044506 1 0.0000 0.78596 1.000 0.000
#> SRR1044507 1 0.2423 0.76015 0.960 0.040
#> SRR1044508 1 0.2423 0.76015 0.960 0.040
#> SRR1044509 1 0.2423 0.76015 0.960 0.040
#> SRR1044510 2 0.0000 0.78325 0.000 1.000
#> SRR1044511 2 0.0000 0.78325 0.000 1.000
#> SRR1044512 2 0.0000 0.78325 0.000 1.000
#> SRR1044513 2 0.9983 0.09547 0.476 0.524
#> SRR1044514 2 0.0000 0.78325 0.000 1.000
#> SRR1044515 2 0.9970 0.12478 0.468 0.532
#> SRR1044516 1 0.9970 0.11957 0.532 0.468
#> SRR1044517 2 0.0000 0.78325 0.000 1.000
#> SRR1044518 2 0.0000 0.78325 0.000 1.000
#> SRR1044519 2 0.0000 0.78325 0.000 1.000
#> SRR1044520 2 0.0000 0.78325 0.000 1.000
#> SRR1044521 1 0.9977 0.10950 0.528 0.472
#> SRR1044522 1 0.9970 0.12198 0.532 0.468
#> SRR1044523 1 1.0000 0.01637 0.504 0.496
#> SRR1044524 2 0.7602 0.70845 0.220 0.780
#> SRR1044525 1 0.0000 0.78596 1.000 0.000
#> SRR1044526 1 0.0000 0.78596 1.000 0.000
#> SRR1044527 1 1.0000 0.01637 0.504 0.496
#> SRR1044528 1 0.9795 0.23371 0.584 0.416
#> SRR1044529 1 0.9970 0.12198 0.532 0.468
#> SRR1044530 1 0.0000 0.78596 1.000 0.000
#> SRR1044531 1 0.0000 0.78596 1.000 0.000
#> SRR1044533 1 0.0000 0.78596 1.000 0.000
#> SRR1044532 1 0.0000 0.78596 1.000 0.000
#> SRR1044534 1 0.9977 0.10950 0.528 0.472
#> SRR1044535 2 0.7602 0.70845 0.220 0.780
#> SRR1044536 1 0.9977 0.10950 0.528 0.472
#> SRR1044537 1 0.0000 0.78596 1.000 0.000
#> SRR1044538 1 0.0000 0.78596 1.000 0.000
#> SRR1044539 1 0.0000 0.78596 1.000 0.000
#> SRR1044540 1 0.0000 0.78596 1.000 0.000
#> SRR1044541 2 0.7950 0.68407 0.240 0.760
#> SRR1044542 1 0.0000 0.78596 1.000 0.000
#> SRR1044543 1 0.0000 0.78596 1.000 0.000
#> SRR1044544 2 0.9286 0.49765 0.344 0.656
#> SRR1044545 1 0.0000 0.78596 1.000 0.000
#> SRR1044546 1 0.0000 0.78596 1.000 0.000
#> SRR1044547 1 0.0000 0.78596 1.000 0.000
#> SRR1044548 1 0.0000 0.78596 1.000 0.000
#> SRR1044549 1 1.0000 0.01637 0.504 0.496
#> SRR1044550 1 0.9977 0.10950 0.528 0.472
#> SRR1044551 1 0.9970 0.12198 0.532 0.468
#> SRR1044552 1 0.0000 0.78596 1.000 0.000
#> SRR1044553 1 0.0000 0.78596 1.000 0.000
#> SRR1044554 1 0.0000 0.78596 1.000 0.000
#> SRR1044555 2 0.7602 0.70845 0.220 0.780
#> SRR1044556 1 0.0000 0.78596 1.000 0.000
#> SRR1044557 1 0.0000 0.78596 1.000 0.000
#> SRR1044558 1 0.0000 0.78596 1.000 0.000
#> SRR1044559 1 0.0000 0.78596 1.000 0.000
#> SRR1044561 1 0.0000 0.78596 1.000 0.000
#> SRR1044560 1 0.9998 0.03332 0.508 0.492
#> SRR1044562 1 0.0000 0.78596 1.000 0.000
#> SRR1044563 1 0.0000 0.78596 1.000 0.000
#> SRR1044564 1 0.0000 0.78596 1.000 0.000
#> SRR1044565 1 0.9970 0.12198 0.532 0.468
#> SRR1044566 1 1.0000 0.01617 0.504 0.496
#> SRR1044567 1 0.0000 0.78596 1.000 0.000
#> SRR1044568 1 0.0000 0.78596 1.000 0.000
#> SRR1044569 1 0.0000 0.78596 1.000 0.000
#> SRR1044570 1 0.0000 0.78596 1.000 0.000
#> SRR1044571 1 0.0000 0.78596 1.000 0.000
#> SRR1044572 1 0.0000 0.78596 1.000 0.000
#> SRR1044573 1 0.0000 0.78596 1.000 0.000
#> SRR1044574 1 0.0000 0.78596 1.000 0.000
#> SRR1044575 1 0.0000 0.78596 1.000 0.000
#> SRR1044576 1 0.9977 0.10950 0.528 0.472
#> SRR1044577 1 0.9970 0.12198 0.532 0.468
#> SRR1044578 1 0.9970 0.12198 0.532 0.468
#> SRR1044579 1 0.0000 0.78596 1.000 0.000
#> SRR1044580 1 0.0000 0.78596 1.000 0.000
#> SRR1044581 1 0.0000 0.78596 1.000 0.000
#> SRR1044582 1 0.0000 0.78596 1.000 0.000
#> SRR1044583 1 0.0000 0.78596 1.000 0.000
#> SRR1044584 1 0.0000 0.78596 1.000 0.000
#> SRR1044585 1 0.0000 0.78596 1.000 0.000
#> SRR1044586 1 0.0000 0.78596 1.000 0.000
#> SRR1044587 1 0.0000 0.78596 1.000 0.000
#> SRR1044588 1 0.0000 0.78596 1.000 0.000
#> SRR1044589 1 0.0000 0.78596 1.000 0.000
#> SRR1044590 1 0.0000 0.78596 1.000 0.000
#> SRR1044591 1 0.0000 0.78596 1.000 0.000
#> SRR1044592 1 0.2423 0.76015 0.960 0.040
#> SRR1044593 1 0.0000 0.78596 1.000 0.000
#> SRR1044594 1 0.0000 0.78596 1.000 0.000
#> SRR1044595 1 0.2423 0.76015 0.960 0.040
#> SRR1044596 1 0.2423 0.76015 0.960 0.040
#> SRR1044597 1 0.3274 0.74253 0.940 0.060
#> SRR1044598 1 0.0000 0.78596 1.000 0.000
#> SRR1044599 1 0.0000 0.78596 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.450 0.8870 0.196 0.804 0.000
#> SRR1044416 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044417 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044418 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044420 2 0.455 0.8888 0.200 0.800 0.000
#> SRR1044419 2 0.517 0.8793 0.192 0.792 0.016
#> SRR1044421 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044422 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044423 2 0.455 0.8888 0.200 0.800 0.000
#> SRR1044424 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044425 1 0.218 0.8946 0.948 0.020 0.032
#> SRR1044426 1 0.243 0.8883 0.940 0.036 0.024
#> SRR1044427 1 0.175 0.8950 0.960 0.012 0.028
#> SRR1044428 1 0.256 0.8779 0.936 0.036 0.028
#> SRR1044429 1 0.205 0.8942 0.952 0.020 0.028
#> SRR1044430 1 0.268 0.8765 0.932 0.040 0.028
#> SRR1044431 1 0.219 0.8955 0.948 0.024 0.028
#> SRR1044433 1 0.691 0.7386 0.724 0.192 0.084
#> SRR1044432 1 0.281 0.8721 0.928 0.040 0.032
#> SRR1044434 1 0.501 0.8683 0.840 0.076 0.084
#> SRR1044435 1 0.447 0.8774 0.864 0.060 0.076
#> SRR1044436 1 0.447 0.8774 0.864 0.060 0.076
#> SRR1044437 1 0.501 0.8683 0.840 0.076 0.084
#> SRR1044439 1 0.447 0.8774 0.864 0.060 0.076
#> SRR1044438 1 0.456 0.8784 0.860 0.064 0.076
#> SRR1044440 1 0.501 0.8683 0.840 0.076 0.084
#> SRR1044441 1 0.501 0.8683 0.840 0.076 0.084
#> SRR1044442 1 0.691 0.7386 0.724 0.192 0.084
#> SRR1044443 1 0.691 0.7386 0.724 0.192 0.084
#> SRR1044444 1 0.501 0.8683 0.840 0.076 0.084
#> SRR1044445 1 0.510 0.8657 0.836 0.080 0.084
#> SRR1044446 2 0.739 -0.5315 0.032 0.500 0.468
#> SRR1044447 2 0.545 0.8024 0.152 0.804 0.044
#> SRR1044449 3 0.536 0.9157 0.000 0.276 0.724
#> SRR1044448 3 0.579 0.8986 0.000 0.332 0.668
#> SRR1044450 3 0.536 0.9157 0.000 0.276 0.724
#> SRR1044451 2 0.539 0.6053 0.072 0.820 0.108
#> SRR1044452 3 0.583 0.8897 0.000 0.340 0.660
#> SRR1044453 3 0.583 0.8897 0.000 0.340 0.660
#> SRR1044454 3 0.583 0.8897 0.000 0.340 0.660
#> SRR1044455 2 0.578 0.8106 0.200 0.768 0.032
#> SRR1044456 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044457 2 0.482 0.7694 0.120 0.840 0.040
#> SRR1044458 2 0.544 0.8751 0.192 0.784 0.024
#> SRR1044459 2 0.629 0.2242 0.036 0.728 0.236
#> SRR1044460 2 0.455 0.8888 0.200 0.800 0.000
#> SRR1044461 2 0.544 0.8751 0.192 0.784 0.024
#> SRR1044462 1 0.255 0.8957 0.936 0.024 0.040
#> SRR1044463 1 0.148 0.8916 0.968 0.012 0.020
#> SRR1044464 1 0.390 0.8851 0.888 0.056 0.056
#> SRR1044466 1 0.148 0.8916 0.968 0.012 0.020
#> SRR1044465 1 0.177 0.8895 0.960 0.016 0.024
#> SRR1044467 1 0.162 0.8904 0.964 0.012 0.024
#> SRR1044468 2 0.450 0.8870 0.196 0.804 0.000
#> SRR1044469 2 0.734 -0.3545 0.036 0.572 0.392
#> SRR1044470 1 0.164 0.8936 0.964 0.016 0.020
#> SRR1044471 1 0.177 0.8895 0.960 0.016 0.024
#> SRR1044472 1 0.148 0.8916 0.968 0.012 0.020
#> SRR1044473 1 0.177 0.8895 0.960 0.016 0.024
#> SRR1044474 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044475 3 0.652 0.6566 0.004 0.488 0.508
#> SRR1044476 2 0.517 0.8793 0.192 0.792 0.016
#> SRR1044477 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044478 2 0.544 0.8751 0.192 0.784 0.024
#> SRR1044479 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044480 1 0.244 0.8947 0.940 0.032 0.028
#> SRR1044481 1 0.145 0.8955 0.968 0.024 0.008
#> SRR1044482 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044483 1 0.510 0.8682 0.836 0.080 0.084
#> SRR1044484 1 0.162 0.8952 0.964 0.024 0.012
#> SRR1044486 1 0.148 0.8949 0.968 0.020 0.012
#> SRR1044485 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044487 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044488 2 0.455 0.8888 0.200 0.800 0.000
#> SRR1044489 2 0.455 0.8888 0.200 0.800 0.000
#> SRR1044490 1 0.132 0.8916 0.972 0.008 0.020
#> SRR1044491 1 0.191 0.8882 0.956 0.016 0.028
#> SRR1044492 1 0.177 0.8895 0.960 0.016 0.024
#> SRR1044493 1 0.191 0.8882 0.956 0.016 0.028
#> SRR1044494 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044496 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044495 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044497 1 0.456 0.8761 0.860 0.064 0.076
#> SRR1044499 2 0.585 0.4402 0.048 0.780 0.172
#> SRR1044498 1 0.132 0.8957 0.972 0.020 0.008
#> SRR1044500 2 0.455 0.8888 0.200 0.800 0.000
#> SRR1044501 2 0.538 0.8715 0.188 0.788 0.024
#> SRR1044502 2 0.694 -0.0402 0.036 0.652 0.312
#> SRR1044503 1 0.465 0.8749 0.856 0.064 0.080
#> SRR1044504 1 0.492 0.8702 0.844 0.072 0.084
#> SRR1044505 1 0.191 0.8938 0.956 0.016 0.028
#> SRR1044506 1 0.510 0.8657 0.836 0.080 0.084
#> SRR1044507 1 0.691 0.7445 0.724 0.192 0.084
#> SRR1044508 1 0.691 0.7386 0.724 0.192 0.084
#> SRR1044509 1 0.691 0.7386 0.724 0.192 0.084
#> SRR1044510 3 0.429 0.9105 0.000 0.180 0.820
#> SRR1044511 3 0.382 0.9040 0.000 0.148 0.852
#> SRR1044512 3 0.382 0.9040 0.000 0.148 0.852
#> SRR1044513 2 0.569 0.8269 0.168 0.788 0.044
#> SRR1044514 3 0.382 0.9040 0.000 0.148 0.852
#> SRR1044515 2 0.579 0.8207 0.168 0.784 0.048
#> SRR1044516 2 0.488 0.8851 0.208 0.788 0.004
#> SRR1044517 3 0.424 0.9102 0.000 0.176 0.824
#> SRR1044518 3 0.388 0.9051 0.000 0.152 0.848
#> SRR1044519 3 0.536 0.9157 0.000 0.276 0.724
#> SRR1044520 3 0.536 0.9157 0.000 0.276 0.724
#> SRR1044521 2 0.455 0.8888 0.200 0.800 0.000
#> SRR1044522 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044523 2 0.525 0.8744 0.188 0.792 0.020
#> SRR1044524 2 0.641 0.1883 0.036 0.716 0.248
#> SRR1044525 1 0.501 0.8683 0.840 0.076 0.084
#> SRR1044526 1 0.203 0.8928 0.952 0.016 0.032
#> SRR1044527 2 0.525 0.8744 0.188 0.792 0.020
#> SRR1044528 2 0.586 0.8271 0.240 0.740 0.020
#> SRR1044529 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044530 1 0.148 0.8916 0.968 0.012 0.020
#> SRR1044531 1 0.162 0.8904 0.964 0.012 0.024
#> SRR1044533 1 0.177 0.8899 0.960 0.016 0.024
#> SRR1044532 1 0.148 0.8916 0.968 0.012 0.020
#> SRR1044534 2 0.455 0.8888 0.200 0.800 0.000
#> SRR1044535 2 0.645 0.1786 0.036 0.712 0.252
#> SRR1044536 2 0.455 0.8888 0.200 0.800 0.000
#> SRR1044537 1 0.205 0.8946 0.952 0.020 0.028
#> SRR1044538 1 0.148 0.8916 0.968 0.012 0.020
#> SRR1044539 1 0.484 0.8718 0.848 0.072 0.080
#> SRR1044540 1 0.117 0.8924 0.976 0.008 0.016
#> SRR1044541 2 0.628 0.2745 0.040 0.736 0.224
#> SRR1044542 1 0.148 0.8916 0.968 0.012 0.020
#> SRR1044543 1 0.117 0.8924 0.976 0.008 0.016
#> SRR1044544 2 0.417 0.5989 0.048 0.876 0.076
#> SRR1044545 1 0.447 0.8788 0.864 0.060 0.076
#> SRR1044546 1 0.191 0.8882 0.956 0.016 0.028
#> SRR1044547 1 0.438 0.8799 0.868 0.060 0.072
#> SRR1044548 1 0.191 0.8882 0.956 0.016 0.028
#> SRR1044549 2 0.525 0.8744 0.188 0.792 0.020
#> SRR1044550 2 0.455 0.8888 0.200 0.800 0.000
#> SRR1044551 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044552 1 0.501 0.8683 0.840 0.076 0.084
#> SRR1044553 1 0.501 0.8683 0.840 0.076 0.084
#> SRR1044554 1 0.191 0.8882 0.956 0.016 0.028
#> SRR1044555 2 0.641 0.1883 0.036 0.716 0.248
#> SRR1044556 1 0.447 0.8774 0.864 0.060 0.076
#> SRR1044557 1 0.191 0.8882 0.956 0.016 0.028
#> SRR1044558 1 0.501 0.8683 0.840 0.076 0.084
#> SRR1044559 1 0.191 0.8882 0.956 0.016 0.028
#> SRR1044561 1 0.501 0.8683 0.840 0.076 0.084
#> SRR1044560 2 0.517 0.8793 0.192 0.792 0.016
#> SRR1044562 1 0.191 0.8882 0.956 0.016 0.028
#> SRR1044563 1 0.483 0.8720 0.848 0.068 0.084
#> SRR1044564 1 0.219 0.8951 0.948 0.024 0.028
#> SRR1044565 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044566 2 0.512 0.8765 0.188 0.796 0.016
#> SRR1044567 1 0.148 0.8916 0.968 0.012 0.020
#> SRR1044568 1 0.359 0.8879 0.900 0.052 0.048
#> SRR1044569 1 0.162 0.8931 0.964 0.012 0.024
#> SRR1044570 1 0.164 0.8910 0.964 0.016 0.020
#> SRR1044571 1 0.177 0.8899 0.960 0.016 0.024
#> SRR1044572 1 0.164 0.8912 0.964 0.016 0.020
#> SRR1044573 1 0.177 0.8895 0.960 0.016 0.024
#> SRR1044574 1 0.164 0.8912 0.964 0.016 0.020
#> SRR1044575 1 0.177 0.8895 0.960 0.016 0.024
#> SRR1044576 2 0.455 0.8888 0.200 0.800 0.000
#> SRR1044577 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044578 2 0.460 0.8883 0.204 0.796 0.000
#> SRR1044579 1 0.501 0.8683 0.840 0.076 0.084
#> SRR1044580 1 0.293 0.8930 0.924 0.036 0.040
#> SRR1044581 1 0.501 0.8683 0.840 0.076 0.084
#> SRR1044582 1 0.162 0.8952 0.964 0.024 0.012
#> SRR1044583 1 0.501 0.8683 0.840 0.076 0.084
#> SRR1044584 1 0.348 0.8879 0.904 0.048 0.048
#> SRR1044585 1 0.501 0.8683 0.840 0.076 0.084
#> SRR1044586 1 0.164 0.8945 0.964 0.020 0.016
#> SRR1044587 1 0.510 0.8657 0.836 0.080 0.084
#> SRR1044588 1 0.510 0.8657 0.836 0.080 0.084
#> SRR1044589 1 0.510 0.8657 0.836 0.080 0.084
#> SRR1044590 1 0.510 0.8657 0.836 0.080 0.084
#> SRR1044591 1 0.510 0.8657 0.836 0.080 0.084
#> SRR1044592 1 0.691 0.7386 0.724 0.192 0.084
#> SRR1044593 1 0.510 0.8657 0.836 0.080 0.084
#> SRR1044594 1 0.510 0.8657 0.836 0.080 0.084
#> SRR1044595 1 0.691 0.7386 0.724 0.192 0.084
#> SRR1044596 1 0.691 0.7386 0.724 0.192 0.084
#> SRR1044597 1 0.684 0.6213 0.704 0.240 0.056
#> SRR1044598 1 0.191 0.8882 0.956 0.016 0.028
#> SRR1044599 1 0.191 0.8882 0.956 0.016 0.028
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 2 0.3024 0.89894 0.000 0.852 0.000 0.148
#> SRR1044416 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044417 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044418 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044420 2 0.3074 0.90080 0.000 0.848 0.000 0.152
#> SRR1044419 2 0.3495 0.89235 0.000 0.844 0.016 0.140
#> SRR1044421 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044422 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044423 2 0.3074 0.90080 0.000 0.848 0.000 0.152
#> SRR1044424 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044425 4 0.5339 0.01670 0.356 0.020 0.000 0.624
#> SRR1044426 4 0.6372 -0.58518 0.376 0.060 0.004 0.560
#> SRR1044427 4 0.5127 0.10888 0.356 0.012 0.000 0.632
#> SRR1044428 4 0.6412 -0.74225 0.456 0.040 0.012 0.492
#> SRR1044429 4 0.5371 0.02358 0.364 0.020 0.000 0.616
#> SRR1044430 1 0.6616 0.71391 0.480 0.052 0.012 0.456
#> SRR1044431 4 0.5252 0.04713 0.336 0.020 0.000 0.644
#> SRR1044433 4 0.2868 0.29338 0.000 0.136 0.000 0.864
#> SRR1044432 1 0.7056 0.76056 0.508 0.088 0.012 0.392
#> SRR1044434 4 0.0524 0.42973 0.004 0.008 0.000 0.988
#> SRR1044435 4 0.1356 0.42692 0.032 0.008 0.000 0.960
#> SRR1044436 4 0.2342 0.41090 0.080 0.008 0.000 0.912
#> SRR1044437 4 0.0524 0.42973 0.004 0.008 0.000 0.988
#> SRR1044439 4 0.2271 0.41260 0.076 0.008 0.000 0.916
#> SRR1044438 4 0.2676 0.40486 0.092 0.012 0.000 0.896
#> SRR1044440 4 0.0524 0.42973 0.004 0.008 0.000 0.988
#> SRR1044441 4 0.0524 0.42973 0.004 0.008 0.000 0.988
#> SRR1044442 4 0.3052 0.29387 0.004 0.136 0.000 0.860
#> SRR1044443 4 0.2868 0.29338 0.000 0.136 0.000 0.864
#> SRR1044444 4 0.0524 0.42973 0.004 0.008 0.000 0.988
#> SRR1044445 4 0.0469 0.42580 0.000 0.012 0.000 0.988
#> SRR1044446 3 0.4624 0.56922 0.000 0.340 0.660 0.000
#> SRR1044447 2 0.4401 0.80479 0.000 0.812 0.076 0.112
#> SRR1044449 3 0.0921 0.83007 0.000 0.028 0.972 0.000
#> SRR1044448 3 0.2281 0.82835 0.000 0.096 0.904 0.000
#> SRR1044450 3 0.0921 0.83007 0.000 0.028 0.972 0.000
#> SRR1044451 2 0.5030 0.62407 0.000 0.752 0.188 0.060
#> SRR1044452 3 0.2921 0.79254 0.000 0.140 0.860 0.000
#> SRR1044453 3 0.2921 0.79254 0.000 0.140 0.860 0.000
#> SRR1044454 3 0.2921 0.79254 0.000 0.140 0.860 0.000
#> SRR1044455 2 0.4176 0.82153 0.008 0.800 0.012 0.180
#> SRR1044456 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044457 2 0.3691 0.78724 0.000 0.856 0.076 0.068
#> SRR1044458 2 0.3554 0.88822 0.000 0.844 0.020 0.136
#> SRR1044459 2 0.4746 0.22960 0.000 0.632 0.368 0.000
#> SRR1044460 2 0.3074 0.90080 0.000 0.848 0.000 0.152
#> SRR1044461 2 0.3554 0.88822 0.000 0.844 0.020 0.136
#> SRR1044462 4 0.4836 0.16704 0.320 0.008 0.000 0.672
#> SRR1044463 4 0.5372 -0.01643 0.444 0.012 0.000 0.544
#> SRR1044464 4 0.3105 0.38114 0.120 0.012 0.000 0.868
#> SRR1044466 4 0.5372 -0.01643 0.444 0.012 0.000 0.544
#> SRR1044465 4 0.5329 0.04609 0.420 0.012 0.000 0.568
#> SRR1044467 4 0.5229 0.02583 0.428 0.008 0.000 0.564
#> SRR1044468 2 0.3024 0.89894 0.000 0.852 0.000 0.148
#> SRR1044469 2 0.4994 -0.19597 0.000 0.520 0.480 0.000
#> SRR1044470 4 0.5466 -0.04110 0.436 0.016 0.000 0.548
#> SRR1044471 4 0.5360 0.02833 0.436 0.012 0.000 0.552
#> SRR1044472 4 0.5250 -0.01045 0.440 0.008 0.000 0.552
#> SRR1044473 4 0.5360 0.02833 0.436 0.012 0.000 0.552
#> SRR1044474 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044475 3 0.4679 0.48185 0.000 0.352 0.648 0.000
#> SRR1044476 2 0.3495 0.89235 0.000 0.844 0.016 0.140
#> SRR1044477 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044478 2 0.3554 0.88822 0.000 0.844 0.020 0.136
#> SRR1044479 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044480 4 0.4248 0.28584 0.220 0.012 0.000 0.768
#> SRR1044481 4 0.5127 0.14934 0.356 0.012 0.000 0.632
#> SRR1044482 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044483 4 0.0937 0.42575 0.012 0.012 0.000 0.976
#> SRR1044484 4 0.5143 0.14566 0.360 0.012 0.000 0.628
#> SRR1044486 4 0.5125 0.09775 0.388 0.008 0.000 0.604
#> SRR1044485 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044487 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044488 2 0.3074 0.90080 0.000 0.848 0.000 0.152
#> SRR1044489 2 0.3074 0.90080 0.000 0.848 0.000 0.152
#> SRR1044490 4 0.5050 0.03198 0.408 0.004 0.000 0.588
#> SRR1044491 4 0.5388 -0.02188 0.456 0.012 0.000 0.532
#> SRR1044492 4 0.5378 -0.00693 0.448 0.012 0.000 0.540
#> SRR1044493 4 0.5277 -0.03089 0.460 0.008 0.000 0.532
#> SRR1044494 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044496 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044495 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044497 4 0.1356 0.42773 0.032 0.008 0.000 0.960
#> SRR1044499 2 0.4155 0.51437 0.000 0.756 0.240 0.004
#> SRR1044498 4 0.4973 0.16337 0.348 0.008 0.000 0.644
#> SRR1044500 2 0.3074 0.90080 0.000 0.848 0.000 0.152
#> SRR1044501 2 0.3606 0.88496 0.000 0.844 0.024 0.132
#> SRR1044502 2 0.4999 -0.18316 0.000 0.508 0.492 0.000
#> SRR1044503 4 0.1151 0.42911 0.024 0.008 0.000 0.968
#> SRR1044504 4 0.0672 0.42989 0.008 0.008 0.000 0.984
#> SRR1044505 4 0.5300 0.06650 0.408 0.012 0.000 0.580
#> SRR1044506 4 0.0469 0.42580 0.000 0.012 0.000 0.988
#> SRR1044507 4 0.3501 0.29542 0.020 0.132 0.000 0.848
#> SRR1044508 4 0.2868 0.29338 0.000 0.136 0.000 0.864
#> SRR1044509 4 0.2868 0.29338 0.000 0.136 0.000 0.864
#> SRR1044510 3 0.6042 0.80258 0.368 0.052 0.580 0.000
#> SRR1044511 3 0.5869 0.80166 0.360 0.044 0.596 0.000
#> SRR1044512 3 0.5869 0.80166 0.360 0.044 0.596 0.000
#> SRR1044513 2 0.4388 0.82874 0.000 0.808 0.060 0.132
#> SRR1044514 3 0.5869 0.80166 0.360 0.044 0.596 0.000
#> SRR1044515 2 0.4552 0.82168 0.000 0.800 0.072 0.128
#> SRR1044516 2 0.3498 0.89625 0.000 0.832 0.008 0.160
#> SRR1044517 3 0.5971 0.80211 0.368 0.048 0.584 0.000
#> SRR1044518 3 0.5793 0.80266 0.360 0.040 0.600 0.000
#> SRR1044519 3 0.0921 0.83007 0.000 0.028 0.972 0.000
#> SRR1044520 3 0.0921 0.83007 0.000 0.028 0.972 0.000
#> SRR1044521 2 0.3074 0.90080 0.000 0.848 0.000 0.152
#> SRR1044522 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044523 2 0.3659 0.88536 0.000 0.840 0.024 0.136
#> SRR1044524 2 0.4790 0.19641 0.000 0.620 0.380 0.000
#> SRR1044525 4 0.0524 0.42973 0.004 0.008 0.000 0.988
#> SRR1044526 4 0.5366 0.01100 0.440 0.012 0.000 0.548
#> SRR1044527 2 0.3659 0.88536 0.000 0.840 0.024 0.136
#> SRR1044528 2 0.3972 0.85048 0.008 0.788 0.000 0.204
#> SRR1044529 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044530 4 0.5372 -0.01643 0.444 0.012 0.000 0.544
#> SRR1044531 4 0.5244 0.02454 0.436 0.008 0.000 0.556
#> SRR1044533 4 0.5366 -0.01171 0.440 0.012 0.000 0.548
#> SRR1044532 4 0.5372 -0.01643 0.444 0.012 0.000 0.544
#> SRR1044534 2 0.3074 0.90080 0.000 0.848 0.000 0.152
#> SRR1044535 2 0.4776 0.21092 0.000 0.624 0.376 0.000
#> SRR1044536 2 0.3074 0.90080 0.000 0.848 0.000 0.152
#> SRR1044537 4 0.5345 0.03540 0.428 0.012 0.000 0.560
#> SRR1044538 4 0.5372 -0.01643 0.444 0.012 0.000 0.544
#> SRR1044539 4 0.1970 0.41707 0.060 0.008 0.000 0.932
#> SRR1044540 4 0.4866 0.06237 0.404 0.000 0.000 0.596
#> SRR1044541 2 0.4661 0.28468 0.000 0.652 0.348 0.000
#> SRR1044542 4 0.5372 -0.01643 0.444 0.012 0.000 0.544
#> SRR1044543 4 0.4830 0.07115 0.392 0.000 0.000 0.608
#> SRR1044544 2 0.3306 0.63819 0.000 0.840 0.156 0.004
#> SRR1044545 4 0.2676 0.40440 0.092 0.012 0.000 0.896
#> SRR1044546 4 0.5388 -0.01681 0.456 0.012 0.000 0.532
#> SRR1044547 4 0.2805 0.39969 0.100 0.012 0.000 0.888
#> SRR1044548 4 0.5378 0.00199 0.448 0.012 0.000 0.540
#> SRR1044549 2 0.3659 0.88536 0.000 0.840 0.024 0.136
#> SRR1044550 2 0.3074 0.90080 0.000 0.848 0.000 0.152
#> SRR1044551 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044552 4 0.0524 0.42973 0.004 0.008 0.000 0.988
#> SRR1044553 4 0.0524 0.42973 0.004 0.008 0.000 0.988
#> SRR1044554 4 0.5392 -0.02952 0.460 0.012 0.000 0.528
#> SRR1044555 2 0.4790 0.19641 0.000 0.620 0.380 0.000
#> SRR1044556 4 0.2271 0.41294 0.076 0.008 0.000 0.916
#> SRR1044557 4 0.5388 -0.01681 0.456 0.012 0.000 0.532
#> SRR1044558 4 0.0524 0.42973 0.004 0.008 0.000 0.988
#> SRR1044559 4 0.5388 -0.01681 0.456 0.012 0.000 0.532
#> SRR1044561 4 0.0524 0.42973 0.004 0.008 0.000 0.988
#> SRR1044560 2 0.3495 0.89235 0.000 0.844 0.016 0.140
#> SRR1044562 4 0.5388 -0.01681 0.456 0.012 0.000 0.532
#> SRR1044563 4 0.0927 0.43019 0.016 0.008 0.000 0.976
#> SRR1044564 4 0.5320 0.05144 0.416 0.012 0.000 0.572
#> SRR1044565 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044566 2 0.3554 0.88984 0.000 0.844 0.020 0.136
#> SRR1044567 4 0.5372 -0.01643 0.444 0.012 0.000 0.544
#> SRR1044568 4 0.2976 0.38263 0.120 0.008 0.000 0.872
#> SRR1044569 4 0.5250 0.01514 0.440 0.008 0.000 0.552
#> SRR1044570 4 0.5478 -0.02273 0.444 0.016 0.000 0.540
#> SRR1044571 4 0.5353 -0.05867 0.432 0.012 0.000 0.556
#> SRR1044572 4 0.5212 0.01354 0.420 0.008 0.000 0.572
#> SRR1044573 4 0.5366 0.02185 0.440 0.012 0.000 0.548
#> SRR1044574 4 0.5193 0.04844 0.412 0.008 0.000 0.580
#> SRR1044575 4 0.5366 0.01674 0.440 0.012 0.000 0.548
#> SRR1044576 2 0.3074 0.90080 0.000 0.848 0.000 0.152
#> SRR1044577 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044578 2 0.3123 0.90056 0.000 0.844 0.000 0.156
#> SRR1044579 4 0.0524 0.42973 0.004 0.008 0.000 0.988
#> SRR1044580 4 0.4539 0.22382 0.272 0.008 0.000 0.720
#> SRR1044581 4 0.0336 0.42761 0.000 0.008 0.000 0.992
#> SRR1044582 4 0.5159 0.14076 0.364 0.012 0.000 0.624
#> SRR1044583 4 0.0524 0.42973 0.004 0.008 0.000 0.988
#> SRR1044584 4 0.3196 0.36852 0.136 0.008 0.000 0.856
#> SRR1044585 4 0.0524 0.42973 0.004 0.008 0.000 0.988
#> SRR1044586 4 0.5217 0.11095 0.380 0.012 0.000 0.608
#> SRR1044587 4 0.0469 0.42580 0.000 0.012 0.000 0.988
#> SRR1044588 4 0.0469 0.42580 0.000 0.012 0.000 0.988
#> SRR1044589 4 0.0469 0.42580 0.000 0.012 0.000 0.988
#> SRR1044590 4 0.0469 0.42580 0.000 0.012 0.000 0.988
#> SRR1044591 4 0.0469 0.42580 0.000 0.012 0.000 0.988
#> SRR1044592 4 0.2868 0.29338 0.000 0.136 0.000 0.864
#> SRR1044593 4 0.0469 0.42580 0.000 0.012 0.000 0.988
#> SRR1044594 4 0.0469 0.42580 0.000 0.012 0.000 0.988
#> SRR1044595 4 0.2868 0.29338 0.000 0.136 0.000 0.864
#> SRR1044596 4 0.3052 0.29387 0.004 0.136 0.000 0.860
#> SRR1044597 4 0.6907 -0.02566 0.172 0.240 0.000 0.588
#> SRR1044598 4 0.5388 -0.01681 0.456 0.012 0.000 0.532
#> SRR1044599 4 0.5388 -0.01681 0.456 0.012 0.000 0.532
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.2179 0.9028 0.100 0.896 0.000 0.000 0.004
#> SRR1044416 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044417 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044418 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044420 2 0.2020 0.9039 0.100 0.900 0.000 0.000 0.000
#> SRR1044419 2 0.2775 0.8962 0.100 0.876 0.020 0.000 0.004
#> SRR1044421 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044422 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044423 2 0.2020 0.9039 0.100 0.900 0.000 0.000 0.000
#> SRR1044424 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044425 1 0.5090 0.5846 0.732 0.024 0.000 0.160 0.084
#> SRR1044426 1 0.6722 -0.5118 0.432 0.020 0.000 0.140 0.408
#> SRR1044427 1 0.4530 0.6106 0.780 0.032 0.000 0.136 0.052
#> SRR1044428 5 0.5742 0.6887 0.436 0.020 0.000 0.044 0.500
#> SRR1044429 1 0.5001 0.6046 0.744 0.028 0.000 0.148 0.080
#> SRR1044430 5 0.5598 0.7957 0.384 0.020 0.000 0.040 0.556
#> SRR1044431 1 0.5505 0.5406 0.696 0.028 0.000 0.180 0.096
#> SRR1044433 4 0.6669 0.6910 0.320 0.152 0.000 0.508 0.020
#> SRR1044432 5 0.4932 0.6600 0.280 0.004 0.000 0.048 0.668
#> SRR1044434 4 0.4915 0.8846 0.420 0.020 0.000 0.556 0.004
#> SRR1044435 4 0.4807 0.8345 0.448 0.020 0.000 0.532 0.000
#> SRR1044436 1 0.4743 -0.6684 0.512 0.016 0.000 0.472 0.000
#> SRR1044437 4 0.4915 0.8846 0.420 0.020 0.000 0.556 0.004
#> SRR1044439 1 0.4744 -0.6809 0.508 0.016 0.000 0.476 0.000
#> SRR1044438 1 0.4886 -0.5990 0.528 0.024 0.000 0.448 0.000
#> SRR1044440 4 0.4915 0.8846 0.420 0.020 0.000 0.556 0.004
#> SRR1044441 4 0.4915 0.8846 0.420 0.020 0.000 0.556 0.004
#> SRR1044442 4 0.6691 0.6858 0.328 0.152 0.000 0.500 0.020
#> SRR1044443 4 0.6669 0.6910 0.320 0.152 0.000 0.508 0.020
#> SRR1044444 4 0.4915 0.8846 0.420 0.020 0.000 0.556 0.004
#> SRR1044445 4 0.4841 0.8849 0.416 0.024 0.000 0.560 0.000
#> SRR1044446 3 0.4225 0.4969 0.000 0.364 0.632 0.000 0.004
#> SRR1044447 2 0.3638 0.8078 0.056 0.852 0.068 0.008 0.016
#> SRR1044449 3 0.0162 0.6809 0.000 0.004 0.996 0.000 0.000
#> SRR1044448 3 0.2230 0.6787 0.000 0.116 0.884 0.000 0.000
#> SRR1044450 3 0.0510 0.6810 0.000 0.016 0.984 0.000 0.000
#> SRR1044451 2 0.4533 0.6289 0.020 0.780 0.156 0.020 0.024
#> SRR1044452 3 0.2488 0.6534 0.000 0.124 0.872 0.000 0.004
#> SRR1044453 3 0.2488 0.6534 0.000 0.124 0.872 0.000 0.004
#> SRR1044454 3 0.2488 0.6534 0.000 0.124 0.872 0.000 0.004
#> SRR1044455 2 0.4025 0.8125 0.072 0.832 0.004 0.044 0.048
#> SRR1044456 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044457 2 0.2728 0.7984 0.040 0.888 0.068 0.000 0.004
#> SRR1044458 2 0.2953 0.8922 0.100 0.868 0.028 0.000 0.004
#> SRR1044459 2 0.4306 0.2875 0.000 0.660 0.328 0.000 0.012
#> SRR1044460 2 0.2020 0.9039 0.100 0.900 0.000 0.000 0.000
#> SRR1044461 2 0.2953 0.8922 0.100 0.868 0.028 0.000 0.004
#> SRR1044462 1 0.4231 0.5449 0.776 0.028 0.000 0.176 0.020
#> SRR1044463 1 0.3495 0.6283 0.844 0.024 0.000 0.024 0.108
#> SRR1044464 1 0.5408 -0.6025 0.516 0.024 0.000 0.440 0.020
#> SRR1044466 1 0.3495 0.6283 0.844 0.024 0.000 0.024 0.108
#> SRR1044465 1 0.3255 0.6819 0.868 0.020 0.000 0.056 0.056
#> SRR1044467 1 0.3546 0.6753 0.852 0.024 0.000 0.060 0.064
#> SRR1044468 2 0.2179 0.9028 0.100 0.896 0.000 0.000 0.004
#> SRR1044469 2 0.4287 -0.1232 0.000 0.540 0.460 0.000 0.000
#> SRR1044470 1 0.4082 0.5973 0.804 0.032 0.000 0.028 0.136
#> SRR1044471 1 0.1967 0.6719 0.932 0.020 0.000 0.012 0.036
#> SRR1044472 1 0.3439 0.6341 0.848 0.020 0.000 0.028 0.104
#> SRR1044473 1 0.2151 0.6718 0.924 0.020 0.000 0.016 0.040
#> SRR1044474 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044475 3 0.3966 0.4231 0.000 0.336 0.664 0.000 0.000
#> SRR1044476 2 0.2775 0.8962 0.100 0.876 0.020 0.000 0.004
#> SRR1044477 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044478 2 0.2953 0.8922 0.100 0.868 0.028 0.000 0.004
#> SRR1044479 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044480 1 0.4946 -0.1054 0.636 0.024 0.000 0.328 0.012
#> SRR1044481 1 0.3739 0.5823 0.820 0.024 0.000 0.136 0.020
#> SRR1044482 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044483 4 0.5163 0.8681 0.408 0.028 0.000 0.556 0.008
#> SRR1044484 1 0.3694 0.5893 0.824 0.024 0.000 0.132 0.020
#> SRR1044486 1 0.3246 0.6466 0.860 0.020 0.000 0.096 0.024
#> SRR1044485 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044487 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044488 2 0.2020 0.9039 0.100 0.900 0.000 0.000 0.000
#> SRR1044489 2 0.2020 0.9039 0.100 0.900 0.000 0.000 0.000
#> SRR1044490 1 0.3908 0.6676 0.824 0.016 0.000 0.088 0.072
#> SRR1044491 1 0.3003 0.6444 0.880 0.040 0.000 0.016 0.064
#> SRR1044492 1 0.2339 0.6575 0.912 0.028 0.000 0.008 0.052
#> SRR1044493 1 0.3018 0.6419 0.876 0.020 0.000 0.024 0.080
#> SRR1044494 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044496 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044495 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044497 4 0.4954 0.8365 0.448 0.020 0.000 0.528 0.004
#> SRR1044499 2 0.3398 0.5476 0.000 0.780 0.216 0.000 0.004
#> SRR1044498 1 0.3870 0.5663 0.808 0.024 0.000 0.148 0.020
#> SRR1044500 2 0.2020 0.9039 0.100 0.900 0.000 0.000 0.000
#> SRR1044501 2 0.2899 0.8896 0.096 0.872 0.028 0.000 0.004
#> SRR1044502 2 0.4542 -0.1254 0.000 0.536 0.456 0.000 0.008
#> SRR1044503 4 0.4945 0.8512 0.440 0.020 0.000 0.536 0.004
#> SRR1044504 4 0.4774 0.8784 0.424 0.020 0.000 0.556 0.000
#> SRR1044505 1 0.2987 0.6817 0.884 0.028 0.000 0.056 0.032
#> SRR1044506 4 0.4841 0.8849 0.416 0.024 0.000 0.560 0.000
#> SRR1044507 4 0.6716 0.6609 0.352 0.148 0.000 0.480 0.020
#> SRR1044508 4 0.6669 0.6910 0.320 0.152 0.000 0.508 0.020
#> SRR1044509 4 0.6669 0.6910 0.320 0.152 0.000 0.508 0.020
#> SRR1044510 3 0.7371 0.5945 0.000 0.044 0.396 0.372 0.188
#> SRR1044511 3 0.6325 0.6013 0.000 0.000 0.428 0.416 0.156
#> SRR1044512 3 0.6325 0.6013 0.000 0.000 0.428 0.416 0.156
#> SRR1044513 2 0.3877 0.8310 0.072 0.840 0.060 0.012 0.016
#> SRR1044514 3 0.6325 0.6013 0.000 0.000 0.428 0.416 0.156
#> SRR1044515 2 0.3956 0.8244 0.072 0.832 0.072 0.008 0.016
#> SRR1044516 2 0.2588 0.8997 0.100 0.884 0.008 0.008 0.000
#> SRR1044517 3 0.7317 0.5925 0.000 0.040 0.396 0.376 0.188
#> SRR1044518 3 0.6570 0.6019 0.000 0.008 0.428 0.408 0.156
#> SRR1044519 3 0.0162 0.6809 0.000 0.004 0.996 0.000 0.000
#> SRR1044520 3 0.0162 0.6809 0.000 0.004 0.996 0.000 0.000
#> SRR1044521 2 0.2020 0.9039 0.100 0.900 0.000 0.000 0.000
#> SRR1044522 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044523 2 0.2983 0.8889 0.096 0.868 0.032 0.000 0.004
#> SRR1044524 2 0.4356 0.2577 0.000 0.648 0.340 0.000 0.012
#> SRR1044525 4 0.4915 0.8846 0.420 0.020 0.000 0.556 0.004
#> SRR1044526 1 0.2780 0.6642 0.896 0.032 0.000 0.032 0.040
#> SRR1044527 2 0.2983 0.8889 0.096 0.868 0.032 0.000 0.004
#> SRR1044528 2 0.3930 0.8542 0.104 0.824 0.000 0.028 0.044
#> SRR1044529 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044530 1 0.3391 0.6310 0.852 0.024 0.000 0.024 0.100
#> SRR1044531 1 0.3001 0.6802 0.884 0.032 0.000 0.032 0.052
#> SRR1044533 1 0.3361 0.6579 0.860 0.024 0.000 0.036 0.080
#> SRR1044532 1 0.3391 0.6310 0.852 0.024 0.000 0.024 0.100
#> SRR1044534 2 0.2020 0.9039 0.100 0.900 0.000 0.000 0.000
#> SRR1044535 2 0.4252 0.2725 0.000 0.652 0.340 0.000 0.008
#> SRR1044536 2 0.2020 0.9039 0.100 0.900 0.000 0.000 0.000
#> SRR1044537 1 0.2777 0.6687 0.896 0.036 0.000 0.040 0.028
#> SRR1044538 1 0.3444 0.6302 0.848 0.024 0.000 0.024 0.104
#> SRR1044539 1 0.4747 -0.7215 0.496 0.016 0.000 0.488 0.000
#> SRR1044540 1 0.3907 0.6535 0.820 0.012 0.000 0.100 0.068
#> SRR1044541 2 0.4213 0.3378 0.000 0.680 0.308 0.000 0.012
#> SRR1044542 1 0.3444 0.6302 0.848 0.024 0.000 0.024 0.104
#> SRR1044543 1 0.4120 0.6376 0.804 0.012 0.000 0.112 0.072
#> SRR1044544 2 0.2563 0.6684 0.000 0.872 0.120 0.000 0.008
#> SRR1044545 1 0.4818 -0.6416 0.520 0.020 0.000 0.460 0.000
#> SRR1044546 1 0.3289 0.6247 0.860 0.036 0.000 0.016 0.088
#> SRR1044547 1 0.4872 -0.5508 0.540 0.024 0.000 0.436 0.000
#> SRR1044548 1 0.3406 0.6341 0.856 0.040 0.000 0.020 0.084
#> SRR1044549 2 0.2983 0.8889 0.096 0.868 0.032 0.000 0.004
#> SRR1044550 2 0.2020 0.9039 0.100 0.900 0.000 0.000 0.000
#> SRR1044551 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044552 4 0.4915 0.8846 0.420 0.020 0.000 0.556 0.004
#> SRR1044553 4 0.4915 0.8846 0.420 0.020 0.000 0.556 0.004
#> SRR1044554 1 0.2859 0.6460 0.888 0.036 0.000 0.016 0.060
#> SRR1044555 2 0.4356 0.2577 0.000 0.648 0.340 0.000 0.012
#> SRR1044556 1 0.4744 -0.6809 0.508 0.016 0.000 0.476 0.000
#> SRR1044557 1 0.3289 0.6247 0.860 0.036 0.000 0.016 0.088
#> SRR1044558 4 0.4915 0.8846 0.420 0.020 0.000 0.556 0.004
#> SRR1044559 1 0.3400 0.6209 0.852 0.036 0.000 0.016 0.096
#> SRR1044561 4 0.4915 0.8846 0.420 0.020 0.000 0.556 0.004
#> SRR1044560 2 0.2775 0.8962 0.100 0.876 0.020 0.000 0.004
#> SRR1044562 1 0.2649 0.6527 0.900 0.036 0.000 0.016 0.048
#> SRR1044563 4 0.4928 0.8714 0.428 0.020 0.000 0.548 0.004
#> SRR1044564 1 0.2745 0.6789 0.896 0.028 0.000 0.052 0.024
#> SRR1044565 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044566 2 0.2720 0.8944 0.096 0.880 0.020 0.000 0.004
#> SRR1044567 1 0.3444 0.6302 0.848 0.024 0.000 0.024 0.104
#> SRR1044568 1 0.5146 -0.5863 0.536 0.020 0.000 0.432 0.012
#> SRR1044569 1 0.2966 0.6826 0.884 0.020 0.000 0.040 0.056
#> SRR1044570 1 0.3246 0.6365 0.860 0.024 0.000 0.020 0.096
#> SRR1044571 1 0.4561 0.5842 0.776 0.020 0.000 0.076 0.128
#> SRR1044572 1 0.3748 0.6610 0.836 0.020 0.000 0.056 0.088
#> SRR1044573 1 0.1934 0.6670 0.932 0.020 0.000 0.008 0.040
#> SRR1044574 1 0.3706 0.6730 0.840 0.020 0.000 0.064 0.076
#> SRR1044575 1 0.2581 0.6778 0.904 0.020 0.000 0.028 0.048
#> SRR1044576 2 0.2020 0.9039 0.100 0.900 0.000 0.000 0.000
#> SRR1044577 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044578 2 0.2179 0.9039 0.100 0.896 0.000 0.004 0.000
#> SRR1044579 4 0.4915 0.8846 0.420 0.020 0.000 0.556 0.004
#> SRR1044580 1 0.4716 0.3515 0.716 0.024 0.000 0.236 0.024
#> SRR1044581 4 0.4767 0.8841 0.420 0.020 0.000 0.560 0.000
#> SRR1044582 1 0.3554 0.6064 0.836 0.024 0.000 0.120 0.020
#> SRR1044583 4 0.4915 0.8846 0.420 0.020 0.000 0.556 0.004
#> SRR1044584 1 0.4980 -0.4527 0.576 0.020 0.000 0.396 0.008
#> SRR1044585 4 0.4915 0.8846 0.420 0.020 0.000 0.556 0.004
#> SRR1044586 1 0.3664 0.6347 0.836 0.024 0.000 0.108 0.032
#> SRR1044587 4 0.4841 0.8849 0.416 0.024 0.000 0.560 0.000
#> SRR1044588 4 0.4841 0.8849 0.416 0.024 0.000 0.560 0.000
#> SRR1044589 4 0.4841 0.8849 0.416 0.024 0.000 0.560 0.000
#> SRR1044590 4 0.4841 0.8849 0.416 0.024 0.000 0.560 0.000
#> SRR1044591 4 0.4841 0.8849 0.416 0.024 0.000 0.560 0.000
#> SRR1044592 4 0.6669 0.6910 0.320 0.152 0.000 0.508 0.020
#> SRR1044593 4 0.4841 0.8849 0.416 0.024 0.000 0.560 0.000
#> SRR1044594 4 0.4841 0.8849 0.416 0.024 0.000 0.560 0.000
#> SRR1044595 4 0.6669 0.6910 0.320 0.152 0.000 0.508 0.020
#> SRR1044596 4 0.6691 0.6858 0.328 0.152 0.000 0.500 0.020
#> SRR1044597 1 0.7770 -0.0316 0.428 0.252 0.000 0.244 0.076
#> SRR1044598 1 0.3454 0.6173 0.848 0.036 0.000 0.016 0.100
#> SRR1044599 1 0.3454 0.6173 0.848 0.036 0.000 0.016 0.100
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.1910 0.8996 0.000 0.892 0.000 0.108 0.000 0.000
#> SRR1044416 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044417 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044418 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044420 2 0.2053 0.9008 0.004 0.888 0.000 0.108 0.000 0.000
#> SRR1044419 2 0.2587 0.8915 0.000 0.868 0.020 0.108 0.000 0.004
#> SRR1044421 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044422 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044423 2 0.2053 0.9008 0.004 0.888 0.000 0.108 0.000 0.000
#> SRR1044424 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044425 4 0.5959 -0.4963 0.396 0.012 0.000 0.472 0.108 0.012
#> SRR1044426 5 0.5886 0.5157 0.200 0.008 0.000 0.272 0.520 0.000
#> SRR1044427 4 0.5986 -0.5844 0.424 0.024 0.000 0.460 0.076 0.016
#> SRR1044428 5 0.5888 0.6717 0.236 0.012 0.000 0.148 0.588 0.016
#> SRR1044429 4 0.5943 -0.5468 0.420 0.012 0.000 0.452 0.104 0.012
#> SRR1044430 5 0.5291 0.6771 0.208 0.016 0.000 0.092 0.668 0.016
#> SRR1044431 4 0.6080 -0.4474 0.368 0.012 0.000 0.480 0.128 0.012
#> SRR1044433 4 0.3372 0.6396 0.008 0.132 0.000 0.824 0.008 0.028
#> SRR1044432 5 0.2790 0.4502 0.132 0.000 0.000 0.024 0.844 0.000
#> SRR1044434 4 0.0291 0.7763 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044435 4 0.0790 0.7643 0.032 0.000 0.000 0.968 0.000 0.000
#> SRR1044436 4 0.2234 0.6820 0.124 0.000 0.000 0.872 0.004 0.000
#> SRR1044437 4 0.0291 0.7763 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044439 4 0.2191 0.6861 0.120 0.000 0.000 0.876 0.004 0.000
#> SRR1044438 4 0.2810 0.6412 0.156 0.008 0.000 0.832 0.004 0.000
#> SRR1044440 4 0.0291 0.7763 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044441 4 0.0291 0.7763 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044442 4 0.3561 0.6379 0.016 0.132 0.000 0.816 0.008 0.028
#> SRR1044443 4 0.3372 0.6396 0.008 0.132 0.000 0.824 0.008 0.028
#> SRR1044444 4 0.0291 0.7763 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044445 4 0.0146 0.7755 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1044446 3 0.4150 0.3861 0.004 0.372 0.612 0.000 0.000 0.012
#> SRR1044447 2 0.3126 0.8007 0.004 0.856 0.064 0.064 0.000 0.012
#> SRR1044449 3 0.0798 0.6655 0.004 0.004 0.976 0.000 0.004 0.012
#> SRR1044448 3 0.2494 0.6495 0.000 0.120 0.864 0.000 0.000 0.016
#> SRR1044450 3 0.0909 0.6664 0.000 0.020 0.968 0.000 0.000 0.012
#> SRR1044451 2 0.3923 0.6113 0.004 0.788 0.148 0.032 0.000 0.028
#> SRR1044452 3 0.2821 0.7035 0.004 0.116 0.856 0.000 0.004 0.020
#> SRR1044453 3 0.2821 0.7035 0.004 0.116 0.856 0.000 0.004 0.020
#> SRR1044454 3 0.2821 0.7035 0.004 0.116 0.856 0.000 0.004 0.020
#> SRR1044455 2 0.3431 0.8054 0.008 0.836 0.000 0.092 0.012 0.052
#> SRR1044456 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044457 2 0.2461 0.7907 0.000 0.888 0.064 0.044 0.000 0.004
#> SRR1044458 2 0.2747 0.8875 0.000 0.860 0.028 0.108 0.000 0.004
#> SRR1044459 2 0.4220 0.2427 0.004 0.664 0.304 0.000 0.000 0.028
#> SRR1044460 2 0.2053 0.9008 0.004 0.888 0.000 0.108 0.000 0.000
#> SRR1044461 2 0.2747 0.8875 0.000 0.860 0.028 0.108 0.000 0.004
#> SRR1044462 4 0.4630 -0.5185 0.484 0.012 0.000 0.488 0.012 0.004
#> SRR1044463 1 0.6034 0.7445 0.544 0.012 0.000 0.292 0.136 0.016
#> SRR1044464 4 0.2748 0.6699 0.128 0.000 0.000 0.848 0.024 0.000
#> SRR1044466 1 0.6034 0.7445 0.544 0.012 0.000 0.292 0.136 0.016
#> SRR1044465 1 0.5881 0.7584 0.532 0.012 0.000 0.344 0.092 0.020
#> SRR1044467 1 0.6018 0.7476 0.524 0.012 0.000 0.340 0.100 0.024
#> SRR1044468 2 0.1910 0.8996 0.000 0.892 0.000 0.108 0.000 0.000
#> SRR1044469 2 0.3982 -0.2612 0.000 0.536 0.460 0.000 0.000 0.004
#> SRR1044470 1 0.6228 0.7176 0.524 0.016 0.000 0.276 0.172 0.012
#> SRR1044471 1 0.4910 0.7925 0.632 0.008 0.000 0.308 0.032 0.020
#> SRR1044472 1 0.5932 0.7538 0.552 0.012 0.000 0.300 0.120 0.016
#> SRR1044473 1 0.4952 0.7910 0.636 0.008 0.000 0.300 0.032 0.024
#> SRR1044474 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044475 3 0.3941 0.4353 0.004 0.328 0.660 0.000 0.004 0.004
#> SRR1044476 2 0.2587 0.8915 0.000 0.868 0.020 0.108 0.000 0.004
#> SRR1044477 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044478 2 0.2747 0.8875 0.000 0.860 0.028 0.108 0.000 0.004
#> SRR1044479 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044480 4 0.4001 0.3501 0.268 0.008 0.000 0.704 0.020 0.000
#> SRR1044481 1 0.4706 0.5526 0.500 0.012 0.000 0.468 0.016 0.004
#> SRR1044482 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044483 4 0.1434 0.7491 0.048 0.000 0.000 0.940 0.012 0.000
#> SRR1044484 1 0.4705 0.5615 0.504 0.012 0.000 0.464 0.016 0.004
#> SRR1044486 1 0.4810 0.6532 0.540 0.012 0.000 0.420 0.024 0.004
#> SRR1044485 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044487 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044488 2 0.2053 0.9008 0.004 0.888 0.000 0.108 0.000 0.000
#> SRR1044489 2 0.2053 0.9008 0.004 0.888 0.000 0.108 0.000 0.000
#> SRR1044490 1 0.6273 0.6861 0.444 0.012 0.000 0.400 0.120 0.024
#> SRR1044491 1 0.5669 0.7655 0.612 0.020 0.000 0.272 0.068 0.028
#> SRR1044492 1 0.5669 0.7846 0.596 0.012 0.000 0.280 0.092 0.020
#> SRR1044493 1 0.5699 0.7723 0.596 0.012 0.000 0.284 0.080 0.028
#> SRR1044494 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044496 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044495 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044497 4 0.0935 0.7646 0.032 0.000 0.000 0.964 0.004 0.000
#> SRR1044499 2 0.2994 0.5213 0.000 0.788 0.208 0.000 0.000 0.004
#> SRR1044498 1 0.4709 0.5259 0.488 0.012 0.000 0.480 0.016 0.004
#> SRR1044500 2 0.2053 0.9008 0.004 0.888 0.000 0.108 0.000 0.000
#> SRR1044501 2 0.2701 0.8853 0.000 0.864 0.028 0.104 0.000 0.004
#> SRR1044502 2 0.4432 -0.1773 0.004 0.544 0.432 0.000 0.000 0.020
#> SRR1044503 4 0.0777 0.7688 0.024 0.000 0.000 0.972 0.004 0.000
#> SRR1044504 4 0.0260 0.7751 0.008 0.000 0.000 0.992 0.000 0.000
#> SRR1044505 1 0.4663 0.7793 0.616 0.012 0.000 0.344 0.020 0.008
#> SRR1044506 4 0.0146 0.7755 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1044507 4 0.3975 0.6261 0.040 0.128 0.000 0.796 0.008 0.028
#> SRR1044508 4 0.3372 0.6396 0.008 0.132 0.000 0.824 0.008 0.028
#> SRR1044509 4 0.3372 0.6396 0.008 0.132 0.000 0.824 0.008 0.028
#> SRR1044510 6 0.6745 0.7604 0.224 0.008 0.200 0.000 0.060 0.508
#> SRR1044511 6 0.2527 0.8918 0.000 0.000 0.168 0.000 0.000 0.832
#> SRR1044512 6 0.2664 0.8844 0.000 0.000 0.184 0.000 0.000 0.816
#> SRR1044513 2 0.3280 0.8244 0.004 0.844 0.056 0.084 0.000 0.012
#> SRR1044514 6 0.2527 0.8918 0.000 0.000 0.168 0.000 0.000 0.832
#> SRR1044515 2 0.3403 0.8175 0.004 0.836 0.068 0.080 0.000 0.012
#> SRR1044516 2 0.2497 0.8974 0.004 0.872 0.008 0.112 0.000 0.004
#> SRR1044517 6 0.6463 0.7929 0.216 0.008 0.160 0.000 0.060 0.556
#> SRR1044518 6 0.3053 0.8908 0.012 0.004 0.172 0.000 0.000 0.812
#> SRR1044519 3 0.0508 0.6682 0.000 0.004 0.984 0.000 0.000 0.012
#> SRR1044520 3 0.0508 0.6682 0.000 0.004 0.984 0.000 0.000 0.012
#> SRR1044521 2 0.2053 0.9008 0.004 0.888 0.000 0.108 0.000 0.000
#> SRR1044522 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044523 2 0.2633 0.8862 0.000 0.864 0.032 0.104 0.000 0.000
#> SRR1044524 2 0.4154 0.2041 0.004 0.652 0.324 0.000 0.000 0.020
#> SRR1044525 4 0.0291 0.7763 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044526 1 0.5066 0.7812 0.620 0.016 0.000 0.312 0.040 0.012
#> SRR1044527 2 0.2633 0.8862 0.000 0.864 0.032 0.104 0.000 0.000
#> SRR1044528 2 0.3615 0.8507 0.008 0.812 0.000 0.132 0.012 0.036
#> SRR1044529 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044530 1 0.5855 0.7521 0.560 0.012 0.000 0.292 0.124 0.012
#> SRR1044531 1 0.5694 0.7958 0.568 0.016 0.000 0.320 0.080 0.016
#> SRR1044533 1 0.5885 0.7605 0.560 0.008 0.000 0.300 0.108 0.024
#> SRR1044532 1 0.5855 0.7521 0.560 0.012 0.000 0.292 0.124 0.012
#> SRR1044534 2 0.2053 0.9008 0.004 0.888 0.000 0.108 0.000 0.000
#> SRR1044535 2 0.4004 0.2200 0.004 0.656 0.328 0.000 0.000 0.012
#> SRR1044536 2 0.2053 0.9008 0.004 0.888 0.000 0.108 0.000 0.000
#> SRR1044537 1 0.4698 0.7746 0.636 0.020 0.000 0.316 0.024 0.004
#> SRR1044538 1 0.5869 0.7546 0.564 0.012 0.000 0.292 0.116 0.016
#> SRR1044539 4 0.2053 0.7005 0.108 0.000 0.000 0.888 0.004 0.000
#> SRR1044540 4 0.6125 -0.6034 0.408 0.004 0.000 0.440 0.124 0.024
#> SRR1044541 2 0.4127 0.2984 0.004 0.684 0.284 0.000 0.000 0.028
#> SRR1044542 1 0.5869 0.7546 0.564 0.012 0.000 0.292 0.116 0.016
#> SRR1044543 4 0.6140 -0.5594 0.388 0.004 0.000 0.456 0.128 0.024
#> SRR1044544 2 0.2243 0.6590 0.004 0.880 0.112 0.000 0.000 0.004
#> SRR1044545 4 0.2544 0.6668 0.140 0.004 0.000 0.852 0.004 0.000
#> SRR1044546 1 0.6060 0.7332 0.572 0.020 0.000 0.292 0.068 0.048
#> SRR1044547 4 0.3152 0.5498 0.196 0.008 0.000 0.792 0.004 0.000
#> SRR1044548 1 0.5985 0.7389 0.572 0.020 0.000 0.300 0.064 0.044
#> SRR1044549 2 0.2633 0.8862 0.000 0.864 0.032 0.104 0.000 0.000
#> SRR1044550 2 0.2053 0.9008 0.004 0.888 0.000 0.108 0.000 0.000
#> SRR1044551 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044552 4 0.0291 0.7763 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044553 4 0.0291 0.7763 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044554 1 0.5936 0.7660 0.576 0.020 0.000 0.292 0.084 0.028
#> SRR1044555 2 0.4154 0.2041 0.004 0.652 0.324 0.000 0.000 0.020
#> SRR1044556 4 0.2191 0.6876 0.120 0.000 0.000 0.876 0.004 0.000
#> SRR1044557 1 0.6060 0.7332 0.572 0.020 0.000 0.292 0.068 0.048
#> SRR1044558 4 0.0291 0.7763 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044559 1 0.6119 0.7310 0.568 0.020 0.000 0.292 0.064 0.056
#> SRR1044561 4 0.0291 0.7763 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044560 2 0.2587 0.8915 0.000 0.868 0.020 0.108 0.000 0.004
#> SRR1044562 1 0.4952 0.7837 0.644 0.020 0.000 0.292 0.028 0.016
#> SRR1044563 4 0.0603 0.7721 0.016 0.000 0.000 0.980 0.004 0.000
#> SRR1044564 1 0.4743 0.7732 0.604 0.016 0.000 0.352 0.024 0.004
#> SRR1044565 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044566 2 0.2540 0.8898 0.000 0.872 0.020 0.104 0.000 0.004
#> SRR1044567 1 0.5904 0.7537 0.560 0.012 0.000 0.292 0.120 0.016
#> SRR1044568 4 0.2402 0.6793 0.120 0.000 0.000 0.868 0.012 0.000
#> SRR1044569 1 0.5660 0.7804 0.560 0.008 0.000 0.324 0.092 0.016
#> SRR1044570 1 0.5869 0.7610 0.564 0.012 0.000 0.292 0.116 0.016
#> SRR1044571 1 0.6482 0.6370 0.464 0.012 0.000 0.324 0.180 0.020
#> SRR1044572 1 0.6268 0.7365 0.488 0.012 0.000 0.348 0.128 0.024
#> SRR1044573 1 0.4935 0.7874 0.640 0.008 0.000 0.296 0.032 0.024
#> SRR1044574 1 0.6009 0.7445 0.504 0.008 0.000 0.360 0.104 0.024
#> SRR1044575 1 0.5198 0.7900 0.612 0.008 0.000 0.312 0.040 0.028
#> SRR1044576 2 0.2053 0.9008 0.004 0.888 0.000 0.108 0.000 0.000
#> SRR1044577 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044578 2 0.2100 0.9010 0.004 0.884 0.000 0.112 0.000 0.000
#> SRR1044579 4 0.0291 0.7763 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044580 4 0.4558 -0.0829 0.348 0.008 0.000 0.612 0.032 0.000
#> SRR1044581 4 0.0146 0.7758 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044582 1 0.4697 0.5900 0.516 0.012 0.000 0.452 0.016 0.004
#> SRR1044583 4 0.0291 0.7763 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044584 4 0.2778 0.6065 0.168 0.000 0.000 0.824 0.008 0.000
#> SRR1044585 4 0.0291 0.7763 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044586 1 0.5123 0.6388 0.504 0.012 0.000 0.440 0.036 0.008
#> SRR1044587 4 0.0146 0.7755 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1044588 4 0.0146 0.7755 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1044589 4 0.0146 0.7755 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1044590 4 0.0146 0.7755 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1044591 4 0.0146 0.7755 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1044592 4 0.3372 0.6396 0.008 0.132 0.000 0.824 0.008 0.028
#> SRR1044593 4 0.0146 0.7755 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1044594 4 0.0146 0.7755 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1044595 4 0.3471 0.6383 0.012 0.132 0.000 0.820 0.008 0.028
#> SRR1044596 4 0.3561 0.6379 0.016 0.132 0.000 0.816 0.008 0.028
#> SRR1044597 4 0.7311 0.0456 0.220 0.232 0.000 0.452 0.024 0.072
#> SRR1044598 1 0.6213 0.7222 0.560 0.020 0.000 0.292 0.072 0.056
#> SRR1044599 1 0.6213 0.7222 0.560 0.020 0.000 0.292 0.072 0.056
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.998 0.998 0.4925 0.508 0.508
#> 3 3 0.748 0.886 0.784 0.2507 0.835 0.675
#> 4 4 0.831 0.873 0.870 0.1475 0.909 0.744
#> 5 5 0.786 0.754 0.809 0.0646 0.946 0.808
#> 6 6 0.753 0.680 0.813 0.0360 0.952 0.809
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0.0000 0.999 0.000 1.000
#> SRR1044416 2 0.0000 0.999 0.000 1.000
#> SRR1044417 2 0.0000 0.999 0.000 1.000
#> SRR1044418 2 0.0000 0.999 0.000 1.000
#> SRR1044420 2 0.0000 0.999 0.000 1.000
#> SRR1044419 2 0.0000 0.999 0.000 1.000
#> SRR1044421 2 0.0000 0.999 0.000 1.000
#> SRR1044422 2 0.0000 0.999 0.000 1.000
#> SRR1044423 2 0.0000 0.999 0.000 1.000
#> SRR1044424 2 0.0000 0.999 0.000 1.000
#> SRR1044425 1 0.0000 0.998 1.000 0.000
#> SRR1044426 1 0.0000 0.998 1.000 0.000
#> SRR1044427 1 0.0376 0.998 0.996 0.004
#> SRR1044428 1 0.0376 0.998 0.996 0.004
#> SRR1044429 1 0.0000 0.998 1.000 0.000
#> SRR1044430 1 0.0376 0.998 0.996 0.004
#> SRR1044431 1 0.0376 0.998 0.996 0.004
#> SRR1044433 1 0.0000 0.998 1.000 0.000
#> SRR1044432 1 0.0376 0.998 0.996 0.004
#> SRR1044434 1 0.0000 0.998 1.000 0.000
#> SRR1044435 1 0.0000 0.998 1.000 0.000
#> SRR1044436 1 0.0000 0.998 1.000 0.000
#> SRR1044437 1 0.0000 0.998 1.000 0.000
#> SRR1044439 1 0.0000 0.998 1.000 0.000
#> SRR1044438 1 0.0000 0.998 1.000 0.000
#> SRR1044440 1 0.0000 0.998 1.000 0.000
#> SRR1044441 1 0.0000 0.998 1.000 0.000
#> SRR1044442 1 0.0000 0.998 1.000 0.000
#> SRR1044443 1 0.0000 0.998 1.000 0.000
#> SRR1044444 1 0.0000 0.998 1.000 0.000
#> SRR1044445 1 0.0000 0.998 1.000 0.000
#> SRR1044446 2 0.0376 0.997 0.004 0.996
#> SRR1044447 2 0.0376 0.997 0.004 0.996
#> SRR1044449 2 0.0376 0.997 0.004 0.996
#> SRR1044448 2 0.0376 0.997 0.004 0.996
#> SRR1044450 2 0.0376 0.997 0.004 0.996
#> SRR1044451 2 0.0376 0.997 0.004 0.996
#> SRR1044452 2 0.0376 0.997 0.004 0.996
#> SRR1044453 2 0.0376 0.997 0.004 0.996
#> SRR1044454 2 0.0376 0.997 0.004 0.996
#> SRR1044455 2 0.0000 0.999 0.000 1.000
#> SRR1044456 2 0.0376 0.996 0.004 0.996
#> SRR1044457 2 0.0000 0.999 0.000 1.000
#> SRR1044458 2 0.0000 0.999 0.000 1.000
#> SRR1044459 2 0.0376 0.997 0.004 0.996
#> SRR1044460 2 0.0000 0.999 0.000 1.000
#> SRR1044461 2 0.0000 0.999 0.000 1.000
#> SRR1044462 1 0.0376 0.998 0.996 0.004
#> SRR1044463 1 0.0376 0.998 0.996 0.004
#> SRR1044464 1 0.0000 0.998 1.000 0.000
#> SRR1044466 1 0.0376 0.998 0.996 0.004
#> SRR1044465 1 0.0376 0.998 0.996 0.004
#> SRR1044467 1 0.0376 0.998 0.996 0.004
#> SRR1044468 2 0.0000 0.999 0.000 1.000
#> SRR1044469 2 0.0376 0.997 0.004 0.996
#> SRR1044470 1 0.0376 0.998 0.996 0.004
#> SRR1044471 1 0.0376 0.998 0.996 0.004
#> SRR1044472 1 0.0376 0.998 0.996 0.004
#> SRR1044473 1 0.0376 0.998 0.996 0.004
#> SRR1044474 2 0.0000 0.999 0.000 1.000
#> SRR1044475 2 0.0376 0.997 0.004 0.996
#> SRR1044476 2 0.0000 0.999 0.000 1.000
#> SRR1044477 2 0.0000 0.999 0.000 1.000
#> SRR1044478 2 0.0000 0.999 0.000 1.000
#> SRR1044479 2 0.0000 0.999 0.000 1.000
#> SRR1044480 1 0.0000 0.998 1.000 0.000
#> SRR1044481 1 0.0376 0.998 0.996 0.004
#> SRR1044482 2 0.0000 0.999 0.000 1.000
#> SRR1044483 1 0.0000 0.998 1.000 0.000
#> SRR1044484 1 0.0376 0.998 0.996 0.004
#> SRR1044486 1 0.0376 0.998 0.996 0.004
#> SRR1044485 2 0.0000 0.999 0.000 1.000
#> SRR1044487 2 0.0000 0.999 0.000 1.000
#> SRR1044488 2 0.0000 0.999 0.000 1.000
#> SRR1044489 2 0.0000 0.999 0.000 1.000
#> SRR1044490 1 0.0376 0.998 0.996 0.004
#> SRR1044491 1 0.0376 0.998 0.996 0.004
#> SRR1044492 1 0.0376 0.998 0.996 0.004
#> SRR1044493 1 0.0376 0.998 0.996 0.004
#> SRR1044494 2 0.0000 0.999 0.000 1.000
#> SRR1044496 2 0.0000 0.999 0.000 1.000
#> SRR1044495 2 0.0000 0.999 0.000 1.000
#> SRR1044497 1 0.0000 0.998 1.000 0.000
#> SRR1044499 2 0.0376 0.997 0.004 0.996
#> SRR1044498 1 0.0376 0.998 0.996 0.004
#> SRR1044500 2 0.0000 0.999 0.000 1.000
#> SRR1044501 2 0.0000 0.999 0.000 1.000
#> SRR1044502 2 0.0000 0.999 0.000 1.000
#> SRR1044503 1 0.0000 0.998 1.000 0.000
#> SRR1044504 1 0.0000 0.998 1.000 0.000
#> SRR1044505 1 0.0376 0.998 0.996 0.004
#> SRR1044506 1 0.0000 0.998 1.000 0.000
#> SRR1044507 1 0.0000 0.998 1.000 0.000
#> SRR1044508 1 0.0000 0.998 1.000 0.000
#> SRR1044509 1 0.0000 0.998 1.000 0.000
#> SRR1044510 2 0.0376 0.997 0.004 0.996
#> SRR1044511 2 0.0376 0.997 0.004 0.996
#> SRR1044512 2 0.0376 0.997 0.004 0.996
#> SRR1044513 2 0.0000 0.999 0.000 1.000
#> SRR1044514 2 0.0376 0.997 0.004 0.996
#> SRR1044515 2 0.0000 0.999 0.000 1.000
#> SRR1044516 2 0.0000 0.999 0.000 1.000
#> SRR1044517 2 0.0376 0.997 0.004 0.996
#> SRR1044518 2 0.0376 0.997 0.004 0.996
#> SRR1044519 2 0.0376 0.997 0.004 0.996
#> SRR1044520 2 0.0376 0.997 0.004 0.996
#> SRR1044521 2 0.0000 0.999 0.000 1.000
#> SRR1044522 2 0.0000 0.999 0.000 1.000
#> SRR1044523 2 0.0000 0.999 0.000 1.000
#> SRR1044524 2 0.0376 0.997 0.004 0.996
#> SRR1044525 1 0.0000 0.998 1.000 0.000
#> SRR1044526 1 0.0376 0.998 0.996 0.004
#> SRR1044527 2 0.0000 0.999 0.000 1.000
#> SRR1044528 2 0.0000 0.999 0.000 1.000
#> SRR1044529 2 0.0000 0.999 0.000 1.000
#> SRR1044530 1 0.0376 0.998 0.996 0.004
#> SRR1044531 1 0.0376 0.998 0.996 0.004
#> SRR1044533 1 0.0376 0.998 0.996 0.004
#> SRR1044532 1 0.0376 0.998 0.996 0.004
#> SRR1044534 2 0.0000 0.999 0.000 1.000
#> SRR1044535 2 0.0376 0.997 0.004 0.996
#> SRR1044536 2 0.0000 0.999 0.000 1.000
#> SRR1044537 1 0.0376 0.998 0.996 0.004
#> SRR1044538 1 0.0376 0.998 0.996 0.004
#> SRR1044539 1 0.0000 0.998 1.000 0.000
#> SRR1044540 1 0.0000 0.998 1.000 0.000
#> SRR1044541 2 0.0000 0.999 0.000 1.000
#> SRR1044542 1 0.0376 0.998 0.996 0.004
#> SRR1044543 1 0.0000 0.998 1.000 0.000
#> SRR1044544 2 0.0000 0.999 0.000 1.000
#> SRR1044545 1 0.0000 0.998 1.000 0.000
#> SRR1044546 1 0.0376 0.998 0.996 0.004
#> SRR1044547 1 0.0376 0.998 0.996 0.004
#> SRR1044548 1 0.0376 0.998 0.996 0.004
#> SRR1044549 2 0.0000 0.999 0.000 1.000
#> SRR1044550 2 0.0000 0.999 0.000 1.000
#> SRR1044551 2 0.0000 0.999 0.000 1.000
#> SRR1044552 1 0.0000 0.998 1.000 0.000
#> SRR1044553 1 0.0000 0.998 1.000 0.000
#> SRR1044554 1 0.0376 0.998 0.996 0.004
#> SRR1044555 2 0.0376 0.997 0.004 0.996
#> SRR1044556 1 0.0000 0.998 1.000 0.000
#> SRR1044557 1 0.0376 0.998 0.996 0.004
#> SRR1044558 1 0.0000 0.998 1.000 0.000
#> SRR1044559 1 0.0376 0.998 0.996 0.004
#> SRR1044561 1 0.0000 0.998 1.000 0.000
#> SRR1044560 2 0.0000 0.999 0.000 1.000
#> SRR1044562 1 0.0376 0.998 0.996 0.004
#> SRR1044563 1 0.0000 0.998 1.000 0.000
#> SRR1044564 1 0.0376 0.998 0.996 0.004
#> SRR1044565 2 0.0000 0.999 0.000 1.000
#> SRR1044566 2 0.0000 0.999 0.000 1.000
#> SRR1044567 1 0.0376 0.998 0.996 0.004
#> SRR1044568 1 0.0000 0.998 1.000 0.000
#> SRR1044569 1 0.0376 0.998 0.996 0.004
#> SRR1044570 1 0.0376 0.998 0.996 0.004
#> SRR1044571 1 0.0376 0.998 0.996 0.004
#> SRR1044572 1 0.0376 0.998 0.996 0.004
#> SRR1044573 1 0.0376 0.998 0.996 0.004
#> SRR1044574 1 0.0376 0.998 0.996 0.004
#> SRR1044575 1 0.0376 0.998 0.996 0.004
#> SRR1044576 2 0.0000 0.999 0.000 1.000
#> SRR1044577 2 0.0000 0.999 0.000 1.000
#> SRR1044578 2 0.0000 0.999 0.000 1.000
#> SRR1044579 1 0.0000 0.998 1.000 0.000
#> SRR1044580 1 0.0000 0.998 1.000 0.000
#> SRR1044581 1 0.0000 0.998 1.000 0.000
#> SRR1044582 1 0.0376 0.998 0.996 0.004
#> SRR1044583 1 0.0000 0.998 1.000 0.000
#> SRR1044584 1 0.0000 0.998 1.000 0.000
#> SRR1044585 1 0.0000 0.998 1.000 0.000
#> SRR1044586 1 0.0376 0.998 0.996 0.004
#> SRR1044587 1 0.0000 0.998 1.000 0.000
#> SRR1044588 1 0.0000 0.998 1.000 0.000
#> SRR1044589 1 0.0000 0.998 1.000 0.000
#> SRR1044590 1 0.0000 0.998 1.000 0.000
#> SRR1044591 1 0.0000 0.998 1.000 0.000
#> SRR1044592 1 0.0000 0.998 1.000 0.000
#> SRR1044593 1 0.0000 0.998 1.000 0.000
#> SRR1044594 1 0.0000 0.998 1.000 0.000
#> SRR1044595 1 0.0000 0.998 1.000 0.000
#> SRR1044596 1 0.0000 0.998 1.000 0.000
#> SRR1044597 1 0.0376 0.998 0.996 0.004
#> SRR1044598 1 0.0376 0.998 0.996 0.004
#> SRR1044599 1 0.0376 0.998 0.996 0.004
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044416 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044417 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044418 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044420 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044419 2 0.0237 0.894 0.004 0.996 0.000
#> SRR1044421 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044422 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044423 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044424 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044425 1 0.3412 0.692 0.876 0.000 0.124
#> SRR1044426 3 0.6305 0.934 0.484 0.000 0.516
#> SRR1044427 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044428 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044429 3 0.6280 0.984 0.460 0.000 0.540
#> SRR1044430 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044431 3 0.6280 0.984 0.460 0.000 0.540
#> SRR1044433 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044432 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044434 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044435 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044436 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044437 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044439 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044438 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044440 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044441 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044442 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044443 1 0.0592 0.921 0.988 0.000 0.012
#> SRR1044444 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044445 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044446 2 0.6267 0.717 0.000 0.548 0.452
#> SRR1044447 2 0.5156 0.823 0.008 0.776 0.216
#> SRR1044449 2 0.6267 0.717 0.000 0.548 0.452
#> SRR1044448 2 0.6267 0.717 0.000 0.548 0.452
#> SRR1044450 2 0.6267 0.717 0.000 0.548 0.452
#> SRR1044451 2 0.5397 0.796 0.000 0.720 0.280
#> SRR1044452 2 0.6267 0.717 0.000 0.548 0.452
#> SRR1044453 2 0.6267 0.717 0.000 0.548 0.452
#> SRR1044454 2 0.6267 0.717 0.000 0.548 0.452
#> SRR1044455 2 0.0000 0.893 0.000 1.000 0.000
#> SRR1044456 2 0.2339 0.864 0.012 0.940 0.048
#> SRR1044457 2 0.0237 0.893 0.000 0.996 0.004
#> SRR1044458 2 0.0000 0.893 0.000 1.000 0.000
#> SRR1044459 2 0.6267 0.717 0.000 0.548 0.452
#> SRR1044460 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044461 2 0.0237 0.894 0.004 0.996 0.000
#> SRR1044462 1 0.6260 -0.767 0.552 0.000 0.448
#> SRR1044463 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044464 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044466 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044465 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044467 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044468 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044469 2 0.5465 0.791 0.000 0.712 0.288
#> SRR1044470 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044471 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044472 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044473 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044474 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044475 2 0.5431 0.792 0.000 0.716 0.284
#> SRR1044476 2 0.0000 0.893 0.000 1.000 0.000
#> SRR1044477 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044478 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044479 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044480 1 0.0424 0.929 0.992 0.000 0.008
#> SRR1044481 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044482 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044483 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044484 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044486 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044485 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044487 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044488 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044489 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044490 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044491 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044492 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044493 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044494 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044496 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044495 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044497 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044499 2 0.2711 0.868 0.000 0.912 0.088
#> SRR1044498 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044500 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044501 2 0.0000 0.893 0.000 1.000 0.000
#> SRR1044502 2 0.5178 0.806 0.000 0.744 0.256
#> SRR1044503 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044504 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044505 3 0.6286 0.976 0.464 0.000 0.536
#> SRR1044506 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044507 1 0.0424 0.931 0.992 0.000 0.008
#> SRR1044508 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044509 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044510 2 0.6267 0.717 0.000 0.548 0.452
#> SRR1044511 2 0.6267 0.717 0.000 0.548 0.452
#> SRR1044512 2 0.6267 0.717 0.000 0.548 0.452
#> SRR1044513 2 0.2384 0.881 0.008 0.936 0.056
#> SRR1044514 2 0.6267 0.717 0.000 0.548 0.452
#> SRR1044515 2 0.2384 0.881 0.008 0.936 0.056
#> SRR1044516 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044517 2 0.6267 0.717 0.000 0.548 0.452
#> SRR1044518 2 0.6267 0.717 0.000 0.548 0.452
#> SRR1044519 2 0.6267 0.717 0.000 0.548 0.452
#> SRR1044520 2 0.6267 0.717 0.000 0.548 0.452
#> SRR1044521 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044522 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044523 2 0.0661 0.895 0.008 0.988 0.004
#> SRR1044524 2 0.6062 0.750 0.000 0.616 0.384
#> SRR1044525 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044526 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044527 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044528 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044529 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044530 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044531 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044533 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044532 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044534 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044535 2 0.6244 0.723 0.000 0.560 0.440
#> SRR1044536 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044537 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044538 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044539 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044540 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044541 2 0.0424 0.893 0.000 0.992 0.008
#> SRR1044542 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044543 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044544 2 0.2796 0.869 0.000 0.908 0.092
#> SRR1044545 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044546 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044547 1 0.1860 0.856 0.948 0.000 0.052
#> SRR1044548 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044549 2 0.0829 0.895 0.012 0.984 0.004
#> SRR1044550 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044551 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044552 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044553 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044554 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044555 2 0.6267 0.717 0.000 0.548 0.452
#> SRR1044556 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044557 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044558 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044559 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044561 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044560 2 0.0000 0.893 0.000 1.000 0.000
#> SRR1044562 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044563 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044564 3 0.6274 0.991 0.456 0.000 0.544
#> SRR1044565 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044566 2 0.0000 0.893 0.000 1.000 0.000
#> SRR1044567 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044568 1 0.0424 0.929 0.992 0.000 0.008
#> SRR1044569 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044570 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044571 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044572 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044573 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044574 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044575 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044576 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044577 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044578 2 0.0592 0.895 0.012 0.988 0.000
#> SRR1044579 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044580 1 0.5591 -0.157 0.696 0.000 0.304
#> SRR1044581 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044582 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044583 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044584 1 0.0892 0.913 0.980 0.000 0.020
#> SRR1044585 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044586 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044587 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044588 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044589 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044590 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044591 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044592 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044593 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044594 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044595 1 0.5560 -0.134 0.700 0.000 0.300
#> SRR1044596 1 0.0000 0.942 1.000 0.000 0.000
#> SRR1044597 1 0.5882 -0.394 0.652 0.000 0.348
#> SRR1044598 3 0.6267 0.998 0.452 0.000 0.548
#> SRR1044599 3 0.6267 0.998 0.452 0.000 0.548
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044416 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044417 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044418 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044420 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044419 2 0.0469 0.9207 0.000 0.988 0.000 0.012
#> SRR1044421 2 0.0188 0.9244 0.000 0.996 0.000 0.004
#> SRR1044422 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044423 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044424 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044425 4 0.6685 0.5505 0.268 0.000 0.132 0.600
#> SRR1044426 1 0.4746 0.8271 0.776 0.000 0.168 0.056
#> SRR1044427 1 0.3172 0.8836 0.840 0.000 0.160 0.000
#> SRR1044428 1 0.3266 0.8755 0.832 0.000 0.168 0.000
#> SRR1044429 1 0.4057 0.8558 0.812 0.000 0.160 0.028
#> SRR1044430 1 0.3172 0.8728 0.840 0.000 0.160 0.000
#> SRR1044431 1 0.3625 0.8659 0.828 0.000 0.160 0.012
#> SRR1044433 4 0.4104 0.9406 0.088 0.000 0.080 0.832
#> SRR1044432 1 0.3123 0.8731 0.844 0.000 0.156 0.000
#> SRR1044434 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044435 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044436 4 0.2480 0.9699 0.088 0.000 0.008 0.904
#> SRR1044437 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044439 4 0.2334 0.9709 0.088 0.000 0.004 0.908
#> SRR1044438 4 0.2480 0.9699 0.088 0.000 0.008 0.904
#> SRR1044440 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044441 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044442 4 0.4104 0.9406 0.088 0.000 0.080 0.832
#> SRR1044443 4 0.4104 0.9406 0.088 0.000 0.080 0.832
#> SRR1044444 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044445 4 0.2949 0.9673 0.088 0.000 0.024 0.888
#> SRR1044446 3 0.5237 0.9672 0.000 0.356 0.628 0.016
#> SRR1044447 2 0.5141 0.2244 0.000 0.700 0.268 0.032
#> SRR1044449 3 0.5615 0.9658 0.000 0.356 0.612 0.032
#> SRR1044448 3 0.4872 0.9697 0.000 0.356 0.640 0.004
#> SRR1044450 3 0.5007 0.9699 0.000 0.356 0.636 0.008
#> SRR1044451 2 0.5699 -0.3609 0.000 0.588 0.380 0.032
#> SRR1044452 3 0.5855 0.9607 0.000 0.356 0.600 0.044
#> SRR1044453 3 0.5855 0.9607 0.000 0.356 0.600 0.044
#> SRR1044454 3 0.5855 0.9607 0.000 0.356 0.600 0.044
#> SRR1044455 2 0.0707 0.9149 0.000 0.980 0.000 0.020
#> SRR1044456 2 0.2578 0.7829 0.052 0.912 0.036 0.000
#> SRR1044457 2 0.1022 0.9043 0.000 0.968 0.000 0.032
#> SRR1044458 2 0.0707 0.9149 0.000 0.980 0.000 0.020
#> SRR1044459 3 0.5007 0.9701 0.000 0.356 0.636 0.008
#> SRR1044460 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044461 2 0.0469 0.9207 0.000 0.988 0.000 0.012
#> SRR1044462 1 0.6240 0.6883 0.664 0.000 0.136 0.200
#> SRR1044463 1 0.1022 0.8915 0.968 0.000 0.032 0.000
#> SRR1044464 4 0.2949 0.9682 0.088 0.000 0.024 0.888
#> SRR1044466 1 0.0469 0.8915 0.988 0.000 0.012 0.000
#> SRR1044465 1 0.2973 0.8751 0.856 0.000 0.144 0.000
#> SRR1044467 1 0.3074 0.8727 0.848 0.000 0.152 0.000
#> SRR1044468 2 0.0188 0.9244 0.000 0.996 0.000 0.004
#> SRR1044469 2 0.6223 -0.4672 0.000 0.556 0.384 0.060
#> SRR1044470 1 0.0817 0.8927 0.976 0.000 0.024 0.000
#> SRR1044471 1 0.2921 0.8778 0.860 0.000 0.140 0.000
#> SRR1044472 1 0.1557 0.8895 0.944 0.000 0.056 0.000
#> SRR1044473 1 0.2589 0.8830 0.884 0.000 0.116 0.000
#> SRR1044474 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044475 2 0.5883 -0.4291 0.000 0.572 0.388 0.040
#> SRR1044476 2 0.0469 0.9207 0.000 0.988 0.000 0.012
#> SRR1044477 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044478 2 0.0336 0.9229 0.000 0.992 0.000 0.008
#> SRR1044479 2 0.0188 0.9218 0.000 0.996 0.004 0.000
#> SRR1044480 4 0.2909 0.9636 0.092 0.000 0.020 0.888
#> SRR1044481 1 0.2408 0.8803 0.896 0.000 0.104 0.000
#> SRR1044482 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044483 4 0.2480 0.9699 0.088 0.000 0.008 0.904
#> SRR1044484 1 0.2530 0.8782 0.888 0.000 0.112 0.000
#> SRR1044486 1 0.2530 0.8778 0.888 0.000 0.112 0.000
#> SRR1044485 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044487 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044488 2 0.0188 0.9244 0.000 0.996 0.000 0.004
#> SRR1044489 2 0.0188 0.9244 0.000 0.996 0.000 0.004
#> SRR1044490 1 0.3123 0.8714 0.844 0.000 0.156 0.000
#> SRR1044491 1 0.2281 0.8818 0.904 0.000 0.096 0.000
#> SRR1044492 1 0.1389 0.8924 0.952 0.000 0.048 0.000
#> SRR1044493 1 0.1474 0.8884 0.948 0.000 0.052 0.000
#> SRR1044494 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044496 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044495 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044497 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044499 2 0.3934 0.6801 0.000 0.836 0.116 0.048
#> SRR1044498 1 0.2589 0.8778 0.884 0.000 0.116 0.000
#> SRR1044500 2 0.0188 0.9244 0.000 0.996 0.000 0.004
#> SRR1044501 2 0.0707 0.9149 0.000 0.980 0.000 0.020
#> SRR1044502 2 0.5460 -0.1482 0.000 0.632 0.340 0.028
#> SRR1044503 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044504 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044505 1 0.4406 0.8745 0.780 0.000 0.192 0.028
#> SRR1044506 4 0.2949 0.9673 0.088 0.000 0.024 0.888
#> SRR1044507 4 0.4948 0.8984 0.100 0.000 0.124 0.776
#> SRR1044508 4 0.4104 0.9406 0.088 0.000 0.080 0.832
#> SRR1044509 4 0.4104 0.9406 0.088 0.000 0.080 0.832
#> SRR1044510 3 0.5339 0.9675 0.000 0.356 0.624 0.020
#> SRR1044511 3 0.5339 0.9675 0.000 0.356 0.624 0.020
#> SRR1044512 3 0.5339 0.9675 0.000 0.356 0.624 0.020
#> SRR1044513 2 0.2546 0.8252 0.000 0.912 0.060 0.028
#> SRR1044514 3 0.5339 0.9675 0.000 0.356 0.624 0.020
#> SRR1044515 2 0.2546 0.8252 0.000 0.912 0.060 0.028
#> SRR1044516 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044517 3 0.5339 0.9675 0.000 0.356 0.624 0.020
#> SRR1044518 3 0.5339 0.9675 0.000 0.356 0.624 0.020
#> SRR1044519 3 0.5127 0.9697 0.000 0.356 0.632 0.012
#> SRR1044520 3 0.5127 0.9697 0.000 0.356 0.632 0.012
#> SRR1044521 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044522 2 0.0469 0.9118 0.000 0.988 0.012 0.000
#> SRR1044523 2 0.0921 0.9075 0.000 0.972 0.000 0.028
#> SRR1044524 3 0.5977 0.8326 0.000 0.432 0.528 0.040
#> SRR1044525 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044526 1 0.3757 0.8834 0.828 0.000 0.152 0.020
#> SRR1044527 2 0.0336 0.9230 0.000 0.992 0.000 0.008
#> SRR1044528 2 0.0188 0.9244 0.000 0.996 0.000 0.004
#> SRR1044529 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044530 1 0.0707 0.8916 0.980 0.000 0.020 0.000
#> SRR1044531 1 0.2814 0.8787 0.868 0.000 0.132 0.000
#> SRR1044533 1 0.3123 0.8714 0.844 0.000 0.156 0.000
#> SRR1044532 1 0.0592 0.8915 0.984 0.000 0.016 0.000
#> SRR1044534 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044535 3 0.5923 0.9367 0.000 0.376 0.580 0.044
#> SRR1044536 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044537 1 0.2469 0.8818 0.892 0.000 0.108 0.000
#> SRR1044538 1 0.0817 0.8909 0.976 0.000 0.024 0.000
#> SRR1044539 4 0.2334 0.9709 0.088 0.000 0.004 0.908
#> SRR1044540 1 0.3123 0.8714 0.844 0.000 0.156 0.000
#> SRR1044541 2 0.1624 0.8861 0.000 0.952 0.020 0.028
#> SRR1044542 1 0.1389 0.8886 0.952 0.000 0.048 0.000
#> SRR1044543 1 0.3123 0.8714 0.844 0.000 0.156 0.000
#> SRR1044544 2 0.4274 0.6118 0.000 0.808 0.148 0.044
#> SRR1044545 4 0.2843 0.9638 0.088 0.000 0.020 0.892
#> SRR1044546 1 0.2530 0.8778 0.888 0.000 0.112 0.000
#> SRR1044547 4 0.4656 0.8495 0.160 0.000 0.056 0.784
#> SRR1044548 1 0.2530 0.8778 0.888 0.000 0.112 0.000
#> SRR1044549 2 0.0469 0.9205 0.000 0.988 0.000 0.012
#> SRR1044550 2 0.0188 0.9244 0.000 0.996 0.000 0.004
#> SRR1044551 2 0.0188 0.9244 0.000 0.996 0.000 0.004
#> SRR1044552 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044553 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044554 1 0.2530 0.8778 0.888 0.000 0.112 0.000
#> SRR1044555 3 0.5929 0.9558 0.000 0.356 0.596 0.048
#> SRR1044556 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044557 1 0.2530 0.8778 0.888 0.000 0.112 0.000
#> SRR1044558 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044559 1 0.2530 0.8778 0.888 0.000 0.112 0.000
#> SRR1044561 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044560 2 0.0469 0.9207 0.000 0.988 0.000 0.012
#> SRR1044562 1 0.2408 0.8798 0.896 0.000 0.104 0.000
#> SRR1044563 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044564 1 0.2773 0.8809 0.880 0.000 0.116 0.004
#> SRR1044565 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044566 2 0.0469 0.9207 0.000 0.988 0.000 0.012
#> SRR1044567 1 0.0469 0.8914 0.988 0.000 0.012 0.000
#> SRR1044568 4 0.2480 0.9699 0.088 0.000 0.008 0.904
#> SRR1044569 1 0.3172 0.8732 0.840 0.000 0.160 0.000
#> SRR1044570 1 0.1637 0.8873 0.940 0.000 0.060 0.000
#> SRR1044571 1 0.3123 0.8714 0.844 0.000 0.156 0.000
#> SRR1044572 1 0.3123 0.8714 0.844 0.000 0.156 0.000
#> SRR1044573 1 0.3219 0.8871 0.836 0.000 0.164 0.000
#> SRR1044574 1 0.3123 0.8714 0.844 0.000 0.156 0.000
#> SRR1044575 1 0.3074 0.8727 0.848 0.000 0.152 0.000
#> SRR1044576 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044577 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044578 2 0.0000 0.9253 0.000 1.000 0.000 0.000
#> SRR1044579 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044580 1 0.6797 0.0807 0.468 0.000 0.096 0.436
#> SRR1044581 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044582 1 0.2530 0.8778 0.888 0.000 0.112 0.000
#> SRR1044583 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044584 4 0.3447 0.9279 0.128 0.000 0.020 0.852
#> SRR1044585 4 0.2149 0.9719 0.088 0.000 0.000 0.912
#> SRR1044586 1 0.2530 0.8778 0.888 0.000 0.112 0.000
#> SRR1044587 4 0.2949 0.9673 0.088 0.000 0.024 0.888
#> SRR1044588 4 0.2949 0.9673 0.088 0.000 0.024 0.888
#> SRR1044589 4 0.2949 0.9673 0.088 0.000 0.024 0.888
#> SRR1044590 4 0.2949 0.9673 0.088 0.000 0.024 0.888
#> SRR1044591 4 0.2949 0.9673 0.088 0.000 0.024 0.888
#> SRR1044592 4 0.4104 0.9406 0.088 0.000 0.080 0.832
#> SRR1044593 4 0.2949 0.9673 0.088 0.000 0.024 0.888
#> SRR1044594 4 0.2949 0.9673 0.088 0.000 0.024 0.888
#> SRR1044595 1 0.6993 0.2300 0.532 0.000 0.132 0.336
#> SRR1044596 4 0.4104 0.9406 0.088 0.000 0.080 0.832
#> SRR1044597 1 0.6596 0.5166 0.612 0.004 0.104 0.280
#> SRR1044598 1 0.2714 0.8766 0.884 0.004 0.112 0.000
#> SRR1044599 1 0.2714 0.8766 0.884 0.004 0.112 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044416 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044417 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044418 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044420 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044419 2 0.0794 0.9186 0.000 0.972 0.000 0.000 0.028
#> SRR1044421 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044422 2 0.0162 0.9309 0.004 0.996 0.000 0.000 0.000
#> SRR1044423 2 0.0162 0.9309 0.004 0.996 0.000 0.000 0.000
#> SRR1044424 2 0.0162 0.9309 0.004 0.996 0.000 0.000 0.000
#> SRR1044425 4 0.5996 0.2951 0.072 0.000 0.020 0.548 0.360
#> SRR1044426 5 0.6033 0.7159 0.376 0.000 0.060 0.028 0.536
#> SRR1044427 1 0.2804 0.5566 0.880 0.000 0.016 0.012 0.092
#> SRR1044428 1 0.5754 -0.7984 0.472 0.000 0.056 0.012 0.460
#> SRR1044429 5 0.5632 0.8754 0.464 0.000 0.036 0.020 0.480
#> SRR1044430 5 0.5801 0.8250 0.444 0.000 0.060 0.012 0.484
#> SRR1044431 5 0.5496 0.8845 0.452 0.000 0.024 0.024 0.500
#> SRR1044433 4 0.4334 0.8095 0.000 0.000 0.080 0.764 0.156
#> SRR1044432 5 0.5801 0.8077 0.444 0.000 0.060 0.012 0.484
#> SRR1044434 4 0.0000 0.9300 0.000 0.000 0.000 1.000 0.000
#> SRR1044435 4 0.0000 0.9300 0.000 0.000 0.000 1.000 0.000
#> SRR1044436 4 0.0451 0.9278 0.004 0.000 0.008 0.988 0.000
#> SRR1044437 4 0.0000 0.9300 0.000 0.000 0.000 1.000 0.000
#> SRR1044439 4 0.0162 0.9294 0.000 0.000 0.004 0.996 0.000
#> SRR1044438 4 0.0579 0.9264 0.008 0.000 0.008 0.984 0.000
#> SRR1044440 4 0.0000 0.9300 0.000 0.000 0.000 1.000 0.000
#> SRR1044441 4 0.0000 0.9300 0.000 0.000 0.000 1.000 0.000
#> SRR1044442 4 0.4334 0.8095 0.000 0.000 0.080 0.764 0.156
#> SRR1044443 4 0.4373 0.8064 0.000 0.000 0.080 0.760 0.160
#> SRR1044444 4 0.0000 0.9300 0.000 0.000 0.000 1.000 0.000
#> SRR1044445 4 0.1211 0.9217 0.000 0.000 0.016 0.960 0.024
#> SRR1044446 3 0.4032 0.9012 0.004 0.192 0.772 0.000 0.032
#> SRR1044447 2 0.5811 0.2063 0.004 0.604 0.272 0.000 0.120
#> SRR1044449 3 0.4100 0.9018 0.000 0.192 0.764 0.000 0.044
#> SRR1044448 3 0.3777 0.9026 0.004 0.192 0.784 0.000 0.020
#> SRR1044450 3 0.3831 0.9022 0.004 0.188 0.784 0.000 0.024
#> SRR1044451 2 0.6267 -0.3982 0.004 0.456 0.412 0.000 0.128
#> SRR1044452 3 0.4973 0.8921 0.004 0.192 0.712 0.000 0.092
#> SRR1044453 3 0.4973 0.8921 0.004 0.192 0.712 0.000 0.092
#> SRR1044454 3 0.5005 0.8912 0.004 0.196 0.708 0.000 0.092
#> SRR1044455 2 0.1704 0.8916 0.004 0.928 0.000 0.000 0.068
#> SRR1044456 2 0.1341 0.8716 0.056 0.944 0.000 0.000 0.000
#> SRR1044457 2 0.2464 0.8471 0.000 0.888 0.016 0.000 0.096
#> SRR1044458 2 0.1043 0.9115 0.000 0.960 0.000 0.000 0.040
#> SRR1044459 3 0.4303 0.9002 0.000 0.192 0.752 0.000 0.056
#> SRR1044460 2 0.0162 0.9309 0.004 0.996 0.000 0.000 0.000
#> SRR1044461 2 0.1041 0.9163 0.004 0.964 0.000 0.000 0.032
#> SRR1044462 1 0.5498 0.2710 0.684 0.000 0.020 0.200 0.096
#> SRR1044463 1 0.4857 0.1616 0.688 0.000 0.036 0.012 0.264
#> SRR1044464 4 0.1195 0.9209 0.000 0.000 0.028 0.960 0.012
#> SRR1044466 1 0.4649 0.2919 0.720 0.000 0.036 0.012 0.232
#> SRR1044465 5 0.5175 0.9071 0.464 0.000 0.020 0.012 0.504
#> SRR1044467 5 0.5000 0.9152 0.460 0.000 0.012 0.012 0.516
#> SRR1044468 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044469 3 0.6070 0.5193 0.004 0.428 0.464 0.000 0.104
#> SRR1044470 1 0.4501 0.3670 0.740 0.000 0.036 0.012 0.212
#> SRR1044471 5 0.5180 0.8910 0.476 0.000 0.020 0.012 0.492
#> SRR1044472 1 0.5021 0.0865 0.676 0.000 0.044 0.012 0.268
#> SRR1044473 1 0.5164 -0.7794 0.520 0.000 0.020 0.012 0.448
#> SRR1044474 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044475 3 0.5690 0.5332 0.004 0.436 0.492 0.000 0.068
#> SRR1044476 2 0.1043 0.9115 0.000 0.960 0.000 0.000 0.040
#> SRR1044477 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044478 2 0.0510 0.9250 0.000 0.984 0.000 0.000 0.016
#> SRR1044479 2 0.0162 0.9309 0.004 0.996 0.000 0.000 0.000
#> SRR1044480 4 0.1179 0.9209 0.016 0.000 0.016 0.964 0.004
#> SRR1044481 1 0.1569 0.6419 0.948 0.000 0.008 0.012 0.032
#> SRR1044482 2 0.0162 0.9309 0.004 0.996 0.000 0.000 0.000
#> SRR1044483 4 0.0566 0.9272 0.004 0.000 0.012 0.984 0.000
#> SRR1044484 1 0.0854 0.6490 0.976 0.000 0.004 0.012 0.008
#> SRR1044486 1 0.0727 0.6516 0.980 0.000 0.004 0.012 0.004
#> SRR1044485 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044487 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044488 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044489 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044490 5 0.4644 0.9151 0.460 0.000 0.000 0.012 0.528
#> SRR1044491 1 0.1314 0.6495 0.960 0.000 0.016 0.012 0.012
#> SRR1044492 1 0.4839 -0.0616 0.660 0.000 0.024 0.012 0.304
#> SRR1044493 1 0.3272 0.5710 0.856 0.000 0.032 0.012 0.100
#> SRR1044494 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044496 2 0.0162 0.9309 0.004 0.996 0.000 0.000 0.000
#> SRR1044495 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044497 4 0.0000 0.9300 0.000 0.000 0.000 1.000 0.000
#> SRR1044499 2 0.4749 0.5698 0.004 0.736 0.172 0.000 0.088
#> SRR1044498 1 0.1612 0.6450 0.948 0.000 0.016 0.012 0.024
#> SRR1044500 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044501 2 0.1043 0.9115 0.000 0.960 0.000 0.000 0.040
#> SRR1044502 2 0.5817 -0.2988 0.004 0.496 0.420 0.000 0.080
#> SRR1044503 4 0.0000 0.9300 0.000 0.000 0.000 1.000 0.000
#> SRR1044504 4 0.0000 0.9300 0.000 0.000 0.000 1.000 0.000
#> SRR1044505 1 0.5189 0.0605 0.688 0.000 0.024 0.048 0.240
#> SRR1044506 4 0.1211 0.9217 0.000 0.000 0.016 0.960 0.024
#> SRR1044507 4 0.6168 0.7215 0.092 0.000 0.084 0.664 0.160
#> SRR1044508 4 0.4373 0.8064 0.000 0.000 0.080 0.760 0.160
#> SRR1044509 4 0.4373 0.8064 0.000 0.000 0.080 0.760 0.160
#> SRR1044510 3 0.5104 0.8869 0.000 0.192 0.692 0.000 0.116
#> SRR1044511 3 0.5104 0.8869 0.000 0.192 0.692 0.000 0.116
#> SRR1044512 3 0.5104 0.8869 0.000 0.192 0.692 0.000 0.116
#> SRR1044513 2 0.3906 0.7420 0.004 0.812 0.080 0.000 0.104
#> SRR1044514 3 0.5104 0.8869 0.000 0.192 0.692 0.000 0.116
#> SRR1044515 2 0.3956 0.7379 0.004 0.808 0.080 0.000 0.108
#> SRR1044516 2 0.0162 0.9305 0.000 0.996 0.000 0.000 0.004
#> SRR1044517 3 0.5104 0.8869 0.000 0.192 0.692 0.000 0.116
#> SRR1044518 3 0.5104 0.8869 0.000 0.192 0.692 0.000 0.116
#> SRR1044519 3 0.3710 0.9027 0.000 0.192 0.784 0.000 0.024
#> SRR1044520 3 0.3710 0.9027 0.000 0.192 0.784 0.000 0.024
#> SRR1044521 2 0.0162 0.9309 0.004 0.996 0.000 0.000 0.000
#> SRR1044522 2 0.0290 0.9282 0.008 0.992 0.000 0.000 0.000
#> SRR1044523 2 0.1894 0.8817 0.000 0.920 0.008 0.000 0.072
#> SRR1044524 3 0.5714 0.7734 0.000 0.292 0.592 0.000 0.116
#> SRR1044525 4 0.0000 0.9300 0.000 0.000 0.000 1.000 0.000
#> SRR1044526 1 0.4570 0.3018 0.752 0.000 0.020 0.040 0.188
#> SRR1044527 2 0.0404 0.9270 0.000 0.988 0.000 0.000 0.012
#> SRR1044528 2 0.0880 0.9158 0.000 0.968 0.000 0.000 0.032
#> SRR1044529 2 0.0162 0.9309 0.004 0.996 0.000 0.000 0.000
#> SRR1044530 1 0.4649 0.2919 0.720 0.000 0.036 0.012 0.232
#> SRR1044531 1 0.5097 -0.8359 0.496 0.000 0.016 0.012 0.476
#> SRR1044533 5 0.5090 0.9129 0.460 0.000 0.016 0.012 0.512
#> SRR1044532 1 0.4196 0.4450 0.776 0.000 0.036 0.012 0.176
#> SRR1044534 2 0.0162 0.9309 0.004 0.996 0.000 0.000 0.000
#> SRR1044535 3 0.5506 0.8614 0.004 0.220 0.656 0.000 0.120
#> SRR1044536 2 0.0162 0.9309 0.004 0.996 0.000 0.000 0.000
#> SRR1044537 1 0.1364 0.6426 0.952 0.000 0.000 0.012 0.036
#> SRR1044538 1 0.4338 0.4022 0.760 0.000 0.036 0.012 0.192
#> SRR1044539 4 0.0162 0.9294 0.000 0.000 0.004 0.996 0.000
#> SRR1044540 5 0.4783 0.9156 0.452 0.000 0.004 0.012 0.532
#> SRR1044541 2 0.2293 0.8608 0.000 0.900 0.016 0.000 0.084
#> SRR1044542 1 0.3504 0.5610 0.844 0.000 0.044 0.012 0.100
#> SRR1044543 5 0.4895 0.9167 0.452 0.000 0.008 0.012 0.528
#> SRR1044544 2 0.5212 0.4791 0.004 0.692 0.192 0.000 0.112
#> SRR1044545 4 0.1106 0.9180 0.024 0.000 0.012 0.964 0.000
#> SRR1044546 1 0.0807 0.6514 0.976 0.000 0.012 0.012 0.000
#> SRR1044547 4 0.3318 0.7688 0.180 0.000 0.012 0.808 0.000
#> SRR1044548 1 0.0807 0.6514 0.976 0.000 0.012 0.012 0.000
#> SRR1044549 2 0.1041 0.9120 0.000 0.964 0.004 0.000 0.032
#> SRR1044550 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044551 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044552 4 0.0000 0.9300 0.000 0.000 0.000 1.000 0.000
#> SRR1044553 4 0.0000 0.9300 0.000 0.000 0.000 1.000 0.000
#> SRR1044554 1 0.0807 0.6514 0.976 0.000 0.012 0.012 0.000
#> SRR1044555 3 0.5301 0.8779 0.004 0.192 0.684 0.000 0.120
#> SRR1044556 4 0.0162 0.9294 0.000 0.000 0.004 0.996 0.000
#> SRR1044557 1 0.0807 0.6514 0.976 0.000 0.012 0.012 0.000
#> SRR1044558 4 0.0000 0.9300 0.000 0.000 0.000 1.000 0.000
#> SRR1044559 1 0.0807 0.6514 0.976 0.000 0.012 0.012 0.000
#> SRR1044561 4 0.0000 0.9300 0.000 0.000 0.000 1.000 0.000
#> SRR1044560 2 0.1043 0.9115 0.000 0.960 0.000 0.000 0.040
#> SRR1044562 1 0.1442 0.6461 0.952 0.000 0.004 0.012 0.032
#> SRR1044563 4 0.0000 0.9300 0.000 0.000 0.000 1.000 0.000
#> SRR1044564 1 0.1967 0.6322 0.932 0.000 0.012 0.020 0.036
#> SRR1044565 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044566 2 0.1043 0.9115 0.000 0.960 0.000 0.000 0.040
#> SRR1044567 1 0.4303 0.4149 0.764 0.000 0.036 0.012 0.188
#> SRR1044568 4 0.0807 0.9260 0.000 0.000 0.012 0.976 0.012
#> SRR1044569 5 0.5097 0.8981 0.476 0.000 0.016 0.012 0.496
#> SRR1044570 1 0.3375 0.5671 0.852 0.000 0.040 0.012 0.096
#> SRR1044571 5 0.4887 0.9074 0.444 0.000 0.008 0.012 0.536
#> SRR1044572 5 0.4644 0.9151 0.460 0.000 0.000 0.012 0.528
#> SRR1044573 1 0.4754 -0.2118 0.664 0.000 0.020 0.012 0.304
#> SRR1044574 5 0.5090 0.9151 0.460 0.000 0.016 0.012 0.512
#> SRR1044575 5 0.5253 0.9095 0.464 0.000 0.024 0.012 0.500
#> SRR1044576 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044577 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044578 2 0.0000 0.9315 0.000 1.000 0.000 0.000 0.000
#> SRR1044579 4 0.0000 0.9300 0.000 0.000 0.000 1.000 0.000
#> SRR1044580 4 0.6978 -0.0819 0.292 0.000 0.020 0.472 0.216
#> SRR1044581 4 0.0000 0.9300 0.000 0.000 0.000 1.000 0.000
#> SRR1044582 1 0.0566 0.6519 0.984 0.000 0.004 0.012 0.000
#> SRR1044583 4 0.0000 0.9300 0.000 0.000 0.000 1.000 0.000
#> SRR1044584 4 0.2618 0.8706 0.036 0.000 0.012 0.900 0.052
#> SRR1044585 4 0.0000 0.9300 0.000 0.000 0.000 1.000 0.000
#> SRR1044586 1 0.0693 0.6503 0.980 0.000 0.000 0.012 0.008
#> SRR1044587 4 0.1211 0.9217 0.000 0.000 0.016 0.960 0.024
#> SRR1044588 4 0.1211 0.9217 0.000 0.000 0.016 0.960 0.024
#> SRR1044589 4 0.1211 0.9217 0.000 0.000 0.016 0.960 0.024
#> SRR1044590 4 0.1211 0.9217 0.000 0.000 0.016 0.960 0.024
#> SRR1044591 4 0.1211 0.9217 0.000 0.000 0.016 0.960 0.024
#> SRR1044592 4 0.4317 0.8076 0.000 0.000 0.076 0.764 0.160
#> SRR1044593 4 0.1211 0.9217 0.000 0.000 0.016 0.960 0.024
#> SRR1044594 4 0.1211 0.9217 0.000 0.000 0.016 0.960 0.024
#> SRR1044595 1 0.7455 0.1621 0.504 0.000 0.088 0.244 0.164
#> SRR1044596 4 0.4334 0.8095 0.000 0.000 0.080 0.764 0.156
#> SRR1044597 1 0.5895 0.2085 0.624 0.004 0.028 0.280 0.064
#> SRR1044598 1 0.0807 0.6514 0.976 0.000 0.012 0.012 0.000
#> SRR1044599 1 0.0807 0.6514 0.976 0.000 0.012 0.012 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.0508 0.8999 0.004 0.984 0.000 0.000 0.000 0.012
#> SRR1044416 2 0.0436 0.9009 0.004 0.988 0.000 0.000 0.004 0.004
#> SRR1044417 2 0.0260 0.9009 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1044418 2 0.0260 0.9009 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1044420 2 0.0291 0.9008 0.004 0.992 0.000 0.000 0.000 0.004
#> SRR1044419 2 0.1493 0.8810 0.004 0.936 0.000 0.000 0.004 0.056
#> SRR1044421 2 0.0508 0.9007 0.000 0.984 0.000 0.000 0.004 0.012
#> SRR1044422 2 0.0146 0.9011 0.004 0.996 0.000 0.000 0.000 0.000
#> SRR1044423 2 0.0551 0.8998 0.004 0.984 0.000 0.000 0.004 0.008
#> SRR1044424 2 0.0551 0.9006 0.004 0.984 0.000 0.000 0.004 0.008
#> SRR1044425 4 0.5239 -0.0936 0.436 0.000 0.012 0.504 0.020 0.028
#> SRR1044426 1 0.4445 0.6533 0.772 0.000 0.076 0.016 0.024 0.112
#> SRR1044427 5 0.4940 0.7182 0.308 0.000 0.016 0.016 0.632 0.028
#> SRR1044428 1 0.4791 0.6496 0.756 0.000 0.080 0.016 0.052 0.096
#> SRR1044429 1 0.3280 0.6986 0.860 0.000 0.024 0.040 0.020 0.056
#> SRR1044430 1 0.4363 0.6660 0.780 0.000 0.080 0.016 0.024 0.100
#> SRR1044431 1 0.3054 0.6908 0.868 0.000 0.020 0.052 0.008 0.052
#> SRR1044433 4 0.3944 -0.1208 0.000 0.000 0.000 0.568 0.004 0.428
#> SRR1044432 1 0.4341 0.6658 0.784 0.000 0.076 0.016 0.028 0.096
#> SRR1044434 4 0.0000 0.8072 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044435 4 0.0000 0.8072 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044436 4 0.1592 0.7817 0.000 0.000 0.008 0.940 0.032 0.020
#> SRR1044437 4 0.0000 0.8072 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044439 4 0.1078 0.7959 0.000 0.000 0.008 0.964 0.016 0.012
#> SRR1044438 4 0.1675 0.7797 0.000 0.000 0.008 0.936 0.032 0.024
#> SRR1044440 4 0.0146 0.8075 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044441 4 0.0146 0.8075 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044442 4 0.3955 -0.1420 0.000 0.000 0.000 0.560 0.004 0.436
#> SRR1044443 4 0.3950 -0.1299 0.000 0.000 0.000 0.564 0.004 0.432
#> SRR1044444 4 0.0146 0.8075 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044445 4 0.1745 0.7655 0.000 0.000 0.012 0.920 0.000 0.068
#> SRR1044446 3 0.3837 0.8506 0.000 0.140 0.784 0.000 0.008 0.068
#> SRR1044447 2 0.6598 -0.1001 0.000 0.476 0.296 0.000 0.060 0.168
#> SRR1044449 3 0.4301 0.8486 0.004 0.140 0.764 0.000 0.020 0.072
#> SRR1044448 3 0.3526 0.8525 0.008 0.140 0.812 0.000 0.008 0.032
#> SRR1044450 3 0.3546 0.8511 0.004 0.136 0.812 0.000 0.012 0.036
#> SRR1044451 3 0.6658 0.5265 0.000 0.336 0.440 0.000 0.060 0.164
#> SRR1044452 3 0.5463 0.8334 0.004 0.140 0.676 0.000 0.052 0.128
#> SRR1044453 3 0.5535 0.8321 0.004 0.144 0.668 0.000 0.052 0.132
#> SRR1044454 3 0.5535 0.8321 0.004 0.144 0.668 0.000 0.052 0.132
#> SRR1044455 2 0.2784 0.8199 0.000 0.848 0.000 0.000 0.028 0.124
#> SRR1044456 2 0.1267 0.8532 0.000 0.940 0.000 0.000 0.060 0.000
#> SRR1044457 2 0.3918 0.7064 0.000 0.748 0.008 0.000 0.036 0.208
#> SRR1044458 2 0.2377 0.8351 0.004 0.868 0.000 0.000 0.004 0.124
#> SRR1044459 3 0.4728 0.8513 0.004 0.140 0.728 0.000 0.020 0.108
#> SRR1044460 2 0.0260 0.9009 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1044461 2 0.1788 0.8694 0.004 0.916 0.000 0.000 0.004 0.076
#> SRR1044462 5 0.6810 0.3878 0.248 0.000 0.016 0.200 0.492 0.044
#> SRR1044463 1 0.5406 0.2569 0.592 0.000 0.004 0.016 0.304 0.084
#> SRR1044464 4 0.2044 0.7797 0.004 0.000 0.008 0.920 0.028 0.040
#> SRR1044466 1 0.5500 0.1801 0.564 0.000 0.004 0.016 0.332 0.084
#> SRR1044465 1 0.2202 0.7107 0.916 0.000 0.016 0.016 0.012 0.040
#> SRR1044467 1 0.1426 0.7171 0.948 0.000 0.008 0.016 0.000 0.028
#> SRR1044468 2 0.0603 0.8989 0.004 0.980 0.000 0.000 0.000 0.016
#> SRR1044469 2 0.6871 -0.4691 0.008 0.376 0.376 0.000 0.044 0.196
#> SRR1044470 1 0.5755 0.1375 0.536 0.000 0.008 0.016 0.344 0.096
#> SRR1044471 1 0.2752 0.7012 0.888 0.000 0.020 0.016 0.024 0.052
#> SRR1044472 1 0.5703 0.3951 0.620 0.000 0.020 0.016 0.236 0.108
#> SRR1044473 1 0.3426 0.6735 0.848 0.000 0.020 0.016 0.064 0.052
#> SRR1044474 2 0.0291 0.9011 0.004 0.992 0.000 0.000 0.004 0.000
#> SRR1044475 3 0.6469 0.4641 0.008 0.388 0.440 0.000 0.044 0.120
#> SRR1044476 2 0.2001 0.8593 0.004 0.900 0.000 0.000 0.004 0.092
#> SRR1044477 2 0.0260 0.9009 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1044478 2 0.1226 0.8887 0.004 0.952 0.000 0.000 0.004 0.040
#> SRR1044479 2 0.0363 0.8993 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR1044480 4 0.2599 0.7286 0.004 0.000 0.008 0.884 0.076 0.028
#> SRR1044481 5 0.3970 0.8234 0.260 0.000 0.000 0.016 0.712 0.012
#> SRR1044482 2 0.0291 0.9011 0.004 0.992 0.000 0.000 0.004 0.000
#> SRR1044483 4 0.2027 0.7726 0.000 0.000 0.016 0.920 0.032 0.032
#> SRR1044484 5 0.3801 0.8249 0.232 0.000 0.000 0.016 0.740 0.012
#> SRR1044486 5 0.3534 0.8317 0.244 0.000 0.000 0.016 0.740 0.000
#> SRR1044485 2 0.0260 0.9009 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1044487 2 0.0291 0.9011 0.004 0.992 0.000 0.000 0.004 0.000
#> SRR1044488 2 0.0405 0.9010 0.000 0.988 0.000 0.000 0.004 0.008
#> SRR1044489 2 0.0405 0.9010 0.000 0.988 0.000 0.000 0.004 0.008
#> SRR1044490 1 0.1059 0.7203 0.964 0.000 0.004 0.016 0.000 0.016
#> SRR1044491 5 0.4169 0.8086 0.252 0.000 0.012 0.016 0.712 0.008
#> SRR1044492 1 0.5341 0.2946 0.616 0.000 0.020 0.016 0.296 0.052
#> SRR1044493 5 0.5622 0.4643 0.384 0.000 0.016 0.016 0.524 0.060
#> SRR1044494 2 0.0260 0.9009 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1044496 2 0.0260 0.9009 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1044495 2 0.0260 0.9009 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1044497 4 0.0260 0.8070 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR1044499 2 0.5550 0.4948 0.004 0.640 0.116 0.000 0.032 0.208
#> SRR1044498 5 0.4352 0.8091 0.252 0.000 0.012 0.016 0.704 0.016
#> SRR1044500 2 0.0520 0.9018 0.000 0.984 0.000 0.000 0.008 0.008
#> SRR1044501 2 0.2196 0.8469 0.004 0.884 0.000 0.000 0.004 0.108
#> SRR1044502 2 0.6338 -0.3920 0.000 0.404 0.404 0.000 0.032 0.160
#> SRR1044503 4 0.0146 0.8070 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044504 4 0.0000 0.8072 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044505 1 0.6384 -0.2103 0.452 0.000 0.024 0.052 0.408 0.064
#> SRR1044506 4 0.1802 0.7644 0.000 0.000 0.012 0.916 0.000 0.072
#> SRR1044507 6 0.5520 0.2483 0.004 0.000 0.000 0.440 0.112 0.444
#> SRR1044508 4 0.3955 -0.1420 0.000 0.000 0.000 0.560 0.004 0.436
#> SRR1044509 4 0.3950 -0.1299 0.000 0.000 0.000 0.564 0.004 0.432
#> SRR1044510 3 0.5239 0.8288 0.004 0.140 0.700 0.000 0.100 0.056
#> SRR1044511 3 0.5129 0.8285 0.000 0.140 0.700 0.000 0.108 0.052
#> SRR1044512 3 0.5129 0.8285 0.000 0.140 0.700 0.000 0.108 0.052
#> SRR1044513 2 0.4781 0.6658 0.000 0.724 0.052 0.000 0.064 0.160
#> SRR1044514 3 0.5129 0.8285 0.000 0.140 0.700 0.000 0.108 0.052
#> SRR1044515 2 0.4760 0.6610 0.000 0.724 0.052 0.000 0.060 0.164
#> SRR1044516 2 0.0692 0.8989 0.004 0.976 0.000 0.000 0.000 0.020
#> SRR1044517 3 0.5239 0.8288 0.004 0.140 0.700 0.000 0.100 0.056
#> SRR1044518 3 0.5129 0.8285 0.000 0.140 0.700 0.000 0.108 0.052
#> SRR1044519 3 0.2755 0.8515 0.004 0.140 0.844 0.000 0.000 0.012
#> SRR1044520 3 0.2755 0.8515 0.004 0.140 0.844 0.000 0.000 0.012
#> SRR1044521 2 0.0146 0.9012 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1044522 2 0.0458 0.8969 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1044523 2 0.3257 0.7829 0.000 0.816 0.012 0.000 0.020 0.152
#> SRR1044524 3 0.6407 0.7630 0.000 0.208 0.532 0.000 0.056 0.204
#> SRR1044525 4 0.0146 0.8075 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044526 5 0.6111 0.3554 0.420 0.000 0.016 0.056 0.460 0.048
#> SRR1044527 2 0.1268 0.8887 0.004 0.952 0.000 0.000 0.008 0.036
#> SRR1044528 2 0.1498 0.8811 0.000 0.940 0.000 0.000 0.028 0.032
#> SRR1044529 2 0.0260 0.9009 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1044530 1 0.5500 0.1801 0.564 0.000 0.004 0.016 0.332 0.084
#> SRR1044531 1 0.2127 0.7130 0.920 0.000 0.008 0.016 0.032 0.024
#> SRR1044533 1 0.1406 0.7207 0.952 0.000 0.008 0.016 0.004 0.020
#> SRR1044532 1 0.5595 -0.0856 0.504 0.000 0.004 0.016 0.396 0.080
#> SRR1044534 2 0.0260 0.9009 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1044535 3 0.6013 0.8022 0.000 0.164 0.592 0.000 0.052 0.192
#> SRR1044536 2 0.0260 0.9009 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1044537 5 0.3970 0.8225 0.260 0.000 0.000 0.016 0.712 0.012
#> SRR1044538 1 0.5664 0.0814 0.536 0.000 0.008 0.016 0.356 0.084
#> SRR1044539 4 0.1262 0.7917 0.000 0.000 0.008 0.956 0.016 0.020
#> SRR1044540 1 0.1390 0.7196 0.948 0.000 0.004 0.016 0.000 0.032
#> SRR1044541 2 0.3901 0.7275 0.000 0.764 0.024 0.000 0.024 0.188
#> SRR1044542 5 0.5804 0.3197 0.420 0.000 0.012 0.016 0.472 0.080
#> SRR1044543 1 0.1570 0.7172 0.944 0.000 0.004 0.016 0.008 0.028
#> SRR1044544 2 0.6079 0.3269 0.000 0.572 0.140 0.000 0.052 0.236
#> SRR1044545 4 0.2349 0.7232 0.000 0.000 0.008 0.892 0.080 0.020
#> SRR1044546 5 0.3775 0.8325 0.228 0.000 0.012 0.016 0.744 0.000
#> SRR1044547 4 0.4307 0.2721 0.008 0.000 0.008 0.704 0.252 0.028
#> SRR1044548 5 0.3775 0.8325 0.228 0.000 0.012 0.016 0.744 0.000
#> SRR1044549 2 0.2114 0.8548 0.000 0.904 0.008 0.000 0.012 0.076
#> SRR1044550 2 0.0405 0.9004 0.004 0.988 0.000 0.000 0.000 0.008
#> SRR1044551 2 0.0291 0.9012 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1044552 4 0.0000 0.8072 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044553 4 0.0000 0.8072 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044554 5 0.3914 0.8307 0.228 0.000 0.012 0.016 0.740 0.004
#> SRR1044555 3 0.5958 0.8073 0.000 0.140 0.600 0.000 0.056 0.204
#> SRR1044556 4 0.1078 0.7959 0.000 0.000 0.008 0.964 0.016 0.012
#> SRR1044557 5 0.3775 0.8325 0.228 0.000 0.012 0.016 0.744 0.000
#> SRR1044558 4 0.0146 0.8075 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044559 5 0.3775 0.8325 0.228 0.000 0.012 0.016 0.744 0.000
#> SRR1044561 4 0.0146 0.8075 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044560 2 0.2001 0.8593 0.004 0.900 0.000 0.000 0.004 0.092
#> SRR1044562 5 0.3897 0.8188 0.264 0.000 0.000 0.016 0.712 0.008
#> SRR1044563 4 0.0767 0.8007 0.000 0.000 0.008 0.976 0.012 0.004
#> SRR1044564 5 0.4734 0.7932 0.248 0.000 0.016 0.024 0.688 0.024
#> SRR1044565 2 0.0260 0.9009 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1044566 2 0.1897 0.8638 0.004 0.908 0.000 0.000 0.004 0.084
#> SRR1044567 1 0.5637 0.0265 0.520 0.000 0.004 0.016 0.372 0.088
#> SRR1044568 4 0.1877 0.7811 0.012 0.000 0.008 0.932 0.024 0.024
#> SRR1044569 1 0.2124 0.7124 0.916 0.000 0.016 0.016 0.004 0.048
#> SRR1044570 5 0.5786 0.3892 0.400 0.000 0.012 0.016 0.492 0.080
#> SRR1044571 1 0.1672 0.7198 0.940 0.000 0.012 0.016 0.004 0.028
#> SRR1044572 1 0.1262 0.7192 0.956 0.000 0.008 0.016 0.000 0.020
#> SRR1044573 1 0.5175 0.3304 0.652 0.000 0.020 0.016 0.260 0.052
#> SRR1044574 1 0.1894 0.7186 0.928 0.000 0.012 0.016 0.004 0.040
#> SRR1044575 1 0.2057 0.7156 0.920 0.000 0.016 0.016 0.004 0.044
#> SRR1044576 2 0.0260 0.9009 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1044577 2 0.0291 0.9011 0.004 0.992 0.000 0.000 0.004 0.000
#> SRR1044578 2 0.0291 0.9011 0.004 0.992 0.000 0.000 0.004 0.000
#> SRR1044579 4 0.0146 0.8075 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044580 4 0.5921 -0.2019 0.420 0.000 0.004 0.464 0.072 0.040
#> SRR1044581 4 0.0260 0.8070 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR1044582 5 0.3673 0.8313 0.244 0.000 0.000 0.016 0.736 0.004
#> SRR1044583 4 0.0146 0.8075 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044584 4 0.2969 0.7024 0.052 0.000 0.012 0.876 0.036 0.024
#> SRR1044585 4 0.0146 0.8075 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044586 5 0.3509 0.8316 0.240 0.000 0.000 0.016 0.744 0.000
#> SRR1044587 4 0.1802 0.7644 0.000 0.000 0.012 0.916 0.000 0.072
#> SRR1044588 4 0.1745 0.7655 0.000 0.000 0.012 0.920 0.000 0.068
#> SRR1044589 4 0.1745 0.7655 0.000 0.000 0.012 0.920 0.000 0.068
#> SRR1044590 4 0.1745 0.7655 0.000 0.000 0.012 0.920 0.000 0.068
#> SRR1044591 4 0.1745 0.7655 0.000 0.000 0.012 0.920 0.000 0.068
#> SRR1044592 4 0.3944 -0.1208 0.000 0.000 0.000 0.568 0.004 0.428
#> SRR1044593 4 0.1745 0.7655 0.000 0.000 0.012 0.920 0.000 0.068
#> SRR1044594 4 0.1745 0.7655 0.000 0.000 0.012 0.920 0.000 0.068
#> SRR1044595 6 0.6658 0.3914 0.056 0.000 0.000 0.184 0.304 0.456
#> SRR1044596 4 0.3950 -0.1299 0.000 0.000 0.000 0.564 0.004 0.432
#> SRR1044597 5 0.6603 0.2274 0.160 0.000 0.012 0.248 0.528 0.052
#> SRR1044598 5 0.3775 0.8325 0.228 0.000 0.012 0.016 0.744 0.000
#> SRR1044599 5 0.3775 0.8325 0.228 0.000 0.012 0.016 0.744 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)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.4925 0.508 0.508
#> 3 3 1.000 0.980 0.991 0.3332 0.836 0.677
#> 4 4 0.947 0.933 0.970 0.1330 0.913 0.746
#> 5 5 0.875 0.874 0.912 0.0433 0.972 0.893
#> 6 6 0.853 0.806 0.899 0.0440 0.950 0.787
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0 1 0 1
#> SRR1044416 2 0 1 0 1
#> SRR1044417 2 0 1 0 1
#> SRR1044418 2 0 1 0 1
#> SRR1044420 2 0 1 0 1
#> SRR1044419 2 0 1 0 1
#> SRR1044421 2 0 1 0 1
#> SRR1044422 2 0 1 0 1
#> SRR1044423 2 0 1 0 1
#> SRR1044424 2 0 1 0 1
#> SRR1044425 1 0 1 1 0
#> SRR1044426 1 0 1 1 0
#> SRR1044427 1 0 1 1 0
#> SRR1044428 1 0 1 1 0
#> SRR1044429 1 0 1 1 0
#> SRR1044430 1 0 1 1 0
#> SRR1044431 1 0 1 1 0
#> SRR1044433 1 0 1 1 0
#> SRR1044432 1 0 1 1 0
#> SRR1044434 1 0 1 1 0
#> SRR1044435 1 0 1 1 0
#> SRR1044436 1 0 1 1 0
#> SRR1044437 1 0 1 1 0
#> SRR1044439 1 0 1 1 0
#> SRR1044438 1 0 1 1 0
#> SRR1044440 1 0 1 1 0
#> SRR1044441 1 0 1 1 0
#> SRR1044442 1 0 1 1 0
#> SRR1044443 1 0 1 1 0
#> SRR1044444 1 0 1 1 0
#> SRR1044445 1 0 1 1 0
#> SRR1044446 2 0 1 0 1
#> SRR1044447 2 0 1 0 1
#> SRR1044449 2 0 1 0 1
#> SRR1044448 2 0 1 0 1
#> SRR1044450 2 0 1 0 1
#> SRR1044451 2 0 1 0 1
#> SRR1044452 2 0 1 0 1
#> SRR1044453 2 0 1 0 1
#> SRR1044454 2 0 1 0 1
#> SRR1044455 2 0 1 0 1
#> SRR1044456 2 0 1 0 1
#> SRR1044457 2 0 1 0 1
#> SRR1044458 2 0 1 0 1
#> SRR1044459 2 0 1 0 1
#> SRR1044460 2 0 1 0 1
#> SRR1044461 2 0 1 0 1
#> SRR1044462 1 0 1 1 0
#> SRR1044463 1 0 1 1 0
#> SRR1044464 1 0 1 1 0
#> SRR1044466 1 0 1 1 0
#> SRR1044465 1 0 1 1 0
#> SRR1044467 1 0 1 1 0
#> SRR1044468 2 0 1 0 1
#> SRR1044469 2 0 1 0 1
#> SRR1044470 1 0 1 1 0
#> SRR1044471 1 0 1 1 0
#> SRR1044472 1 0 1 1 0
#> SRR1044473 1 0 1 1 0
#> SRR1044474 2 0 1 0 1
#> SRR1044475 2 0 1 0 1
#> SRR1044476 2 0 1 0 1
#> SRR1044477 2 0 1 0 1
#> SRR1044478 2 0 1 0 1
#> SRR1044479 2 0 1 0 1
#> SRR1044480 1 0 1 1 0
#> SRR1044481 1 0 1 1 0
#> SRR1044482 2 0 1 0 1
#> SRR1044483 1 0 1 1 0
#> SRR1044484 1 0 1 1 0
#> SRR1044486 1 0 1 1 0
#> SRR1044485 2 0 1 0 1
#> SRR1044487 2 0 1 0 1
#> SRR1044488 2 0 1 0 1
#> SRR1044489 2 0 1 0 1
#> SRR1044490 1 0 1 1 0
#> SRR1044491 1 0 1 1 0
#> SRR1044492 1 0 1 1 0
#> SRR1044493 1 0 1 1 0
#> SRR1044494 2 0 1 0 1
#> SRR1044496 2 0 1 0 1
#> SRR1044495 2 0 1 0 1
#> SRR1044497 1 0 1 1 0
#> SRR1044499 2 0 1 0 1
#> SRR1044498 1 0 1 1 0
#> SRR1044500 2 0 1 0 1
#> SRR1044501 2 0 1 0 1
#> SRR1044502 2 0 1 0 1
#> SRR1044503 1 0 1 1 0
#> SRR1044504 1 0 1 1 0
#> SRR1044505 1 0 1 1 0
#> SRR1044506 1 0 1 1 0
#> SRR1044507 1 0 1 1 0
#> SRR1044508 1 0 1 1 0
#> SRR1044509 1 0 1 1 0
#> SRR1044510 2 0 1 0 1
#> SRR1044511 2 0 1 0 1
#> SRR1044512 2 0 1 0 1
#> SRR1044513 2 0 1 0 1
#> SRR1044514 2 0 1 0 1
#> SRR1044515 2 0 1 0 1
#> SRR1044516 2 0 1 0 1
#> SRR1044517 2 0 1 0 1
#> SRR1044518 2 0 1 0 1
#> SRR1044519 2 0 1 0 1
#> SRR1044520 2 0 1 0 1
#> SRR1044521 2 0 1 0 1
#> SRR1044522 2 0 1 0 1
#> SRR1044523 2 0 1 0 1
#> SRR1044524 2 0 1 0 1
#> SRR1044525 1 0 1 1 0
#> SRR1044526 1 0 1 1 0
#> SRR1044527 2 0 1 0 1
#> SRR1044528 2 0 1 0 1
#> SRR1044529 2 0 1 0 1
#> SRR1044530 1 0 1 1 0
#> SRR1044531 1 0 1 1 0
#> SRR1044533 1 0 1 1 0
#> SRR1044532 1 0 1 1 0
#> SRR1044534 2 0 1 0 1
#> SRR1044535 2 0 1 0 1
#> SRR1044536 2 0 1 0 1
#> SRR1044537 1 0 1 1 0
#> SRR1044538 1 0 1 1 0
#> SRR1044539 1 0 1 1 0
#> SRR1044540 1 0 1 1 0
#> SRR1044541 2 0 1 0 1
#> SRR1044542 1 0 1 1 0
#> SRR1044543 1 0 1 1 0
#> SRR1044544 2 0 1 0 1
#> SRR1044545 1 0 1 1 0
#> SRR1044546 1 0 1 1 0
#> SRR1044547 1 0 1 1 0
#> SRR1044548 1 0 1 1 0
#> SRR1044549 2 0 1 0 1
#> SRR1044550 2 0 1 0 1
#> SRR1044551 2 0 1 0 1
#> SRR1044552 1 0 1 1 0
#> SRR1044553 1 0 1 1 0
#> SRR1044554 1 0 1 1 0
#> SRR1044555 2 0 1 0 1
#> SRR1044556 1 0 1 1 0
#> SRR1044557 1 0 1 1 0
#> SRR1044558 1 0 1 1 0
#> SRR1044559 1 0 1 1 0
#> SRR1044561 1 0 1 1 0
#> SRR1044560 2 0 1 0 1
#> SRR1044562 1 0 1 1 0
#> SRR1044563 1 0 1 1 0
#> SRR1044564 1 0 1 1 0
#> SRR1044565 2 0 1 0 1
#> SRR1044566 2 0 1 0 1
#> SRR1044567 1 0 1 1 0
#> SRR1044568 1 0 1 1 0
#> SRR1044569 1 0 1 1 0
#> SRR1044570 1 0 1 1 0
#> SRR1044571 1 0 1 1 0
#> SRR1044572 1 0 1 1 0
#> SRR1044573 1 0 1 1 0
#> SRR1044574 1 0 1 1 0
#> SRR1044575 1 0 1 1 0
#> SRR1044576 2 0 1 0 1
#> SRR1044577 2 0 1 0 1
#> SRR1044578 2 0 1 0 1
#> SRR1044579 1 0 1 1 0
#> SRR1044580 1 0 1 1 0
#> SRR1044581 1 0 1 1 0
#> SRR1044582 1 0 1 1 0
#> SRR1044583 1 0 1 1 0
#> SRR1044584 1 0 1 1 0
#> SRR1044585 1 0 1 1 0
#> SRR1044586 1 0 1 1 0
#> SRR1044587 1 0 1 1 0
#> SRR1044588 1 0 1 1 0
#> SRR1044589 1 0 1 1 0
#> SRR1044590 1 0 1 1 0
#> SRR1044591 1 0 1 1 0
#> SRR1044592 1 0 1 1 0
#> SRR1044593 1 0 1 1 0
#> SRR1044594 1 0 1 1 0
#> SRR1044595 1 0 1 1 0
#> SRR1044596 1 0 1 1 0
#> SRR1044597 1 0 1 1 0
#> SRR1044598 1 0 1 1 0
#> SRR1044599 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.0000 1.000 0.000 1 0.000
#> SRR1044416 2 0.0000 1.000 0.000 1 0.000
#> SRR1044417 2 0.0000 1.000 0.000 1 0.000
#> SRR1044418 2 0.0000 1.000 0.000 1 0.000
#> SRR1044420 2 0.0000 1.000 0.000 1 0.000
#> SRR1044419 2 0.0000 1.000 0.000 1 0.000
#> SRR1044421 2 0.0000 1.000 0.000 1 0.000
#> SRR1044422 2 0.0000 1.000 0.000 1 0.000
#> SRR1044423 2 0.0000 1.000 0.000 1 0.000
#> SRR1044424 2 0.0000 1.000 0.000 1 0.000
#> SRR1044425 3 0.4555 0.752 0.200 0 0.800
#> SRR1044426 1 0.3879 0.820 0.848 0 0.152
#> SRR1044427 1 0.0000 0.978 1.000 0 0.000
#> SRR1044428 1 0.0000 0.978 1.000 0 0.000
#> SRR1044429 1 0.1753 0.936 0.952 0 0.048
#> SRR1044430 1 0.0000 0.978 1.000 0 0.000
#> SRR1044431 1 0.0237 0.975 0.996 0 0.004
#> SRR1044433 3 0.0000 0.990 0.000 0 1.000
#> SRR1044432 1 0.0000 0.978 1.000 0 0.000
#> SRR1044434 3 0.0000 0.990 0.000 0 1.000
#> SRR1044435 3 0.0000 0.990 0.000 0 1.000
#> SRR1044436 3 0.0000 0.990 0.000 0 1.000
#> SRR1044437 3 0.0000 0.990 0.000 0 1.000
#> SRR1044439 3 0.0000 0.990 0.000 0 1.000
#> SRR1044438 3 0.0000 0.990 0.000 0 1.000
#> SRR1044440 3 0.0000 0.990 0.000 0 1.000
#> SRR1044441 3 0.0000 0.990 0.000 0 1.000
#> SRR1044442 3 0.0237 0.988 0.004 0 0.996
#> SRR1044443 3 0.0237 0.988 0.004 0 0.996
#> SRR1044444 3 0.0000 0.990 0.000 0 1.000
#> SRR1044445 3 0.0000 0.990 0.000 0 1.000
#> SRR1044446 2 0.0000 1.000 0.000 1 0.000
#> SRR1044447 2 0.0000 1.000 0.000 1 0.000
#> SRR1044449 2 0.0000 1.000 0.000 1 0.000
#> SRR1044448 2 0.0000 1.000 0.000 1 0.000
#> SRR1044450 2 0.0000 1.000 0.000 1 0.000
#> SRR1044451 2 0.0000 1.000 0.000 1 0.000
#> SRR1044452 2 0.0000 1.000 0.000 1 0.000
#> SRR1044453 2 0.0000 1.000 0.000 1 0.000
#> SRR1044454 2 0.0000 1.000 0.000 1 0.000
#> SRR1044455 2 0.0000 1.000 0.000 1 0.000
#> SRR1044456 2 0.0000 1.000 0.000 1 0.000
#> SRR1044457 2 0.0000 1.000 0.000 1 0.000
#> SRR1044458 2 0.0000 1.000 0.000 1 0.000
#> SRR1044459 2 0.0000 1.000 0.000 1 0.000
#> SRR1044460 2 0.0000 1.000 0.000 1 0.000
#> SRR1044461 2 0.0000 1.000 0.000 1 0.000
#> SRR1044462 1 0.2878 0.888 0.904 0 0.096
#> SRR1044463 1 0.0000 0.978 1.000 0 0.000
#> SRR1044464 3 0.0592 0.981 0.012 0 0.988
#> SRR1044466 1 0.0000 0.978 1.000 0 0.000
#> SRR1044465 1 0.0000 0.978 1.000 0 0.000
#> SRR1044467 1 0.0000 0.978 1.000 0 0.000
#> SRR1044468 2 0.0000 1.000 0.000 1 0.000
#> SRR1044469 2 0.0000 1.000 0.000 1 0.000
#> SRR1044470 1 0.0000 0.978 1.000 0 0.000
#> SRR1044471 1 0.0000 0.978 1.000 0 0.000
#> SRR1044472 1 0.0000 0.978 1.000 0 0.000
#> SRR1044473 1 0.0000 0.978 1.000 0 0.000
#> SRR1044474 2 0.0000 1.000 0.000 1 0.000
#> SRR1044475 2 0.0000 1.000 0.000 1 0.000
#> SRR1044476 2 0.0000 1.000 0.000 1 0.000
#> SRR1044477 2 0.0000 1.000 0.000 1 0.000
#> SRR1044478 2 0.0000 1.000 0.000 1 0.000
#> SRR1044479 2 0.0000 1.000 0.000 1 0.000
#> SRR1044480 3 0.1753 0.947 0.048 0 0.952
#> SRR1044481 1 0.0000 0.978 1.000 0 0.000
#> SRR1044482 2 0.0000 1.000 0.000 1 0.000
#> SRR1044483 3 0.0000 0.990 0.000 0 1.000
#> SRR1044484 1 0.0000 0.978 1.000 0 0.000
#> SRR1044486 1 0.0000 0.978 1.000 0 0.000
#> SRR1044485 2 0.0000 1.000 0.000 1 0.000
#> SRR1044487 2 0.0000 1.000 0.000 1 0.000
#> SRR1044488 2 0.0000 1.000 0.000 1 0.000
#> SRR1044489 2 0.0000 1.000 0.000 1 0.000
#> SRR1044490 1 0.0000 0.978 1.000 0 0.000
#> SRR1044491 1 0.0000 0.978 1.000 0 0.000
#> SRR1044492 1 0.0000 0.978 1.000 0 0.000
#> SRR1044493 1 0.0000 0.978 1.000 0 0.000
#> SRR1044494 2 0.0000 1.000 0.000 1 0.000
#> SRR1044496 2 0.0000 1.000 0.000 1 0.000
#> SRR1044495 2 0.0000 1.000 0.000 1 0.000
#> SRR1044497 3 0.0000 0.990 0.000 0 1.000
#> SRR1044499 2 0.0000 1.000 0.000 1 0.000
#> SRR1044498 1 0.0000 0.978 1.000 0 0.000
#> SRR1044500 2 0.0000 1.000 0.000 1 0.000
#> SRR1044501 2 0.0000 1.000 0.000 1 0.000
#> SRR1044502 2 0.0000 1.000 0.000 1 0.000
#> SRR1044503 3 0.0000 0.990 0.000 0 1.000
#> SRR1044504 3 0.0000 0.990 0.000 0 1.000
#> SRR1044505 1 0.0592 0.968 0.988 0 0.012
#> SRR1044506 3 0.0000 0.990 0.000 0 1.000
#> SRR1044507 3 0.0237 0.988 0.004 0 0.996
#> SRR1044508 3 0.0237 0.988 0.004 0 0.996
#> SRR1044509 3 0.0237 0.988 0.004 0 0.996
#> SRR1044510 2 0.0000 1.000 0.000 1 0.000
#> SRR1044511 2 0.0000 1.000 0.000 1 0.000
#> SRR1044512 2 0.0000 1.000 0.000 1 0.000
#> SRR1044513 2 0.0000 1.000 0.000 1 0.000
#> SRR1044514 2 0.0000 1.000 0.000 1 0.000
#> SRR1044515 2 0.0000 1.000 0.000 1 0.000
#> SRR1044516 2 0.0000 1.000 0.000 1 0.000
#> SRR1044517 2 0.0000 1.000 0.000 1 0.000
#> SRR1044518 2 0.0000 1.000 0.000 1 0.000
#> SRR1044519 2 0.0000 1.000 0.000 1 0.000
#> SRR1044520 2 0.0000 1.000 0.000 1 0.000
#> SRR1044521 2 0.0000 1.000 0.000 1 0.000
#> SRR1044522 2 0.0000 1.000 0.000 1 0.000
#> SRR1044523 2 0.0000 1.000 0.000 1 0.000
#> SRR1044524 2 0.0000 1.000 0.000 1 0.000
#> SRR1044525 3 0.0000 0.990 0.000 0 1.000
#> SRR1044526 1 0.0000 0.978 1.000 0 0.000
#> SRR1044527 2 0.0000 1.000 0.000 1 0.000
#> SRR1044528 2 0.0000 1.000 0.000 1 0.000
#> SRR1044529 2 0.0000 1.000 0.000 1 0.000
#> SRR1044530 1 0.0000 0.978 1.000 0 0.000
#> SRR1044531 1 0.0000 0.978 1.000 0 0.000
#> SRR1044533 1 0.0000 0.978 1.000 0 0.000
#> SRR1044532 1 0.0000 0.978 1.000 0 0.000
#> SRR1044534 2 0.0000 1.000 0.000 1 0.000
#> SRR1044535 2 0.0000 1.000 0.000 1 0.000
#> SRR1044536 2 0.0000 1.000 0.000 1 0.000
#> SRR1044537 1 0.0000 0.978 1.000 0 0.000
#> SRR1044538 1 0.0000 0.978 1.000 0 0.000
#> SRR1044539 3 0.0000 0.990 0.000 0 1.000
#> SRR1044540 1 0.0000 0.978 1.000 0 0.000
#> SRR1044541 2 0.0000 1.000 0.000 1 0.000
#> SRR1044542 1 0.0000 0.978 1.000 0 0.000
#> SRR1044543 1 0.0237 0.975 0.996 0 0.004
#> SRR1044544 2 0.0000 1.000 0.000 1 0.000
#> SRR1044545 3 0.0000 0.990 0.000 0 1.000
#> SRR1044546 1 0.0000 0.978 1.000 0 0.000
#> SRR1044547 3 0.1031 0.970 0.024 0 0.976
#> SRR1044548 1 0.0000 0.978 1.000 0 0.000
#> SRR1044549 2 0.0000 1.000 0.000 1 0.000
#> SRR1044550 2 0.0000 1.000 0.000 1 0.000
#> SRR1044551 2 0.0000 1.000 0.000 1 0.000
#> SRR1044552 3 0.0000 0.990 0.000 0 1.000
#> SRR1044553 3 0.0000 0.990 0.000 0 1.000
#> SRR1044554 1 0.0000 0.978 1.000 0 0.000
#> SRR1044555 2 0.0000 1.000 0.000 1 0.000
#> SRR1044556 3 0.0000 0.990 0.000 0 1.000
#> SRR1044557 1 0.0000 0.978 1.000 0 0.000
#> SRR1044558 3 0.0000 0.990 0.000 0 1.000
#> SRR1044559 1 0.0000 0.978 1.000 0 0.000
#> SRR1044561 3 0.0000 0.990 0.000 0 1.000
#> SRR1044560 2 0.0000 1.000 0.000 1 0.000
#> SRR1044562 1 0.0000 0.978 1.000 0 0.000
#> SRR1044563 3 0.0000 0.990 0.000 0 1.000
#> SRR1044564 1 0.0000 0.978 1.000 0 0.000
#> SRR1044565 2 0.0000 1.000 0.000 1 0.000
#> SRR1044566 2 0.0000 1.000 0.000 1 0.000
#> SRR1044567 1 0.0000 0.978 1.000 0 0.000
#> SRR1044568 3 0.0747 0.977 0.016 0 0.984
#> SRR1044569 1 0.0000 0.978 1.000 0 0.000
#> SRR1044570 1 0.0000 0.978 1.000 0 0.000
#> SRR1044571 1 0.0000 0.978 1.000 0 0.000
#> SRR1044572 1 0.0000 0.978 1.000 0 0.000
#> SRR1044573 1 0.0000 0.978 1.000 0 0.000
#> SRR1044574 1 0.0000 0.978 1.000 0 0.000
#> SRR1044575 1 0.0000 0.978 1.000 0 0.000
#> SRR1044576 2 0.0000 1.000 0.000 1 0.000
#> SRR1044577 2 0.0000 1.000 0.000 1 0.000
#> SRR1044578 2 0.0000 1.000 0.000 1 0.000
#> SRR1044579 3 0.0000 0.990 0.000 0 1.000
#> SRR1044580 1 0.5591 0.576 0.696 0 0.304
#> SRR1044581 3 0.0000 0.990 0.000 0 1.000
#> SRR1044582 1 0.0000 0.978 1.000 0 0.000
#> SRR1044583 3 0.0000 0.990 0.000 0 1.000
#> SRR1044584 3 0.3686 0.837 0.140 0 0.860
#> SRR1044585 3 0.0000 0.990 0.000 0 1.000
#> SRR1044586 1 0.0000 0.978 1.000 0 0.000
#> SRR1044587 3 0.0000 0.990 0.000 0 1.000
#> SRR1044588 3 0.0000 0.990 0.000 0 1.000
#> SRR1044589 3 0.0000 0.990 0.000 0 1.000
#> SRR1044590 3 0.0000 0.990 0.000 0 1.000
#> SRR1044591 3 0.0000 0.990 0.000 0 1.000
#> SRR1044592 3 0.0000 0.990 0.000 0 1.000
#> SRR1044593 3 0.0000 0.990 0.000 0 1.000
#> SRR1044594 3 0.0000 0.990 0.000 0 1.000
#> SRR1044595 1 0.5497 0.601 0.708 0 0.292
#> SRR1044596 3 0.0237 0.988 0.004 0 0.996
#> SRR1044597 1 0.5560 0.581 0.700 0 0.300
#> SRR1044598 1 0.0000 0.978 1.000 0 0.000
#> SRR1044599 1 0.0000 0.978 1.000 0 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044416 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044417 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044418 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044420 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044419 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044421 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044422 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044423 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044424 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044425 4 0.3569 0.7581 0.196 0.000 0.000 0.804
#> SRR1044426 1 0.3355 0.8078 0.836 0.000 0.004 0.160
#> SRR1044427 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044428 1 0.0188 0.9738 0.996 0.000 0.004 0.000
#> SRR1044429 1 0.1576 0.9307 0.948 0.000 0.004 0.048
#> SRR1044430 1 0.0188 0.9738 0.996 0.000 0.004 0.000
#> SRR1044431 1 0.0376 0.9716 0.992 0.000 0.004 0.004
#> SRR1044433 4 0.0592 0.9712 0.000 0.000 0.016 0.984
#> SRR1044432 1 0.0188 0.9738 0.996 0.000 0.004 0.000
#> SRR1044434 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044435 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044436 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044437 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044439 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044438 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044440 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044441 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044442 4 0.0524 0.9740 0.008 0.000 0.004 0.988
#> SRR1044443 4 0.4624 0.5080 0.000 0.000 0.340 0.660
#> SRR1044444 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044445 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044446 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044447 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044449 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044448 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044450 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044451 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044452 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044453 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044454 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044455 3 0.2408 0.8760 0.000 0.104 0.896 0.000
#> SRR1044456 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044457 3 0.2216 0.8876 0.000 0.092 0.908 0.000
#> SRR1044458 2 0.4164 0.6332 0.000 0.736 0.264 0.000
#> SRR1044459 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044460 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044461 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044462 1 0.2654 0.8699 0.888 0.000 0.004 0.108
#> SRR1044463 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044464 4 0.0592 0.9690 0.016 0.000 0.000 0.984
#> SRR1044466 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044465 1 0.0188 0.9738 0.996 0.000 0.004 0.000
#> SRR1044467 1 0.0188 0.9738 0.996 0.000 0.004 0.000
#> SRR1044468 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044469 3 0.3801 0.7350 0.000 0.220 0.780 0.000
#> SRR1044470 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044471 1 0.0188 0.9738 0.996 0.000 0.004 0.000
#> SRR1044472 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044473 1 0.0188 0.9738 0.996 0.000 0.004 0.000
#> SRR1044474 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044475 3 0.3801 0.7350 0.000 0.220 0.780 0.000
#> SRR1044476 2 0.2868 0.8281 0.000 0.864 0.136 0.000
#> SRR1044477 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044478 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044479 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044480 4 0.1389 0.9375 0.048 0.000 0.000 0.952
#> SRR1044481 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044482 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044483 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044484 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044486 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044485 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044487 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044488 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044489 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044490 1 0.0188 0.9738 0.996 0.000 0.004 0.000
#> SRR1044491 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044492 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044493 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044494 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044496 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044495 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044497 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044499 3 0.4967 0.2028 0.000 0.452 0.548 0.000
#> SRR1044498 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044500 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044501 2 0.4072 0.6553 0.000 0.748 0.252 0.000
#> SRR1044502 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044503 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044504 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044505 1 0.0657 0.9648 0.984 0.000 0.004 0.012
#> SRR1044506 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044507 4 0.1042 0.9628 0.020 0.000 0.008 0.972
#> SRR1044508 4 0.1004 0.9640 0.004 0.000 0.024 0.972
#> SRR1044509 4 0.1004 0.9640 0.004 0.000 0.024 0.972
#> SRR1044510 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044511 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044512 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044513 3 0.1118 0.9315 0.000 0.036 0.964 0.000
#> SRR1044514 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044515 3 0.1022 0.9344 0.000 0.032 0.968 0.000
#> SRR1044516 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044517 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044518 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044519 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044520 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044521 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044522 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044523 2 0.4998 -0.0175 0.000 0.512 0.488 0.000
#> SRR1044524 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044525 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044526 1 0.0376 0.9717 0.992 0.000 0.004 0.004
#> SRR1044527 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044528 2 0.2345 0.8663 0.000 0.900 0.100 0.000
#> SRR1044529 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044530 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044531 1 0.0188 0.9738 0.996 0.000 0.004 0.000
#> SRR1044533 1 0.0188 0.9738 0.996 0.000 0.004 0.000
#> SRR1044532 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044534 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044535 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044536 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044537 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044538 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044539 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044540 1 0.0188 0.9738 0.996 0.000 0.004 0.000
#> SRR1044541 3 0.4356 0.6021 0.000 0.292 0.708 0.000
#> SRR1044542 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044543 1 0.0376 0.9716 0.992 0.000 0.004 0.004
#> SRR1044544 3 0.1474 0.9201 0.000 0.052 0.948 0.000
#> SRR1044545 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044546 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044547 4 0.0817 0.9609 0.024 0.000 0.000 0.976
#> SRR1044548 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044549 2 0.3610 0.7334 0.000 0.800 0.200 0.000
#> SRR1044550 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044551 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044552 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044553 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044554 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044555 3 0.0336 0.9490 0.000 0.008 0.992 0.000
#> SRR1044556 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044557 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044558 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044559 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044561 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044560 2 0.2921 0.8232 0.000 0.860 0.140 0.000
#> SRR1044562 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044563 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044564 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044565 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044566 2 0.2216 0.8773 0.000 0.908 0.092 0.000
#> SRR1044567 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044568 4 0.0469 0.9720 0.012 0.000 0.000 0.988
#> SRR1044569 1 0.0188 0.9738 0.996 0.000 0.004 0.000
#> SRR1044570 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044571 1 0.0188 0.9738 0.996 0.000 0.004 0.000
#> SRR1044572 1 0.0188 0.9738 0.996 0.000 0.004 0.000
#> SRR1044573 1 0.0188 0.9738 0.996 0.000 0.004 0.000
#> SRR1044574 1 0.0188 0.9738 0.996 0.000 0.004 0.000
#> SRR1044575 1 0.0188 0.9738 0.996 0.000 0.004 0.000
#> SRR1044576 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044577 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044578 2 0.0000 0.9612 0.000 1.000 0.000 0.000
#> SRR1044579 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044580 1 0.4761 0.5170 0.664 0.000 0.004 0.332
#> SRR1044581 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044582 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044583 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044584 4 0.2704 0.8482 0.124 0.000 0.000 0.876
#> SRR1044585 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044586 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044587 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044588 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044589 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044590 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044591 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044592 4 0.0921 0.9625 0.000 0.000 0.028 0.972
#> SRR1044593 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044594 4 0.0000 0.9801 0.000 0.000 0.000 1.000
#> SRR1044595 1 0.4482 0.6423 0.728 0.000 0.008 0.264
#> SRR1044596 4 0.0376 0.9764 0.004 0.000 0.004 0.992
#> SRR1044597 1 0.4356 0.5946 0.708 0.000 0.000 0.292
#> SRR1044598 1 0.0000 0.9744 1.000 0.000 0.000 0.000
#> SRR1044599 1 0.0000 0.9744 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.0162 0.965 0.000 0.996 0.000 0.000 0.004
#> SRR1044416 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044417 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044418 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044420 2 0.0162 0.965 0.000 0.996 0.000 0.000 0.004
#> SRR1044419 2 0.0290 0.963 0.000 0.992 0.000 0.000 0.008
#> SRR1044421 2 0.0162 0.965 0.000 0.996 0.000 0.000 0.004
#> SRR1044422 2 0.0162 0.965 0.000 0.996 0.000 0.000 0.004
#> SRR1044423 2 0.0162 0.965 0.000 0.996 0.000 0.000 0.004
#> SRR1044424 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044425 4 0.4901 0.390 0.216 0.000 0.000 0.700 0.084
#> SRR1044426 1 0.3885 0.688 0.724 0.000 0.000 0.008 0.268
#> SRR1044427 1 0.3480 0.826 0.752 0.000 0.000 0.000 0.248
#> SRR1044428 1 0.2377 0.846 0.872 0.000 0.000 0.000 0.128
#> SRR1044429 1 0.2848 0.824 0.868 0.000 0.000 0.028 0.104
#> SRR1044430 1 0.2127 0.841 0.892 0.000 0.000 0.000 0.108
#> SRR1044431 1 0.2358 0.838 0.888 0.000 0.000 0.008 0.104
#> SRR1044433 5 0.3966 0.892 0.000 0.000 0.000 0.336 0.664
#> SRR1044432 1 0.2230 0.844 0.884 0.000 0.000 0.000 0.116
#> SRR1044434 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044435 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044436 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044437 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044439 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044438 4 0.0162 0.951 0.000 0.000 0.000 0.996 0.004
#> SRR1044440 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044441 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044442 5 0.3966 0.892 0.000 0.000 0.000 0.336 0.664
#> SRR1044443 5 0.5018 0.836 0.000 0.000 0.068 0.268 0.664
#> SRR1044444 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044445 4 0.1043 0.927 0.000 0.000 0.000 0.960 0.040
#> SRR1044446 3 0.0000 0.922 0.000 0.000 1.000 0.000 0.000
#> SRR1044447 3 0.0000 0.922 0.000 0.000 1.000 0.000 0.000
#> SRR1044449 3 0.0000 0.922 0.000 0.000 1.000 0.000 0.000
#> SRR1044448 3 0.0000 0.922 0.000 0.000 1.000 0.000 0.000
#> SRR1044450 3 0.0000 0.922 0.000 0.000 1.000 0.000 0.000
#> SRR1044451 3 0.0000 0.922 0.000 0.000 1.000 0.000 0.000
#> SRR1044452 3 0.0290 0.920 0.000 0.000 0.992 0.000 0.008
#> SRR1044453 3 0.0290 0.920 0.000 0.000 0.992 0.000 0.008
#> SRR1044454 3 0.0290 0.920 0.000 0.000 0.992 0.000 0.008
#> SRR1044455 3 0.2077 0.848 0.000 0.084 0.908 0.000 0.008
#> SRR1044456 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044457 3 0.1701 0.882 0.000 0.048 0.936 0.000 0.016
#> SRR1044458 2 0.3992 0.617 0.000 0.720 0.268 0.000 0.012
#> SRR1044459 3 0.0162 0.921 0.000 0.000 0.996 0.000 0.004
#> SRR1044460 2 0.0162 0.965 0.000 0.996 0.000 0.000 0.004
#> SRR1044461 2 0.0404 0.961 0.000 0.988 0.000 0.000 0.012
#> SRR1044462 1 0.5923 0.679 0.572 0.000 0.000 0.140 0.288
#> SRR1044463 1 0.0290 0.853 0.992 0.000 0.000 0.000 0.008
#> SRR1044464 4 0.1907 0.879 0.028 0.000 0.000 0.928 0.044
#> SRR1044466 1 0.0290 0.853 0.992 0.000 0.000 0.000 0.008
#> SRR1044465 1 0.2074 0.841 0.896 0.000 0.000 0.000 0.104
#> SRR1044467 1 0.2074 0.841 0.896 0.000 0.000 0.000 0.104
#> SRR1044468 2 0.0162 0.965 0.000 0.996 0.000 0.000 0.004
#> SRR1044469 3 0.3455 0.706 0.000 0.208 0.784 0.000 0.008
#> SRR1044470 1 0.0703 0.855 0.976 0.000 0.000 0.000 0.024
#> SRR1044471 1 0.2179 0.843 0.888 0.000 0.000 0.000 0.112
#> SRR1044472 1 0.0703 0.852 0.976 0.000 0.000 0.000 0.024
#> SRR1044473 1 0.2230 0.844 0.884 0.000 0.000 0.000 0.116
#> SRR1044474 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044475 3 0.3455 0.706 0.000 0.208 0.784 0.000 0.008
#> SRR1044476 2 0.2929 0.809 0.000 0.840 0.152 0.000 0.008
#> SRR1044477 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044478 2 0.0290 0.963 0.000 0.992 0.000 0.000 0.008
#> SRR1044479 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044480 4 0.2344 0.820 0.064 0.000 0.000 0.904 0.032
#> SRR1044481 1 0.3143 0.822 0.796 0.000 0.000 0.000 0.204
#> SRR1044482 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044483 4 0.0162 0.951 0.000 0.000 0.000 0.996 0.004
#> SRR1044484 1 0.3210 0.818 0.788 0.000 0.000 0.000 0.212
#> SRR1044486 1 0.3210 0.818 0.788 0.000 0.000 0.000 0.212
#> SRR1044485 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044487 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044488 2 0.0162 0.965 0.000 0.996 0.000 0.000 0.004
#> SRR1044489 2 0.0162 0.965 0.000 0.996 0.000 0.000 0.004
#> SRR1044490 1 0.2074 0.841 0.896 0.000 0.000 0.000 0.104
#> SRR1044491 1 0.3074 0.825 0.804 0.000 0.000 0.000 0.196
#> SRR1044492 1 0.0703 0.856 0.976 0.000 0.000 0.000 0.024
#> SRR1044493 1 0.1197 0.852 0.952 0.000 0.000 0.000 0.048
#> SRR1044494 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044496 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044495 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044497 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044499 3 0.4597 0.277 0.000 0.424 0.564 0.000 0.012
#> SRR1044498 1 0.3242 0.820 0.784 0.000 0.000 0.000 0.216
#> SRR1044500 2 0.0162 0.965 0.000 0.996 0.000 0.000 0.004
#> SRR1044501 2 0.3890 0.648 0.000 0.736 0.252 0.000 0.012
#> SRR1044502 3 0.0000 0.922 0.000 0.000 1.000 0.000 0.000
#> SRR1044503 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044504 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044505 1 0.4797 0.795 0.660 0.000 0.000 0.044 0.296
#> SRR1044506 4 0.1043 0.927 0.000 0.000 0.000 0.960 0.040
#> SRR1044507 5 0.3508 0.830 0.000 0.000 0.000 0.252 0.748
#> SRR1044508 5 0.3966 0.892 0.000 0.000 0.000 0.336 0.664
#> SRR1044509 5 0.3966 0.892 0.000 0.000 0.000 0.336 0.664
#> SRR1044510 3 0.0000 0.922 0.000 0.000 1.000 0.000 0.000
#> SRR1044511 3 0.0000 0.922 0.000 0.000 1.000 0.000 0.000
#> SRR1044512 3 0.0000 0.922 0.000 0.000 1.000 0.000 0.000
#> SRR1044513 3 0.0703 0.906 0.000 0.024 0.976 0.000 0.000
#> SRR1044514 3 0.0000 0.922 0.000 0.000 1.000 0.000 0.000
#> SRR1044515 3 0.0898 0.909 0.000 0.020 0.972 0.000 0.008
#> SRR1044516 2 0.0162 0.965 0.000 0.996 0.000 0.000 0.004
#> SRR1044517 3 0.0000 0.922 0.000 0.000 1.000 0.000 0.000
#> SRR1044518 3 0.0000 0.922 0.000 0.000 1.000 0.000 0.000
#> SRR1044519 3 0.0000 0.922 0.000 0.000 1.000 0.000 0.000
#> SRR1044520 3 0.0000 0.922 0.000 0.000 1.000 0.000 0.000
#> SRR1044521 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044522 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044523 3 0.4702 0.254 0.000 0.432 0.552 0.000 0.016
#> SRR1044524 3 0.0290 0.920 0.000 0.000 0.992 0.000 0.008
#> SRR1044525 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044526 1 0.4430 0.807 0.708 0.000 0.000 0.036 0.256
#> SRR1044527 2 0.0162 0.963 0.000 0.996 0.000 0.000 0.004
#> SRR1044528 2 0.2536 0.838 0.000 0.868 0.128 0.000 0.004
#> SRR1044529 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044530 1 0.0290 0.853 0.992 0.000 0.000 0.000 0.008
#> SRR1044531 1 0.2020 0.842 0.900 0.000 0.000 0.000 0.100
#> SRR1044533 1 0.2074 0.841 0.896 0.000 0.000 0.000 0.104
#> SRR1044532 1 0.0880 0.854 0.968 0.000 0.000 0.000 0.032
#> SRR1044534 2 0.0162 0.965 0.000 0.996 0.000 0.000 0.004
#> SRR1044535 3 0.0162 0.921 0.000 0.000 0.996 0.000 0.004
#> SRR1044536 2 0.0162 0.965 0.000 0.996 0.000 0.000 0.004
#> SRR1044537 1 0.3177 0.819 0.792 0.000 0.000 0.000 0.208
#> SRR1044538 1 0.0703 0.852 0.976 0.000 0.000 0.000 0.024
#> SRR1044539 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044540 1 0.2074 0.841 0.896 0.000 0.000 0.000 0.104
#> SRR1044541 3 0.3890 0.641 0.000 0.252 0.736 0.000 0.012
#> SRR1044542 1 0.1270 0.852 0.948 0.000 0.000 0.000 0.052
#> SRR1044543 1 0.2074 0.841 0.896 0.000 0.000 0.000 0.104
#> SRR1044544 3 0.1106 0.904 0.000 0.024 0.964 0.000 0.012
#> SRR1044545 4 0.0880 0.921 0.000 0.000 0.000 0.968 0.032
#> SRR1044546 1 0.3242 0.817 0.784 0.000 0.000 0.000 0.216
#> SRR1044547 4 0.2798 0.722 0.008 0.000 0.000 0.852 0.140
#> SRR1044548 1 0.3242 0.817 0.784 0.000 0.000 0.000 0.216
#> SRR1044549 2 0.3398 0.705 0.000 0.780 0.216 0.000 0.004
#> SRR1044550 2 0.0162 0.965 0.000 0.996 0.000 0.000 0.004
#> SRR1044551 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044552 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044553 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044554 1 0.3242 0.817 0.784 0.000 0.000 0.000 0.216
#> SRR1044555 3 0.0290 0.920 0.000 0.000 0.992 0.000 0.008
#> SRR1044556 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044557 1 0.3242 0.817 0.784 0.000 0.000 0.000 0.216
#> SRR1044558 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044559 1 0.3242 0.817 0.784 0.000 0.000 0.000 0.216
#> SRR1044561 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044560 2 0.2971 0.804 0.000 0.836 0.156 0.000 0.008
#> SRR1044562 1 0.3177 0.819 0.792 0.000 0.000 0.000 0.208
#> SRR1044563 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044564 1 0.3177 0.823 0.792 0.000 0.000 0.000 0.208
#> SRR1044565 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044566 2 0.2358 0.866 0.000 0.888 0.104 0.000 0.008
#> SRR1044567 1 0.0794 0.852 0.972 0.000 0.000 0.000 0.028
#> SRR1044568 4 0.1117 0.917 0.016 0.000 0.000 0.964 0.020
#> SRR1044569 1 0.2127 0.842 0.892 0.000 0.000 0.000 0.108
#> SRR1044570 1 0.1410 0.852 0.940 0.000 0.000 0.000 0.060
#> SRR1044571 1 0.2074 0.841 0.896 0.000 0.000 0.000 0.104
#> SRR1044572 1 0.2074 0.841 0.896 0.000 0.000 0.000 0.104
#> SRR1044573 1 0.3366 0.840 0.768 0.000 0.000 0.000 0.232
#> SRR1044574 1 0.2074 0.841 0.896 0.000 0.000 0.000 0.104
#> SRR1044575 1 0.2074 0.841 0.896 0.000 0.000 0.000 0.104
#> SRR1044576 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044577 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044578 2 0.0000 0.966 0.000 1.000 0.000 0.000 0.000
#> SRR1044579 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044580 1 0.5952 0.139 0.480 0.000 0.000 0.412 0.108
#> SRR1044581 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044582 1 0.3242 0.817 0.784 0.000 0.000 0.000 0.216
#> SRR1044583 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044584 4 0.1768 0.848 0.072 0.000 0.000 0.924 0.004
#> SRR1044585 4 0.0000 0.954 0.000 0.000 0.000 1.000 0.000
#> SRR1044586 1 0.3210 0.818 0.788 0.000 0.000 0.000 0.212
#> SRR1044587 4 0.1043 0.927 0.000 0.000 0.000 0.960 0.040
#> SRR1044588 4 0.1043 0.927 0.000 0.000 0.000 0.960 0.040
#> SRR1044589 4 0.1043 0.927 0.000 0.000 0.000 0.960 0.040
#> SRR1044590 4 0.1043 0.927 0.000 0.000 0.000 0.960 0.040
#> SRR1044591 4 0.1043 0.927 0.000 0.000 0.000 0.960 0.040
#> SRR1044592 5 0.3966 0.892 0.000 0.000 0.000 0.336 0.664
#> SRR1044593 4 0.1043 0.927 0.000 0.000 0.000 0.960 0.040
#> SRR1044594 4 0.1043 0.927 0.000 0.000 0.000 0.960 0.040
#> SRR1044595 5 0.3141 0.538 0.152 0.000 0.000 0.016 0.832
#> SRR1044596 5 0.3966 0.892 0.000 0.000 0.000 0.336 0.664
#> SRR1044597 1 0.6526 0.293 0.468 0.000 0.000 0.216 0.316
#> SRR1044598 1 0.3242 0.817 0.784 0.000 0.000 0.000 0.216
#> SRR1044599 1 0.3242 0.817 0.784 0.000 0.000 0.000 0.216
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.1408 0.9317 0.020 0.944 0.000 0.000 0.000 0.036
#> SRR1044416 2 0.0000 0.9470 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044417 2 0.0000 0.9470 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044418 2 0.0000 0.9470 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044420 2 0.0622 0.9456 0.012 0.980 0.000 0.000 0.000 0.008
#> SRR1044419 2 0.2451 0.8937 0.060 0.884 0.000 0.000 0.000 0.056
#> SRR1044421 2 0.0993 0.9417 0.024 0.964 0.000 0.000 0.000 0.012
#> SRR1044422 2 0.1334 0.9337 0.020 0.948 0.000 0.000 0.000 0.032
#> SRR1044423 2 0.0972 0.9417 0.028 0.964 0.000 0.000 0.000 0.008
#> SRR1044424 2 0.0508 0.9466 0.012 0.984 0.000 0.000 0.000 0.004
#> SRR1044425 1 0.4264 -0.0560 0.492 0.000 0.000 0.492 0.016 0.000
#> SRR1044426 1 0.2420 0.7622 0.884 0.000 0.000 0.000 0.076 0.040
#> SRR1044427 5 0.2454 0.6487 0.160 0.000 0.000 0.000 0.840 0.000
#> SRR1044428 1 0.2738 0.7506 0.820 0.000 0.000 0.000 0.176 0.004
#> SRR1044429 1 0.2118 0.7877 0.888 0.000 0.000 0.008 0.104 0.000
#> SRR1044430 1 0.2278 0.7864 0.868 0.000 0.000 0.000 0.128 0.004
#> SRR1044431 1 0.1910 0.7921 0.892 0.000 0.000 0.000 0.108 0.000
#> SRR1044433 6 0.1910 0.9699 0.000 0.000 0.000 0.108 0.000 0.892
#> SRR1044432 1 0.2520 0.7674 0.844 0.000 0.000 0.000 0.152 0.004
#> SRR1044434 4 0.0000 0.9682 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044435 4 0.0000 0.9682 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044436 4 0.0405 0.9651 0.008 0.000 0.000 0.988 0.000 0.004
#> SRR1044437 4 0.0000 0.9682 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044439 4 0.0405 0.9651 0.008 0.000 0.000 0.988 0.000 0.004
#> SRR1044438 4 0.0551 0.9640 0.008 0.000 0.000 0.984 0.004 0.004
#> SRR1044440 4 0.0000 0.9682 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044441 4 0.0000 0.9682 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044442 6 0.1910 0.9699 0.000 0.000 0.000 0.108 0.000 0.892
#> SRR1044443 6 0.2199 0.9543 0.000 0.000 0.020 0.088 0.000 0.892
#> SRR1044444 4 0.0146 0.9676 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044445 4 0.0909 0.9555 0.012 0.000 0.000 0.968 0.000 0.020
#> SRR1044446 3 0.0260 0.8977 0.008 0.000 0.992 0.000 0.000 0.000
#> SRR1044447 3 0.0260 0.8977 0.008 0.000 0.992 0.000 0.000 0.000
#> SRR1044449 3 0.0260 0.8977 0.008 0.000 0.992 0.000 0.000 0.000
#> SRR1044448 3 0.0260 0.8977 0.008 0.000 0.992 0.000 0.000 0.000
#> SRR1044450 3 0.0260 0.8977 0.008 0.000 0.992 0.000 0.000 0.000
#> SRR1044451 3 0.0260 0.8977 0.008 0.000 0.992 0.000 0.000 0.000
#> SRR1044452 3 0.1003 0.8900 0.020 0.000 0.964 0.000 0.000 0.016
#> SRR1044453 3 0.1088 0.8885 0.024 0.000 0.960 0.000 0.000 0.016
#> SRR1044454 3 0.1168 0.8869 0.028 0.000 0.956 0.000 0.000 0.016
#> SRR1044455 3 0.3275 0.8030 0.032 0.088 0.844 0.000 0.000 0.036
#> SRR1044456 2 0.0000 0.9470 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044457 3 0.3516 0.8078 0.076 0.036 0.832 0.000 0.000 0.056
#> SRR1044458 2 0.5211 0.6475 0.076 0.680 0.188 0.000 0.000 0.056
#> SRR1044459 3 0.0146 0.8980 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1044460 2 0.0622 0.9457 0.008 0.980 0.000 0.000 0.000 0.012
#> SRR1044461 2 0.2625 0.8858 0.072 0.872 0.000 0.000 0.000 0.056
#> SRR1044462 5 0.5150 0.3231 0.324 0.000 0.000 0.092 0.580 0.004
#> SRR1044463 1 0.4726 0.2818 0.528 0.000 0.000 0.000 0.424 0.048
#> SRR1044464 4 0.2999 0.8439 0.068 0.000 0.000 0.856 0.008 0.068
#> SRR1044466 1 0.4753 0.1999 0.496 0.000 0.000 0.000 0.456 0.048
#> SRR1044465 1 0.1957 0.7916 0.888 0.000 0.000 0.000 0.112 0.000
#> SRR1044467 1 0.1910 0.7927 0.892 0.000 0.000 0.000 0.108 0.000
#> SRR1044468 2 0.0993 0.9417 0.024 0.964 0.000 0.000 0.000 0.012
#> SRR1044469 3 0.4913 0.6433 0.060 0.200 0.696 0.000 0.000 0.044
#> SRR1044470 1 0.4742 0.2416 0.512 0.000 0.000 0.000 0.440 0.048
#> SRR1044471 1 0.2092 0.7873 0.876 0.000 0.000 0.000 0.124 0.000
#> SRR1044472 1 0.4757 0.1568 0.480 0.000 0.000 0.000 0.472 0.048
#> SRR1044473 1 0.2527 0.7541 0.832 0.000 0.000 0.000 0.168 0.000
#> SRR1044474 2 0.0000 0.9470 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044475 3 0.4851 0.6460 0.060 0.200 0.700 0.000 0.000 0.040
#> SRR1044476 2 0.4394 0.7808 0.068 0.768 0.108 0.000 0.000 0.056
#> SRR1044477 2 0.0000 0.9470 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044478 2 0.2384 0.8972 0.064 0.888 0.000 0.000 0.000 0.048
#> SRR1044479 2 0.0000 0.9470 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044480 4 0.2594 0.8668 0.056 0.000 0.000 0.880 0.060 0.004
#> SRR1044481 5 0.1007 0.7652 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1044482 2 0.0000 0.9470 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044483 4 0.0508 0.9635 0.012 0.000 0.000 0.984 0.000 0.004
#> SRR1044484 5 0.0363 0.7753 0.012 0.000 0.000 0.000 0.988 0.000
#> SRR1044486 5 0.0146 0.7767 0.004 0.000 0.000 0.000 0.996 0.000
#> SRR1044485 2 0.0000 0.9470 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044487 2 0.0000 0.9470 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044488 2 0.0909 0.9428 0.020 0.968 0.000 0.000 0.000 0.012
#> SRR1044489 2 0.0909 0.9428 0.020 0.968 0.000 0.000 0.000 0.012
#> SRR1044490 1 0.1910 0.7927 0.892 0.000 0.000 0.000 0.108 0.000
#> SRR1044491 5 0.1075 0.7539 0.048 0.000 0.000 0.000 0.952 0.000
#> SRR1044492 1 0.4261 0.3608 0.572 0.000 0.000 0.000 0.408 0.020
#> SRR1044493 5 0.4332 0.3259 0.316 0.000 0.000 0.000 0.644 0.040
#> SRR1044494 2 0.0000 0.9470 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044496 2 0.0000 0.9470 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044495 2 0.0000 0.9470 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044497 4 0.0146 0.9676 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044499 3 0.6019 0.1889 0.076 0.396 0.472 0.000 0.000 0.056
#> SRR1044498 5 0.0260 0.7766 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1044500 2 0.0717 0.9450 0.016 0.976 0.000 0.000 0.000 0.008
#> SRR1044501 2 0.5052 0.6715 0.068 0.696 0.180 0.000 0.000 0.056
#> SRR1044502 3 0.0000 0.8982 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044503 4 0.0000 0.9682 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044504 4 0.0000 0.9682 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044505 5 0.4256 0.1748 0.420 0.000 0.000 0.012 0.564 0.004
#> SRR1044506 4 0.0909 0.9555 0.012 0.000 0.000 0.968 0.000 0.020
#> SRR1044507 6 0.2308 0.9343 0.000 0.000 0.000 0.068 0.040 0.892
#> SRR1044508 6 0.1910 0.9699 0.000 0.000 0.000 0.108 0.000 0.892
#> SRR1044509 6 0.1910 0.9699 0.000 0.000 0.000 0.108 0.000 0.892
#> SRR1044510 3 0.0000 0.8982 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044511 3 0.0000 0.8982 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044512 3 0.0000 0.8982 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044513 3 0.1151 0.8782 0.012 0.032 0.956 0.000 0.000 0.000
#> SRR1044514 3 0.0000 0.8982 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044515 3 0.1780 0.8740 0.028 0.028 0.932 0.000 0.000 0.012
#> SRR1044516 2 0.0909 0.9436 0.020 0.968 0.000 0.000 0.000 0.012
#> SRR1044517 3 0.0000 0.8982 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044518 3 0.0000 0.8982 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044519 3 0.0260 0.8977 0.008 0.000 0.992 0.000 0.000 0.000
#> SRR1044520 3 0.0260 0.8977 0.008 0.000 0.992 0.000 0.000 0.000
#> SRR1044521 2 0.0405 0.9465 0.004 0.988 0.000 0.000 0.000 0.008
#> SRR1044522 2 0.0000 0.9470 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044523 3 0.5299 0.2446 0.052 0.404 0.520 0.000 0.000 0.024
#> SRR1044524 3 0.0820 0.8924 0.016 0.000 0.972 0.000 0.000 0.012
#> SRR1044525 4 0.0000 0.9682 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044526 5 0.4134 0.3717 0.340 0.000 0.000 0.016 0.640 0.004
#> SRR1044527 2 0.0363 0.9452 0.012 0.988 0.000 0.000 0.000 0.000
#> SRR1044528 2 0.2667 0.8178 0.020 0.852 0.128 0.000 0.000 0.000
#> SRR1044529 2 0.0000 0.9470 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044530 1 0.4751 0.2136 0.500 0.000 0.000 0.000 0.452 0.048
#> SRR1044531 1 0.2520 0.7700 0.844 0.000 0.000 0.000 0.152 0.004
#> SRR1044533 1 0.1957 0.7929 0.888 0.000 0.000 0.000 0.112 0.000
#> SRR1044532 5 0.4715 0.0217 0.416 0.000 0.000 0.000 0.536 0.048
#> SRR1044534 2 0.0508 0.9464 0.012 0.984 0.000 0.000 0.000 0.004
#> SRR1044535 3 0.0260 0.8972 0.008 0.000 0.992 0.000 0.000 0.000
#> SRR1044536 2 0.0820 0.9439 0.016 0.972 0.000 0.000 0.000 0.012
#> SRR1044537 5 0.1204 0.7591 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1044538 5 0.4703 0.0487 0.408 0.000 0.000 0.000 0.544 0.048
#> SRR1044539 4 0.0508 0.9635 0.012 0.000 0.000 0.984 0.000 0.004
#> SRR1044540 1 0.1863 0.7913 0.896 0.000 0.000 0.000 0.104 0.000
#> SRR1044541 3 0.5398 0.5863 0.076 0.216 0.652 0.000 0.000 0.056
#> SRR1044542 5 0.4467 0.3071 0.320 0.000 0.000 0.000 0.632 0.048
#> SRR1044543 1 0.1863 0.7913 0.896 0.000 0.000 0.000 0.104 0.000
#> SRR1044544 3 0.2823 0.8375 0.068 0.016 0.872 0.000 0.000 0.044
#> SRR1044545 4 0.1296 0.9381 0.012 0.000 0.000 0.952 0.032 0.004
#> SRR1044546 5 0.0000 0.7776 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1044547 4 0.3219 0.7195 0.012 0.000 0.000 0.792 0.192 0.004
#> SRR1044548 5 0.0000 0.7776 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1044549 2 0.3586 0.6785 0.028 0.756 0.216 0.000 0.000 0.000
#> SRR1044550 2 0.0909 0.9428 0.020 0.968 0.000 0.000 0.000 0.012
#> SRR1044551 2 0.0260 0.9467 0.008 0.992 0.000 0.000 0.000 0.000
#> SRR1044552 4 0.0000 0.9682 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044553 4 0.0146 0.9673 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044554 5 0.0146 0.7767 0.004 0.000 0.000 0.000 0.996 0.000
#> SRR1044555 3 0.0909 0.8913 0.020 0.000 0.968 0.000 0.000 0.012
#> SRR1044556 4 0.0405 0.9651 0.008 0.000 0.000 0.988 0.000 0.004
#> SRR1044557 5 0.0000 0.7776 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1044558 4 0.0000 0.9682 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044559 5 0.0000 0.7776 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1044561 4 0.0000 0.9682 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044560 2 0.4467 0.7691 0.064 0.760 0.120 0.000 0.000 0.056
#> SRR1044562 5 0.0713 0.7715 0.028 0.000 0.000 0.000 0.972 0.000
#> SRR1044563 4 0.0405 0.9651 0.008 0.000 0.000 0.988 0.000 0.004
#> SRR1044564 5 0.1663 0.7331 0.088 0.000 0.000 0.000 0.912 0.000
#> SRR1044565 2 0.0000 0.9470 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044566 2 0.3955 0.8199 0.064 0.804 0.076 0.000 0.000 0.056
#> SRR1044567 5 0.4682 0.0894 0.396 0.000 0.000 0.000 0.556 0.048
#> SRR1044568 4 0.1732 0.9058 0.072 0.000 0.000 0.920 0.004 0.004
#> SRR1044569 1 0.1957 0.7916 0.888 0.000 0.000 0.000 0.112 0.000
#> SRR1044570 5 0.4436 0.3246 0.312 0.000 0.000 0.000 0.640 0.048
#> SRR1044571 1 0.1910 0.7927 0.892 0.000 0.000 0.000 0.108 0.000
#> SRR1044572 1 0.1957 0.7929 0.888 0.000 0.000 0.000 0.112 0.000
#> SRR1044573 1 0.3860 0.1188 0.528 0.000 0.000 0.000 0.472 0.000
#> SRR1044574 1 0.1957 0.7929 0.888 0.000 0.000 0.000 0.112 0.000
#> SRR1044575 1 0.1957 0.7929 0.888 0.000 0.000 0.000 0.112 0.000
#> SRR1044576 2 0.0000 0.9470 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044577 2 0.0000 0.9470 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044578 2 0.0000 0.9470 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044579 4 0.0000 0.9682 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044580 1 0.5115 0.3192 0.560 0.000 0.000 0.356 0.080 0.004
#> SRR1044581 4 0.0146 0.9676 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044582 5 0.0000 0.7776 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1044583 4 0.0000 0.9682 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044584 4 0.2848 0.8198 0.104 0.000 0.000 0.856 0.036 0.004
#> SRR1044585 4 0.0146 0.9676 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044586 5 0.0146 0.7767 0.004 0.000 0.000 0.000 0.996 0.000
#> SRR1044587 4 0.0909 0.9555 0.012 0.000 0.000 0.968 0.000 0.020
#> SRR1044588 4 0.0820 0.9578 0.012 0.000 0.000 0.972 0.000 0.016
#> SRR1044589 4 0.0820 0.9578 0.012 0.000 0.000 0.972 0.000 0.016
#> SRR1044590 4 0.0820 0.9578 0.012 0.000 0.000 0.972 0.000 0.016
#> SRR1044591 4 0.0909 0.9555 0.012 0.000 0.000 0.968 0.000 0.020
#> SRR1044592 6 0.1910 0.9699 0.000 0.000 0.000 0.108 0.000 0.892
#> SRR1044593 4 0.0820 0.9578 0.012 0.000 0.000 0.972 0.000 0.016
#> SRR1044594 4 0.0820 0.9578 0.012 0.000 0.000 0.972 0.000 0.016
#> SRR1044595 6 0.1584 0.8475 0.008 0.000 0.000 0.000 0.064 0.928
#> SRR1044596 6 0.1910 0.9699 0.000 0.000 0.000 0.108 0.000 0.892
#> SRR1044597 5 0.6207 0.4604 0.128 0.000 0.000 0.132 0.600 0.140
#> SRR1044598 5 0.0000 0.7776 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1044599 5 0.0000 0.7776 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)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.991 0.995 0.4935 0.508 0.508
#> 3 3 0.737 0.910 0.896 0.3052 0.835 0.676
#> 4 4 0.869 0.867 0.939 0.1443 0.918 0.760
#> 5 5 0.769 0.632 0.828 0.0487 0.954 0.831
#> 6 6 0.745 0.571 0.741 0.0370 0.906 0.643
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0.0000 1.000 0.000 1.000
#> SRR1044416 2 0.0000 1.000 0.000 1.000
#> SRR1044417 2 0.0000 1.000 0.000 1.000
#> SRR1044418 2 0.0000 1.000 0.000 1.000
#> SRR1044420 2 0.0000 1.000 0.000 1.000
#> SRR1044419 2 0.0000 1.000 0.000 1.000
#> SRR1044421 2 0.0000 1.000 0.000 1.000
#> SRR1044422 2 0.0000 1.000 0.000 1.000
#> SRR1044423 2 0.0000 1.000 0.000 1.000
#> SRR1044424 2 0.0000 1.000 0.000 1.000
#> SRR1044425 1 0.0000 0.991 1.000 0.000
#> SRR1044426 1 0.0000 0.991 1.000 0.000
#> SRR1044427 1 0.0000 0.991 1.000 0.000
#> SRR1044428 1 0.0000 0.991 1.000 0.000
#> SRR1044429 1 0.0000 0.991 1.000 0.000
#> SRR1044430 1 0.7376 0.751 0.792 0.208
#> SRR1044431 1 0.0000 0.991 1.000 0.000
#> SRR1044433 1 0.0000 0.991 1.000 0.000
#> SRR1044432 1 0.0000 0.991 1.000 0.000
#> SRR1044434 1 0.0000 0.991 1.000 0.000
#> SRR1044435 1 0.0000 0.991 1.000 0.000
#> SRR1044436 1 0.0000 0.991 1.000 0.000
#> SRR1044437 1 0.0000 0.991 1.000 0.000
#> SRR1044439 1 0.0000 0.991 1.000 0.000
#> SRR1044438 1 0.0000 0.991 1.000 0.000
#> SRR1044440 1 0.0000 0.991 1.000 0.000
#> SRR1044441 1 0.0000 0.991 1.000 0.000
#> SRR1044442 1 0.0000 0.991 1.000 0.000
#> SRR1044443 1 0.0000 0.991 1.000 0.000
#> SRR1044444 1 0.0000 0.991 1.000 0.000
#> SRR1044445 1 0.0000 0.991 1.000 0.000
#> SRR1044446 2 0.0000 1.000 0.000 1.000
#> SRR1044447 2 0.0000 1.000 0.000 1.000
#> SRR1044449 2 0.0000 1.000 0.000 1.000
#> SRR1044448 2 0.0000 1.000 0.000 1.000
#> SRR1044450 2 0.0000 1.000 0.000 1.000
#> SRR1044451 2 0.0000 1.000 0.000 1.000
#> SRR1044452 2 0.0000 1.000 0.000 1.000
#> SRR1044453 2 0.0000 1.000 0.000 1.000
#> SRR1044454 2 0.0000 1.000 0.000 1.000
#> SRR1044455 2 0.0000 1.000 0.000 1.000
#> SRR1044456 2 0.0000 1.000 0.000 1.000
#> SRR1044457 2 0.0000 1.000 0.000 1.000
#> SRR1044458 2 0.0000 1.000 0.000 1.000
#> SRR1044459 2 0.0000 1.000 0.000 1.000
#> SRR1044460 2 0.0000 1.000 0.000 1.000
#> SRR1044461 2 0.0000 1.000 0.000 1.000
#> SRR1044462 1 0.0000 0.991 1.000 0.000
#> SRR1044463 1 0.1414 0.979 0.980 0.020
#> SRR1044464 1 0.0000 0.991 1.000 0.000
#> SRR1044466 1 0.2236 0.966 0.964 0.036
#> SRR1044465 1 0.0000 0.991 1.000 0.000
#> SRR1044467 1 0.0000 0.991 1.000 0.000
#> SRR1044468 2 0.0000 1.000 0.000 1.000
#> SRR1044469 2 0.0000 1.000 0.000 1.000
#> SRR1044470 1 0.3274 0.943 0.940 0.060
#> SRR1044471 1 0.0000 0.991 1.000 0.000
#> SRR1044472 1 0.5059 0.880 0.888 0.112
#> SRR1044473 1 0.1184 0.982 0.984 0.016
#> SRR1044474 2 0.0000 1.000 0.000 1.000
#> SRR1044475 2 0.0000 1.000 0.000 1.000
#> SRR1044476 2 0.0000 1.000 0.000 1.000
#> SRR1044477 2 0.0000 1.000 0.000 1.000
#> SRR1044478 2 0.0000 1.000 0.000 1.000
#> SRR1044479 2 0.0000 1.000 0.000 1.000
#> SRR1044480 1 0.0000 0.991 1.000 0.000
#> SRR1044481 1 0.0000 0.991 1.000 0.000
#> SRR1044482 2 0.0000 1.000 0.000 1.000
#> SRR1044483 1 0.0000 0.991 1.000 0.000
#> SRR1044484 1 0.0000 0.991 1.000 0.000
#> SRR1044486 1 0.0000 0.991 1.000 0.000
#> SRR1044485 2 0.0000 1.000 0.000 1.000
#> SRR1044487 2 0.0000 1.000 0.000 1.000
#> SRR1044488 2 0.0000 1.000 0.000 1.000
#> SRR1044489 2 0.0000 1.000 0.000 1.000
#> SRR1044490 1 0.0000 0.991 1.000 0.000
#> SRR1044491 1 0.2043 0.969 0.968 0.032
#> SRR1044492 1 0.2043 0.969 0.968 0.032
#> SRR1044493 1 0.0000 0.991 1.000 0.000
#> SRR1044494 2 0.0000 1.000 0.000 1.000
#> SRR1044496 2 0.0000 1.000 0.000 1.000
#> SRR1044495 2 0.0000 1.000 0.000 1.000
#> SRR1044497 1 0.0000 0.991 1.000 0.000
#> SRR1044499 2 0.0000 1.000 0.000 1.000
#> SRR1044498 1 0.0000 0.991 1.000 0.000
#> SRR1044500 2 0.0000 1.000 0.000 1.000
#> SRR1044501 2 0.0000 1.000 0.000 1.000
#> SRR1044502 2 0.0000 1.000 0.000 1.000
#> SRR1044503 1 0.0000 0.991 1.000 0.000
#> SRR1044504 1 0.0000 0.991 1.000 0.000
#> SRR1044505 1 0.0000 0.991 1.000 0.000
#> SRR1044506 1 0.0000 0.991 1.000 0.000
#> SRR1044507 1 0.0000 0.991 1.000 0.000
#> SRR1044508 1 0.0000 0.991 1.000 0.000
#> SRR1044509 1 0.0000 0.991 1.000 0.000
#> SRR1044510 2 0.0000 1.000 0.000 1.000
#> SRR1044511 2 0.0000 1.000 0.000 1.000
#> SRR1044512 2 0.0000 1.000 0.000 1.000
#> SRR1044513 2 0.0000 1.000 0.000 1.000
#> SRR1044514 2 0.0000 1.000 0.000 1.000
#> SRR1044515 2 0.0000 1.000 0.000 1.000
#> SRR1044516 2 0.0000 1.000 0.000 1.000
#> SRR1044517 2 0.0000 1.000 0.000 1.000
#> SRR1044518 2 0.0000 1.000 0.000 1.000
#> SRR1044519 2 0.0000 1.000 0.000 1.000
#> SRR1044520 2 0.0376 0.996 0.004 0.996
#> SRR1044521 2 0.0000 1.000 0.000 1.000
#> SRR1044522 2 0.0000 1.000 0.000 1.000
#> SRR1044523 2 0.0000 1.000 0.000 1.000
#> SRR1044524 2 0.0000 1.000 0.000 1.000
#> SRR1044525 1 0.0000 0.991 1.000 0.000
#> SRR1044526 1 0.0000 0.991 1.000 0.000
#> SRR1044527 2 0.0000 1.000 0.000 1.000
#> SRR1044528 2 0.0000 1.000 0.000 1.000
#> SRR1044529 2 0.0000 1.000 0.000 1.000
#> SRR1044530 1 0.0938 0.984 0.988 0.012
#> SRR1044531 1 0.0000 0.991 1.000 0.000
#> SRR1044533 1 0.0000 0.991 1.000 0.000
#> SRR1044532 1 0.1414 0.979 0.980 0.020
#> SRR1044534 2 0.0000 1.000 0.000 1.000
#> SRR1044535 2 0.0000 1.000 0.000 1.000
#> SRR1044536 2 0.0000 1.000 0.000 1.000
#> SRR1044537 1 0.1184 0.981 0.984 0.016
#> SRR1044538 1 0.0938 0.984 0.988 0.012
#> SRR1044539 1 0.0000 0.991 1.000 0.000
#> SRR1044540 1 0.0000 0.991 1.000 0.000
#> SRR1044541 2 0.0000 1.000 0.000 1.000
#> SRR1044542 1 0.1633 0.976 0.976 0.024
#> SRR1044543 1 0.0000 0.991 1.000 0.000
#> SRR1044544 2 0.0000 1.000 0.000 1.000
#> SRR1044545 1 0.0000 0.991 1.000 0.000
#> SRR1044546 1 0.0376 0.989 0.996 0.004
#> SRR1044547 1 0.0000 0.991 1.000 0.000
#> SRR1044548 1 0.1414 0.979 0.980 0.020
#> SRR1044549 2 0.0000 1.000 0.000 1.000
#> SRR1044550 2 0.0000 1.000 0.000 1.000
#> SRR1044551 2 0.0000 1.000 0.000 1.000
#> SRR1044552 1 0.0000 0.991 1.000 0.000
#> SRR1044553 1 0.0000 0.991 1.000 0.000
#> SRR1044554 1 0.1633 0.976 0.976 0.024
#> SRR1044555 2 0.0000 1.000 0.000 1.000
#> SRR1044556 1 0.0000 0.991 1.000 0.000
#> SRR1044557 1 0.2603 0.959 0.956 0.044
#> SRR1044558 1 0.0000 0.991 1.000 0.000
#> SRR1044559 1 0.2778 0.955 0.952 0.048
#> SRR1044561 1 0.0000 0.991 1.000 0.000
#> SRR1044560 2 0.0000 1.000 0.000 1.000
#> SRR1044562 1 0.1184 0.982 0.984 0.016
#> SRR1044563 1 0.0000 0.991 1.000 0.000
#> SRR1044564 1 0.0000 0.991 1.000 0.000
#> SRR1044565 2 0.0000 1.000 0.000 1.000
#> SRR1044566 2 0.0000 1.000 0.000 1.000
#> SRR1044567 1 0.0672 0.986 0.992 0.008
#> SRR1044568 1 0.0000 0.991 1.000 0.000
#> SRR1044569 1 0.0000 0.991 1.000 0.000
#> SRR1044570 1 0.1633 0.976 0.976 0.024
#> SRR1044571 1 0.0000 0.991 1.000 0.000
#> SRR1044572 1 0.0000 0.991 1.000 0.000
#> SRR1044573 1 0.0000 0.991 1.000 0.000
#> SRR1044574 1 0.0000 0.991 1.000 0.000
#> SRR1044575 1 0.0000 0.991 1.000 0.000
#> SRR1044576 2 0.0000 1.000 0.000 1.000
#> SRR1044577 2 0.0000 1.000 0.000 1.000
#> SRR1044578 2 0.0000 1.000 0.000 1.000
#> SRR1044579 1 0.0000 0.991 1.000 0.000
#> SRR1044580 1 0.0000 0.991 1.000 0.000
#> SRR1044581 1 0.0000 0.991 1.000 0.000
#> SRR1044582 1 0.0000 0.991 1.000 0.000
#> SRR1044583 1 0.0000 0.991 1.000 0.000
#> SRR1044584 1 0.0000 0.991 1.000 0.000
#> SRR1044585 1 0.0000 0.991 1.000 0.000
#> SRR1044586 1 0.0000 0.991 1.000 0.000
#> SRR1044587 1 0.0000 0.991 1.000 0.000
#> SRR1044588 1 0.0000 0.991 1.000 0.000
#> SRR1044589 1 0.0000 0.991 1.000 0.000
#> SRR1044590 1 0.0000 0.991 1.000 0.000
#> SRR1044591 1 0.0000 0.991 1.000 0.000
#> SRR1044592 1 0.0000 0.991 1.000 0.000
#> SRR1044593 1 0.0000 0.991 1.000 0.000
#> SRR1044594 1 0.0000 0.991 1.000 0.000
#> SRR1044595 1 0.0000 0.991 1.000 0.000
#> SRR1044596 1 0.0000 0.991 1.000 0.000
#> SRR1044597 1 0.2948 0.951 0.948 0.052
#> SRR1044598 1 0.3114 0.947 0.944 0.056
#> SRR1044599 1 0.3431 0.939 0.936 0.064
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.1999 0.935 0.036 0.952 0.012
#> SRR1044416 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044417 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044418 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044420 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044419 2 0.3267 0.928 0.116 0.884 0.000
#> SRR1044421 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044422 2 0.1877 0.935 0.032 0.956 0.012
#> SRR1044423 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044424 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044425 1 0.4346 0.927 0.816 0.000 0.184
#> SRR1044426 1 0.6295 0.413 0.528 0.000 0.472
#> SRR1044427 3 0.5810 0.385 0.336 0.000 0.664
#> SRR1044428 3 0.1163 0.941 0.028 0.000 0.972
#> SRR1044429 1 0.6140 0.597 0.596 0.000 0.404
#> SRR1044430 3 0.3583 0.881 0.044 0.056 0.900
#> SRR1044431 1 0.5948 0.685 0.640 0.000 0.360
#> SRR1044433 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044432 3 0.1163 0.941 0.028 0.000 0.972
#> SRR1044434 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044435 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044436 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044437 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044439 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044438 1 0.4002 0.948 0.840 0.000 0.160
#> SRR1044440 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044441 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044442 1 0.4121 0.942 0.832 0.000 0.168
#> SRR1044443 1 0.4399 0.926 0.812 0.000 0.188
#> SRR1044444 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044445 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044446 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044447 2 0.3607 0.930 0.112 0.880 0.008
#> SRR1044449 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044448 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044450 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044451 2 0.2774 0.933 0.072 0.920 0.008
#> SRR1044452 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044453 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044454 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044455 2 0.3267 0.928 0.116 0.884 0.000
#> SRR1044456 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044457 2 0.3412 0.927 0.124 0.876 0.000
#> SRR1044458 2 0.3267 0.928 0.116 0.884 0.000
#> SRR1044459 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044460 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044461 2 0.3267 0.928 0.116 0.884 0.000
#> SRR1044462 1 0.6008 0.663 0.628 0.000 0.372
#> SRR1044463 3 0.0892 0.942 0.020 0.000 0.980
#> SRR1044464 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044466 3 0.0848 0.934 0.008 0.008 0.984
#> SRR1044465 3 0.1289 0.941 0.032 0.000 0.968
#> SRR1044467 3 0.1163 0.941 0.028 0.000 0.972
#> SRR1044468 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044469 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044470 3 0.0424 0.927 0.000 0.008 0.992
#> SRR1044471 3 0.1163 0.941 0.028 0.000 0.972
#> SRR1044472 3 0.1163 0.941 0.028 0.000 0.972
#> SRR1044473 3 0.2261 0.908 0.068 0.000 0.932
#> SRR1044474 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044475 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044476 2 0.3267 0.928 0.116 0.884 0.000
#> SRR1044477 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044478 2 0.3267 0.928 0.116 0.884 0.000
#> SRR1044479 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044480 1 0.4974 0.876 0.764 0.000 0.236
#> SRR1044481 3 0.1411 0.938 0.036 0.000 0.964
#> SRR1044482 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044483 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044484 3 0.4235 0.764 0.176 0.000 0.824
#> SRR1044486 3 0.1411 0.938 0.036 0.000 0.964
#> SRR1044485 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044487 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044488 2 0.1129 0.935 0.004 0.976 0.020
#> SRR1044489 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044490 3 0.1289 0.940 0.032 0.000 0.968
#> SRR1044491 3 0.0000 0.934 0.000 0.000 1.000
#> SRR1044492 3 0.0237 0.936 0.004 0.000 0.996
#> SRR1044493 3 0.0747 0.941 0.016 0.000 0.984
#> SRR1044494 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044496 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044495 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044497 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044499 2 0.3686 0.923 0.140 0.860 0.000
#> SRR1044498 3 0.5621 0.455 0.308 0.000 0.692
#> SRR1044500 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044501 2 0.3267 0.928 0.116 0.884 0.000
#> SRR1044502 2 0.3267 0.928 0.116 0.884 0.000
#> SRR1044503 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044504 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044505 1 0.6280 0.443 0.540 0.000 0.460
#> SRR1044506 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044507 1 0.4504 0.918 0.804 0.000 0.196
#> SRR1044508 1 0.4235 0.935 0.824 0.000 0.176
#> SRR1044509 1 0.4121 0.942 0.832 0.000 0.168
#> SRR1044510 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044511 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044512 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044513 2 0.1399 0.935 0.004 0.968 0.028
#> SRR1044514 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044515 2 0.3755 0.929 0.120 0.872 0.008
#> SRR1044516 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044517 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044518 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044519 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044520 2 0.4002 0.917 0.160 0.840 0.000
#> SRR1044521 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044522 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044523 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044524 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044525 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044526 3 0.4887 0.678 0.228 0.000 0.772
#> SRR1044527 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044528 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044529 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044530 3 0.1031 0.942 0.024 0.000 0.976
#> SRR1044531 3 0.1163 0.941 0.028 0.000 0.972
#> SRR1044533 3 0.1163 0.941 0.028 0.000 0.972
#> SRR1044532 3 0.0237 0.936 0.004 0.000 0.996
#> SRR1044534 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044535 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044536 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044537 3 0.0892 0.933 0.020 0.000 0.980
#> SRR1044538 3 0.1031 0.942 0.024 0.000 0.976
#> SRR1044539 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044540 3 0.1289 0.941 0.032 0.000 0.968
#> SRR1044541 2 0.3116 0.930 0.108 0.892 0.000
#> SRR1044542 3 0.0237 0.931 0.000 0.004 0.996
#> SRR1044543 3 0.2625 0.896 0.084 0.000 0.916
#> SRR1044544 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044545 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044546 3 0.0000 0.934 0.000 0.000 1.000
#> SRR1044547 1 0.4062 0.945 0.836 0.000 0.164
#> SRR1044548 3 0.0000 0.934 0.000 0.000 1.000
#> SRR1044549 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044550 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044551 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044552 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044553 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044554 3 0.0000 0.934 0.000 0.000 1.000
#> SRR1044555 2 0.3941 0.919 0.156 0.844 0.000
#> SRR1044556 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044557 3 0.0237 0.930 0.000 0.004 0.996
#> SRR1044558 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044559 3 0.0592 0.935 0.012 0.000 0.988
#> SRR1044561 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044560 2 0.3267 0.928 0.116 0.884 0.000
#> SRR1044562 3 0.0000 0.934 0.000 0.000 1.000
#> SRR1044563 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044564 3 0.3816 0.816 0.148 0.000 0.852
#> SRR1044565 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044566 2 0.3267 0.928 0.116 0.884 0.000
#> SRR1044567 3 0.1031 0.942 0.024 0.000 0.976
#> SRR1044568 1 0.4002 0.948 0.840 0.000 0.160
#> SRR1044569 3 0.1289 0.940 0.032 0.000 0.968
#> SRR1044570 3 0.0237 0.936 0.004 0.000 0.996
#> SRR1044571 3 0.1163 0.941 0.028 0.000 0.972
#> SRR1044572 3 0.1163 0.941 0.028 0.000 0.972
#> SRR1044573 3 0.1289 0.940 0.032 0.000 0.968
#> SRR1044574 3 0.2165 0.916 0.064 0.000 0.936
#> SRR1044575 3 0.1411 0.938 0.036 0.000 0.964
#> SRR1044576 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044577 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044578 2 0.1163 0.935 0.000 0.972 0.028
#> SRR1044579 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044580 1 0.6215 0.534 0.572 0.000 0.428
#> SRR1044581 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044582 3 0.0747 0.941 0.016 0.000 0.984
#> SRR1044583 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044584 1 0.5178 0.846 0.744 0.000 0.256
#> SRR1044585 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044586 3 0.1163 0.940 0.028 0.000 0.972
#> SRR1044587 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044588 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044589 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044590 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044591 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044592 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044593 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044594 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044595 3 0.5291 0.580 0.268 0.000 0.732
#> SRR1044596 1 0.3941 0.950 0.844 0.000 0.156
#> SRR1044597 1 0.7424 0.583 0.572 0.040 0.388
#> SRR1044598 3 0.0892 0.913 0.000 0.020 0.980
#> SRR1044599 3 0.1031 0.908 0.000 0.024 0.976
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 2 0.1389 0.888 0.000 0.952 0.048 0.000
#> SRR1044416 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044417 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044418 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044420 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044419 2 0.4040 0.683 0.000 0.752 0.248 0.000
#> SRR1044421 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044422 2 0.1389 0.889 0.000 0.952 0.048 0.000
#> SRR1044423 2 0.0188 0.915 0.000 0.996 0.004 0.000
#> SRR1044424 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044425 4 0.0921 0.932 0.028 0.000 0.000 0.972
#> SRR1044426 4 0.4543 0.556 0.324 0.000 0.000 0.676
#> SRR1044427 1 0.4830 0.365 0.608 0.000 0.000 0.392
#> SRR1044428 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044429 4 0.4072 0.685 0.252 0.000 0.000 0.748
#> SRR1044430 1 0.1022 0.933 0.968 0.000 0.000 0.032
#> SRR1044431 4 0.3764 0.735 0.216 0.000 0.000 0.784
#> SRR1044433 4 0.0592 0.946 0.000 0.000 0.016 0.984
#> SRR1044432 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044434 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044435 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044436 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044437 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044439 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044438 4 0.0188 0.947 0.004 0.000 0.000 0.996
#> SRR1044440 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044441 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044442 4 0.1059 0.941 0.012 0.000 0.016 0.972
#> SRR1044443 4 0.2036 0.920 0.032 0.000 0.032 0.936
#> SRR1044444 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044445 4 0.0592 0.946 0.000 0.000 0.016 0.984
#> SRR1044446 3 0.0592 0.885 0.000 0.016 0.984 0.000
#> SRR1044447 3 0.4925 0.267 0.000 0.428 0.572 0.000
#> SRR1044449 3 0.0592 0.885 0.000 0.016 0.984 0.000
#> SRR1044448 3 0.0592 0.885 0.000 0.016 0.984 0.000
#> SRR1044450 3 0.0592 0.885 0.000 0.016 0.984 0.000
#> SRR1044451 3 0.3801 0.713 0.000 0.220 0.780 0.000
#> SRR1044452 3 0.0592 0.885 0.000 0.016 0.984 0.000
#> SRR1044453 3 0.0921 0.882 0.000 0.028 0.972 0.000
#> SRR1044454 3 0.0921 0.882 0.000 0.028 0.972 0.000
#> SRR1044455 2 0.4103 0.672 0.000 0.744 0.256 0.000
#> SRR1044456 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044457 3 0.4977 0.155 0.000 0.460 0.540 0.000
#> SRR1044458 2 0.4040 0.683 0.000 0.752 0.248 0.000
#> SRR1044459 3 0.0707 0.885 0.000 0.020 0.980 0.000
#> SRR1044460 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044461 2 0.4040 0.683 0.000 0.752 0.248 0.000
#> SRR1044462 4 0.3975 0.700 0.240 0.000 0.000 0.760
#> SRR1044463 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044464 4 0.0336 0.947 0.000 0.000 0.008 0.992
#> SRR1044466 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044465 1 0.0336 0.948 0.992 0.000 0.000 0.008
#> SRR1044467 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044468 2 0.1022 0.900 0.000 0.968 0.032 0.000
#> SRR1044469 3 0.4250 0.622 0.000 0.276 0.724 0.000
#> SRR1044470 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044471 1 0.0336 0.948 0.992 0.000 0.000 0.008
#> SRR1044472 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044473 1 0.1474 0.916 0.948 0.000 0.000 0.052
#> SRR1044474 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044475 3 0.4746 0.438 0.000 0.368 0.632 0.000
#> SRR1044476 2 0.4040 0.683 0.000 0.752 0.248 0.000
#> SRR1044477 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044478 2 0.4040 0.683 0.000 0.752 0.248 0.000
#> SRR1044479 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044480 4 0.2334 0.886 0.088 0.000 0.004 0.908
#> SRR1044481 1 0.0336 0.948 0.992 0.000 0.000 0.008
#> SRR1044482 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044483 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044484 1 0.3837 0.710 0.776 0.000 0.000 0.224
#> SRR1044486 1 0.0336 0.948 0.992 0.000 0.000 0.008
#> SRR1044485 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044487 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044488 2 0.0921 0.902 0.000 0.972 0.028 0.000
#> SRR1044489 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044490 1 0.0336 0.948 0.992 0.000 0.000 0.008
#> SRR1044491 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044492 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044493 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044494 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044496 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044495 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044497 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044499 2 0.4697 0.465 0.000 0.644 0.356 0.000
#> SRR1044498 1 0.4898 0.274 0.584 0.000 0.000 0.416
#> SRR1044500 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044501 2 0.4040 0.683 0.000 0.752 0.248 0.000
#> SRR1044502 3 0.4477 0.547 0.000 0.312 0.688 0.000
#> SRR1044503 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044504 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044505 4 0.4643 0.498 0.344 0.000 0.000 0.656
#> SRR1044506 4 0.0592 0.946 0.000 0.000 0.016 0.984
#> SRR1044507 4 0.1798 0.924 0.040 0.000 0.016 0.944
#> SRR1044508 4 0.1297 0.937 0.016 0.000 0.020 0.964
#> SRR1044509 4 0.1182 0.939 0.016 0.000 0.016 0.968
#> SRR1044510 3 0.0921 0.882 0.000 0.028 0.972 0.000
#> SRR1044511 3 0.0592 0.885 0.000 0.016 0.984 0.000
#> SRR1044512 3 0.0592 0.885 0.000 0.016 0.984 0.000
#> SRR1044513 2 0.3975 0.630 0.000 0.760 0.240 0.000
#> SRR1044514 3 0.0592 0.885 0.000 0.016 0.984 0.000
#> SRR1044515 3 0.4948 0.230 0.000 0.440 0.560 0.000
#> SRR1044516 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044517 3 0.0592 0.885 0.000 0.016 0.984 0.000
#> SRR1044518 3 0.0921 0.880 0.000 0.028 0.972 0.000
#> SRR1044519 3 0.0592 0.885 0.000 0.016 0.984 0.000
#> SRR1044520 3 0.0592 0.885 0.000 0.016 0.984 0.000
#> SRR1044521 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044522 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044523 2 0.2921 0.792 0.000 0.860 0.140 0.000
#> SRR1044524 3 0.0817 0.884 0.000 0.024 0.976 0.000
#> SRR1044525 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044526 1 0.4250 0.639 0.724 0.000 0.000 0.276
#> SRR1044527 2 0.0469 0.909 0.000 0.988 0.012 0.000
#> SRR1044528 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044529 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044530 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044531 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044533 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044532 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044534 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044535 3 0.0592 0.885 0.000 0.016 0.984 0.000
#> SRR1044536 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044537 1 0.0707 0.941 0.980 0.000 0.000 0.020
#> SRR1044538 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044539 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044540 1 0.0469 0.946 0.988 0.000 0.000 0.012
#> SRR1044541 2 0.4382 0.605 0.000 0.704 0.296 0.000
#> SRR1044542 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044543 1 0.2469 0.861 0.892 0.000 0.000 0.108
#> SRR1044544 3 0.2760 0.806 0.000 0.128 0.872 0.000
#> SRR1044545 4 0.0592 0.946 0.000 0.000 0.016 0.984
#> SRR1044546 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044547 4 0.0672 0.946 0.008 0.000 0.008 0.984
#> SRR1044548 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044549 2 0.1474 0.878 0.000 0.948 0.052 0.000
#> SRR1044550 2 0.0188 0.915 0.000 0.996 0.004 0.000
#> SRR1044551 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044552 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044553 4 0.0592 0.946 0.000 0.000 0.016 0.984
#> SRR1044554 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044555 3 0.0707 0.885 0.000 0.020 0.980 0.000
#> SRR1044556 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044557 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044558 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044559 1 0.0469 0.946 0.988 0.000 0.000 0.012
#> SRR1044561 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044560 2 0.4040 0.683 0.000 0.752 0.248 0.000
#> SRR1044562 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044563 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044564 1 0.2647 0.854 0.880 0.000 0.000 0.120
#> SRR1044565 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044566 2 0.4040 0.683 0.000 0.752 0.248 0.000
#> SRR1044567 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044568 4 0.0188 0.947 0.004 0.000 0.000 0.996
#> SRR1044569 1 0.0188 0.950 0.996 0.000 0.000 0.004
#> SRR1044570 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044571 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044572 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044573 1 0.0336 0.949 0.992 0.000 0.000 0.008
#> SRR1044574 1 0.1557 0.912 0.944 0.000 0.000 0.056
#> SRR1044575 1 0.0336 0.948 0.992 0.000 0.000 0.008
#> SRR1044576 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044577 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044578 2 0.0000 0.916 0.000 1.000 0.000 0.000
#> SRR1044579 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044580 4 0.4356 0.608 0.292 0.000 0.000 0.708
#> SRR1044581 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044582 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044583 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044584 4 0.2345 0.871 0.100 0.000 0.000 0.900
#> SRR1044585 4 0.0000 0.948 0.000 0.000 0.000 1.000
#> SRR1044586 1 0.0592 0.944 0.984 0.000 0.000 0.016
#> SRR1044587 4 0.0592 0.946 0.000 0.000 0.016 0.984
#> SRR1044588 4 0.0592 0.946 0.000 0.000 0.016 0.984
#> SRR1044589 4 0.0592 0.946 0.000 0.000 0.016 0.984
#> SRR1044590 4 0.0592 0.946 0.000 0.000 0.016 0.984
#> SRR1044591 4 0.0592 0.946 0.000 0.000 0.016 0.984
#> SRR1044592 4 0.0707 0.944 0.000 0.000 0.020 0.980
#> SRR1044593 4 0.0592 0.946 0.000 0.000 0.016 0.984
#> SRR1044594 4 0.0592 0.946 0.000 0.000 0.016 0.984
#> SRR1044595 1 0.4690 0.637 0.724 0.000 0.016 0.260
#> SRR1044596 4 0.0592 0.946 0.000 0.000 0.016 0.984
#> SRR1044597 4 0.6538 0.551 0.232 0.140 0.000 0.628
#> SRR1044598 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1044599 1 0.0000 0.951 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.1270 0.8504 0.000 0.948 0.052 0.000 0.000
#> SRR1044416 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044417 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044418 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044420 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044419 2 0.4511 0.5160 0.000 0.628 0.356 0.000 0.016
#> SRR1044421 2 0.0162 0.8762 0.000 0.996 0.004 0.000 0.000
#> SRR1044422 2 0.1197 0.8530 0.000 0.952 0.048 0.000 0.000
#> SRR1044423 2 0.0451 0.8735 0.000 0.988 0.004 0.000 0.008
#> SRR1044424 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044425 4 0.0880 0.4823 0.000 0.000 0.000 0.968 0.032
#> SRR1044426 4 0.6641 -0.0826 0.256 0.000 0.000 0.448 0.296
#> SRR1044427 4 0.5795 0.0757 0.412 0.000 0.000 0.496 0.092
#> SRR1044428 1 0.1608 0.9388 0.928 0.000 0.000 0.000 0.072
#> SRR1044429 4 0.5365 0.2589 0.228 0.000 0.000 0.656 0.116
#> SRR1044430 1 0.1918 0.9325 0.928 0.000 0.000 0.036 0.036
#> SRR1044431 4 0.4430 0.3524 0.172 0.000 0.000 0.752 0.076
#> SRR1044433 5 0.4297 0.9767 0.000 0.000 0.000 0.472 0.528
#> SRR1044432 1 0.1043 0.9434 0.960 0.000 0.000 0.000 0.040
#> SRR1044434 4 0.3177 0.2639 0.000 0.000 0.000 0.792 0.208
#> SRR1044435 4 0.2516 0.3743 0.000 0.000 0.000 0.860 0.140
#> SRR1044436 4 0.2230 0.4029 0.000 0.000 0.000 0.884 0.116
#> SRR1044437 4 0.1341 0.4790 0.000 0.000 0.000 0.944 0.056
#> SRR1044439 4 0.1732 0.4421 0.000 0.000 0.000 0.920 0.080
#> SRR1044438 4 0.2280 0.3972 0.000 0.000 0.000 0.880 0.120
#> SRR1044440 4 0.3177 0.2448 0.000 0.000 0.000 0.792 0.208
#> SRR1044441 4 0.3003 0.2999 0.000 0.000 0.000 0.812 0.188
#> SRR1044442 5 0.4302 0.9663 0.000 0.000 0.000 0.480 0.520
#> SRR1044443 5 0.4297 0.9767 0.000 0.000 0.000 0.472 0.528
#> SRR1044444 4 0.1197 0.4759 0.000 0.000 0.000 0.952 0.048
#> SRR1044445 5 0.4306 0.9278 0.000 0.000 0.000 0.492 0.508
#> SRR1044446 3 0.0510 0.8335 0.000 0.000 0.984 0.000 0.016
#> SRR1044447 3 0.4269 0.4648 0.000 0.300 0.684 0.000 0.016
#> SRR1044449 3 0.4015 0.7210 0.000 0.000 0.652 0.000 0.348
#> SRR1044448 3 0.0609 0.8340 0.000 0.000 0.980 0.000 0.020
#> SRR1044450 3 0.1908 0.8280 0.000 0.000 0.908 0.000 0.092
#> SRR1044451 3 0.3304 0.7383 0.000 0.168 0.816 0.000 0.016
#> SRR1044452 3 0.3949 0.7261 0.000 0.000 0.668 0.000 0.332
#> SRR1044453 3 0.4323 0.7286 0.000 0.012 0.656 0.000 0.332
#> SRR1044454 3 0.4339 0.7290 0.000 0.012 0.652 0.000 0.336
#> SRR1044455 2 0.4538 0.5022 0.000 0.620 0.364 0.000 0.016
#> SRR1044456 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044457 3 0.4482 0.3299 0.000 0.348 0.636 0.000 0.016
#> SRR1044458 2 0.4511 0.5160 0.000 0.628 0.356 0.000 0.016
#> SRR1044459 3 0.0451 0.8329 0.000 0.004 0.988 0.000 0.008
#> SRR1044460 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044461 2 0.4511 0.5160 0.000 0.628 0.356 0.000 0.016
#> SRR1044462 4 0.4704 0.3499 0.152 0.000 0.000 0.736 0.112
#> SRR1044463 1 0.0000 0.9405 1.000 0.000 0.000 0.000 0.000
#> SRR1044464 4 0.2806 0.3230 0.004 0.000 0.000 0.844 0.152
#> SRR1044466 1 0.0000 0.9405 1.000 0.000 0.000 0.000 0.000
#> SRR1044465 1 0.1195 0.9351 0.960 0.000 0.000 0.028 0.012
#> SRR1044467 1 0.0451 0.9409 0.988 0.000 0.000 0.004 0.008
#> SRR1044468 2 0.1740 0.8424 0.000 0.932 0.056 0.000 0.012
#> SRR1044469 3 0.4206 0.5122 0.000 0.272 0.708 0.000 0.020
#> SRR1044470 1 0.0162 0.9394 0.996 0.000 0.000 0.000 0.004
#> SRR1044471 1 0.0451 0.9386 0.988 0.000 0.000 0.008 0.004
#> SRR1044472 1 0.0162 0.9394 0.996 0.000 0.000 0.000 0.004
#> SRR1044473 1 0.2179 0.8732 0.896 0.000 0.000 0.100 0.004
#> SRR1044474 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044475 2 0.6795 -0.2370 0.000 0.364 0.288 0.000 0.348
#> SRR1044476 2 0.4511 0.5160 0.000 0.628 0.356 0.000 0.016
#> SRR1044477 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044478 2 0.4511 0.5160 0.000 0.628 0.356 0.000 0.016
#> SRR1044479 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044480 4 0.2830 0.4428 0.080 0.000 0.000 0.876 0.044
#> SRR1044481 1 0.2390 0.9261 0.896 0.000 0.000 0.020 0.084
#> SRR1044482 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044483 4 0.0404 0.4809 0.000 0.000 0.000 0.988 0.012
#> SRR1044484 1 0.5580 0.4208 0.576 0.000 0.000 0.336 0.088
#> SRR1044486 1 0.2077 0.9310 0.908 0.000 0.000 0.008 0.084
#> SRR1044485 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044487 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044488 2 0.1205 0.8570 0.000 0.956 0.040 0.000 0.004
#> SRR1044489 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044490 1 0.1281 0.9422 0.956 0.000 0.000 0.012 0.032
#> SRR1044491 1 0.1608 0.9369 0.928 0.000 0.000 0.000 0.072
#> SRR1044492 1 0.0404 0.9415 0.988 0.000 0.000 0.000 0.012
#> SRR1044493 1 0.0963 0.9432 0.964 0.000 0.000 0.000 0.036
#> SRR1044494 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044496 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044495 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044497 4 0.0404 0.4800 0.000 0.000 0.000 0.988 0.012
#> SRR1044499 2 0.4658 0.4082 0.000 0.576 0.408 0.000 0.016
#> SRR1044498 4 0.5831 0.1586 0.408 0.000 0.000 0.496 0.096
#> SRR1044500 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044501 2 0.4511 0.5160 0.000 0.628 0.356 0.000 0.016
#> SRR1044502 3 0.3419 0.6694 0.000 0.180 0.804 0.000 0.016
#> SRR1044503 4 0.1197 0.4787 0.000 0.000 0.000 0.952 0.048
#> SRR1044504 4 0.3636 -0.0307 0.000 0.000 0.000 0.728 0.272
#> SRR1044505 4 0.5449 0.2736 0.256 0.000 0.000 0.636 0.108
#> SRR1044506 5 0.4307 0.9294 0.000 0.000 0.000 0.496 0.504
#> SRR1044507 4 0.5148 -0.7010 0.040 0.000 0.000 0.528 0.432
#> SRR1044508 5 0.4297 0.9767 0.000 0.000 0.000 0.472 0.528
#> SRR1044509 5 0.4297 0.9767 0.000 0.000 0.000 0.472 0.528
#> SRR1044510 3 0.1195 0.8324 0.000 0.012 0.960 0.000 0.028
#> SRR1044511 3 0.0703 0.8335 0.000 0.000 0.976 0.000 0.024
#> SRR1044512 3 0.2929 0.8048 0.000 0.000 0.820 0.000 0.180
#> SRR1044513 2 0.3774 0.5225 0.000 0.704 0.296 0.000 0.000
#> SRR1044514 3 0.0703 0.8335 0.000 0.000 0.976 0.000 0.024
#> SRR1044515 3 0.4451 0.3636 0.000 0.340 0.644 0.000 0.016
#> SRR1044516 2 0.0162 0.8763 0.000 0.996 0.004 0.000 0.000
#> SRR1044517 3 0.3534 0.7741 0.000 0.000 0.744 0.000 0.256
#> SRR1044518 3 0.0992 0.8335 0.000 0.008 0.968 0.000 0.024
#> SRR1044519 3 0.1965 0.8273 0.000 0.000 0.904 0.000 0.096
#> SRR1044520 3 0.3966 0.7292 0.000 0.000 0.664 0.000 0.336
#> SRR1044521 2 0.0404 0.8735 0.000 0.988 0.000 0.000 0.012
#> SRR1044522 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044523 2 0.2970 0.7321 0.000 0.828 0.168 0.000 0.004
#> SRR1044524 3 0.0451 0.8296 0.000 0.008 0.988 0.000 0.004
#> SRR1044525 4 0.2891 0.3195 0.000 0.000 0.000 0.824 0.176
#> SRR1044526 4 0.5650 -0.1107 0.460 0.000 0.000 0.464 0.076
#> SRR1044527 2 0.0671 0.8692 0.000 0.980 0.016 0.000 0.004
#> SRR1044528 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044529 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044530 1 0.0000 0.9405 1.000 0.000 0.000 0.000 0.000
#> SRR1044531 1 0.1043 0.9432 0.960 0.000 0.000 0.000 0.040
#> SRR1044533 1 0.0609 0.9427 0.980 0.000 0.000 0.000 0.020
#> SRR1044532 1 0.0000 0.9405 1.000 0.000 0.000 0.000 0.000
#> SRR1044534 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044535 3 0.0290 0.8330 0.000 0.000 0.992 0.000 0.008
#> SRR1044536 2 0.0162 0.8762 0.000 0.996 0.000 0.000 0.004
#> SRR1044537 1 0.2423 0.9248 0.896 0.000 0.000 0.024 0.080
#> SRR1044538 1 0.0162 0.9413 0.996 0.000 0.000 0.000 0.004
#> SRR1044539 4 0.2329 0.3883 0.000 0.000 0.000 0.876 0.124
#> SRR1044540 1 0.1628 0.9410 0.936 0.000 0.000 0.008 0.056
#> SRR1044541 2 0.4557 0.4215 0.000 0.584 0.404 0.000 0.012
#> SRR1044542 1 0.0000 0.9405 1.000 0.000 0.000 0.000 0.000
#> SRR1044543 1 0.3438 0.7701 0.808 0.000 0.000 0.172 0.020
#> SRR1044544 3 0.2677 0.7524 0.000 0.112 0.872 0.000 0.016
#> SRR1044545 4 0.3534 -0.0473 0.000 0.000 0.000 0.744 0.256
#> SRR1044546 1 0.1831 0.9350 0.920 0.000 0.000 0.004 0.076
#> SRR1044547 4 0.2674 0.3773 0.004 0.000 0.000 0.856 0.140
#> SRR1044548 1 0.1792 0.9332 0.916 0.000 0.000 0.000 0.084
#> SRR1044549 2 0.1270 0.8394 0.000 0.948 0.052 0.000 0.000
#> SRR1044550 2 0.0324 0.8749 0.000 0.992 0.004 0.000 0.004
#> SRR1044551 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044552 4 0.2773 0.3451 0.000 0.000 0.000 0.836 0.164
#> SRR1044553 4 0.4273 -0.7459 0.000 0.000 0.000 0.552 0.448
#> SRR1044554 1 0.1544 0.9378 0.932 0.000 0.000 0.000 0.068
#> SRR1044555 3 0.0162 0.8315 0.000 0.004 0.996 0.000 0.000
#> SRR1044556 4 0.2074 0.4187 0.000 0.000 0.000 0.896 0.104
#> SRR1044557 1 0.1732 0.9344 0.920 0.000 0.000 0.000 0.080
#> SRR1044558 4 0.2020 0.4438 0.000 0.000 0.000 0.900 0.100
#> SRR1044559 1 0.2903 0.9092 0.872 0.000 0.000 0.048 0.080
#> SRR1044561 4 0.2773 0.3522 0.000 0.000 0.000 0.836 0.164
#> SRR1044560 2 0.4511 0.5160 0.000 0.628 0.356 0.000 0.016
#> SRR1044562 1 0.1732 0.9349 0.920 0.000 0.000 0.000 0.080
#> SRR1044563 4 0.0510 0.4807 0.000 0.000 0.000 0.984 0.016
#> SRR1044564 1 0.4036 0.8110 0.788 0.000 0.000 0.144 0.068
#> SRR1044565 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044566 2 0.4511 0.5160 0.000 0.628 0.356 0.000 0.016
#> SRR1044567 1 0.0162 0.9413 0.996 0.000 0.000 0.000 0.004
#> SRR1044568 4 0.1043 0.4808 0.000 0.000 0.000 0.960 0.040
#> SRR1044569 1 0.1205 0.9440 0.956 0.000 0.000 0.004 0.040
#> SRR1044570 1 0.0000 0.9405 1.000 0.000 0.000 0.000 0.000
#> SRR1044571 1 0.0162 0.9394 0.996 0.000 0.000 0.000 0.004
#> SRR1044572 1 0.1638 0.9408 0.932 0.000 0.000 0.004 0.064
#> SRR1044573 1 0.1485 0.9414 0.948 0.000 0.000 0.020 0.032
#> SRR1044574 1 0.3134 0.8528 0.848 0.000 0.000 0.120 0.032
#> SRR1044575 1 0.1195 0.9367 0.960 0.000 0.000 0.028 0.012
#> SRR1044576 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044577 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044578 2 0.0000 0.8773 0.000 1.000 0.000 0.000 0.000
#> SRR1044579 4 0.3274 0.2118 0.000 0.000 0.000 0.780 0.220
#> SRR1044580 4 0.4183 0.3803 0.136 0.000 0.000 0.780 0.084
#> SRR1044581 4 0.1851 0.4541 0.000 0.000 0.000 0.912 0.088
#> SRR1044582 1 0.1792 0.9332 0.916 0.000 0.000 0.000 0.084
#> SRR1044583 4 0.2516 0.3928 0.000 0.000 0.000 0.860 0.140
#> SRR1044584 4 0.1408 0.4752 0.008 0.000 0.000 0.948 0.044
#> SRR1044585 4 0.1792 0.4573 0.000 0.000 0.000 0.916 0.084
#> SRR1044586 1 0.2390 0.9260 0.896 0.000 0.000 0.020 0.084
#> SRR1044587 4 0.4307 -0.9231 0.000 0.000 0.000 0.504 0.496
#> SRR1044588 4 0.4302 -0.8641 0.000 0.000 0.000 0.520 0.480
#> SRR1044589 4 0.4302 -0.8641 0.000 0.000 0.000 0.520 0.480
#> SRR1044590 4 0.4273 -0.8048 0.000 0.000 0.000 0.552 0.448
#> SRR1044591 4 0.4305 -0.8899 0.000 0.000 0.000 0.512 0.488
#> SRR1044592 5 0.4297 0.9767 0.000 0.000 0.000 0.472 0.528
#> SRR1044593 4 0.4305 -0.8897 0.000 0.000 0.000 0.512 0.488
#> SRR1044594 4 0.4302 -0.8641 0.000 0.000 0.000 0.520 0.480
#> SRR1044595 1 0.5557 0.5169 0.624 0.000 0.000 0.116 0.260
#> SRR1044596 5 0.4300 0.9711 0.000 0.000 0.000 0.476 0.524
#> SRR1044597 4 0.6328 0.2750 0.108 0.136 0.000 0.656 0.100
#> SRR1044598 1 0.0671 0.9426 0.980 0.000 0.000 0.004 0.016
#> SRR1044599 1 0.0865 0.9431 0.972 0.000 0.000 0.004 0.024
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.1141 0.9169 0.000 0.948 0.052 0.000 0.000 0.000
#> SRR1044416 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044417 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044418 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044420 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044419 3 0.4944 0.3215 0.000 0.432 0.516 0.000 0.040 0.012
#> SRR1044421 2 0.0405 0.9559 0.000 0.988 0.008 0.000 0.004 0.000
#> SRR1044422 2 0.1219 0.9182 0.000 0.948 0.048 0.000 0.004 0.000
#> SRR1044423 2 0.1888 0.8857 0.000 0.916 0.068 0.000 0.012 0.004
#> SRR1044424 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044425 4 0.1152 0.6260 0.004 0.000 0.000 0.952 0.000 0.044
#> SRR1044426 4 0.7207 -0.0873 0.252 0.000 0.000 0.404 0.104 0.240
#> SRR1044427 5 0.6396 0.4392 0.244 0.000 0.000 0.364 0.376 0.016
#> SRR1044428 1 0.3672 0.3367 0.632 0.000 0.000 0.000 0.368 0.000
#> SRR1044429 4 0.6736 0.1964 0.136 0.000 0.000 0.488 0.276 0.100
#> SRR1044430 1 0.3420 0.5492 0.748 0.000 0.000 0.012 0.240 0.000
#> SRR1044431 4 0.5285 0.4458 0.136 0.000 0.000 0.692 0.096 0.076
#> SRR1044433 6 0.4634 0.7700 0.000 0.000 0.000 0.400 0.044 0.556
#> SRR1044432 1 0.3050 0.5717 0.764 0.000 0.000 0.000 0.236 0.000
#> SRR1044434 4 0.2664 0.4906 0.000 0.000 0.000 0.816 0.000 0.184
#> SRR1044435 4 0.2912 0.4491 0.000 0.000 0.000 0.784 0.000 0.216
#> SRR1044436 4 0.3394 0.4875 0.000 0.000 0.000 0.776 0.024 0.200
#> SRR1044437 4 0.1444 0.6191 0.000 0.000 0.000 0.928 0.000 0.072
#> SRR1044439 4 0.3062 0.5413 0.000 0.000 0.000 0.816 0.024 0.160
#> SRR1044438 4 0.3374 0.4594 0.000 0.000 0.000 0.772 0.020 0.208
#> SRR1044440 4 0.2631 0.4788 0.000 0.000 0.000 0.820 0.000 0.180
#> SRR1044441 4 0.2491 0.5068 0.000 0.000 0.000 0.836 0.000 0.164
#> SRR1044442 6 0.4648 0.7651 0.000 0.000 0.000 0.408 0.044 0.548
#> SRR1044443 6 0.4634 0.7700 0.000 0.000 0.000 0.400 0.044 0.556
#> SRR1044444 4 0.0790 0.6203 0.000 0.000 0.000 0.968 0.000 0.032
#> SRR1044445 6 0.3797 0.7698 0.000 0.000 0.000 0.420 0.000 0.580
#> SRR1044446 3 0.3283 0.6299 0.000 0.000 0.804 0.000 0.160 0.036
#> SRR1044447 3 0.3415 0.6400 0.000 0.152 0.808 0.000 0.028 0.012
#> SRR1044449 3 0.5847 0.4792 0.000 0.000 0.444 0.000 0.196 0.360
#> SRR1044448 3 0.3387 0.6290 0.000 0.000 0.796 0.000 0.164 0.040
#> SRR1044450 3 0.4601 0.6060 0.000 0.000 0.688 0.000 0.200 0.112
#> SRR1044451 3 0.5247 0.6122 0.000 0.168 0.672 0.000 0.128 0.032
#> SRR1044452 3 0.4923 0.5148 0.000 0.000 0.560 0.000 0.072 0.368
#> SRR1044453 3 0.4799 0.5252 0.000 0.008 0.580 0.000 0.044 0.368
#> SRR1044454 3 0.4740 0.5259 0.000 0.008 0.584 0.000 0.040 0.368
#> SRR1044455 3 0.4948 0.3142 0.000 0.436 0.512 0.000 0.040 0.012
#> SRR1044456 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044457 3 0.4023 0.5941 0.000 0.200 0.748 0.000 0.040 0.012
#> SRR1044458 3 0.4935 0.3367 0.000 0.424 0.524 0.000 0.040 0.012
#> SRR1044459 3 0.1889 0.6497 0.000 0.004 0.920 0.000 0.056 0.020
#> SRR1044460 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044461 3 0.4935 0.3367 0.000 0.424 0.524 0.000 0.040 0.012
#> SRR1044462 4 0.5977 0.0565 0.088 0.000 0.000 0.528 0.332 0.052
#> SRR1044463 1 0.0458 0.6470 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1044464 4 0.3642 0.4456 0.000 0.000 0.000 0.760 0.036 0.204
#> SRR1044466 1 0.0363 0.6450 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1044465 1 0.2212 0.6361 0.880 0.000 0.000 0.008 0.112 0.000
#> SRR1044467 1 0.0508 0.6375 0.984 0.000 0.000 0.004 0.012 0.000
#> SRR1044468 2 0.3206 0.7403 0.000 0.816 0.152 0.000 0.028 0.004
#> SRR1044469 3 0.4426 0.5549 0.000 0.248 0.696 0.000 0.040 0.016
#> SRR1044470 1 0.0547 0.6496 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1044471 1 0.1584 0.6526 0.928 0.000 0.000 0.008 0.064 0.000
#> SRR1044472 1 0.0865 0.6526 0.964 0.000 0.000 0.000 0.036 0.000
#> SRR1044473 1 0.1498 0.6316 0.940 0.000 0.000 0.028 0.032 0.000
#> SRR1044474 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044475 6 0.7062 -0.5111 0.000 0.336 0.224 0.000 0.076 0.364
#> SRR1044476 3 0.4940 0.3317 0.000 0.428 0.520 0.000 0.040 0.012
#> SRR1044477 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044478 3 0.4935 0.3367 0.000 0.424 0.524 0.000 0.040 0.012
#> SRR1044479 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044480 4 0.3749 0.4899 0.028 0.000 0.000 0.776 0.180 0.016
#> SRR1044481 5 0.4184 0.0528 0.488 0.000 0.000 0.012 0.500 0.000
#> SRR1044482 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044483 4 0.1720 0.6194 0.000 0.000 0.000 0.928 0.040 0.032
#> SRR1044484 5 0.5815 0.4372 0.316 0.000 0.000 0.164 0.512 0.008
#> SRR1044486 1 0.3937 0.1450 0.572 0.000 0.000 0.004 0.424 0.000
#> SRR1044485 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044487 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044488 2 0.1349 0.9121 0.000 0.940 0.056 0.000 0.000 0.004
#> SRR1044489 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044490 1 0.1913 0.6423 0.908 0.000 0.000 0.012 0.080 0.000
#> SRR1044491 1 0.3843 0.0669 0.548 0.000 0.000 0.000 0.452 0.000
#> SRR1044492 1 0.1204 0.6556 0.944 0.000 0.000 0.000 0.056 0.000
#> SRR1044493 1 0.2823 0.5890 0.796 0.000 0.000 0.000 0.204 0.000
#> SRR1044494 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044496 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044495 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044497 4 0.0000 0.6203 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044499 3 0.4925 0.3503 0.000 0.416 0.532 0.000 0.040 0.012
#> SRR1044498 5 0.5764 0.4878 0.216 0.000 0.000 0.280 0.504 0.000
#> SRR1044500 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044501 3 0.4935 0.3367 0.000 0.424 0.524 0.000 0.040 0.012
#> SRR1044502 3 0.3076 0.6571 0.000 0.064 0.856 0.000 0.064 0.016
#> SRR1044503 4 0.1501 0.6153 0.000 0.000 0.000 0.924 0.000 0.076
#> SRR1044504 4 0.3578 0.0746 0.000 0.000 0.000 0.660 0.000 0.340
#> SRR1044505 5 0.6564 0.3480 0.164 0.000 0.000 0.388 0.400 0.048
#> SRR1044506 6 0.3797 0.7693 0.000 0.000 0.000 0.420 0.000 0.580
#> SRR1044507 6 0.5703 0.5666 0.036 0.000 0.000 0.444 0.068 0.452
#> SRR1044508 6 0.4634 0.7700 0.000 0.000 0.000 0.400 0.044 0.556
#> SRR1044509 6 0.4634 0.7700 0.000 0.000 0.000 0.400 0.044 0.556
#> SRR1044510 3 0.2699 0.6514 0.000 0.008 0.864 0.000 0.108 0.020
#> SRR1044511 3 0.4139 0.5883 0.000 0.000 0.640 0.000 0.336 0.024
#> SRR1044512 3 0.5285 0.5393 0.000 0.000 0.524 0.000 0.368 0.108
#> SRR1044513 2 0.3748 0.4676 0.000 0.688 0.300 0.000 0.012 0.000
#> SRR1044514 3 0.4092 0.5868 0.000 0.000 0.636 0.000 0.344 0.020
#> SRR1044515 3 0.4213 0.5863 0.000 0.224 0.724 0.000 0.036 0.016
#> SRR1044516 2 0.0146 0.9603 0.000 0.996 0.004 0.000 0.000 0.000
#> SRR1044517 3 0.5595 0.5461 0.000 0.000 0.540 0.000 0.192 0.268
#> SRR1044518 3 0.4153 0.5875 0.000 0.000 0.636 0.000 0.340 0.024
#> SRR1044519 3 0.4532 0.6086 0.000 0.000 0.696 0.000 0.196 0.108
#> SRR1044520 3 0.5877 0.4884 0.000 0.000 0.456 0.000 0.212 0.332
#> SRR1044521 2 0.1296 0.9274 0.000 0.952 0.032 0.000 0.012 0.004
#> SRR1044522 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044523 2 0.3619 0.6262 0.000 0.744 0.232 0.000 0.024 0.000
#> SRR1044524 3 0.0862 0.6509 0.000 0.008 0.972 0.000 0.004 0.016
#> SRR1044525 4 0.2664 0.4981 0.000 0.000 0.000 0.816 0.000 0.184
#> SRR1044526 1 0.6239 -0.4534 0.352 0.000 0.000 0.344 0.300 0.004
#> SRR1044527 2 0.1367 0.9240 0.000 0.944 0.044 0.000 0.012 0.000
#> SRR1044528 2 0.0146 0.9603 0.000 0.996 0.004 0.000 0.000 0.000
#> SRR1044529 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044530 1 0.0790 0.6518 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1044531 1 0.2631 0.5930 0.820 0.000 0.000 0.000 0.180 0.000
#> SRR1044533 1 0.1327 0.6486 0.936 0.000 0.000 0.000 0.064 0.000
#> SRR1044532 1 0.0713 0.6512 0.972 0.000 0.000 0.000 0.028 0.000
#> SRR1044534 2 0.0260 0.9584 0.000 0.992 0.008 0.000 0.000 0.000
#> SRR1044535 3 0.1829 0.6471 0.000 0.000 0.920 0.000 0.056 0.024
#> SRR1044536 2 0.0291 0.9584 0.000 0.992 0.004 0.000 0.000 0.004
#> SRR1044537 1 0.4185 -0.1823 0.496 0.000 0.000 0.012 0.492 0.000
#> SRR1044538 1 0.2178 0.6336 0.868 0.000 0.000 0.000 0.132 0.000
#> SRR1044539 4 0.3333 0.5032 0.000 0.000 0.000 0.784 0.024 0.192
#> SRR1044540 1 0.3271 0.5491 0.760 0.000 0.000 0.008 0.232 0.000
#> SRR1044541 3 0.4770 0.4009 0.000 0.380 0.572 0.000 0.040 0.008
#> SRR1044542 1 0.1204 0.6545 0.944 0.000 0.000 0.000 0.056 0.000
#> SRR1044543 1 0.3681 0.4304 0.796 0.000 0.000 0.144 0.048 0.012
#> SRR1044544 3 0.3032 0.6537 0.000 0.096 0.852 0.000 0.040 0.012
#> SRR1044545 4 0.4206 -0.0580 0.000 0.000 0.000 0.620 0.024 0.356
#> SRR1044546 1 0.3862 -0.0569 0.524 0.000 0.000 0.000 0.476 0.000
#> SRR1044547 4 0.3671 0.4632 0.000 0.000 0.000 0.756 0.036 0.208
#> SRR1044548 1 0.3868 -0.1004 0.508 0.000 0.000 0.000 0.492 0.000
#> SRR1044549 2 0.1501 0.8916 0.000 0.924 0.076 0.000 0.000 0.000
#> SRR1044550 2 0.0603 0.9499 0.000 0.980 0.016 0.000 0.000 0.004
#> SRR1044551 2 0.0146 0.9603 0.000 0.996 0.004 0.000 0.000 0.000
#> SRR1044552 4 0.2730 0.5136 0.000 0.000 0.000 0.808 0.000 0.192
#> SRR1044553 4 0.3868 -0.6209 0.000 0.000 0.000 0.504 0.000 0.496
#> SRR1044554 1 0.3817 0.1308 0.568 0.000 0.000 0.000 0.432 0.000
#> SRR1044555 3 0.0862 0.6498 0.000 0.004 0.972 0.000 0.008 0.016
#> SRR1044556 4 0.3269 0.5120 0.000 0.000 0.000 0.792 0.024 0.184
#> SRR1044557 1 0.3868 -0.1150 0.508 0.000 0.000 0.000 0.492 0.000
#> SRR1044558 4 0.1838 0.6208 0.000 0.000 0.000 0.916 0.016 0.068
#> SRR1044559 5 0.4407 0.0777 0.480 0.000 0.000 0.024 0.496 0.000
#> SRR1044561 4 0.2520 0.5314 0.000 0.000 0.000 0.844 0.004 0.152
#> SRR1044560 3 0.4935 0.3367 0.000 0.424 0.524 0.000 0.040 0.012
#> SRR1044562 1 0.3862 -0.0601 0.524 0.000 0.000 0.000 0.476 0.000
#> SRR1044563 4 0.0891 0.6191 0.000 0.000 0.000 0.968 0.024 0.008
#> SRR1044564 1 0.5556 -0.0678 0.544 0.000 0.000 0.112 0.332 0.012
#> SRR1044565 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044566 3 0.4940 0.3298 0.000 0.428 0.520 0.000 0.040 0.012
#> SRR1044567 1 0.1387 0.6541 0.932 0.000 0.000 0.000 0.068 0.000
#> SRR1044568 4 0.2331 0.6108 0.000 0.000 0.000 0.888 0.032 0.080
#> SRR1044569 1 0.2178 0.6377 0.868 0.000 0.000 0.000 0.132 0.000
#> SRR1044570 1 0.1007 0.6536 0.956 0.000 0.000 0.000 0.044 0.000
#> SRR1044571 1 0.0363 0.6386 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1044572 1 0.3189 0.5508 0.760 0.000 0.000 0.004 0.236 0.000
#> SRR1044573 1 0.3240 0.5235 0.752 0.000 0.000 0.004 0.244 0.000
#> SRR1044574 1 0.3946 0.4703 0.756 0.000 0.000 0.076 0.168 0.000
#> SRR1044575 1 0.1584 0.6523 0.928 0.000 0.000 0.008 0.064 0.000
#> SRR1044576 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044577 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044578 2 0.0000 0.9621 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044579 4 0.2730 0.4571 0.000 0.000 0.000 0.808 0.000 0.192
#> SRR1044580 4 0.5235 0.1974 0.088 0.000 0.000 0.612 0.284 0.016
#> SRR1044581 4 0.1556 0.6022 0.000 0.000 0.000 0.920 0.000 0.080
#> SRR1044582 5 0.3868 0.0113 0.496 0.000 0.000 0.000 0.504 0.000
#> SRR1044583 4 0.2135 0.5572 0.000 0.000 0.000 0.872 0.000 0.128
#> SRR1044584 4 0.1007 0.6105 0.000 0.000 0.000 0.956 0.044 0.000
#> SRR1044585 4 0.1327 0.6109 0.000 0.000 0.000 0.936 0.000 0.064
#> SRR1044586 1 0.3868 -0.1163 0.508 0.000 0.000 0.000 0.492 0.000
#> SRR1044587 6 0.3804 0.7669 0.000 0.000 0.000 0.424 0.000 0.576
#> SRR1044588 6 0.3828 0.7464 0.000 0.000 0.000 0.440 0.000 0.560
#> SRR1044589 6 0.3828 0.7464 0.000 0.000 0.000 0.440 0.000 0.560
#> SRR1044590 6 0.3860 0.6915 0.000 0.000 0.000 0.472 0.000 0.528
#> SRR1044591 6 0.3817 0.7591 0.000 0.000 0.000 0.432 0.000 0.568
#> SRR1044592 6 0.4634 0.7700 0.000 0.000 0.000 0.400 0.044 0.556
#> SRR1044593 6 0.3817 0.7591 0.000 0.000 0.000 0.432 0.000 0.568
#> SRR1044594 6 0.3828 0.7464 0.000 0.000 0.000 0.440 0.000 0.560
#> SRR1044595 1 0.6322 0.0724 0.544 0.000 0.000 0.068 0.136 0.252
#> SRR1044596 6 0.4641 0.7675 0.000 0.000 0.000 0.404 0.044 0.552
#> SRR1044597 4 0.6659 0.1643 0.064 0.088 0.000 0.532 0.284 0.032
#> SRR1044598 1 0.3076 0.5417 0.760 0.000 0.000 0.000 0.240 0.000
#> SRR1044599 1 0.3620 0.3710 0.648 0.000 0.000 0.000 0.352 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)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.4925 0.508 0.508
#> 3 3 0.656 0.561 0.747 0.2847 0.856 0.717
#> 4 4 0.833 0.868 0.934 0.1684 0.805 0.522
#> 5 5 0.788 0.768 0.858 0.0413 0.963 0.856
#> 6 6 0.819 0.806 0.876 0.0376 0.964 0.844
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0 1 0 1
#> SRR1044416 2 0 1 0 1
#> SRR1044417 2 0 1 0 1
#> SRR1044418 2 0 1 0 1
#> SRR1044420 2 0 1 0 1
#> SRR1044419 2 0 1 0 1
#> SRR1044421 2 0 1 0 1
#> SRR1044422 2 0 1 0 1
#> SRR1044423 2 0 1 0 1
#> SRR1044424 2 0 1 0 1
#> SRR1044425 1 0 1 1 0
#> SRR1044426 1 0 1 1 0
#> SRR1044427 1 0 1 1 0
#> SRR1044428 1 0 1 1 0
#> SRR1044429 1 0 1 1 0
#> SRR1044430 1 0 1 1 0
#> SRR1044431 1 0 1 1 0
#> SRR1044433 1 0 1 1 0
#> SRR1044432 1 0 1 1 0
#> SRR1044434 1 0 1 1 0
#> SRR1044435 1 0 1 1 0
#> SRR1044436 1 0 1 1 0
#> SRR1044437 1 0 1 1 0
#> SRR1044439 1 0 1 1 0
#> SRR1044438 1 0 1 1 0
#> SRR1044440 1 0 1 1 0
#> SRR1044441 1 0 1 1 0
#> SRR1044442 1 0 1 1 0
#> SRR1044443 1 0 1 1 0
#> SRR1044444 1 0 1 1 0
#> SRR1044445 1 0 1 1 0
#> SRR1044446 2 0 1 0 1
#> SRR1044447 2 0 1 0 1
#> SRR1044449 2 0 1 0 1
#> SRR1044448 2 0 1 0 1
#> SRR1044450 2 0 1 0 1
#> SRR1044451 2 0 1 0 1
#> SRR1044452 2 0 1 0 1
#> SRR1044453 2 0 1 0 1
#> SRR1044454 2 0 1 0 1
#> SRR1044455 2 0 1 0 1
#> SRR1044456 2 0 1 0 1
#> SRR1044457 2 0 1 0 1
#> SRR1044458 2 0 1 0 1
#> SRR1044459 2 0 1 0 1
#> SRR1044460 2 0 1 0 1
#> SRR1044461 2 0 1 0 1
#> SRR1044462 1 0 1 1 0
#> SRR1044463 1 0 1 1 0
#> SRR1044464 1 0 1 1 0
#> SRR1044466 1 0 1 1 0
#> SRR1044465 1 0 1 1 0
#> SRR1044467 1 0 1 1 0
#> SRR1044468 2 0 1 0 1
#> SRR1044469 2 0 1 0 1
#> SRR1044470 1 0 1 1 0
#> SRR1044471 1 0 1 1 0
#> SRR1044472 1 0 1 1 0
#> SRR1044473 1 0 1 1 0
#> SRR1044474 2 0 1 0 1
#> SRR1044475 2 0 1 0 1
#> SRR1044476 2 0 1 0 1
#> SRR1044477 2 0 1 0 1
#> SRR1044478 2 0 1 0 1
#> SRR1044479 2 0 1 0 1
#> SRR1044480 1 0 1 1 0
#> SRR1044481 1 0 1 1 0
#> SRR1044482 2 0 1 0 1
#> SRR1044483 1 0 1 1 0
#> SRR1044484 1 0 1 1 0
#> SRR1044486 1 0 1 1 0
#> SRR1044485 2 0 1 0 1
#> SRR1044487 2 0 1 0 1
#> SRR1044488 2 0 1 0 1
#> SRR1044489 2 0 1 0 1
#> SRR1044490 1 0 1 1 0
#> SRR1044491 1 0 1 1 0
#> SRR1044492 1 0 1 1 0
#> SRR1044493 1 0 1 1 0
#> SRR1044494 2 0 1 0 1
#> SRR1044496 2 0 1 0 1
#> SRR1044495 2 0 1 0 1
#> SRR1044497 1 0 1 1 0
#> SRR1044499 2 0 1 0 1
#> SRR1044498 1 0 1 1 0
#> SRR1044500 2 0 1 0 1
#> SRR1044501 2 0 1 0 1
#> SRR1044502 2 0 1 0 1
#> SRR1044503 1 0 1 1 0
#> SRR1044504 1 0 1 1 0
#> SRR1044505 1 0 1 1 0
#> SRR1044506 1 0 1 1 0
#> SRR1044507 1 0 1 1 0
#> SRR1044508 1 0 1 1 0
#> SRR1044509 1 0 1 1 0
#> SRR1044510 2 0 1 0 1
#> SRR1044511 2 0 1 0 1
#> SRR1044512 2 0 1 0 1
#> SRR1044513 2 0 1 0 1
#> SRR1044514 2 0 1 0 1
#> SRR1044515 2 0 1 0 1
#> SRR1044516 2 0 1 0 1
#> SRR1044517 2 0 1 0 1
#> SRR1044518 2 0 1 0 1
#> SRR1044519 2 0 1 0 1
#> SRR1044520 2 0 1 0 1
#> SRR1044521 2 0 1 0 1
#> SRR1044522 2 0 1 0 1
#> SRR1044523 2 0 1 0 1
#> SRR1044524 2 0 1 0 1
#> SRR1044525 1 0 1 1 0
#> SRR1044526 1 0 1 1 0
#> SRR1044527 2 0 1 0 1
#> SRR1044528 2 0 1 0 1
#> SRR1044529 2 0 1 0 1
#> SRR1044530 1 0 1 1 0
#> SRR1044531 1 0 1 1 0
#> SRR1044533 1 0 1 1 0
#> SRR1044532 1 0 1 1 0
#> SRR1044534 2 0 1 0 1
#> SRR1044535 2 0 1 0 1
#> SRR1044536 2 0 1 0 1
#> SRR1044537 1 0 1 1 0
#> SRR1044538 1 0 1 1 0
#> SRR1044539 1 0 1 1 0
#> SRR1044540 1 0 1 1 0
#> SRR1044541 2 0 1 0 1
#> SRR1044542 1 0 1 1 0
#> SRR1044543 1 0 1 1 0
#> SRR1044544 2 0 1 0 1
#> SRR1044545 1 0 1 1 0
#> SRR1044546 1 0 1 1 0
#> SRR1044547 1 0 1 1 0
#> SRR1044548 1 0 1 1 0
#> SRR1044549 2 0 1 0 1
#> SRR1044550 2 0 1 0 1
#> SRR1044551 2 0 1 0 1
#> SRR1044552 1 0 1 1 0
#> SRR1044553 1 0 1 1 0
#> SRR1044554 1 0 1 1 0
#> SRR1044555 2 0 1 0 1
#> SRR1044556 1 0 1 1 0
#> SRR1044557 1 0 1 1 0
#> SRR1044558 1 0 1 1 0
#> SRR1044559 1 0 1 1 0
#> SRR1044561 1 0 1 1 0
#> SRR1044560 2 0 1 0 1
#> SRR1044562 1 0 1 1 0
#> SRR1044563 1 0 1 1 0
#> SRR1044564 1 0 1 1 0
#> SRR1044565 2 0 1 0 1
#> SRR1044566 2 0 1 0 1
#> SRR1044567 1 0 1 1 0
#> SRR1044568 1 0 1 1 0
#> SRR1044569 1 0 1 1 0
#> SRR1044570 1 0 1 1 0
#> SRR1044571 1 0 1 1 0
#> SRR1044572 1 0 1 1 0
#> SRR1044573 1 0 1 1 0
#> SRR1044574 1 0 1 1 0
#> SRR1044575 1 0 1 1 0
#> SRR1044576 2 0 1 0 1
#> SRR1044577 2 0 1 0 1
#> SRR1044578 2 0 1 0 1
#> SRR1044579 1 0 1 1 0
#> SRR1044580 1 0 1 1 0
#> SRR1044581 1 0 1 1 0
#> SRR1044582 1 0 1 1 0
#> SRR1044583 1 0 1 1 0
#> SRR1044584 1 0 1 1 0
#> SRR1044585 1 0 1 1 0
#> SRR1044586 1 0 1 1 0
#> SRR1044587 1 0 1 1 0
#> SRR1044588 1 0 1 1 0
#> SRR1044589 1 0 1 1 0
#> SRR1044590 1 0 1 1 0
#> SRR1044591 1 0 1 1 0
#> SRR1044592 1 0 1 1 0
#> SRR1044593 1 0 1 1 0
#> SRR1044594 1 0 1 1 0
#> SRR1044595 1 0 1 1 0
#> SRR1044596 1 0 1 1 0
#> SRR1044597 1 0 1 1 0
#> SRR1044598 1 0 1 1 0
#> SRR1044599 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044416 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044417 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044418 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044420 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044419 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044421 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044422 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044423 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044424 2 0.2448 0.863 0.000 0.924 0.076
#> SRR1044425 1 0.6299 -0.807 0.524 0.000 0.476
#> SRR1044426 3 0.5560 0.588 0.300 0.000 0.700
#> SRR1044427 1 0.6274 -0.755 0.544 0.000 0.456
#> SRR1044428 3 0.6244 0.880 0.440 0.000 0.560
#> SRR1044429 1 0.6305 -0.820 0.516 0.000 0.484
#> SRR1044430 3 0.5733 0.682 0.324 0.000 0.676
#> SRR1044431 3 0.6305 0.876 0.484 0.000 0.516
#> SRR1044433 1 0.6225 0.302 0.568 0.000 0.432
#> SRR1044432 3 0.5529 0.636 0.296 0.000 0.704
#> SRR1044434 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044435 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044436 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044437 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044439 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044438 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044440 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044441 1 0.0237 0.594 0.996 0.000 0.004
#> SRR1044442 1 0.5948 0.343 0.640 0.000 0.360
#> SRR1044443 1 0.6225 0.302 0.568 0.000 0.432
#> SRR1044444 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044445 1 0.0592 0.593 0.988 0.000 0.012
#> SRR1044446 2 0.6280 0.706 0.000 0.540 0.460
#> SRR1044447 2 0.6280 0.706 0.000 0.540 0.460
#> SRR1044449 2 0.6295 0.698 0.000 0.528 0.472
#> SRR1044448 2 0.6299 0.695 0.000 0.524 0.476
#> SRR1044450 2 0.6299 0.695 0.000 0.524 0.476
#> SRR1044451 2 0.6225 0.723 0.000 0.568 0.432
#> SRR1044452 2 0.6244 0.721 0.000 0.560 0.440
#> SRR1044453 2 0.5926 0.766 0.000 0.644 0.356
#> SRR1044454 2 0.5859 0.771 0.000 0.656 0.344
#> SRR1044455 2 0.6045 0.752 0.000 0.620 0.380
#> SRR1044456 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044457 2 0.0424 0.877 0.000 0.992 0.008
#> SRR1044458 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044459 2 0.6299 0.695 0.000 0.524 0.476
#> SRR1044460 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044461 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044462 1 0.5859 -0.459 0.656 0.000 0.344
#> SRR1044463 3 0.6274 0.887 0.456 0.000 0.544
#> SRR1044464 1 0.5291 0.394 0.732 0.000 0.268
#> SRR1044466 3 0.6244 0.879 0.440 0.000 0.560
#> SRR1044465 3 0.6307 0.871 0.488 0.000 0.512
#> SRR1044467 3 0.6295 0.883 0.472 0.000 0.528
#> SRR1044468 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044469 2 0.3686 0.845 0.000 0.860 0.140
#> SRR1044470 3 0.6267 0.886 0.452 0.000 0.548
#> SRR1044471 1 0.6305 -0.818 0.516 0.000 0.484
#> SRR1044472 3 0.5882 0.729 0.348 0.000 0.652
#> SRR1044473 1 0.6291 -0.780 0.532 0.000 0.468
#> SRR1044474 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044475 2 0.4654 0.824 0.000 0.792 0.208
#> SRR1044476 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044477 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044478 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044479 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044480 1 0.0592 0.584 0.988 0.000 0.012
#> SRR1044481 1 0.6280 -0.764 0.540 0.000 0.460
#> SRR1044482 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044483 1 0.0237 0.594 0.996 0.000 0.004
#> SRR1044484 1 0.6291 -0.782 0.532 0.000 0.468
#> SRR1044486 1 0.6291 -0.781 0.532 0.000 0.468
#> SRR1044485 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044487 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044488 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044489 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044490 3 0.6260 0.880 0.448 0.000 0.552
#> SRR1044491 3 0.6307 0.866 0.488 0.000 0.512
#> SRR1044492 3 0.6307 0.870 0.488 0.000 0.512
#> SRR1044493 3 0.6260 0.884 0.448 0.000 0.552
#> SRR1044494 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044496 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044495 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044497 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044499 2 0.3482 0.848 0.000 0.872 0.128
#> SRR1044498 1 0.6280 -0.764 0.540 0.000 0.460
#> SRR1044500 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044501 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044502 2 0.6140 0.739 0.000 0.596 0.404
#> SRR1044503 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044504 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044505 1 0.6267 -0.743 0.548 0.000 0.452
#> SRR1044506 1 0.0592 0.593 0.988 0.000 0.012
#> SRR1044507 1 0.6140 0.318 0.596 0.000 0.404
#> SRR1044508 1 0.6225 0.302 0.568 0.000 0.432
#> SRR1044509 1 0.6225 0.302 0.568 0.000 0.432
#> SRR1044510 2 0.6299 0.695 0.000 0.524 0.476
#> SRR1044511 2 0.6299 0.695 0.000 0.524 0.476
#> SRR1044512 2 0.6299 0.695 0.000 0.524 0.476
#> SRR1044513 2 0.5859 0.768 0.000 0.656 0.344
#> SRR1044514 2 0.6299 0.695 0.000 0.524 0.476
#> SRR1044515 2 0.5291 0.800 0.000 0.732 0.268
#> SRR1044516 2 0.0424 0.877 0.000 0.992 0.008
#> SRR1044517 2 0.6299 0.695 0.000 0.524 0.476
#> SRR1044518 2 0.6299 0.695 0.000 0.524 0.476
#> SRR1044519 2 0.6295 0.698 0.000 0.528 0.472
#> SRR1044520 2 0.6295 0.698 0.000 0.528 0.472
#> SRR1044521 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044522 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044523 2 0.0424 0.877 0.000 0.992 0.008
#> SRR1044524 2 0.5138 0.811 0.000 0.748 0.252
#> SRR1044525 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044526 1 0.6260 -0.733 0.552 0.000 0.448
#> SRR1044527 2 0.0237 0.878 0.000 0.996 0.004
#> SRR1044528 2 0.4702 0.817 0.000 0.788 0.212
#> SRR1044529 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044530 3 0.6286 0.887 0.464 0.000 0.536
#> SRR1044531 3 0.6299 0.884 0.476 0.000 0.524
#> SRR1044533 3 0.6244 0.874 0.440 0.000 0.560
#> SRR1044532 3 0.6302 0.877 0.480 0.000 0.520
#> SRR1044534 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044535 2 0.6154 0.737 0.000 0.592 0.408
#> SRR1044536 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044537 1 0.6302 -0.810 0.520 0.000 0.480
#> SRR1044538 3 0.6291 0.885 0.468 0.000 0.532
#> SRR1044539 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044540 3 0.6140 0.824 0.404 0.000 0.596
#> SRR1044541 2 0.5835 0.774 0.000 0.660 0.340
#> SRR1044542 3 0.6307 0.866 0.488 0.000 0.512
#> SRR1044543 3 0.6126 0.814 0.400 0.000 0.600
#> SRR1044544 2 0.3116 0.855 0.000 0.892 0.108
#> SRR1044545 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044546 1 0.6309 -0.840 0.504 0.000 0.496
#> SRR1044547 1 0.1163 0.563 0.972 0.000 0.028
#> SRR1044548 3 0.6309 0.840 0.500 0.000 0.500
#> SRR1044549 2 0.1031 0.874 0.000 0.976 0.024
#> SRR1044550 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044551 2 0.0237 0.878 0.000 0.996 0.004
#> SRR1044552 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044553 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044554 1 0.6308 -0.831 0.508 0.000 0.492
#> SRR1044555 2 0.5706 0.784 0.000 0.680 0.320
#> SRR1044556 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044557 3 0.6309 0.846 0.496 0.000 0.504
#> SRR1044558 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044559 3 0.6295 0.856 0.472 0.000 0.528
#> SRR1044561 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044560 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044562 1 0.6308 -0.831 0.508 0.000 0.492
#> SRR1044563 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044564 1 0.6267 -0.747 0.548 0.000 0.452
#> SRR1044565 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044566 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044567 3 0.6305 0.872 0.484 0.000 0.516
#> SRR1044568 1 0.0237 0.594 0.996 0.000 0.004
#> SRR1044569 1 0.6307 -0.828 0.512 0.000 0.488
#> SRR1044570 3 0.6302 0.877 0.480 0.000 0.520
#> SRR1044571 3 0.6215 0.855 0.428 0.000 0.572
#> SRR1044572 3 0.6286 0.887 0.464 0.000 0.536
#> SRR1044573 1 0.6291 -0.780 0.532 0.000 0.468
#> SRR1044574 3 0.6295 0.886 0.472 0.000 0.528
#> SRR1044575 3 0.6305 0.876 0.484 0.000 0.516
#> SRR1044576 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044577 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044578 2 0.0000 0.879 0.000 1.000 0.000
#> SRR1044579 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044580 1 0.6180 -0.671 0.584 0.000 0.416
#> SRR1044581 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044582 1 0.6308 -0.831 0.508 0.000 0.492
#> SRR1044583 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044584 1 0.0237 0.594 0.996 0.000 0.004
#> SRR1044585 1 0.0000 0.597 1.000 0.000 0.000
#> SRR1044586 1 0.6291 -0.781 0.532 0.000 0.468
#> SRR1044587 1 0.0592 0.593 0.988 0.000 0.012
#> SRR1044588 1 0.0592 0.593 0.988 0.000 0.012
#> SRR1044589 1 0.0592 0.593 0.988 0.000 0.012
#> SRR1044590 1 0.0592 0.593 0.988 0.000 0.012
#> SRR1044591 1 0.0592 0.593 0.988 0.000 0.012
#> SRR1044592 1 0.6225 0.302 0.568 0.000 0.432
#> SRR1044593 1 0.0592 0.593 0.988 0.000 0.012
#> SRR1044594 1 0.0592 0.593 0.988 0.000 0.012
#> SRR1044595 1 0.6225 0.295 0.568 0.000 0.432
#> SRR1044596 1 0.5216 0.406 0.740 0.000 0.260
#> SRR1044597 1 0.5178 0.405 0.744 0.000 0.256
#> SRR1044598 3 0.6260 0.847 0.448 0.000 0.552
#> SRR1044599 3 0.6260 0.847 0.448 0.000 0.552
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044416 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044417 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044418 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044420 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044419 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044421 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044422 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044423 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044424 2 0.3801 0.688 0.000 0.780 0.220 0.000
#> SRR1044425 1 0.4284 0.730 0.780 0.000 0.020 0.200
#> SRR1044426 1 0.2589 0.852 0.884 0.000 0.116 0.000
#> SRR1044427 1 0.2281 0.885 0.904 0.000 0.000 0.096
#> SRR1044428 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044429 1 0.0707 0.953 0.980 0.000 0.000 0.020
#> SRR1044430 1 0.1174 0.944 0.968 0.000 0.012 0.020
#> SRR1044431 1 0.0469 0.957 0.988 0.000 0.000 0.012
#> SRR1044433 4 0.7612 0.436 0.260 0.000 0.264 0.476
#> SRR1044432 1 0.0188 0.959 0.996 0.000 0.004 0.000
#> SRR1044434 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044435 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044436 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044437 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044439 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044438 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044440 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044441 4 0.1256 0.847 0.008 0.000 0.028 0.964
#> SRR1044442 4 0.7612 0.436 0.260 0.000 0.264 0.476
#> SRR1044443 4 0.7612 0.436 0.260 0.000 0.264 0.476
#> SRR1044444 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044445 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044446 3 0.0188 0.894 0.000 0.004 0.996 0.000
#> SRR1044447 3 0.1389 0.885 0.000 0.048 0.952 0.000
#> SRR1044449 3 0.0000 0.893 0.000 0.000 1.000 0.000
#> SRR1044448 3 0.0000 0.893 0.000 0.000 1.000 0.000
#> SRR1044450 3 0.0000 0.893 0.000 0.000 1.000 0.000
#> SRR1044451 3 0.1211 0.888 0.000 0.040 0.960 0.000
#> SRR1044452 3 0.0188 0.893 0.000 0.004 0.996 0.000
#> SRR1044453 3 0.0469 0.893 0.000 0.012 0.988 0.000
#> SRR1044454 3 0.0921 0.888 0.000 0.028 0.972 0.000
#> SRR1044455 3 0.3610 0.755 0.000 0.200 0.800 0.000
#> SRR1044456 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044457 2 0.3024 0.811 0.000 0.852 0.148 0.000
#> SRR1044458 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044459 3 0.0000 0.893 0.000 0.000 1.000 0.000
#> SRR1044460 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044461 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044462 1 0.4776 0.361 0.624 0.000 0.000 0.376
#> SRR1044463 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044464 4 0.7612 0.437 0.264 0.000 0.260 0.476
#> SRR1044466 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044465 1 0.0188 0.961 0.996 0.000 0.000 0.004
#> SRR1044467 1 0.0188 0.961 0.996 0.000 0.000 0.004
#> SRR1044468 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044469 3 0.4605 0.563 0.000 0.336 0.664 0.000
#> SRR1044470 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044471 1 0.0188 0.961 0.996 0.000 0.000 0.004
#> SRR1044472 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044473 1 0.0188 0.961 0.996 0.000 0.000 0.004
#> SRR1044474 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044475 3 0.4790 0.470 0.000 0.380 0.620 0.000
#> SRR1044476 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044477 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044478 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044479 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044480 4 0.3726 0.705 0.212 0.000 0.000 0.788
#> SRR1044481 1 0.2011 0.900 0.920 0.000 0.000 0.080
#> SRR1044482 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044483 4 0.0469 0.859 0.012 0.000 0.000 0.988
#> SRR1044484 1 0.3219 0.798 0.836 0.000 0.000 0.164
#> SRR1044486 1 0.0707 0.951 0.980 0.000 0.000 0.020
#> SRR1044485 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044487 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044488 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044489 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044490 1 0.0188 0.961 0.996 0.000 0.000 0.004
#> SRR1044491 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044492 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044493 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044494 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044496 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044495 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044497 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044499 3 0.4925 0.354 0.000 0.428 0.572 0.000
#> SRR1044498 1 0.3610 0.742 0.800 0.000 0.000 0.200
#> SRR1044500 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044501 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044502 3 0.1211 0.888 0.000 0.040 0.960 0.000
#> SRR1044503 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044504 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044505 1 0.1792 0.916 0.932 0.000 0.000 0.068
#> SRR1044506 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044507 4 0.7612 0.436 0.260 0.000 0.264 0.476
#> SRR1044508 4 0.7612 0.436 0.260 0.000 0.264 0.476
#> SRR1044509 4 0.7612 0.436 0.260 0.000 0.264 0.476
#> SRR1044510 3 0.0000 0.893 0.000 0.000 1.000 0.000
#> SRR1044511 3 0.0000 0.893 0.000 0.000 1.000 0.000
#> SRR1044512 3 0.0000 0.893 0.000 0.000 1.000 0.000
#> SRR1044513 3 0.4761 0.470 0.000 0.372 0.628 0.000
#> SRR1044514 3 0.0000 0.893 0.000 0.000 1.000 0.000
#> SRR1044515 3 0.4730 0.492 0.000 0.364 0.636 0.000
#> SRR1044516 2 0.0921 0.949 0.000 0.972 0.028 0.000
#> SRR1044517 3 0.0000 0.893 0.000 0.000 1.000 0.000
#> SRR1044518 3 0.0000 0.893 0.000 0.000 1.000 0.000
#> SRR1044519 3 0.0000 0.893 0.000 0.000 1.000 0.000
#> SRR1044520 3 0.0000 0.893 0.000 0.000 1.000 0.000
#> SRR1044521 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044522 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044523 2 0.2530 0.856 0.000 0.888 0.112 0.000
#> SRR1044524 3 0.1389 0.885 0.000 0.048 0.952 0.000
#> SRR1044525 4 0.0895 0.853 0.020 0.000 0.004 0.976
#> SRR1044526 1 0.2281 0.888 0.904 0.000 0.000 0.096
#> SRR1044527 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044528 2 0.4679 0.401 0.000 0.648 0.352 0.000
#> SRR1044529 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044530 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044531 1 0.0188 0.961 0.996 0.000 0.000 0.004
#> SRR1044533 1 0.0188 0.961 0.996 0.000 0.000 0.004
#> SRR1044532 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044534 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044535 3 0.1022 0.890 0.000 0.032 0.968 0.000
#> SRR1044536 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044537 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044538 1 0.0188 0.961 0.996 0.000 0.000 0.004
#> SRR1044539 4 0.0336 0.860 0.008 0.000 0.000 0.992
#> SRR1044540 1 0.0188 0.961 0.996 0.000 0.000 0.004
#> SRR1044541 3 0.1637 0.879 0.000 0.060 0.940 0.000
#> SRR1044542 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044543 1 0.0188 0.961 0.996 0.000 0.000 0.004
#> SRR1044544 3 0.4382 0.618 0.000 0.296 0.704 0.000
#> SRR1044545 4 0.0336 0.860 0.008 0.000 0.000 0.992
#> SRR1044546 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044547 4 0.2647 0.789 0.120 0.000 0.000 0.880
#> SRR1044548 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044549 2 0.3311 0.774 0.000 0.828 0.172 0.000
#> SRR1044550 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044551 2 0.0188 0.972 0.000 0.996 0.004 0.000
#> SRR1044552 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044553 4 0.0188 0.862 0.004 0.000 0.000 0.996
#> SRR1044554 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044555 3 0.0817 0.893 0.000 0.024 0.976 0.000
#> SRR1044556 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044557 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044558 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044559 1 0.2521 0.897 0.912 0.000 0.024 0.064
#> SRR1044561 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044560 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044562 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044563 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044564 1 0.0592 0.955 0.984 0.000 0.000 0.016
#> SRR1044565 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044566 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044567 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044568 4 0.2918 0.788 0.116 0.000 0.008 0.876
#> SRR1044569 1 0.0188 0.961 0.996 0.000 0.000 0.004
#> SRR1044570 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044571 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044572 1 0.0188 0.961 0.996 0.000 0.000 0.004
#> SRR1044573 1 0.0188 0.961 0.996 0.000 0.000 0.004
#> SRR1044574 1 0.0188 0.961 0.996 0.000 0.000 0.004
#> SRR1044575 1 0.0188 0.961 0.996 0.000 0.000 0.004
#> SRR1044576 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044577 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044578 2 0.0000 0.976 0.000 1.000 0.000 0.000
#> SRR1044579 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044580 1 0.4485 0.663 0.740 0.000 0.012 0.248
#> SRR1044581 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044582 1 0.0336 0.960 0.992 0.000 0.000 0.008
#> SRR1044583 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044584 4 0.2345 0.803 0.100 0.000 0.000 0.900
#> SRR1044585 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044586 1 0.0817 0.950 0.976 0.000 0.000 0.024
#> SRR1044587 4 0.0188 0.862 0.004 0.000 0.000 0.996
#> SRR1044588 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044589 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044590 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044591 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044592 4 0.7612 0.436 0.260 0.000 0.264 0.476
#> SRR1044593 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044594 4 0.0000 0.863 0.000 0.000 0.000 1.000
#> SRR1044595 4 0.7676 0.414 0.276 0.000 0.264 0.460
#> SRR1044596 4 0.7594 0.439 0.256 0.000 0.264 0.480
#> SRR1044597 4 0.7612 0.437 0.264 0.000 0.260 0.476
#> SRR1044598 1 0.0000 0.961 1.000 0.000 0.000 0.000
#> SRR1044599 1 0.0000 0.961 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.0290 0.9205 0.000 0.992 0.000 0.000 0.008
#> SRR1044416 2 0.0703 0.9207 0.000 0.976 0.000 0.000 0.024
#> SRR1044417 2 0.0609 0.9219 0.000 0.980 0.000 0.000 0.020
#> SRR1044418 2 0.0703 0.9216 0.000 0.976 0.000 0.000 0.024
#> SRR1044420 2 0.0000 0.9210 0.000 1.000 0.000 0.000 0.000
#> SRR1044419 2 0.1197 0.9055 0.000 0.952 0.000 0.000 0.048
#> SRR1044421 2 0.1197 0.9086 0.000 0.952 0.000 0.000 0.048
#> SRR1044422 2 0.0290 0.9198 0.000 0.992 0.000 0.000 0.008
#> SRR1044423 2 0.0162 0.9218 0.000 0.996 0.000 0.000 0.004
#> SRR1044424 2 0.4835 0.6819 0.000 0.724 0.120 0.000 0.156
#> SRR1044425 1 0.6035 0.3820 0.580 0.000 0.000 0.216 0.204
#> SRR1044426 1 0.3496 0.8063 0.832 0.000 0.040 0.004 0.124
#> SRR1044427 1 0.4351 0.7346 0.768 0.000 0.000 0.100 0.132
#> SRR1044428 1 0.1544 0.8793 0.932 0.000 0.000 0.000 0.068
#> SRR1044429 1 0.2669 0.8552 0.876 0.000 0.000 0.020 0.104
#> SRR1044430 1 0.2635 0.8545 0.888 0.000 0.016 0.008 0.088
#> SRR1044431 1 0.2011 0.8733 0.908 0.000 0.000 0.004 0.088
#> SRR1044433 5 0.7742 0.4672 0.192 0.000 0.076 0.336 0.396
#> SRR1044432 1 0.1928 0.8653 0.920 0.000 0.004 0.004 0.072
#> SRR1044434 4 0.0000 0.9420 0.000 0.000 0.000 1.000 0.000
#> SRR1044435 4 0.0000 0.9420 0.000 0.000 0.000 1.000 0.000
#> SRR1044436 4 0.0162 0.9405 0.000 0.000 0.000 0.996 0.004
#> SRR1044437 4 0.0000 0.9420 0.000 0.000 0.000 1.000 0.000
#> SRR1044439 4 0.0162 0.9405 0.000 0.000 0.000 0.996 0.004
#> SRR1044438 4 0.1195 0.9065 0.028 0.000 0.000 0.960 0.012
#> SRR1044440 4 0.0000 0.9420 0.000 0.000 0.000 1.000 0.000
#> SRR1044441 4 0.0932 0.9269 0.004 0.000 0.004 0.972 0.020
#> SRR1044442 5 0.7742 0.4672 0.192 0.000 0.076 0.336 0.396
#> SRR1044443 5 0.7742 0.4672 0.192 0.000 0.076 0.336 0.396
#> SRR1044444 4 0.0000 0.9420 0.000 0.000 0.000 1.000 0.000
#> SRR1044445 4 0.0290 0.9402 0.000 0.000 0.000 0.992 0.008
#> SRR1044446 3 0.1831 0.7540 0.000 0.004 0.920 0.000 0.076
#> SRR1044447 3 0.5998 0.4984 0.000 0.112 0.464 0.000 0.424
#> SRR1044449 3 0.0162 0.7731 0.000 0.000 0.996 0.000 0.004
#> SRR1044448 3 0.0000 0.7730 0.000 0.000 1.000 0.000 0.000
#> SRR1044450 3 0.0290 0.7698 0.000 0.000 0.992 0.000 0.008
#> SRR1044451 3 0.5867 0.5287 0.000 0.100 0.496 0.000 0.404
#> SRR1044452 3 0.1626 0.7641 0.000 0.016 0.940 0.000 0.044
#> SRR1044453 3 0.2110 0.7556 0.000 0.016 0.912 0.000 0.072
#> SRR1044454 3 0.2793 0.7431 0.000 0.036 0.876 0.000 0.088
#> SRR1044455 3 0.6162 0.4579 0.000 0.132 0.436 0.000 0.432
#> SRR1044456 2 0.1041 0.9206 0.000 0.964 0.004 0.000 0.032
#> SRR1044457 5 0.5964 -0.2399 0.000 0.428 0.108 0.000 0.464
#> SRR1044458 2 0.3837 0.6450 0.000 0.692 0.000 0.000 0.308
#> SRR1044459 3 0.0162 0.7735 0.000 0.000 0.996 0.000 0.004
#> SRR1044460 2 0.0404 0.9217 0.000 0.988 0.000 0.000 0.012
#> SRR1044461 2 0.1478 0.8952 0.000 0.936 0.000 0.000 0.064
#> SRR1044462 1 0.6564 -0.0513 0.444 0.000 0.000 0.344 0.212
#> SRR1044463 1 0.1410 0.8788 0.940 0.000 0.000 0.000 0.060
#> SRR1044464 5 0.7742 0.4672 0.192 0.000 0.076 0.336 0.396
#> SRR1044466 1 0.1608 0.8761 0.928 0.000 0.000 0.000 0.072
#> SRR1044465 1 0.1341 0.8831 0.944 0.000 0.000 0.000 0.056
#> SRR1044467 1 0.0794 0.8879 0.972 0.000 0.000 0.000 0.028
#> SRR1044468 2 0.0162 0.9203 0.000 0.996 0.000 0.000 0.004
#> SRR1044469 5 0.6738 -0.2766 0.000 0.308 0.280 0.000 0.412
#> SRR1044470 1 0.0609 0.8884 0.980 0.000 0.000 0.000 0.020
#> SRR1044471 1 0.1043 0.8879 0.960 0.000 0.000 0.000 0.040
#> SRR1044472 1 0.2179 0.8634 0.896 0.000 0.000 0.004 0.100
#> SRR1044473 1 0.1597 0.8868 0.940 0.000 0.000 0.012 0.048
#> SRR1044474 2 0.0703 0.9207 0.000 0.976 0.000 0.000 0.024
#> SRR1044475 3 0.6660 0.3130 0.000 0.324 0.432 0.000 0.244
#> SRR1044476 2 0.3074 0.7778 0.000 0.804 0.000 0.000 0.196
#> SRR1044477 2 0.0703 0.9207 0.000 0.976 0.000 0.000 0.024
#> SRR1044478 2 0.1410 0.9011 0.000 0.940 0.000 0.000 0.060
#> SRR1044479 2 0.0703 0.9207 0.000 0.976 0.000 0.000 0.024
#> SRR1044480 4 0.4548 0.5706 0.156 0.000 0.000 0.748 0.096
#> SRR1044481 1 0.3459 0.8170 0.832 0.000 0.000 0.052 0.116
#> SRR1044482 2 0.0703 0.9207 0.000 0.976 0.000 0.000 0.024
#> SRR1044483 4 0.0290 0.9392 0.000 0.000 0.000 0.992 0.008
#> SRR1044484 1 0.4720 0.6779 0.736 0.000 0.000 0.124 0.140
#> SRR1044486 1 0.1981 0.8794 0.920 0.000 0.000 0.016 0.064
#> SRR1044485 2 0.0703 0.9207 0.000 0.976 0.000 0.000 0.024
#> SRR1044487 2 0.0703 0.9207 0.000 0.976 0.000 0.000 0.024
#> SRR1044488 2 0.0510 0.9186 0.000 0.984 0.000 0.000 0.016
#> SRR1044489 2 0.0510 0.9186 0.000 0.984 0.000 0.000 0.016
#> SRR1044490 1 0.1197 0.8842 0.952 0.000 0.000 0.000 0.048
#> SRR1044491 1 0.1478 0.8771 0.936 0.000 0.000 0.000 0.064
#> SRR1044492 1 0.1341 0.8805 0.944 0.000 0.000 0.000 0.056
#> SRR1044493 1 0.1478 0.8771 0.936 0.000 0.000 0.000 0.064
#> SRR1044494 2 0.0703 0.9207 0.000 0.976 0.000 0.000 0.024
#> SRR1044496 2 0.0703 0.9207 0.000 0.976 0.000 0.000 0.024
#> SRR1044495 2 0.0703 0.9207 0.000 0.976 0.000 0.000 0.024
#> SRR1044497 4 0.0162 0.9405 0.000 0.000 0.000 0.996 0.004
#> SRR1044499 5 0.6685 -0.2322 0.000 0.340 0.244 0.000 0.416
#> SRR1044498 1 0.5819 0.4531 0.612 0.000 0.000 0.188 0.200
#> SRR1044500 2 0.0404 0.9192 0.000 0.988 0.000 0.000 0.012
#> SRR1044501 2 0.3913 0.6222 0.000 0.676 0.000 0.000 0.324
#> SRR1044502 3 0.5717 0.5540 0.000 0.092 0.540 0.000 0.368
#> SRR1044503 4 0.0162 0.9405 0.000 0.000 0.000 0.996 0.004
#> SRR1044504 4 0.0000 0.9420 0.000 0.000 0.000 1.000 0.000
#> SRR1044505 1 0.3657 0.8088 0.820 0.000 0.000 0.064 0.116
#> SRR1044506 4 0.0290 0.9402 0.000 0.000 0.000 0.992 0.008
#> SRR1044507 5 0.7742 0.4672 0.192 0.000 0.076 0.336 0.396
#> SRR1044508 5 0.7742 0.4672 0.192 0.000 0.076 0.336 0.396
#> SRR1044509 5 0.7742 0.4672 0.192 0.000 0.076 0.336 0.396
#> SRR1044510 3 0.0000 0.7730 0.000 0.000 1.000 0.000 0.000
#> SRR1044511 3 0.0404 0.7727 0.000 0.000 0.988 0.000 0.012
#> SRR1044512 3 0.0000 0.7730 0.000 0.000 1.000 0.000 0.000
#> SRR1044513 5 0.6475 -0.4372 0.000 0.184 0.388 0.000 0.428
#> SRR1044514 3 0.0000 0.7730 0.000 0.000 1.000 0.000 0.000
#> SRR1044515 5 0.6503 -0.3809 0.000 0.204 0.332 0.000 0.464
#> SRR1044516 2 0.2653 0.8558 0.000 0.880 0.024 0.000 0.096
#> SRR1044517 3 0.0000 0.7730 0.000 0.000 1.000 0.000 0.000
#> SRR1044518 3 0.0000 0.7730 0.000 0.000 1.000 0.000 0.000
#> SRR1044519 3 0.0290 0.7733 0.000 0.000 0.992 0.000 0.008
#> SRR1044520 3 0.0290 0.7733 0.000 0.000 0.992 0.000 0.008
#> SRR1044521 2 0.0798 0.9179 0.000 0.976 0.008 0.000 0.016
#> SRR1044522 2 0.0703 0.9207 0.000 0.976 0.000 0.000 0.024
#> SRR1044523 2 0.5666 0.4699 0.000 0.592 0.108 0.000 0.300
#> SRR1044524 3 0.5884 0.5257 0.000 0.100 0.480 0.000 0.420
#> SRR1044525 4 0.1478 0.8874 0.000 0.000 0.000 0.936 0.064
#> SRR1044526 1 0.3758 0.8028 0.816 0.000 0.000 0.096 0.088
#> SRR1044527 2 0.0955 0.9151 0.000 0.968 0.004 0.000 0.028
#> SRR1044528 2 0.6309 0.2697 0.000 0.528 0.208 0.000 0.264
#> SRR1044529 2 0.0703 0.9207 0.000 0.976 0.000 0.000 0.024
#> SRR1044530 1 0.1410 0.8788 0.940 0.000 0.000 0.000 0.060
#> SRR1044531 1 0.0794 0.8893 0.972 0.000 0.000 0.000 0.028
#> SRR1044533 1 0.1121 0.8853 0.956 0.000 0.000 0.000 0.044
#> SRR1044532 1 0.1478 0.8771 0.936 0.000 0.000 0.000 0.064
#> SRR1044534 2 0.0771 0.9176 0.000 0.976 0.004 0.000 0.020
#> SRR1044535 3 0.5627 0.5664 0.000 0.084 0.548 0.000 0.368
#> SRR1044536 2 0.0671 0.9186 0.000 0.980 0.004 0.000 0.016
#> SRR1044537 1 0.1877 0.8815 0.924 0.000 0.000 0.012 0.064
#> SRR1044538 1 0.1270 0.8811 0.948 0.000 0.000 0.000 0.052
#> SRR1044539 4 0.0404 0.9376 0.000 0.000 0.000 0.988 0.012
#> SRR1044540 1 0.1197 0.8842 0.952 0.000 0.000 0.000 0.048
#> SRR1044541 3 0.6127 0.4894 0.000 0.128 0.456 0.000 0.416
#> SRR1044542 1 0.1478 0.8771 0.936 0.000 0.000 0.000 0.064
#> SRR1044543 1 0.1197 0.8842 0.952 0.000 0.000 0.000 0.048
#> SRR1044544 5 0.6402 -0.4116 0.000 0.180 0.348 0.000 0.472
#> SRR1044545 4 0.0798 0.9258 0.016 0.000 0.000 0.976 0.008
#> SRR1044546 1 0.1732 0.8778 0.920 0.000 0.000 0.000 0.080
#> SRR1044547 4 0.3967 0.6888 0.092 0.000 0.000 0.800 0.108
#> SRR1044548 1 0.1671 0.8811 0.924 0.000 0.000 0.000 0.076
#> SRR1044549 2 0.5184 0.6084 0.000 0.688 0.136 0.000 0.176
#> SRR1044550 2 0.0162 0.9203 0.000 0.996 0.000 0.000 0.004
#> SRR1044551 2 0.1357 0.9055 0.000 0.948 0.004 0.000 0.048
#> SRR1044552 4 0.0000 0.9420 0.000 0.000 0.000 1.000 0.000
#> SRR1044553 4 0.0000 0.9420 0.000 0.000 0.000 1.000 0.000
#> SRR1044554 1 0.1671 0.8779 0.924 0.000 0.000 0.000 0.076
#> SRR1044555 3 0.5415 0.5847 0.000 0.064 0.552 0.000 0.384
#> SRR1044556 4 0.0162 0.9405 0.000 0.000 0.000 0.996 0.004
#> SRR1044557 1 0.1792 0.8765 0.916 0.000 0.000 0.000 0.084
#> SRR1044558 4 0.0000 0.9420 0.000 0.000 0.000 1.000 0.000
#> SRR1044559 1 0.3455 0.8457 0.844 0.000 0.020 0.024 0.112
#> SRR1044561 4 0.0000 0.9420 0.000 0.000 0.000 1.000 0.000
#> SRR1044560 2 0.3210 0.7627 0.000 0.788 0.000 0.000 0.212
#> SRR1044562 1 0.1671 0.8796 0.924 0.000 0.000 0.000 0.076
#> SRR1044563 4 0.0000 0.9420 0.000 0.000 0.000 1.000 0.000
#> SRR1044564 1 0.2795 0.8523 0.872 0.000 0.000 0.028 0.100
#> SRR1044565 2 0.0703 0.9207 0.000 0.976 0.000 0.000 0.024
#> SRR1044566 2 0.2813 0.8053 0.000 0.832 0.000 0.000 0.168
#> SRR1044567 1 0.1608 0.8792 0.928 0.000 0.000 0.000 0.072
#> SRR1044568 4 0.4521 0.6021 0.088 0.000 0.000 0.748 0.164
#> SRR1044569 1 0.1197 0.8865 0.952 0.000 0.000 0.000 0.048
#> SRR1044570 1 0.1478 0.8771 0.936 0.000 0.000 0.000 0.064
#> SRR1044571 1 0.1197 0.8859 0.952 0.000 0.000 0.000 0.048
#> SRR1044572 1 0.1197 0.8842 0.952 0.000 0.000 0.000 0.048
#> SRR1044573 1 0.1410 0.8833 0.940 0.000 0.000 0.000 0.060
#> SRR1044574 1 0.1341 0.8840 0.944 0.000 0.000 0.000 0.056
#> SRR1044575 1 0.1197 0.8842 0.952 0.000 0.000 0.000 0.048
#> SRR1044576 2 0.0510 0.9216 0.000 0.984 0.000 0.000 0.016
#> SRR1044577 2 0.0290 0.9217 0.000 0.992 0.000 0.000 0.008
#> SRR1044578 2 0.0703 0.9207 0.000 0.976 0.000 0.000 0.024
#> SRR1044579 4 0.0000 0.9420 0.000 0.000 0.000 1.000 0.000
#> SRR1044580 1 0.6199 0.3439 0.552 0.000 0.000 0.236 0.212
#> SRR1044581 4 0.0000 0.9420 0.000 0.000 0.000 1.000 0.000
#> SRR1044582 1 0.1608 0.8859 0.928 0.000 0.000 0.000 0.072
#> SRR1044583 4 0.0000 0.9420 0.000 0.000 0.000 1.000 0.000
#> SRR1044584 4 0.3476 0.7454 0.076 0.000 0.000 0.836 0.088
#> SRR1044585 4 0.0000 0.9420 0.000 0.000 0.000 1.000 0.000
#> SRR1044586 1 0.2046 0.8771 0.916 0.000 0.000 0.016 0.068
#> SRR1044587 4 0.0404 0.9386 0.000 0.000 0.000 0.988 0.012
#> SRR1044588 4 0.0290 0.9402 0.000 0.000 0.000 0.992 0.008
#> SRR1044589 4 0.0290 0.9402 0.000 0.000 0.000 0.992 0.008
#> SRR1044590 4 0.0290 0.9402 0.000 0.000 0.000 0.992 0.008
#> SRR1044591 4 0.0290 0.9402 0.000 0.000 0.000 0.992 0.008
#> SRR1044592 5 0.7742 0.4672 0.192 0.000 0.076 0.336 0.396
#> SRR1044593 4 0.0290 0.9402 0.000 0.000 0.000 0.992 0.008
#> SRR1044594 4 0.0290 0.9402 0.000 0.000 0.000 0.992 0.008
#> SRR1044595 5 0.7899 0.4423 0.244 0.000 0.076 0.312 0.368
#> SRR1044596 5 0.7749 0.4540 0.192 0.000 0.076 0.344 0.388
#> SRR1044597 4 0.7780 -0.4005 0.204 0.000 0.076 0.396 0.324
#> SRR1044598 1 0.1851 0.8761 0.912 0.000 0.000 0.000 0.088
#> SRR1044599 1 0.1851 0.8761 0.912 0.000 0.000 0.000 0.088
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.0865 0.898 0.000 0.964 0.000 0.000 0.000 0.036
#> SRR1044416 2 0.0935 0.893 0.000 0.964 0.000 0.000 0.004 0.032
#> SRR1044417 2 0.0632 0.898 0.000 0.976 0.000 0.000 0.000 0.024
#> SRR1044418 2 0.0508 0.898 0.000 0.984 0.000 0.000 0.004 0.012
#> SRR1044420 2 0.0363 0.900 0.000 0.988 0.000 0.000 0.000 0.012
#> SRR1044419 2 0.1204 0.893 0.000 0.944 0.000 0.000 0.000 0.056
#> SRR1044421 2 0.2135 0.851 0.000 0.872 0.000 0.000 0.000 0.128
#> SRR1044422 2 0.1007 0.894 0.000 0.956 0.000 0.000 0.000 0.044
#> SRR1044423 2 0.0547 0.899 0.000 0.980 0.000 0.000 0.000 0.020
#> SRR1044424 2 0.3766 0.603 0.000 0.736 0.032 0.000 0.000 0.232
#> SRR1044425 5 0.5813 0.261 0.388 0.000 0.004 0.096 0.492 0.020
#> SRR1044426 1 0.3452 0.718 0.736 0.000 0.004 0.000 0.256 0.004
#> SRR1044427 1 0.5374 0.339 0.548 0.000 0.000 0.064 0.364 0.024
#> SRR1044428 1 0.0909 0.860 0.968 0.000 0.000 0.000 0.020 0.012
#> SRR1044429 1 0.4076 0.737 0.724 0.000 0.000 0.016 0.236 0.024
#> SRR1044430 1 0.2562 0.787 0.828 0.000 0.000 0.000 0.172 0.000
#> SRR1044431 1 0.3352 0.817 0.800 0.000 0.000 0.012 0.172 0.016
#> SRR1044433 5 0.2038 0.784 0.028 0.000 0.020 0.032 0.920 0.000
#> SRR1044432 1 0.2278 0.824 0.868 0.000 0.000 0.000 0.128 0.004
#> SRR1044434 4 0.0000 0.936 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044435 4 0.0000 0.936 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044436 4 0.0520 0.933 0.000 0.000 0.000 0.984 0.008 0.008
#> SRR1044437 4 0.0146 0.935 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1044439 4 0.0260 0.935 0.000 0.000 0.000 0.992 0.000 0.008
#> SRR1044438 4 0.0717 0.930 0.000 0.000 0.000 0.976 0.016 0.008
#> SRR1044440 4 0.0000 0.936 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044441 4 0.1082 0.916 0.000 0.000 0.004 0.956 0.040 0.000
#> SRR1044442 5 0.2038 0.784 0.028 0.000 0.020 0.032 0.920 0.000
#> SRR1044443 5 0.2038 0.784 0.028 0.000 0.020 0.032 0.920 0.000
#> SRR1044444 4 0.0000 0.936 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044445 4 0.0806 0.929 0.000 0.000 0.000 0.972 0.020 0.008
#> SRR1044446 3 0.2048 0.817 0.000 0.000 0.880 0.000 0.000 0.120
#> SRR1044447 6 0.4041 0.708 0.000 0.040 0.216 0.000 0.008 0.736
#> SRR1044449 3 0.0632 0.929 0.000 0.000 0.976 0.000 0.000 0.024
#> SRR1044448 3 0.0260 0.932 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1044450 3 0.0405 0.930 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1044451 6 0.4139 0.686 0.000 0.036 0.260 0.000 0.004 0.700
#> SRR1044452 3 0.2473 0.833 0.000 0.008 0.856 0.000 0.000 0.136
#> SRR1044453 3 0.3071 0.773 0.000 0.016 0.804 0.000 0.000 0.180
#> SRR1044454 3 0.3834 0.605 0.000 0.024 0.708 0.000 0.000 0.268
#> SRR1044455 6 0.4817 0.755 0.000 0.120 0.200 0.000 0.004 0.676
#> SRR1044456 2 0.1588 0.891 0.000 0.924 0.000 0.000 0.004 0.072
#> SRR1044457 6 0.3841 0.666 0.000 0.244 0.032 0.000 0.000 0.724
#> SRR1044458 2 0.3482 0.566 0.000 0.684 0.000 0.000 0.000 0.316
#> SRR1044459 3 0.0692 0.930 0.000 0.004 0.976 0.000 0.000 0.020
#> SRR1044460 2 0.0458 0.898 0.000 0.984 0.000 0.000 0.000 0.016
#> SRR1044461 2 0.1556 0.883 0.000 0.920 0.000 0.000 0.000 0.080
#> SRR1044462 5 0.6003 0.458 0.276 0.000 0.000 0.164 0.536 0.024
#> SRR1044463 1 0.0622 0.859 0.980 0.000 0.000 0.000 0.008 0.012
#> SRR1044464 5 0.2307 0.783 0.048 0.000 0.016 0.032 0.904 0.000
#> SRR1044466 1 0.0909 0.852 0.968 0.000 0.000 0.000 0.020 0.012
#> SRR1044465 1 0.2302 0.857 0.872 0.000 0.000 0.000 0.120 0.008
#> SRR1044467 1 0.1970 0.866 0.900 0.000 0.000 0.000 0.092 0.008
#> SRR1044468 2 0.1007 0.894 0.000 0.956 0.000 0.000 0.000 0.044
#> SRR1044469 6 0.4633 0.707 0.000 0.224 0.100 0.000 0.000 0.676
#> SRR1044470 1 0.1267 0.868 0.940 0.000 0.000 0.000 0.060 0.000
#> SRR1044471 1 0.2170 0.866 0.888 0.000 0.000 0.000 0.100 0.012
#> SRR1044472 1 0.1625 0.825 0.928 0.000 0.000 0.000 0.060 0.012
#> SRR1044473 1 0.2013 0.870 0.908 0.000 0.000 0.008 0.076 0.008
#> SRR1044474 2 0.0858 0.894 0.000 0.968 0.000 0.000 0.004 0.028
#> SRR1044475 6 0.5786 0.591 0.000 0.240 0.256 0.000 0.000 0.504
#> SRR1044476 2 0.3101 0.705 0.000 0.756 0.000 0.000 0.000 0.244
#> SRR1044477 2 0.0935 0.893 0.000 0.964 0.000 0.000 0.004 0.032
#> SRR1044478 2 0.1910 0.862 0.000 0.892 0.000 0.000 0.000 0.108
#> SRR1044479 2 0.0935 0.893 0.000 0.964 0.000 0.000 0.004 0.032
#> SRR1044480 4 0.5015 0.295 0.072 0.000 0.000 0.572 0.352 0.004
#> SRR1044481 1 0.4671 0.654 0.672 0.000 0.000 0.040 0.264 0.024
#> SRR1044482 2 0.0858 0.894 0.000 0.968 0.000 0.000 0.004 0.028
#> SRR1044483 4 0.1141 0.908 0.000 0.000 0.000 0.948 0.052 0.000
#> SRR1044484 1 0.5387 0.236 0.520 0.000 0.000 0.060 0.396 0.024
#> SRR1044486 1 0.3124 0.843 0.828 0.000 0.000 0.008 0.140 0.024
#> SRR1044485 2 0.0858 0.894 0.000 0.968 0.000 0.000 0.004 0.028
#> SRR1044487 2 0.0935 0.893 0.000 0.964 0.000 0.000 0.004 0.032
#> SRR1044488 2 0.0937 0.894 0.000 0.960 0.000 0.000 0.000 0.040
#> SRR1044489 2 0.0937 0.894 0.000 0.960 0.000 0.000 0.000 0.040
#> SRR1044490 1 0.2191 0.857 0.876 0.000 0.000 0.000 0.120 0.004
#> SRR1044491 1 0.0363 0.857 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1044492 1 0.0725 0.862 0.976 0.000 0.000 0.000 0.012 0.012
#> SRR1044493 1 0.0508 0.857 0.984 0.000 0.000 0.000 0.004 0.012
#> SRR1044494 2 0.0935 0.893 0.000 0.964 0.000 0.000 0.004 0.032
#> SRR1044496 2 0.0935 0.893 0.000 0.964 0.000 0.000 0.004 0.032
#> SRR1044495 2 0.0858 0.894 0.000 0.968 0.000 0.000 0.004 0.028
#> SRR1044497 4 0.0291 0.935 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR1044499 6 0.4793 0.669 0.000 0.288 0.084 0.000 0.000 0.628
#> SRR1044498 5 0.5604 -0.019 0.448 0.000 0.000 0.076 0.452 0.024
#> SRR1044500 2 0.1007 0.894 0.000 0.956 0.000 0.000 0.000 0.044
#> SRR1044501 2 0.3765 0.335 0.000 0.596 0.000 0.000 0.000 0.404
#> SRR1044502 6 0.4774 0.663 0.000 0.068 0.332 0.000 0.000 0.600
#> SRR1044503 4 0.0146 0.935 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1044504 4 0.0000 0.936 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044505 1 0.5032 0.532 0.604 0.000 0.000 0.052 0.324 0.020
#> SRR1044506 4 0.0806 0.929 0.000 0.000 0.000 0.972 0.020 0.008
#> SRR1044507 5 0.2182 0.783 0.028 0.000 0.020 0.032 0.916 0.004
#> SRR1044508 5 0.2038 0.784 0.028 0.000 0.020 0.032 0.920 0.000
#> SRR1044509 5 0.2038 0.784 0.028 0.000 0.020 0.032 0.920 0.000
#> SRR1044510 3 0.0260 0.932 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1044511 3 0.0713 0.924 0.000 0.000 0.972 0.000 0.000 0.028
#> SRR1044512 3 0.0000 0.931 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044513 6 0.4168 0.742 0.000 0.088 0.148 0.000 0.008 0.756
#> SRR1044514 3 0.0260 0.932 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1044515 6 0.3469 0.742 0.000 0.104 0.088 0.000 0.000 0.808
#> SRR1044516 2 0.2793 0.774 0.000 0.800 0.000 0.000 0.000 0.200
#> SRR1044517 3 0.0146 0.932 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1044518 3 0.0146 0.932 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1044519 3 0.0713 0.928 0.000 0.000 0.972 0.000 0.000 0.028
#> SRR1044520 3 0.0632 0.929 0.000 0.000 0.976 0.000 0.000 0.024
#> SRR1044521 2 0.1444 0.887 0.000 0.928 0.000 0.000 0.000 0.072
#> SRR1044522 2 0.1010 0.893 0.000 0.960 0.000 0.000 0.004 0.036
#> SRR1044523 2 0.4328 0.112 0.000 0.520 0.020 0.000 0.000 0.460
#> SRR1044524 6 0.3999 0.649 0.000 0.032 0.272 0.000 0.000 0.696
#> SRR1044525 4 0.3109 0.703 0.000 0.000 0.000 0.772 0.224 0.004
#> SRR1044526 1 0.5501 0.455 0.580 0.000 0.000 0.100 0.300 0.020
#> SRR1044527 2 0.1714 0.878 0.000 0.908 0.000 0.000 0.000 0.092
#> SRR1044528 6 0.4918 0.647 0.000 0.276 0.088 0.000 0.004 0.632
#> SRR1044529 2 0.0858 0.894 0.000 0.968 0.000 0.000 0.004 0.028
#> SRR1044530 1 0.0508 0.859 0.984 0.000 0.000 0.000 0.004 0.012
#> SRR1044531 1 0.2019 0.869 0.900 0.000 0.000 0.000 0.088 0.012
#> SRR1044533 1 0.2053 0.861 0.888 0.000 0.000 0.000 0.108 0.004
#> SRR1044532 1 0.0363 0.857 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1044534 2 0.1141 0.894 0.000 0.948 0.000 0.000 0.000 0.052
#> SRR1044535 6 0.3967 0.545 0.000 0.012 0.356 0.000 0.000 0.632
#> SRR1044536 2 0.1141 0.894 0.000 0.948 0.000 0.000 0.000 0.052
#> SRR1044537 1 0.3058 0.849 0.840 0.000 0.000 0.012 0.124 0.024
#> SRR1044538 1 0.0725 0.862 0.976 0.000 0.000 0.000 0.012 0.012
#> SRR1044539 4 0.1285 0.906 0.000 0.000 0.000 0.944 0.052 0.004
#> SRR1044540 1 0.2257 0.857 0.876 0.000 0.000 0.000 0.116 0.008
#> SRR1044541 6 0.5032 0.744 0.000 0.148 0.216 0.000 0.000 0.636
#> SRR1044542 1 0.0363 0.857 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1044543 1 0.2257 0.857 0.876 0.000 0.000 0.000 0.116 0.008
#> SRR1044544 6 0.4352 0.752 0.000 0.148 0.128 0.000 0.000 0.724
#> SRR1044545 4 0.1124 0.916 0.000 0.000 0.000 0.956 0.036 0.008
#> SRR1044546 1 0.1492 0.857 0.940 0.000 0.000 0.000 0.036 0.024
#> SRR1044547 4 0.4345 0.440 0.020 0.000 0.000 0.624 0.348 0.008
#> SRR1044548 1 0.1788 0.857 0.928 0.000 0.000 0.004 0.040 0.028
#> SRR1044549 2 0.4609 0.174 0.000 0.540 0.040 0.000 0.000 0.420
#> SRR1044550 2 0.1007 0.893 0.000 0.956 0.000 0.000 0.000 0.044
#> SRR1044551 2 0.1957 0.860 0.000 0.888 0.000 0.000 0.000 0.112
#> SRR1044552 4 0.0000 0.936 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044553 4 0.0260 0.935 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR1044554 1 0.1088 0.859 0.960 0.000 0.000 0.000 0.016 0.024
#> SRR1044555 6 0.3778 0.605 0.000 0.016 0.288 0.000 0.000 0.696
#> SRR1044556 4 0.0260 0.935 0.000 0.000 0.000 0.992 0.000 0.008
#> SRR1044557 1 0.1418 0.858 0.944 0.000 0.000 0.000 0.032 0.024
#> SRR1044558 4 0.0000 0.936 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044559 1 0.3146 0.821 0.844 0.000 0.004 0.012 0.112 0.028
#> SRR1044561 4 0.0000 0.936 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044560 2 0.2883 0.745 0.000 0.788 0.000 0.000 0.000 0.212
#> SRR1044562 1 0.1418 0.860 0.944 0.000 0.000 0.000 0.032 0.024
#> SRR1044563 4 0.0000 0.936 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044564 1 0.4475 0.705 0.692 0.000 0.000 0.032 0.252 0.024
#> SRR1044565 2 0.0858 0.894 0.000 0.968 0.000 0.000 0.004 0.028
#> SRR1044566 2 0.2454 0.805 0.000 0.840 0.000 0.000 0.000 0.160
#> SRR1044567 1 0.0862 0.862 0.972 0.000 0.000 0.004 0.008 0.016
#> SRR1044568 4 0.4452 0.238 0.016 0.000 0.000 0.548 0.428 0.008
#> SRR1044569 1 0.1866 0.866 0.908 0.000 0.000 0.000 0.084 0.008
#> SRR1044570 1 0.0508 0.858 0.984 0.000 0.000 0.000 0.004 0.012
#> SRR1044571 1 0.2212 0.861 0.880 0.000 0.000 0.000 0.112 0.008
#> SRR1044572 1 0.2191 0.858 0.876 0.000 0.000 0.000 0.120 0.004
#> SRR1044573 1 0.2633 0.860 0.864 0.000 0.000 0.004 0.112 0.020
#> SRR1044574 1 0.2531 0.854 0.856 0.000 0.000 0.000 0.132 0.012
#> SRR1044575 1 0.2146 0.857 0.880 0.000 0.000 0.000 0.116 0.004
#> SRR1044576 2 0.0458 0.899 0.000 0.984 0.000 0.000 0.000 0.016
#> SRR1044577 2 0.0865 0.899 0.000 0.964 0.000 0.000 0.000 0.036
#> SRR1044578 2 0.0858 0.894 0.000 0.968 0.000 0.000 0.004 0.028
#> SRR1044579 4 0.0000 0.936 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044580 5 0.6084 0.324 0.340 0.000 0.004 0.140 0.496 0.020
#> SRR1044581 4 0.0000 0.936 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044582 1 0.2651 0.859 0.872 0.000 0.000 0.004 0.088 0.036
#> SRR1044583 4 0.0000 0.936 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044584 4 0.4183 0.577 0.036 0.000 0.000 0.692 0.268 0.004
#> SRR1044585 4 0.0000 0.936 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044586 1 0.3411 0.826 0.804 0.000 0.000 0.012 0.160 0.024
#> SRR1044587 4 0.1049 0.926 0.000 0.000 0.000 0.960 0.032 0.008
#> SRR1044588 4 0.0806 0.929 0.000 0.000 0.000 0.972 0.020 0.008
#> SRR1044589 4 0.0717 0.931 0.000 0.000 0.000 0.976 0.016 0.008
#> SRR1044590 4 0.0717 0.931 0.000 0.000 0.000 0.976 0.016 0.008
#> SRR1044591 4 0.0806 0.929 0.000 0.000 0.000 0.972 0.020 0.008
#> SRR1044592 5 0.2038 0.784 0.028 0.000 0.020 0.032 0.920 0.000
#> SRR1044593 4 0.0806 0.929 0.000 0.000 0.000 0.972 0.020 0.008
#> SRR1044594 4 0.0806 0.929 0.000 0.000 0.000 0.972 0.020 0.008
#> SRR1044595 5 0.3552 0.728 0.148 0.000 0.020 0.028 0.804 0.000
#> SRR1044596 5 0.2507 0.772 0.028 0.000 0.020 0.060 0.892 0.000
#> SRR1044597 5 0.4320 0.735 0.116 0.000 0.016 0.100 0.764 0.004
#> SRR1044598 1 0.1492 0.857 0.940 0.000 0.000 0.000 0.036 0.024
#> SRR1044599 1 0.1492 0.857 0.940 0.000 0.000 0.000 0.036 0.024
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.994 0.997 0.4932 0.508 0.508
#> 3 3 0.736 0.843 0.797 0.2715 0.835 0.675
#> 4 4 0.933 0.912 0.956 0.1656 0.900 0.717
#> 5 5 0.815 0.609 0.857 0.0432 0.965 0.875
#> 6 6 0.796 0.656 0.827 0.0290 0.945 0.800
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0.0000 1.000 0.000 1.000
#> SRR1044416 2 0.0000 1.000 0.000 1.000
#> SRR1044417 2 0.0000 1.000 0.000 1.000
#> SRR1044418 2 0.0000 1.000 0.000 1.000
#> SRR1044420 2 0.0000 1.000 0.000 1.000
#> SRR1044419 2 0.0000 1.000 0.000 1.000
#> SRR1044421 2 0.0000 1.000 0.000 1.000
#> SRR1044422 2 0.0000 1.000 0.000 1.000
#> SRR1044423 2 0.0000 1.000 0.000 1.000
#> SRR1044424 2 0.0000 1.000 0.000 1.000
#> SRR1044425 1 0.0000 0.995 1.000 0.000
#> SRR1044426 1 0.0000 0.995 1.000 0.000
#> SRR1044427 1 0.0000 0.995 1.000 0.000
#> SRR1044428 1 0.0000 0.995 1.000 0.000
#> SRR1044429 1 0.0000 0.995 1.000 0.000
#> SRR1044430 1 0.0000 0.995 1.000 0.000
#> SRR1044431 1 0.0000 0.995 1.000 0.000
#> SRR1044433 1 0.0000 0.995 1.000 0.000
#> SRR1044432 1 0.0000 0.995 1.000 0.000
#> SRR1044434 1 0.0000 0.995 1.000 0.000
#> SRR1044435 1 0.0000 0.995 1.000 0.000
#> SRR1044436 1 0.0000 0.995 1.000 0.000
#> SRR1044437 1 0.0000 0.995 1.000 0.000
#> SRR1044439 1 0.0000 0.995 1.000 0.000
#> SRR1044438 1 0.0000 0.995 1.000 0.000
#> SRR1044440 1 0.0000 0.995 1.000 0.000
#> SRR1044441 1 0.0000 0.995 1.000 0.000
#> SRR1044442 1 0.0000 0.995 1.000 0.000
#> SRR1044443 1 0.9209 0.497 0.664 0.336
#> SRR1044444 1 0.0000 0.995 1.000 0.000
#> SRR1044445 1 0.0000 0.995 1.000 0.000
#> SRR1044446 2 0.0000 1.000 0.000 1.000
#> SRR1044447 2 0.0000 1.000 0.000 1.000
#> SRR1044449 2 0.0000 1.000 0.000 1.000
#> SRR1044448 2 0.0000 1.000 0.000 1.000
#> SRR1044450 2 0.0000 1.000 0.000 1.000
#> SRR1044451 2 0.0000 1.000 0.000 1.000
#> SRR1044452 2 0.0000 1.000 0.000 1.000
#> SRR1044453 2 0.0000 1.000 0.000 1.000
#> SRR1044454 2 0.0000 1.000 0.000 1.000
#> SRR1044455 2 0.0000 1.000 0.000 1.000
#> SRR1044456 2 0.0000 1.000 0.000 1.000
#> SRR1044457 2 0.0000 1.000 0.000 1.000
#> SRR1044458 2 0.0000 1.000 0.000 1.000
#> SRR1044459 2 0.0000 1.000 0.000 1.000
#> SRR1044460 2 0.0000 1.000 0.000 1.000
#> SRR1044461 2 0.0000 1.000 0.000 1.000
#> SRR1044462 1 0.0000 0.995 1.000 0.000
#> SRR1044463 1 0.0000 0.995 1.000 0.000
#> SRR1044464 1 0.0000 0.995 1.000 0.000
#> SRR1044466 1 0.0000 0.995 1.000 0.000
#> SRR1044465 1 0.0000 0.995 1.000 0.000
#> SRR1044467 1 0.0000 0.995 1.000 0.000
#> SRR1044468 2 0.0000 1.000 0.000 1.000
#> SRR1044469 2 0.0000 1.000 0.000 1.000
#> SRR1044470 1 0.0000 0.995 1.000 0.000
#> SRR1044471 1 0.0000 0.995 1.000 0.000
#> SRR1044472 1 0.0000 0.995 1.000 0.000
#> SRR1044473 1 0.0000 0.995 1.000 0.000
#> SRR1044474 2 0.0000 1.000 0.000 1.000
#> SRR1044475 2 0.0000 1.000 0.000 1.000
#> SRR1044476 2 0.0000 1.000 0.000 1.000
#> SRR1044477 2 0.0000 1.000 0.000 1.000
#> SRR1044478 2 0.0000 1.000 0.000 1.000
#> SRR1044479 2 0.0000 1.000 0.000 1.000
#> SRR1044480 1 0.0000 0.995 1.000 0.000
#> SRR1044481 1 0.0000 0.995 1.000 0.000
#> SRR1044482 2 0.0000 1.000 0.000 1.000
#> SRR1044483 1 0.0000 0.995 1.000 0.000
#> SRR1044484 1 0.0000 0.995 1.000 0.000
#> SRR1044486 1 0.0000 0.995 1.000 0.000
#> SRR1044485 2 0.0000 1.000 0.000 1.000
#> SRR1044487 2 0.0000 1.000 0.000 1.000
#> SRR1044488 2 0.0000 1.000 0.000 1.000
#> SRR1044489 2 0.0000 1.000 0.000 1.000
#> SRR1044490 1 0.0000 0.995 1.000 0.000
#> SRR1044491 1 0.0000 0.995 1.000 0.000
#> SRR1044492 1 0.0000 0.995 1.000 0.000
#> SRR1044493 1 0.0000 0.995 1.000 0.000
#> SRR1044494 2 0.0000 1.000 0.000 1.000
#> SRR1044496 2 0.0000 1.000 0.000 1.000
#> SRR1044495 2 0.0000 1.000 0.000 1.000
#> SRR1044497 1 0.0000 0.995 1.000 0.000
#> SRR1044499 2 0.0000 1.000 0.000 1.000
#> SRR1044498 1 0.0000 0.995 1.000 0.000
#> SRR1044500 2 0.0000 1.000 0.000 1.000
#> SRR1044501 2 0.0000 1.000 0.000 1.000
#> SRR1044502 2 0.0000 1.000 0.000 1.000
#> SRR1044503 1 0.0000 0.995 1.000 0.000
#> SRR1044504 1 0.0000 0.995 1.000 0.000
#> SRR1044505 1 0.0000 0.995 1.000 0.000
#> SRR1044506 1 0.0376 0.992 0.996 0.004
#> SRR1044507 1 0.0938 0.984 0.988 0.012
#> SRR1044508 1 0.0376 0.992 0.996 0.004
#> SRR1044509 1 0.0376 0.992 0.996 0.004
#> SRR1044510 2 0.0000 1.000 0.000 1.000
#> SRR1044511 2 0.0000 1.000 0.000 1.000
#> SRR1044512 2 0.0000 1.000 0.000 1.000
#> SRR1044513 2 0.0000 1.000 0.000 1.000
#> SRR1044514 2 0.0000 1.000 0.000 1.000
#> SRR1044515 2 0.0000 1.000 0.000 1.000
#> SRR1044516 2 0.0000 1.000 0.000 1.000
#> SRR1044517 2 0.0000 1.000 0.000 1.000
#> SRR1044518 2 0.0000 1.000 0.000 1.000
#> SRR1044519 2 0.0000 1.000 0.000 1.000
#> SRR1044520 2 0.0000 1.000 0.000 1.000
#> SRR1044521 2 0.0000 1.000 0.000 1.000
#> SRR1044522 2 0.0000 1.000 0.000 1.000
#> SRR1044523 2 0.0000 1.000 0.000 1.000
#> SRR1044524 2 0.0000 1.000 0.000 1.000
#> SRR1044525 1 0.0000 0.995 1.000 0.000
#> SRR1044526 1 0.0000 0.995 1.000 0.000
#> SRR1044527 2 0.0000 1.000 0.000 1.000
#> SRR1044528 2 0.0000 1.000 0.000 1.000
#> SRR1044529 2 0.0000 1.000 0.000 1.000
#> SRR1044530 1 0.0000 0.995 1.000 0.000
#> SRR1044531 1 0.0000 0.995 1.000 0.000
#> SRR1044533 1 0.0000 0.995 1.000 0.000
#> SRR1044532 1 0.0000 0.995 1.000 0.000
#> SRR1044534 2 0.0000 1.000 0.000 1.000
#> SRR1044535 2 0.0000 1.000 0.000 1.000
#> SRR1044536 2 0.0000 1.000 0.000 1.000
#> SRR1044537 1 0.0000 0.995 1.000 0.000
#> SRR1044538 1 0.0000 0.995 1.000 0.000
#> SRR1044539 1 0.0000 0.995 1.000 0.000
#> SRR1044540 1 0.0000 0.995 1.000 0.000
#> SRR1044541 2 0.0000 1.000 0.000 1.000
#> SRR1044542 1 0.0000 0.995 1.000 0.000
#> SRR1044543 1 0.0000 0.995 1.000 0.000
#> SRR1044544 2 0.0000 1.000 0.000 1.000
#> SRR1044545 1 0.0000 0.995 1.000 0.000
#> SRR1044546 1 0.0000 0.995 1.000 0.000
#> SRR1044547 1 0.0000 0.995 1.000 0.000
#> SRR1044548 1 0.0000 0.995 1.000 0.000
#> SRR1044549 2 0.0000 1.000 0.000 1.000
#> SRR1044550 2 0.0000 1.000 0.000 1.000
#> SRR1044551 2 0.0000 1.000 0.000 1.000
#> SRR1044552 1 0.0000 0.995 1.000 0.000
#> SRR1044553 1 0.0000 0.995 1.000 0.000
#> SRR1044554 1 0.0000 0.995 1.000 0.000
#> SRR1044555 2 0.0000 1.000 0.000 1.000
#> SRR1044556 1 0.0000 0.995 1.000 0.000
#> SRR1044557 1 0.0000 0.995 1.000 0.000
#> SRR1044558 1 0.0000 0.995 1.000 0.000
#> SRR1044559 1 0.0000 0.995 1.000 0.000
#> SRR1044561 1 0.0000 0.995 1.000 0.000
#> SRR1044560 2 0.0000 1.000 0.000 1.000
#> SRR1044562 1 0.0000 0.995 1.000 0.000
#> SRR1044563 1 0.0000 0.995 1.000 0.000
#> SRR1044564 1 0.0000 0.995 1.000 0.000
#> SRR1044565 2 0.0000 1.000 0.000 1.000
#> SRR1044566 2 0.0000 1.000 0.000 1.000
#> SRR1044567 1 0.0000 0.995 1.000 0.000
#> SRR1044568 1 0.0000 0.995 1.000 0.000
#> SRR1044569 1 0.0000 0.995 1.000 0.000
#> SRR1044570 1 0.0000 0.995 1.000 0.000
#> SRR1044571 1 0.0000 0.995 1.000 0.000
#> SRR1044572 1 0.0000 0.995 1.000 0.000
#> SRR1044573 1 0.0000 0.995 1.000 0.000
#> SRR1044574 1 0.0000 0.995 1.000 0.000
#> SRR1044575 1 0.0000 0.995 1.000 0.000
#> SRR1044576 2 0.0000 1.000 0.000 1.000
#> SRR1044577 2 0.0000 1.000 0.000 1.000
#> SRR1044578 2 0.0000 1.000 0.000 1.000
#> SRR1044579 1 0.0000 0.995 1.000 0.000
#> SRR1044580 1 0.0000 0.995 1.000 0.000
#> SRR1044581 1 0.0000 0.995 1.000 0.000
#> SRR1044582 1 0.0000 0.995 1.000 0.000
#> SRR1044583 1 0.0000 0.995 1.000 0.000
#> SRR1044584 1 0.0000 0.995 1.000 0.000
#> SRR1044585 1 0.0000 0.995 1.000 0.000
#> SRR1044586 1 0.0000 0.995 1.000 0.000
#> SRR1044587 1 0.0000 0.995 1.000 0.000
#> SRR1044588 1 0.0672 0.988 0.992 0.008
#> SRR1044589 1 0.0000 0.995 1.000 0.000
#> SRR1044590 1 0.0000 0.995 1.000 0.000
#> SRR1044591 1 0.0000 0.995 1.000 0.000
#> SRR1044592 1 0.1843 0.968 0.972 0.028
#> SRR1044593 1 0.0000 0.995 1.000 0.000
#> SRR1044594 1 0.0000 0.995 1.000 0.000
#> SRR1044595 1 0.0000 0.995 1.000 0.000
#> SRR1044596 1 0.0000 0.995 1.000 0.000
#> SRR1044597 1 0.4690 0.888 0.900 0.100
#> SRR1044598 1 0.0000 0.995 1.000 0.000
#> SRR1044599 1 0.0000 0.995 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044416 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044417 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044418 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044420 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044419 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044421 2 0.0592 0.897 0.000 0.988 0.012
#> SRR1044422 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044423 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044424 2 0.0237 0.898 0.000 0.996 0.004
#> SRR1044425 3 0.6305 0.799 0.484 0.000 0.516
#> SRR1044426 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044427 3 0.6140 0.940 0.404 0.000 0.596
#> SRR1044428 1 0.0747 0.892 0.984 0.000 0.016
#> SRR1044429 1 0.5905 -0.222 0.648 0.000 0.352
#> SRR1044430 1 0.2711 0.780 0.912 0.000 0.088
#> SRR1044431 1 0.0237 0.906 0.996 0.000 0.004
#> SRR1044433 3 0.6140 0.915 0.404 0.000 0.596
#> SRR1044432 1 0.1163 0.875 0.972 0.000 0.028
#> SRR1044434 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044435 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044436 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044437 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044439 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044438 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044440 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044441 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044442 3 0.6180 0.925 0.416 0.000 0.584
#> SRR1044443 3 0.6184 0.347 0.108 0.112 0.780
#> SRR1044444 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044445 3 0.6483 0.936 0.392 0.008 0.600
#> SRR1044446 2 0.6126 0.772 0.000 0.600 0.400
#> SRR1044447 2 0.5591 0.813 0.000 0.696 0.304
#> SRR1044449 2 0.6126 0.772 0.000 0.600 0.400
#> SRR1044448 2 0.6126 0.772 0.000 0.600 0.400
#> SRR1044450 2 0.6126 0.772 0.000 0.600 0.400
#> SRR1044451 2 0.6079 0.778 0.000 0.612 0.388
#> SRR1044452 2 0.6045 0.782 0.000 0.620 0.380
#> SRR1044453 2 0.5988 0.788 0.000 0.632 0.368
#> SRR1044454 2 0.5988 0.788 0.000 0.632 0.368
#> SRR1044455 2 0.6045 0.783 0.000 0.620 0.380
#> SRR1044456 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044457 2 0.2165 0.887 0.000 0.936 0.064
#> SRR1044458 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044459 2 0.6126 0.772 0.000 0.600 0.400
#> SRR1044460 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044461 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044462 3 0.6192 0.919 0.420 0.000 0.580
#> SRR1044463 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044464 3 0.6280 0.850 0.460 0.000 0.540
#> SRR1044466 1 0.0424 0.901 0.992 0.000 0.008
#> SRR1044465 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044467 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044468 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044469 2 0.4399 0.852 0.000 0.812 0.188
#> SRR1044470 1 0.0237 0.905 0.996 0.000 0.004
#> SRR1044471 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044472 1 0.0892 0.886 0.980 0.000 0.020
#> SRR1044473 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044474 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044475 2 0.4555 0.848 0.000 0.800 0.200
#> SRR1044476 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044477 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044478 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044479 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044480 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044481 1 0.0237 0.906 0.996 0.000 0.004
#> SRR1044482 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044483 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044484 1 0.6302 -0.715 0.520 0.000 0.480
#> SRR1044486 1 0.1289 0.876 0.968 0.000 0.032
#> SRR1044485 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044487 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044488 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044489 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044490 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044491 1 0.0237 0.905 0.996 0.000 0.004
#> SRR1044492 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044493 1 0.0424 0.901 0.992 0.000 0.008
#> SRR1044494 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044496 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044495 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044497 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044499 2 0.0424 0.897 0.000 0.992 0.008
#> SRR1044498 1 0.6008 -0.336 0.628 0.000 0.372
#> SRR1044500 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044501 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044502 2 0.6079 0.778 0.000 0.612 0.388
#> SRR1044503 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044504 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044505 1 0.6299 -0.701 0.524 0.000 0.476
#> SRR1044506 3 0.7050 0.909 0.372 0.028 0.600
#> SRR1044507 3 0.5706 0.833 0.320 0.000 0.680
#> SRR1044508 3 0.5728 0.703 0.272 0.008 0.720
#> SRR1044509 3 0.5560 0.742 0.300 0.000 0.700
#> SRR1044510 2 0.6111 0.774 0.000 0.604 0.396
#> SRR1044511 2 0.6111 0.774 0.000 0.604 0.396
#> SRR1044512 2 0.6126 0.772 0.000 0.600 0.400
#> SRR1044513 2 0.4121 0.859 0.000 0.832 0.168
#> SRR1044514 2 0.6126 0.772 0.000 0.600 0.400
#> SRR1044515 2 0.2356 0.884 0.000 0.928 0.072
#> SRR1044516 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044517 2 0.6126 0.772 0.000 0.600 0.400
#> SRR1044518 2 0.6126 0.772 0.000 0.600 0.400
#> SRR1044519 2 0.6062 0.780 0.000 0.616 0.384
#> SRR1044520 2 0.6095 0.776 0.000 0.608 0.392
#> SRR1044521 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044522 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044523 2 0.1411 0.892 0.000 0.964 0.036
#> SRR1044524 2 0.5465 0.819 0.000 0.712 0.288
#> SRR1044525 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044526 1 0.6252 -0.599 0.556 0.000 0.444
#> SRR1044527 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044528 2 0.2625 0.882 0.000 0.916 0.084
#> SRR1044529 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044530 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044531 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044533 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044532 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044534 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044535 2 0.6045 0.782 0.000 0.620 0.380
#> SRR1044536 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044537 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044538 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044539 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044540 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044541 2 0.5905 0.795 0.000 0.648 0.352
#> SRR1044542 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044543 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044544 2 0.4452 0.853 0.000 0.808 0.192
#> SRR1044545 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044546 1 0.1163 0.881 0.972 0.000 0.028
#> SRR1044547 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044548 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044549 2 0.3192 0.874 0.000 0.888 0.112
#> SRR1044550 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044551 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044552 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044553 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044554 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044555 2 0.5882 0.796 0.000 0.652 0.348
#> SRR1044556 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044557 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044558 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044559 1 0.1031 0.885 0.976 0.000 0.024
#> SRR1044561 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044560 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044562 1 0.0592 0.899 0.988 0.000 0.012
#> SRR1044563 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044564 1 0.3619 0.690 0.864 0.000 0.136
#> SRR1044565 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044566 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044567 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044568 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044569 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044570 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044571 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044572 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044573 1 0.0424 0.903 0.992 0.000 0.008
#> SRR1044574 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044575 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044576 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044577 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044578 2 0.0000 0.898 0.000 1.000 0.000
#> SRR1044579 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044580 1 0.3686 0.682 0.860 0.000 0.140
#> SRR1044581 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044582 1 0.0000 0.909 1.000 0.000 0.000
#> SRR1044583 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044584 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044585 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044586 1 0.0237 0.906 0.996 0.000 0.004
#> SRR1044587 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044588 3 0.7727 0.848 0.336 0.064 0.600
#> SRR1044589 3 0.6737 0.926 0.384 0.016 0.600
#> SRR1044590 3 0.7310 0.890 0.360 0.040 0.600
#> SRR1044591 3 0.7141 0.903 0.368 0.032 0.600
#> SRR1044592 3 0.5810 0.858 0.336 0.000 0.664
#> SRR1044593 3 0.6330 0.941 0.396 0.004 0.600
#> SRR1044594 3 0.6126 0.945 0.400 0.000 0.600
#> SRR1044595 1 0.3896 0.763 0.864 0.008 0.128
#> SRR1044596 3 0.6140 0.940 0.404 0.000 0.596
#> SRR1044597 3 0.8972 0.643 0.412 0.128 0.460
#> SRR1044598 1 0.0424 0.903 0.992 0.000 0.008
#> SRR1044599 1 0.1643 0.858 0.956 0.000 0.044
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044416 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044417 2 0.0188 0.979 0.000 0.996 0.004 0.000
#> SRR1044418 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044420 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044419 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044421 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044422 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044423 2 0.0188 0.979 0.000 0.996 0.004 0.000
#> SRR1044424 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044425 4 0.4391 0.662 0.252 0.000 0.008 0.740
#> SRR1044426 1 0.0657 0.957 0.984 0.000 0.012 0.004
#> SRR1044427 4 0.0817 0.938 0.024 0.000 0.000 0.976
#> SRR1044428 1 0.0779 0.956 0.980 0.000 0.016 0.004
#> SRR1044429 1 0.5119 0.217 0.556 0.000 0.004 0.440
#> SRR1044430 1 0.0779 0.956 0.980 0.000 0.016 0.004
#> SRR1044431 1 0.0804 0.955 0.980 0.000 0.008 0.012
#> SRR1044433 4 0.1940 0.894 0.000 0.000 0.076 0.924
#> SRR1044432 1 0.0657 0.957 0.984 0.000 0.012 0.004
#> SRR1044434 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044435 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044436 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044437 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044439 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044438 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044440 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044441 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044442 4 0.0188 0.953 0.000 0.000 0.004 0.996
#> SRR1044443 3 0.4164 0.584 0.000 0.000 0.736 0.264
#> SRR1044444 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044445 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044446 3 0.0921 0.900 0.000 0.028 0.972 0.000
#> SRR1044447 3 0.3688 0.767 0.000 0.208 0.792 0.000
#> SRR1044449 3 0.0921 0.900 0.000 0.028 0.972 0.000
#> SRR1044448 3 0.0921 0.900 0.000 0.028 0.972 0.000
#> SRR1044450 3 0.0921 0.900 0.000 0.028 0.972 0.000
#> SRR1044451 3 0.1118 0.898 0.000 0.036 0.964 0.000
#> SRR1044452 3 0.1211 0.896 0.000 0.040 0.960 0.000
#> SRR1044453 3 0.2760 0.842 0.000 0.128 0.872 0.000
#> SRR1044454 3 0.2408 0.861 0.000 0.104 0.896 0.000
#> SRR1044455 2 0.3688 0.710 0.000 0.792 0.208 0.000
#> SRR1044456 2 0.0376 0.977 0.004 0.992 0.004 0.000
#> SRR1044457 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044458 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044459 3 0.0921 0.900 0.000 0.028 0.972 0.000
#> SRR1044460 2 0.0188 0.979 0.000 0.996 0.004 0.000
#> SRR1044461 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044462 4 0.1284 0.930 0.024 0.000 0.012 0.964
#> SRR1044463 1 0.0376 0.956 0.992 0.000 0.004 0.004
#> SRR1044464 4 0.0895 0.939 0.020 0.000 0.004 0.976
#> SRR1044466 1 0.0376 0.956 0.992 0.000 0.004 0.004
#> SRR1044465 1 0.0779 0.956 0.980 0.000 0.016 0.004
#> SRR1044467 1 0.0779 0.956 0.980 0.000 0.016 0.004
#> SRR1044468 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044469 2 0.0707 0.963 0.000 0.980 0.020 0.000
#> SRR1044470 1 0.0376 0.956 0.992 0.000 0.004 0.004
#> SRR1044471 1 0.0779 0.956 0.980 0.000 0.016 0.004
#> SRR1044472 1 0.0376 0.956 0.992 0.000 0.004 0.004
#> SRR1044473 1 0.0895 0.955 0.976 0.000 0.020 0.004
#> SRR1044474 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044475 2 0.4543 0.470 0.000 0.676 0.324 0.000
#> SRR1044476 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044477 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044478 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044479 2 0.0188 0.979 0.000 0.996 0.004 0.000
#> SRR1044480 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044481 1 0.0817 0.947 0.976 0.000 0.000 0.024
#> SRR1044482 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044483 4 0.0188 0.953 0.000 0.000 0.004 0.996
#> SRR1044484 4 0.4920 0.418 0.368 0.000 0.004 0.628
#> SRR1044486 1 0.1489 0.931 0.952 0.000 0.004 0.044
#> SRR1044485 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044487 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044488 2 0.0188 0.979 0.000 0.996 0.004 0.000
#> SRR1044489 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044490 1 0.0779 0.956 0.980 0.000 0.016 0.004
#> SRR1044491 1 0.0779 0.956 0.980 0.000 0.016 0.004
#> SRR1044492 1 0.0779 0.957 0.980 0.000 0.016 0.004
#> SRR1044493 1 0.0524 0.956 0.988 0.000 0.008 0.004
#> SRR1044494 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044496 2 0.0188 0.979 0.000 0.996 0.004 0.000
#> SRR1044495 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044497 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044499 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044498 1 0.4877 0.305 0.592 0.000 0.000 0.408
#> SRR1044500 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044501 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044502 3 0.3074 0.824 0.000 0.152 0.848 0.000
#> SRR1044503 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044504 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044505 4 0.4542 0.685 0.228 0.000 0.020 0.752
#> SRR1044506 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044507 4 0.0921 0.936 0.000 0.000 0.028 0.972
#> SRR1044508 4 0.4134 0.657 0.000 0.000 0.260 0.740
#> SRR1044509 4 0.4122 0.692 0.004 0.000 0.236 0.760
#> SRR1044510 3 0.0921 0.900 0.000 0.028 0.972 0.000
#> SRR1044511 3 0.0921 0.900 0.000 0.028 0.972 0.000
#> SRR1044512 3 0.0921 0.900 0.000 0.028 0.972 0.000
#> SRR1044513 2 0.2216 0.886 0.000 0.908 0.092 0.000
#> SRR1044514 3 0.0921 0.900 0.000 0.028 0.972 0.000
#> SRR1044515 2 0.0921 0.955 0.000 0.972 0.028 0.000
#> SRR1044516 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044517 3 0.0921 0.900 0.000 0.028 0.972 0.000
#> SRR1044518 3 0.0921 0.900 0.000 0.028 0.972 0.000
#> SRR1044519 3 0.0921 0.900 0.000 0.028 0.972 0.000
#> SRR1044520 3 0.0921 0.900 0.000 0.028 0.972 0.000
#> SRR1044521 2 0.0188 0.979 0.000 0.996 0.004 0.000
#> SRR1044522 2 0.0188 0.979 0.000 0.996 0.004 0.000
#> SRR1044523 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044524 2 0.3610 0.719 0.000 0.800 0.200 0.000
#> SRR1044525 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044526 4 0.5349 0.456 0.336 0.000 0.024 0.640
#> SRR1044527 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044528 2 0.0336 0.977 0.000 0.992 0.008 0.000
#> SRR1044529 2 0.0188 0.979 0.000 0.996 0.004 0.000
#> SRR1044530 1 0.0376 0.956 0.992 0.000 0.004 0.004
#> SRR1044531 1 0.0895 0.955 0.976 0.000 0.020 0.004
#> SRR1044533 1 0.0895 0.955 0.976 0.000 0.020 0.004
#> SRR1044532 1 0.0376 0.956 0.992 0.000 0.004 0.004
#> SRR1044534 2 0.0188 0.979 0.000 0.996 0.004 0.000
#> SRR1044535 3 0.3942 0.732 0.000 0.236 0.764 0.000
#> SRR1044536 2 0.0188 0.979 0.000 0.996 0.004 0.000
#> SRR1044537 1 0.1284 0.946 0.964 0.000 0.012 0.024
#> SRR1044538 1 0.0376 0.956 0.992 0.000 0.004 0.004
#> SRR1044539 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044540 1 0.0657 0.956 0.984 0.000 0.012 0.004
#> SRR1044541 3 0.4955 0.309 0.000 0.444 0.556 0.000
#> SRR1044542 1 0.0376 0.956 0.992 0.000 0.004 0.004
#> SRR1044543 1 0.0895 0.955 0.976 0.000 0.020 0.004
#> SRR1044544 2 0.0188 0.978 0.000 0.996 0.004 0.000
#> SRR1044545 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044546 1 0.2402 0.898 0.912 0.000 0.012 0.076
#> SRR1044547 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044548 1 0.0672 0.956 0.984 0.000 0.008 0.008
#> SRR1044549 2 0.0188 0.978 0.000 0.996 0.004 0.000
#> SRR1044550 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044551 2 0.0188 0.979 0.000 0.996 0.004 0.000
#> SRR1044552 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044553 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044554 1 0.0524 0.956 0.988 0.000 0.008 0.004
#> SRR1044555 3 0.5000 0.145 0.000 0.496 0.504 0.000
#> SRR1044556 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044557 1 0.0657 0.956 0.984 0.000 0.012 0.004
#> SRR1044558 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044559 1 0.3286 0.866 0.876 0.000 0.044 0.080
#> SRR1044561 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044560 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044562 1 0.0672 0.956 0.984 0.000 0.008 0.008
#> SRR1044563 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044564 1 0.4123 0.722 0.772 0.000 0.008 0.220
#> SRR1044565 2 0.0188 0.979 0.000 0.996 0.004 0.000
#> SRR1044566 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044567 1 0.0376 0.956 0.992 0.000 0.004 0.004
#> SRR1044568 4 0.0469 0.947 0.012 0.000 0.000 0.988
#> SRR1044569 1 0.0779 0.956 0.980 0.000 0.016 0.004
#> SRR1044570 1 0.0376 0.956 0.992 0.000 0.004 0.004
#> SRR1044571 1 0.0779 0.956 0.980 0.000 0.016 0.004
#> SRR1044572 1 0.0657 0.956 0.984 0.000 0.012 0.004
#> SRR1044573 1 0.1174 0.953 0.968 0.000 0.020 0.012
#> SRR1044574 1 0.0779 0.956 0.980 0.000 0.016 0.004
#> SRR1044575 1 0.0895 0.955 0.976 0.000 0.020 0.004
#> SRR1044576 2 0.0188 0.979 0.000 0.996 0.004 0.000
#> SRR1044577 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044578 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1044579 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044580 1 0.2216 0.884 0.908 0.000 0.000 0.092
#> SRR1044581 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044582 1 0.0376 0.956 0.992 0.000 0.004 0.004
#> SRR1044583 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044584 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044585 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044586 1 0.0524 0.955 0.988 0.000 0.004 0.008
#> SRR1044587 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044588 4 0.0188 0.951 0.000 0.004 0.000 0.996
#> SRR1044589 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044590 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044591 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044592 4 0.1118 0.929 0.000 0.000 0.036 0.964
#> SRR1044593 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044594 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044595 3 0.6065 0.511 0.276 0.000 0.644 0.080
#> SRR1044596 4 0.0000 0.955 0.000 0.000 0.000 1.000
#> SRR1044597 4 0.4136 0.823 0.060 0.008 0.092 0.840
#> SRR1044598 1 0.0895 0.950 0.976 0.000 0.004 0.020
#> SRR1044599 1 0.2334 0.886 0.908 0.000 0.004 0.088
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.0290 0.95080 0.000 0.992 0.000 0.000 0.008
#> SRR1044416 2 0.0290 0.95080 0.000 0.992 0.000 0.000 0.008
#> SRR1044417 2 0.0703 0.94795 0.000 0.976 0.000 0.000 0.024
#> SRR1044418 2 0.0404 0.95119 0.000 0.988 0.000 0.000 0.012
#> SRR1044420 2 0.0510 0.95170 0.000 0.984 0.000 0.000 0.016
#> SRR1044419 2 0.0510 0.94909 0.000 0.984 0.000 0.000 0.016
#> SRR1044421 2 0.0510 0.95035 0.000 0.984 0.000 0.000 0.016
#> SRR1044422 2 0.0290 0.95080 0.000 0.992 0.000 0.000 0.008
#> SRR1044423 2 0.0290 0.95080 0.000 0.992 0.000 0.000 0.008
#> SRR1044424 2 0.0404 0.95025 0.000 0.988 0.000 0.000 0.012
#> SRR1044425 4 0.4637 0.56437 0.292 0.000 0.000 0.672 0.036
#> SRR1044426 1 0.3684 -0.09181 0.720 0.000 0.000 0.000 0.280
#> SRR1044427 4 0.1741 0.88671 0.024 0.000 0.000 0.936 0.040
#> SRR1044428 1 0.2848 0.35775 0.840 0.000 0.004 0.000 0.156
#> SRR1044429 4 0.6037 -0.11844 0.440 0.000 0.000 0.444 0.116
#> SRR1044430 1 0.3821 0.33354 0.780 0.008 0.004 0.008 0.200
#> SRR1044431 1 0.4818 0.11609 0.720 0.000 0.000 0.100 0.180
#> SRR1044433 4 0.2471 0.82109 0.000 0.000 0.136 0.864 0.000
#> SRR1044432 1 0.3305 0.22715 0.776 0.000 0.000 0.000 0.224
#> SRR1044434 4 0.0703 0.90736 0.000 0.000 0.000 0.976 0.024
#> SRR1044435 4 0.0290 0.91038 0.000 0.000 0.000 0.992 0.008
#> SRR1044436 4 0.0162 0.91119 0.000 0.000 0.000 0.996 0.004
#> SRR1044437 4 0.0290 0.91061 0.000 0.000 0.000 0.992 0.008
#> SRR1044439 4 0.0000 0.91092 0.000 0.000 0.000 1.000 0.000
#> SRR1044438 4 0.0162 0.91119 0.000 0.000 0.000 0.996 0.004
#> SRR1044440 4 0.0404 0.91000 0.000 0.000 0.000 0.988 0.012
#> SRR1044441 4 0.0794 0.90483 0.000 0.000 0.000 0.972 0.028
#> SRR1044442 4 0.1300 0.90083 0.000 0.000 0.016 0.956 0.028
#> SRR1044443 3 0.2966 0.71250 0.000 0.000 0.816 0.184 0.000
#> SRR1044444 4 0.0510 0.90901 0.000 0.000 0.000 0.984 0.016
#> SRR1044445 4 0.0404 0.91061 0.000 0.000 0.000 0.988 0.012
#> SRR1044446 3 0.0000 0.88193 0.000 0.000 1.000 0.000 0.000
#> SRR1044447 3 0.1965 0.83500 0.000 0.096 0.904 0.000 0.000
#> SRR1044449 3 0.2377 0.85917 0.000 0.000 0.872 0.000 0.128
#> SRR1044448 3 0.0000 0.88193 0.000 0.000 1.000 0.000 0.000
#> SRR1044450 3 0.0404 0.88067 0.000 0.000 0.988 0.000 0.012
#> SRR1044451 3 0.0912 0.88062 0.000 0.016 0.972 0.000 0.012
#> SRR1044452 3 0.4066 0.82041 0.000 0.044 0.768 0.000 0.188
#> SRR1044453 3 0.5450 0.73061 0.000 0.132 0.652 0.000 0.216
#> SRR1044454 3 0.5449 0.73484 0.000 0.108 0.636 0.000 0.256
#> SRR1044455 2 0.4134 0.71226 0.000 0.760 0.196 0.000 0.044
#> SRR1044456 2 0.0609 0.94923 0.000 0.980 0.000 0.000 0.020
#> SRR1044457 2 0.0609 0.94790 0.000 0.980 0.000 0.000 0.020
#> SRR1044458 2 0.0162 0.95128 0.000 0.996 0.000 0.000 0.004
#> SRR1044459 3 0.2069 0.87832 0.000 0.012 0.912 0.000 0.076
#> SRR1044460 2 0.0609 0.94948 0.000 0.980 0.000 0.000 0.020
#> SRR1044461 2 0.0880 0.94309 0.000 0.968 0.000 0.000 0.032
#> SRR1044462 4 0.6154 0.25933 0.348 0.000 0.000 0.508 0.144
#> SRR1044463 1 0.4210 -0.53662 0.588 0.000 0.000 0.000 0.412
#> SRR1044464 4 0.1300 0.89639 0.016 0.000 0.000 0.956 0.028
#> SRR1044466 1 0.4242 -0.55822 0.572 0.000 0.000 0.000 0.428
#> SRR1044465 1 0.1704 0.37997 0.928 0.000 0.000 0.004 0.068
#> SRR1044467 1 0.1121 0.37350 0.956 0.000 0.000 0.000 0.044
#> SRR1044468 2 0.0290 0.95146 0.000 0.992 0.000 0.000 0.008
#> SRR1044469 2 0.2848 0.82548 0.000 0.840 0.004 0.000 0.156
#> SRR1044470 1 0.4210 -0.53666 0.588 0.000 0.000 0.000 0.412
#> SRR1044471 1 0.2127 0.37579 0.892 0.000 0.000 0.000 0.108
#> SRR1044472 1 0.4235 -0.55639 0.576 0.000 0.000 0.000 0.424
#> SRR1044473 1 0.2795 0.35963 0.872 0.000 0.000 0.028 0.100
#> SRR1044474 2 0.0290 0.95189 0.000 0.992 0.000 0.000 0.008
#> SRR1044475 2 0.5886 0.41695 0.000 0.600 0.224 0.000 0.176
#> SRR1044476 2 0.0703 0.94680 0.000 0.976 0.000 0.000 0.024
#> SRR1044477 2 0.0162 0.95180 0.000 0.996 0.000 0.000 0.004
#> SRR1044478 2 0.0000 0.95169 0.000 1.000 0.000 0.000 0.000
#> SRR1044479 2 0.0404 0.95110 0.000 0.988 0.000 0.000 0.012
#> SRR1044480 4 0.2304 0.85314 0.008 0.000 0.000 0.892 0.100
#> SRR1044481 1 0.5027 -0.28299 0.640 0.000 0.000 0.056 0.304
#> SRR1044482 2 0.0404 0.95023 0.000 0.988 0.000 0.000 0.012
#> SRR1044483 4 0.3460 0.79721 0.044 0.000 0.000 0.828 0.128
#> SRR1044484 4 0.5254 0.50860 0.272 0.000 0.000 0.644 0.084
#> SRR1044486 1 0.5778 -0.81087 0.460 0.000 0.000 0.088 0.452
#> SRR1044485 2 0.0162 0.95180 0.000 0.996 0.000 0.000 0.004
#> SRR1044487 2 0.0162 0.95180 0.000 0.996 0.000 0.000 0.004
#> SRR1044488 2 0.0510 0.95052 0.000 0.984 0.000 0.000 0.016
#> SRR1044489 2 0.0162 0.95180 0.000 0.996 0.000 0.000 0.004
#> SRR1044490 1 0.1270 0.36766 0.948 0.000 0.000 0.000 0.052
#> SRR1044491 1 0.1608 0.34792 0.928 0.000 0.000 0.000 0.072
#> SRR1044492 1 0.2690 0.22143 0.844 0.000 0.000 0.000 0.156
#> SRR1044493 1 0.3730 -0.13551 0.712 0.000 0.000 0.000 0.288
#> SRR1044494 2 0.0162 0.95180 0.000 0.996 0.000 0.000 0.004
#> SRR1044496 2 0.0609 0.94923 0.000 0.980 0.000 0.000 0.020
#> SRR1044495 2 0.0000 0.95169 0.000 1.000 0.000 0.000 0.000
#> SRR1044497 4 0.0000 0.91092 0.000 0.000 0.000 1.000 0.000
#> SRR1044499 2 0.1410 0.92169 0.000 0.940 0.000 0.000 0.060
#> SRR1044498 4 0.6507 -0.10477 0.212 0.000 0.000 0.472 0.316
#> SRR1044500 2 0.0290 0.95176 0.000 0.992 0.000 0.000 0.008
#> SRR1044501 2 0.0290 0.95189 0.000 0.992 0.000 0.000 0.008
#> SRR1044502 3 0.2953 0.79205 0.000 0.144 0.844 0.000 0.012
#> SRR1044503 4 0.0404 0.91058 0.000 0.000 0.000 0.988 0.012
#> SRR1044504 4 0.0290 0.91038 0.000 0.000 0.000 0.992 0.008
#> SRR1044505 1 0.6448 0.07419 0.464 0.000 0.000 0.348 0.188
#> SRR1044506 4 0.0794 0.90616 0.000 0.000 0.000 0.972 0.028
#> SRR1044507 4 0.1836 0.88533 0.000 0.000 0.036 0.932 0.032
#> SRR1044508 4 0.5568 0.21201 0.000 0.000 0.412 0.516 0.072
#> SRR1044509 4 0.4597 0.55097 0.004 0.000 0.300 0.672 0.024
#> SRR1044510 3 0.2077 0.87802 0.000 0.008 0.908 0.000 0.084
#> SRR1044511 3 0.0963 0.88413 0.000 0.000 0.964 0.000 0.036
#> SRR1044512 3 0.1043 0.88373 0.000 0.000 0.960 0.000 0.040
#> SRR1044513 2 0.3355 0.81408 0.000 0.832 0.132 0.000 0.036
#> SRR1044514 3 0.0880 0.88429 0.000 0.000 0.968 0.000 0.032
#> SRR1044515 2 0.1281 0.93339 0.000 0.956 0.032 0.000 0.012
#> SRR1044516 2 0.0404 0.95191 0.000 0.988 0.000 0.000 0.012
#> SRR1044517 3 0.1502 0.88264 0.000 0.004 0.940 0.000 0.056
#> SRR1044518 3 0.0880 0.88429 0.000 0.000 0.968 0.000 0.032
#> SRR1044519 3 0.0000 0.88193 0.000 0.000 1.000 0.000 0.000
#> SRR1044520 3 0.0000 0.88193 0.000 0.000 1.000 0.000 0.000
#> SRR1044521 2 0.0609 0.94948 0.000 0.980 0.000 0.000 0.020
#> SRR1044522 2 0.0609 0.94899 0.000 0.980 0.000 0.000 0.020
#> SRR1044523 2 0.0992 0.94249 0.000 0.968 0.008 0.000 0.024
#> SRR1044524 2 0.3236 0.79705 0.000 0.828 0.152 0.000 0.020
#> SRR1044525 4 0.0162 0.91112 0.000 0.000 0.000 0.996 0.004
#> SRR1044526 1 0.6196 0.07990 0.508 0.000 0.000 0.340 0.152
#> SRR1044527 2 0.0162 0.95128 0.000 0.996 0.000 0.000 0.004
#> SRR1044528 2 0.1197 0.93533 0.000 0.952 0.000 0.000 0.048
#> SRR1044529 2 0.0290 0.95159 0.000 0.992 0.000 0.000 0.008
#> SRR1044530 1 0.4210 -0.54420 0.588 0.000 0.000 0.000 0.412
#> SRR1044531 1 0.1851 0.38483 0.912 0.000 0.000 0.000 0.088
#> SRR1044533 1 0.0703 0.38227 0.976 0.000 0.000 0.000 0.024
#> SRR1044532 1 0.3932 -0.31750 0.672 0.000 0.000 0.000 0.328
#> SRR1044534 2 0.0510 0.95045 0.000 0.984 0.000 0.000 0.016
#> SRR1044535 3 0.3231 0.73617 0.000 0.196 0.800 0.000 0.004
#> SRR1044536 2 0.0703 0.94795 0.000 0.976 0.000 0.000 0.024
#> SRR1044537 1 0.4087 0.30799 0.756 0.000 0.000 0.036 0.208
#> SRR1044538 1 0.4256 -0.58658 0.564 0.000 0.000 0.000 0.436
#> SRR1044539 4 0.0703 0.90853 0.000 0.000 0.000 0.976 0.024
#> SRR1044540 1 0.1043 0.36857 0.960 0.000 0.000 0.000 0.040
#> SRR1044541 2 0.6081 0.00277 0.000 0.476 0.400 0.000 0.124
#> SRR1044542 1 0.4262 -0.58460 0.560 0.000 0.000 0.000 0.440
#> SRR1044543 1 0.1671 0.38643 0.924 0.000 0.000 0.000 0.076
#> SRR1044544 2 0.1732 0.90769 0.000 0.920 0.000 0.000 0.080
#> SRR1044545 4 0.0510 0.91036 0.000 0.000 0.000 0.984 0.016
#> SRR1044546 1 0.5747 -0.36410 0.504 0.000 0.000 0.088 0.408
#> SRR1044547 4 0.1341 0.89281 0.000 0.000 0.000 0.944 0.056
#> SRR1044548 1 0.4937 -0.52722 0.544 0.000 0.000 0.028 0.428
#> SRR1044549 2 0.1211 0.93888 0.000 0.960 0.016 0.000 0.024
#> SRR1044550 2 0.0162 0.95180 0.000 0.996 0.000 0.000 0.004
#> SRR1044551 2 0.0609 0.94948 0.000 0.980 0.000 0.000 0.020
#> SRR1044552 4 0.0290 0.91061 0.000 0.000 0.000 0.992 0.008
#> SRR1044553 4 0.0404 0.91062 0.000 0.000 0.000 0.988 0.012
#> SRR1044554 1 0.4273 -0.36833 0.552 0.000 0.000 0.000 0.448
#> SRR1044555 2 0.5401 0.15815 0.000 0.536 0.404 0.000 0.060
#> SRR1044556 4 0.0000 0.91092 0.000 0.000 0.000 1.000 0.000
#> SRR1044557 1 0.4015 0.10682 0.652 0.000 0.000 0.000 0.348
#> SRR1044558 4 0.0000 0.91092 0.000 0.000 0.000 1.000 0.000
#> SRR1044559 1 0.5723 0.13398 0.640 0.000 0.040 0.052 0.268
#> SRR1044561 4 0.0290 0.91061 0.000 0.000 0.000 0.992 0.008
#> SRR1044560 2 0.0703 0.94632 0.000 0.976 0.000 0.000 0.024
#> SRR1044562 1 0.3266 0.33276 0.796 0.000 0.000 0.004 0.200
#> SRR1044563 4 0.0290 0.91108 0.000 0.000 0.000 0.992 0.008
#> SRR1044564 1 0.6661 -0.03170 0.444 0.000 0.000 0.284 0.272
#> SRR1044565 2 0.0290 0.95159 0.000 0.992 0.000 0.000 0.008
#> SRR1044566 2 0.0290 0.95116 0.000 0.992 0.000 0.000 0.008
#> SRR1044567 1 0.4256 -0.61223 0.564 0.000 0.000 0.000 0.436
#> SRR1044568 4 0.3791 0.77855 0.112 0.000 0.000 0.812 0.076
#> SRR1044569 1 0.1478 0.38612 0.936 0.000 0.000 0.000 0.064
#> SRR1044570 1 0.4242 -0.56876 0.572 0.000 0.000 0.000 0.428
#> SRR1044571 1 0.1792 0.32663 0.916 0.000 0.000 0.000 0.084
#> SRR1044572 1 0.2074 0.30662 0.896 0.000 0.000 0.000 0.104
#> SRR1044573 1 0.3934 0.29815 0.800 0.000 0.000 0.076 0.124
#> SRR1044574 1 0.1410 0.37770 0.940 0.000 0.000 0.000 0.060
#> SRR1044575 1 0.2561 0.36878 0.884 0.000 0.000 0.020 0.096
#> SRR1044576 2 0.0290 0.95186 0.000 0.992 0.000 0.000 0.008
#> SRR1044577 2 0.0000 0.95169 0.000 1.000 0.000 0.000 0.000
#> SRR1044578 2 0.0162 0.95180 0.000 0.996 0.000 0.000 0.004
#> SRR1044579 4 0.0404 0.91058 0.000 0.000 0.000 0.988 0.012
#> SRR1044580 1 0.6606 -0.11912 0.420 0.000 0.000 0.364 0.216
#> SRR1044581 4 0.0162 0.91084 0.000 0.000 0.000 0.996 0.004
#> SRR1044582 1 0.4030 -0.30122 0.648 0.000 0.000 0.000 0.352
#> SRR1044583 4 0.0794 0.90483 0.000 0.000 0.000 0.972 0.028
#> SRR1044584 4 0.1251 0.89784 0.008 0.000 0.000 0.956 0.036
#> SRR1044585 4 0.0290 0.91061 0.000 0.000 0.000 0.992 0.008
#> SRR1044586 5 0.5293 0.00000 0.460 0.000 0.000 0.048 0.492
#> SRR1044587 4 0.0290 0.91038 0.000 0.000 0.000 0.992 0.008
#> SRR1044588 4 0.0609 0.90958 0.000 0.000 0.000 0.980 0.020
#> SRR1044589 4 0.0404 0.91061 0.000 0.000 0.000 0.988 0.012
#> SRR1044590 4 0.0510 0.91019 0.000 0.000 0.000 0.984 0.016
#> SRR1044591 4 0.0404 0.91061 0.000 0.000 0.000 0.988 0.012
#> SRR1044592 4 0.2124 0.87201 0.000 0.000 0.056 0.916 0.028
#> SRR1044593 4 0.0290 0.91038 0.000 0.000 0.000 0.992 0.008
#> SRR1044594 4 0.0404 0.91061 0.000 0.000 0.000 0.988 0.012
#> SRR1044595 3 0.7387 -0.03957 0.160 0.000 0.444 0.060 0.336
#> SRR1044596 4 0.0404 0.91029 0.000 0.000 0.000 0.988 0.012
#> SRR1044597 4 0.6655 0.57146 0.056 0.020 0.092 0.632 0.200
#> SRR1044598 1 0.4906 -0.77445 0.496 0.000 0.000 0.024 0.480
#> SRR1044599 1 0.4650 -0.70434 0.520 0.000 0.000 0.012 0.468
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.0363 0.9271 0.000 0.988 0.000 0.000 0.000 0.012
#> SRR1044416 2 0.0146 0.9287 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044417 2 0.0405 0.9275 0.000 0.988 0.000 0.000 0.004 0.008
#> SRR1044418 2 0.0405 0.9275 0.000 0.988 0.000 0.000 0.004 0.008
#> SRR1044420 2 0.0260 0.9291 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044419 2 0.0458 0.9265 0.000 0.984 0.000 0.000 0.000 0.016
#> SRR1044421 2 0.0405 0.9275 0.000 0.988 0.000 0.000 0.004 0.008
#> SRR1044422 2 0.0458 0.9265 0.000 0.984 0.000 0.000 0.000 0.016
#> SRR1044423 2 0.0777 0.9246 0.000 0.972 0.000 0.000 0.004 0.024
#> SRR1044424 2 0.0790 0.9203 0.000 0.968 0.000 0.000 0.000 0.032
#> SRR1044425 4 0.4845 0.5077 0.052 0.000 0.000 0.636 0.296 0.016
#> SRR1044426 1 0.4585 0.3890 0.692 0.000 0.000 0.000 0.192 0.116
#> SRR1044427 4 0.3235 0.8157 0.008 0.000 0.000 0.824 0.136 0.032
#> SRR1044428 5 0.5171 0.3484 0.336 0.000 0.000 0.000 0.560 0.104
#> SRR1044429 4 0.6340 0.1360 0.244 0.000 0.000 0.500 0.224 0.032
#> SRR1044430 5 0.5752 0.3072 0.288 0.004 0.000 0.000 0.524 0.184
#> SRR1044431 1 0.5742 -0.1367 0.488 0.000 0.000 0.080 0.400 0.032
#> SRR1044433 4 0.3812 0.7203 0.004 0.000 0.204 0.760 0.008 0.024
#> SRR1044432 1 0.5560 -0.1230 0.444 0.000 0.000 0.000 0.420 0.136
#> SRR1044434 4 0.1765 0.8874 0.000 0.000 0.000 0.924 0.052 0.024
#> SRR1044435 4 0.1003 0.8975 0.000 0.000 0.000 0.964 0.016 0.020
#> SRR1044436 4 0.0622 0.8985 0.000 0.000 0.000 0.980 0.012 0.008
#> SRR1044437 4 0.1168 0.8952 0.000 0.000 0.000 0.956 0.028 0.016
#> SRR1044439 4 0.0520 0.8975 0.000 0.000 0.000 0.984 0.008 0.008
#> SRR1044438 4 0.0993 0.8976 0.000 0.000 0.000 0.964 0.012 0.024
#> SRR1044440 4 0.1461 0.8923 0.000 0.000 0.000 0.940 0.044 0.016
#> SRR1044441 4 0.1297 0.8938 0.000 0.000 0.000 0.948 0.040 0.012
#> SRR1044442 4 0.3096 0.8434 0.008 0.000 0.020 0.864 0.040 0.068
#> SRR1044443 3 0.2326 0.5648 0.000 0.000 0.888 0.092 0.008 0.012
#> SRR1044444 4 0.1528 0.8901 0.000 0.000 0.000 0.936 0.048 0.016
#> SRR1044445 4 0.0547 0.8978 0.000 0.000 0.000 0.980 0.000 0.020
#> SRR1044446 3 0.0146 0.6970 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1044447 3 0.1951 0.5837 0.000 0.076 0.908 0.000 0.000 0.016
#> SRR1044449 3 0.3782 -0.1235 0.000 0.000 0.636 0.000 0.004 0.360
#> SRR1044448 3 0.0146 0.6980 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1044450 3 0.1049 0.6833 0.000 0.000 0.960 0.000 0.008 0.032
#> SRR1044451 3 0.1003 0.6805 0.000 0.020 0.964 0.000 0.000 0.016
#> SRR1044452 3 0.4449 -0.4971 0.000 0.028 0.532 0.000 0.000 0.440
#> SRR1044453 6 0.5449 0.9153 0.000 0.108 0.388 0.000 0.004 0.500
#> SRR1044454 6 0.5417 0.9191 0.000 0.112 0.352 0.000 0.004 0.532
#> SRR1044455 2 0.4789 0.5476 0.000 0.700 0.164 0.000 0.012 0.124
#> SRR1044456 2 0.0146 0.9288 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1044457 2 0.0603 0.9249 0.000 0.980 0.004 0.000 0.000 0.016
#> SRR1044458 2 0.0260 0.9283 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044459 3 0.2669 0.5918 0.000 0.000 0.836 0.000 0.008 0.156
#> SRR1044460 2 0.0405 0.9275 0.000 0.988 0.000 0.000 0.004 0.008
#> SRR1044461 2 0.0790 0.9204 0.000 0.968 0.000 0.000 0.000 0.032
#> SRR1044462 5 0.5190 0.2689 0.024 0.000 0.000 0.304 0.608 0.064
#> SRR1044463 1 0.1657 0.5754 0.928 0.000 0.000 0.000 0.056 0.016
#> SRR1044464 4 0.2450 0.8532 0.000 0.000 0.000 0.868 0.116 0.016
#> SRR1044466 1 0.1421 0.5844 0.944 0.000 0.000 0.000 0.028 0.028
#> SRR1044465 5 0.3728 0.5568 0.344 0.000 0.000 0.000 0.652 0.004
#> SRR1044467 5 0.3993 0.5070 0.400 0.000 0.000 0.000 0.592 0.008
#> SRR1044468 2 0.0363 0.9271 0.000 0.988 0.000 0.000 0.000 0.012
#> SRR1044469 2 0.3944 0.2037 0.000 0.568 0.004 0.000 0.000 0.428
#> SRR1044470 1 0.2199 0.5629 0.892 0.000 0.000 0.000 0.088 0.020
#> SRR1044471 5 0.3468 0.5821 0.284 0.000 0.000 0.000 0.712 0.004
#> SRR1044472 1 0.1176 0.5841 0.956 0.000 0.000 0.000 0.020 0.024
#> SRR1044473 5 0.3784 0.5784 0.236 0.000 0.000 0.024 0.736 0.004
#> SRR1044474 2 0.0260 0.9290 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044475 2 0.5139 -0.1460 0.000 0.492 0.084 0.000 0.000 0.424
#> SRR1044476 2 0.0865 0.9170 0.000 0.964 0.000 0.000 0.000 0.036
#> SRR1044477 2 0.0000 0.9289 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044478 2 0.0363 0.9288 0.000 0.988 0.000 0.000 0.000 0.012
#> SRR1044479 2 0.0291 0.9283 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1044480 4 0.4300 0.6942 0.000 0.000 0.000 0.712 0.208 0.080
#> SRR1044481 1 0.5125 0.4305 0.684 0.000 0.000 0.048 0.192 0.076
#> SRR1044482 2 0.0458 0.9265 0.000 0.984 0.000 0.000 0.000 0.016
#> SRR1044483 4 0.4168 0.6503 0.000 0.000 0.000 0.696 0.256 0.048
#> SRR1044484 4 0.5987 0.4947 0.120 0.000 0.000 0.604 0.204 0.072
#> SRR1044486 1 0.3662 0.5263 0.824 0.000 0.000 0.072 0.056 0.048
#> SRR1044485 2 0.0000 0.9289 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044487 2 0.0260 0.9282 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044488 2 0.0405 0.9275 0.000 0.988 0.000 0.000 0.004 0.008
#> SRR1044489 2 0.0146 0.9287 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044490 5 0.4141 0.4581 0.432 0.000 0.000 0.000 0.556 0.012
#> SRR1044491 1 0.4644 -0.3099 0.504 0.000 0.000 0.000 0.456 0.040
#> SRR1044492 1 0.4258 -0.2699 0.516 0.000 0.000 0.000 0.468 0.016
#> SRR1044493 1 0.3587 0.4754 0.792 0.000 0.000 0.000 0.140 0.068
#> SRR1044494 2 0.0260 0.9290 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044496 2 0.0291 0.9283 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1044495 2 0.0000 0.9289 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044497 4 0.0363 0.8973 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR1044499 2 0.2135 0.8235 0.000 0.872 0.000 0.000 0.000 0.128
#> SRR1044498 1 0.5726 0.1989 0.532 0.000 0.000 0.356 0.060 0.052
#> SRR1044500 2 0.0146 0.9287 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1044501 2 0.0260 0.9290 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044502 3 0.3694 0.1010 0.000 0.232 0.740 0.000 0.000 0.028
#> SRR1044503 4 0.1549 0.8916 0.000 0.000 0.000 0.936 0.044 0.020
#> SRR1044504 4 0.0622 0.8974 0.000 0.000 0.000 0.980 0.008 0.012
#> SRR1044505 5 0.3381 0.4366 0.004 0.000 0.000 0.148 0.808 0.040
#> SRR1044506 4 0.1168 0.8910 0.000 0.000 0.000 0.956 0.016 0.028
#> SRR1044507 4 0.3535 0.8150 0.000 0.000 0.068 0.832 0.040 0.060
#> SRR1044508 3 0.6162 0.1044 0.000 0.000 0.552 0.276 0.076 0.096
#> SRR1044509 4 0.5280 0.3380 0.004 0.000 0.372 0.556 0.036 0.032
#> SRR1044510 3 0.2909 0.5882 0.000 0.004 0.828 0.000 0.012 0.156
#> SRR1044511 3 0.1524 0.6854 0.000 0.000 0.932 0.000 0.008 0.060
#> SRR1044512 3 0.1563 0.6849 0.000 0.000 0.932 0.000 0.012 0.056
#> SRR1044513 2 0.4333 0.6090 0.008 0.736 0.188 0.000 0.004 0.064
#> SRR1044514 3 0.1265 0.6928 0.000 0.000 0.948 0.000 0.008 0.044
#> SRR1044515 2 0.1176 0.9122 0.000 0.956 0.024 0.000 0.000 0.020
#> SRR1044516 2 0.0291 0.9292 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1044517 3 0.2312 0.6363 0.000 0.000 0.876 0.000 0.012 0.112
#> SRR1044518 3 0.1196 0.6934 0.000 0.000 0.952 0.000 0.008 0.040
#> SRR1044519 3 0.0405 0.6964 0.000 0.000 0.988 0.000 0.008 0.004
#> SRR1044520 3 0.0291 0.6969 0.000 0.000 0.992 0.000 0.004 0.004
#> SRR1044521 2 0.0622 0.9251 0.000 0.980 0.000 0.000 0.012 0.008
#> SRR1044522 2 0.0260 0.9290 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1044523 2 0.1245 0.9061 0.000 0.952 0.032 0.000 0.000 0.016
#> SRR1044524 2 0.3283 0.7190 0.000 0.804 0.160 0.000 0.000 0.036
#> SRR1044525 4 0.0820 0.8982 0.000 0.000 0.000 0.972 0.016 0.012
#> SRR1044526 5 0.3889 0.4387 0.044 0.000 0.000 0.164 0.776 0.016
#> SRR1044527 2 0.0260 0.9279 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044528 2 0.0993 0.9170 0.000 0.964 0.000 0.000 0.012 0.024
#> SRR1044529 2 0.0146 0.9288 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1044530 1 0.1500 0.5792 0.936 0.000 0.000 0.000 0.052 0.012
#> SRR1044531 5 0.3915 0.5071 0.412 0.000 0.000 0.000 0.584 0.004
#> SRR1044533 5 0.4109 0.5015 0.412 0.000 0.000 0.000 0.576 0.012
#> SRR1044532 1 0.1812 0.5634 0.912 0.000 0.000 0.000 0.080 0.008
#> SRR1044534 2 0.0291 0.9283 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1044535 3 0.4172 -0.0358 0.000 0.280 0.680 0.000 0.000 0.040
#> SRR1044536 2 0.0291 0.9283 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1044537 5 0.5505 0.3627 0.204 0.000 0.000 0.056 0.648 0.092
#> SRR1044538 1 0.1168 0.5850 0.956 0.000 0.000 0.000 0.016 0.028
#> SRR1044539 4 0.1049 0.8918 0.000 0.000 0.000 0.960 0.032 0.008
#> SRR1044540 5 0.3899 0.5065 0.404 0.000 0.000 0.000 0.592 0.004
#> SRR1044541 2 0.6034 -0.3948 0.000 0.412 0.260 0.000 0.000 0.328
#> SRR1044542 1 0.0725 0.5864 0.976 0.000 0.000 0.000 0.012 0.012
#> SRR1044543 5 0.3756 0.5764 0.316 0.000 0.000 0.004 0.676 0.004
#> SRR1044544 2 0.2915 0.7428 0.000 0.808 0.008 0.000 0.000 0.184
#> SRR1044545 4 0.1367 0.8852 0.000 0.000 0.000 0.944 0.044 0.012
#> SRR1044546 1 0.5878 0.2354 0.552 0.000 0.000 0.044 0.308 0.096
#> SRR1044547 4 0.2949 0.8094 0.000 0.000 0.000 0.832 0.140 0.028
#> SRR1044548 1 0.5667 0.3819 0.612 0.000 0.000 0.048 0.244 0.096
#> SRR1044549 2 0.0909 0.9206 0.000 0.968 0.012 0.000 0.000 0.020
#> SRR1044550 2 0.0260 0.9282 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1044551 2 0.0405 0.9275 0.000 0.988 0.000 0.000 0.004 0.008
#> SRR1044552 4 0.1003 0.8961 0.000 0.000 0.000 0.964 0.020 0.016
#> SRR1044553 4 0.0820 0.8978 0.000 0.000 0.000 0.972 0.016 0.012
#> SRR1044554 1 0.4812 0.2267 0.588 0.000 0.000 0.000 0.344 0.068
#> SRR1044555 2 0.5726 -0.1559 0.000 0.496 0.316 0.000 0.000 0.188
#> SRR1044556 4 0.0405 0.8959 0.000 0.000 0.000 0.988 0.004 0.008
#> SRR1044557 5 0.5630 -0.0174 0.416 0.000 0.000 0.012 0.468 0.104
#> SRR1044558 4 0.0547 0.8981 0.000 0.000 0.000 0.980 0.020 0.000
#> SRR1044559 5 0.6674 0.1415 0.324 0.000 0.032 0.044 0.496 0.104
#> SRR1044561 4 0.0972 0.8963 0.000 0.000 0.000 0.964 0.028 0.008
#> SRR1044560 2 0.1327 0.8924 0.000 0.936 0.000 0.000 0.000 0.064
#> SRR1044562 5 0.5025 0.4277 0.276 0.000 0.000 0.012 0.632 0.080
#> SRR1044563 4 0.0935 0.8982 0.000 0.000 0.000 0.964 0.032 0.004
#> SRR1044564 5 0.6760 0.2029 0.252 0.000 0.000 0.176 0.488 0.084
#> SRR1044565 2 0.0291 0.9283 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1044566 2 0.0363 0.9275 0.000 0.988 0.000 0.000 0.000 0.012
#> SRR1044567 1 0.1934 0.5742 0.916 0.000 0.000 0.000 0.044 0.040
#> SRR1044568 4 0.5133 0.6151 0.056 0.000 0.000 0.668 0.224 0.052
#> SRR1044569 5 0.3684 0.5685 0.332 0.000 0.000 0.000 0.664 0.004
#> SRR1044570 1 0.1498 0.5821 0.940 0.000 0.000 0.000 0.032 0.028
#> SRR1044571 1 0.4472 -0.3227 0.496 0.000 0.000 0.000 0.476 0.028
#> SRR1044572 1 0.4591 -0.2979 0.500 0.000 0.000 0.000 0.464 0.036
#> SRR1044573 5 0.4056 0.5515 0.184 0.000 0.000 0.064 0.748 0.004
#> SRR1044574 5 0.4026 0.5355 0.376 0.000 0.000 0.000 0.612 0.012
#> SRR1044575 5 0.3897 0.5835 0.264 0.000 0.000 0.016 0.712 0.008
#> SRR1044576 2 0.0291 0.9283 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1044577 2 0.0363 0.9271 0.000 0.988 0.000 0.000 0.000 0.012
#> SRR1044578 2 0.0291 0.9292 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1044579 4 0.0914 0.8970 0.000 0.000 0.000 0.968 0.016 0.016
#> SRR1044580 1 0.6669 0.0785 0.416 0.000 0.000 0.332 0.208 0.044
#> SRR1044581 4 0.0508 0.8976 0.000 0.000 0.000 0.984 0.012 0.004
#> SRR1044582 1 0.3646 0.5040 0.776 0.000 0.000 0.000 0.172 0.052
#> SRR1044583 4 0.1434 0.8912 0.000 0.000 0.000 0.940 0.048 0.012
#> SRR1044584 4 0.2425 0.8659 0.004 0.000 0.000 0.884 0.088 0.024
#> SRR1044585 4 0.1461 0.8920 0.000 0.000 0.000 0.940 0.044 0.016
#> SRR1044586 1 0.4676 0.4883 0.744 0.000 0.000 0.056 0.120 0.080
#> SRR1044587 4 0.0622 0.8948 0.000 0.000 0.000 0.980 0.012 0.008
#> SRR1044588 4 0.1082 0.8962 0.000 0.000 0.000 0.956 0.004 0.040
#> SRR1044589 4 0.0777 0.8959 0.000 0.000 0.000 0.972 0.004 0.024
#> SRR1044590 4 0.0858 0.8954 0.000 0.000 0.000 0.968 0.004 0.028
#> SRR1044591 4 0.0777 0.8961 0.000 0.000 0.000 0.972 0.004 0.024
#> SRR1044592 4 0.2816 0.8469 0.000 0.000 0.060 0.876 0.036 0.028
#> SRR1044593 4 0.0820 0.8935 0.000 0.000 0.000 0.972 0.016 0.012
#> SRR1044594 4 0.0993 0.8968 0.000 0.000 0.000 0.964 0.012 0.024
#> SRR1044595 1 0.7360 0.0466 0.396 0.000 0.376 0.060 0.076 0.092
#> SRR1044596 4 0.1418 0.8833 0.000 0.000 0.000 0.944 0.032 0.024
#> SRR1044597 4 0.7916 0.2633 0.208 0.000 0.108 0.456 0.100 0.128
#> SRR1044598 1 0.3498 0.5375 0.828 0.000 0.000 0.024 0.056 0.092
#> SRR1044599 1 0.2862 0.5560 0.864 0.000 0.000 0.008 0.048 0.080
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) are extracted by 'ATC' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> There is no best k.
#>
#> 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.850 0.924 0.963 0.2340 0.757 0.757
#> 3 3 0.760 0.863 0.948 0.3364 0.941 0.922
#> 4 4 0.714 0.831 0.929 0.0364 0.988 0.984
#> 5 5 0.702 0.796 0.915 0.0357 0.989 0.984
#> 6 6 0.667 0.779 0.900 0.0706 0.995 0.992
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] NA
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 1 0.9170 0.3956 0.668 0.332
#> SRR1044416 1 0.0000 0.9763 1.000 0.000
#> SRR1044417 1 0.0000 0.9763 1.000 0.000
#> SRR1044418 1 0.0000 0.9763 1.000 0.000
#> SRR1044420 1 0.1633 0.9550 0.976 0.024
#> SRR1044419 1 0.9044 0.4301 0.680 0.320
#> SRR1044421 1 0.0376 0.9730 0.996 0.004
#> SRR1044422 1 0.5629 0.8190 0.868 0.132
#> SRR1044423 1 0.3431 0.9114 0.936 0.064
#> SRR1044424 1 0.1414 0.9588 0.980 0.020
#> SRR1044425 1 0.0000 0.9763 1.000 0.000
#> SRR1044426 1 0.0000 0.9763 1.000 0.000
#> SRR1044427 1 0.0000 0.9763 1.000 0.000
#> SRR1044428 1 0.0000 0.9763 1.000 0.000
#> SRR1044429 1 0.0000 0.9763 1.000 0.000
#> SRR1044430 1 0.0000 0.9763 1.000 0.000
#> SRR1044431 1 0.0000 0.9763 1.000 0.000
#> SRR1044433 1 0.0000 0.9763 1.000 0.000
#> SRR1044432 1 0.0000 0.9763 1.000 0.000
#> SRR1044434 1 0.0000 0.9763 1.000 0.000
#> SRR1044435 1 0.0000 0.9763 1.000 0.000
#> SRR1044436 1 0.0000 0.9763 1.000 0.000
#> SRR1044437 1 0.0000 0.9763 1.000 0.000
#> SRR1044439 1 0.0000 0.9763 1.000 0.000
#> SRR1044438 1 0.0000 0.9763 1.000 0.000
#> SRR1044440 1 0.0000 0.9763 1.000 0.000
#> SRR1044441 1 0.0000 0.9763 1.000 0.000
#> SRR1044442 1 0.0000 0.9763 1.000 0.000
#> SRR1044443 1 0.0000 0.9763 1.000 0.000
#> SRR1044444 1 0.0000 0.9763 1.000 0.000
#> SRR1044445 1 0.0000 0.9763 1.000 0.000
#> SRR1044446 2 0.9209 0.6716 0.336 0.664
#> SRR1044447 1 0.3584 0.9060 0.932 0.068
#> SRR1044449 2 0.0376 0.8401 0.004 0.996
#> SRR1044448 2 0.7453 0.8217 0.212 0.788
#> SRR1044450 2 0.8443 0.7757 0.272 0.728
#> SRR1044451 1 0.0938 0.9660 0.988 0.012
#> SRR1044452 2 0.0000 0.8398 0.000 1.000
#> SRR1044453 2 0.0000 0.8398 0.000 1.000
#> SRR1044454 2 0.0000 0.8398 0.000 1.000
#> SRR1044455 1 0.8144 0.6004 0.748 0.252
#> SRR1044456 1 0.0000 0.9763 1.000 0.000
#> SRR1044457 1 0.9815 0.0773 0.580 0.420
#> SRR1044458 1 0.9427 0.3070 0.640 0.360
#> SRR1044459 2 0.8016 0.8036 0.244 0.756
#> SRR1044460 1 0.1843 0.9511 0.972 0.028
#> SRR1044461 1 0.7950 0.6252 0.760 0.240
#> SRR1044462 1 0.0000 0.9763 1.000 0.000
#> SRR1044463 1 0.0000 0.9763 1.000 0.000
#> SRR1044464 1 0.0000 0.9763 1.000 0.000
#> SRR1044466 1 0.0000 0.9763 1.000 0.000
#> SRR1044465 1 0.0000 0.9763 1.000 0.000
#> SRR1044467 1 0.0000 0.9763 1.000 0.000
#> SRR1044468 1 0.1843 0.9511 0.972 0.028
#> SRR1044469 2 0.5059 0.8412 0.112 0.888
#> SRR1044470 1 0.0000 0.9763 1.000 0.000
#> SRR1044471 1 0.0000 0.9763 1.000 0.000
#> SRR1044472 1 0.0000 0.9763 1.000 0.000
#> SRR1044473 1 0.0000 0.9763 1.000 0.000
#> SRR1044474 1 0.0000 0.9763 1.000 0.000
#> SRR1044475 2 0.0000 0.8398 0.000 1.000
#> SRR1044476 2 0.8499 0.7718 0.276 0.724
#> SRR1044477 1 0.0000 0.9763 1.000 0.000
#> SRR1044478 1 0.2948 0.9256 0.948 0.052
#> SRR1044479 1 0.0000 0.9763 1.000 0.000
#> SRR1044480 1 0.0000 0.9763 1.000 0.000
#> SRR1044481 1 0.0000 0.9763 1.000 0.000
#> SRR1044482 1 0.0000 0.9763 1.000 0.000
#> SRR1044483 1 0.0000 0.9763 1.000 0.000
#> SRR1044484 1 0.0000 0.9763 1.000 0.000
#> SRR1044486 1 0.0000 0.9763 1.000 0.000
#> SRR1044485 1 0.1184 0.9625 0.984 0.016
#> SRR1044487 1 0.0000 0.9763 1.000 0.000
#> SRR1044488 1 0.1843 0.9511 0.972 0.028
#> SRR1044489 1 0.1843 0.9511 0.972 0.028
#> SRR1044490 1 0.0000 0.9763 1.000 0.000
#> SRR1044491 1 0.0000 0.9763 1.000 0.000
#> SRR1044492 1 0.0000 0.9763 1.000 0.000
#> SRR1044493 1 0.0000 0.9763 1.000 0.000
#> SRR1044494 1 0.0000 0.9763 1.000 0.000
#> SRR1044496 1 0.0000 0.9763 1.000 0.000
#> SRR1044495 1 0.0000 0.9763 1.000 0.000
#> SRR1044497 1 0.0000 0.9763 1.000 0.000
#> SRR1044499 2 0.5059 0.8412 0.112 0.888
#> SRR1044498 1 0.0000 0.9763 1.000 0.000
#> SRR1044500 1 0.1414 0.9588 0.980 0.020
#> SRR1044501 1 0.9000 0.4416 0.684 0.316
#> SRR1044502 1 0.1184 0.9625 0.984 0.016
#> SRR1044503 1 0.0000 0.9763 1.000 0.000
#> SRR1044504 1 0.0000 0.9763 1.000 0.000
#> SRR1044505 1 0.0000 0.9763 1.000 0.000
#> SRR1044506 1 0.0000 0.9763 1.000 0.000
#> SRR1044507 1 0.0000 0.9763 1.000 0.000
#> SRR1044508 1 0.0000 0.9763 1.000 0.000
#> SRR1044509 1 0.0000 0.9763 1.000 0.000
#> SRR1044510 2 0.0000 0.8398 0.000 1.000
#> SRR1044511 2 0.0000 0.8398 0.000 1.000
#> SRR1044512 2 0.0000 0.8398 0.000 1.000
#> SRR1044513 1 0.0376 0.9730 0.996 0.004
#> SRR1044514 2 0.0000 0.8398 0.000 1.000
#> SRR1044515 1 0.0376 0.9730 0.996 0.004
#> SRR1044516 1 0.3584 0.9066 0.932 0.068
#> SRR1044517 2 0.0000 0.8398 0.000 1.000
#> SRR1044518 2 0.0000 0.8398 0.000 1.000
#> SRR1044519 2 0.7453 0.8217 0.212 0.788
#> SRR1044520 2 0.7453 0.8217 0.212 0.788
#> SRR1044521 1 0.0938 0.9662 0.988 0.012
#> SRR1044522 1 0.0000 0.9763 1.000 0.000
#> SRR1044523 1 0.0376 0.9730 0.996 0.004
#> SRR1044524 2 0.9996 0.2759 0.488 0.512
#> SRR1044525 1 0.0000 0.9763 1.000 0.000
#> SRR1044526 1 0.0000 0.9763 1.000 0.000
#> SRR1044527 1 0.0000 0.9763 1.000 0.000
#> SRR1044528 1 0.0000 0.9763 1.000 0.000
#> SRR1044529 1 0.0000 0.9763 1.000 0.000
#> SRR1044530 1 0.0000 0.9763 1.000 0.000
#> SRR1044531 1 0.0000 0.9763 1.000 0.000
#> SRR1044533 1 0.0000 0.9763 1.000 0.000
#> SRR1044532 1 0.0000 0.9763 1.000 0.000
#> SRR1044534 1 0.1414 0.9588 0.980 0.020
#> SRR1044535 1 0.7139 0.7145 0.804 0.196
#> SRR1044536 1 0.2043 0.9470 0.968 0.032
#> SRR1044537 1 0.0000 0.9763 1.000 0.000
#> SRR1044538 1 0.0000 0.9763 1.000 0.000
#> SRR1044539 1 0.0000 0.9763 1.000 0.000
#> SRR1044540 1 0.0000 0.9763 1.000 0.000
#> SRR1044541 2 0.8144 0.7973 0.252 0.748
#> SRR1044542 1 0.0000 0.9763 1.000 0.000
#> SRR1044543 1 0.0000 0.9763 1.000 0.000
#> SRR1044544 2 0.8144 0.7974 0.252 0.748
#> SRR1044545 1 0.0000 0.9763 1.000 0.000
#> SRR1044546 1 0.0000 0.9763 1.000 0.000
#> SRR1044547 1 0.0000 0.9763 1.000 0.000
#> SRR1044548 1 0.0000 0.9763 1.000 0.000
#> SRR1044549 1 0.0000 0.9763 1.000 0.000
#> SRR1044550 1 0.2043 0.9470 0.968 0.032
#> SRR1044551 1 0.0000 0.9763 1.000 0.000
#> SRR1044552 1 0.0000 0.9763 1.000 0.000
#> SRR1044553 1 0.0000 0.9763 1.000 0.000
#> SRR1044554 1 0.0000 0.9763 1.000 0.000
#> SRR1044555 2 0.7950 0.8064 0.240 0.760
#> SRR1044556 1 0.0000 0.9763 1.000 0.000
#> SRR1044557 1 0.0000 0.9763 1.000 0.000
#> SRR1044558 1 0.0000 0.9763 1.000 0.000
#> SRR1044559 1 0.0000 0.9763 1.000 0.000
#> SRR1044561 1 0.0000 0.9763 1.000 0.000
#> SRR1044560 2 0.8499 0.7718 0.276 0.724
#> SRR1044562 1 0.0000 0.9763 1.000 0.000
#> SRR1044563 1 0.0000 0.9763 1.000 0.000
#> SRR1044564 1 0.0000 0.9763 1.000 0.000
#> SRR1044565 1 0.0000 0.9763 1.000 0.000
#> SRR1044566 2 0.8555 0.7662 0.280 0.720
#> SRR1044567 1 0.0000 0.9763 1.000 0.000
#> SRR1044568 1 0.0000 0.9763 1.000 0.000
#> SRR1044569 1 0.0000 0.9763 1.000 0.000
#> SRR1044570 1 0.0000 0.9763 1.000 0.000
#> SRR1044571 1 0.0000 0.9763 1.000 0.000
#> SRR1044572 1 0.0000 0.9763 1.000 0.000
#> SRR1044573 1 0.0000 0.9763 1.000 0.000
#> SRR1044574 1 0.0000 0.9763 1.000 0.000
#> SRR1044575 1 0.0000 0.9763 1.000 0.000
#> SRR1044576 1 0.0000 0.9763 1.000 0.000
#> SRR1044577 1 0.0000 0.9763 1.000 0.000
#> SRR1044578 1 0.0000 0.9763 1.000 0.000
#> SRR1044579 1 0.0000 0.9763 1.000 0.000
#> SRR1044580 1 0.0000 0.9763 1.000 0.000
#> SRR1044581 1 0.0000 0.9763 1.000 0.000
#> SRR1044582 1 0.0000 0.9763 1.000 0.000
#> SRR1044583 1 0.0000 0.9763 1.000 0.000
#> SRR1044584 1 0.0000 0.9763 1.000 0.000
#> SRR1044585 1 0.0000 0.9763 1.000 0.000
#> SRR1044586 1 0.0000 0.9763 1.000 0.000
#> SRR1044587 1 0.0000 0.9763 1.000 0.000
#> SRR1044588 1 0.0000 0.9763 1.000 0.000
#> SRR1044589 1 0.0000 0.9763 1.000 0.000
#> SRR1044590 1 0.0000 0.9763 1.000 0.000
#> SRR1044591 1 0.0000 0.9763 1.000 0.000
#> SRR1044592 1 0.0000 0.9763 1.000 0.000
#> SRR1044593 1 0.0000 0.9763 1.000 0.000
#> SRR1044594 1 0.0000 0.9763 1.000 0.000
#> SRR1044595 1 0.0000 0.9763 1.000 0.000
#> SRR1044596 1 0.0000 0.9763 1.000 0.000
#> SRR1044597 1 0.0000 0.9763 1.000 0.000
#> SRR1044598 1 0.0000 0.9763 1.000 0.000
#> SRR1044599 1 0.0000 0.9763 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.6252 0.3169 0.444 0.556 0.000
#> SRR1044416 1 0.0892 0.9398 0.980 0.020 0.000
#> SRR1044417 1 0.0592 0.9458 0.988 0.012 0.000
#> SRR1044418 1 0.0424 0.9488 0.992 0.008 0.000
#> SRR1044420 1 0.4002 0.7952 0.840 0.160 0.000
#> SRR1044419 2 0.6274 0.2805 0.456 0.544 0.000
#> SRR1044421 1 0.3192 0.8534 0.888 0.112 0.000
#> SRR1044422 1 0.5905 0.4111 0.648 0.352 0.000
#> SRR1044423 1 0.5465 0.5727 0.712 0.288 0.000
#> SRR1044424 1 0.3816 0.8113 0.852 0.148 0.000
#> SRR1044425 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044426 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044427 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044428 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044429 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044430 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044431 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044433 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044432 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044434 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044435 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044436 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044437 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044439 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044438 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044440 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044441 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044442 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044443 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044444 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044445 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044446 2 0.2959 0.5905 0.100 0.900 0.000
#> SRR1044447 1 0.5327 0.6072 0.728 0.272 0.000
#> SRR1044449 3 0.2356 0.9329 0.000 0.072 0.928
#> SRR1044448 2 0.1163 0.5731 0.000 0.972 0.028
#> SRR1044450 2 0.1411 0.6185 0.036 0.964 0.000
#> SRR1044451 1 0.4555 0.7361 0.800 0.200 0.000
#> SRR1044452 3 0.0000 0.9740 0.000 0.000 1.000
#> SRR1044453 3 0.0000 0.9740 0.000 0.000 1.000
#> SRR1044454 3 0.0000 0.9740 0.000 0.000 1.000
#> SRR1044455 1 0.6299 -0.0574 0.524 0.476 0.000
#> SRR1044456 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044457 2 0.5905 0.4633 0.352 0.648 0.000
#> SRR1044458 2 0.6168 0.4006 0.412 0.588 0.000
#> SRR1044459 2 0.0424 0.6011 0.008 0.992 0.000
#> SRR1044460 1 0.4178 0.7791 0.828 0.172 0.000
#> SRR1044461 1 0.6280 0.0120 0.540 0.460 0.000
#> SRR1044462 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044463 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044464 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044466 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044465 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044467 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044468 1 0.4178 0.7794 0.828 0.172 0.000
#> SRR1044469 2 0.5431 0.1857 0.000 0.716 0.284
#> SRR1044470 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044471 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044472 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044473 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044474 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044475 3 0.0000 0.9740 0.000 0.000 1.000
#> SRR1044476 2 0.1529 0.6226 0.040 0.960 0.000
#> SRR1044477 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044478 1 0.4654 0.7249 0.792 0.208 0.000
#> SRR1044479 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044480 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044481 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044482 1 0.0747 0.9430 0.984 0.016 0.000
#> SRR1044483 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044484 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044486 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044485 1 0.2959 0.8657 0.900 0.100 0.000
#> SRR1044487 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044488 1 0.4121 0.7845 0.832 0.168 0.000
#> SRR1044489 1 0.4121 0.7845 0.832 0.168 0.000
#> SRR1044490 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044491 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044492 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044493 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044494 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044496 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044495 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044497 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044499 2 0.5431 0.1857 0.000 0.716 0.284
#> SRR1044498 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044500 1 0.3941 0.8004 0.844 0.156 0.000
#> SRR1044501 2 0.6280 0.2671 0.460 0.540 0.000
#> SRR1044502 1 0.4504 0.7426 0.804 0.196 0.000
#> SRR1044503 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044504 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044505 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044506 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044507 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044508 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044509 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044510 3 0.0000 0.9740 0.000 0.000 1.000
#> SRR1044511 3 0.2261 0.9523 0.000 0.068 0.932
#> SRR1044512 3 0.1031 0.9699 0.000 0.024 0.976
#> SRR1044513 1 0.4399 0.7554 0.812 0.188 0.000
#> SRR1044514 3 0.2066 0.9565 0.000 0.060 0.940
#> SRR1044515 1 0.4399 0.7554 0.812 0.188 0.000
#> SRR1044516 1 0.5465 0.5727 0.712 0.288 0.000
#> SRR1044517 3 0.0000 0.9740 0.000 0.000 1.000
#> SRR1044518 3 0.2261 0.9523 0.000 0.068 0.932
#> SRR1044519 2 0.1163 0.5731 0.000 0.972 0.028
#> SRR1044520 2 0.1163 0.5731 0.000 0.972 0.028
#> SRR1044521 1 0.2959 0.8656 0.900 0.100 0.000
#> SRR1044522 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044523 1 0.3551 0.8316 0.868 0.132 0.000
#> SRR1044524 2 0.5138 0.5069 0.252 0.748 0.000
#> SRR1044525 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044526 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044527 1 0.2537 0.8865 0.920 0.080 0.000
#> SRR1044528 1 0.1411 0.9268 0.964 0.036 0.000
#> SRR1044529 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044530 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044531 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044533 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044532 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044534 1 0.3879 0.8055 0.848 0.152 0.000
#> SRR1044535 1 0.6225 0.1490 0.568 0.432 0.000
#> SRR1044536 1 0.4178 0.7790 0.828 0.172 0.000
#> SRR1044537 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044538 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044539 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044540 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044541 2 0.0747 0.6104 0.016 0.984 0.000
#> SRR1044542 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044543 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044544 2 0.0983 0.6089 0.016 0.980 0.004
#> SRR1044545 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044546 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044547 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044548 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044549 1 0.2625 0.8825 0.916 0.084 0.000
#> SRR1044550 1 0.4235 0.7734 0.824 0.176 0.000
#> SRR1044551 1 0.1289 0.9303 0.968 0.032 0.000
#> SRR1044552 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044553 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044554 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044555 2 0.0475 0.5932 0.004 0.992 0.004
#> SRR1044556 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044557 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044558 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044559 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044561 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044560 2 0.1529 0.6226 0.040 0.960 0.000
#> SRR1044562 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044563 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044564 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044565 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044566 2 0.1643 0.6220 0.044 0.956 0.000
#> SRR1044567 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044568 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044569 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044570 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044571 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044572 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044573 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044574 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044575 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044576 1 0.0747 0.9428 0.984 0.016 0.000
#> SRR1044577 1 0.0592 0.9461 0.988 0.012 0.000
#> SRR1044578 1 0.0424 0.9489 0.992 0.008 0.000
#> SRR1044579 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044580 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044581 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044582 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044583 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044584 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044585 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044586 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044587 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044588 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044589 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044590 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044591 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044592 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044593 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044594 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044595 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044596 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044597 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044598 1 0.0000 0.9546 1.000 0.000 0.000
#> SRR1044599 1 0.0000 0.9546 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 2 0.4898 0.3751 0.416 0.584 0.000 0.000
#> SRR1044416 1 0.1022 0.9291 0.968 0.032 0.000 0.000
#> SRR1044417 1 0.0817 0.9350 0.976 0.024 0.000 0.000
#> SRR1044418 1 0.0707 0.9381 0.980 0.020 0.000 0.000
#> SRR1044420 1 0.3486 0.7612 0.812 0.188 0.000 0.000
#> SRR1044419 2 0.4925 0.3430 0.428 0.572 0.000 0.000
#> SRR1044421 1 0.3217 0.8234 0.860 0.128 0.000 0.012
#> SRR1044422 1 0.4790 0.3440 0.620 0.380 0.000 0.000
#> SRR1044423 1 0.4500 0.5213 0.684 0.316 0.000 0.000
#> SRR1044424 1 0.3356 0.7779 0.824 0.176 0.000 0.000
#> SRR1044425 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044426 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044427 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044428 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044429 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044430 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044431 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044433 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044432 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044434 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044435 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044436 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044437 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044439 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044438 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044440 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044441 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044442 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044443 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044444 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044445 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044446 2 0.5473 0.4390 0.084 0.724 0.000 0.192
#> SRR1044447 1 0.5200 0.5596 0.700 0.264 0.000 0.036
#> SRR1044449 3 0.2521 0.7691 0.000 0.024 0.912 0.064
#> SRR1044448 2 0.4277 0.3396 0.000 0.720 0.000 0.280
#> SRR1044450 2 0.4426 0.4285 0.024 0.772 0.000 0.204
#> SRR1044451 1 0.4426 0.6980 0.772 0.204 0.000 0.024
#> SRR1044452 3 0.0000 0.8514 0.000 0.000 1.000 0.000
#> SRR1044453 3 0.0000 0.8514 0.000 0.000 1.000 0.000
#> SRR1044454 3 0.0000 0.8514 0.000 0.000 1.000 0.000
#> SRR1044455 2 0.5000 0.1054 0.496 0.504 0.000 0.000
#> SRR1044456 1 0.0188 0.9489 0.996 0.004 0.000 0.000
#> SRR1044457 2 0.4897 0.4201 0.332 0.660 0.000 0.008
#> SRR1044458 2 0.4978 0.4091 0.384 0.612 0.000 0.004
#> SRR1044459 2 0.1302 0.4524 0.000 0.956 0.000 0.044
#> SRR1044460 1 0.3610 0.7440 0.800 0.200 0.000 0.000
#> SRR1044461 1 0.4998 -0.0930 0.512 0.488 0.000 0.000
#> SRR1044462 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044463 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044464 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044466 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044465 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044467 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044468 1 0.3610 0.7442 0.800 0.200 0.000 0.000
#> SRR1044469 2 0.5334 0.0981 0.000 0.680 0.284 0.036
#> SRR1044470 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044471 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044472 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044473 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044474 1 0.0336 0.9466 0.992 0.008 0.000 0.000
#> SRR1044475 3 0.0000 0.8514 0.000 0.000 1.000 0.000
#> SRR1044476 2 0.1520 0.4830 0.024 0.956 0.000 0.020
#> SRR1044477 1 0.0336 0.9466 0.992 0.008 0.000 0.000
#> SRR1044478 1 0.3942 0.6855 0.764 0.236 0.000 0.000
#> SRR1044479 1 0.0188 0.9489 0.996 0.004 0.000 0.000
#> SRR1044480 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044481 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044482 1 0.0921 0.9325 0.972 0.028 0.000 0.000
#> SRR1044483 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044484 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044486 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044485 1 0.2589 0.8495 0.884 0.116 0.000 0.000
#> SRR1044487 1 0.0336 0.9466 0.992 0.008 0.000 0.000
#> SRR1044488 1 0.3569 0.7497 0.804 0.196 0.000 0.000
#> SRR1044489 1 0.3569 0.7497 0.804 0.196 0.000 0.000
#> SRR1044490 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044491 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044492 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044493 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044494 1 0.0336 0.9466 0.992 0.008 0.000 0.000
#> SRR1044496 1 0.0336 0.9466 0.992 0.008 0.000 0.000
#> SRR1044495 1 0.0336 0.9466 0.992 0.008 0.000 0.000
#> SRR1044497 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044499 2 0.5334 0.0981 0.000 0.680 0.284 0.036
#> SRR1044498 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044500 1 0.3444 0.7666 0.816 0.184 0.000 0.000
#> SRR1044501 2 0.5105 0.3346 0.432 0.564 0.000 0.004
#> SRR1044502 1 0.4253 0.7039 0.776 0.208 0.000 0.016
#> SRR1044503 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044504 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044505 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044506 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044507 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044508 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044509 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044510 3 0.1637 0.8258 0.000 0.000 0.940 0.060
#> SRR1044511 4 0.4477 0.9931 0.000 0.000 0.312 0.688
#> SRR1044512 3 0.4998 -0.5902 0.000 0.000 0.512 0.488
#> SRR1044513 1 0.4307 0.7188 0.784 0.192 0.000 0.024
#> SRR1044514 4 0.4522 0.9861 0.000 0.000 0.320 0.680
#> SRR1044515 1 0.4307 0.7188 0.784 0.192 0.000 0.024
#> SRR1044516 1 0.4500 0.5215 0.684 0.316 0.000 0.000
#> SRR1044517 3 0.1557 0.8222 0.000 0.000 0.944 0.056
#> SRR1044518 4 0.4477 0.9931 0.000 0.000 0.312 0.688
#> SRR1044519 2 0.4250 0.3427 0.000 0.724 0.000 0.276
#> SRR1044520 2 0.4250 0.3427 0.000 0.724 0.000 0.276
#> SRR1044521 1 0.2647 0.8449 0.880 0.120 0.000 0.000
#> SRR1044522 1 0.0188 0.9489 0.996 0.004 0.000 0.000
#> SRR1044523 1 0.3547 0.7999 0.840 0.144 0.000 0.016
#> SRR1044524 2 0.5820 0.4309 0.232 0.684 0.000 0.084
#> SRR1044525 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044526 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044527 1 0.2345 0.8661 0.900 0.100 0.000 0.000
#> SRR1044528 1 0.1557 0.9088 0.944 0.056 0.000 0.000
#> SRR1044529 1 0.0336 0.9466 0.992 0.008 0.000 0.000
#> SRR1044530 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044531 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044533 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044532 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044534 1 0.3400 0.7719 0.820 0.180 0.000 0.000
#> SRR1044535 1 0.6500 0.0824 0.544 0.376 0.000 0.080
#> SRR1044536 1 0.3610 0.7439 0.800 0.200 0.000 0.000
#> SRR1044537 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044538 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044539 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044540 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044541 2 0.1635 0.4646 0.008 0.948 0.000 0.044
#> SRR1044542 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044543 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044544 2 0.1191 0.4636 0.004 0.968 0.004 0.024
#> SRR1044545 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044546 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044547 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044548 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044549 1 0.2408 0.8618 0.896 0.104 0.000 0.000
#> SRR1044550 1 0.3649 0.7380 0.796 0.204 0.000 0.000
#> SRR1044551 1 0.1302 0.9194 0.956 0.044 0.000 0.000
#> SRR1044552 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044553 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044554 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044555 2 0.1978 0.4509 0.000 0.928 0.004 0.068
#> SRR1044556 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044557 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044558 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044559 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044561 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044560 2 0.1520 0.4830 0.024 0.956 0.000 0.020
#> SRR1044562 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044563 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044564 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044565 1 0.0336 0.9466 0.992 0.008 0.000 0.000
#> SRR1044566 2 0.1624 0.4845 0.028 0.952 0.000 0.020
#> SRR1044567 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044568 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044569 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044570 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044571 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044572 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044573 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044574 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044575 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044576 1 0.0921 0.9319 0.972 0.028 0.000 0.000
#> SRR1044577 1 0.0817 0.9356 0.976 0.024 0.000 0.000
#> SRR1044578 1 0.0592 0.9411 0.984 0.016 0.000 0.000
#> SRR1044579 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044580 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044581 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044582 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044583 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044584 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044585 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044586 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044587 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044588 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044589 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044590 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044591 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044592 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044593 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044594 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044595 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044596 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044597 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044598 1 0.0000 0.9513 1.000 0.000 0.000 0.000
#> SRR1044599 1 0.0000 0.9513 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.4299 0.4027 0.388 0.608 0.000 0.000 0.004
#> SRR1044416 1 0.1444 0.9091 0.948 0.040 0.000 0.000 0.012
#> SRR1044417 1 0.1281 0.9154 0.956 0.032 0.000 0.000 0.012
#> SRR1044418 1 0.0771 0.9310 0.976 0.020 0.000 0.000 0.004
#> SRR1044420 1 0.3596 0.7099 0.776 0.212 0.000 0.000 0.012
#> SRR1044419 2 0.4192 0.3977 0.404 0.596 0.000 0.000 0.000
#> SRR1044421 1 0.3430 0.7781 0.824 0.152 0.000 0.012 0.012
#> SRR1044422 1 0.4557 0.2456 0.584 0.404 0.000 0.000 0.012
#> SRR1044423 1 0.4356 0.4448 0.648 0.340 0.000 0.000 0.012
#> SRR1044424 1 0.3496 0.7282 0.788 0.200 0.000 0.000 0.012
#> SRR1044425 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044426 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044427 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044428 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044429 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044430 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044431 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044433 1 0.0324 0.9422 0.992 0.004 0.000 0.000 0.004
#> SRR1044432 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044434 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044435 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044436 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044437 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044439 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044438 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044440 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044441 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044442 1 0.0162 0.9441 0.996 0.000 0.000 0.000 0.004
#> SRR1044443 1 0.0324 0.9422 0.992 0.004 0.000 0.000 0.004
#> SRR1044444 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044445 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044446 2 0.5255 0.2948 0.072 0.624 0.000 0.304 0.000
#> SRR1044447 1 0.5192 0.4975 0.668 0.264 0.000 0.056 0.012
#> SRR1044449 3 0.2632 0.6282 0.000 0.000 0.888 0.072 0.040
#> SRR1044448 2 0.4305 0.0623 0.000 0.512 0.000 0.488 0.000
#> SRR1044450 2 0.4467 0.2302 0.016 0.640 0.000 0.344 0.000
#> SRR1044451 1 0.4353 0.6475 0.740 0.224 0.000 0.024 0.012
#> SRR1044452 3 0.0000 0.7741 0.000 0.000 1.000 0.000 0.000
#> SRR1044453 3 0.0000 0.7741 0.000 0.000 1.000 0.000 0.000
#> SRR1044454 3 0.0000 0.7741 0.000 0.000 1.000 0.000 0.000
#> SRR1044455 2 0.4549 0.2111 0.464 0.528 0.000 0.000 0.008
#> SRR1044456 1 0.0162 0.9441 0.996 0.004 0.000 0.000 0.000
#> SRR1044457 2 0.4607 0.4100 0.320 0.656 0.000 0.004 0.020
#> SRR1044458 2 0.4211 0.4102 0.360 0.636 0.000 0.004 0.000
#> SRR1044459 2 0.2260 0.3266 0.000 0.908 0.000 0.028 0.064
#> SRR1044460 1 0.3690 0.6910 0.764 0.224 0.000 0.000 0.012
#> SRR1044461 2 0.4655 0.1698 0.476 0.512 0.000 0.000 0.012
#> SRR1044462 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044463 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044464 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044466 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044465 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044467 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044468 1 0.3690 0.6913 0.764 0.224 0.000 0.000 0.012
#> SRR1044469 2 0.5785 -0.0641 0.000 0.628 0.280 0.040 0.052
#> SRR1044470 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044471 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044472 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044473 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044474 1 0.0451 0.9396 0.988 0.008 0.000 0.000 0.004
#> SRR1044475 3 0.0000 0.7741 0.000 0.000 1.000 0.000 0.000
#> SRR1044476 2 0.2362 0.3694 0.024 0.916 0.000 0.032 0.028
#> SRR1044477 1 0.0451 0.9396 0.988 0.008 0.000 0.000 0.004
#> SRR1044478 1 0.3942 0.6269 0.728 0.260 0.000 0.000 0.012
#> SRR1044479 1 0.0162 0.9441 0.996 0.004 0.000 0.000 0.000
#> SRR1044480 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044481 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044482 1 0.1082 0.9223 0.964 0.028 0.000 0.000 0.008
#> SRR1044483 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044484 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044486 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044485 1 0.2864 0.8118 0.852 0.136 0.000 0.000 0.012
#> SRR1044487 1 0.0290 0.9418 0.992 0.008 0.000 0.000 0.000
#> SRR1044488 1 0.3659 0.6973 0.768 0.220 0.000 0.000 0.012
#> SRR1044489 1 0.3659 0.6973 0.768 0.220 0.000 0.000 0.012
#> SRR1044490 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044491 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044492 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044493 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044494 1 0.0451 0.9396 0.988 0.008 0.000 0.000 0.004
#> SRR1044496 1 0.0290 0.9418 0.992 0.008 0.000 0.000 0.000
#> SRR1044495 1 0.0451 0.9396 0.988 0.008 0.000 0.000 0.004
#> SRR1044497 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044499 2 0.5785 -0.0641 0.000 0.628 0.280 0.040 0.052
#> SRR1044498 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044500 1 0.3563 0.7159 0.780 0.208 0.000 0.000 0.012
#> SRR1044501 2 0.4490 0.3972 0.404 0.588 0.000 0.004 0.004
#> SRR1044502 1 0.4231 0.6476 0.740 0.232 0.000 0.016 0.012
#> SRR1044503 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044504 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044505 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044506 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044507 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044508 1 0.0324 0.9422 0.992 0.004 0.000 0.000 0.004
#> SRR1044509 1 0.0324 0.9422 0.992 0.004 0.000 0.000 0.004
#> SRR1044510 3 0.5454 -0.8123 0.000 0.000 0.532 0.404 0.064
#> SRR1044511 5 0.2249 0.8424 0.000 0.000 0.096 0.008 0.896
#> SRR1044512 5 0.4746 0.4652 0.000 0.000 0.376 0.024 0.600
#> SRR1044513 1 0.4292 0.6638 0.748 0.216 0.000 0.024 0.012
#> SRR1044514 5 0.2329 0.8402 0.000 0.000 0.124 0.000 0.876
#> SRR1044515 1 0.4292 0.6638 0.748 0.216 0.000 0.024 0.012
#> SRR1044516 1 0.4356 0.4452 0.648 0.340 0.000 0.000 0.012
#> SRR1044517 4 0.5351 0.0000 0.000 0.000 0.464 0.484 0.052
#> SRR1044518 5 0.1965 0.8440 0.000 0.000 0.096 0.000 0.904
#> SRR1044519 2 0.4449 0.0609 0.000 0.512 0.000 0.484 0.004
#> SRR1044520 2 0.4449 0.0609 0.000 0.512 0.000 0.484 0.004
#> SRR1044521 1 0.2953 0.8021 0.844 0.144 0.000 0.000 0.012
#> SRR1044522 1 0.0162 0.9441 0.996 0.004 0.000 0.000 0.000
#> SRR1044523 1 0.3693 0.7526 0.804 0.168 0.000 0.016 0.012
#> SRR1044524 2 0.5437 0.3884 0.204 0.680 0.000 0.104 0.012
#> SRR1044525 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044526 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044527 1 0.2462 0.8427 0.880 0.112 0.000 0.000 0.008
#> SRR1044528 1 0.1830 0.8878 0.924 0.068 0.000 0.000 0.008
#> SRR1044529 1 0.0451 0.9396 0.988 0.008 0.000 0.000 0.004
#> SRR1044530 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044531 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044533 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044532 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044534 1 0.3530 0.7216 0.784 0.204 0.000 0.000 0.012
#> SRR1044535 1 0.6107 -0.0319 0.512 0.384 0.000 0.092 0.012
#> SRR1044536 1 0.3690 0.6909 0.764 0.224 0.000 0.000 0.012
#> SRR1044537 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044538 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044539 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044540 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044541 2 0.2544 0.3404 0.008 0.900 0.000 0.028 0.064
#> SRR1044542 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044543 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044544 2 0.1753 0.3392 0.000 0.936 0.000 0.032 0.032
#> SRR1044545 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044546 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044547 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044548 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044549 1 0.2563 0.8340 0.872 0.120 0.000 0.000 0.008
#> SRR1044550 1 0.3720 0.6843 0.760 0.228 0.000 0.000 0.012
#> SRR1044551 1 0.1670 0.8989 0.936 0.052 0.000 0.000 0.012
#> SRR1044552 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044553 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044554 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044555 2 0.2708 0.3300 0.000 0.884 0.000 0.072 0.044
#> SRR1044556 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044557 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044558 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044559 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044561 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044560 2 0.2362 0.3694 0.024 0.916 0.000 0.032 0.028
#> SRR1044562 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044563 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044564 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044565 1 0.0451 0.9396 0.988 0.008 0.000 0.000 0.004
#> SRR1044566 2 0.2273 0.3699 0.024 0.920 0.000 0.032 0.024
#> SRR1044567 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044568 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044569 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044570 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044571 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044572 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044573 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044574 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044575 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044576 1 0.1364 0.9121 0.952 0.036 0.000 0.000 0.012
#> SRR1044577 1 0.1281 0.9160 0.956 0.032 0.000 0.000 0.012
#> SRR1044578 1 0.0671 0.9341 0.980 0.016 0.000 0.000 0.004
#> SRR1044579 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044580 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044581 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044582 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044583 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044584 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044585 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044586 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044587 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044588 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044589 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044590 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044591 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044592 1 0.0324 0.9422 0.992 0.004 0.000 0.000 0.004
#> SRR1044593 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044594 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044595 1 0.0324 0.9422 0.992 0.004 0.000 0.000 0.004
#> SRR1044596 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044597 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044598 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
#> SRR1044599 1 0.0000 0.9461 1.000 0.000 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.4224 0.417473 0.000 0.632 0.000 0.340 0.000 0.028
#> SRR1044416 4 0.2149 0.843508 0.000 0.104 0.004 0.888 0.000 0.004
#> SRR1044417 4 0.1949 0.858032 0.000 0.088 0.004 0.904 0.000 0.004
#> SRR1044418 4 0.1555 0.881903 0.000 0.060 0.004 0.932 0.000 0.004
#> SRR1044420 4 0.3508 0.591022 0.000 0.292 0.004 0.704 0.000 0.000
#> SRR1044419 2 0.4264 0.416320 0.000 0.620 0.000 0.352 0.000 0.028
#> SRR1044421 4 0.3570 0.673250 0.000 0.228 0.016 0.752 0.004 0.000
#> SRR1044422 4 0.3996 -0.000981 0.000 0.484 0.004 0.512 0.000 0.000
#> SRR1044423 4 0.3930 0.260375 0.000 0.420 0.004 0.576 0.000 0.000
#> SRR1044424 4 0.3448 0.613163 0.000 0.280 0.004 0.716 0.000 0.000
#> SRR1044425 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044426 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044427 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044428 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044429 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044430 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044431 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044433 4 0.0935 0.905860 0.000 0.032 0.000 0.964 0.000 0.004
#> SRR1044432 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044434 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044435 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044436 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044437 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044439 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044438 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044440 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044441 4 0.0146 0.921959 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1044442 4 0.0508 0.916624 0.000 0.012 0.000 0.984 0.000 0.004
#> SRR1044443 4 0.0935 0.905860 0.000 0.032 0.000 0.964 0.000 0.004
#> SRR1044444 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044445 4 0.0291 0.920478 0.000 0.004 0.000 0.992 0.000 0.004
#> SRR1044446 3 0.4786 0.564702 0.000 0.412 0.540 0.044 0.004 0.000
#> SRR1044447 4 0.4980 0.339054 0.000 0.328 0.064 0.600 0.004 0.004
#> SRR1044449 1 0.3038 0.775534 0.856 0.000 0.072 0.000 0.012 0.060
#> SRR1044448 3 0.2762 0.782237 0.000 0.196 0.804 0.000 0.000 0.000
#> SRR1044450 3 0.3714 0.714576 0.000 0.340 0.656 0.000 0.004 0.000
#> SRR1044451 4 0.4339 0.507648 0.000 0.300 0.028 0.664 0.004 0.004
#> SRR1044452 1 0.0000 0.944763 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044453 1 0.0000 0.944763 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044454 1 0.0000 0.944763 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044455 2 0.3881 0.383480 0.000 0.600 0.000 0.396 0.000 0.004
#> SRR1044456 4 0.0508 0.916543 0.000 0.012 0.000 0.984 0.000 0.004
#> SRR1044457 2 0.4853 0.398576 0.000 0.628 0.004 0.292 0.000 0.076
#> SRR1044458 2 0.4316 0.415375 0.000 0.648 0.000 0.312 0.000 0.040
#> SRR1044459 2 0.3430 -0.054517 0.000 0.772 0.016 0.000 0.004 0.208
#> SRR1044460 4 0.3565 0.567869 0.000 0.304 0.004 0.692 0.000 0.000
#> SRR1044461 2 0.3774 0.371945 0.000 0.592 0.000 0.408 0.000 0.000
#> SRR1044462 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044463 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044464 4 0.0146 0.921959 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1044466 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044465 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044467 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044468 4 0.3565 0.568111 0.000 0.304 0.004 0.692 0.000 0.000
#> SRR1044469 2 0.5949 -0.249924 0.276 0.544 0.024 0.000 0.000 0.156
#> SRR1044470 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044471 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044472 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044473 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044474 4 0.1080 0.902723 0.000 0.032 0.004 0.960 0.000 0.004
#> SRR1044475 1 0.0000 0.944763 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044476 2 0.3257 0.077517 0.000 0.816 0.012 0.020 0.000 0.152
#> SRR1044477 4 0.1080 0.902723 0.000 0.032 0.004 0.960 0.000 0.004
#> SRR1044478 4 0.3714 0.488463 0.000 0.340 0.004 0.656 0.000 0.000
#> SRR1044479 4 0.0922 0.907596 0.000 0.024 0.004 0.968 0.000 0.004
#> SRR1044480 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044481 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044482 4 0.1788 0.869347 0.000 0.076 0.004 0.916 0.000 0.004
#> SRR1044483 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044484 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044486 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044485 4 0.3023 0.720077 0.000 0.212 0.004 0.784 0.000 0.000
#> SRR1044487 4 0.1003 0.905164 0.000 0.028 0.004 0.964 0.000 0.004
#> SRR1044488 4 0.3547 0.575573 0.000 0.300 0.004 0.696 0.000 0.000
#> SRR1044489 4 0.3547 0.575573 0.000 0.300 0.004 0.696 0.000 0.000
#> SRR1044490 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044491 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044492 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044493 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044494 4 0.1080 0.902723 0.000 0.032 0.004 0.960 0.000 0.004
#> SRR1044496 4 0.1003 0.905164 0.000 0.028 0.004 0.964 0.000 0.004
#> SRR1044495 4 0.1080 0.902723 0.000 0.032 0.004 0.960 0.000 0.004
#> SRR1044497 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044499 2 0.5949 -0.249924 0.276 0.544 0.024 0.000 0.000 0.156
#> SRR1044498 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044500 4 0.3489 0.598267 0.000 0.288 0.004 0.708 0.000 0.000
#> SRR1044501 2 0.4167 0.416880 0.000 0.632 0.000 0.344 0.000 0.024
#> SRR1044502 4 0.4225 0.507741 0.000 0.308 0.020 0.664 0.004 0.004
#> SRR1044503 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044504 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044505 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044506 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044507 4 0.0291 0.920236 0.000 0.004 0.000 0.992 0.000 0.004
#> SRR1044508 4 0.0935 0.905860 0.000 0.032 0.000 0.964 0.000 0.004
#> SRR1044509 4 0.0935 0.905860 0.000 0.032 0.000 0.964 0.000 0.004
#> SRR1044510 6 0.6356 0.782103 0.324 0.000 0.168 0.000 0.036 0.472
#> SRR1044511 5 0.0767 0.834894 0.012 0.000 0.008 0.000 0.976 0.004
#> SRR1044512 5 0.5507 0.455657 0.256 0.000 0.076 0.000 0.620 0.048
#> SRR1044513 4 0.4283 0.535924 0.000 0.288 0.028 0.676 0.004 0.004
#> SRR1044514 5 0.1082 0.833556 0.040 0.000 0.000 0.000 0.956 0.004
#> SRR1044515 4 0.4283 0.535924 0.000 0.288 0.028 0.676 0.004 0.004
#> SRR1044516 4 0.3930 0.260666 0.000 0.420 0.004 0.576 0.000 0.000
#> SRR1044517 6 0.4024 0.797048 0.264 0.000 0.000 0.000 0.036 0.700
#> SRR1044518 5 0.0363 0.837357 0.012 0.000 0.000 0.000 0.988 0.000
#> SRR1044519 3 0.2902 0.782359 0.000 0.196 0.800 0.000 0.000 0.004
#> SRR1044520 3 0.2902 0.782359 0.000 0.196 0.800 0.000 0.000 0.004
#> SRR1044521 4 0.3081 0.708517 0.000 0.220 0.004 0.776 0.000 0.000
#> SRR1044522 4 0.0603 0.914436 0.000 0.016 0.000 0.980 0.000 0.004
#> SRR1044523 4 0.3755 0.644406 0.000 0.244 0.020 0.732 0.000 0.004
#> SRR1044524 2 0.5638 0.216435 0.000 0.644 0.132 0.180 0.004 0.040
#> SRR1044525 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044526 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044527 4 0.2913 0.758204 0.000 0.180 0.004 0.812 0.000 0.004
#> SRR1044528 4 0.2420 0.819299 0.000 0.128 0.004 0.864 0.000 0.004
#> SRR1044529 4 0.1226 0.897298 0.000 0.040 0.004 0.952 0.000 0.004
#> SRR1044530 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044531 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044533 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044532 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044534 4 0.3468 0.605354 0.000 0.284 0.004 0.712 0.000 0.000
#> SRR1044535 4 0.5897 -0.188279 0.000 0.400 0.104 0.472 0.004 0.020
#> SRR1044536 4 0.3565 0.567678 0.000 0.304 0.004 0.692 0.000 0.000
#> SRR1044537 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044538 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044539 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044540 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044541 2 0.3451 -0.028089 0.000 0.776 0.012 0.004 0.004 0.204
#> SRR1044542 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044543 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044544 2 0.2907 0.007029 0.000 0.828 0.020 0.000 0.000 0.152
#> SRR1044545 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044546 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044547 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044548 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044549 4 0.2979 0.747840 0.000 0.188 0.004 0.804 0.000 0.004
#> SRR1044550 4 0.3584 0.559644 0.000 0.308 0.004 0.688 0.000 0.000
#> SRR1044551 4 0.2288 0.831961 0.000 0.116 0.004 0.876 0.000 0.004
#> SRR1044552 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044553 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044554 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044555 2 0.3985 -0.129938 0.000 0.760 0.100 0.000 0.000 0.140
#> SRR1044556 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044557 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044558 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044559 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044561 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044560 2 0.3257 0.077517 0.000 0.816 0.012 0.020 0.000 0.152
#> SRR1044562 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044563 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044564 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044565 4 0.1080 0.902723 0.000 0.032 0.004 0.960 0.000 0.004
#> SRR1044566 2 0.3219 0.078705 0.000 0.820 0.012 0.020 0.000 0.148
#> SRR1044567 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044568 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044569 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044570 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044571 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044572 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044573 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044574 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044575 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044576 4 0.2101 0.847013 0.000 0.100 0.004 0.892 0.000 0.004
#> SRR1044577 4 0.2051 0.851534 0.000 0.096 0.004 0.896 0.000 0.004
#> SRR1044578 4 0.1429 0.888417 0.000 0.052 0.004 0.940 0.000 0.004
#> SRR1044579 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044580 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044581 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044582 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044583 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044584 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044585 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044586 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044587 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044588 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044589 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044590 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044591 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044592 4 0.0935 0.905860 0.000 0.032 0.000 0.964 0.000 0.004
#> SRR1044593 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044594 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044595 4 0.0935 0.905860 0.000 0.032 0.000 0.964 0.000 0.004
#> SRR1044596 4 0.0291 0.920236 0.000 0.004 0.000 0.992 0.000 0.004
#> SRR1044597 4 0.0291 0.920236 0.000 0.004 0.000 0.992 0.000 0.004
#> SRR1044598 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044599 4 0.0000 0.923754 0.000 0.000 0.000 1.000 0.000 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)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.988 0.995 0.2997 0.705 0.705
#> 3 3 0.938 0.920 0.970 0.7977 0.674 0.559
#> 4 4 0.665 0.733 0.848 0.1729 0.884 0.754
#> 5 5 0.657 0.646 0.796 0.0811 0.934 0.832
#> 6 6 0.638 0.283 0.669 0.0614 0.855 0.629
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0.1184 0.9831 0.016 0.984
#> SRR1044416 1 0.0000 0.9949 1.000 0.000
#> SRR1044417 1 0.0000 0.9949 1.000 0.000
#> SRR1044418 1 0.0000 0.9949 1.000 0.000
#> SRR1044420 1 0.0376 0.9918 0.996 0.004
#> SRR1044419 2 0.1184 0.9830 0.016 0.984
#> SRR1044421 1 0.0376 0.9918 0.996 0.004
#> SRR1044422 1 0.2948 0.9439 0.948 0.052
#> SRR1044423 1 0.2603 0.9525 0.956 0.044
#> SRR1044424 1 0.0000 0.9949 1.000 0.000
#> SRR1044425 1 0.0000 0.9949 1.000 0.000
#> SRR1044426 1 0.0000 0.9949 1.000 0.000
#> SRR1044427 1 0.0000 0.9949 1.000 0.000
#> SRR1044428 1 0.0000 0.9949 1.000 0.000
#> SRR1044429 1 0.0000 0.9949 1.000 0.000
#> SRR1044430 1 0.0000 0.9949 1.000 0.000
#> SRR1044431 1 0.0000 0.9949 1.000 0.000
#> SRR1044433 1 0.0000 0.9949 1.000 0.000
#> SRR1044432 1 0.0000 0.9949 1.000 0.000
#> SRR1044434 1 0.0000 0.9949 1.000 0.000
#> SRR1044435 1 0.0000 0.9949 1.000 0.000
#> SRR1044436 1 0.0000 0.9949 1.000 0.000
#> SRR1044437 1 0.0000 0.9949 1.000 0.000
#> SRR1044439 1 0.0000 0.9949 1.000 0.000
#> SRR1044438 1 0.0000 0.9949 1.000 0.000
#> SRR1044440 1 0.0000 0.9949 1.000 0.000
#> SRR1044441 1 0.0000 0.9949 1.000 0.000
#> SRR1044442 1 0.0000 0.9949 1.000 0.000
#> SRR1044443 1 0.0000 0.9949 1.000 0.000
#> SRR1044444 1 0.0000 0.9949 1.000 0.000
#> SRR1044445 1 0.0000 0.9949 1.000 0.000
#> SRR1044446 2 0.0000 0.9962 0.000 1.000
#> SRR1044447 1 0.2043 0.9648 0.968 0.032
#> SRR1044449 2 0.0000 0.9962 0.000 1.000
#> SRR1044448 2 0.0000 0.9962 0.000 1.000
#> SRR1044450 2 0.0000 0.9962 0.000 1.000
#> SRR1044451 1 0.0376 0.9918 0.996 0.004
#> SRR1044452 2 0.0000 0.9962 0.000 1.000
#> SRR1044453 2 0.0000 0.9962 0.000 1.000
#> SRR1044454 2 0.0000 0.9962 0.000 1.000
#> SRR1044455 2 0.3879 0.9186 0.076 0.924
#> SRR1044456 1 0.0000 0.9949 1.000 0.000
#> SRR1044457 2 0.0000 0.9962 0.000 1.000
#> SRR1044458 2 0.0000 0.9962 0.000 1.000
#> SRR1044459 2 0.0000 0.9962 0.000 1.000
#> SRR1044460 1 0.0376 0.9918 0.996 0.004
#> SRR1044461 1 0.9998 0.0272 0.508 0.492
#> SRR1044462 1 0.0000 0.9949 1.000 0.000
#> SRR1044463 1 0.0000 0.9949 1.000 0.000
#> SRR1044464 1 0.0000 0.9949 1.000 0.000
#> SRR1044466 1 0.0000 0.9949 1.000 0.000
#> SRR1044465 1 0.0000 0.9949 1.000 0.000
#> SRR1044467 1 0.0000 0.9949 1.000 0.000
#> SRR1044468 1 0.0376 0.9918 0.996 0.004
#> SRR1044469 2 0.0000 0.9962 0.000 1.000
#> SRR1044470 1 0.0000 0.9949 1.000 0.000
#> SRR1044471 1 0.0000 0.9949 1.000 0.000
#> SRR1044472 1 0.0000 0.9949 1.000 0.000
#> SRR1044473 1 0.0000 0.9949 1.000 0.000
#> SRR1044474 1 0.0000 0.9949 1.000 0.000
#> SRR1044475 2 0.0000 0.9962 0.000 1.000
#> SRR1044476 2 0.0000 0.9962 0.000 1.000
#> SRR1044477 1 0.0000 0.9949 1.000 0.000
#> SRR1044478 1 0.0376 0.9918 0.996 0.004
#> SRR1044479 1 0.0000 0.9949 1.000 0.000
#> SRR1044480 1 0.0000 0.9949 1.000 0.000
#> SRR1044481 1 0.0000 0.9949 1.000 0.000
#> SRR1044482 1 0.0000 0.9949 1.000 0.000
#> SRR1044483 1 0.0000 0.9949 1.000 0.000
#> SRR1044484 1 0.0000 0.9949 1.000 0.000
#> SRR1044486 1 0.0000 0.9949 1.000 0.000
#> SRR1044485 1 0.0000 0.9949 1.000 0.000
#> SRR1044487 1 0.0000 0.9949 1.000 0.000
#> SRR1044488 1 0.0376 0.9918 0.996 0.004
#> SRR1044489 1 0.0376 0.9918 0.996 0.004
#> SRR1044490 1 0.0000 0.9949 1.000 0.000
#> SRR1044491 1 0.0000 0.9949 1.000 0.000
#> SRR1044492 1 0.0000 0.9949 1.000 0.000
#> SRR1044493 1 0.0000 0.9949 1.000 0.000
#> SRR1044494 1 0.0000 0.9949 1.000 0.000
#> SRR1044496 1 0.0000 0.9949 1.000 0.000
#> SRR1044495 1 0.0000 0.9949 1.000 0.000
#> SRR1044497 1 0.0000 0.9949 1.000 0.000
#> SRR1044499 2 0.0000 0.9962 0.000 1.000
#> SRR1044498 1 0.0000 0.9949 1.000 0.000
#> SRR1044500 1 0.0000 0.9949 1.000 0.000
#> SRR1044501 2 0.0000 0.9962 0.000 1.000
#> SRR1044502 1 0.0376 0.9918 0.996 0.004
#> SRR1044503 1 0.0000 0.9949 1.000 0.000
#> SRR1044504 1 0.0000 0.9949 1.000 0.000
#> SRR1044505 1 0.0000 0.9949 1.000 0.000
#> SRR1044506 1 0.0000 0.9949 1.000 0.000
#> SRR1044507 1 0.0000 0.9949 1.000 0.000
#> SRR1044508 1 0.0000 0.9949 1.000 0.000
#> SRR1044509 1 0.0000 0.9949 1.000 0.000
#> SRR1044510 2 0.0000 0.9962 0.000 1.000
#> SRR1044511 2 0.0000 0.9962 0.000 1.000
#> SRR1044512 2 0.0000 0.9962 0.000 1.000
#> SRR1044513 1 0.0000 0.9949 1.000 0.000
#> SRR1044514 2 0.0000 0.9962 0.000 1.000
#> SRR1044515 1 0.0376 0.9918 0.996 0.004
#> SRR1044516 1 0.4431 0.8984 0.908 0.092
#> SRR1044517 2 0.0000 0.9962 0.000 1.000
#> SRR1044518 2 0.0000 0.9962 0.000 1.000
#> SRR1044519 2 0.0000 0.9962 0.000 1.000
#> SRR1044520 2 0.0000 0.9962 0.000 1.000
#> SRR1044521 1 0.0000 0.9949 1.000 0.000
#> SRR1044522 1 0.0000 0.9949 1.000 0.000
#> SRR1044523 1 0.0376 0.9918 0.996 0.004
#> SRR1044524 2 0.0000 0.9962 0.000 1.000
#> SRR1044525 1 0.0000 0.9949 1.000 0.000
#> SRR1044526 1 0.0000 0.9949 1.000 0.000
#> SRR1044527 1 0.0000 0.9949 1.000 0.000
#> SRR1044528 1 0.0000 0.9949 1.000 0.000
#> SRR1044529 1 0.0000 0.9949 1.000 0.000
#> SRR1044530 1 0.0000 0.9949 1.000 0.000
#> SRR1044531 1 0.0000 0.9949 1.000 0.000
#> SRR1044533 1 0.0000 0.9949 1.000 0.000
#> SRR1044532 1 0.0000 0.9949 1.000 0.000
#> SRR1044534 1 0.0000 0.9949 1.000 0.000
#> SRR1044535 2 0.0000 0.9962 0.000 1.000
#> SRR1044536 1 0.0376 0.9918 0.996 0.004
#> SRR1044537 1 0.0000 0.9949 1.000 0.000
#> SRR1044538 1 0.0000 0.9949 1.000 0.000
#> SRR1044539 1 0.0000 0.9949 1.000 0.000
#> SRR1044540 1 0.0000 0.9949 1.000 0.000
#> SRR1044541 2 0.0938 0.9866 0.012 0.988
#> SRR1044542 1 0.0000 0.9949 1.000 0.000
#> SRR1044543 1 0.0000 0.9949 1.000 0.000
#> SRR1044544 2 0.0000 0.9962 0.000 1.000
#> SRR1044545 1 0.0000 0.9949 1.000 0.000
#> SRR1044546 1 0.0000 0.9949 1.000 0.000
#> SRR1044547 1 0.0000 0.9949 1.000 0.000
#> SRR1044548 1 0.0000 0.9949 1.000 0.000
#> SRR1044549 1 0.0000 0.9949 1.000 0.000
#> SRR1044550 1 0.0376 0.9918 0.996 0.004
#> SRR1044551 1 0.0000 0.9949 1.000 0.000
#> SRR1044552 1 0.0000 0.9949 1.000 0.000
#> SRR1044553 1 0.0000 0.9949 1.000 0.000
#> SRR1044554 1 0.0000 0.9949 1.000 0.000
#> SRR1044555 2 0.0000 0.9962 0.000 1.000
#> SRR1044556 1 0.0000 0.9949 1.000 0.000
#> SRR1044557 1 0.0000 0.9949 1.000 0.000
#> SRR1044558 1 0.0000 0.9949 1.000 0.000
#> SRR1044559 1 0.0000 0.9949 1.000 0.000
#> SRR1044561 1 0.0000 0.9949 1.000 0.000
#> SRR1044560 2 0.0000 0.9962 0.000 1.000
#> SRR1044562 1 0.0000 0.9949 1.000 0.000
#> SRR1044563 1 0.0000 0.9949 1.000 0.000
#> SRR1044564 1 0.0000 0.9949 1.000 0.000
#> SRR1044565 1 0.0000 0.9949 1.000 0.000
#> SRR1044566 2 0.0000 0.9962 0.000 1.000
#> SRR1044567 1 0.0000 0.9949 1.000 0.000
#> SRR1044568 1 0.0000 0.9949 1.000 0.000
#> SRR1044569 1 0.0000 0.9949 1.000 0.000
#> SRR1044570 1 0.0000 0.9949 1.000 0.000
#> SRR1044571 1 0.0000 0.9949 1.000 0.000
#> SRR1044572 1 0.0000 0.9949 1.000 0.000
#> SRR1044573 1 0.0000 0.9949 1.000 0.000
#> SRR1044574 1 0.0000 0.9949 1.000 0.000
#> SRR1044575 1 0.0000 0.9949 1.000 0.000
#> SRR1044576 1 0.0000 0.9949 1.000 0.000
#> SRR1044577 1 0.0000 0.9949 1.000 0.000
#> SRR1044578 1 0.0000 0.9949 1.000 0.000
#> SRR1044579 1 0.0000 0.9949 1.000 0.000
#> SRR1044580 1 0.0000 0.9949 1.000 0.000
#> SRR1044581 1 0.0000 0.9949 1.000 0.000
#> SRR1044582 1 0.0000 0.9949 1.000 0.000
#> SRR1044583 1 0.0000 0.9949 1.000 0.000
#> SRR1044584 1 0.0000 0.9949 1.000 0.000
#> SRR1044585 1 0.0000 0.9949 1.000 0.000
#> SRR1044586 1 0.0000 0.9949 1.000 0.000
#> SRR1044587 1 0.0000 0.9949 1.000 0.000
#> SRR1044588 1 0.0000 0.9949 1.000 0.000
#> SRR1044589 1 0.0000 0.9949 1.000 0.000
#> SRR1044590 1 0.0000 0.9949 1.000 0.000
#> SRR1044591 1 0.0000 0.9949 1.000 0.000
#> SRR1044592 1 0.0000 0.9949 1.000 0.000
#> SRR1044593 1 0.0000 0.9949 1.000 0.000
#> SRR1044594 1 0.0000 0.9949 1.000 0.000
#> SRR1044595 1 0.0000 0.9949 1.000 0.000
#> SRR1044596 1 0.0000 0.9949 1.000 0.000
#> SRR1044597 1 0.0000 0.9949 1.000 0.000
#> SRR1044598 1 0.0000 0.9949 1.000 0.000
#> SRR1044599 1 0.0000 0.9949 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044416 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044417 2 0.1163 0.870 0.028 0.972 0.000
#> SRR1044418 2 0.5327 0.602 0.272 0.728 0.000
#> SRR1044420 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044419 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044421 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044422 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044423 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044424 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044425 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044426 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044427 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044428 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044429 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044430 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044431 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044433 1 0.6168 0.220 0.588 0.412 0.000
#> SRR1044432 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044434 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044435 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044436 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044437 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044439 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044438 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044440 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044441 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044442 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044443 1 0.0892 0.970 0.980 0.020 0.000
#> SRR1044444 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044445 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044446 2 0.0237 0.893 0.000 0.996 0.004
#> SRR1044447 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044449 3 0.0000 0.937 0.000 0.000 1.000
#> SRR1044448 3 0.4452 0.799 0.000 0.192 0.808
#> SRR1044450 3 0.6274 0.307 0.000 0.456 0.544
#> SRR1044451 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044452 3 0.0000 0.937 0.000 0.000 1.000
#> SRR1044453 3 0.0000 0.937 0.000 0.000 1.000
#> SRR1044454 3 0.0000 0.937 0.000 0.000 1.000
#> SRR1044455 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044456 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044457 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044458 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044459 3 0.2165 0.902 0.000 0.064 0.936
#> SRR1044460 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044461 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044462 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044463 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044464 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044466 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044465 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044467 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044468 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044469 3 0.0000 0.937 0.000 0.000 1.000
#> SRR1044470 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044471 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044472 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044473 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044474 2 0.5327 0.602 0.272 0.728 0.000
#> SRR1044475 3 0.0000 0.937 0.000 0.000 1.000
#> SRR1044476 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044477 2 0.5810 0.513 0.336 0.664 0.000
#> SRR1044478 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044479 1 0.2066 0.923 0.940 0.060 0.000
#> SRR1044480 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044481 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044482 2 0.4555 0.684 0.200 0.800 0.000
#> SRR1044483 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044484 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044486 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044485 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044487 2 0.5497 0.577 0.292 0.708 0.000
#> SRR1044488 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044489 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044490 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044491 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044492 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044493 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044494 2 0.5591 0.561 0.304 0.696 0.000
#> SRR1044496 2 0.6308 0.146 0.492 0.508 0.000
#> SRR1044495 2 0.5678 0.543 0.316 0.684 0.000
#> SRR1044497 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044499 3 0.0000 0.937 0.000 0.000 1.000
#> SRR1044498 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044500 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044501 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044502 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044503 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044504 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044505 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044506 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044507 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044508 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044509 1 0.0592 0.978 0.988 0.012 0.000
#> SRR1044510 3 0.0000 0.937 0.000 0.000 1.000
#> SRR1044511 3 0.0000 0.937 0.000 0.000 1.000
#> SRR1044512 3 0.0000 0.937 0.000 0.000 1.000
#> SRR1044513 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044514 3 0.0000 0.937 0.000 0.000 1.000
#> SRR1044515 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044516 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044517 3 0.0000 0.937 0.000 0.000 1.000
#> SRR1044518 3 0.0000 0.937 0.000 0.000 1.000
#> SRR1044519 3 0.4796 0.768 0.000 0.220 0.780
#> SRR1044520 3 0.0892 0.928 0.000 0.020 0.980
#> SRR1044521 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044522 1 0.2537 0.898 0.920 0.080 0.000
#> SRR1044523 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044524 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044525 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044526 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044527 2 0.4062 0.724 0.164 0.836 0.000
#> SRR1044528 2 0.0237 0.893 0.004 0.996 0.000
#> SRR1044529 2 0.5431 0.587 0.284 0.716 0.000
#> SRR1044530 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044531 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044533 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044532 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044534 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044535 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044536 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044537 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044538 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044539 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044540 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044541 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044542 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044543 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044544 2 0.0237 0.893 0.000 0.996 0.004
#> SRR1044545 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044546 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044547 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044548 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044549 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044550 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044551 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044552 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044553 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044554 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044555 3 0.4654 0.782 0.000 0.208 0.792
#> SRR1044556 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044557 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044558 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044559 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044561 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044560 2 0.1643 0.855 0.000 0.956 0.044
#> SRR1044562 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044563 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044564 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044565 2 0.5560 0.566 0.300 0.700 0.000
#> SRR1044566 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044567 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044568 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044569 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044570 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044571 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044572 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044573 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044574 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044575 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044576 2 0.0000 0.896 0.000 1.000 0.000
#> SRR1044577 2 0.0237 0.893 0.004 0.996 0.000
#> SRR1044578 2 0.4842 0.658 0.224 0.776 0.000
#> SRR1044579 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044580 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044581 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044582 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044583 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044584 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044585 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044586 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044587 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044588 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044589 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044590 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044591 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044592 1 0.5678 0.487 0.684 0.316 0.000
#> SRR1044593 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044594 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044595 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044596 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044597 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044598 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1044599 1 0.0000 0.991 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 4 0.1302 0.7180 0.000 0.044 0.000 0.956
#> SRR1044416 2 0.4522 0.7032 0.000 0.680 0.000 0.320
#> SRR1044417 2 0.4454 0.7035 0.000 0.692 0.000 0.308
#> SRR1044418 2 0.5022 0.6907 0.028 0.708 0.000 0.264
#> SRR1044420 2 0.4933 0.6261 0.000 0.568 0.000 0.432
#> SRR1044419 4 0.1389 0.7135 0.000 0.048 0.000 0.952
#> SRR1044421 2 0.4925 0.6286 0.000 0.572 0.000 0.428
#> SRR1044422 4 0.4989 -0.4490 0.000 0.472 0.000 0.528
#> SRR1044423 4 0.5000 -0.5087 0.000 0.496 0.000 0.504
#> SRR1044424 2 0.4790 0.6753 0.000 0.620 0.000 0.380
#> SRR1044425 1 0.0707 0.9015 0.980 0.020 0.000 0.000
#> SRR1044426 1 0.4898 0.6512 0.584 0.416 0.000 0.000
#> SRR1044427 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044428 1 0.0469 0.8973 0.988 0.012 0.000 0.000
#> SRR1044429 1 0.2530 0.8853 0.888 0.112 0.000 0.000
#> SRR1044430 1 0.1474 0.8735 0.948 0.052 0.000 0.000
#> SRR1044431 1 0.0188 0.9026 0.996 0.004 0.000 0.000
#> SRR1044433 2 0.3647 0.4079 0.108 0.852 0.000 0.040
#> SRR1044432 1 0.2469 0.8427 0.892 0.108 0.000 0.000
#> SRR1044434 1 0.3486 0.8650 0.812 0.188 0.000 0.000
#> SRR1044435 1 0.3486 0.8650 0.812 0.188 0.000 0.000
#> SRR1044436 1 0.3444 0.8668 0.816 0.184 0.000 0.000
#> SRR1044437 1 0.3486 0.8650 0.812 0.188 0.000 0.000
#> SRR1044439 1 0.3444 0.8668 0.816 0.184 0.000 0.000
#> SRR1044438 1 0.3444 0.8668 0.816 0.184 0.000 0.000
#> SRR1044440 1 0.3486 0.8650 0.812 0.188 0.000 0.000
#> SRR1044441 1 0.3837 0.8463 0.776 0.224 0.000 0.000
#> SRR1044442 1 0.4790 0.6848 0.620 0.380 0.000 0.000
#> SRR1044443 2 0.3610 0.3252 0.200 0.800 0.000 0.000
#> SRR1044444 1 0.3444 0.8668 0.816 0.184 0.000 0.000
#> SRR1044445 1 0.4643 0.7373 0.656 0.344 0.000 0.000
#> SRR1044446 4 0.0657 0.7034 0.000 0.012 0.004 0.984
#> SRR1044447 2 0.4985 0.5474 0.000 0.532 0.000 0.468
#> SRR1044449 3 0.0469 0.9076 0.000 0.000 0.988 0.012
#> SRR1044448 4 0.4790 -0.0922 0.000 0.000 0.380 0.620
#> SRR1044450 4 0.4820 0.1546 0.000 0.012 0.296 0.692
#> SRR1044451 2 0.4898 0.6414 0.000 0.584 0.000 0.416
#> SRR1044452 3 0.0000 0.9079 0.000 0.000 1.000 0.000
#> SRR1044453 3 0.0000 0.9079 0.000 0.000 1.000 0.000
#> SRR1044454 3 0.0000 0.9079 0.000 0.000 1.000 0.000
#> SRR1044455 4 0.1302 0.7180 0.000 0.044 0.000 0.956
#> SRR1044456 1 0.4250 0.7241 0.724 0.276 0.000 0.000
#> SRR1044457 4 0.1211 0.7212 0.000 0.040 0.000 0.960
#> SRR1044458 4 0.1211 0.7212 0.000 0.040 0.000 0.960
#> SRR1044459 4 0.4746 -0.0438 0.000 0.000 0.368 0.632
#> SRR1044460 2 0.4941 0.6200 0.000 0.564 0.000 0.436
#> SRR1044461 4 0.4585 0.0162 0.000 0.332 0.000 0.668
#> SRR1044462 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044463 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044464 1 0.4888 0.6363 0.588 0.412 0.000 0.000
#> SRR1044466 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044465 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044467 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044468 2 0.4907 0.6408 0.000 0.580 0.000 0.420
#> SRR1044469 3 0.4804 0.5156 0.000 0.000 0.616 0.384
#> SRR1044470 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044471 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044472 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044473 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044474 2 0.4993 0.6887 0.028 0.712 0.000 0.260
#> SRR1044475 3 0.0000 0.9079 0.000 0.000 1.000 0.000
#> SRR1044476 4 0.1211 0.7212 0.000 0.040 0.000 0.960
#> SRR1044477 2 0.5168 0.6785 0.040 0.712 0.000 0.248
#> SRR1044478 2 0.4933 0.6261 0.000 0.568 0.000 0.432
#> SRR1044479 2 0.6223 0.2350 0.384 0.556 0.000 0.060
#> SRR1044480 1 0.0817 0.9011 0.976 0.024 0.000 0.000
#> SRR1044481 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044482 2 0.4868 0.7044 0.012 0.684 0.000 0.304
#> SRR1044483 1 0.2408 0.8877 0.896 0.104 0.000 0.000
#> SRR1044484 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044486 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044485 2 0.4543 0.7024 0.000 0.676 0.000 0.324
#> SRR1044487 2 0.5143 0.6833 0.036 0.708 0.000 0.256
#> SRR1044488 2 0.4925 0.6317 0.000 0.572 0.000 0.428
#> SRR1044489 2 0.4933 0.6261 0.000 0.568 0.000 0.432
#> SRR1044490 1 0.0469 0.8973 0.988 0.012 0.000 0.000
#> SRR1044491 1 0.0188 0.9010 0.996 0.004 0.000 0.000
#> SRR1044492 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044493 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044494 2 0.5055 0.6864 0.032 0.712 0.000 0.256
#> SRR1044496 2 0.5982 0.5874 0.112 0.684 0.000 0.204
#> SRR1044495 2 0.5113 0.6828 0.036 0.712 0.000 0.252
#> SRR1044497 1 0.3356 0.8695 0.824 0.176 0.000 0.000
#> SRR1044499 3 0.4746 0.5409 0.000 0.000 0.632 0.368
#> SRR1044498 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044500 2 0.4746 0.6831 0.000 0.632 0.000 0.368
#> SRR1044501 4 0.1211 0.7212 0.000 0.040 0.000 0.960
#> SRR1044502 2 0.4877 0.6426 0.000 0.592 0.000 0.408
#> SRR1044503 1 0.3356 0.8695 0.824 0.176 0.000 0.000
#> SRR1044504 1 0.3486 0.8650 0.812 0.188 0.000 0.000
#> SRR1044505 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044506 1 0.4134 0.8172 0.740 0.260 0.000 0.000
#> SRR1044507 1 0.4605 0.7473 0.664 0.336 0.000 0.000
#> SRR1044508 2 0.4564 0.0971 0.328 0.672 0.000 0.000
#> SRR1044509 2 0.3569 0.3294 0.196 0.804 0.000 0.000
#> SRR1044510 3 0.0376 0.9079 0.000 0.004 0.992 0.004
#> SRR1044511 3 0.0779 0.9074 0.000 0.004 0.980 0.016
#> SRR1044512 3 0.0779 0.9074 0.000 0.004 0.980 0.016
#> SRR1044513 2 0.4804 0.6659 0.000 0.616 0.000 0.384
#> SRR1044514 3 0.0779 0.9074 0.000 0.004 0.980 0.016
#> SRR1044515 2 0.4898 0.6332 0.000 0.584 0.000 0.416
#> SRR1044516 4 0.4989 -0.4497 0.000 0.472 0.000 0.528
#> SRR1044517 3 0.0188 0.9084 0.000 0.000 0.996 0.004
#> SRR1044518 3 0.0779 0.9074 0.000 0.004 0.980 0.016
#> SRR1044519 4 0.5158 -0.2955 0.000 0.004 0.472 0.524
#> SRR1044520 3 0.4661 0.5909 0.000 0.000 0.652 0.348
#> SRR1044521 2 0.4522 0.7032 0.000 0.680 0.000 0.320
#> SRR1044522 2 0.6306 0.2053 0.392 0.544 0.000 0.064
#> SRR1044523 2 0.4866 0.6478 0.000 0.596 0.000 0.404
#> SRR1044524 4 0.1022 0.7170 0.000 0.032 0.000 0.968
#> SRR1044525 1 0.3444 0.8668 0.816 0.184 0.000 0.000
#> SRR1044526 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044527 2 0.4744 0.6992 0.012 0.704 0.000 0.284
#> SRR1044528 2 0.4477 0.7023 0.000 0.688 0.000 0.312
#> SRR1044529 2 0.5055 0.6864 0.032 0.712 0.000 0.256
#> SRR1044530 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044531 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044533 1 0.0188 0.9010 0.996 0.004 0.000 0.000
#> SRR1044532 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044534 2 0.4713 0.6879 0.000 0.640 0.000 0.360
#> SRR1044535 4 0.1118 0.7157 0.000 0.036 0.000 0.964
#> SRR1044536 2 0.4925 0.6316 0.000 0.572 0.000 0.428
#> SRR1044537 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044538 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044539 1 0.3444 0.8668 0.816 0.184 0.000 0.000
#> SRR1044540 1 0.0469 0.8975 0.988 0.012 0.000 0.000
#> SRR1044541 4 0.1211 0.7198 0.000 0.040 0.000 0.960
#> SRR1044542 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044543 1 0.1118 0.8830 0.964 0.036 0.000 0.000
#> SRR1044544 4 0.0817 0.7190 0.000 0.024 0.000 0.976
#> SRR1044545 1 0.3074 0.8772 0.848 0.152 0.000 0.000
#> SRR1044546 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044547 1 0.1716 0.8960 0.936 0.064 0.000 0.000
#> SRR1044548 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044549 2 0.4500 0.7030 0.000 0.684 0.000 0.316
#> SRR1044550 2 0.4933 0.6261 0.000 0.568 0.000 0.432
#> SRR1044551 2 0.4522 0.7032 0.000 0.680 0.000 0.320
#> SRR1044552 1 0.3486 0.8650 0.812 0.188 0.000 0.000
#> SRR1044553 1 0.3486 0.8650 0.812 0.188 0.000 0.000
#> SRR1044554 1 0.0188 0.9010 0.996 0.004 0.000 0.000
#> SRR1044555 4 0.4331 0.1772 0.000 0.000 0.288 0.712
#> SRR1044556 1 0.3444 0.8668 0.816 0.184 0.000 0.000
#> SRR1044557 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044558 1 0.3444 0.8668 0.816 0.184 0.000 0.000
#> SRR1044559 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044561 1 0.3444 0.8668 0.816 0.184 0.000 0.000
#> SRR1044560 4 0.1211 0.7212 0.000 0.040 0.000 0.960
#> SRR1044562 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044563 1 0.3356 0.8697 0.824 0.176 0.000 0.000
#> SRR1044564 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044565 2 0.5055 0.6864 0.032 0.712 0.000 0.256
#> SRR1044566 4 0.1211 0.7212 0.000 0.040 0.000 0.960
#> SRR1044567 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044568 1 0.2081 0.8922 0.916 0.084 0.000 0.000
#> SRR1044569 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044570 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044571 1 0.0188 0.9010 0.996 0.004 0.000 0.000
#> SRR1044572 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044573 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044574 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044575 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044576 2 0.4522 0.7032 0.000 0.680 0.000 0.320
#> SRR1044577 2 0.4500 0.7033 0.000 0.684 0.000 0.316
#> SRR1044578 2 0.4882 0.6936 0.020 0.708 0.000 0.272
#> SRR1044579 1 0.3486 0.8650 0.812 0.188 0.000 0.000
#> SRR1044580 1 0.0817 0.9011 0.976 0.024 0.000 0.000
#> SRR1044581 1 0.3444 0.8668 0.816 0.184 0.000 0.000
#> SRR1044582 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044583 1 0.3444 0.8668 0.816 0.184 0.000 0.000
#> SRR1044584 1 0.3024 0.8769 0.852 0.148 0.000 0.000
#> SRR1044585 1 0.3444 0.8668 0.816 0.184 0.000 0.000
#> SRR1044586 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044587 1 0.4164 0.8144 0.736 0.264 0.000 0.000
#> SRR1044588 1 0.4134 0.8172 0.740 0.260 0.000 0.000
#> SRR1044589 1 0.4103 0.8206 0.744 0.256 0.000 0.000
#> SRR1044590 1 0.3975 0.8329 0.760 0.240 0.000 0.000
#> SRR1044591 1 0.4277 0.8024 0.720 0.280 0.000 0.000
#> SRR1044592 2 0.3731 0.3970 0.120 0.844 0.000 0.036
#> SRR1044593 1 0.4134 0.8172 0.740 0.260 0.000 0.000
#> SRR1044594 1 0.4134 0.8172 0.740 0.260 0.000 0.000
#> SRR1044595 2 0.4994 -0.4150 0.480 0.520 0.000 0.000
#> SRR1044596 1 0.4522 0.7661 0.680 0.320 0.000 0.000
#> SRR1044597 1 0.3837 0.7859 0.776 0.224 0.000 0.000
#> SRR1044598 1 0.0000 0.9026 1.000 0.000 0.000 0.000
#> SRR1044599 1 0.0000 0.9026 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 5 0.3932 0.74046 0.000 0.328 0.000 0.000 0.672
#> SRR1044416 2 0.1544 0.79627 0.000 0.932 0.000 0.068 0.000
#> SRR1044417 2 0.2648 0.77433 0.000 0.848 0.000 0.152 0.000
#> SRR1044418 2 0.3381 0.74039 0.016 0.808 0.000 0.176 0.000
#> SRR1044420 2 0.2074 0.73945 0.000 0.896 0.000 0.000 0.104
#> SRR1044419 5 0.3949 0.73586 0.000 0.332 0.000 0.000 0.668
#> SRR1044421 2 0.1197 0.77476 0.000 0.952 0.000 0.000 0.048
#> SRR1044422 2 0.3143 0.60288 0.000 0.796 0.000 0.000 0.204
#> SRR1044423 2 0.3210 0.59062 0.000 0.788 0.000 0.000 0.212
#> SRR1044424 2 0.0794 0.78578 0.000 0.972 0.000 0.000 0.028
#> SRR1044425 1 0.0771 0.77472 0.976 0.000 0.000 0.020 0.004
#> SRR1044426 4 0.6205 0.57526 0.240 0.052 0.000 0.624 0.084
#> SRR1044427 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044428 1 0.0798 0.76680 0.976 0.000 0.000 0.008 0.016
#> SRR1044429 1 0.3074 0.68378 0.804 0.000 0.000 0.196 0.000
#> SRR1044430 1 0.4150 0.53131 0.772 0.004 0.000 0.180 0.044
#> SRR1044431 1 0.1041 0.77105 0.964 0.000 0.000 0.032 0.004
#> SRR1044433 4 0.5870 0.31531 0.020 0.400 0.000 0.524 0.056
#> SRR1044432 1 0.6012 0.17312 0.572 0.000 0.000 0.264 0.164
#> SRR1044434 1 0.3913 0.57023 0.676 0.000 0.000 0.324 0.000
#> SRR1044435 1 0.3895 0.57642 0.680 0.000 0.000 0.320 0.000
#> SRR1044436 1 0.3857 0.58703 0.688 0.000 0.000 0.312 0.000
#> SRR1044437 1 0.3876 0.58229 0.684 0.000 0.000 0.316 0.000
#> SRR1044439 1 0.3837 0.59157 0.692 0.000 0.000 0.308 0.000
#> SRR1044438 1 0.3857 0.58703 0.688 0.000 0.000 0.312 0.000
#> SRR1044440 1 0.3913 0.57055 0.676 0.000 0.000 0.324 0.000
#> SRR1044441 1 0.5059 0.24377 0.548 0.036 0.000 0.416 0.000
#> SRR1044442 4 0.6505 0.51871 0.344 0.088 0.000 0.528 0.040
#> SRR1044443 4 0.6031 0.40478 0.032 0.368 0.000 0.544 0.056
#> SRR1044444 1 0.3816 0.59594 0.696 0.000 0.000 0.304 0.000
#> SRR1044445 4 0.5697 0.30981 0.404 0.084 0.000 0.512 0.000
#> SRR1044446 5 0.5776 0.68648 0.000 0.204 0.004 0.160 0.632
#> SRR1044447 2 0.3912 0.66684 0.000 0.804 0.000 0.088 0.108
#> SRR1044449 3 0.2962 0.84495 0.000 0.000 0.868 0.084 0.048
#> SRR1044448 5 0.5957 0.27993 0.000 0.000 0.236 0.176 0.588
#> SRR1044450 5 0.6194 0.39042 0.000 0.020 0.180 0.184 0.616
#> SRR1044451 2 0.2974 0.75073 0.000 0.868 0.000 0.080 0.052
#> SRR1044452 3 0.0451 0.89629 0.000 0.000 0.988 0.008 0.004
#> SRR1044453 3 0.0451 0.89629 0.000 0.000 0.988 0.008 0.004
#> SRR1044454 3 0.0451 0.89629 0.000 0.000 0.988 0.008 0.004
#> SRR1044455 5 0.3990 0.76156 0.000 0.308 0.000 0.004 0.688
#> SRR1044456 1 0.6374 -0.22183 0.504 0.196 0.000 0.300 0.000
#> SRR1044457 5 0.3730 0.77525 0.000 0.288 0.000 0.000 0.712
#> SRR1044458 5 0.3684 0.77916 0.000 0.280 0.000 0.000 0.720
#> SRR1044459 5 0.4799 0.41088 0.000 0.004 0.228 0.060 0.708
#> SRR1044460 2 0.2471 0.70587 0.000 0.864 0.000 0.000 0.136
#> SRR1044461 2 0.4283 -0.23964 0.000 0.544 0.000 0.000 0.456
#> SRR1044462 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044463 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044464 4 0.6492 0.58768 0.292 0.124 0.000 0.556 0.028
#> SRR1044466 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044465 1 0.0162 0.77793 0.996 0.000 0.000 0.000 0.004
#> SRR1044467 1 0.0162 0.77793 0.996 0.000 0.000 0.000 0.004
#> SRR1044468 2 0.2074 0.73979 0.000 0.896 0.000 0.000 0.104
#> SRR1044469 5 0.4747 -0.13490 0.000 0.000 0.484 0.016 0.500
#> SRR1044470 1 0.0579 0.77362 0.984 0.000 0.000 0.008 0.008
#> SRR1044471 1 0.0290 0.77738 0.992 0.000 0.000 0.000 0.008
#> SRR1044472 1 0.0290 0.77738 0.992 0.000 0.000 0.000 0.008
#> SRR1044473 1 0.0162 0.77689 0.996 0.000 0.000 0.004 0.000
#> SRR1044474 2 0.3381 0.74039 0.016 0.808 0.000 0.176 0.000
#> SRR1044475 3 0.0451 0.89629 0.000 0.000 0.988 0.008 0.004
#> SRR1044476 5 0.3534 0.78396 0.000 0.256 0.000 0.000 0.744
#> SRR1044477 2 0.3381 0.74039 0.016 0.808 0.000 0.176 0.000
#> SRR1044478 2 0.2230 0.72836 0.000 0.884 0.000 0.000 0.116
#> SRR1044479 2 0.6253 0.00327 0.188 0.532 0.000 0.280 0.000
#> SRR1044480 1 0.1410 0.75971 0.940 0.000 0.000 0.060 0.000
#> SRR1044481 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044482 2 0.2674 0.77933 0.004 0.856 0.000 0.140 0.000
#> SRR1044483 1 0.3242 0.67653 0.784 0.000 0.000 0.216 0.000
#> SRR1044484 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044486 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044485 2 0.1043 0.79731 0.000 0.960 0.000 0.040 0.000
#> SRR1044487 2 0.3381 0.74039 0.016 0.808 0.000 0.176 0.000
#> SRR1044488 2 0.1478 0.76729 0.000 0.936 0.000 0.000 0.064
#> SRR1044489 2 0.2127 0.73592 0.000 0.892 0.000 0.000 0.108
#> SRR1044490 1 0.2370 0.71157 0.904 0.000 0.000 0.056 0.040
#> SRR1044491 1 0.0671 0.76652 0.980 0.000 0.000 0.016 0.004
#> SRR1044492 1 0.0451 0.77431 0.988 0.000 0.000 0.008 0.004
#> SRR1044493 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044494 2 0.3381 0.74039 0.016 0.808 0.000 0.176 0.000
#> SRR1044496 2 0.4010 0.67133 0.032 0.760 0.000 0.208 0.000
#> SRR1044495 2 0.3381 0.74039 0.016 0.808 0.000 0.176 0.000
#> SRR1044497 1 0.3684 0.61898 0.720 0.000 0.000 0.280 0.000
#> SRR1044499 3 0.4746 0.08153 0.000 0.000 0.504 0.016 0.480
#> SRR1044498 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044500 2 0.0609 0.78673 0.000 0.980 0.000 0.000 0.020
#> SRR1044501 5 0.3876 0.75407 0.000 0.316 0.000 0.000 0.684
#> SRR1044502 2 0.2054 0.77088 0.000 0.920 0.000 0.028 0.052
#> SRR1044503 1 0.3796 0.60006 0.700 0.000 0.000 0.300 0.000
#> SRR1044504 1 0.3966 0.54979 0.664 0.000 0.000 0.336 0.000
#> SRR1044505 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044506 1 0.4872 0.21796 0.540 0.024 0.000 0.436 0.000
#> SRR1044507 4 0.5842 0.39053 0.392 0.040 0.000 0.536 0.032
#> SRR1044508 4 0.6799 0.57461 0.120 0.280 0.000 0.548 0.052
#> SRR1044509 4 0.6146 0.42337 0.040 0.360 0.000 0.544 0.056
#> SRR1044510 3 0.0290 0.89612 0.000 0.000 0.992 0.008 0.000
#> SRR1044511 3 0.1168 0.89298 0.000 0.000 0.960 0.032 0.008
#> SRR1044512 3 0.0794 0.89509 0.000 0.000 0.972 0.028 0.000
#> SRR1044513 2 0.2067 0.77900 0.000 0.920 0.000 0.048 0.032
#> SRR1044514 3 0.1168 0.89298 0.000 0.000 0.960 0.032 0.008
#> SRR1044515 2 0.2067 0.77010 0.000 0.920 0.000 0.032 0.048
#> SRR1044516 2 0.3177 0.59677 0.000 0.792 0.000 0.000 0.208
#> SRR1044517 3 0.0162 0.89594 0.000 0.000 0.996 0.004 0.000
#> SRR1044518 3 0.1168 0.89298 0.000 0.000 0.960 0.032 0.008
#> SRR1044519 5 0.6417 -0.17564 0.000 0.000 0.404 0.172 0.424
#> SRR1044520 3 0.6275 0.39053 0.000 0.000 0.516 0.176 0.308
#> SRR1044521 2 0.0771 0.79511 0.000 0.976 0.000 0.020 0.004
#> SRR1044522 2 0.6303 -0.03143 0.196 0.524 0.000 0.280 0.000
#> SRR1044523 2 0.1469 0.78154 0.000 0.948 0.000 0.016 0.036
#> SRR1044524 5 0.4615 0.77323 0.000 0.252 0.000 0.048 0.700
#> SRR1044525 1 0.3876 0.58229 0.684 0.000 0.000 0.316 0.000
#> SRR1044526 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044527 2 0.3211 0.75695 0.008 0.824 0.000 0.164 0.004
#> SRR1044528 2 0.2843 0.77802 0.000 0.848 0.000 0.144 0.008
#> SRR1044529 2 0.3381 0.74039 0.016 0.808 0.000 0.176 0.000
#> SRR1044530 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044531 1 0.0162 0.77689 0.996 0.000 0.000 0.004 0.000
#> SRR1044533 1 0.0566 0.77286 0.984 0.000 0.000 0.004 0.012
#> SRR1044532 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044534 2 0.0609 0.78768 0.000 0.980 0.000 0.000 0.020
#> SRR1044535 5 0.5224 0.75517 0.000 0.276 0.000 0.080 0.644
#> SRR1044536 2 0.2127 0.73592 0.000 0.892 0.000 0.000 0.108
#> SRR1044537 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044538 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044539 1 0.3857 0.58720 0.688 0.000 0.000 0.312 0.000
#> SRR1044540 1 0.1997 0.73124 0.924 0.000 0.000 0.040 0.036
#> SRR1044541 5 0.3707 0.77741 0.000 0.284 0.000 0.000 0.716
#> SRR1044542 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044543 1 0.2951 0.64549 0.860 0.000 0.000 0.112 0.028
#> SRR1044544 5 0.3424 0.78008 0.000 0.240 0.000 0.000 0.760
#> SRR1044545 1 0.3612 0.63020 0.732 0.000 0.000 0.268 0.000
#> SRR1044546 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044547 1 0.2690 0.70978 0.844 0.000 0.000 0.156 0.000
#> SRR1044548 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044549 2 0.1430 0.79798 0.000 0.944 0.000 0.052 0.004
#> SRR1044550 2 0.2329 0.71979 0.000 0.876 0.000 0.000 0.124
#> SRR1044551 2 0.1792 0.79470 0.000 0.916 0.000 0.084 0.000
#> SRR1044552 1 0.3895 0.57642 0.680 0.000 0.000 0.320 0.000
#> SRR1044553 1 0.3999 0.53547 0.656 0.000 0.000 0.344 0.000
#> SRR1044554 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044555 5 0.4771 0.51635 0.000 0.028 0.168 0.052 0.752
#> SRR1044556 1 0.3876 0.58229 0.684 0.000 0.000 0.316 0.000
#> SRR1044557 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044558 1 0.3876 0.58229 0.684 0.000 0.000 0.316 0.000
#> SRR1044559 1 0.0162 0.77835 0.996 0.000 0.000 0.004 0.000
#> SRR1044561 1 0.3876 0.58229 0.684 0.000 0.000 0.316 0.000
#> SRR1044560 5 0.3508 0.78377 0.000 0.252 0.000 0.000 0.748
#> SRR1044562 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044563 1 0.3857 0.58720 0.688 0.000 0.000 0.312 0.000
#> SRR1044564 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044565 2 0.3381 0.74039 0.016 0.808 0.000 0.176 0.000
#> SRR1044566 5 0.3661 0.78044 0.000 0.276 0.000 0.000 0.724
#> SRR1044567 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044568 1 0.2813 0.70015 0.832 0.000 0.000 0.168 0.000
#> SRR1044569 1 0.0324 0.77651 0.992 0.000 0.000 0.004 0.004
#> SRR1044570 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044571 1 0.0510 0.77487 0.984 0.000 0.000 0.000 0.016
#> SRR1044572 1 0.0566 0.77417 0.984 0.000 0.000 0.004 0.012
#> SRR1044573 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044574 1 0.0404 0.77665 0.988 0.000 0.000 0.000 0.012
#> SRR1044575 1 0.0162 0.77793 0.996 0.000 0.000 0.000 0.004
#> SRR1044576 2 0.1732 0.79569 0.000 0.920 0.000 0.080 0.000
#> SRR1044577 2 0.2329 0.78604 0.000 0.876 0.000 0.124 0.000
#> SRR1044578 2 0.3381 0.74039 0.016 0.808 0.000 0.176 0.000
#> SRR1044579 1 0.3876 0.58229 0.684 0.000 0.000 0.316 0.000
#> SRR1044580 1 0.0955 0.77233 0.968 0.000 0.000 0.028 0.004
#> SRR1044581 1 0.3837 0.59169 0.692 0.000 0.000 0.308 0.000
#> SRR1044582 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044583 1 0.3876 0.58229 0.684 0.000 0.000 0.316 0.000
#> SRR1044584 1 0.3612 0.62984 0.732 0.000 0.000 0.268 0.000
#> SRR1044585 1 0.3876 0.58229 0.684 0.000 0.000 0.316 0.000
#> SRR1044586 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044587 1 0.4718 0.22153 0.540 0.016 0.000 0.444 0.000
#> SRR1044588 1 0.4872 0.21796 0.540 0.024 0.000 0.436 0.000
#> SRR1044589 1 0.4696 0.27543 0.556 0.016 0.000 0.428 0.000
#> SRR1044590 1 0.4574 0.33911 0.576 0.012 0.000 0.412 0.000
#> SRR1044591 1 0.4897 0.12499 0.516 0.024 0.000 0.460 0.000
#> SRR1044592 4 0.5870 0.31531 0.020 0.400 0.000 0.524 0.056
#> SRR1044593 1 0.4702 0.26151 0.552 0.016 0.000 0.432 0.000
#> SRR1044594 1 0.4793 0.23306 0.544 0.020 0.000 0.436 0.000
#> SRR1044595 4 0.6968 0.66168 0.216 0.180 0.000 0.552 0.052
#> SRR1044596 4 0.5537 0.29120 0.420 0.024 0.000 0.528 0.028
#> SRR1044597 1 0.6276 -0.08641 0.548 0.096 0.000 0.332 0.024
#> SRR1044598 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
#> SRR1044599 1 0.0000 0.77863 1.000 0.000 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 6 0.2941 0.7473 0.000 0.220 0.000 0.000 0.000 0.780
#> SRR1044416 2 0.0632 0.7934 0.024 0.976 0.000 0.000 0.000 0.000
#> SRR1044417 2 0.2748 0.7728 0.128 0.848 0.000 0.000 0.024 0.000
#> SRR1044418 2 0.3233 0.7669 0.132 0.828 0.000 0.016 0.024 0.000
#> SRR1044420 2 0.2048 0.7406 0.000 0.880 0.000 0.000 0.000 0.120
#> SRR1044419 6 0.3175 0.7181 0.000 0.256 0.000 0.000 0.000 0.744
#> SRR1044421 2 0.1411 0.7728 0.004 0.936 0.000 0.000 0.000 0.060
#> SRR1044422 2 0.2793 0.6586 0.000 0.800 0.000 0.000 0.000 0.200
#> SRR1044423 2 0.2823 0.6539 0.000 0.796 0.000 0.000 0.000 0.204
#> SRR1044424 2 0.1267 0.7763 0.000 0.940 0.000 0.000 0.000 0.060
#> SRR1044425 4 0.4336 -0.6618 0.408 0.000 0.000 0.572 0.008 0.012
#> SRR1044426 4 0.7385 -0.4963 0.328 0.048 0.000 0.352 0.244 0.028
#> SRR1044427 4 0.4227 -0.8281 0.488 0.000 0.000 0.500 0.008 0.004
#> SRR1044428 1 0.4385 0.7315 0.540 0.000 0.000 0.440 0.012 0.008
#> SRR1044429 4 0.3488 -0.0982 0.244 0.000 0.000 0.744 0.008 0.004
#> SRR1044430 1 0.6203 -0.4426 0.552 0.000 0.000 0.208 0.196 0.044
#> SRR1044431 4 0.4364 -0.6921 0.424 0.000 0.000 0.556 0.012 0.008
#> SRR1044433 2 0.7683 -0.0163 0.216 0.308 0.000 0.228 0.248 0.000
#> SRR1044432 5 0.6932 0.0000 0.360 0.000 0.000 0.160 0.392 0.088
#> SRR1044434 4 0.0146 0.3992 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1044435 4 0.0000 0.4000 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044436 4 0.0291 0.3969 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044437 4 0.0000 0.4000 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044439 4 0.0405 0.3946 0.008 0.000 0.000 0.988 0.004 0.000
#> SRR1044438 4 0.0405 0.3946 0.008 0.000 0.000 0.988 0.004 0.000
#> SRR1044440 4 0.0000 0.4000 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044441 4 0.3886 0.2094 0.160 0.024 0.000 0.780 0.036 0.000
#> SRR1044442 4 0.6438 -0.1439 0.204 0.072 0.000 0.544 0.180 0.000
#> SRR1044443 4 0.7708 -0.3391 0.216 0.248 0.000 0.288 0.248 0.000
#> SRR1044444 4 0.0260 0.3959 0.008 0.000 0.000 0.992 0.000 0.000
#> SRR1044445 4 0.4365 0.1664 0.132 0.088 0.000 0.756 0.024 0.000
#> SRR1044446 6 0.5310 0.6533 0.004 0.108 0.004 0.000 0.288 0.596
#> SRR1044447 2 0.4700 0.6125 0.020 0.716 0.000 0.000 0.168 0.096
#> SRR1044449 3 0.3219 0.8204 0.008 0.000 0.808 0.000 0.168 0.016
#> SRR1044448 6 0.5560 0.4396 0.000 0.004 0.140 0.000 0.320 0.536
#> SRR1044450 6 0.5498 0.4796 0.004 0.004 0.116 0.000 0.320 0.556
#> SRR1044451 2 0.3883 0.7124 0.028 0.788 0.000 0.000 0.144 0.040
#> SRR1044452 3 0.0891 0.9068 0.008 0.000 0.968 0.000 0.024 0.000
#> SRR1044453 3 0.0891 0.9068 0.008 0.000 0.968 0.000 0.024 0.000
#> SRR1044454 3 0.0891 0.9068 0.008 0.000 0.968 0.000 0.024 0.000
#> SRR1044455 6 0.2854 0.7563 0.000 0.208 0.000 0.000 0.000 0.792
#> SRR1044456 4 0.6160 -0.1618 0.228 0.264 0.000 0.492 0.016 0.000
#> SRR1044457 6 0.2597 0.7710 0.000 0.176 0.000 0.000 0.000 0.824
#> SRR1044458 6 0.2593 0.7777 0.008 0.148 0.000 0.000 0.000 0.844
#> SRR1044459 6 0.4289 0.6062 0.016 0.000 0.136 0.000 0.092 0.756
#> SRR1044460 2 0.2491 0.7032 0.000 0.836 0.000 0.000 0.000 0.164
#> SRR1044461 6 0.3866 0.2309 0.000 0.484 0.000 0.000 0.000 0.516
#> SRR1044462 4 0.4326 -0.8205 0.484 0.000 0.000 0.500 0.008 0.008
#> SRR1044463 1 0.3999 0.8339 0.500 0.000 0.000 0.496 0.000 0.004
#> SRR1044464 4 0.6253 -0.1709 0.264 0.084 0.000 0.560 0.088 0.004
#> SRR1044466 1 0.3868 0.8366 0.504 0.000 0.000 0.496 0.000 0.000
#> SRR1044465 4 0.4326 -0.8274 0.488 0.000 0.000 0.496 0.008 0.008
#> SRR1044467 4 0.4719 -0.7994 0.464 0.000 0.000 0.500 0.012 0.024
#> SRR1044468 2 0.2092 0.7393 0.000 0.876 0.000 0.000 0.000 0.124
#> SRR1044469 6 0.4913 0.3611 0.020 0.000 0.340 0.000 0.040 0.600
#> SRR1044470 1 0.4326 0.8267 0.496 0.000 0.000 0.488 0.008 0.008
#> SRR1044471 4 0.4721 -0.7988 0.472 0.000 0.000 0.492 0.012 0.024
#> SRR1044472 4 0.3997 -0.8239 0.488 0.000 0.000 0.508 0.000 0.004
#> SRR1044473 4 0.4326 -0.8274 0.488 0.000 0.000 0.496 0.008 0.008
#> SRR1044474 2 0.3233 0.7669 0.132 0.828 0.000 0.016 0.024 0.000
#> SRR1044475 3 0.0891 0.9068 0.008 0.000 0.968 0.000 0.024 0.000
#> SRR1044476 6 0.2573 0.7769 0.008 0.132 0.000 0.000 0.004 0.856
#> SRR1044477 2 0.3233 0.7669 0.132 0.828 0.000 0.016 0.024 0.000
#> SRR1044478 2 0.2260 0.7254 0.000 0.860 0.000 0.000 0.000 0.140
#> SRR1044479 2 0.6264 0.1765 0.192 0.476 0.000 0.308 0.024 0.000
#> SRR1044480 4 0.4221 -0.6261 0.396 0.000 0.000 0.588 0.008 0.008
#> SRR1044481 4 0.3862 -0.7960 0.476 0.000 0.000 0.524 0.000 0.000
#> SRR1044482 2 0.2706 0.7743 0.124 0.852 0.000 0.000 0.024 0.000
#> SRR1044483 4 0.3812 -0.0461 0.248 0.000 0.000 0.728 0.012 0.012
#> SRR1044484 4 0.4227 -0.8281 0.488 0.000 0.000 0.500 0.008 0.004
#> SRR1044486 4 0.3868 -0.8330 0.496 0.000 0.000 0.504 0.000 0.000
#> SRR1044485 2 0.0508 0.7925 0.012 0.984 0.000 0.000 0.000 0.004
#> SRR1044487 2 0.3233 0.7669 0.132 0.828 0.000 0.016 0.024 0.000
#> SRR1044488 2 0.1765 0.7567 0.000 0.904 0.000 0.000 0.000 0.096
#> SRR1044489 2 0.2178 0.7324 0.000 0.868 0.000 0.000 0.000 0.132
#> SRR1044490 1 0.5876 0.5616 0.460 0.000 0.000 0.412 0.100 0.028
#> SRR1044491 1 0.4097 0.7862 0.504 0.000 0.000 0.488 0.008 0.000
#> SRR1044492 1 0.4097 0.8313 0.504 0.000 0.000 0.488 0.008 0.000
#> SRR1044493 4 0.3866 -0.8086 0.484 0.000 0.000 0.516 0.000 0.000
#> SRR1044494 2 0.3233 0.7669 0.132 0.828 0.000 0.016 0.024 0.000
#> SRR1044496 2 0.3706 0.7429 0.148 0.796 0.000 0.032 0.024 0.000
#> SRR1044495 2 0.3233 0.7669 0.132 0.828 0.000 0.016 0.024 0.000
#> SRR1044497 4 0.1075 0.3556 0.048 0.000 0.000 0.952 0.000 0.000
#> SRR1044499 6 0.4938 0.3455 0.020 0.000 0.348 0.000 0.040 0.592
#> SRR1044498 1 0.3999 0.8324 0.500 0.000 0.000 0.496 0.004 0.000
#> SRR1044500 2 0.0865 0.7847 0.000 0.964 0.000 0.000 0.000 0.036
#> SRR1044501 6 0.2854 0.7556 0.000 0.208 0.000 0.000 0.000 0.792
#> SRR1044502 2 0.2164 0.7733 0.008 0.908 0.000 0.000 0.028 0.056
#> SRR1044503 4 0.0508 0.3912 0.012 0.000 0.000 0.984 0.004 0.000
#> SRR1044504 4 0.0260 0.4003 0.008 0.000 0.000 0.992 0.000 0.000
#> SRR1044505 4 0.4227 -0.8310 0.488 0.000 0.000 0.500 0.004 0.008
#> SRR1044506 4 0.2900 0.3442 0.088 0.044 0.000 0.860 0.008 0.000
#> SRR1044507 4 0.5759 -0.0226 0.212 0.048 0.000 0.616 0.124 0.000
#> SRR1044508 4 0.7630 -0.3230 0.216 0.204 0.000 0.332 0.248 0.000
#> SRR1044509 4 0.7695 -0.3349 0.216 0.236 0.000 0.300 0.248 0.000
#> SRR1044510 3 0.0260 0.9086 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1044511 3 0.1340 0.9054 0.004 0.000 0.948 0.000 0.040 0.008
#> SRR1044512 3 0.1340 0.9054 0.004 0.000 0.948 0.000 0.040 0.008
#> SRR1044513 2 0.3104 0.7351 0.020 0.844 0.000 0.000 0.112 0.024
#> SRR1044514 3 0.1340 0.9054 0.004 0.000 0.948 0.000 0.040 0.008
#> SRR1044515 2 0.1777 0.7754 0.004 0.928 0.000 0.000 0.024 0.044
#> SRR1044516 2 0.2730 0.6690 0.000 0.808 0.000 0.000 0.000 0.192
#> SRR1044517 3 0.0000 0.9081 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044518 3 0.1340 0.9054 0.004 0.000 0.948 0.000 0.040 0.008
#> SRR1044519 6 0.6174 0.1535 0.000 0.004 0.268 0.000 0.324 0.404
#> SRR1044520 3 0.6063 0.1773 0.000 0.000 0.400 0.000 0.328 0.272
#> SRR1044521 2 0.0363 0.7899 0.000 0.988 0.000 0.000 0.000 0.012
#> SRR1044522 2 0.6262 0.2089 0.200 0.484 0.000 0.292 0.024 0.000
#> SRR1044523 2 0.1536 0.7798 0.004 0.940 0.000 0.000 0.016 0.040
#> SRR1044524 6 0.3766 0.7681 0.004 0.144 0.000 0.000 0.068 0.784
#> SRR1044525 4 0.0291 0.3969 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR1044526 4 0.4227 -0.8281 0.488 0.000 0.000 0.500 0.008 0.004
#> SRR1044527 2 0.2932 0.7704 0.132 0.840 0.000 0.004 0.024 0.000
#> SRR1044528 2 0.2930 0.7733 0.124 0.840 0.000 0.000 0.036 0.000
#> SRR1044529 2 0.3233 0.7669 0.132 0.828 0.000 0.016 0.024 0.000
#> SRR1044530 4 0.3868 -0.8244 0.492 0.000 0.000 0.508 0.000 0.000
#> SRR1044531 4 0.4225 -0.8186 0.480 0.000 0.000 0.508 0.004 0.008
#> SRR1044533 4 0.3999 -0.8290 0.496 0.000 0.000 0.500 0.000 0.004
#> SRR1044532 4 0.3869 -0.8429 0.500 0.000 0.000 0.500 0.000 0.000
#> SRR1044534 2 0.0790 0.7860 0.000 0.968 0.000 0.000 0.000 0.032
#> SRR1044535 6 0.4725 0.7403 0.004 0.204 0.000 0.000 0.108 0.684
#> SRR1044536 2 0.2219 0.7288 0.000 0.864 0.000 0.000 0.000 0.136
#> SRR1044537 1 0.3869 0.8322 0.500 0.000 0.000 0.500 0.000 0.000
#> SRR1044538 1 0.3868 0.8366 0.504 0.000 0.000 0.496 0.000 0.000
#> SRR1044539 4 0.0405 0.3946 0.008 0.000 0.000 0.988 0.004 0.000
#> SRR1044540 4 0.5626 -0.6284 0.440 0.000 0.000 0.460 0.072 0.028
#> SRR1044541 6 0.2662 0.7777 0.004 0.152 0.000 0.000 0.004 0.840
#> SRR1044542 1 0.3868 0.8366 0.504 0.000 0.000 0.496 0.000 0.000
#> SRR1044543 1 0.6289 0.2796 0.484 0.000 0.000 0.340 0.128 0.048
#> SRR1044544 6 0.2685 0.7761 0.008 0.132 0.000 0.000 0.008 0.852
#> SRR1044545 4 0.1542 0.3481 0.052 0.000 0.000 0.936 0.008 0.004
#> SRR1044546 4 0.3869 -0.8429 0.500 0.000 0.000 0.500 0.000 0.000
#> SRR1044547 4 0.2958 0.1507 0.160 0.000 0.000 0.824 0.008 0.008
#> SRR1044548 4 0.3866 -0.8066 0.484 0.000 0.000 0.516 0.000 0.000
#> SRR1044549 2 0.0603 0.7936 0.016 0.980 0.000 0.000 0.004 0.000
#> SRR1044550 2 0.2300 0.7226 0.000 0.856 0.000 0.000 0.000 0.144
#> SRR1044551 2 0.1219 0.7925 0.048 0.948 0.000 0.000 0.004 0.000
#> SRR1044552 4 0.0000 0.4000 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044553 4 0.0547 0.3996 0.020 0.000 0.000 0.980 0.000 0.000
#> SRR1044554 1 0.3997 0.8270 0.508 0.000 0.000 0.488 0.004 0.000
#> SRR1044555 6 0.4293 0.6318 0.016 0.008 0.112 0.000 0.092 0.772
#> SRR1044556 4 0.0405 0.3946 0.008 0.000 0.000 0.988 0.004 0.000
#> SRR1044557 4 0.3866 -0.8118 0.484 0.000 0.000 0.516 0.000 0.000
#> SRR1044558 4 0.0146 0.3989 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1044559 4 0.3868 -0.8336 0.496 0.000 0.000 0.504 0.000 0.000
#> SRR1044561 4 0.0000 0.4000 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044560 6 0.2673 0.7769 0.012 0.132 0.000 0.000 0.004 0.852
#> SRR1044562 1 0.3869 0.8322 0.500 0.000 0.000 0.500 0.000 0.000
#> SRR1044563 4 0.0508 0.3914 0.012 0.000 0.000 0.984 0.004 0.000
#> SRR1044564 1 0.3868 0.8366 0.504 0.000 0.000 0.496 0.000 0.000
#> SRR1044565 2 0.3233 0.7669 0.132 0.828 0.000 0.016 0.024 0.000
#> SRR1044566 6 0.2734 0.7779 0.008 0.148 0.000 0.000 0.004 0.840
#> SRR1044567 4 0.3868 -0.8310 0.496 0.000 0.000 0.504 0.000 0.000
#> SRR1044568 4 0.2655 0.1946 0.140 0.000 0.000 0.848 0.008 0.004
#> SRR1044569 4 0.4649 -0.8009 0.464 0.000 0.000 0.504 0.012 0.020
#> SRR1044570 1 0.3868 0.8366 0.504 0.000 0.000 0.496 0.000 0.000
#> SRR1044571 4 0.4848 -0.7955 0.468 0.000 0.000 0.488 0.012 0.032
#> SRR1044572 4 0.4789 -0.7833 0.448 0.000 0.000 0.512 0.016 0.024
#> SRR1044573 4 0.4411 -0.8127 0.476 0.000 0.000 0.504 0.008 0.012
#> SRR1044574 4 0.4698 -0.7606 0.436 0.000 0.000 0.528 0.012 0.024
#> SRR1044575 4 0.4574 -0.7996 0.464 0.000 0.000 0.508 0.012 0.016
#> SRR1044576 2 0.0935 0.7936 0.032 0.964 0.000 0.000 0.004 0.000
#> SRR1044577 2 0.2282 0.7835 0.088 0.888 0.000 0.000 0.024 0.000
#> SRR1044578 2 0.3233 0.7669 0.132 0.828 0.000 0.016 0.024 0.000
#> SRR1044579 4 0.0000 0.4000 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044580 4 0.4440 -0.7067 0.420 0.000 0.000 0.556 0.008 0.016
#> SRR1044581 4 0.0000 0.4000 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044582 1 0.3868 0.8366 0.504 0.000 0.000 0.496 0.000 0.000
#> SRR1044583 4 0.0000 0.4000 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044584 4 0.1555 0.3366 0.060 0.000 0.000 0.932 0.004 0.004
#> SRR1044585 4 0.0000 0.4000 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1044586 4 0.3867 -0.8168 0.488 0.000 0.000 0.512 0.000 0.000
#> SRR1044587 4 0.2883 0.3473 0.092 0.040 0.000 0.860 0.008 0.000
#> SRR1044588 4 0.2900 0.3442 0.088 0.044 0.000 0.860 0.008 0.000
#> SRR1044589 4 0.2900 0.3442 0.088 0.044 0.000 0.860 0.008 0.000
#> SRR1044590 4 0.2398 0.3743 0.080 0.028 0.000 0.888 0.004 0.000
#> SRR1044591 4 0.2900 0.3442 0.088 0.044 0.000 0.860 0.008 0.000
#> SRR1044592 2 0.7689 -0.0286 0.216 0.304 0.000 0.232 0.248 0.000
#> SRR1044593 4 0.2900 0.3442 0.088 0.044 0.000 0.860 0.008 0.000
#> SRR1044594 4 0.2900 0.3442 0.088 0.044 0.000 0.860 0.008 0.000
#> SRR1044595 4 0.7409 -0.3018 0.224 0.144 0.000 0.384 0.248 0.000
#> SRR1044596 4 0.5415 0.0269 0.204 0.036 0.000 0.648 0.112 0.000
#> SRR1044597 4 0.6170 -0.1911 0.416 0.052 0.000 0.436 0.096 0.000
#> SRR1044598 1 0.3869 0.8322 0.500 0.000 0.000 0.500 0.000 0.000
#> SRR1044599 4 0.3869 -0.8429 0.500 0.000 0.000 0.500 0.000 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)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.955 0.944 0.978 0.4724 0.533 0.533
#> 3 3 0.936 0.932 0.970 0.2176 0.875 0.770
#> 4 4 0.730 0.675 0.845 0.1713 0.945 0.873
#> 5 5 0.727 0.736 0.792 0.0786 0.815 0.531
#> 6 6 0.789 0.841 0.874 0.0565 0.920 0.690
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0.000 0.98357 0.000 1.000
#> SRR1044416 2 0.000 0.98357 0.000 1.000
#> SRR1044417 2 0.000 0.98357 0.000 1.000
#> SRR1044418 2 1.000 0.00366 0.488 0.512
#> SRR1044420 2 0.000 0.98357 0.000 1.000
#> SRR1044419 2 0.000 0.98357 0.000 1.000
#> SRR1044421 2 0.000 0.98357 0.000 1.000
#> SRR1044422 2 0.000 0.98357 0.000 1.000
#> SRR1044423 2 0.000 0.98357 0.000 1.000
#> SRR1044424 2 0.000 0.98357 0.000 1.000
#> SRR1044425 1 0.000 0.97316 1.000 0.000
#> SRR1044426 1 0.000 0.97316 1.000 0.000
#> SRR1044427 1 0.000 0.97316 1.000 0.000
#> SRR1044428 1 0.000 0.97316 1.000 0.000
#> SRR1044429 1 0.000 0.97316 1.000 0.000
#> SRR1044430 1 0.000 0.97316 1.000 0.000
#> SRR1044431 1 0.000 0.97316 1.000 0.000
#> SRR1044433 1 0.998 0.09135 0.524 0.476
#> SRR1044432 1 0.000 0.97316 1.000 0.000
#> SRR1044434 1 0.000 0.97316 1.000 0.000
#> SRR1044435 1 0.000 0.97316 1.000 0.000
#> SRR1044436 1 0.000 0.97316 1.000 0.000
#> SRR1044437 1 0.000 0.97316 1.000 0.000
#> SRR1044439 1 0.000 0.97316 1.000 0.000
#> SRR1044438 1 0.000 0.97316 1.000 0.000
#> SRR1044440 1 0.000 0.97316 1.000 0.000
#> SRR1044441 1 0.000 0.97316 1.000 0.000
#> SRR1044442 1 0.000 0.97316 1.000 0.000
#> SRR1044443 1 0.000 0.97316 1.000 0.000
#> SRR1044444 1 0.000 0.97316 1.000 0.000
#> SRR1044445 1 0.000 0.97316 1.000 0.000
#> SRR1044446 2 0.000 0.98357 0.000 1.000
#> SRR1044447 2 0.000 0.98357 0.000 1.000
#> SRR1044449 2 0.000 0.98357 0.000 1.000
#> SRR1044448 2 0.000 0.98357 0.000 1.000
#> SRR1044450 2 0.000 0.98357 0.000 1.000
#> SRR1044451 2 0.000 0.98357 0.000 1.000
#> SRR1044452 2 0.000 0.98357 0.000 1.000
#> SRR1044453 2 0.000 0.98357 0.000 1.000
#> SRR1044454 2 0.000 0.98357 0.000 1.000
#> SRR1044455 2 0.000 0.98357 0.000 1.000
#> SRR1044456 1 0.000 0.97316 1.000 0.000
#> SRR1044457 2 0.000 0.98357 0.000 1.000
#> SRR1044458 2 0.000 0.98357 0.000 1.000
#> SRR1044459 2 0.000 0.98357 0.000 1.000
#> SRR1044460 2 0.000 0.98357 0.000 1.000
#> SRR1044461 2 0.000 0.98357 0.000 1.000
#> SRR1044462 1 0.000 0.97316 1.000 0.000
#> SRR1044463 1 0.000 0.97316 1.000 0.000
#> SRR1044464 1 0.000 0.97316 1.000 0.000
#> SRR1044466 1 0.000 0.97316 1.000 0.000
#> SRR1044465 1 0.000 0.97316 1.000 0.000
#> SRR1044467 1 0.000 0.97316 1.000 0.000
#> SRR1044468 2 0.000 0.98357 0.000 1.000
#> SRR1044469 2 0.000 0.98357 0.000 1.000
#> SRR1044470 1 0.000 0.97316 1.000 0.000
#> SRR1044471 1 0.000 0.97316 1.000 0.000
#> SRR1044472 1 0.000 0.97316 1.000 0.000
#> SRR1044473 1 0.000 0.97316 1.000 0.000
#> SRR1044474 1 1.000 0.06980 0.512 0.488
#> SRR1044475 2 0.000 0.98357 0.000 1.000
#> SRR1044476 2 0.000 0.98357 0.000 1.000
#> SRR1044477 1 0.781 0.69979 0.768 0.232
#> SRR1044478 2 0.000 0.98357 0.000 1.000
#> SRR1044479 1 0.000 0.97316 1.000 0.000
#> SRR1044480 1 0.000 0.97316 1.000 0.000
#> SRR1044481 1 0.000 0.97316 1.000 0.000
#> SRR1044482 2 0.529 0.85257 0.120 0.880
#> SRR1044483 1 0.000 0.97316 1.000 0.000
#> SRR1044484 1 0.000 0.97316 1.000 0.000
#> SRR1044486 1 0.000 0.97316 1.000 0.000
#> SRR1044485 2 0.000 0.98357 0.000 1.000
#> SRR1044487 1 0.886 0.57447 0.696 0.304
#> SRR1044488 2 0.000 0.98357 0.000 1.000
#> SRR1044489 2 0.000 0.98357 0.000 1.000
#> SRR1044490 1 0.000 0.97316 1.000 0.000
#> SRR1044491 1 0.000 0.97316 1.000 0.000
#> SRR1044492 1 0.000 0.97316 1.000 0.000
#> SRR1044493 1 0.000 0.97316 1.000 0.000
#> SRR1044494 1 0.839 0.64094 0.732 0.268
#> SRR1044496 1 0.697 0.76368 0.812 0.188
#> SRR1044495 1 0.839 0.64094 0.732 0.268
#> SRR1044497 1 0.000 0.97316 1.000 0.000
#> SRR1044499 2 0.000 0.98357 0.000 1.000
#> SRR1044498 1 0.000 0.97316 1.000 0.000
#> SRR1044500 2 0.000 0.98357 0.000 1.000
#> SRR1044501 2 0.000 0.98357 0.000 1.000
#> SRR1044502 2 0.000 0.98357 0.000 1.000
#> SRR1044503 1 0.000 0.97316 1.000 0.000
#> SRR1044504 1 0.000 0.97316 1.000 0.000
#> SRR1044505 1 0.000 0.97316 1.000 0.000
#> SRR1044506 1 0.000 0.97316 1.000 0.000
#> SRR1044507 1 0.000 0.97316 1.000 0.000
#> SRR1044508 1 0.000 0.97316 1.000 0.000
#> SRR1044509 1 0.000 0.97316 1.000 0.000
#> SRR1044510 2 0.000 0.98357 0.000 1.000
#> SRR1044511 2 0.000 0.98357 0.000 1.000
#> SRR1044512 2 0.000 0.98357 0.000 1.000
#> SRR1044513 2 0.000 0.98357 0.000 1.000
#> SRR1044514 2 0.000 0.98357 0.000 1.000
#> SRR1044515 2 0.000 0.98357 0.000 1.000
#> SRR1044516 2 0.000 0.98357 0.000 1.000
#> SRR1044517 2 0.000 0.98357 0.000 1.000
#> SRR1044518 2 0.000 0.98357 0.000 1.000
#> SRR1044519 2 0.000 0.98357 0.000 1.000
#> SRR1044520 2 0.000 0.98357 0.000 1.000
#> SRR1044521 2 0.000 0.98357 0.000 1.000
#> SRR1044522 1 0.000 0.97316 1.000 0.000
#> SRR1044523 2 0.000 0.98357 0.000 1.000
#> SRR1044524 2 0.000 0.98357 0.000 1.000
#> SRR1044525 1 0.000 0.97316 1.000 0.000
#> SRR1044526 1 0.000 0.97316 1.000 0.000
#> SRR1044527 2 0.584 0.82632 0.140 0.860
#> SRR1044528 2 0.000 0.98357 0.000 1.000
#> SRR1044529 1 0.925 0.49964 0.660 0.340
#> SRR1044530 1 0.000 0.97316 1.000 0.000
#> SRR1044531 1 0.000 0.97316 1.000 0.000
#> SRR1044533 1 0.000 0.97316 1.000 0.000
#> SRR1044532 1 0.000 0.97316 1.000 0.000
#> SRR1044534 2 0.000 0.98357 0.000 1.000
#> SRR1044535 2 0.000 0.98357 0.000 1.000
#> SRR1044536 2 0.000 0.98357 0.000 1.000
#> SRR1044537 1 0.000 0.97316 1.000 0.000
#> SRR1044538 1 0.000 0.97316 1.000 0.000
#> SRR1044539 1 0.000 0.97316 1.000 0.000
#> SRR1044540 1 0.000 0.97316 1.000 0.000
#> SRR1044541 2 0.000 0.98357 0.000 1.000
#> SRR1044542 1 0.000 0.97316 1.000 0.000
#> SRR1044543 1 0.000 0.97316 1.000 0.000
#> SRR1044544 2 0.000 0.98357 0.000 1.000
#> SRR1044545 1 0.000 0.97316 1.000 0.000
#> SRR1044546 1 0.000 0.97316 1.000 0.000
#> SRR1044547 1 0.000 0.97316 1.000 0.000
#> SRR1044548 1 0.000 0.97316 1.000 0.000
#> SRR1044549 2 0.000 0.98357 0.000 1.000
#> SRR1044550 2 0.000 0.98357 0.000 1.000
#> SRR1044551 2 0.000 0.98357 0.000 1.000
#> SRR1044552 1 0.000 0.97316 1.000 0.000
#> SRR1044553 1 0.000 0.97316 1.000 0.000
#> SRR1044554 1 0.000 0.97316 1.000 0.000
#> SRR1044555 2 0.000 0.98357 0.000 1.000
#> SRR1044556 1 0.000 0.97316 1.000 0.000
#> SRR1044557 1 0.000 0.97316 1.000 0.000
#> SRR1044558 1 0.000 0.97316 1.000 0.000
#> SRR1044559 1 0.000 0.97316 1.000 0.000
#> SRR1044561 1 0.000 0.97316 1.000 0.000
#> SRR1044560 2 0.000 0.98357 0.000 1.000
#> SRR1044562 1 0.000 0.97316 1.000 0.000
#> SRR1044563 1 0.000 0.97316 1.000 0.000
#> SRR1044564 1 0.000 0.97316 1.000 0.000
#> SRR1044565 1 0.871 0.59746 0.708 0.292
#> SRR1044566 2 0.000 0.98357 0.000 1.000
#> SRR1044567 1 0.000 0.97316 1.000 0.000
#> SRR1044568 1 0.000 0.97316 1.000 0.000
#> SRR1044569 1 0.000 0.97316 1.000 0.000
#> SRR1044570 1 0.000 0.97316 1.000 0.000
#> SRR1044571 1 0.000 0.97316 1.000 0.000
#> SRR1044572 1 0.000 0.97316 1.000 0.000
#> SRR1044573 1 0.000 0.97316 1.000 0.000
#> SRR1044574 1 0.000 0.97316 1.000 0.000
#> SRR1044575 1 0.000 0.97316 1.000 0.000
#> SRR1044576 2 0.000 0.98357 0.000 1.000
#> SRR1044577 2 0.000 0.98357 0.000 1.000
#> SRR1044578 2 0.886 0.54757 0.304 0.696
#> SRR1044579 1 0.000 0.97316 1.000 0.000
#> SRR1044580 1 0.000 0.97316 1.000 0.000
#> SRR1044581 1 0.000 0.97316 1.000 0.000
#> SRR1044582 1 0.000 0.97316 1.000 0.000
#> SRR1044583 1 0.000 0.97316 1.000 0.000
#> SRR1044584 1 0.000 0.97316 1.000 0.000
#> SRR1044585 1 0.000 0.97316 1.000 0.000
#> SRR1044586 1 0.000 0.97316 1.000 0.000
#> SRR1044587 1 0.000 0.97316 1.000 0.000
#> SRR1044588 1 0.000 0.97316 1.000 0.000
#> SRR1044589 1 0.000 0.97316 1.000 0.000
#> SRR1044590 1 0.000 0.97316 1.000 0.000
#> SRR1044591 1 0.000 0.97316 1.000 0.000
#> SRR1044592 1 0.625 0.80726 0.844 0.156
#> SRR1044593 1 0.000 0.97316 1.000 0.000
#> SRR1044594 1 0.000 0.97316 1.000 0.000
#> SRR1044595 1 0.000 0.97316 1.000 0.000
#> SRR1044596 1 0.000 0.97316 1.000 0.000
#> SRR1044597 1 0.000 0.97316 1.000 0.000
#> SRR1044598 1 0.000 0.97316 1.000 0.000
#> SRR1044599 1 0.000 0.97316 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044416 3 0.2878 0.8486 0.000 0.096 0.904
#> SRR1044417 3 0.0000 0.9115 0.000 0.000 1.000
#> SRR1044418 3 0.0424 0.9156 0.008 0.000 0.992
#> SRR1044420 2 0.1860 0.9148 0.000 0.948 0.052
#> SRR1044419 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044421 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044422 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044423 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044424 2 0.5678 0.5456 0.000 0.684 0.316
#> SRR1044425 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044426 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044427 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044428 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044429 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044430 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044431 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044433 2 0.9561 0.1239 0.316 0.468 0.216
#> SRR1044432 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044434 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044435 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044436 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044437 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044439 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044438 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044440 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044441 1 0.2356 0.9144 0.928 0.000 0.072
#> SRR1044442 1 0.2165 0.9228 0.936 0.000 0.064
#> SRR1044443 1 0.4842 0.7173 0.776 0.000 0.224
#> SRR1044444 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044445 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044446 2 0.0592 0.9477 0.000 0.988 0.012
#> SRR1044447 2 0.1411 0.9305 0.000 0.964 0.036
#> SRR1044449 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044448 2 0.0424 0.9499 0.000 0.992 0.008
#> SRR1044450 2 0.0592 0.9477 0.000 0.988 0.012
#> SRR1044451 2 0.4452 0.7716 0.000 0.808 0.192
#> SRR1044452 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044453 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044454 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044455 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044456 3 0.6008 0.4787 0.372 0.000 0.628
#> SRR1044457 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044458 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044459 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044460 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044461 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044462 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044463 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044464 1 0.1643 0.9424 0.956 0.000 0.044
#> SRR1044466 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044465 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044467 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044468 2 0.0237 0.9516 0.000 0.996 0.004
#> SRR1044469 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044470 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044471 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044472 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044473 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044474 3 0.0592 0.9171 0.012 0.000 0.988
#> SRR1044475 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044476 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044477 3 0.0592 0.9171 0.012 0.000 0.988
#> SRR1044478 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044479 3 0.4504 0.7694 0.196 0.000 0.804
#> SRR1044480 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044481 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044482 3 0.1647 0.9070 0.036 0.004 0.960
#> SRR1044483 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044484 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044486 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044485 3 0.4291 0.7515 0.000 0.180 0.820
#> SRR1044487 3 0.1643 0.9029 0.044 0.000 0.956
#> SRR1044488 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044489 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044490 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044491 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044492 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044493 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044494 3 0.0592 0.9171 0.012 0.000 0.988
#> SRR1044496 3 0.3116 0.8549 0.108 0.000 0.892
#> SRR1044495 3 0.0592 0.9171 0.012 0.000 0.988
#> SRR1044497 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044499 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044498 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044500 2 0.5016 0.6857 0.000 0.760 0.240
#> SRR1044501 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044502 2 0.2796 0.8824 0.000 0.908 0.092
#> SRR1044503 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044504 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044505 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044506 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044507 1 0.0747 0.9693 0.984 0.000 0.016
#> SRR1044508 1 0.4605 0.7477 0.796 0.000 0.204
#> SRR1044509 1 0.4605 0.7477 0.796 0.000 0.204
#> SRR1044510 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044511 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044512 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044513 2 0.3752 0.8293 0.000 0.856 0.144
#> SRR1044514 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044515 2 0.4887 0.7233 0.000 0.772 0.228
#> SRR1044516 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044517 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044518 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044519 2 0.0424 0.9499 0.000 0.992 0.008
#> SRR1044520 2 0.0424 0.9499 0.000 0.992 0.008
#> SRR1044521 2 0.5621 0.5620 0.000 0.692 0.308
#> SRR1044522 3 0.4605 0.7611 0.204 0.000 0.796
#> SRR1044523 2 0.4605 0.7655 0.000 0.796 0.204
#> SRR1044524 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044525 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044526 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044527 3 0.0000 0.9115 0.000 0.000 1.000
#> SRR1044528 3 0.0000 0.9115 0.000 0.000 1.000
#> SRR1044529 3 0.3340 0.8446 0.120 0.000 0.880
#> SRR1044530 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044531 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044533 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044532 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044534 2 0.1289 0.9313 0.000 0.968 0.032
#> SRR1044535 2 0.0592 0.9477 0.000 0.988 0.012
#> SRR1044536 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044537 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044538 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044539 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044540 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044541 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044542 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044543 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044544 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044545 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044546 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044547 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044548 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044549 3 0.1031 0.9032 0.000 0.024 0.976
#> SRR1044550 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044551 3 0.0592 0.9088 0.000 0.012 0.988
#> SRR1044552 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044553 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044554 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044555 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044556 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044557 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044558 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044559 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044561 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044560 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044562 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044563 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044564 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044565 3 0.0592 0.9171 0.012 0.000 0.988
#> SRR1044566 2 0.0000 0.9538 0.000 1.000 0.000
#> SRR1044567 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044568 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044569 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044570 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044571 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044572 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044573 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044574 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044575 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044576 3 0.1411 0.8958 0.000 0.036 0.964
#> SRR1044577 3 0.0000 0.9115 0.000 0.000 1.000
#> SRR1044578 3 0.0592 0.9171 0.012 0.000 0.988
#> SRR1044579 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044580 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044581 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044582 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044583 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044584 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044585 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044586 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044587 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044588 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044589 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044590 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044591 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044592 1 0.8865 -0.0209 0.476 0.120 0.404
#> SRR1044593 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044594 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044595 1 0.4504 0.7586 0.804 0.000 0.196
#> SRR1044596 1 0.0747 0.9693 0.984 0.000 0.016
#> SRR1044597 1 0.3038 0.8789 0.896 0.000 0.104
#> SRR1044598 1 0.0000 0.9833 1.000 0.000 0.000
#> SRR1044599 1 0.0000 0.9833 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044416 2 0.3966 0.8354 0.000 0.840 0.072 0.088
#> SRR1044417 2 0.3400 0.8347 0.000 0.820 0.000 0.180
#> SRR1044418 2 0.0000 0.8858 0.000 1.000 0.000 0.000
#> SRR1044420 3 0.1398 0.8643 0.000 0.040 0.956 0.004
#> SRR1044419 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044421 3 0.3649 0.7797 0.000 0.000 0.796 0.204
#> SRR1044422 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044423 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044424 3 0.4277 0.5565 0.000 0.280 0.720 0.000
#> SRR1044425 1 0.1474 0.7208 0.948 0.000 0.000 0.052
#> SRR1044426 1 0.3528 0.6146 0.808 0.000 0.000 0.192
#> SRR1044427 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044428 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044429 1 0.3610 0.6054 0.800 0.000 0.000 0.200
#> SRR1044430 1 0.0336 0.7420 0.992 0.008 0.000 0.000
#> SRR1044431 1 0.0188 0.7478 0.996 0.000 0.000 0.004
#> SRR1044433 4 0.2995 0.5391 0.016 0.064 0.020 0.900
#> SRR1044432 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044434 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044435 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044436 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044437 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044439 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044438 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044440 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044441 1 0.7319 -0.1667 0.460 0.156 0.000 0.384
#> SRR1044442 4 0.6837 0.5086 0.340 0.116 0.000 0.544
#> SRR1044443 4 0.4332 0.6663 0.072 0.112 0.000 0.816
#> SRR1044444 1 0.4830 0.3836 0.608 0.000 0.000 0.392
#> SRR1044445 4 0.5268 0.0543 0.452 0.008 0.000 0.540
#> SRR1044446 3 0.4866 0.6193 0.000 0.000 0.596 0.404
#> SRR1044447 3 0.4877 0.6151 0.000 0.000 0.592 0.408
#> SRR1044449 3 0.0921 0.8834 0.000 0.000 0.972 0.028
#> SRR1044448 3 0.4730 0.6575 0.000 0.000 0.636 0.364
#> SRR1044450 3 0.4855 0.6233 0.000 0.000 0.600 0.400
#> SRR1044451 3 0.5088 0.5932 0.000 0.004 0.572 0.424
#> SRR1044452 3 0.0188 0.8901 0.000 0.000 0.996 0.004
#> SRR1044453 3 0.0188 0.8901 0.000 0.000 0.996 0.004
#> SRR1044454 3 0.0188 0.8901 0.000 0.000 0.996 0.004
#> SRR1044455 3 0.0188 0.8901 0.000 0.000 0.996 0.004
#> SRR1044456 2 0.4538 0.5063 0.216 0.760 0.000 0.024
#> SRR1044457 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044458 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044459 3 0.0336 0.8895 0.000 0.000 0.992 0.008
#> SRR1044460 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044461 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044462 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044463 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044464 1 0.7098 -0.0343 0.492 0.132 0.000 0.376
#> SRR1044466 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044465 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044467 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044468 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044469 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044470 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044471 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044472 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044473 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044474 2 0.0000 0.8858 0.000 1.000 0.000 0.000
#> SRR1044475 3 0.0188 0.8901 0.000 0.000 0.996 0.004
#> SRR1044476 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044477 2 0.0000 0.8858 0.000 1.000 0.000 0.000
#> SRR1044478 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044479 2 0.1867 0.8252 0.072 0.928 0.000 0.000
#> SRR1044480 1 0.0336 0.7459 0.992 0.000 0.000 0.008
#> SRR1044481 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044482 2 0.0817 0.8768 0.024 0.976 0.000 0.000
#> SRR1044483 1 0.4500 0.4841 0.684 0.000 0.000 0.316
#> SRR1044484 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044486 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044485 2 0.3311 0.7632 0.000 0.828 0.172 0.000
#> SRR1044487 2 0.0000 0.8858 0.000 1.000 0.000 0.000
#> SRR1044488 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044489 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044490 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044491 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044492 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044493 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044494 2 0.0000 0.8858 0.000 1.000 0.000 0.000
#> SRR1044496 2 0.0336 0.8835 0.008 0.992 0.000 0.000
#> SRR1044495 2 0.0000 0.8858 0.000 1.000 0.000 0.000
#> SRR1044497 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044499 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044498 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044500 3 0.3356 0.7238 0.000 0.176 0.824 0.000
#> SRR1044501 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044502 3 0.4907 0.6021 0.000 0.000 0.580 0.420
#> SRR1044503 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044504 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044505 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044506 1 0.4994 0.1527 0.520 0.000 0.000 0.480
#> SRR1044507 4 0.6748 0.5210 0.328 0.112 0.000 0.560
#> SRR1044508 4 0.4843 0.6867 0.104 0.112 0.000 0.784
#> SRR1044509 4 0.4274 0.6663 0.072 0.108 0.000 0.820
#> SRR1044510 3 0.0336 0.8895 0.000 0.000 0.992 0.008
#> SRR1044511 3 0.0921 0.8834 0.000 0.000 0.972 0.028
#> SRR1044512 3 0.0921 0.8834 0.000 0.000 0.972 0.028
#> SRR1044513 3 0.5080 0.5975 0.000 0.004 0.576 0.420
#> SRR1044514 3 0.0921 0.8834 0.000 0.000 0.972 0.028
#> SRR1044515 3 0.5950 0.5505 0.000 0.040 0.544 0.416
#> SRR1044516 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044517 3 0.0336 0.8895 0.000 0.000 0.992 0.008
#> SRR1044518 3 0.0921 0.8834 0.000 0.000 0.972 0.028
#> SRR1044519 3 0.4713 0.6611 0.000 0.000 0.640 0.360
#> SRR1044520 3 0.4431 0.7081 0.000 0.000 0.696 0.304
#> SRR1044521 3 0.4382 0.5252 0.000 0.296 0.704 0.000
#> SRR1044522 2 0.2867 0.7699 0.104 0.884 0.000 0.012
#> SRR1044523 3 0.6998 0.4259 0.000 0.116 0.468 0.416
#> SRR1044524 3 0.2760 0.8309 0.000 0.000 0.872 0.128
#> SRR1044525 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044526 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044527 2 0.2081 0.8731 0.000 0.916 0.000 0.084
#> SRR1044528 2 0.4830 0.6607 0.000 0.608 0.000 0.392
#> SRR1044529 2 0.0921 0.8735 0.028 0.972 0.000 0.000
#> SRR1044530 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044531 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044533 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044532 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044534 3 0.0592 0.8816 0.000 0.016 0.984 0.000
#> SRR1044535 3 0.4730 0.6578 0.000 0.000 0.636 0.364
#> SRR1044536 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044537 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044538 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044539 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044540 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044541 3 0.0188 0.8901 0.000 0.000 0.996 0.004
#> SRR1044542 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044543 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044544 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044545 1 0.4643 0.4502 0.656 0.000 0.000 0.344
#> SRR1044546 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044547 1 0.1867 0.7099 0.928 0.000 0.000 0.072
#> SRR1044548 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044549 2 0.4790 0.6731 0.000 0.620 0.000 0.380
#> SRR1044550 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044551 2 0.3400 0.8346 0.000 0.820 0.000 0.180
#> SRR1044552 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044553 1 0.4898 0.3479 0.584 0.000 0.000 0.416
#> SRR1044554 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044555 3 0.0336 0.8895 0.000 0.000 0.992 0.008
#> SRR1044556 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044557 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044558 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044559 1 0.0188 0.7459 0.996 0.004 0.000 0.000
#> SRR1044561 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044560 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044562 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044563 1 0.4866 0.3732 0.596 0.000 0.000 0.404
#> SRR1044564 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044565 2 0.0000 0.8858 0.000 1.000 0.000 0.000
#> SRR1044566 3 0.0000 0.8904 0.000 0.000 1.000 0.000
#> SRR1044567 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044568 1 0.2814 0.6654 0.868 0.000 0.000 0.132
#> SRR1044569 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044570 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044571 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044572 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044573 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044574 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044575 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044576 2 0.3024 0.8485 0.000 0.852 0.000 0.148
#> SRR1044577 2 0.2704 0.8573 0.000 0.876 0.000 0.124
#> SRR1044578 2 0.0000 0.8858 0.000 1.000 0.000 0.000
#> SRR1044579 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044580 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044581 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044582 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044583 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044584 1 0.4624 0.4512 0.660 0.000 0.000 0.340
#> SRR1044585 1 0.4877 0.3673 0.592 0.000 0.000 0.408
#> SRR1044586 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044587 1 0.4994 0.1527 0.520 0.000 0.000 0.480
#> SRR1044588 1 0.4994 0.1527 0.520 0.000 0.000 0.480
#> SRR1044589 1 0.4994 0.1527 0.520 0.000 0.000 0.480
#> SRR1044590 1 0.4994 0.1527 0.520 0.000 0.000 0.480
#> SRR1044591 1 0.4994 0.1527 0.520 0.000 0.000 0.480
#> SRR1044592 4 0.2773 0.5601 0.004 0.116 0.000 0.880
#> SRR1044593 1 0.4994 0.1527 0.520 0.000 0.000 0.480
#> SRR1044594 1 0.4994 0.1527 0.520 0.000 0.000 0.480
#> SRR1044595 4 0.6317 0.6484 0.240 0.116 0.000 0.644
#> SRR1044596 4 0.6649 0.4897 0.340 0.100 0.000 0.560
#> SRR1044597 1 0.4356 0.4875 0.812 0.124 0.000 0.064
#> SRR1044598 1 0.0000 0.7496 1.000 0.000 0.000 0.000
#> SRR1044599 1 0.0000 0.7496 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.0000 0.819 0.000 1.000 0.000 0.000 0.000
#> SRR1044416 5 0.3765 0.811 0.004 0.064 0.112 0.000 0.820
#> SRR1044417 5 0.3074 0.804 0.000 0.000 0.196 0.000 0.804
#> SRR1044418 5 0.0000 0.883 0.000 0.000 0.000 0.000 1.000
#> SRR1044420 2 0.0854 0.806 0.004 0.976 0.008 0.000 0.012
#> SRR1044419 2 0.0000 0.819 0.000 1.000 0.000 0.000 0.000
#> SRR1044421 2 0.3999 0.248 0.000 0.656 0.344 0.000 0.000
#> SRR1044422 2 0.0162 0.818 0.000 0.996 0.004 0.000 0.000
#> SRR1044423 2 0.0162 0.818 0.000 0.996 0.004 0.000 0.000
#> SRR1044424 2 0.2877 0.626 0.004 0.848 0.004 0.000 0.144
#> SRR1044425 1 0.4201 0.758 0.592 0.000 0.000 0.408 0.000
#> SRR1044426 4 0.4744 -0.405 0.476 0.000 0.016 0.508 0.000
#> SRR1044427 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044428 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044429 4 0.4262 -0.320 0.440 0.000 0.000 0.560 0.000
#> SRR1044430 1 0.4009 0.880 0.684 0.000 0.000 0.312 0.004
#> SRR1044431 1 0.4101 0.831 0.628 0.000 0.000 0.372 0.000
#> SRR1044433 3 0.5338 0.257 0.324 0.000 0.604 0.072 0.000
#> SRR1044432 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044434 4 0.0609 0.895 0.020 0.000 0.000 0.980 0.000
#> SRR1044435 4 0.0609 0.895 0.020 0.000 0.000 0.980 0.000
#> SRR1044436 4 0.0609 0.895 0.020 0.000 0.000 0.980 0.000
#> SRR1044437 4 0.0609 0.895 0.020 0.000 0.000 0.980 0.000
#> SRR1044439 4 0.0609 0.895 0.020 0.000 0.000 0.980 0.000
#> SRR1044438 4 0.0609 0.895 0.020 0.000 0.000 0.980 0.000
#> SRR1044440 4 0.0609 0.895 0.020 0.000 0.000 0.980 0.000
#> SRR1044441 4 0.5778 0.471 0.280 0.000 0.000 0.592 0.128
#> SRR1044442 1 0.6572 -0.317 0.452 0.000 0.328 0.220 0.000
#> SRR1044443 3 0.6683 0.182 0.372 0.000 0.424 0.200 0.004
#> SRR1044444 4 0.2127 0.788 0.108 0.000 0.000 0.892 0.000
#> SRR1044445 4 0.0609 0.859 0.020 0.000 0.000 0.980 0.000
#> SRR1044446 3 0.4045 0.500 0.000 0.356 0.644 0.000 0.000
#> SRR1044447 3 0.3983 0.514 0.000 0.340 0.660 0.000 0.000
#> SRR1044449 2 0.3966 0.494 0.000 0.664 0.336 0.000 0.000
#> SRR1044448 3 0.4161 0.443 0.000 0.392 0.608 0.000 0.000
#> SRR1044450 3 0.4030 0.504 0.000 0.352 0.648 0.000 0.000
#> SRR1044451 3 0.4084 0.520 0.004 0.328 0.668 0.000 0.000
#> SRR1044452 2 0.3561 0.622 0.000 0.740 0.260 0.000 0.000
#> SRR1044453 2 0.3561 0.622 0.000 0.740 0.260 0.000 0.000
#> SRR1044454 2 0.3561 0.622 0.000 0.740 0.260 0.000 0.000
#> SRR1044455 2 0.2929 0.707 0.000 0.820 0.180 0.000 0.000
#> SRR1044456 5 0.3949 0.506 0.000 0.000 0.000 0.332 0.668
#> SRR1044457 2 0.0162 0.819 0.000 0.996 0.004 0.000 0.000
#> SRR1044458 2 0.0162 0.819 0.000 0.996 0.004 0.000 0.000
#> SRR1044459 2 0.3730 0.582 0.000 0.712 0.288 0.000 0.000
#> SRR1044460 2 0.0324 0.817 0.004 0.992 0.004 0.000 0.000
#> SRR1044461 2 0.0162 0.818 0.000 0.996 0.004 0.000 0.000
#> SRR1044462 1 0.3983 0.885 0.660 0.000 0.000 0.340 0.000
#> SRR1044463 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044464 4 0.5778 0.448 0.280 0.000 0.000 0.592 0.128
#> SRR1044466 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044465 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044467 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044468 2 0.0324 0.817 0.004 0.992 0.004 0.000 0.000
#> SRR1044469 2 0.2074 0.765 0.000 0.896 0.104 0.000 0.000
#> SRR1044470 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044471 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044472 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044473 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044474 5 0.0000 0.883 0.000 0.000 0.000 0.000 1.000
#> SRR1044475 2 0.3109 0.687 0.000 0.800 0.200 0.000 0.000
#> SRR1044476 2 0.0162 0.819 0.000 0.996 0.004 0.000 0.000
#> SRR1044477 5 0.0000 0.883 0.000 0.000 0.000 0.000 1.000
#> SRR1044478 2 0.0162 0.818 0.000 0.996 0.004 0.000 0.000
#> SRR1044479 5 0.1197 0.848 0.000 0.000 0.000 0.048 0.952
#> SRR1044480 1 0.3983 0.886 0.660 0.000 0.000 0.340 0.000
#> SRR1044481 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044482 5 0.0162 0.883 0.004 0.000 0.000 0.000 0.996
#> SRR1044483 4 0.3074 0.633 0.196 0.000 0.000 0.804 0.000
#> SRR1044484 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044486 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044485 5 0.3196 0.705 0.004 0.192 0.000 0.000 0.804
#> SRR1044487 5 0.0000 0.883 0.000 0.000 0.000 0.000 1.000
#> SRR1044488 2 0.0324 0.817 0.004 0.992 0.004 0.000 0.000
#> SRR1044489 2 0.0324 0.817 0.004 0.992 0.004 0.000 0.000
#> SRR1044490 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044491 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044492 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044493 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044494 5 0.0000 0.883 0.000 0.000 0.000 0.000 1.000
#> SRR1044496 5 0.0000 0.883 0.000 0.000 0.000 0.000 1.000
#> SRR1044495 5 0.0000 0.883 0.000 0.000 0.000 0.000 1.000
#> SRR1044497 4 0.0794 0.888 0.028 0.000 0.000 0.972 0.000
#> SRR1044499 2 0.0162 0.819 0.000 0.996 0.004 0.000 0.000
#> SRR1044498 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044500 2 0.2339 0.696 0.004 0.892 0.004 0.000 0.100
#> SRR1044501 2 0.0162 0.819 0.000 0.996 0.004 0.000 0.000
#> SRR1044502 3 0.4135 0.514 0.004 0.340 0.656 0.000 0.000
#> SRR1044503 4 0.0609 0.895 0.020 0.000 0.000 0.980 0.000
#> SRR1044504 4 0.0609 0.895 0.020 0.000 0.000 0.980 0.000
#> SRR1044505 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044506 4 0.0000 0.883 0.000 0.000 0.000 1.000 0.000
#> SRR1044507 1 0.6808 -0.316 0.368 0.000 0.324 0.308 0.000
#> SRR1044508 3 0.6771 0.161 0.384 0.000 0.392 0.220 0.004
#> SRR1044509 3 0.6664 0.184 0.372 0.000 0.428 0.196 0.004
#> SRR1044510 2 0.3816 0.556 0.000 0.696 0.304 0.000 0.000
#> SRR1044511 2 0.3966 0.494 0.000 0.664 0.336 0.000 0.000
#> SRR1044512 2 0.3966 0.494 0.000 0.664 0.336 0.000 0.000
#> SRR1044513 3 0.4066 0.519 0.004 0.324 0.672 0.000 0.000
#> SRR1044514 2 0.3966 0.494 0.000 0.664 0.336 0.000 0.000
#> SRR1044515 3 0.5075 0.503 0.004 0.324 0.628 0.000 0.044
#> SRR1044516 2 0.0290 0.819 0.000 0.992 0.008 0.000 0.000
#> SRR1044517 2 0.3796 0.563 0.000 0.700 0.300 0.000 0.000
#> SRR1044518 2 0.3966 0.494 0.000 0.664 0.336 0.000 0.000
#> SRR1044519 3 0.4161 0.443 0.000 0.392 0.608 0.000 0.000
#> SRR1044520 3 0.4171 0.434 0.000 0.396 0.604 0.000 0.000
#> SRR1044521 2 0.2843 0.639 0.000 0.848 0.008 0.000 0.144
#> SRR1044522 5 0.2732 0.727 0.000 0.000 0.000 0.160 0.840
#> SRR1044523 3 0.6059 0.379 0.004 0.364 0.520 0.000 0.112
#> SRR1044524 3 0.4283 0.258 0.000 0.456 0.544 0.000 0.000
#> SRR1044525 4 0.0609 0.895 0.020 0.000 0.000 0.980 0.000
#> SRR1044526 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044527 5 0.1544 0.869 0.000 0.000 0.068 0.000 0.932
#> SRR1044528 5 0.4211 0.643 0.004 0.000 0.360 0.000 0.636
#> SRR1044529 5 0.0404 0.878 0.000 0.000 0.000 0.012 0.988
#> SRR1044530 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044531 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044533 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044532 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044534 2 0.0451 0.813 0.000 0.988 0.004 0.000 0.008
#> SRR1044535 3 0.4138 0.458 0.000 0.384 0.616 0.000 0.000
#> SRR1044536 2 0.0162 0.818 0.000 0.996 0.004 0.000 0.000
#> SRR1044537 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044538 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044539 4 0.0609 0.895 0.020 0.000 0.000 0.980 0.000
#> SRR1044540 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044541 2 0.0880 0.810 0.000 0.968 0.032 0.000 0.000
#> SRR1044542 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044543 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044544 2 0.0510 0.816 0.000 0.984 0.016 0.000 0.000
#> SRR1044545 4 0.1410 0.853 0.060 0.000 0.000 0.940 0.000
#> SRR1044546 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044547 4 0.3774 0.329 0.296 0.000 0.000 0.704 0.000
#> SRR1044548 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044549 5 0.4196 0.641 0.004 0.000 0.356 0.000 0.640
#> SRR1044550 2 0.0324 0.817 0.004 0.992 0.004 0.000 0.000
#> SRR1044551 5 0.3266 0.801 0.004 0.000 0.200 0.000 0.796
#> SRR1044552 4 0.0609 0.895 0.020 0.000 0.000 0.980 0.000
#> SRR1044553 4 0.0290 0.888 0.008 0.000 0.000 0.992 0.000
#> SRR1044554 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044555 2 0.3684 0.595 0.000 0.720 0.280 0.000 0.000
#> SRR1044556 4 0.0609 0.895 0.020 0.000 0.000 0.980 0.000
#> SRR1044557 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044558 4 0.0609 0.895 0.020 0.000 0.000 0.980 0.000
#> SRR1044559 1 0.3949 0.897 0.668 0.000 0.000 0.332 0.000
#> SRR1044561 4 0.0609 0.895 0.020 0.000 0.000 0.980 0.000
#> SRR1044560 2 0.0162 0.819 0.000 0.996 0.004 0.000 0.000
#> SRR1044562 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044563 4 0.0703 0.892 0.024 0.000 0.000 0.976 0.000
#> SRR1044564 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044565 5 0.0000 0.883 0.000 0.000 0.000 0.000 1.000
#> SRR1044566 2 0.0162 0.819 0.000 0.996 0.004 0.000 0.000
#> SRR1044567 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044568 4 0.3395 0.524 0.236 0.000 0.000 0.764 0.000
#> SRR1044569 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044570 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044571 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044572 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044573 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044574 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044575 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044576 5 0.3123 0.811 0.004 0.000 0.184 0.000 0.812
#> SRR1044577 5 0.1792 0.863 0.000 0.000 0.084 0.000 0.916
#> SRR1044578 5 0.0000 0.883 0.000 0.000 0.000 0.000 1.000
#> SRR1044579 4 0.0609 0.895 0.020 0.000 0.000 0.980 0.000
#> SRR1044580 1 0.3949 0.897 0.668 0.000 0.000 0.332 0.000
#> SRR1044581 4 0.0609 0.895 0.020 0.000 0.000 0.980 0.000
#> SRR1044582 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044583 4 0.0609 0.895 0.020 0.000 0.000 0.980 0.000
#> SRR1044584 4 0.3452 0.509 0.244 0.000 0.000 0.756 0.000
#> SRR1044585 4 0.0609 0.895 0.020 0.000 0.000 0.980 0.000
#> SRR1044586 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044587 4 0.0000 0.883 0.000 0.000 0.000 1.000 0.000
#> SRR1044588 4 0.0000 0.883 0.000 0.000 0.000 1.000 0.000
#> SRR1044589 4 0.0000 0.883 0.000 0.000 0.000 1.000 0.000
#> SRR1044590 4 0.0000 0.883 0.000 0.000 0.000 1.000 0.000
#> SRR1044591 4 0.0000 0.883 0.000 0.000 0.000 1.000 0.000
#> SRR1044592 3 0.6587 0.205 0.328 0.000 0.488 0.176 0.008
#> SRR1044593 4 0.0000 0.883 0.000 0.000 0.000 1.000 0.000
#> SRR1044594 4 0.0000 0.883 0.000 0.000 0.000 1.000 0.000
#> SRR1044595 1 0.6468 -0.372 0.456 0.000 0.380 0.160 0.004
#> SRR1044596 1 0.6823 -0.277 0.348 0.000 0.324 0.328 0.000
#> SRR1044597 1 0.1547 0.402 0.948 0.000 0.032 0.016 0.004
#> SRR1044598 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
#> SRR1044599 1 0.3932 0.903 0.672 0.000 0.000 0.328 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.0717 0.922 0.000 0.976 0.016 0.000 0.008 0.000
#> SRR1044416 6 0.3517 0.827 0.000 0.048 0.024 0.104 0.000 0.824
#> SRR1044417 6 0.3558 0.811 0.000 0.000 0.088 0.112 0.000 0.800
#> SRR1044418 6 0.0000 0.875 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044420 2 0.0865 0.908 0.000 0.964 0.000 0.036 0.000 0.000
#> SRR1044419 2 0.0520 0.923 0.000 0.984 0.008 0.000 0.008 0.000
#> SRR1044421 2 0.4766 0.228 0.000 0.552 0.400 0.044 0.004 0.000
#> SRR1044422 2 0.0146 0.924 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1044423 2 0.0146 0.924 0.000 0.996 0.004 0.000 0.000 0.000
#> SRR1044424 2 0.0862 0.912 0.000 0.972 0.004 0.016 0.000 0.008
#> SRR1044425 1 0.2257 0.794 0.876 0.000 0.000 0.116 0.008 0.000
#> SRR1044426 1 0.4577 0.578 0.708 0.000 0.016 0.208 0.068 0.000
#> SRR1044427 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044428 1 0.0458 0.930 0.984 0.000 0.000 0.016 0.000 0.000
#> SRR1044429 1 0.3298 0.534 0.756 0.000 0.000 0.236 0.008 0.000
#> SRR1044430 1 0.1767 0.882 0.932 0.000 0.012 0.036 0.020 0.000
#> SRR1044431 1 0.2062 0.828 0.900 0.000 0.004 0.088 0.008 0.000
#> SRR1044433 5 0.0725 0.932 0.000 0.000 0.012 0.012 0.976 0.000
#> SRR1044432 1 0.1577 0.894 0.940 0.000 0.016 0.036 0.008 0.000
#> SRR1044434 4 0.2996 0.944 0.228 0.000 0.000 0.772 0.000 0.000
#> SRR1044435 4 0.2969 0.942 0.224 0.000 0.000 0.776 0.000 0.000
#> SRR1044436 4 0.3023 0.945 0.232 0.000 0.000 0.768 0.000 0.000
#> SRR1044437 4 0.3050 0.946 0.236 0.000 0.000 0.764 0.000 0.000
#> SRR1044439 4 0.3050 0.946 0.236 0.000 0.000 0.764 0.000 0.000
#> SRR1044438 4 0.3023 0.945 0.232 0.000 0.000 0.768 0.000 0.000
#> SRR1044440 4 0.3050 0.946 0.236 0.000 0.000 0.764 0.000 0.000
#> SRR1044441 4 0.5944 0.227 0.424 0.000 0.000 0.424 0.016 0.136
#> SRR1044442 5 0.1780 0.916 0.048 0.000 0.000 0.028 0.924 0.000
#> SRR1044443 5 0.0632 0.941 0.000 0.000 0.000 0.024 0.976 0.000
#> SRR1044444 4 0.3737 0.715 0.392 0.000 0.000 0.608 0.000 0.000
#> SRR1044445 4 0.3133 0.932 0.212 0.000 0.000 0.780 0.008 0.000
#> SRR1044446 3 0.1408 0.772 0.000 0.020 0.944 0.036 0.000 0.000
#> SRR1044447 3 0.1926 0.759 0.000 0.020 0.912 0.068 0.000 0.000
#> SRR1044449 3 0.2854 0.801 0.000 0.208 0.792 0.000 0.000 0.000
#> SRR1044448 3 0.0632 0.784 0.000 0.024 0.976 0.000 0.000 0.000
#> SRR1044450 3 0.1088 0.781 0.000 0.024 0.960 0.016 0.000 0.000
#> SRR1044451 3 0.3414 0.695 0.000 0.016 0.820 0.128 0.036 0.000
#> SRR1044452 3 0.3271 0.785 0.000 0.232 0.760 0.000 0.008 0.000
#> SRR1044453 3 0.3271 0.785 0.000 0.232 0.760 0.000 0.008 0.000
#> SRR1044454 3 0.3349 0.774 0.000 0.244 0.748 0.000 0.008 0.000
#> SRR1044455 3 0.4018 0.493 0.000 0.412 0.580 0.000 0.008 0.000
#> SRR1044456 6 0.4673 0.451 0.080 0.000 0.000 0.272 0.000 0.648
#> SRR1044457 2 0.1049 0.917 0.000 0.960 0.032 0.000 0.008 0.000
#> SRR1044458 2 0.0972 0.918 0.000 0.964 0.028 0.000 0.008 0.000
#> SRR1044459 3 0.3298 0.782 0.000 0.236 0.756 0.000 0.008 0.000
#> SRR1044460 2 0.0363 0.923 0.000 0.988 0.000 0.012 0.000 0.000
#> SRR1044461 2 0.0000 0.924 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044462 1 0.0603 0.925 0.980 0.000 0.000 0.016 0.004 0.000
#> SRR1044463 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044464 1 0.5797 -0.166 0.444 0.000 0.012 0.432 0.004 0.108
#> SRR1044466 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044465 1 0.0291 0.933 0.992 0.000 0.004 0.000 0.004 0.000
#> SRR1044467 1 0.0405 0.932 0.988 0.000 0.004 0.000 0.008 0.000
#> SRR1044468 2 0.0363 0.923 0.000 0.988 0.000 0.012 0.000 0.000
#> SRR1044469 2 0.3595 0.511 0.000 0.704 0.288 0.000 0.008 0.000
#> SRR1044470 1 0.0146 0.934 0.996 0.000 0.004 0.000 0.000 0.000
#> SRR1044471 1 0.0405 0.932 0.988 0.000 0.004 0.000 0.008 0.000
#> SRR1044472 1 0.0146 0.934 0.996 0.000 0.004 0.000 0.000 0.000
#> SRR1044473 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044474 6 0.0000 0.875 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044475 3 0.3861 0.609 0.000 0.352 0.640 0.000 0.008 0.000
#> SRR1044476 2 0.0972 0.918 0.000 0.964 0.028 0.000 0.008 0.000
#> SRR1044477 6 0.0000 0.875 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044478 2 0.0363 0.923 0.000 0.988 0.000 0.012 0.000 0.000
#> SRR1044479 6 0.0777 0.865 0.004 0.000 0.000 0.024 0.000 0.972
#> SRR1044480 1 0.1082 0.901 0.956 0.000 0.000 0.040 0.004 0.000
#> SRR1044481 1 0.0260 0.932 0.992 0.000 0.000 0.008 0.000 0.000
#> SRR1044482 6 0.0790 0.870 0.000 0.000 0.000 0.032 0.000 0.968
#> SRR1044483 4 0.3999 0.454 0.496 0.000 0.000 0.500 0.004 0.000
#> SRR1044484 1 0.0146 0.934 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1044486 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044485 6 0.3848 0.678 0.000 0.224 0.000 0.040 0.000 0.736
#> SRR1044487 6 0.0000 0.875 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044488 2 0.0260 0.924 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1044489 2 0.0363 0.923 0.000 0.988 0.000 0.012 0.000 0.000
#> SRR1044490 1 0.0520 0.931 0.984 0.000 0.008 0.000 0.008 0.000
#> SRR1044491 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044492 1 0.0146 0.934 0.996 0.000 0.004 0.000 0.000 0.000
#> SRR1044493 1 0.0146 0.934 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1044494 6 0.0000 0.875 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044496 6 0.0146 0.874 0.000 0.000 0.000 0.004 0.000 0.996
#> SRR1044495 6 0.0000 0.875 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044497 4 0.3390 0.877 0.296 0.000 0.000 0.704 0.000 0.000
#> SRR1044499 2 0.1524 0.896 0.000 0.932 0.060 0.000 0.008 0.000
#> SRR1044498 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044500 2 0.1390 0.893 0.000 0.948 0.004 0.032 0.000 0.016
#> SRR1044501 2 0.0972 0.918 0.000 0.964 0.028 0.000 0.008 0.000
#> SRR1044502 3 0.3730 0.690 0.000 0.036 0.804 0.128 0.032 0.000
#> SRR1044503 4 0.3050 0.946 0.236 0.000 0.000 0.764 0.000 0.000
#> SRR1044504 4 0.3023 0.945 0.232 0.000 0.000 0.768 0.000 0.000
#> SRR1044505 1 0.0146 0.934 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1044506 4 0.3052 0.937 0.216 0.000 0.000 0.780 0.004 0.000
#> SRR1044507 5 0.2448 0.892 0.052 0.000 0.000 0.064 0.884 0.000
#> SRR1044508 5 0.0713 0.943 0.000 0.000 0.000 0.028 0.972 0.000
#> SRR1044509 5 0.0713 0.943 0.000 0.000 0.000 0.028 0.972 0.000
#> SRR1044510 3 0.3163 0.786 0.000 0.232 0.764 0.000 0.004 0.000
#> SRR1044511 3 0.2854 0.801 0.000 0.208 0.792 0.000 0.000 0.000
#> SRR1044512 3 0.2854 0.801 0.000 0.208 0.792 0.000 0.000 0.000
#> SRR1044513 3 0.3509 0.697 0.000 0.024 0.816 0.128 0.032 0.000
#> SRR1044514 3 0.2854 0.801 0.000 0.208 0.792 0.000 0.000 0.000
#> SRR1044515 3 0.4682 0.647 0.000 0.044 0.760 0.128 0.032 0.036
#> SRR1044516 2 0.2378 0.796 0.000 0.848 0.152 0.000 0.000 0.000
#> SRR1044517 3 0.3271 0.785 0.000 0.232 0.760 0.000 0.008 0.000
#> SRR1044518 3 0.2823 0.801 0.000 0.204 0.796 0.000 0.000 0.000
#> SRR1044519 3 0.0632 0.784 0.000 0.024 0.976 0.000 0.000 0.000
#> SRR1044520 3 0.0790 0.787 0.000 0.032 0.968 0.000 0.000 0.000
#> SRR1044521 2 0.2527 0.847 0.000 0.876 0.084 0.000 0.000 0.040
#> SRR1044522 6 0.2618 0.786 0.052 0.000 0.000 0.076 0.000 0.872
#> SRR1044523 3 0.6337 0.510 0.000 0.156 0.620 0.128 0.032 0.064
#> SRR1044524 3 0.1477 0.793 0.000 0.048 0.940 0.008 0.004 0.000
#> SRR1044525 4 0.3050 0.946 0.236 0.000 0.000 0.764 0.000 0.000
#> SRR1044526 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044527 6 0.2436 0.848 0.000 0.000 0.032 0.088 0.000 0.880
#> SRR1044528 6 0.6067 0.634 0.000 0.020 0.216 0.128 0.032 0.604
#> SRR1044529 6 0.0146 0.874 0.000 0.000 0.000 0.004 0.000 0.996
#> SRR1044530 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044531 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044533 1 0.0405 0.929 0.988 0.000 0.004 0.008 0.000 0.000
#> SRR1044532 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044534 2 0.0363 0.923 0.000 0.988 0.000 0.012 0.000 0.000
#> SRR1044535 3 0.1549 0.769 0.000 0.020 0.936 0.044 0.000 0.000
#> SRR1044536 2 0.0146 0.924 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1044537 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044538 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044539 4 0.3050 0.946 0.236 0.000 0.000 0.764 0.000 0.000
#> SRR1044540 1 0.0551 0.931 0.984 0.000 0.004 0.004 0.008 0.000
#> SRR1044541 2 0.2882 0.749 0.000 0.812 0.180 0.000 0.008 0.000
#> SRR1044542 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044543 1 0.0881 0.925 0.972 0.000 0.008 0.012 0.008 0.000
#> SRR1044544 2 0.1970 0.868 0.000 0.900 0.092 0.000 0.008 0.000
#> SRR1044545 4 0.3198 0.924 0.260 0.000 0.000 0.740 0.000 0.000
#> SRR1044546 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044547 1 0.3868 -0.447 0.508 0.000 0.000 0.492 0.000 0.000
#> SRR1044548 1 0.0146 0.934 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1044549 6 0.5541 0.671 0.000 0.004 0.200 0.128 0.028 0.640
#> SRR1044550 2 0.0363 0.923 0.000 0.988 0.000 0.012 0.000 0.000
#> SRR1044551 6 0.4890 0.770 0.000 0.028 0.076 0.160 0.012 0.724
#> SRR1044552 4 0.3023 0.945 0.232 0.000 0.000 0.768 0.000 0.000
#> SRR1044553 4 0.2941 0.939 0.220 0.000 0.000 0.780 0.000 0.000
#> SRR1044554 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044555 3 0.3298 0.782 0.000 0.236 0.756 0.000 0.008 0.000
#> SRR1044556 4 0.3050 0.946 0.236 0.000 0.000 0.764 0.000 0.000
#> SRR1044557 1 0.0146 0.934 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1044558 4 0.3050 0.946 0.236 0.000 0.000 0.764 0.000 0.000
#> SRR1044559 1 0.0363 0.930 0.988 0.000 0.000 0.012 0.000 0.000
#> SRR1044561 4 0.3050 0.946 0.236 0.000 0.000 0.764 0.000 0.000
#> SRR1044560 2 0.0972 0.918 0.000 0.964 0.028 0.000 0.008 0.000
#> SRR1044562 1 0.0363 0.930 0.988 0.000 0.000 0.012 0.000 0.000
#> SRR1044563 4 0.3050 0.946 0.236 0.000 0.000 0.764 0.000 0.000
#> SRR1044564 1 0.0363 0.930 0.988 0.000 0.000 0.012 0.000 0.000
#> SRR1044565 6 0.0000 0.875 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044566 2 0.0972 0.918 0.000 0.964 0.028 0.000 0.008 0.000
#> SRR1044567 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044568 4 0.3828 0.623 0.440 0.000 0.000 0.560 0.000 0.000
#> SRR1044569 1 0.0405 0.932 0.988 0.000 0.004 0.000 0.008 0.000
#> SRR1044570 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044571 1 0.0405 0.932 0.988 0.000 0.004 0.000 0.008 0.000
#> SRR1044572 1 0.0405 0.932 0.988 0.000 0.004 0.000 0.008 0.000
#> SRR1044573 1 0.0291 0.934 0.992 0.000 0.000 0.004 0.004 0.000
#> SRR1044574 1 0.0862 0.924 0.972 0.000 0.004 0.016 0.008 0.000
#> SRR1044575 1 0.0767 0.927 0.976 0.000 0.004 0.012 0.008 0.000
#> SRR1044576 6 0.4018 0.809 0.000 0.024 0.056 0.140 0.000 0.780
#> SRR1044577 6 0.2858 0.837 0.000 0.000 0.032 0.124 0.000 0.844
#> SRR1044578 6 0.0000 0.875 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1044579 4 0.3023 0.945 0.232 0.000 0.000 0.768 0.000 0.000
#> SRR1044580 1 0.0551 0.931 0.984 0.000 0.004 0.004 0.008 0.000
#> SRR1044581 4 0.3050 0.946 0.236 0.000 0.000 0.764 0.000 0.000
#> SRR1044582 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044583 4 0.3050 0.946 0.236 0.000 0.000 0.764 0.000 0.000
#> SRR1044584 1 0.3966 -0.277 0.552 0.000 0.000 0.444 0.004 0.000
#> SRR1044585 4 0.3050 0.946 0.236 0.000 0.000 0.764 0.000 0.000
#> SRR1044586 1 0.0000 0.935 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044587 4 0.3052 0.937 0.216 0.000 0.000 0.780 0.004 0.000
#> SRR1044588 4 0.3052 0.937 0.216 0.000 0.000 0.780 0.004 0.000
#> SRR1044589 4 0.3052 0.937 0.216 0.000 0.000 0.780 0.004 0.000
#> SRR1044590 4 0.3052 0.937 0.216 0.000 0.000 0.780 0.004 0.000
#> SRR1044591 4 0.3052 0.937 0.216 0.000 0.000 0.780 0.004 0.000
#> SRR1044592 5 0.0713 0.943 0.000 0.000 0.000 0.028 0.972 0.000
#> SRR1044593 4 0.3052 0.937 0.216 0.000 0.000 0.780 0.004 0.000
#> SRR1044594 4 0.3052 0.937 0.216 0.000 0.000 0.780 0.004 0.000
#> SRR1044595 5 0.0806 0.930 0.020 0.000 0.000 0.008 0.972 0.000
#> SRR1044596 5 0.3055 0.828 0.096 0.000 0.000 0.064 0.840 0.000
#> SRR1044597 1 0.4002 0.208 0.588 0.000 0.000 0.008 0.404 0.000
#> SRR1044598 1 0.0146 0.934 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1044599 1 0.0146 0.934 0.996 0.000 0.000 0.004 0.000 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)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.910 0.925 0.969 0.4475 0.559 0.559
#> 3 3 0.873 0.916 0.963 0.2371 0.770 0.628
#> 4 4 0.924 0.924 0.967 0.1048 0.938 0.863
#> 5 5 0.725 0.604 0.832 0.1325 0.892 0.725
#> 6 6 0.710 0.755 0.825 0.0395 0.909 0.704
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0.0000 0.9702 0.000 1.000
#> SRR1044416 2 0.8608 0.5983 0.284 0.716
#> SRR1044417 1 0.9427 0.4587 0.640 0.360
#> SRR1044418 1 0.5737 0.8336 0.864 0.136
#> SRR1044420 2 0.0000 0.9702 0.000 1.000
#> SRR1044419 2 0.0000 0.9702 0.000 1.000
#> SRR1044421 2 0.0000 0.9702 0.000 1.000
#> SRR1044422 2 0.0000 0.9702 0.000 1.000
#> SRR1044423 2 0.0000 0.9702 0.000 1.000
#> SRR1044424 2 0.0376 0.9675 0.004 0.996
#> SRR1044425 1 0.0000 0.9653 1.000 0.000
#> SRR1044426 1 0.0000 0.9653 1.000 0.000
#> SRR1044427 1 0.0000 0.9653 1.000 0.000
#> SRR1044428 1 0.0000 0.9653 1.000 0.000
#> SRR1044429 1 0.0000 0.9653 1.000 0.000
#> SRR1044430 1 0.0000 0.9653 1.000 0.000
#> SRR1044431 1 0.0000 0.9653 1.000 0.000
#> SRR1044433 1 0.4562 0.8773 0.904 0.096
#> SRR1044432 1 0.0000 0.9653 1.000 0.000
#> SRR1044434 1 0.0000 0.9653 1.000 0.000
#> SRR1044435 1 0.0000 0.9653 1.000 0.000
#> SRR1044436 1 0.0000 0.9653 1.000 0.000
#> SRR1044437 1 0.0000 0.9653 1.000 0.000
#> SRR1044439 1 0.0000 0.9653 1.000 0.000
#> SRR1044438 1 0.0000 0.9653 1.000 0.000
#> SRR1044440 1 0.0000 0.9653 1.000 0.000
#> SRR1044441 1 0.0000 0.9653 1.000 0.000
#> SRR1044442 1 0.0000 0.9653 1.000 0.000
#> SRR1044443 1 0.0672 0.9592 0.992 0.008
#> SRR1044444 1 0.0000 0.9653 1.000 0.000
#> SRR1044445 1 0.0000 0.9653 1.000 0.000
#> SRR1044446 2 0.0000 0.9702 0.000 1.000
#> SRR1044447 2 0.0000 0.9702 0.000 1.000
#> SRR1044449 2 0.0000 0.9702 0.000 1.000
#> SRR1044448 2 0.0000 0.9702 0.000 1.000
#> SRR1044450 2 0.0000 0.9702 0.000 1.000
#> SRR1044451 2 0.2948 0.9243 0.052 0.948
#> SRR1044452 2 0.0000 0.9702 0.000 1.000
#> SRR1044453 2 0.0000 0.9702 0.000 1.000
#> SRR1044454 2 0.0000 0.9702 0.000 1.000
#> SRR1044455 2 0.0000 0.9702 0.000 1.000
#> SRR1044456 1 0.0000 0.9653 1.000 0.000
#> SRR1044457 2 0.0000 0.9702 0.000 1.000
#> SRR1044458 2 0.0000 0.9702 0.000 1.000
#> SRR1044459 2 0.0000 0.9702 0.000 1.000
#> SRR1044460 2 0.0000 0.9702 0.000 1.000
#> SRR1044461 2 0.0000 0.9702 0.000 1.000
#> SRR1044462 1 0.0000 0.9653 1.000 0.000
#> SRR1044463 1 0.0000 0.9653 1.000 0.000
#> SRR1044464 1 0.0000 0.9653 1.000 0.000
#> SRR1044466 1 0.0000 0.9653 1.000 0.000
#> SRR1044465 1 0.0000 0.9653 1.000 0.000
#> SRR1044467 1 0.0000 0.9653 1.000 0.000
#> SRR1044468 2 0.0000 0.9702 0.000 1.000
#> SRR1044469 2 0.0000 0.9702 0.000 1.000
#> SRR1044470 1 0.0000 0.9653 1.000 0.000
#> SRR1044471 1 0.0000 0.9653 1.000 0.000
#> SRR1044472 1 0.0000 0.9653 1.000 0.000
#> SRR1044473 1 0.0000 0.9653 1.000 0.000
#> SRR1044474 1 0.8555 0.6207 0.720 0.280
#> SRR1044475 2 0.0000 0.9702 0.000 1.000
#> SRR1044476 2 0.0000 0.9702 0.000 1.000
#> SRR1044477 1 0.2948 0.9217 0.948 0.052
#> SRR1044478 2 0.0000 0.9702 0.000 1.000
#> SRR1044479 1 0.0000 0.9653 1.000 0.000
#> SRR1044480 1 0.0000 0.9653 1.000 0.000
#> SRR1044481 1 0.0000 0.9653 1.000 0.000
#> SRR1044482 1 0.9460 0.4491 0.636 0.364
#> SRR1044483 1 0.0000 0.9653 1.000 0.000
#> SRR1044484 1 0.0000 0.9653 1.000 0.000
#> SRR1044486 1 0.0000 0.9653 1.000 0.000
#> SRR1044485 2 0.7139 0.7503 0.196 0.804
#> SRR1044487 1 0.6048 0.8180 0.852 0.148
#> SRR1044488 2 0.0000 0.9702 0.000 1.000
#> SRR1044489 2 0.0000 0.9702 0.000 1.000
#> SRR1044490 1 0.0000 0.9653 1.000 0.000
#> SRR1044491 1 0.0000 0.9653 1.000 0.000
#> SRR1044492 1 0.0000 0.9653 1.000 0.000
#> SRR1044493 1 0.0000 0.9653 1.000 0.000
#> SRR1044494 1 0.3584 0.9064 0.932 0.068
#> SRR1044496 1 0.2603 0.9286 0.956 0.044
#> SRR1044495 1 0.3274 0.9141 0.940 0.060
#> SRR1044497 1 0.0000 0.9653 1.000 0.000
#> SRR1044499 2 0.0000 0.9702 0.000 1.000
#> SRR1044498 1 0.0000 0.9653 1.000 0.000
#> SRR1044500 2 0.0672 0.9645 0.008 0.992
#> SRR1044501 2 0.0000 0.9702 0.000 1.000
#> SRR1044502 2 0.0376 0.9675 0.004 0.996
#> SRR1044503 1 0.0000 0.9653 1.000 0.000
#> SRR1044504 1 0.0000 0.9653 1.000 0.000
#> SRR1044505 1 0.0000 0.9653 1.000 0.000
#> SRR1044506 1 0.0000 0.9653 1.000 0.000
#> SRR1044507 1 0.0000 0.9653 1.000 0.000
#> SRR1044508 1 0.0376 0.9622 0.996 0.004
#> SRR1044509 1 0.1184 0.9527 0.984 0.016
#> SRR1044510 2 0.0000 0.9702 0.000 1.000
#> SRR1044511 2 0.0000 0.9702 0.000 1.000
#> SRR1044512 2 0.0000 0.9702 0.000 1.000
#> SRR1044513 2 0.5842 0.8264 0.140 0.860
#> SRR1044514 2 0.0000 0.9702 0.000 1.000
#> SRR1044515 2 0.0376 0.9675 0.004 0.996
#> SRR1044516 2 0.0000 0.9702 0.000 1.000
#> SRR1044517 2 0.0000 0.9702 0.000 1.000
#> SRR1044518 2 0.0000 0.9702 0.000 1.000
#> SRR1044519 2 0.0000 0.9702 0.000 1.000
#> SRR1044520 2 0.0000 0.9702 0.000 1.000
#> SRR1044521 2 0.6973 0.7621 0.188 0.812
#> SRR1044522 1 0.0000 0.9653 1.000 0.000
#> SRR1044523 2 0.0672 0.9644 0.008 0.992
#> SRR1044524 2 0.0000 0.9702 0.000 1.000
#> SRR1044525 1 0.0000 0.9653 1.000 0.000
#> SRR1044526 1 0.0000 0.9653 1.000 0.000
#> SRR1044527 1 0.9393 0.4678 0.644 0.356
#> SRR1044528 1 0.9635 0.3892 0.612 0.388
#> SRR1044529 1 0.6887 0.7708 0.816 0.184
#> SRR1044530 1 0.0000 0.9653 1.000 0.000
#> SRR1044531 1 0.0000 0.9653 1.000 0.000
#> SRR1044533 1 0.0000 0.9653 1.000 0.000
#> SRR1044532 1 0.0000 0.9653 1.000 0.000
#> SRR1044534 2 0.0672 0.9645 0.008 0.992
#> SRR1044535 2 0.0000 0.9702 0.000 1.000
#> SRR1044536 2 0.0000 0.9702 0.000 1.000
#> SRR1044537 1 0.0000 0.9653 1.000 0.000
#> SRR1044538 1 0.0000 0.9653 1.000 0.000
#> SRR1044539 1 0.0000 0.9653 1.000 0.000
#> SRR1044540 1 0.0000 0.9653 1.000 0.000
#> SRR1044541 2 0.0000 0.9702 0.000 1.000
#> SRR1044542 1 0.0000 0.9653 1.000 0.000
#> SRR1044543 1 0.0000 0.9653 1.000 0.000
#> SRR1044544 2 0.0000 0.9702 0.000 1.000
#> SRR1044545 1 0.0000 0.9653 1.000 0.000
#> SRR1044546 1 0.0000 0.9653 1.000 0.000
#> SRR1044547 1 0.0000 0.9653 1.000 0.000
#> SRR1044548 1 0.0000 0.9653 1.000 0.000
#> SRR1044549 2 0.9815 0.2543 0.420 0.580
#> SRR1044550 2 0.0000 0.9702 0.000 1.000
#> SRR1044551 1 0.9815 0.3007 0.580 0.420
#> SRR1044552 1 0.0000 0.9653 1.000 0.000
#> SRR1044553 1 0.0000 0.9653 1.000 0.000
#> SRR1044554 1 0.0000 0.9653 1.000 0.000
#> SRR1044555 2 0.0000 0.9702 0.000 1.000
#> SRR1044556 1 0.0000 0.9653 1.000 0.000
#> SRR1044557 1 0.0000 0.9653 1.000 0.000
#> SRR1044558 1 0.0000 0.9653 1.000 0.000
#> SRR1044559 1 0.0000 0.9653 1.000 0.000
#> SRR1044561 1 0.0000 0.9653 1.000 0.000
#> SRR1044560 2 0.0000 0.9702 0.000 1.000
#> SRR1044562 1 0.0000 0.9653 1.000 0.000
#> SRR1044563 1 0.0000 0.9653 1.000 0.000
#> SRR1044564 1 0.0000 0.9653 1.000 0.000
#> SRR1044565 1 0.6887 0.7728 0.816 0.184
#> SRR1044566 2 0.0000 0.9702 0.000 1.000
#> SRR1044567 1 0.0000 0.9653 1.000 0.000
#> SRR1044568 1 0.0000 0.9653 1.000 0.000
#> SRR1044569 1 0.0000 0.9653 1.000 0.000
#> SRR1044570 1 0.0000 0.9653 1.000 0.000
#> SRR1044571 1 0.0000 0.9653 1.000 0.000
#> SRR1044572 1 0.0000 0.9653 1.000 0.000
#> SRR1044573 1 0.0000 0.9653 1.000 0.000
#> SRR1044574 1 0.0000 0.9653 1.000 0.000
#> SRR1044575 1 0.0000 0.9653 1.000 0.000
#> SRR1044576 2 0.9170 0.4957 0.332 0.668
#> SRR1044577 1 0.9993 0.0845 0.516 0.484
#> SRR1044578 1 0.9393 0.4678 0.644 0.356
#> SRR1044579 1 0.0000 0.9653 1.000 0.000
#> SRR1044580 1 0.0000 0.9653 1.000 0.000
#> SRR1044581 1 0.0000 0.9653 1.000 0.000
#> SRR1044582 1 0.0000 0.9653 1.000 0.000
#> SRR1044583 1 0.0000 0.9653 1.000 0.000
#> SRR1044584 1 0.0000 0.9653 1.000 0.000
#> SRR1044585 1 0.0000 0.9653 1.000 0.000
#> SRR1044586 1 0.0000 0.9653 1.000 0.000
#> SRR1044587 1 0.0000 0.9653 1.000 0.000
#> SRR1044588 1 0.0000 0.9653 1.000 0.000
#> SRR1044589 1 0.0000 0.9653 1.000 0.000
#> SRR1044590 1 0.0000 0.9653 1.000 0.000
#> SRR1044591 1 0.0000 0.9653 1.000 0.000
#> SRR1044592 1 0.4431 0.8818 0.908 0.092
#> SRR1044593 1 0.0000 0.9653 1.000 0.000
#> SRR1044594 1 0.0000 0.9653 1.000 0.000
#> SRR1044595 1 0.0376 0.9622 0.996 0.004
#> SRR1044596 1 0.0000 0.9653 1.000 0.000
#> SRR1044597 1 0.0000 0.9653 1.000 0.000
#> SRR1044598 1 0.0000 0.9653 1.000 0.000
#> SRR1044599 1 0.0000 0.9653 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.1643 0.868 0.000 0.956 0.044
#> SRR1044416 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044417 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044418 2 0.4062 0.745 0.164 0.836 0.000
#> SRR1044420 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044419 2 0.1643 0.868 0.000 0.956 0.044
#> SRR1044421 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044422 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044423 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044424 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044425 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044426 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044427 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044428 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044429 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044430 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044431 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044433 2 0.4291 0.724 0.180 0.820 0.000
#> SRR1044432 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044434 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044435 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044436 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044437 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044439 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044438 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044440 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044441 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044442 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044443 2 0.4555 0.703 0.200 0.800 0.000
#> SRR1044444 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044445 1 0.1411 0.949 0.964 0.036 0.000
#> SRR1044446 2 0.1643 0.868 0.000 0.956 0.044
#> SRR1044447 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044449 3 0.0000 0.988 0.000 0.000 1.000
#> SRR1044448 2 0.5291 0.649 0.000 0.732 0.268
#> SRR1044450 2 0.1753 0.866 0.000 0.952 0.048
#> SRR1044451 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044452 3 0.0000 0.988 0.000 0.000 1.000
#> SRR1044453 3 0.0000 0.988 0.000 0.000 1.000
#> SRR1044454 3 0.0000 0.988 0.000 0.000 1.000
#> SRR1044455 2 0.1643 0.868 0.000 0.956 0.044
#> SRR1044456 1 0.6079 0.319 0.612 0.388 0.000
#> SRR1044457 2 0.1643 0.868 0.000 0.956 0.044
#> SRR1044458 2 0.4555 0.735 0.000 0.800 0.200
#> SRR1044459 2 0.6192 0.390 0.000 0.580 0.420
#> SRR1044460 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044461 2 0.1643 0.868 0.000 0.956 0.044
#> SRR1044462 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044463 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044464 1 0.0237 0.988 0.996 0.004 0.000
#> SRR1044466 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044465 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044467 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044468 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044469 3 0.0000 0.988 0.000 0.000 1.000
#> SRR1044470 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044471 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044472 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044473 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044474 2 0.2625 0.825 0.084 0.916 0.000
#> SRR1044475 3 0.0000 0.988 0.000 0.000 1.000
#> SRR1044476 2 0.5560 0.601 0.000 0.700 0.300
#> SRR1044477 2 0.4399 0.717 0.188 0.812 0.000
#> SRR1044478 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044479 2 0.4702 0.685 0.212 0.788 0.000
#> SRR1044480 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044481 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044482 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044483 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044484 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044486 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044485 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044487 2 0.4555 0.702 0.200 0.800 0.000
#> SRR1044488 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044489 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044490 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044491 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044492 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044493 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044494 2 0.4235 0.731 0.176 0.824 0.000
#> SRR1044496 2 0.4605 0.696 0.204 0.796 0.000
#> SRR1044495 2 0.4346 0.722 0.184 0.816 0.000
#> SRR1044497 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044499 3 0.0000 0.988 0.000 0.000 1.000
#> SRR1044498 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044500 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044501 2 0.1643 0.868 0.000 0.956 0.044
#> SRR1044502 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044503 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044504 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044505 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044506 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044507 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044508 1 0.5058 0.640 0.756 0.244 0.000
#> SRR1044509 2 0.6062 0.425 0.384 0.616 0.000
#> SRR1044510 3 0.0000 0.988 0.000 0.000 1.000
#> SRR1044511 3 0.0592 0.977 0.000 0.012 0.988
#> SRR1044512 3 0.0000 0.988 0.000 0.000 1.000
#> SRR1044513 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044514 3 0.0000 0.988 0.000 0.000 1.000
#> SRR1044515 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044516 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044517 3 0.0000 0.988 0.000 0.000 1.000
#> SRR1044518 3 0.0000 0.988 0.000 0.000 1.000
#> SRR1044519 2 0.5529 0.607 0.000 0.704 0.296
#> SRR1044520 3 0.3551 0.842 0.000 0.132 0.868
#> SRR1044521 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044522 2 0.5465 0.565 0.288 0.712 0.000
#> SRR1044523 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044524 2 0.1643 0.868 0.000 0.956 0.044
#> SRR1044525 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044526 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044527 2 0.0892 0.873 0.020 0.980 0.000
#> SRR1044528 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044529 2 0.4555 0.702 0.200 0.800 0.000
#> SRR1044530 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044531 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044533 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044532 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044534 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044535 2 0.1643 0.868 0.000 0.956 0.044
#> SRR1044536 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044537 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044538 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044539 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044540 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044541 2 0.1643 0.868 0.000 0.956 0.044
#> SRR1044542 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044543 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044544 2 0.5560 0.601 0.000 0.700 0.300
#> SRR1044545 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044546 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044547 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044548 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044549 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044550 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044551 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044552 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044553 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044554 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044555 2 0.5591 0.594 0.000 0.696 0.304
#> SRR1044556 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044557 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044558 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044559 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044561 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044560 2 0.5560 0.601 0.000 0.700 0.300
#> SRR1044562 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044563 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044564 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044565 2 0.2448 0.832 0.076 0.924 0.000
#> SRR1044566 2 0.5178 0.666 0.000 0.744 0.256
#> SRR1044567 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044568 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044569 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044570 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044571 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044572 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044573 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044574 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044575 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044576 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044577 2 0.0000 0.883 0.000 1.000 0.000
#> SRR1044578 2 0.0747 0.875 0.016 0.984 0.000
#> SRR1044579 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044580 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044581 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044582 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044583 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044584 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044585 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044586 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044587 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044588 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044589 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044590 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044591 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044592 2 0.4002 0.753 0.160 0.840 0.000
#> SRR1044593 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044594 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044595 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044596 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044597 1 0.0237 0.988 0.996 0.004 0.000
#> SRR1044598 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1044599 1 0.0000 0.992 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 4 0.0336 0.949 0.000 0.008 0.000 0.992
#> SRR1044416 2 0.0000 0.939 0.000 1.000 0.000 0.000
#> SRR1044417 2 0.0000 0.939 0.000 1.000 0.000 0.000
#> SRR1044418 2 0.0000 0.939 0.000 1.000 0.000 0.000
#> SRR1044420 2 0.0592 0.936 0.000 0.984 0.000 0.016
#> SRR1044419 4 0.0336 0.949 0.000 0.008 0.000 0.992
#> SRR1044421 2 0.0707 0.934 0.000 0.980 0.000 0.020
#> SRR1044422 2 0.4877 0.350 0.000 0.592 0.000 0.408
#> SRR1044423 2 0.3907 0.714 0.000 0.768 0.000 0.232
#> SRR1044424 2 0.0469 0.938 0.000 0.988 0.000 0.012
#> SRR1044425 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044426 1 0.1635 0.938 0.948 0.044 0.008 0.000
#> SRR1044427 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044428 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044429 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044430 1 0.0336 0.972 0.992 0.008 0.000 0.000
#> SRR1044431 1 0.0188 0.977 0.996 0.000 0.004 0.000
#> SRR1044433 2 0.3142 0.756 0.132 0.860 0.008 0.000
#> SRR1044432 1 0.0188 0.975 0.996 0.004 0.000 0.000
#> SRR1044434 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044435 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044436 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044437 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044439 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044438 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044440 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044441 1 0.2480 0.889 0.904 0.088 0.008 0.000
#> SRR1044442 1 0.3142 0.836 0.860 0.132 0.008 0.000
#> SRR1044443 2 0.0927 0.920 0.016 0.976 0.008 0.000
#> SRR1044444 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044445 1 0.1452 0.943 0.956 0.036 0.008 0.000
#> SRR1044446 4 0.2408 0.839 0.000 0.104 0.000 0.896
#> SRR1044447 2 0.0000 0.939 0.000 1.000 0.000 0.000
#> SRR1044449 3 0.0336 0.914 0.000 0.000 0.992 0.008
#> SRR1044448 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1044450 4 0.4040 0.605 0.000 0.248 0.000 0.752
#> SRR1044451 2 0.0000 0.939 0.000 1.000 0.000 0.000
#> SRR1044452 3 0.0336 0.914 0.000 0.000 0.992 0.008
#> SRR1044453 3 0.0336 0.914 0.000 0.000 0.992 0.008
#> SRR1044454 3 0.0336 0.914 0.000 0.000 0.992 0.008
#> SRR1044455 4 0.0336 0.949 0.000 0.008 0.000 0.992
#> SRR1044456 1 0.4961 0.184 0.552 0.448 0.000 0.000
#> SRR1044457 4 0.0336 0.949 0.000 0.008 0.000 0.992
#> SRR1044458 4 0.0188 0.949 0.000 0.004 0.000 0.996
#> SRR1044459 4 0.0188 0.944 0.000 0.000 0.004 0.996
#> SRR1044460 2 0.3123 0.811 0.000 0.844 0.000 0.156
#> SRR1044461 4 0.1118 0.924 0.000 0.036 0.000 0.964
#> SRR1044462 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044463 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044464 1 0.3681 0.777 0.816 0.176 0.008 0.000
#> SRR1044466 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044465 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044467 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044468 2 0.0817 0.932 0.000 0.976 0.000 0.024
#> SRR1044469 4 0.2011 0.876 0.000 0.000 0.080 0.920
#> SRR1044470 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044471 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044472 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044473 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044474 2 0.0000 0.939 0.000 1.000 0.000 0.000
#> SRR1044475 3 0.0336 0.914 0.000 0.000 0.992 0.008
#> SRR1044476 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1044477 2 0.0000 0.939 0.000 1.000 0.000 0.000
#> SRR1044478 2 0.0921 0.929 0.000 0.972 0.000 0.028
#> SRR1044479 2 0.2868 0.764 0.136 0.864 0.000 0.000
#> SRR1044480 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044481 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044482 2 0.0000 0.939 0.000 1.000 0.000 0.000
#> SRR1044483 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044484 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044486 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044485 2 0.0469 0.938 0.000 0.988 0.000 0.012
#> SRR1044487 2 0.0336 0.934 0.008 0.992 0.000 0.000
#> SRR1044488 2 0.0707 0.934 0.000 0.980 0.000 0.020
#> SRR1044489 2 0.0921 0.929 0.000 0.972 0.000 0.028
#> SRR1044490 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044491 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044492 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044493 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044494 2 0.0000 0.939 0.000 1.000 0.000 0.000
#> SRR1044496 2 0.0000 0.939 0.000 1.000 0.000 0.000
#> SRR1044495 2 0.0000 0.939 0.000 1.000 0.000 0.000
#> SRR1044497 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044499 4 0.1302 0.913 0.000 0.000 0.044 0.956
#> SRR1044498 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044500 2 0.0469 0.938 0.000 0.988 0.000 0.012
#> SRR1044501 4 0.0336 0.949 0.000 0.008 0.000 0.992
#> SRR1044502 2 0.0469 0.938 0.000 0.988 0.000 0.012
#> SRR1044503 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044504 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044505 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044506 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044507 1 0.1356 0.950 0.960 0.032 0.008 0.000
#> SRR1044508 1 0.5229 0.263 0.564 0.428 0.008 0.000
#> SRR1044509 2 0.4011 0.624 0.208 0.784 0.008 0.000
#> SRR1044510 3 0.0707 0.910 0.000 0.000 0.980 0.020
#> SRR1044511 3 0.4888 0.363 0.000 0.000 0.588 0.412
#> SRR1044512 3 0.0336 0.914 0.000 0.000 0.992 0.008
#> SRR1044513 2 0.0188 0.939 0.000 0.996 0.000 0.004
#> SRR1044514 3 0.0469 0.913 0.000 0.000 0.988 0.012
#> SRR1044515 2 0.0188 0.939 0.000 0.996 0.000 0.004
#> SRR1044516 2 0.3801 0.733 0.000 0.780 0.000 0.220
#> SRR1044517 3 0.0921 0.904 0.000 0.000 0.972 0.028
#> SRR1044518 3 0.4776 0.449 0.000 0.000 0.624 0.376
#> SRR1044519 4 0.0336 0.947 0.000 0.008 0.000 0.992
#> SRR1044520 4 0.1637 0.903 0.000 0.000 0.060 0.940
#> SRR1044521 2 0.0336 0.939 0.000 0.992 0.000 0.008
#> SRR1044522 2 0.3688 0.642 0.208 0.792 0.000 0.000
#> SRR1044523 2 0.0336 0.939 0.000 0.992 0.000 0.008
#> SRR1044524 4 0.0336 0.949 0.000 0.008 0.000 0.992
#> SRR1044525 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044526 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044527 2 0.0000 0.939 0.000 1.000 0.000 0.000
#> SRR1044528 2 0.0000 0.939 0.000 1.000 0.000 0.000
#> SRR1044529 2 0.0000 0.939 0.000 1.000 0.000 0.000
#> SRR1044530 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044531 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044533 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044532 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044534 2 0.0469 0.938 0.000 0.988 0.000 0.012
#> SRR1044535 4 0.2921 0.783 0.000 0.140 0.000 0.860
#> SRR1044536 2 0.1211 0.920 0.000 0.960 0.000 0.040
#> SRR1044537 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044538 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044539 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044540 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044541 4 0.0469 0.946 0.000 0.012 0.000 0.988
#> SRR1044542 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044543 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044544 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1044545 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044546 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044547 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044548 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044549 2 0.0188 0.939 0.000 0.996 0.000 0.004
#> SRR1044550 2 0.2281 0.871 0.000 0.904 0.000 0.096
#> SRR1044551 2 0.0188 0.939 0.000 0.996 0.000 0.004
#> SRR1044552 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044553 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044554 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044555 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1044556 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044557 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044558 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044559 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044561 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044560 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1044562 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044563 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044564 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044565 2 0.0000 0.939 0.000 1.000 0.000 0.000
#> SRR1044566 4 0.0188 0.949 0.000 0.004 0.000 0.996
#> SRR1044567 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044568 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044569 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044570 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044571 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044572 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044573 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044574 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044575 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044576 2 0.0000 0.939 0.000 1.000 0.000 0.000
#> SRR1044577 2 0.0000 0.939 0.000 1.000 0.000 0.000
#> SRR1044578 2 0.0000 0.939 0.000 1.000 0.000 0.000
#> SRR1044579 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044580 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044581 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044582 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044583 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044584 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044585 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044586 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044587 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044588 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044589 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044590 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044591 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044592 2 0.2675 0.807 0.100 0.892 0.008 0.000
#> SRR1044593 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044594 1 0.0336 0.976 0.992 0.000 0.008 0.000
#> SRR1044595 1 0.3751 0.748 0.800 0.196 0.004 0.000
#> SRR1044596 1 0.1151 0.957 0.968 0.024 0.008 0.000
#> SRR1044597 1 0.3123 0.806 0.844 0.156 0.000 0.000
#> SRR1044598 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> SRR1044599 1 0.0000 0.977 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 3 0.0000 0.8903 0.000 0.000 1.000 0.000 0.000
#> SRR1044416 2 0.0000 0.9076 0.000 1.000 0.000 0.000 0.000
#> SRR1044417 2 0.0000 0.9076 0.000 1.000 0.000 0.000 0.000
#> SRR1044418 2 0.0000 0.9076 0.000 1.000 0.000 0.000 0.000
#> SRR1044420 2 0.1281 0.9029 0.000 0.956 0.012 0.032 0.000
#> SRR1044419 3 0.0162 0.8896 0.000 0.000 0.996 0.004 0.000
#> SRR1044421 2 0.1281 0.9029 0.000 0.956 0.012 0.032 0.000
#> SRR1044422 2 0.4898 0.4102 0.000 0.592 0.376 0.032 0.000
#> SRR1044423 2 0.3977 0.7307 0.000 0.764 0.204 0.032 0.000
#> SRR1044424 2 0.1041 0.9047 0.000 0.964 0.004 0.032 0.000
#> SRR1044425 1 0.2605 0.5535 0.852 0.000 0.000 0.148 0.000
#> SRR1044426 1 0.5431 -0.5855 0.516 0.060 0.000 0.424 0.000
#> SRR1044427 1 0.0794 0.7082 0.972 0.000 0.000 0.028 0.000
#> SRR1044428 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044429 1 0.3707 0.1621 0.716 0.000 0.000 0.284 0.000
#> SRR1044430 1 0.2046 0.6479 0.916 0.016 0.000 0.068 0.000
#> SRR1044431 1 0.2852 0.5089 0.828 0.000 0.000 0.172 0.000
#> SRR1044433 2 0.4689 0.5373 0.048 0.688 0.000 0.264 0.000
#> SRR1044432 1 0.1430 0.6815 0.944 0.004 0.000 0.052 0.000
#> SRR1044434 4 0.4300 0.7901 0.476 0.000 0.000 0.524 0.000
#> SRR1044435 4 0.4302 0.7822 0.480 0.000 0.000 0.520 0.000
#> SRR1044436 1 0.4302 -0.6839 0.520 0.000 0.000 0.480 0.000
#> SRR1044437 1 0.4306 -0.7174 0.508 0.000 0.000 0.492 0.000
#> SRR1044439 1 0.4291 -0.6343 0.536 0.000 0.000 0.464 0.000
#> SRR1044438 1 0.4278 -0.5979 0.548 0.000 0.000 0.452 0.000
#> SRR1044440 1 0.4305 -0.7060 0.512 0.000 0.000 0.488 0.000
#> SRR1044441 4 0.5948 0.6766 0.408 0.108 0.000 0.484 0.000
#> SRR1044442 4 0.6269 0.5690 0.408 0.148 0.000 0.444 0.000
#> SRR1044443 2 0.3612 0.6606 0.008 0.764 0.000 0.228 0.000
#> SRR1044444 1 0.4249 -0.5294 0.568 0.000 0.000 0.432 0.000
#> SRR1044445 4 0.4300 0.7901 0.476 0.000 0.000 0.524 0.000
#> SRR1044446 3 0.3910 0.7752 0.000 0.032 0.772 0.196 0.000
#> SRR1044447 2 0.1197 0.8955 0.000 0.952 0.000 0.048 0.000
#> SRR1044449 5 0.2516 0.8391 0.000 0.000 0.000 0.140 0.860
#> SRR1044448 3 0.4101 0.6265 0.000 0.000 0.628 0.372 0.000
#> SRR1044450 3 0.6239 0.3886 0.000 0.144 0.452 0.404 0.000
#> SRR1044451 2 0.0880 0.9012 0.000 0.968 0.000 0.032 0.000
#> SRR1044452 5 0.0000 0.8815 0.000 0.000 0.000 0.000 1.000
#> SRR1044453 5 0.0000 0.8815 0.000 0.000 0.000 0.000 1.000
#> SRR1044454 5 0.0000 0.8815 0.000 0.000 0.000 0.000 1.000
#> SRR1044455 3 0.0290 0.8889 0.000 0.000 0.992 0.008 0.000
#> SRR1044456 4 0.6821 0.3883 0.316 0.336 0.000 0.348 0.000
#> SRR1044457 3 0.0000 0.8903 0.000 0.000 1.000 0.000 0.000
#> SRR1044458 3 0.0000 0.8903 0.000 0.000 1.000 0.000 0.000
#> SRR1044459 3 0.0324 0.8885 0.000 0.000 0.992 0.004 0.004
#> SRR1044460 2 0.3276 0.8088 0.000 0.836 0.132 0.032 0.000
#> SRR1044461 3 0.1579 0.8586 0.000 0.024 0.944 0.032 0.000
#> SRR1044462 1 0.2020 0.6327 0.900 0.000 0.000 0.100 0.000
#> SRR1044463 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044464 4 0.6301 0.5841 0.308 0.180 0.000 0.512 0.000
#> SRR1044466 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044465 1 0.0880 0.7051 0.968 0.000 0.000 0.032 0.000
#> SRR1044467 1 0.0404 0.7150 0.988 0.000 0.000 0.012 0.000
#> SRR1044468 2 0.1485 0.8996 0.000 0.948 0.020 0.032 0.000
#> SRR1044469 3 0.1478 0.8573 0.000 0.000 0.936 0.000 0.064
#> SRR1044470 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044471 1 0.0404 0.7150 0.988 0.000 0.000 0.012 0.000
#> SRR1044472 1 0.0404 0.7139 0.988 0.000 0.000 0.012 0.000
#> SRR1044473 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044474 2 0.0000 0.9076 0.000 1.000 0.000 0.000 0.000
#> SRR1044475 5 0.0000 0.8815 0.000 0.000 0.000 0.000 1.000
#> SRR1044476 3 0.0000 0.8903 0.000 0.000 1.000 0.000 0.000
#> SRR1044477 2 0.0000 0.9076 0.000 1.000 0.000 0.000 0.000
#> SRR1044478 2 0.1386 0.9016 0.000 0.952 0.016 0.032 0.000
#> SRR1044479 2 0.3555 0.7180 0.124 0.824 0.000 0.052 0.000
#> SRR1044480 1 0.2813 0.5211 0.832 0.000 0.000 0.168 0.000
#> SRR1044481 1 0.0404 0.7152 0.988 0.000 0.000 0.012 0.000
#> SRR1044482 2 0.0000 0.9076 0.000 1.000 0.000 0.000 0.000
#> SRR1044483 1 0.2929 0.4886 0.820 0.000 0.000 0.180 0.000
#> SRR1044484 1 0.1121 0.6965 0.956 0.000 0.000 0.044 0.000
#> SRR1044486 1 0.0290 0.7160 0.992 0.000 0.000 0.008 0.000
#> SRR1044485 2 0.1041 0.9047 0.000 0.964 0.004 0.032 0.000
#> SRR1044487 2 0.0162 0.9062 0.004 0.996 0.000 0.000 0.000
#> SRR1044488 2 0.1281 0.9028 0.000 0.956 0.012 0.032 0.000
#> SRR1044489 2 0.1579 0.8976 0.000 0.944 0.024 0.032 0.000
#> SRR1044490 1 0.0609 0.7120 0.980 0.000 0.000 0.020 0.000
#> SRR1044491 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044492 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044493 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044494 2 0.0000 0.9076 0.000 1.000 0.000 0.000 0.000
#> SRR1044496 2 0.0963 0.8893 0.000 0.964 0.000 0.036 0.000
#> SRR1044495 2 0.0000 0.9076 0.000 1.000 0.000 0.000 0.000
#> SRR1044497 1 0.4114 -0.2960 0.624 0.000 0.000 0.376 0.000
#> SRR1044499 3 0.1043 0.8735 0.000 0.000 0.960 0.000 0.040
#> SRR1044498 1 0.1270 0.6890 0.948 0.000 0.000 0.052 0.000
#> SRR1044500 2 0.1041 0.9047 0.000 0.964 0.004 0.032 0.000
#> SRR1044501 3 0.0404 0.8871 0.000 0.000 0.988 0.012 0.000
#> SRR1044502 2 0.1704 0.8901 0.000 0.928 0.004 0.068 0.000
#> SRR1044503 1 0.4294 -0.6483 0.532 0.000 0.000 0.468 0.000
#> SRR1044504 4 0.4307 0.7399 0.496 0.000 0.000 0.504 0.000
#> SRR1044505 1 0.0404 0.7153 0.988 0.000 0.000 0.012 0.000
#> SRR1044506 4 0.4300 0.7901 0.476 0.000 0.000 0.524 0.000
#> SRR1044507 4 0.5153 0.7535 0.436 0.040 0.000 0.524 0.000
#> SRR1044508 4 0.6584 0.3657 0.208 0.380 0.000 0.412 0.000
#> SRR1044509 2 0.5351 0.3023 0.060 0.560 0.000 0.380 0.000
#> SRR1044510 5 0.0510 0.8800 0.000 0.000 0.016 0.000 0.984
#> SRR1044511 5 0.6454 0.3996 0.000 0.000 0.304 0.208 0.488
#> SRR1044512 5 0.1792 0.8670 0.000 0.000 0.000 0.084 0.916
#> SRR1044513 2 0.1041 0.9027 0.000 0.964 0.004 0.032 0.000
#> SRR1044514 5 0.2719 0.8497 0.000 0.000 0.004 0.144 0.852
#> SRR1044515 2 0.1282 0.9023 0.000 0.952 0.004 0.044 0.000
#> SRR1044516 2 0.3876 0.7461 0.000 0.776 0.192 0.032 0.000
#> SRR1044517 5 0.0609 0.8787 0.000 0.000 0.020 0.000 0.980
#> SRR1044518 5 0.6658 0.3791 0.000 0.000 0.292 0.264 0.444
#> SRR1044519 3 0.4138 0.6204 0.000 0.000 0.616 0.384 0.000
#> SRR1044520 3 0.4651 0.6023 0.000 0.000 0.608 0.372 0.020
#> SRR1044521 2 0.0771 0.9068 0.000 0.976 0.004 0.020 0.000
#> SRR1044522 2 0.5243 0.5130 0.132 0.680 0.000 0.188 0.000
#> SRR1044523 2 0.1205 0.9036 0.000 0.956 0.004 0.040 0.000
#> SRR1044524 3 0.1197 0.8746 0.000 0.000 0.952 0.048 0.000
#> SRR1044525 1 0.4101 -0.2642 0.628 0.000 0.000 0.372 0.000
#> SRR1044526 1 0.0880 0.7057 0.968 0.000 0.000 0.032 0.000
#> SRR1044527 2 0.0000 0.9076 0.000 1.000 0.000 0.000 0.000
#> SRR1044528 2 0.0000 0.9076 0.000 1.000 0.000 0.000 0.000
#> SRR1044529 2 0.0000 0.9076 0.000 1.000 0.000 0.000 0.000
#> SRR1044530 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044531 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044533 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044532 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044534 2 0.1041 0.9047 0.000 0.964 0.004 0.032 0.000
#> SRR1044535 3 0.4069 0.7134 0.000 0.136 0.788 0.076 0.000
#> SRR1044536 2 0.1753 0.8928 0.000 0.936 0.032 0.032 0.000
#> SRR1044537 1 0.0510 0.7139 0.984 0.000 0.000 0.016 0.000
#> SRR1044538 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044539 1 0.4306 -0.7174 0.508 0.000 0.000 0.492 0.000
#> SRR1044540 1 0.1671 0.6620 0.924 0.000 0.000 0.076 0.000
#> SRR1044541 3 0.0671 0.8832 0.000 0.004 0.980 0.016 0.000
#> SRR1044542 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044543 1 0.1671 0.6657 0.924 0.000 0.000 0.076 0.000
#> SRR1044544 3 0.0000 0.8903 0.000 0.000 1.000 0.000 0.000
#> SRR1044545 1 0.4182 -0.3970 0.600 0.000 0.000 0.400 0.000
#> SRR1044546 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044547 1 0.3774 0.1064 0.704 0.000 0.000 0.296 0.000
#> SRR1044548 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044549 2 0.0162 0.9077 0.000 0.996 0.004 0.000 0.000
#> SRR1044550 2 0.2535 0.8603 0.000 0.892 0.076 0.032 0.000
#> SRR1044551 2 0.0324 0.9079 0.000 0.992 0.004 0.004 0.000
#> SRR1044552 4 0.4306 0.7560 0.492 0.000 0.000 0.508 0.000
#> SRR1044553 4 0.4300 0.7901 0.476 0.000 0.000 0.524 0.000
#> SRR1044554 1 0.0162 0.7158 0.996 0.000 0.000 0.004 0.000
#> SRR1044555 3 0.1043 0.8783 0.000 0.000 0.960 0.040 0.000
#> SRR1044556 1 0.4305 -0.7060 0.512 0.000 0.000 0.488 0.000
#> SRR1044557 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044558 1 0.4302 -0.6878 0.520 0.000 0.000 0.480 0.000
#> SRR1044559 1 0.0404 0.7155 0.988 0.000 0.000 0.012 0.000
#> SRR1044561 4 0.4305 0.7641 0.488 0.000 0.000 0.512 0.000
#> SRR1044560 3 0.0000 0.8903 0.000 0.000 1.000 0.000 0.000
#> SRR1044562 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044563 1 0.4291 -0.6355 0.536 0.000 0.000 0.464 0.000
#> SRR1044564 1 0.0290 0.7160 0.992 0.000 0.000 0.008 0.000
#> SRR1044565 2 0.0000 0.9076 0.000 1.000 0.000 0.000 0.000
#> SRR1044566 3 0.0000 0.8903 0.000 0.000 1.000 0.000 0.000
#> SRR1044567 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044568 1 0.3796 0.0933 0.700 0.000 0.000 0.300 0.000
#> SRR1044569 1 0.0510 0.7136 0.984 0.000 0.000 0.016 0.000
#> SRR1044570 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044571 1 0.0162 0.7161 0.996 0.000 0.000 0.004 0.000
#> SRR1044572 1 0.0703 0.7108 0.976 0.000 0.000 0.024 0.000
#> SRR1044573 1 0.0404 0.7152 0.988 0.000 0.000 0.012 0.000
#> SRR1044574 1 0.0290 0.7158 0.992 0.000 0.000 0.008 0.000
#> SRR1044575 1 0.0794 0.7081 0.972 0.000 0.000 0.028 0.000
#> SRR1044576 2 0.0000 0.9076 0.000 1.000 0.000 0.000 0.000
#> SRR1044577 2 0.0000 0.9076 0.000 1.000 0.000 0.000 0.000
#> SRR1044578 2 0.0000 0.9076 0.000 1.000 0.000 0.000 0.000
#> SRR1044579 1 0.4306 -0.7174 0.508 0.000 0.000 0.492 0.000
#> SRR1044580 1 0.2605 0.5581 0.852 0.000 0.000 0.148 0.000
#> SRR1044581 1 0.4304 -0.6949 0.516 0.000 0.000 0.484 0.000
#> SRR1044582 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044583 1 0.4305 -0.7068 0.512 0.000 0.000 0.488 0.000
#> SRR1044584 1 0.3913 -0.0292 0.676 0.000 0.000 0.324 0.000
#> SRR1044585 1 0.4304 -0.6948 0.516 0.000 0.000 0.484 0.000
#> SRR1044586 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044587 4 0.4300 0.7901 0.476 0.000 0.000 0.524 0.000
#> SRR1044588 4 0.4300 0.7901 0.476 0.000 0.000 0.524 0.000
#> SRR1044589 4 0.4300 0.7901 0.476 0.000 0.000 0.524 0.000
#> SRR1044590 4 0.4300 0.7901 0.476 0.000 0.000 0.524 0.000
#> SRR1044591 4 0.4300 0.7901 0.476 0.000 0.000 0.524 0.000
#> SRR1044592 2 0.4645 0.5412 0.044 0.688 0.000 0.268 0.000
#> SRR1044593 4 0.4300 0.7901 0.476 0.000 0.000 0.524 0.000
#> SRR1044594 4 0.4300 0.7901 0.476 0.000 0.000 0.524 0.000
#> SRR1044595 4 0.6554 0.4660 0.392 0.200 0.000 0.408 0.000
#> SRR1044596 4 0.4890 0.7705 0.452 0.024 0.000 0.524 0.000
#> SRR1044597 1 0.5083 0.2562 0.700 0.160 0.000 0.140 0.000
#> SRR1044598 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
#> SRR1044599 1 0.0000 0.7159 1.000 0.000 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 6 0.0363 0.9191 0.000 0.000 0.000 0.012 0.000 0.988
#> SRR1044416 2 0.0000 0.8534 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044417 2 0.0000 0.8534 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044418 2 0.0146 0.8529 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1044420 2 0.2527 0.8335 0.000 0.832 0.000 0.168 0.000 0.000
#> SRR1044419 6 0.0547 0.9163 0.000 0.000 0.000 0.020 0.000 0.980
#> SRR1044421 2 0.2562 0.8321 0.000 0.828 0.000 0.172 0.000 0.000
#> SRR1044422 2 0.5383 0.5318 0.000 0.576 0.000 0.164 0.000 0.260
#> SRR1044423 2 0.4520 0.7293 0.000 0.704 0.000 0.168 0.000 0.128
#> SRR1044424 2 0.2454 0.8360 0.000 0.840 0.000 0.160 0.000 0.000
#> SRR1044425 1 0.2854 0.5676 0.792 0.000 0.000 0.208 0.000 0.000
#> SRR1044426 4 0.5345 0.6710 0.364 0.116 0.000 0.520 0.000 0.000
#> SRR1044427 1 0.0865 0.8558 0.964 0.000 0.000 0.036 0.000 0.000
#> SRR1044428 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044429 1 0.3672 -0.1052 0.632 0.000 0.000 0.368 0.000 0.000
#> SRR1044430 1 0.2786 0.7303 0.860 0.056 0.000 0.084 0.000 0.000
#> SRR1044431 1 0.3050 0.4962 0.764 0.000 0.000 0.236 0.000 0.000
#> SRR1044433 2 0.3927 0.4145 0.012 0.644 0.000 0.344 0.000 0.000
#> SRR1044432 1 0.1644 0.8103 0.920 0.004 0.000 0.076 0.000 0.000
#> SRR1044434 4 0.3647 0.8587 0.360 0.000 0.000 0.640 0.000 0.000
#> SRR1044435 4 0.3659 0.8587 0.364 0.000 0.000 0.636 0.000 0.000
#> SRR1044436 4 0.3765 0.8396 0.404 0.000 0.000 0.596 0.000 0.000
#> SRR1044437 4 0.3737 0.8500 0.392 0.000 0.000 0.608 0.000 0.000
#> SRR1044439 4 0.3797 0.8171 0.420 0.000 0.000 0.580 0.000 0.000
#> SRR1044438 4 0.3817 0.7965 0.432 0.000 0.000 0.568 0.000 0.000
#> SRR1044440 4 0.3747 0.8474 0.396 0.000 0.000 0.604 0.000 0.000
#> SRR1044441 4 0.5237 0.6801 0.220 0.172 0.000 0.608 0.000 0.000
#> SRR1044442 4 0.5472 0.6282 0.256 0.180 0.000 0.564 0.000 0.000
#> SRR1044443 2 0.3547 0.5081 0.004 0.696 0.000 0.300 0.000 0.000
#> SRR1044444 4 0.3854 0.7277 0.464 0.000 0.000 0.536 0.000 0.000
#> SRR1044445 4 0.3634 0.8559 0.356 0.000 0.000 0.644 0.000 0.000
#> SRR1044446 6 0.4698 0.5054 0.000 0.008 0.000 0.076 0.240 0.676
#> SRR1044447 2 0.2747 0.8105 0.000 0.860 0.000 0.044 0.096 0.000
#> SRR1044449 3 0.3448 0.5306 0.000 0.000 0.716 0.004 0.280 0.000
#> SRR1044448 5 0.2969 0.7836 0.000 0.000 0.000 0.000 0.776 0.224
#> SRR1044450 5 0.3133 0.7866 0.000 0.008 0.000 0.000 0.780 0.212
#> SRR1044451 2 0.0891 0.8548 0.000 0.968 0.000 0.024 0.008 0.000
#> SRR1044452 3 0.0000 0.7889 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044453 3 0.0000 0.7889 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044454 3 0.0000 0.7889 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044455 6 0.0865 0.9068 0.000 0.000 0.000 0.036 0.000 0.964
#> SRR1044456 4 0.5954 0.3921 0.220 0.372 0.000 0.408 0.000 0.000
#> SRR1044457 6 0.0260 0.9188 0.000 0.000 0.000 0.008 0.000 0.992
#> SRR1044458 6 0.0260 0.9188 0.000 0.000 0.000 0.008 0.000 0.992
#> SRR1044459 6 0.0713 0.9098 0.000 0.000 0.000 0.028 0.000 0.972
#> SRR1044460 2 0.3422 0.8112 0.000 0.792 0.000 0.168 0.000 0.040
#> SRR1044461 6 0.2491 0.7396 0.000 0.000 0.000 0.164 0.000 0.836
#> SRR1044462 1 0.2178 0.7331 0.868 0.000 0.000 0.132 0.000 0.000
#> SRR1044463 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044464 4 0.5093 0.6462 0.176 0.192 0.000 0.632 0.000 0.000
#> SRR1044466 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044465 1 0.1075 0.8464 0.952 0.000 0.000 0.048 0.000 0.000
#> SRR1044467 1 0.0363 0.8670 0.988 0.000 0.000 0.012 0.000 0.000
#> SRR1044468 2 0.2778 0.8298 0.000 0.824 0.000 0.168 0.000 0.008
#> SRR1044469 6 0.1341 0.8931 0.000 0.000 0.024 0.028 0.000 0.948
#> SRR1044470 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044471 1 0.0458 0.8658 0.984 0.000 0.000 0.016 0.000 0.000
#> SRR1044472 1 0.0632 0.8613 0.976 0.000 0.000 0.024 0.000 0.000
#> SRR1044473 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044474 2 0.0146 0.8529 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1044475 3 0.0000 0.7889 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1044476 6 0.0146 0.9180 0.000 0.000 0.000 0.004 0.000 0.996
#> SRR1044477 2 0.0146 0.8529 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1044478 2 0.2668 0.8322 0.000 0.828 0.000 0.168 0.000 0.004
#> SRR1044479 2 0.2910 0.7461 0.068 0.852 0.000 0.080 0.000 0.000
#> SRR1044480 1 0.2996 0.5269 0.772 0.000 0.000 0.228 0.000 0.000
#> SRR1044481 1 0.0632 0.8636 0.976 0.000 0.000 0.024 0.000 0.000
#> SRR1044482 2 0.0146 0.8529 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1044483 1 0.3076 0.4710 0.760 0.000 0.000 0.240 0.000 0.000
#> SRR1044484 1 0.1327 0.8318 0.936 0.000 0.000 0.064 0.000 0.000
#> SRR1044486 1 0.0363 0.8678 0.988 0.000 0.000 0.012 0.000 0.000
#> SRR1044485 2 0.2340 0.8394 0.000 0.852 0.000 0.148 0.000 0.000
#> SRR1044487 2 0.0260 0.8515 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1044488 2 0.2527 0.8335 0.000 0.832 0.000 0.168 0.000 0.000
#> SRR1044489 2 0.2668 0.8318 0.000 0.828 0.000 0.168 0.000 0.004
#> SRR1044490 1 0.0713 0.8600 0.972 0.000 0.000 0.028 0.000 0.000
#> SRR1044491 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044492 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044493 1 0.0363 0.8666 0.988 0.000 0.000 0.012 0.000 0.000
#> SRR1044494 2 0.0146 0.8529 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1044496 2 0.1007 0.8321 0.000 0.956 0.000 0.044 0.000 0.000
#> SRR1044495 2 0.0146 0.8529 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1044497 1 0.3862 -0.5660 0.524 0.000 0.000 0.476 0.000 0.000
#> SRR1044499 6 0.0891 0.9073 0.000 0.000 0.008 0.024 0.000 0.968
#> SRR1044498 1 0.1327 0.8292 0.936 0.000 0.000 0.064 0.000 0.000
#> SRR1044500 2 0.2527 0.8335 0.000 0.832 0.000 0.168 0.000 0.000
#> SRR1044501 6 0.0790 0.9096 0.000 0.000 0.000 0.032 0.000 0.968
#> SRR1044502 2 0.2920 0.8303 0.000 0.820 0.000 0.168 0.008 0.004
#> SRR1044503 4 0.3789 0.8239 0.416 0.000 0.000 0.584 0.000 0.000
#> SRR1044504 4 0.3717 0.8546 0.384 0.000 0.000 0.616 0.000 0.000
#> SRR1044505 1 0.0458 0.8663 0.984 0.000 0.000 0.016 0.000 0.000
#> SRR1044506 4 0.3647 0.8587 0.360 0.000 0.000 0.640 0.000 0.000
#> SRR1044507 4 0.4792 0.7518 0.260 0.096 0.000 0.644 0.000 0.000
#> SRR1044508 4 0.5285 0.3611 0.108 0.368 0.000 0.524 0.000 0.000
#> SRR1044509 2 0.4325 0.1817 0.020 0.524 0.000 0.456 0.000 0.000
#> SRR1044510 3 0.0458 0.7821 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1044511 3 0.5781 0.3531 0.000 0.000 0.440 0.152 0.404 0.004
#> SRR1044512 3 0.5124 0.5774 0.000 0.000 0.620 0.148 0.232 0.000
#> SRR1044513 2 0.1007 0.8552 0.000 0.956 0.000 0.044 0.000 0.000
#> SRR1044514 3 0.5645 0.3777 0.000 0.000 0.456 0.152 0.392 0.000
#> SRR1044515 2 0.2048 0.8469 0.000 0.880 0.000 0.120 0.000 0.000
#> SRR1044516 2 0.4187 0.7643 0.000 0.736 0.000 0.168 0.000 0.096
#> SRR1044517 3 0.0632 0.7755 0.000 0.000 0.976 0.000 0.000 0.024
#> SRR1044518 5 0.5605 -0.4016 0.000 0.000 0.360 0.152 0.488 0.000
#> SRR1044519 5 0.2883 0.7901 0.000 0.000 0.000 0.000 0.788 0.212
#> SRR1044520 5 0.3141 0.7831 0.000 0.000 0.012 0.000 0.788 0.200
#> SRR1044521 2 0.2135 0.8443 0.000 0.872 0.000 0.128 0.000 0.000
#> SRR1044522 2 0.4281 0.5261 0.068 0.704 0.000 0.228 0.000 0.000
#> SRR1044523 2 0.2454 0.8368 0.000 0.840 0.000 0.160 0.000 0.000
#> SRR1044524 6 0.0914 0.9131 0.000 0.000 0.000 0.016 0.016 0.968
#> SRR1044525 1 0.3854 -0.5152 0.536 0.000 0.000 0.464 0.000 0.000
#> SRR1044526 1 0.0865 0.8560 0.964 0.000 0.000 0.036 0.000 0.000
#> SRR1044527 2 0.0146 0.8529 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1044528 2 0.0146 0.8536 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1044529 2 0.0146 0.8529 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1044530 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044531 1 0.0146 0.8675 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1044533 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044532 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044534 2 0.2527 0.8335 0.000 0.832 0.000 0.168 0.000 0.000
#> SRR1044535 6 0.4590 0.5480 0.000 0.116 0.000 0.140 0.016 0.728
#> SRR1044536 2 0.2778 0.8301 0.000 0.824 0.000 0.168 0.000 0.008
#> SRR1044537 1 0.0547 0.8653 0.980 0.000 0.000 0.020 0.000 0.000
#> SRR1044538 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044539 4 0.3737 0.8500 0.392 0.000 0.000 0.608 0.000 0.000
#> SRR1044540 1 0.2003 0.7570 0.884 0.000 0.000 0.116 0.000 0.000
#> SRR1044541 6 0.0972 0.9055 0.000 0.008 0.000 0.028 0.000 0.964
#> SRR1044542 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044543 1 0.1863 0.7808 0.896 0.000 0.000 0.104 0.000 0.000
#> SRR1044544 6 0.0146 0.9180 0.000 0.000 0.000 0.004 0.000 0.996
#> SRR1044545 4 0.3867 0.6591 0.488 0.000 0.000 0.512 0.000 0.000
#> SRR1044546 1 0.0146 0.8676 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1044547 1 0.3634 -0.0318 0.644 0.000 0.000 0.356 0.000 0.000
#> SRR1044548 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044549 2 0.0363 0.8544 0.000 0.988 0.000 0.012 0.000 0.000
#> SRR1044550 2 0.3210 0.8200 0.000 0.804 0.000 0.168 0.000 0.028
#> SRR1044551 2 0.0937 0.8556 0.000 0.960 0.000 0.040 0.000 0.000
#> SRR1044552 4 0.3695 0.8573 0.376 0.000 0.000 0.624 0.000 0.000
#> SRR1044553 4 0.3647 0.8587 0.360 0.000 0.000 0.640 0.000 0.000
#> SRR1044554 1 0.0146 0.8674 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1044555 6 0.1168 0.9040 0.000 0.000 0.000 0.028 0.016 0.956
#> SRR1044556 4 0.3756 0.8443 0.400 0.000 0.000 0.600 0.000 0.000
#> SRR1044557 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044558 4 0.3765 0.8412 0.404 0.000 0.000 0.596 0.000 0.000
#> SRR1044559 1 0.0865 0.8568 0.964 0.000 0.000 0.036 0.000 0.000
#> SRR1044561 4 0.3684 0.8579 0.372 0.000 0.000 0.628 0.000 0.000
#> SRR1044560 6 0.0146 0.9180 0.000 0.000 0.000 0.004 0.000 0.996
#> SRR1044562 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044563 4 0.3810 0.8044 0.428 0.000 0.000 0.572 0.000 0.000
#> SRR1044564 1 0.0363 0.8675 0.988 0.000 0.000 0.012 0.000 0.000
#> SRR1044565 2 0.0146 0.8529 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1044566 6 0.0146 0.9180 0.000 0.000 0.000 0.004 0.000 0.996
#> SRR1044567 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044568 1 0.3684 -0.1142 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1044569 1 0.0547 0.8641 0.980 0.000 0.000 0.020 0.000 0.000
#> SRR1044570 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044571 1 0.0458 0.8671 0.984 0.000 0.000 0.016 0.000 0.000
#> SRR1044572 1 0.0937 0.8541 0.960 0.000 0.000 0.040 0.000 0.000
#> SRR1044573 1 0.0458 0.8661 0.984 0.000 0.000 0.016 0.000 0.000
#> SRR1044574 1 0.0458 0.8673 0.984 0.000 0.000 0.016 0.000 0.000
#> SRR1044575 1 0.0937 0.8534 0.960 0.000 0.000 0.040 0.000 0.000
#> SRR1044576 2 0.0146 0.8543 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1044577 2 0.0000 0.8534 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1044578 2 0.0146 0.8529 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1044579 4 0.3737 0.8500 0.392 0.000 0.000 0.608 0.000 0.000
#> SRR1044580 1 0.2762 0.6069 0.804 0.000 0.000 0.196 0.000 0.000
#> SRR1044581 4 0.3765 0.8402 0.404 0.000 0.000 0.596 0.000 0.000
#> SRR1044582 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044583 4 0.3747 0.8479 0.396 0.000 0.000 0.604 0.000 0.000
#> SRR1044584 1 0.3782 -0.3103 0.588 0.000 0.000 0.412 0.000 0.000
#> SRR1044585 4 0.3765 0.8404 0.404 0.000 0.000 0.596 0.000 0.000
#> SRR1044586 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044587 4 0.3634 0.8559 0.356 0.000 0.000 0.644 0.000 0.000
#> SRR1044588 4 0.3647 0.8587 0.360 0.000 0.000 0.640 0.000 0.000
#> SRR1044589 4 0.3647 0.8587 0.360 0.000 0.000 0.640 0.000 0.000
#> SRR1044590 4 0.3647 0.8587 0.360 0.000 0.000 0.640 0.000 0.000
#> SRR1044591 4 0.3647 0.8587 0.360 0.000 0.000 0.640 0.000 0.000
#> SRR1044592 2 0.3912 0.4249 0.012 0.648 0.000 0.340 0.000 0.000
#> SRR1044593 4 0.3647 0.8587 0.360 0.000 0.000 0.640 0.000 0.000
#> SRR1044594 4 0.3647 0.8587 0.360 0.000 0.000 0.640 0.000 0.000
#> SRR1044595 4 0.5680 0.5474 0.292 0.192 0.000 0.516 0.000 0.000
#> SRR1044596 4 0.4603 0.7871 0.288 0.068 0.000 0.644 0.000 0.000
#> SRR1044597 1 0.5039 0.3185 0.640 0.180 0.000 0.180 0.000 0.000
#> SRR1044598 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1044599 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 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)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.818 0.914 0.963 0.4996 0.498 0.498
#> 3 3 0.802 0.817 0.904 0.2295 0.889 0.778
#> 4 4 0.623 0.717 0.822 0.1325 0.911 0.779
#> 5 5 0.603 0.647 0.755 0.0699 0.956 0.866
#> 6 6 0.628 0.565 0.726 0.0477 0.939 0.799
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0.0000 0.9481 0.000 1.000
#> SRR1044416 2 0.0000 0.9481 0.000 1.000
#> SRR1044417 2 0.0938 0.9413 0.012 0.988
#> SRR1044418 2 0.4298 0.8872 0.088 0.912
#> SRR1044420 2 0.0000 0.9481 0.000 1.000
#> SRR1044419 2 0.0000 0.9481 0.000 1.000
#> SRR1044421 2 0.0000 0.9481 0.000 1.000
#> SRR1044422 2 0.0000 0.9481 0.000 1.000
#> SRR1044423 2 0.0000 0.9481 0.000 1.000
#> SRR1044424 2 0.0000 0.9481 0.000 1.000
#> SRR1044425 1 0.0000 0.9722 1.000 0.000
#> SRR1044426 2 0.9866 0.2601 0.432 0.568
#> SRR1044427 1 0.0000 0.9722 1.000 0.000
#> SRR1044428 1 0.0000 0.9722 1.000 0.000
#> SRR1044429 1 0.0672 0.9650 0.992 0.008
#> SRR1044430 1 0.8763 0.5553 0.704 0.296
#> SRR1044431 1 0.0000 0.9722 1.000 0.000
#> SRR1044433 2 0.5294 0.8551 0.120 0.880
#> SRR1044432 1 0.9850 0.2152 0.572 0.428
#> SRR1044434 1 0.0000 0.9722 1.000 0.000
#> SRR1044435 1 0.0000 0.9722 1.000 0.000
#> SRR1044436 1 0.0000 0.9722 1.000 0.000
#> SRR1044437 1 0.0000 0.9722 1.000 0.000
#> SRR1044439 1 0.0000 0.9722 1.000 0.000
#> SRR1044438 1 0.0000 0.9722 1.000 0.000
#> SRR1044440 1 0.0000 0.9722 1.000 0.000
#> SRR1044441 1 0.9754 0.2719 0.592 0.408
#> SRR1044442 2 0.8327 0.6570 0.264 0.736
#> SRR1044443 2 0.5294 0.8551 0.120 0.880
#> SRR1044444 1 0.0000 0.9722 1.000 0.000
#> SRR1044445 1 0.9170 0.4767 0.668 0.332
#> SRR1044446 2 0.0000 0.9481 0.000 1.000
#> SRR1044447 2 0.0000 0.9481 0.000 1.000
#> SRR1044449 2 0.0000 0.9481 0.000 1.000
#> SRR1044448 2 0.0000 0.9481 0.000 1.000
#> SRR1044450 2 0.0000 0.9481 0.000 1.000
#> SRR1044451 2 0.0000 0.9481 0.000 1.000
#> SRR1044452 2 0.0000 0.9481 0.000 1.000
#> SRR1044453 2 0.0000 0.9481 0.000 1.000
#> SRR1044454 2 0.0000 0.9481 0.000 1.000
#> SRR1044455 2 0.0000 0.9481 0.000 1.000
#> SRR1044456 2 0.9491 0.4557 0.368 0.632
#> SRR1044457 2 0.0000 0.9481 0.000 1.000
#> SRR1044458 2 0.0000 0.9481 0.000 1.000
#> SRR1044459 2 0.0000 0.9481 0.000 1.000
#> SRR1044460 2 0.0000 0.9481 0.000 1.000
#> SRR1044461 2 0.0000 0.9481 0.000 1.000
#> SRR1044462 1 0.0000 0.9722 1.000 0.000
#> SRR1044463 1 0.0000 0.9722 1.000 0.000
#> SRR1044464 1 0.9661 0.3202 0.608 0.392
#> SRR1044466 1 0.0000 0.9722 1.000 0.000
#> SRR1044465 1 0.0000 0.9722 1.000 0.000
#> SRR1044467 1 0.0000 0.9722 1.000 0.000
#> SRR1044468 2 0.0000 0.9481 0.000 1.000
#> SRR1044469 2 0.0000 0.9481 0.000 1.000
#> SRR1044470 1 0.0000 0.9722 1.000 0.000
#> SRR1044471 1 0.0376 0.9687 0.996 0.004
#> SRR1044472 1 0.0000 0.9722 1.000 0.000
#> SRR1044473 1 0.0000 0.9722 1.000 0.000
#> SRR1044474 2 0.3274 0.9093 0.060 0.940
#> SRR1044475 2 0.0000 0.9481 0.000 1.000
#> SRR1044476 2 0.0000 0.9481 0.000 1.000
#> SRR1044477 2 0.5842 0.8376 0.140 0.860
#> SRR1044478 2 0.0000 0.9481 0.000 1.000
#> SRR1044479 2 0.6801 0.7907 0.180 0.820
#> SRR1044480 1 0.0000 0.9722 1.000 0.000
#> SRR1044481 1 0.0000 0.9722 1.000 0.000
#> SRR1044482 2 0.0000 0.9481 0.000 1.000
#> SRR1044483 1 0.0000 0.9722 1.000 0.000
#> SRR1044484 1 0.0000 0.9722 1.000 0.000
#> SRR1044486 1 0.0000 0.9722 1.000 0.000
#> SRR1044485 2 0.0000 0.9481 0.000 1.000
#> SRR1044487 2 0.4815 0.8734 0.104 0.896
#> SRR1044488 2 0.0000 0.9481 0.000 1.000
#> SRR1044489 2 0.0000 0.9481 0.000 1.000
#> SRR1044490 1 0.7056 0.7399 0.808 0.192
#> SRR1044491 1 0.0376 0.9687 0.996 0.004
#> SRR1044492 1 0.0000 0.9722 1.000 0.000
#> SRR1044493 1 0.0000 0.9722 1.000 0.000
#> SRR1044494 2 0.5519 0.8502 0.128 0.872
#> SRR1044496 2 0.6438 0.8103 0.164 0.836
#> SRR1044495 2 0.5629 0.8460 0.132 0.868
#> SRR1044497 1 0.0000 0.9722 1.000 0.000
#> SRR1044499 2 0.0000 0.9481 0.000 1.000
#> SRR1044498 1 0.0000 0.9722 1.000 0.000
#> SRR1044500 2 0.0000 0.9481 0.000 1.000
#> SRR1044501 2 0.0000 0.9481 0.000 1.000
#> SRR1044502 2 0.0000 0.9481 0.000 1.000
#> SRR1044503 1 0.0000 0.9722 1.000 0.000
#> SRR1044504 1 0.0376 0.9687 0.996 0.004
#> SRR1044505 1 0.0000 0.9722 1.000 0.000
#> SRR1044506 1 0.0000 0.9722 1.000 0.000
#> SRR1044507 2 0.9209 0.5246 0.336 0.664
#> SRR1044508 2 0.5294 0.8551 0.120 0.880
#> SRR1044509 2 0.5519 0.8467 0.128 0.872
#> SRR1044510 2 0.0000 0.9481 0.000 1.000
#> SRR1044511 2 0.0000 0.9481 0.000 1.000
#> SRR1044512 2 0.0000 0.9481 0.000 1.000
#> SRR1044513 2 0.0000 0.9481 0.000 1.000
#> SRR1044514 2 0.0000 0.9481 0.000 1.000
#> SRR1044515 2 0.0000 0.9481 0.000 1.000
#> SRR1044516 2 0.0000 0.9481 0.000 1.000
#> SRR1044517 2 0.0000 0.9481 0.000 1.000
#> SRR1044518 2 0.0000 0.9481 0.000 1.000
#> SRR1044519 2 0.0000 0.9481 0.000 1.000
#> SRR1044520 2 0.0000 0.9481 0.000 1.000
#> SRR1044521 2 0.0000 0.9481 0.000 1.000
#> SRR1044522 2 0.8608 0.6318 0.284 0.716
#> SRR1044523 2 0.0000 0.9481 0.000 1.000
#> SRR1044524 2 0.0000 0.9481 0.000 1.000
#> SRR1044525 1 0.0000 0.9722 1.000 0.000
#> SRR1044526 1 0.0000 0.9722 1.000 0.000
#> SRR1044527 2 0.0000 0.9481 0.000 1.000
#> SRR1044528 2 0.0000 0.9481 0.000 1.000
#> SRR1044529 2 0.0938 0.9412 0.012 0.988
#> SRR1044530 1 0.0000 0.9722 1.000 0.000
#> SRR1044531 1 0.0000 0.9722 1.000 0.000
#> SRR1044533 1 0.0000 0.9722 1.000 0.000
#> SRR1044532 1 0.0000 0.9722 1.000 0.000
#> SRR1044534 2 0.0000 0.9481 0.000 1.000
#> SRR1044535 2 0.0000 0.9481 0.000 1.000
#> SRR1044536 2 0.0000 0.9481 0.000 1.000
#> SRR1044537 1 0.0000 0.9722 1.000 0.000
#> SRR1044538 1 0.0000 0.9722 1.000 0.000
#> SRR1044539 1 0.0000 0.9722 1.000 0.000
#> SRR1044540 1 0.0000 0.9722 1.000 0.000
#> SRR1044541 2 0.0000 0.9481 0.000 1.000
#> SRR1044542 1 0.0000 0.9722 1.000 0.000
#> SRR1044543 1 0.1414 0.9532 0.980 0.020
#> SRR1044544 2 0.0000 0.9481 0.000 1.000
#> SRR1044545 1 0.0000 0.9722 1.000 0.000
#> SRR1044546 1 0.0000 0.9722 1.000 0.000
#> SRR1044547 1 0.0000 0.9722 1.000 0.000
#> SRR1044548 1 0.0000 0.9722 1.000 0.000
#> SRR1044549 2 0.0000 0.9481 0.000 1.000
#> SRR1044550 2 0.0000 0.9481 0.000 1.000
#> SRR1044551 2 0.0000 0.9481 0.000 1.000
#> SRR1044552 1 0.0000 0.9722 1.000 0.000
#> SRR1044553 1 0.0000 0.9722 1.000 0.000
#> SRR1044554 1 0.0000 0.9722 1.000 0.000
#> SRR1044555 2 0.0000 0.9481 0.000 1.000
#> SRR1044556 1 0.0000 0.9722 1.000 0.000
#> SRR1044557 1 0.0000 0.9722 1.000 0.000
#> SRR1044558 1 0.0000 0.9722 1.000 0.000
#> SRR1044559 1 0.9000 0.5127 0.684 0.316
#> SRR1044561 1 0.0000 0.9722 1.000 0.000
#> SRR1044560 2 0.0000 0.9481 0.000 1.000
#> SRR1044562 1 0.0000 0.9722 1.000 0.000
#> SRR1044563 1 0.0000 0.9722 1.000 0.000
#> SRR1044564 1 0.0000 0.9722 1.000 0.000
#> SRR1044565 2 0.5178 0.8622 0.116 0.884
#> SRR1044566 2 0.0000 0.9481 0.000 1.000
#> SRR1044567 1 0.0000 0.9722 1.000 0.000
#> SRR1044568 1 0.0376 0.9687 0.996 0.004
#> SRR1044569 1 0.0000 0.9722 1.000 0.000
#> SRR1044570 1 0.0000 0.9722 1.000 0.000
#> SRR1044571 1 0.0000 0.9722 1.000 0.000
#> SRR1044572 1 0.0000 0.9722 1.000 0.000
#> SRR1044573 1 0.0000 0.9722 1.000 0.000
#> SRR1044574 1 0.0000 0.9722 1.000 0.000
#> SRR1044575 1 0.0000 0.9722 1.000 0.000
#> SRR1044576 2 0.0000 0.9481 0.000 1.000
#> SRR1044577 2 0.0000 0.9481 0.000 1.000
#> SRR1044578 2 0.2423 0.9232 0.040 0.960
#> SRR1044579 1 0.0000 0.9722 1.000 0.000
#> SRR1044580 1 0.0000 0.9722 1.000 0.000
#> SRR1044581 1 0.0000 0.9722 1.000 0.000
#> SRR1044582 1 0.0000 0.9722 1.000 0.000
#> SRR1044583 1 0.0000 0.9722 1.000 0.000
#> SRR1044584 1 0.0000 0.9722 1.000 0.000
#> SRR1044585 1 0.0000 0.9722 1.000 0.000
#> SRR1044586 1 0.0000 0.9722 1.000 0.000
#> SRR1044587 1 0.0000 0.9722 1.000 0.000
#> SRR1044588 1 0.0000 0.9722 1.000 0.000
#> SRR1044589 1 0.0000 0.9722 1.000 0.000
#> SRR1044590 1 0.0000 0.9722 1.000 0.000
#> SRR1044591 1 0.0000 0.9722 1.000 0.000
#> SRR1044592 2 0.5294 0.8551 0.120 0.880
#> SRR1044593 1 0.0000 0.9722 1.000 0.000
#> SRR1044594 1 0.0000 0.9722 1.000 0.000
#> SRR1044595 2 0.5294 0.8551 0.120 0.880
#> SRR1044596 2 0.8813 0.5934 0.300 0.700
#> SRR1044597 2 0.9996 0.0808 0.488 0.512
#> SRR1044598 1 0.0000 0.9722 1.000 0.000
#> SRR1044599 1 0.0000 0.9722 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 2 0.1964 0.8009 0.000 0.944 0.056
#> SRR1044416 2 0.0424 0.8143 0.000 0.992 0.008
#> SRR1044417 2 0.0475 0.8136 0.004 0.992 0.004
#> SRR1044418 2 0.0237 0.8126 0.004 0.996 0.000
#> SRR1044420 2 0.0747 0.8150 0.000 0.984 0.016
#> SRR1044419 2 0.1289 0.8105 0.000 0.968 0.032
#> SRR1044421 2 0.1753 0.8075 0.000 0.952 0.048
#> SRR1044422 2 0.0892 0.8139 0.000 0.980 0.020
#> SRR1044423 2 0.0892 0.8139 0.000 0.980 0.020
#> SRR1044424 2 0.0747 0.8150 0.000 0.984 0.016
#> SRR1044425 1 0.0747 0.9477 0.984 0.000 0.016
#> SRR1044426 2 0.9724 0.2357 0.252 0.448 0.300
#> SRR1044427 1 0.0424 0.9485 0.992 0.000 0.008
#> SRR1044428 1 0.1163 0.9440 0.972 0.000 0.028
#> SRR1044429 1 0.1774 0.9413 0.960 0.016 0.024
#> SRR1044430 1 0.8226 0.3450 0.584 0.320 0.096
#> SRR1044431 1 0.0747 0.9477 0.984 0.000 0.016
#> SRR1044433 2 0.8165 0.2602 0.072 0.512 0.416
#> SRR1044432 1 0.9858 -0.2280 0.376 0.372 0.252
#> SRR1044434 1 0.1267 0.9463 0.972 0.004 0.024
#> SRR1044435 1 0.1267 0.9463 0.972 0.004 0.024
#> SRR1044436 1 0.1267 0.9463 0.972 0.004 0.024
#> SRR1044437 1 0.1267 0.9463 0.972 0.004 0.024
#> SRR1044439 1 0.1267 0.9463 0.972 0.004 0.024
#> SRR1044438 1 0.1453 0.9451 0.968 0.008 0.024
#> SRR1044440 1 0.1267 0.9463 0.972 0.004 0.024
#> SRR1044441 1 0.8264 0.0196 0.488 0.436 0.076
#> SRR1044442 2 0.8955 0.3192 0.140 0.516 0.344
#> SRR1044443 2 0.8149 0.2806 0.072 0.520 0.408
#> SRR1044444 1 0.1031 0.9467 0.976 0.000 0.024
#> SRR1044445 1 0.8249 0.0641 0.500 0.424 0.076
#> SRR1044446 3 0.2165 0.9444 0.000 0.064 0.936
#> SRR1044447 3 0.2878 0.9282 0.000 0.096 0.904
#> SRR1044449 3 0.1964 0.9464 0.000 0.056 0.944
#> SRR1044448 3 0.1964 0.9464 0.000 0.056 0.944
#> SRR1044450 3 0.1964 0.9464 0.000 0.056 0.944
#> SRR1044451 3 0.2796 0.9313 0.000 0.092 0.908
#> SRR1044452 3 0.1964 0.9464 0.000 0.056 0.944
#> SRR1044453 3 0.1964 0.9464 0.000 0.056 0.944
#> SRR1044454 3 0.1964 0.9464 0.000 0.056 0.944
#> SRR1044455 2 0.6280 0.1811 0.000 0.540 0.460
#> SRR1044456 2 0.7926 0.5211 0.216 0.656 0.128
#> SRR1044457 2 0.2711 0.7862 0.000 0.912 0.088
#> SRR1044458 2 0.3340 0.7509 0.000 0.880 0.120
#> SRR1044459 3 0.2356 0.9421 0.000 0.072 0.928
#> SRR1044460 2 0.0747 0.8150 0.000 0.984 0.016
#> SRR1044461 2 0.1031 0.8130 0.000 0.976 0.024
#> SRR1044462 1 0.0237 0.9497 0.996 0.000 0.004
#> SRR1044463 1 0.0848 0.9494 0.984 0.008 0.008
#> SRR1044464 2 0.9221 0.1978 0.404 0.444 0.152
#> SRR1044466 1 0.0848 0.9494 0.984 0.008 0.008
#> SRR1044465 1 0.1315 0.9452 0.972 0.008 0.020
#> SRR1044467 1 0.0424 0.9485 0.992 0.000 0.008
#> SRR1044468 2 0.0747 0.8150 0.000 0.984 0.016
#> SRR1044469 3 0.2537 0.9387 0.000 0.080 0.920
#> SRR1044470 1 0.0661 0.9487 0.988 0.004 0.008
#> SRR1044471 1 0.0829 0.9483 0.984 0.004 0.012
#> SRR1044472 1 0.1399 0.9469 0.968 0.004 0.028
#> SRR1044473 1 0.0424 0.9495 0.992 0.000 0.008
#> SRR1044474 2 0.1337 0.8025 0.012 0.972 0.016
#> SRR1044475 3 0.1964 0.9464 0.000 0.056 0.944
#> SRR1044476 2 0.5254 0.5528 0.000 0.736 0.264
#> SRR1044477 2 0.1337 0.8025 0.012 0.972 0.016
#> SRR1044478 2 0.0747 0.8150 0.000 0.984 0.016
#> SRR1044479 2 0.2297 0.7872 0.036 0.944 0.020
#> SRR1044480 1 0.0424 0.9502 0.992 0.000 0.008
#> SRR1044481 1 0.0237 0.9493 0.996 0.000 0.004
#> SRR1044482 2 0.0424 0.8143 0.000 0.992 0.008
#> SRR1044483 1 0.0475 0.9500 0.992 0.004 0.004
#> SRR1044484 1 0.0424 0.9496 0.992 0.000 0.008
#> SRR1044486 1 0.0424 0.9485 0.992 0.000 0.008
#> SRR1044485 2 0.0747 0.8150 0.000 0.984 0.016
#> SRR1044487 2 0.1337 0.8025 0.012 0.972 0.016
#> SRR1044488 2 0.0747 0.8150 0.000 0.984 0.016
#> SRR1044489 2 0.0747 0.8150 0.000 0.984 0.016
#> SRR1044490 1 0.6742 0.6138 0.708 0.240 0.052
#> SRR1044491 1 0.2031 0.9398 0.952 0.016 0.032
#> SRR1044492 1 0.0892 0.9467 0.980 0.000 0.020
#> SRR1044493 1 0.0237 0.9493 0.996 0.000 0.004
#> SRR1044494 2 0.1337 0.8025 0.012 0.972 0.016
#> SRR1044496 2 0.1636 0.7994 0.020 0.964 0.016
#> SRR1044495 2 0.1337 0.8025 0.012 0.972 0.016
#> SRR1044497 1 0.0892 0.9477 0.980 0.000 0.020
#> SRR1044499 3 0.3192 0.9106 0.000 0.112 0.888
#> SRR1044498 1 0.0829 0.9499 0.984 0.004 0.012
#> SRR1044500 2 0.0747 0.8150 0.000 0.984 0.016
#> SRR1044501 2 0.2066 0.7962 0.000 0.940 0.060
#> SRR1044502 3 0.5058 0.7257 0.000 0.244 0.756
#> SRR1044503 1 0.1267 0.9463 0.972 0.004 0.024
#> SRR1044504 1 0.1774 0.9424 0.960 0.016 0.024
#> SRR1044505 1 0.0592 0.9483 0.988 0.000 0.012
#> SRR1044506 1 0.4995 0.8066 0.824 0.144 0.032
#> SRR1044507 2 0.9376 0.3345 0.228 0.512 0.260
#> SRR1044508 2 0.8149 0.2806 0.072 0.520 0.408
#> SRR1044509 2 0.8211 0.2841 0.076 0.520 0.404
#> SRR1044510 3 0.1964 0.9464 0.000 0.056 0.944
#> SRR1044511 3 0.1964 0.9464 0.000 0.056 0.944
#> SRR1044512 3 0.1964 0.9464 0.000 0.056 0.944
#> SRR1044513 3 0.4504 0.8218 0.000 0.196 0.804
#> SRR1044514 3 0.1964 0.9464 0.000 0.056 0.944
#> SRR1044515 3 0.4399 0.8237 0.000 0.188 0.812
#> SRR1044516 2 0.3879 0.7320 0.000 0.848 0.152
#> SRR1044517 3 0.1964 0.9464 0.000 0.056 0.944
#> SRR1044518 3 0.1964 0.9464 0.000 0.056 0.944
#> SRR1044519 3 0.1964 0.9464 0.000 0.056 0.944
#> SRR1044520 3 0.1964 0.9464 0.000 0.056 0.944
#> SRR1044521 2 0.2356 0.7932 0.000 0.928 0.072
#> SRR1044522 2 0.4324 0.7185 0.112 0.860 0.028
#> SRR1044523 3 0.6244 0.2145 0.000 0.440 0.560
#> SRR1044524 3 0.3267 0.9121 0.000 0.116 0.884
#> SRR1044525 1 0.1267 0.9463 0.972 0.004 0.024
#> SRR1044526 1 0.1585 0.9478 0.964 0.008 0.028
#> SRR1044527 2 0.1411 0.8101 0.000 0.964 0.036
#> SRR1044528 2 0.5291 0.5737 0.000 0.732 0.268
#> SRR1044529 2 0.0237 0.8124 0.000 0.996 0.004
#> SRR1044530 1 0.0424 0.9485 0.992 0.000 0.008
#> SRR1044531 1 0.0829 0.9496 0.984 0.004 0.012
#> SRR1044533 1 0.1267 0.9459 0.972 0.004 0.024
#> SRR1044532 1 0.0424 0.9485 0.992 0.000 0.008
#> SRR1044534 2 0.1289 0.8127 0.000 0.968 0.032
#> SRR1044535 3 0.3038 0.9237 0.000 0.104 0.896
#> SRR1044536 2 0.0747 0.8150 0.000 0.984 0.016
#> SRR1044537 1 0.0237 0.9493 0.996 0.000 0.004
#> SRR1044538 1 0.0424 0.9485 0.992 0.000 0.008
#> SRR1044539 1 0.1267 0.9463 0.972 0.004 0.024
#> SRR1044540 1 0.0983 0.9482 0.980 0.004 0.016
#> SRR1044541 2 0.2878 0.7739 0.000 0.904 0.096
#> SRR1044542 1 0.0237 0.9493 0.996 0.000 0.004
#> SRR1044543 1 0.2569 0.9227 0.936 0.032 0.032
#> SRR1044544 2 0.5988 0.3629 0.000 0.632 0.368
#> SRR1044545 1 0.1267 0.9463 0.972 0.004 0.024
#> SRR1044546 1 0.0424 0.9485 0.992 0.000 0.008
#> SRR1044547 1 0.0747 0.9485 0.984 0.000 0.016
#> SRR1044548 1 0.0237 0.9493 0.996 0.000 0.004
#> SRR1044549 2 0.2165 0.7985 0.000 0.936 0.064
#> SRR1044550 2 0.0747 0.8150 0.000 0.984 0.016
#> SRR1044551 2 0.0237 0.8140 0.000 0.996 0.004
#> SRR1044552 1 0.1267 0.9463 0.972 0.004 0.024
#> SRR1044553 1 0.1877 0.9428 0.956 0.012 0.032
#> SRR1044554 1 0.0592 0.9498 0.988 0.000 0.012
#> SRR1044555 3 0.2711 0.9345 0.000 0.088 0.912
#> SRR1044556 1 0.1267 0.9463 0.972 0.004 0.024
#> SRR1044557 1 0.0592 0.9493 0.988 0.000 0.012
#> SRR1044558 1 0.1267 0.9463 0.972 0.004 0.024
#> SRR1044559 1 0.7271 0.3719 0.608 0.352 0.040
#> SRR1044561 1 0.1031 0.9467 0.976 0.000 0.024
#> SRR1044560 2 0.5905 0.3711 0.000 0.648 0.352
#> SRR1044562 1 0.0661 0.9499 0.988 0.004 0.008
#> SRR1044563 1 0.1267 0.9463 0.972 0.004 0.024
#> SRR1044564 1 0.1031 0.9455 0.976 0.000 0.024
#> SRR1044565 2 0.1337 0.8025 0.012 0.972 0.016
#> SRR1044566 2 0.4887 0.6129 0.000 0.772 0.228
#> SRR1044567 1 0.0892 0.9467 0.980 0.000 0.020
#> SRR1044568 1 0.0892 0.9477 0.980 0.000 0.020
#> SRR1044569 1 0.1031 0.9452 0.976 0.000 0.024
#> SRR1044570 1 0.0424 0.9485 0.992 0.000 0.008
#> SRR1044571 1 0.0661 0.9491 0.988 0.004 0.008
#> SRR1044572 1 0.1491 0.9439 0.968 0.016 0.016
#> SRR1044573 1 0.1525 0.9471 0.964 0.004 0.032
#> SRR1044574 1 0.1289 0.9420 0.968 0.000 0.032
#> SRR1044575 1 0.0424 0.9485 0.992 0.000 0.008
#> SRR1044576 2 0.0424 0.8147 0.000 0.992 0.008
#> SRR1044577 2 0.0237 0.8140 0.000 0.996 0.004
#> SRR1044578 2 0.1337 0.8025 0.012 0.972 0.016
#> SRR1044579 1 0.1031 0.9467 0.976 0.000 0.024
#> SRR1044580 1 0.0424 0.9494 0.992 0.000 0.008
#> SRR1044581 1 0.1031 0.9467 0.976 0.000 0.024
#> SRR1044582 1 0.0424 0.9485 0.992 0.000 0.008
#> SRR1044583 1 0.1031 0.9467 0.976 0.000 0.024
#> SRR1044584 1 0.0237 0.9493 0.996 0.000 0.004
#> SRR1044585 1 0.1031 0.9467 0.976 0.000 0.024
#> SRR1044586 1 0.0000 0.9496 1.000 0.000 0.000
#> SRR1044587 1 0.4712 0.8440 0.848 0.108 0.044
#> SRR1044588 1 0.2663 0.9233 0.932 0.044 0.024
#> SRR1044589 1 0.2443 0.9312 0.940 0.032 0.028
#> SRR1044590 1 0.2663 0.9233 0.932 0.044 0.024
#> SRR1044591 1 0.4058 0.8818 0.880 0.076 0.044
#> SRR1044592 2 0.8149 0.2806 0.072 0.520 0.408
#> SRR1044593 1 0.2918 0.9201 0.924 0.044 0.032
#> SRR1044594 1 0.3337 0.9052 0.908 0.060 0.032
#> SRR1044595 2 0.8149 0.2806 0.072 0.520 0.408
#> SRR1044596 2 0.9284 0.3271 0.192 0.512 0.296
#> SRR1044597 2 0.9328 0.2713 0.372 0.460 0.168
#> SRR1044598 1 0.0424 0.9485 0.992 0.000 0.008
#> SRR1044599 1 0.0424 0.9485 0.992 0.000 0.008
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 2 0.1637 0.8067 0.000 0.940 0.060 0.000
#> SRR1044416 2 0.2266 0.7835 0.000 0.912 0.004 0.084
#> SRR1044417 2 0.4585 0.6020 0.000 0.668 0.000 0.332
#> SRR1044418 2 0.4817 0.5400 0.000 0.612 0.000 0.388
#> SRR1044420 2 0.1118 0.8115 0.000 0.964 0.036 0.000
#> SRR1044419 2 0.1743 0.8070 0.000 0.940 0.056 0.004
#> SRR1044421 2 0.3732 0.7778 0.000 0.852 0.092 0.056
#> SRR1044422 2 0.1398 0.8105 0.000 0.956 0.040 0.004
#> SRR1044423 2 0.1118 0.8115 0.000 0.964 0.036 0.000
#> SRR1044424 2 0.1118 0.8115 0.000 0.964 0.036 0.000
#> SRR1044425 1 0.2469 0.8410 0.892 0.000 0.000 0.108
#> SRR1044426 4 0.9013 0.5615 0.240 0.116 0.172 0.472
#> SRR1044427 1 0.1792 0.8530 0.932 0.000 0.000 0.068
#> SRR1044428 1 0.4193 0.7024 0.732 0.000 0.000 0.268
#> SRR1044429 1 0.3751 0.7949 0.800 0.000 0.004 0.196
#> SRR1044430 4 0.6950 0.3553 0.380 0.056 0.028 0.536
#> SRR1044431 1 0.2760 0.8329 0.872 0.000 0.000 0.128
#> SRR1044433 4 0.5905 0.5646 0.004 0.096 0.200 0.700
#> SRR1044432 4 0.7302 0.3940 0.352 0.024 0.092 0.532
#> SRR1044434 1 0.2860 0.8415 0.888 0.008 0.004 0.100
#> SRR1044435 1 0.2796 0.8405 0.892 0.008 0.004 0.096
#> SRR1044436 1 0.2796 0.8405 0.892 0.008 0.004 0.096
#> SRR1044437 1 0.2796 0.8405 0.892 0.008 0.004 0.096
#> SRR1044439 1 0.2796 0.8405 0.892 0.008 0.004 0.096
#> SRR1044438 1 0.2796 0.8405 0.892 0.008 0.004 0.096
#> SRR1044440 1 0.2922 0.8390 0.884 0.008 0.004 0.104
#> SRR1044441 4 0.7405 0.6361 0.192 0.088 0.084 0.636
#> SRR1044442 4 0.6098 0.5904 0.020 0.092 0.176 0.712
#> SRR1044443 4 0.5869 0.5683 0.004 0.096 0.196 0.704
#> SRR1044444 1 0.2860 0.8415 0.888 0.008 0.004 0.100
#> SRR1044445 4 0.7169 0.6310 0.200 0.084 0.068 0.648
#> SRR1044446 3 0.1182 0.8520 0.000 0.016 0.968 0.016
#> SRR1044447 3 0.4199 0.7291 0.000 0.032 0.804 0.164
#> SRR1044449 3 0.0188 0.8575 0.000 0.004 0.996 0.000
#> SRR1044448 3 0.0524 0.8567 0.000 0.004 0.988 0.008
#> SRR1044450 3 0.0524 0.8567 0.000 0.004 0.988 0.008
#> SRR1044451 3 0.5198 0.6090 0.000 0.040 0.708 0.252
#> SRR1044452 3 0.0188 0.8575 0.000 0.004 0.996 0.000
#> SRR1044453 3 0.0188 0.8575 0.000 0.004 0.996 0.000
#> SRR1044454 3 0.0188 0.8575 0.000 0.004 0.996 0.000
#> SRR1044455 3 0.5396 0.1864 0.000 0.464 0.524 0.012
#> SRR1044456 4 0.6445 0.1500 0.096 0.304 0.000 0.600
#> SRR1044457 2 0.3610 0.7166 0.000 0.800 0.200 0.000
#> SRR1044458 2 0.2266 0.7961 0.000 0.912 0.084 0.004
#> SRR1044459 3 0.0921 0.8512 0.000 0.028 0.972 0.000
#> SRR1044460 2 0.1118 0.8115 0.000 0.964 0.036 0.000
#> SRR1044461 2 0.1661 0.8076 0.000 0.944 0.052 0.004
#> SRR1044462 1 0.1118 0.8605 0.964 0.000 0.000 0.036
#> SRR1044463 1 0.2530 0.8416 0.888 0.000 0.000 0.112
#> SRR1044464 4 0.8182 0.6086 0.248 0.100 0.100 0.552
#> SRR1044466 1 0.2921 0.8284 0.860 0.000 0.000 0.140
#> SRR1044465 1 0.3311 0.8083 0.828 0.000 0.000 0.172
#> SRR1044467 1 0.1867 0.8570 0.928 0.000 0.000 0.072
#> SRR1044468 2 0.1305 0.8109 0.000 0.960 0.036 0.004
#> SRR1044469 3 0.2053 0.8233 0.000 0.072 0.924 0.004
#> SRR1044470 1 0.2530 0.8421 0.888 0.000 0.000 0.112
#> SRR1044471 1 0.3172 0.8280 0.840 0.000 0.000 0.160
#> SRR1044472 1 0.3444 0.8244 0.816 0.000 0.000 0.184
#> SRR1044473 1 0.2469 0.8524 0.892 0.000 0.000 0.108
#> SRR1044474 2 0.4836 0.6349 0.008 0.672 0.000 0.320
#> SRR1044475 3 0.0188 0.8575 0.000 0.004 0.996 0.000
#> SRR1044476 2 0.3105 0.7656 0.000 0.856 0.140 0.004
#> SRR1044477 2 0.5143 0.5795 0.012 0.628 0.000 0.360
#> SRR1044478 2 0.1398 0.8105 0.000 0.956 0.040 0.004
#> SRR1044479 2 0.5850 0.3697 0.032 0.512 0.000 0.456
#> SRR1044480 1 0.1792 0.8570 0.932 0.000 0.000 0.068
#> SRR1044481 1 0.1118 0.8615 0.964 0.000 0.000 0.036
#> SRR1044482 2 0.2469 0.7754 0.000 0.892 0.000 0.108
#> SRR1044483 1 0.2345 0.8558 0.900 0.000 0.000 0.100
#> SRR1044484 1 0.0921 0.8589 0.972 0.000 0.000 0.028
#> SRR1044486 1 0.0707 0.8581 0.980 0.000 0.000 0.020
#> SRR1044485 2 0.1022 0.8108 0.000 0.968 0.032 0.000
#> SRR1044487 2 0.4877 0.6283 0.008 0.664 0.000 0.328
#> SRR1044488 2 0.1118 0.8115 0.000 0.964 0.036 0.000
#> SRR1044489 2 0.1118 0.8115 0.000 0.964 0.036 0.000
#> SRR1044490 4 0.5869 0.1882 0.428 0.012 0.016 0.544
#> SRR1044491 1 0.4422 0.7480 0.736 0.008 0.000 0.256
#> SRR1044492 1 0.3356 0.8042 0.824 0.000 0.000 0.176
#> SRR1044493 1 0.1302 0.8605 0.956 0.000 0.000 0.044
#> SRR1044494 2 0.4897 0.6223 0.008 0.660 0.000 0.332
#> SRR1044496 2 0.5290 0.5095 0.012 0.584 0.000 0.404
#> SRR1044495 2 0.4877 0.6263 0.008 0.664 0.000 0.328
#> SRR1044497 1 0.2796 0.8405 0.892 0.008 0.004 0.096
#> SRR1044499 3 0.2125 0.8196 0.000 0.076 0.920 0.004
#> SRR1044498 1 0.1022 0.8583 0.968 0.000 0.000 0.032
#> SRR1044500 2 0.1118 0.8115 0.000 0.964 0.036 0.000
#> SRR1044501 2 0.1824 0.8053 0.000 0.936 0.060 0.004
#> SRR1044502 3 0.7214 0.2450 0.000 0.144 0.476 0.380
#> SRR1044503 1 0.2860 0.8410 0.888 0.008 0.004 0.100
#> SRR1044504 1 0.3721 0.7913 0.816 0.004 0.004 0.176
#> SRR1044505 1 0.2281 0.8481 0.904 0.000 0.000 0.096
#> SRR1044506 1 0.5755 0.2395 0.528 0.028 0.000 0.444
#> SRR1044507 4 0.6781 0.6200 0.060 0.112 0.136 0.692
#> SRR1044508 4 0.5925 0.5679 0.004 0.100 0.196 0.700
#> SRR1044509 4 0.5869 0.5683 0.004 0.096 0.196 0.704
#> SRR1044510 3 0.0188 0.8575 0.000 0.004 0.996 0.000
#> SRR1044511 3 0.0188 0.8575 0.000 0.004 0.996 0.000
#> SRR1044512 3 0.0188 0.8575 0.000 0.004 0.996 0.000
#> SRR1044513 3 0.7227 0.2547 0.000 0.148 0.484 0.368
#> SRR1044514 3 0.0188 0.8575 0.000 0.004 0.996 0.000
#> SRR1044515 3 0.7179 0.2538 0.000 0.140 0.480 0.380
#> SRR1044516 2 0.3427 0.7635 0.000 0.860 0.112 0.028
#> SRR1044517 3 0.0188 0.8575 0.000 0.004 0.996 0.000
#> SRR1044518 3 0.0188 0.8575 0.000 0.004 0.996 0.000
#> SRR1044519 3 0.0524 0.8567 0.000 0.004 0.988 0.008
#> SRR1044520 3 0.0524 0.8567 0.000 0.004 0.988 0.008
#> SRR1044521 2 0.3463 0.7710 0.000 0.864 0.096 0.040
#> SRR1044522 4 0.6475 -0.1747 0.052 0.424 0.008 0.516
#> SRR1044523 3 0.7746 0.0703 0.000 0.232 0.392 0.376
#> SRR1044524 3 0.3245 0.7927 0.000 0.100 0.872 0.028
#> SRR1044525 1 0.2773 0.8476 0.880 0.000 0.004 0.116
#> SRR1044526 1 0.3528 0.7887 0.808 0.000 0.000 0.192
#> SRR1044527 2 0.5387 0.4610 0.000 0.584 0.016 0.400
#> SRR1044528 4 0.7082 -0.0866 0.000 0.428 0.124 0.448
#> SRR1044529 2 0.4655 0.6430 0.004 0.684 0.000 0.312
#> SRR1044530 1 0.1867 0.8449 0.928 0.000 0.000 0.072
#> SRR1044531 1 0.2704 0.8408 0.876 0.000 0.000 0.124
#> SRR1044533 1 0.3528 0.7841 0.808 0.000 0.000 0.192
#> SRR1044532 1 0.1867 0.8449 0.928 0.000 0.000 0.072
#> SRR1044534 2 0.1022 0.8108 0.000 0.968 0.032 0.000
#> SRR1044535 3 0.3320 0.8050 0.000 0.068 0.876 0.056
#> SRR1044536 2 0.1118 0.8115 0.000 0.964 0.036 0.000
#> SRR1044537 1 0.1118 0.8559 0.964 0.000 0.000 0.036
#> SRR1044538 1 0.1940 0.8448 0.924 0.000 0.000 0.076
#> SRR1044539 1 0.2796 0.8405 0.892 0.008 0.004 0.096
#> SRR1044540 1 0.3219 0.8222 0.836 0.000 0.000 0.164
#> SRR1044541 2 0.3448 0.7536 0.000 0.828 0.168 0.004
#> SRR1044542 1 0.1389 0.8551 0.952 0.000 0.000 0.048
#> SRR1044543 1 0.4335 0.7531 0.752 0.004 0.004 0.240
#> SRR1044544 2 0.4741 0.5065 0.000 0.668 0.328 0.004
#> SRR1044545 1 0.2796 0.8405 0.892 0.008 0.004 0.096
#> SRR1044546 1 0.1211 0.8543 0.960 0.000 0.000 0.040
#> SRR1044547 1 0.2665 0.8435 0.900 0.008 0.004 0.088
#> SRR1044548 1 0.1389 0.8615 0.952 0.000 0.000 0.048
#> SRR1044549 2 0.5872 0.4172 0.000 0.576 0.040 0.384
#> SRR1044550 2 0.1118 0.8115 0.000 0.964 0.036 0.000
#> SRR1044551 2 0.3668 0.7207 0.000 0.808 0.004 0.188
#> SRR1044552 1 0.2983 0.8373 0.880 0.008 0.004 0.108
#> SRR1044553 1 0.4746 0.7035 0.712 0.008 0.004 0.276
#> SRR1044554 1 0.0921 0.8618 0.972 0.000 0.000 0.028
#> SRR1044555 3 0.1022 0.8494 0.000 0.032 0.968 0.000
#> SRR1044556 1 0.2796 0.8405 0.892 0.008 0.004 0.096
#> SRR1044557 1 0.1302 0.8558 0.956 0.000 0.000 0.044
#> SRR1044558 1 0.2796 0.8405 0.892 0.008 0.004 0.096
#> SRR1044559 1 0.7297 -0.2029 0.464 0.088 0.020 0.428
#> SRR1044561 1 0.2796 0.8405 0.892 0.008 0.004 0.096
#> SRR1044560 2 0.3870 0.7047 0.000 0.788 0.208 0.004
#> SRR1044562 1 0.2149 0.8480 0.912 0.000 0.000 0.088
#> SRR1044563 1 0.2860 0.8399 0.888 0.008 0.004 0.100
#> SRR1044564 1 0.3764 0.7560 0.784 0.000 0.000 0.216
#> SRR1044565 2 0.4836 0.6346 0.008 0.672 0.000 0.320
#> SRR1044566 2 0.3105 0.7662 0.000 0.856 0.140 0.004
#> SRR1044567 1 0.3123 0.8158 0.844 0.000 0.000 0.156
#> SRR1044568 1 0.3272 0.8322 0.860 0.008 0.004 0.128
#> SRR1044569 1 0.3311 0.7943 0.828 0.000 0.000 0.172
#> SRR1044570 1 0.1940 0.8432 0.924 0.000 0.000 0.076
#> SRR1044571 1 0.2149 0.8523 0.912 0.000 0.000 0.088
#> SRR1044572 1 0.3172 0.8183 0.840 0.000 0.000 0.160
#> SRR1044573 1 0.3219 0.8088 0.836 0.000 0.000 0.164
#> SRR1044574 1 0.4134 0.7145 0.740 0.000 0.000 0.260
#> SRR1044575 1 0.2149 0.8488 0.912 0.000 0.000 0.088
#> SRR1044576 2 0.2342 0.7883 0.000 0.912 0.008 0.080
#> SRR1044577 2 0.3649 0.7291 0.000 0.796 0.000 0.204
#> SRR1044578 2 0.4621 0.6657 0.008 0.708 0.000 0.284
#> SRR1044579 1 0.2796 0.8405 0.892 0.008 0.004 0.096
#> SRR1044580 1 0.1940 0.8565 0.924 0.000 0.000 0.076
#> SRR1044581 1 0.2796 0.8405 0.892 0.008 0.004 0.096
#> SRR1044582 1 0.1211 0.8532 0.960 0.000 0.000 0.040
#> SRR1044583 1 0.2796 0.8405 0.892 0.008 0.004 0.096
#> SRR1044584 1 0.1474 0.8610 0.948 0.000 0.000 0.052
#> SRR1044585 1 0.2860 0.8415 0.888 0.008 0.004 0.100
#> SRR1044586 1 0.0469 0.8588 0.988 0.000 0.000 0.012
#> SRR1044587 4 0.5435 0.1210 0.420 0.016 0.000 0.564
#> SRR1044588 1 0.5028 0.4527 0.596 0.000 0.004 0.400
#> SRR1044589 1 0.4978 0.4978 0.612 0.000 0.004 0.384
#> SRR1044590 1 0.4872 0.5482 0.640 0.000 0.004 0.356
#> SRR1044591 4 0.5675 -0.1280 0.472 0.016 0.004 0.508
#> SRR1044592 4 0.5869 0.5683 0.004 0.096 0.196 0.704
#> SRR1044593 1 0.5039 0.4473 0.592 0.000 0.004 0.404
#> SRR1044594 1 0.5252 0.3908 0.572 0.004 0.004 0.420
#> SRR1044595 4 0.5869 0.5683 0.004 0.096 0.196 0.704
#> SRR1044596 4 0.6626 0.6062 0.040 0.112 0.156 0.692
#> SRR1044597 4 0.7240 0.6391 0.136 0.100 0.100 0.664
#> SRR1044598 1 0.1792 0.8469 0.932 0.000 0.000 0.068
#> SRR1044599 1 0.1792 0.8469 0.932 0.000 0.000 0.068
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.2046 0.719069 0.000 0.916 0.068 0.000 0.016
#> SRR1044416 2 0.3877 0.392649 0.000 0.764 0.000 0.024 0.212
#> SRR1044417 2 0.6265 -0.386897 0.000 0.540 0.000 0.220 0.240
#> SRR1044418 2 0.6570 -0.768829 0.000 0.408 0.000 0.204 0.388
#> SRR1044420 2 0.0324 0.734590 0.000 0.992 0.000 0.004 0.004
#> SRR1044419 2 0.1800 0.725628 0.000 0.932 0.048 0.000 0.020
#> SRR1044421 2 0.3380 0.684145 0.000 0.864 0.032 0.052 0.052
#> SRR1044422 2 0.0404 0.736015 0.000 0.988 0.000 0.000 0.012
#> SRR1044423 2 0.0324 0.736485 0.000 0.992 0.000 0.004 0.004
#> SRR1044424 2 0.0162 0.735919 0.000 0.996 0.000 0.004 0.000
#> SRR1044425 1 0.3476 0.777696 0.836 0.000 0.000 0.076 0.088
#> SRR1044426 4 0.7493 0.483172 0.160 0.036 0.040 0.544 0.220
#> SRR1044427 1 0.2761 0.809702 0.872 0.000 0.000 0.024 0.104
#> SRR1044428 1 0.5572 0.549938 0.628 0.000 0.000 0.248 0.124
#> SRR1044429 1 0.5037 0.730079 0.684 0.000 0.000 0.088 0.228
#> SRR1044430 4 0.6387 0.479448 0.168 0.012 0.004 0.584 0.232
#> SRR1044431 1 0.3971 0.764587 0.800 0.000 0.000 0.100 0.100
#> SRR1044433 4 0.1547 0.588187 0.000 0.016 0.032 0.948 0.004
#> SRR1044432 4 0.6831 0.443808 0.216 0.004 0.008 0.488 0.284
#> SRR1044434 1 0.3710 0.786034 0.784 0.000 0.000 0.024 0.192
#> SRR1044435 1 0.3527 0.773592 0.792 0.000 0.000 0.016 0.192
#> SRR1044436 1 0.3123 0.779000 0.812 0.000 0.000 0.004 0.184
#> SRR1044437 1 0.3123 0.780653 0.812 0.000 0.000 0.004 0.184
#> SRR1044439 1 0.3318 0.779069 0.800 0.000 0.000 0.008 0.192
#> SRR1044438 1 0.3231 0.780916 0.800 0.000 0.000 0.004 0.196
#> SRR1044440 1 0.3421 0.779756 0.788 0.000 0.000 0.008 0.204
#> SRR1044441 4 0.3594 0.575255 0.056 0.004 0.012 0.848 0.080
#> SRR1044442 4 0.0932 0.586359 0.000 0.004 0.020 0.972 0.004
#> SRR1044443 4 0.1646 0.587660 0.000 0.020 0.032 0.944 0.004
#> SRR1044444 1 0.2763 0.791156 0.848 0.000 0.000 0.004 0.148
#> SRR1044445 4 0.5820 0.506049 0.128 0.004 0.012 0.656 0.200
#> SRR1044446 3 0.3308 0.857574 0.000 0.028 0.864 0.032 0.076
#> SRR1044447 3 0.6728 0.543969 0.000 0.112 0.584 0.236 0.068
#> SRR1044449 3 0.0324 0.896884 0.000 0.000 0.992 0.004 0.004
#> SRR1044448 3 0.1522 0.889294 0.000 0.000 0.944 0.012 0.044
#> SRR1044450 3 0.1522 0.889294 0.000 0.000 0.944 0.012 0.044
#> SRR1044451 3 0.7278 0.390398 0.000 0.132 0.496 0.296 0.076
#> SRR1044452 3 0.0000 0.896688 0.000 0.000 1.000 0.000 0.000
#> SRR1044453 3 0.0000 0.896688 0.000 0.000 1.000 0.000 0.000
#> SRR1044454 3 0.0000 0.896688 0.000 0.000 1.000 0.000 0.000
#> SRR1044455 2 0.5416 0.251299 0.000 0.584 0.364 0.028 0.024
#> SRR1044456 5 0.6773 0.374100 0.044 0.116 0.000 0.316 0.524
#> SRR1044457 2 0.3355 0.665836 0.000 0.832 0.132 0.000 0.036
#> SRR1044458 2 0.2761 0.693124 0.000 0.872 0.104 0.000 0.024
#> SRR1044459 3 0.2473 0.862694 0.000 0.072 0.896 0.000 0.032
#> SRR1044460 2 0.0162 0.735919 0.000 0.996 0.000 0.004 0.000
#> SRR1044461 2 0.1862 0.727492 0.000 0.932 0.048 0.004 0.016
#> SRR1044462 1 0.2305 0.818022 0.896 0.000 0.000 0.012 0.092
#> SRR1044463 1 0.3116 0.797405 0.860 0.000 0.000 0.064 0.076
#> SRR1044464 4 0.5778 0.516009 0.112 0.016 0.012 0.684 0.176
#> SRR1044466 1 0.3916 0.776340 0.804 0.000 0.000 0.092 0.104
#> SRR1044465 1 0.4365 0.740411 0.768 0.000 0.000 0.116 0.116
#> SRR1044467 1 0.1965 0.809399 0.924 0.000 0.000 0.024 0.052
#> SRR1044468 2 0.0324 0.736417 0.000 0.992 0.000 0.004 0.004
#> SRR1044469 3 0.2540 0.852669 0.000 0.088 0.888 0.000 0.024
#> SRR1044470 1 0.2962 0.802146 0.868 0.000 0.000 0.048 0.084
#> SRR1044471 1 0.5045 0.693562 0.696 0.000 0.000 0.108 0.196
#> SRR1044472 1 0.4155 0.777020 0.780 0.000 0.000 0.076 0.144
#> SRR1044473 1 0.3846 0.788123 0.800 0.000 0.000 0.056 0.144
#> SRR1044474 5 0.6347 0.793517 0.000 0.408 0.000 0.160 0.432
#> SRR1044475 3 0.0000 0.896688 0.000 0.000 1.000 0.000 0.000
#> SRR1044476 2 0.3321 0.667172 0.000 0.832 0.136 0.000 0.032
#> SRR1044477 5 0.6482 0.803758 0.000 0.372 0.000 0.188 0.440
#> SRR1044478 2 0.0451 0.736853 0.000 0.988 0.000 0.004 0.008
#> SRR1044479 5 0.6863 0.738352 0.008 0.272 0.000 0.268 0.452
#> SRR1044480 1 0.2470 0.818050 0.884 0.000 0.000 0.012 0.104
#> SRR1044481 1 0.1357 0.812693 0.948 0.000 0.000 0.004 0.048
#> SRR1044482 2 0.4161 0.366437 0.000 0.752 0.000 0.040 0.208
#> SRR1044483 1 0.3555 0.809629 0.824 0.000 0.000 0.052 0.124
#> SRR1044484 1 0.1124 0.811306 0.960 0.000 0.000 0.004 0.036
#> SRR1044486 1 0.0566 0.807173 0.984 0.000 0.000 0.004 0.012
#> SRR1044485 2 0.0324 0.734590 0.000 0.992 0.000 0.004 0.004
#> SRR1044487 5 0.6347 0.794415 0.000 0.408 0.000 0.160 0.432
#> SRR1044488 2 0.0162 0.735919 0.000 0.996 0.000 0.004 0.000
#> SRR1044489 2 0.0162 0.735919 0.000 0.996 0.000 0.004 0.000
#> SRR1044490 4 0.6378 0.402491 0.288 0.004 0.000 0.528 0.180
#> SRR1044491 1 0.6021 0.565348 0.580 0.000 0.000 0.232 0.188
#> SRR1044492 1 0.4535 0.716972 0.752 0.000 0.000 0.140 0.108
#> SRR1044493 1 0.1168 0.811799 0.960 0.000 0.000 0.008 0.032
#> SRR1044494 5 0.6415 0.800194 0.000 0.400 0.000 0.172 0.428
#> SRR1044496 5 0.6614 0.776731 0.000 0.316 0.000 0.236 0.448
#> SRR1044495 5 0.6390 0.804740 0.000 0.396 0.000 0.168 0.436
#> SRR1044497 1 0.2806 0.788701 0.844 0.000 0.000 0.004 0.152
#> SRR1044499 3 0.2653 0.846233 0.000 0.096 0.880 0.000 0.024
#> SRR1044498 1 0.1877 0.813817 0.924 0.000 0.000 0.012 0.064
#> SRR1044500 2 0.0162 0.735919 0.000 0.996 0.000 0.004 0.000
#> SRR1044501 2 0.1800 0.725628 0.000 0.932 0.048 0.000 0.020
#> SRR1044502 4 0.7972 0.110232 0.000 0.236 0.240 0.420 0.104
#> SRR1044503 1 0.3530 0.778052 0.784 0.000 0.000 0.012 0.204
#> SRR1044504 1 0.5013 0.715817 0.680 0.000 0.000 0.080 0.240
#> SRR1044505 1 0.2729 0.803705 0.884 0.000 0.000 0.056 0.060
#> SRR1044506 1 0.6728 0.187899 0.404 0.000 0.000 0.336 0.260
#> SRR1044507 4 0.1467 0.582423 0.004 0.008 0.016 0.956 0.016
#> SRR1044508 4 0.1739 0.586061 0.000 0.024 0.032 0.940 0.004
#> SRR1044509 4 0.1372 0.589784 0.000 0.016 0.024 0.956 0.004
#> SRR1044510 3 0.0162 0.896003 0.000 0.000 0.996 0.000 0.004
#> SRR1044511 3 0.0324 0.896586 0.000 0.000 0.992 0.004 0.004
#> SRR1044512 3 0.0324 0.896586 0.000 0.000 0.992 0.004 0.004
#> SRR1044513 4 0.8021 0.134466 0.000 0.224 0.248 0.416 0.112
#> SRR1044514 3 0.0324 0.896586 0.000 0.000 0.992 0.004 0.004
#> SRR1044515 4 0.7988 0.120428 0.000 0.224 0.248 0.420 0.108
#> SRR1044516 2 0.2856 0.700590 0.000 0.892 0.032 0.032 0.044
#> SRR1044517 3 0.0162 0.896003 0.000 0.000 0.996 0.000 0.004
#> SRR1044518 3 0.0324 0.896586 0.000 0.000 0.992 0.004 0.004
#> SRR1044519 3 0.1597 0.889181 0.000 0.000 0.940 0.012 0.048
#> SRR1044520 3 0.1484 0.889969 0.000 0.000 0.944 0.008 0.048
#> SRR1044521 2 0.3227 0.681437 0.000 0.868 0.072 0.040 0.020
#> SRR1044522 5 0.7019 0.487678 0.028 0.168 0.000 0.368 0.436
#> SRR1044523 4 0.7915 -0.030830 0.000 0.320 0.160 0.404 0.116
#> SRR1044524 3 0.5814 0.630565 0.000 0.232 0.656 0.044 0.068
#> SRR1044525 1 0.4967 0.755581 0.704 0.000 0.000 0.104 0.192
#> SRR1044526 1 0.5446 0.661061 0.660 0.000 0.000 0.164 0.176
#> SRR1044527 2 0.6483 -0.324279 0.000 0.508 0.004 0.296 0.192
#> SRR1044528 4 0.5839 0.000719 0.000 0.336 0.016 0.576 0.072
#> SRR1044529 2 0.6349 -0.788582 0.000 0.424 0.000 0.160 0.416
#> SRR1044530 1 0.1764 0.804022 0.928 0.000 0.000 0.008 0.064
#> SRR1044531 1 0.3608 0.785852 0.824 0.000 0.000 0.064 0.112
#> SRR1044533 1 0.5043 0.682537 0.704 0.000 0.000 0.160 0.136
#> SRR1044532 1 0.1697 0.801267 0.932 0.000 0.000 0.008 0.060
#> SRR1044534 2 0.0798 0.732545 0.000 0.976 0.000 0.008 0.016
#> SRR1044535 3 0.6150 0.660758 0.000 0.176 0.660 0.076 0.088
#> SRR1044536 2 0.0162 0.735919 0.000 0.996 0.000 0.004 0.000
#> SRR1044537 1 0.1774 0.812137 0.932 0.000 0.000 0.016 0.052
#> SRR1044538 1 0.1408 0.803169 0.948 0.000 0.000 0.008 0.044
#> SRR1044539 1 0.3048 0.781201 0.820 0.000 0.000 0.004 0.176
#> SRR1044540 1 0.4724 0.726842 0.732 0.000 0.000 0.104 0.164
#> SRR1044541 2 0.2824 0.702242 0.000 0.872 0.096 0.000 0.032
#> SRR1044542 1 0.1469 0.809568 0.948 0.000 0.000 0.016 0.036
#> SRR1044543 1 0.6224 0.460289 0.548 0.000 0.000 0.232 0.220
#> SRR1044544 2 0.4297 0.548564 0.000 0.728 0.236 0.000 0.036
#> SRR1044545 1 0.3300 0.776500 0.792 0.000 0.000 0.004 0.204
#> SRR1044546 1 0.1774 0.805941 0.932 0.000 0.000 0.016 0.052
#> SRR1044547 1 0.2929 0.792739 0.840 0.000 0.000 0.008 0.152
#> SRR1044548 1 0.1836 0.815114 0.932 0.000 0.000 0.032 0.036
#> SRR1044549 2 0.6816 -0.166059 0.000 0.484 0.024 0.336 0.156
#> SRR1044550 2 0.0324 0.736417 0.000 0.992 0.000 0.004 0.004
#> SRR1044551 2 0.5087 0.268053 0.000 0.700 0.000 0.148 0.152
#> SRR1044552 1 0.3819 0.767309 0.756 0.000 0.000 0.016 0.228
#> SRR1044553 1 0.6491 0.470503 0.492 0.000 0.000 0.264 0.244
#> SRR1044554 1 0.2136 0.816360 0.904 0.000 0.000 0.008 0.088
#> SRR1044555 3 0.2813 0.851501 0.000 0.084 0.876 0.000 0.040
#> SRR1044556 1 0.3123 0.778278 0.812 0.000 0.000 0.004 0.184
#> SRR1044557 1 0.1914 0.813884 0.924 0.000 0.000 0.016 0.060
#> SRR1044558 1 0.2891 0.782674 0.824 0.000 0.000 0.000 0.176
#> SRR1044559 4 0.6302 0.288300 0.356 0.016 0.000 0.520 0.108
#> SRR1044561 1 0.2891 0.784454 0.824 0.000 0.000 0.000 0.176
#> SRR1044560 2 0.3656 0.637449 0.000 0.800 0.168 0.000 0.032
#> SRR1044562 1 0.3215 0.791695 0.852 0.000 0.000 0.056 0.092
#> SRR1044563 1 0.3455 0.774108 0.784 0.000 0.000 0.008 0.208
#> SRR1044564 1 0.5164 0.617698 0.672 0.000 0.000 0.232 0.096
#> SRR1044565 5 0.6344 0.800550 0.000 0.400 0.000 0.160 0.440
#> SRR1044566 2 0.3106 0.675254 0.000 0.844 0.132 0.000 0.024
#> SRR1044567 1 0.3269 0.785681 0.848 0.000 0.000 0.096 0.056
#> SRR1044568 1 0.4674 0.747642 0.708 0.000 0.000 0.060 0.232
#> SRR1044569 1 0.4593 0.695003 0.736 0.000 0.000 0.184 0.080
#> SRR1044570 1 0.2006 0.798524 0.916 0.000 0.000 0.012 0.072
#> SRR1044571 1 0.2722 0.803969 0.872 0.000 0.000 0.020 0.108
#> SRR1044572 1 0.4711 0.733347 0.736 0.000 0.000 0.116 0.148
#> SRR1044573 1 0.4879 0.704296 0.720 0.000 0.000 0.156 0.124
#> SRR1044574 1 0.6049 0.494648 0.576 0.000 0.000 0.232 0.192
#> SRR1044575 1 0.3110 0.796480 0.860 0.000 0.000 0.060 0.080
#> SRR1044576 2 0.2989 0.617816 0.000 0.868 0.000 0.060 0.072
#> SRR1044577 2 0.5974 -0.364568 0.000 0.564 0.000 0.144 0.292
#> SRR1044578 5 0.6349 0.784942 0.000 0.412 0.000 0.160 0.428
#> SRR1044579 1 0.2891 0.785097 0.824 0.000 0.000 0.000 0.176
#> SRR1044580 1 0.2293 0.816215 0.900 0.000 0.000 0.016 0.084
#> SRR1044581 1 0.3086 0.781568 0.816 0.000 0.000 0.004 0.180
#> SRR1044582 1 0.1012 0.807229 0.968 0.000 0.000 0.012 0.020
#> SRR1044583 1 0.2930 0.790254 0.832 0.000 0.000 0.004 0.164
#> SRR1044584 1 0.3327 0.815512 0.828 0.000 0.000 0.028 0.144
#> SRR1044585 1 0.2890 0.787376 0.836 0.000 0.000 0.004 0.160
#> SRR1044586 1 0.0992 0.809168 0.968 0.000 0.000 0.008 0.024
#> SRR1044587 4 0.6890 0.144817 0.292 0.004 0.000 0.404 0.300
#> SRR1044588 1 0.6581 0.364998 0.468 0.000 0.000 0.280 0.252
#> SRR1044589 1 0.6612 0.362854 0.460 0.000 0.000 0.276 0.264
#> SRR1044590 1 0.6541 0.388973 0.480 0.000 0.000 0.264 0.256
#> SRR1044591 4 0.6698 0.090632 0.316 0.000 0.000 0.424 0.260
#> SRR1044592 4 0.1461 0.588885 0.000 0.016 0.028 0.952 0.004
#> SRR1044593 1 0.6649 0.329718 0.448 0.000 0.000 0.284 0.268
#> SRR1044594 1 0.6745 0.222183 0.408 0.000 0.000 0.312 0.280
#> SRR1044595 4 0.1461 0.588885 0.000 0.016 0.028 0.952 0.004
#> SRR1044596 4 0.1617 0.581728 0.000 0.012 0.020 0.948 0.020
#> SRR1044597 4 0.3117 0.586101 0.036 0.016 0.012 0.884 0.052
#> SRR1044598 1 0.2616 0.794130 0.880 0.000 0.000 0.020 0.100
#> SRR1044599 1 0.2561 0.795988 0.884 0.000 0.000 0.020 0.096
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.2926 0.7800 0.000 0.876 0.048 0.048 0.008 0.020
#> SRR1044416 6 0.3996 0.2537 0.000 0.484 0.000 0.004 0.000 0.512
#> SRR1044417 6 0.4794 0.5705 0.000 0.328 0.000 0.004 0.060 0.608
#> SRR1044418 6 0.2831 0.7517 0.000 0.136 0.000 0.000 0.024 0.840
#> SRR1044420 2 0.1843 0.8157 0.000 0.912 0.000 0.004 0.004 0.080
#> SRR1044419 2 0.2444 0.7925 0.000 0.904 0.032 0.036 0.008 0.020
#> SRR1044421 2 0.4015 0.7653 0.000 0.804 0.028 0.016 0.044 0.108
#> SRR1044422 2 0.1471 0.8169 0.000 0.932 0.000 0.004 0.000 0.064
#> SRR1044423 2 0.1531 0.8174 0.000 0.928 0.000 0.004 0.000 0.068
#> SRR1044424 2 0.1858 0.8078 0.000 0.904 0.000 0.004 0.000 0.092
#> SRR1044425 1 0.3930 0.5474 0.744 0.000 0.000 0.216 0.028 0.012
#> SRR1044426 4 0.7550 -0.2597 0.088 0.036 0.008 0.380 0.376 0.112
#> SRR1044427 1 0.2703 0.6457 0.824 0.000 0.000 0.172 0.000 0.004
#> SRR1044428 1 0.5292 0.2580 0.580 0.000 0.000 0.312 0.100 0.008
#> SRR1044429 1 0.4888 0.3976 0.592 0.000 0.000 0.352 0.020 0.036
#> SRR1044430 5 0.6847 0.1433 0.112 0.004 0.000 0.348 0.436 0.100
#> SRR1044431 1 0.3849 0.5555 0.752 0.000 0.000 0.208 0.032 0.008
#> SRR1044433 5 0.1555 0.6163 0.000 0.004 0.004 0.000 0.932 0.060
#> SRR1044432 4 0.6865 -0.1477 0.112 0.004 0.004 0.448 0.344 0.088
#> SRR1044434 1 0.3725 0.5177 0.676 0.000 0.000 0.316 0.008 0.000
#> SRR1044435 1 0.3464 0.4940 0.688 0.000 0.000 0.312 0.000 0.000
#> SRR1044436 1 0.3198 0.5323 0.740 0.000 0.000 0.260 0.000 0.000
#> SRR1044437 1 0.3409 0.5129 0.700 0.000 0.000 0.300 0.000 0.000
#> SRR1044439 1 0.3330 0.5199 0.716 0.000 0.000 0.284 0.000 0.000
#> SRR1044438 1 0.3351 0.5134 0.712 0.000 0.000 0.288 0.000 0.000
#> SRR1044440 1 0.3531 0.4869 0.672 0.000 0.000 0.328 0.000 0.000
#> SRR1044441 5 0.5305 0.4240 0.028 0.000 0.000 0.260 0.628 0.084
#> SRR1044442 5 0.2507 0.6139 0.000 0.004 0.000 0.040 0.884 0.072
#> SRR1044443 5 0.1812 0.6156 0.000 0.008 0.004 0.004 0.924 0.060
#> SRR1044444 1 0.3076 0.5689 0.760 0.000 0.000 0.240 0.000 0.000
#> SRR1044445 5 0.6715 0.0803 0.096 0.000 0.000 0.328 0.456 0.120
#> SRR1044446 3 0.5187 0.7258 0.000 0.032 0.716 0.040 0.156 0.056
#> SRR1044447 5 0.6874 -0.1241 0.000 0.092 0.376 0.044 0.440 0.048
#> SRR1044449 3 0.0551 0.8625 0.000 0.000 0.984 0.004 0.004 0.008
#> SRR1044448 3 0.2566 0.8396 0.000 0.000 0.888 0.028 0.064 0.020
#> SRR1044450 3 0.2642 0.8386 0.000 0.000 0.884 0.032 0.064 0.020
#> SRR1044451 5 0.7028 0.0617 0.000 0.100 0.316 0.040 0.476 0.068
#> SRR1044452 3 0.0508 0.8619 0.000 0.000 0.984 0.004 0.000 0.012
#> SRR1044453 3 0.0508 0.8619 0.000 0.000 0.984 0.004 0.000 0.012
#> SRR1044454 3 0.0508 0.8619 0.000 0.000 0.984 0.004 0.000 0.012
#> SRR1044455 2 0.5409 0.6053 0.000 0.680 0.200 0.036 0.036 0.048
#> SRR1044456 6 0.6494 0.2165 0.028 0.020 0.004 0.176 0.216 0.556
#> SRR1044457 2 0.4752 0.6860 0.000 0.736 0.144 0.084 0.008 0.028
#> SRR1044458 2 0.4336 0.7042 0.000 0.768 0.116 0.092 0.008 0.016
#> SRR1044459 3 0.4742 0.7672 0.000 0.116 0.760 0.056 0.032 0.036
#> SRR1044460 2 0.1531 0.8178 0.000 0.928 0.000 0.004 0.000 0.068
#> SRR1044461 2 0.1599 0.8105 0.000 0.940 0.024 0.008 0.000 0.028
#> SRR1044462 1 0.2146 0.6566 0.880 0.000 0.000 0.116 0.000 0.004
#> SRR1044463 1 0.3499 0.6062 0.812 0.000 0.000 0.132 0.044 0.012
#> SRR1044464 5 0.7064 0.2889 0.068 0.016 0.004 0.288 0.476 0.148
#> SRR1044466 1 0.4361 0.5165 0.724 0.000 0.000 0.196 0.072 0.008
#> SRR1044465 1 0.4610 0.4475 0.664 0.000 0.000 0.272 0.056 0.008
#> SRR1044467 1 0.2118 0.6605 0.888 0.000 0.000 0.104 0.000 0.008
#> SRR1044468 2 0.1588 0.8156 0.000 0.924 0.000 0.004 0.000 0.072
#> SRR1044469 3 0.5240 0.7047 0.000 0.172 0.692 0.088 0.008 0.040
#> SRR1044470 1 0.3048 0.6237 0.824 0.000 0.000 0.152 0.020 0.004
#> SRR1044471 1 0.5307 0.3274 0.588 0.000 0.000 0.324 0.052 0.036
#> SRR1044472 1 0.4283 0.5317 0.696 0.000 0.000 0.252 0.048 0.004
#> SRR1044473 1 0.3897 0.5682 0.712 0.000 0.000 0.264 0.016 0.008
#> SRR1044474 6 0.2165 0.7503 0.000 0.108 0.000 0.000 0.008 0.884
#> SRR1044475 3 0.0508 0.8619 0.000 0.000 0.984 0.004 0.000 0.012
#> SRR1044476 2 0.4864 0.6667 0.000 0.720 0.148 0.104 0.008 0.020
#> SRR1044477 6 0.2537 0.7448 0.000 0.096 0.000 0.000 0.032 0.872
#> SRR1044478 2 0.1588 0.8175 0.000 0.924 0.000 0.004 0.000 0.072
#> SRR1044479 6 0.4044 0.6723 0.004 0.076 0.000 0.028 0.096 0.796
#> SRR1044480 1 0.3152 0.6384 0.792 0.000 0.000 0.196 0.008 0.004
#> SRR1044481 1 0.1663 0.6553 0.912 0.000 0.000 0.088 0.000 0.000
#> SRR1044482 6 0.3998 0.2076 0.000 0.492 0.000 0.004 0.000 0.504
#> SRR1044483 1 0.3852 0.6014 0.732 0.000 0.000 0.240 0.016 0.012
#> SRR1044484 1 0.1285 0.6597 0.944 0.000 0.000 0.052 0.000 0.004
#> SRR1044486 1 0.1204 0.6562 0.944 0.000 0.000 0.056 0.000 0.000
#> SRR1044485 2 0.1814 0.8037 0.000 0.900 0.000 0.000 0.000 0.100
#> SRR1044487 6 0.2501 0.7511 0.000 0.108 0.000 0.004 0.016 0.872
#> SRR1044488 2 0.1958 0.8104 0.000 0.896 0.000 0.004 0.000 0.100
#> SRR1044489 2 0.1644 0.8142 0.000 0.920 0.000 0.004 0.000 0.076
#> SRR1044490 5 0.7387 -0.0435 0.200 0.012 0.000 0.304 0.392 0.092
#> SRR1044491 1 0.5817 0.0688 0.500 0.000 0.000 0.348 0.140 0.012
#> SRR1044492 1 0.4394 0.4557 0.676 0.000 0.000 0.276 0.040 0.008
#> SRR1044493 1 0.1714 0.6581 0.908 0.000 0.000 0.092 0.000 0.000
#> SRR1044494 6 0.2404 0.7535 0.000 0.112 0.000 0.000 0.016 0.872
#> SRR1044496 6 0.3016 0.7320 0.000 0.092 0.000 0.008 0.048 0.852
#> SRR1044495 6 0.2350 0.7494 0.000 0.100 0.000 0.000 0.020 0.880
#> SRR1044497 1 0.2969 0.5753 0.776 0.000 0.000 0.224 0.000 0.000
#> SRR1044499 3 0.5240 0.7047 0.000 0.172 0.692 0.088 0.008 0.040
#> SRR1044498 1 0.1556 0.6537 0.920 0.000 0.000 0.080 0.000 0.000
#> SRR1044500 2 0.1958 0.8039 0.000 0.896 0.000 0.004 0.000 0.100
#> SRR1044501 2 0.2990 0.7714 0.000 0.872 0.052 0.048 0.008 0.020
#> SRR1044502 5 0.7783 0.2649 0.000 0.216 0.148 0.044 0.444 0.148
#> SRR1044503 1 0.3390 0.5236 0.704 0.000 0.000 0.296 0.000 0.000
#> SRR1044504 1 0.4762 0.3112 0.576 0.000 0.000 0.380 0.020 0.024
#> SRR1044505 1 0.2572 0.6228 0.852 0.000 0.000 0.136 0.012 0.000
#> SRR1044506 4 0.6794 0.6254 0.312 0.000 0.000 0.428 0.200 0.060
#> SRR1044507 5 0.2712 0.6074 0.000 0.000 0.000 0.048 0.864 0.088
#> SRR1044508 5 0.1769 0.6150 0.000 0.012 0.004 0.000 0.924 0.060
#> SRR1044509 5 0.1913 0.6183 0.000 0.004 0.004 0.012 0.920 0.060
#> SRR1044510 3 0.0405 0.8623 0.000 0.000 0.988 0.008 0.000 0.004
#> SRR1044511 3 0.0551 0.8615 0.000 0.000 0.984 0.008 0.004 0.004
#> SRR1044512 3 0.0551 0.8615 0.000 0.000 0.984 0.008 0.004 0.004
#> SRR1044513 5 0.7353 0.3404 0.000 0.144 0.148 0.048 0.524 0.136
#> SRR1044514 3 0.0551 0.8615 0.000 0.000 0.984 0.008 0.004 0.004
#> SRR1044515 5 0.7635 0.3033 0.000 0.180 0.160 0.044 0.476 0.140
#> SRR1044516 2 0.2763 0.8028 0.000 0.876 0.008 0.016 0.016 0.084
#> SRR1044517 3 0.0520 0.8622 0.000 0.000 0.984 0.008 0.000 0.008
#> SRR1044518 3 0.0551 0.8615 0.000 0.000 0.984 0.008 0.004 0.004
#> SRR1044519 3 0.2714 0.8387 0.000 0.000 0.880 0.036 0.064 0.020
#> SRR1044520 3 0.2642 0.8396 0.000 0.000 0.884 0.032 0.064 0.020
#> SRR1044521 2 0.4375 0.7265 0.000 0.764 0.040 0.012 0.032 0.152
#> SRR1044522 6 0.5892 0.3281 0.008 0.048 0.000 0.084 0.268 0.592
#> SRR1044523 5 0.7883 0.1944 0.000 0.272 0.120 0.044 0.396 0.168
#> SRR1044524 3 0.7111 0.4831 0.000 0.244 0.520 0.064 0.112 0.060
#> SRR1044525 1 0.4500 0.3581 0.572 0.000 0.000 0.392 0.036 0.000
#> SRR1044526 1 0.5130 0.3826 0.600 0.000 0.000 0.296 0.100 0.004
#> SRR1044527 6 0.6266 0.4156 0.000 0.304 0.000 0.012 0.248 0.436
#> SRR1044528 5 0.6100 0.2145 0.000 0.248 0.000 0.020 0.520 0.212
#> SRR1044529 6 0.2673 0.7537 0.000 0.132 0.000 0.004 0.012 0.852
#> SRR1044530 1 0.1387 0.6533 0.932 0.000 0.000 0.068 0.000 0.000
#> SRR1044531 1 0.3761 0.6020 0.764 0.000 0.000 0.196 0.032 0.008
#> SRR1044533 1 0.4817 0.3749 0.612 0.000 0.000 0.320 0.064 0.004
#> SRR1044532 1 0.1531 0.6475 0.928 0.000 0.000 0.068 0.000 0.004
#> SRR1044534 2 0.2053 0.8059 0.000 0.888 0.000 0.004 0.000 0.108
#> SRR1044535 3 0.7348 0.4468 0.000 0.196 0.496 0.048 0.188 0.072
#> SRR1044536 2 0.1753 0.8129 0.000 0.912 0.000 0.004 0.000 0.084
#> SRR1044537 1 0.2454 0.6509 0.876 0.000 0.000 0.104 0.016 0.004
#> SRR1044538 1 0.1610 0.6516 0.916 0.000 0.000 0.084 0.000 0.000
#> SRR1044539 1 0.3175 0.5402 0.744 0.000 0.000 0.256 0.000 0.000
#> SRR1044540 1 0.4488 0.4288 0.652 0.000 0.000 0.304 0.032 0.012
#> SRR1044541 2 0.3608 0.7551 0.000 0.828 0.052 0.092 0.008 0.020
#> SRR1044542 1 0.2053 0.6601 0.888 0.000 0.000 0.108 0.000 0.004
#> SRR1044543 1 0.6423 -0.1469 0.436 0.000 0.000 0.348 0.184 0.032
#> SRR1044544 2 0.5440 0.6127 0.000 0.668 0.184 0.104 0.008 0.036
#> SRR1044545 1 0.3371 0.5131 0.708 0.000 0.000 0.292 0.000 0.000
#> SRR1044546 1 0.2113 0.6469 0.896 0.000 0.000 0.092 0.008 0.004
#> SRR1044547 1 0.2941 0.5841 0.780 0.000 0.000 0.220 0.000 0.000
#> SRR1044548 1 0.2624 0.6569 0.856 0.000 0.000 0.124 0.020 0.000
#> SRR1044549 6 0.7353 0.2481 0.000 0.280 0.052 0.024 0.260 0.384
#> SRR1044550 2 0.1588 0.8156 0.000 0.924 0.000 0.004 0.000 0.072
#> SRR1044551 6 0.4602 0.1725 0.000 0.480 0.000 0.004 0.028 0.488
#> SRR1044552 1 0.3607 0.4631 0.652 0.000 0.000 0.348 0.000 0.000
#> SRR1044553 4 0.6082 0.3256 0.392 0.000 0.000 0.456 0.120 0.032
#> SRR1044554 1 0.2920 0.6494 0.820 0.000 0.000 0.168 0.008 0.004
#> SRR1044555 3 0.4996 0.7538 0.000 0.124 0.740 0.064 0.028 0.044
#> SRR1044556 1 0.3288 0.5196 0.724 0.000 0.000 0.276 0.000 0.000
#> SRR1044557 1 0.2615 0.6597 0.852 0.000 0.000 0.136 0.008 0.004
#> SRR1044558 1 0.3351 0.5241 0.712 0.000 0.000 0.288 0.000 0.000
#> SRR1044559 5 0.7400 -0.2898 0.272 0.008 0.000 0.236 0.388 0.096
#> SRR1044561 1 0.3371 0.5259 0.708 0.000 0.000 0.292 0.000 0.000
#> SRR1044560 2 0.4967 0.6543 0.000 0.708 0.160 0.104 0.008 0.020
#> SRR1044562 1 0.3535 0.5744 0.760 0.000 0.000 0.220 0.008 0.012
#> SRR1044563 1 0.3428 0.5100 0.696 0.000 0.000 0.304 0.000 0.000
#> SRR1044564 1 0.5280 0.3093 0.616 0.000 0.000 0.248 0.128 0.008
#> SRR1044565 6 0.2311 0.7503 0.000 0.104 0.000 0.000 0.016 0.880
#> SRR1044566 2 0.4776 0.6732 0.000 0.728 0.148 0.096 0.008 0.020
#> SRR1044567 1 0.3301 0.6141 0.828 0.000 0.000 0.100 0.068 0.004
#> SRR1044568 1 0.4411 0.4141 0.612 0.000 0.000 0.356 0.028 0.004
#> SRR1044569 1 0.4219 0.5089 0.720 0.000 0.000 0.224 0.048 0.008
#> SRR1044570 1 0.2053 0.6428 0.888 0.000 0.000 0.108 0.000 0.004
#> SRR1044571 1 0.3219 0.6219 0.792 0.000 0.000 0.192 0.012 0.004
#> SRR1044572 1 0.5079 0.3910 0.620 0.000 0.000 0.288 0.080 0.012
#> SRR1044573 1 0.4468 0.4544 0.660 0.000 0.000 0.288 0.048 0.004
#> SRR1044574 1 0.5583 0.1668 0.516 0.000 0.000 0.372 0.096 0.016
#> SRR1044575 1 0.2778 0.6207 0.824 0.000 0.000 0.168 0.008 0.000
#> SRR1044576 2 0.3652 0.4335 0.000 0.672 0.000 0.004 0.000 0.324
#> SRR1044577 6 0.3713 0.6446 0.000 0.284 0.000 0.004 0.008 0.704
#> SRR1044578 6 0.2362 0.7526 0.000 0.136 0.000 0.000 0.004 0.860
#> SRR1044579 1 0.3428 0.5247 0.696 0.000 0.000 0.304 0.000 0.000
#> SRR1044580 1 0.2562 0.6369 0.828 0.000 0.000 0.172 0.000 0.000
#> SRR1044581 1 0.3244 0.5357 0.732 0.000 0.000 0.268 0.000 0.000
#> SRR1044582 1 0.1141 0.6565 0.948 0.000 0.000 0.052 0.000 0.000
#> SRR1044583 1 0.3349 0.5609 0.748 0.000 0.000 0.244 0.008 0.000
#> SRR1044584 1 0.3290 0.5970 0.744 0.000 0.000 0.252 0.004 0.000
#> SRR1044585 1 0.3266 0.5436 0.728 0.000 0.000 0.272 0.000 0.000
#> SRR1044586 1 0.1411 0.6567 0.936 0.000 0.000 0.060 0.000 0.004
#> SRR1044587 4 0.6917 0.6236 0.240 0.000 0.000 0.464 0.208 0.088
#> SRR1044588 4 0.6510 0.4830 0.396 0.000 0.000 0.416 0.124 0.064
#> SRR1044589 4 0.6180 0.5035 0.376 0.000 0.000 0.464 0.120 0.040
#> SRR1044590 1 0.6364 -0.4620 0.436 0.000 0.000 0.392 0.116 0.056
#> SRR1044591 4 0.6769 0.6230 0.256 0.000 0.000 0.456 0.228 0.060
#> SRR1044592 5 0.1555 0.6163 0.000 0.004 0.004 0.000 0.932 0.060
#> SRR1044593 4 0.6470 0.5565 0.356 0.000 0.000 0.452 0.136 0.056
#> SRR1044594 4 0.6716 0.6236 0.300 0.000 0.000 0.464 0.164 0.072
#> SRR1044595 5 0.1411 0.6160 0.000 0.004 0.000 0.000 0.936 0.060
#> SRR1044596 5 0.2579 0.6085 0.000 0.000 0.000 0.040 0.872 0.088
#> SRR1044597 5 0.4291 0.5245 0.012 0.004 0.000 0.164 0.752 0.068
#> SRR1044598 1 0.2573 0.6308 0.856 0.000 0.000 0.132 0.008 0.004
#> SRR1044599 1 0.2573 0.6308 0.856 0.000 0.000 0.132 0.008 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)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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 714 rows and 185 columns.
#> Top rows (71, 142, 214, 286, 357) 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)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
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 0.259 0.761 0.836 0.4905 0.508 0.508
#> 3 3 0.327 0.593 0.746 0.2653 0.900 0.805
#> 4 4 0.437 0.596 0.713 0.1421 0.807 0.580
#> 5 5 0.521 0.573 0.709 0.0879 0.790 0.445
#> 6 6 0.582 0.566 0.705 0.0323 0.975 0.900
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.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1044415 2 0.0000 0.7883 0.000 1.000
#> SRR1044416 2 0.8555 0.7446 0.280 0.720
#> SRR1044417 2 0.9732 0.6887 0.404 0.596
#> SRR1044418 2 0.9754 0.6850 0.408 0.592
#> SRR1044420 2 0.7219 0.7508 0.200 0.800
#> SRR1044419 2 0.0000 0.7883 0.000 1.000
#> SRR1044421 2 0.9393 0.7147 0.356 0.644
#> SRR1044422 2 0.1633 0.7901 0.024 0.976
#> SRR1044423 2 0.0376 0.7888 0.004 0.996
#> SRR1044424 2 0.7139 0.7498 0.196 0.804
#> SRR1044425 1 0.5946 0.8103 0.856 0.144
#> SRR1044426 1 0.9286 0.7057 0.656 0.344
#> SRR1044427 1 0.8267 0.7262 0.740 0.260
#> SRR1044428 1 0.7299 0.7857 0.796 0.204
#> SRR1044429 1 0.7528 0.7540 0.784 0.216
#> SRR1044430 1 0.9881 0.5728 0.564 0.436
#> SRR1044431 1 0.5519 0.8311 0.872 0.128
#> SRR1044433 1 0.9460 0.5062 0.636 0.364
#> SRR1044432 1 0.7815 0.7802 0.768 0.232
#> SRR1044434 1 0.1414 0.8235 0.980 0.020
#> SRR1044435 1 0.6623 0.7567 0.828 0.172
#> SRR1044436 1 0.1843 0.8235 0.972 0.028
#> SRR1044437 1 0.3431 0.8222 0.936 0.064
#> SRR1044439 1 0.0938 0.8214 0.988 0.012
#> SRR1044438 1 0.1843 0.8237 0.972 0.028
#> SRR1044440 1 0.2236 0.8249 0.964 0.036
#> SRR1044441 1 0.0000 0.8175 1.000 0.000
#> SRR1044442 1 0.3274 0.8291 0.940 0.060
#> SRR1044443 1 0.8386 0.4646 0.732 0.268
#> SRR1044444 1 0.3274 0.8229 0.940 0.060
#> SRR1044445 1 0.0000 0.8175 1.000 0.000
#> SRR1044446 2 0.7219 0.7288 0.200 0.800
#> SRR1044447 2 0.7453 0.7291 0.212 0.788
#> SRR1044449 2 0.4690 0.7719 0.100 0.900
#> SRR1044448 2 0.7219 0.7288 0.200 0.800
#> SRR1044450 2 0.7219 0.7288 0.200 0.800
#> SRR1044451 2 0.8081 0.7281 0.248 0.752
#> SRR1044452 2 0.0000 0.7883 0.000 1.000
#> SRR1044453 2 0.0000 0.7883 0.000 1.000
#> SRR1044454 2 0.0000 0.7883 0.000 1.000
#> SRR1044455 2 0.0000 0.7883 0.000 1.000
#> SRR1044456 2 0.9977 0.5874 0.472 0.528
#> SRR1044457 2 0.0000 0.7883 0.000 1.000
#> SRR1044458 2 0.0000 0.7883 0.000 1.000
#> SRR1044459 2 0.0000 0.7883 0.000 1.000
#> SRR1044460 2 0.3431 0.7877 0.064 0.936
#> SRR1044461 2 0.2778 0.7891 0.048 0.952
#> SRR1044462 1 0.4298 0.8308 0.912 0.088
#> SRR1044463 1 0.6973 0.7960 0.812 0.188
#> SRR1044464 1 0.5178 0.8242 0.884 0.116
#> SRR1044466 1 0.6887 0.7987 0.816 0.184
#> SRR1044465 1 0.7219 0.7915 0.800 0.200
#> SRR1044467 1 0.6801 0.8178 0.820 0.180
#> SRR1044468 2 0.7056 0.7522 0.192 0.808
#> SRR1044469 2 0.0000 0.7883 0.000 1.000
#> SRR1044470 1 0.8144 0.7659 0.748 0.252
#> SRR1044471 1 0.7453 0.7818 0.788 0.212
#> SRR1044472 1 0.7602 0.7783 0.780 0.220
#> SRR1044473 1 0.9170 0.7085 0.668 0.332
#> SRR1044474 2 0.9833 0.6676 0.424 0.576
#> SRR1044475 2 0.0000 0.7883 0.000 1.000
#> SRR1044476 2 0.0000 0.7883 0.000 1.000
#> SRR1044477 2 0.9815 0.6724 0.420 0.580
#> SRR1044478 2 0.6887 0.7566 0.184 0.816
#> SRR1044479 2 0.9909 0.6382 0.444 0.556
#> SRR1044480 1 0.3274 0.8352 0.940 0.060
#> SRR1044481 1 0.7219 0.8154 0.800 0.200
#> SRR1044482 2 0.7602 0.7374 0.220 0.780
#> SRR1044483 1 0.7883 0.7369 0.764 0.236
#> SRR1044484 1 0.5178 0.8020 0.884 0.116
#> SRR1044486 1 0.7453 0.7895 0.788 0.212
#> SRR1044485 2 0.7299 0.7483 0.204 0.796
#> SRR1044487 2 0.9944 0.6179 0.456 0.544
#> SRR1044488 2 0.6623 0.7665 0.172 0.828
#> SRR1044489 2 0.5294 0.7773 0.120 0.880
#> SRR1044490 1 0.7528 0.7810 0.784 0.216
#> SRR1044491 1 0.9850 0.6034 0.572 0.428
#> SRR1044492 1 0.7376 0.7982 0.792 0.208
#> SRR1044493 1 0.7056 0.8121 0.808 0.192
#> SRR1044494 2 0.9866 0.6564 0.432 0.568
#> SRR1044496 2 0.9732 0.6833 0.404 0.596
#> SRR1044495 2 0.9833 0.6675 0.424 0.576
#> SRR1044497 1 0.5178 0.7999 0.884 0.116
#> SRR1044499 2 0.0000 0.7883 0.000 1.000
#> SRR1044498 1 0.0000 0.8175 1.000 0.000
#> SRR1044500 2 0.7219 0.7508 0.200 0.800
#> SRR1044501 2 0.0000 0.7883 0.000 1.000
#> SRR1044502 2 0.9491 0.7054 0.368 0.632
#> SRR1044503 1 0.3879 0.8186 0.924 0.076
#> SRR1044504 1 0.6712 0.7520 0.824 0.176
#> SRR1044505 1 0.3733 0.8314 0.928 0.072
#> SRR1044506 1 0.0000 0.8175 1.000 0.000
#> SRR1044507 1 0.0000 0.8175 1.000 0.000
#> SRR1044508 1 0.1843 0.8228 0.972 0.028
#> SRR1044509 1 0.8207 0.7083 0.744 0.256
#> SRR1044510 2 0.0000 0.7883 0.000 1.000
#> SRR1044511 2 0.0672 0.7890 0.008 0.992
#> SRR1044512 2 0.0000 0.7883 0.000 1.000
#> SRR1044513 2 0.7453 0.7301 0.212 0.788
#> SRR1044514 2 0.1184 0.7887 0.016 0.984
#> SRR1044515 2 0.9710 0.6920 0.400 0.600
#> SRR1044516 2 0.1184 0.7880 0.016 0.984
#> SRR1044517 2 0.0000 0.7883 0.000 1.000
#> SRR1044518 2 0.3733 0.7798 0.072 0.928
#> SRR1044519 2 0.7299 0.7293 0.204 0.796
#> SRR1044520 2 0.7219 0.7288 0.200 0.800
#> SRR1044521 2 0.0000 0.7883 0.000 1.000
#> SRR1044522 2 0.9815 0.6598 0.420 0.580
#> SRR1044523 2 0.9580 0.7017 0.380 0.620
#> SRR1044524 2 0.6973 0.7363 0.188 0.812
#> SRR1044525 1 0.2778 0.8240 0.952 0.048
#> SRR1044526 1 0.9209 0.6986 0.664 0.336
#> SRR1044527 2 0.9795 0.6769 0.416 0.584
#> SRR1044528 2 0.9661 0.6965 0.392 0.608
#> SRR1044529 2 0.9209 0.7149 0.336 0.664
#> SRR1044530 1 0.7602 0.7790 0.780 0.220
#> SRR1044531 1 0.8909 0.7362 0.692 0.308
#> SRR1044533 1 0.7602 0.7792 0.780 0.220
#> SRR1044532 1 0.7453 0.7808 0.788 0.212
#> SRR1044534 2 0.6887 0.7560 0.184 0.816
#> SRR1044535 2 0.7219 0.7288 0.200 0.800
#> SRR1044536 2 0.2423 0.7902 0.040 0.960
#> SRR1044537 1 0.1843 0.8270 0.972 0.028
#> SRR1044538 1 0.7528 0.7812 0.784 0.216
#> SRR1044539 1 0.3274 0.8222 0.940 0.060
#> SRR1044540 1 0.7056 0.7966 0.808 0.192
#> SRR1044541 2 0.0000 0.7883 0.000 1.000
#> SRR1044542 1 0.5178 0.8254 0.884 0.116
#> SRR1044543 1 0.9775 0.6229 0.588 0.412
#> SRR1044544 2 0.0000 0.7883 0.000 1.000
#> SRR1044545 1 0.5737 0.7879 0.864 0.136
#> SRR1044546 1 0.3431 0.8253 0.936 0.064
#> SRR1044547 1 0.3431 0.8232 0.936 0.064
#> SRR1044548 1 0.6801 0.8172 0.820 0.180
#> SRR1044549 2 0.9710 0.6920 0.400 0.600
#> SRR1044550 2 0.6531 0.7627 0.168 0.832
#> SRR1044551 2 0.9710 0.6920 0.400 0.600
#> SRR1044552 1 0.4690 0.8094 0.900 0.100
#> SRR1044553 1 0.0000 0.8175 1.000 0.000
#> SRR1044554 1 0.8207 0.7758 0.744 0.256
#> SRR1044555 2 0.0672 0.7889 0.008 0.992
#> SRR1044556 1 0.6247 0.7716 0.844 0.156
#> SRR1044557 1 0.8267 0.7739 0.740 0.260
#> SRR1044558 1 0.4690 0.8095 0.900 0.100
#> SRR1044559 1 0.2778 0.8291 0.952 0.048
#> SRR1044561 1 0.6438 0.7642 0.836 0.164
#> SRR1044560 2 0.0000 0.7883 0.000 1.000
#> SRR1044562 1 0.0000 0.8175 1.000 0.000
#> SRR1044563 1 0.1414 0.8225 0.980 0.020
#> SRR1044564 1 0.0000 0.8175 1.000 0.000
#> SRR1044565 2 0.9815 0.6724 0.420 0.580
#> SRR1044566 2 0.0000 0.7883 0.000 1.000
#> SRR1044567 1 0.6247 0.8121 0.844 0.156
#> SRR1044568 1 0.0938 0.8211 0.988 0.012
#> SRR1044569 1 0.8267 0.7699 0.740 0.260
#> SRR1044570 1 0.7056 0.7933 0.808 0.192
#> SRR1044571 1 0.8608 0.7506 0.716 0.284
#> SRR1044572 1 0.9286 0.7036 0.656 0.344
#> SRR1044573 1 0.9754 0.6294 0.592 0.408
#> SRR1044574 1 0.8327 0.7692 0.736 0.264
#> SRR1044575 1 0.9608 0.6522 0.616 0.384
#> SRR1044576 2 0.9710 0.6920 0.400 0.600
#> SRR1044577 2 0.9795 0.6769 0.416 0.584
#> SRR1044578 2 0.9833 0.6675 0.424 0.576
#> SRR1044579 1 0.5842 0.7842 0.860 0.140
#> SRR1044580 1 0.2603 0.8274 0.956 0.044
#> SRR1044581 1 0.3431 0.8216 0.936 0.064
#> SRR1044582 1 0.7139 0.7904 0.804 0.196
#> SRR1044583 1 0.5519 0.7935 0.872 0.128
#> SRR1044584 1 0.0672 0.8201 0.992 0.008
#> SRR1044585 1 0.5178 0.8000 0.884 0.116
#> SRR1044586 1 0.3431 0.8366 0.936 0.064
#> SRR1044587 1 0.0000 0.8175 1.000 0.000
#> SRR1044588 1 0.1414 0.8229 0.980 0.020
#> SRR1044589 1 0.0938 0.8217 0.988 0.012
#> SRR1044590 1 0.0376 0.8189 0.996 0.004
#> SRR1044591 1 0.0000 0.8175 1.000 0.000
#> SRR1044592 1 0.6801 0.7414 0.820 0.180
#> SRR1044593 1 0.0000 0.8175 1.000 0.000
#> SRR1044594 1 0.0000 0.8175 1.000 0.000
#> SRR1044595 1 0.5842 0.8169 0.860 0.140
#> SRR1044596 1 0.0000 0.8175 1.000 0.000
#> SRR1044597 1 1.0000 0.0575 0.504 0.496
#> SRR1044598 1 0.4939 0.8261 0.892 0.108
#> SRR1044599 1 0.7219 0.8086 0.800 0.200
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1044415 3 0.6045 0.31097 0.000 0.380 0.620
#> SRR1044416 2 0.4062 0.65904 0.000 0.836 0.164
#> SRR1044417 2 0.0000 0.74711 0.000 1.000 0.000
#> SRR1044418 2 0.0000 0.74711 0.000 1.000 0.000
#> SRR1044420 2 0.5363 0.54245 0.000 0.724 0.276
#> SRR1044419 3 0.6126 0.27253 0.000 0.400 0.600
#> SRR1044421 2 0.6228 0.38641 0.012 0.672 0.316
#> SRR1044422 3 0.6309 0.00780 0.000 0.500 0.500
#> SRR1044423 3 0.6647 0.27981 0.012 0.396 0.592
#> SRR1044424 2 0.5365 0.57183 0.004 0.744 0.252
#> SRR1044425 1 0.4099 0.77518 0.852 0.140 0.008
#> SRR1044426 1 0.4978 0.69200 0.780 0.004 0.216
#> SRR1044427 1 0.7932 0.69335 0.660 0.140 0.200
#> SRR1044428 1 0.6662 0.68698 0.736 0.192 0.072
#> SRR1044429 1 0.8170 0.65219 0.624 0.120 0.256
#> SRR1044430 1 0.6955 0.13577 0.496 0.016 0.488
#> SRR1044431 1 0.5791 0.75441 0.792 0.148 0.060
#> SRR1044433 1 0.9408 0.22022 0.488 0.196 0.316
#> SRR1044432 1 0.5899 0.52225 0.736 0.020 0.244
#> SRR1044434 1 0.4796 0.75986 0.780 0.220 0.000
#> SRR1044435 1 0.5506 0.75021 0.764 0.220 0.016
#> SRR1044436 1 0.4750 0.75896 0.784 0.216 0.000
#> SRR1044437 1 0.4931 0.75648 0.784 0.212 0.004
#> SRR1044439 1 0.4842 0.75686 0.776 0.224 0.000
#> SRR1044438 1 0.5138 0.75646 0.748 0.252 0.000
#> SRR1044440 1 0.5024 0.75980 0.776 0.220 0.004
#> SRR1044441 1 0.4702 0.72236 0.788 0.212 0.000
#> SRR1044442 1 0.5660 0.70448 0.772 0.200 0.028
#> SRR1044443 1 0.9606 0.06649 0.428 0.204 0.368
#> SRR1044444 1 0.4834 0.75990 0.792 0.204 0.004
#> SRR1044445 1 0.5216 0.76050 0.740 0.260 0.000
#> SRR1044446 3 0.8767 0.34143 0.204 0.208 0.588
#> SRR1044447 3 0.8842 0.34149 0.212 0.208 0.580
#> SRR1044449 3 0.6470 0.38624 0.356 0.012 0.632
#> SRR1044448 3 0.8787 0.34816 0.228 0.188 0.584
#> SRR1044450 3 0.8804 0.34182 0.212 0.204 0.584
#> SRR1044451 3 0.8805 0.33953 0.208 0.208 0.584
#> SRR1044452 3 0.4269 0.45750 0.052 0.076 0.872
#> SRR1044453 3 0.3325 0.45060 0.076 0.020 0.904
#> SRR1044454 3 0.3886 0.45907 0.024 0.096 0.880
#> SRR1044455 3 0.5201 0.42282 0.004 0.236 0.760
#> SRR1044456 2 0.0424 0.74557 0.008 0.992 0.000
#> SRR1044457 3 0.5988 0.32987 0.000 0.368 0.632
#> SRR1044458 3 0.5988 0.33030 0.000 0.368 0.632
#> SRR1044459 3 0.4045 0.45869 0.024 0.104 0.872
#> SRR1044460 3 0.6308 0.03777 0.000 0.492 0.508
#> SRR1044461 3 0.6260 0.16000 0.000 0.448 0.552
#> SRR1044462 1 0.6998 0.74125 0.664 0.292 0.044
#> SRR1044463 1 0.5223 0.72476 0.800 0.176 0.024
#> SRR1044464 1 0.5061 0.73982 0.784 0.208 0.008
#> SRR1044466 1 0.5356 0.70910 0.784 0.196 0.020
#> SRR1044465 1 0.5147 0.71946 0.800 0.180 0.020
#> SRR1044467 1 0.7766 0.74623 0.676 0.176 0.148
#> SRR1044468 2 0.5835 0.41783 0.000 0.660 0.340
#> SRR1044469 3 0.5560 0.39424 0.000 0.300 0.700
#> SRR1044470 1 0.5998 0.72593 0.788 0.128 0.084
#> SRR1044471 1 0.6488 0.71924 0.756 0.160 0.084
#> SRR1044472 1 0.4652 0.72731 0.856 0.064 0.080
#> SRR1044473 1 0.8141 0.64853 0.624 0.116 0.260
#> SRR1044474 2 0.0237 0.74593 0.004 0.996 0.000
#> SRR1044475 3 0.4994 0.44634 0.024 0.160 0.816
#> SRR1044476 3 0.5948 0.34081 0.000 0.360 0.640
#> SRR1044477 2 0.0424 0.74557 0.008 0.992 0.000
#> SRR1044478 2 0.5706 0.46067 0.000 0.680 0.320
#> SRR1044479 2 0.0237 0.74593 0.004 0.996 0.000
#> SRR1044480 1 0.3267 0.78284 0.884 0.116 0.000
#> SRR1044481 1 0.2176 0.76650 0.948 0.032 0.020
#> SRR1044482 2 0.4504 0.62308 0.000 0.804 0.196
#> SRR1044483 1 0.8005 0.67645 0.648 0.128 0.224
#> SRR1044484 1 0.5455 0.76065 0.776 0.204 0.020
#> SRR1044486 1 0.1129 0.75499 0.976 0.004 0.020
#> SRR1044485 2 0.4702 0.60755 0.000 0.788 0.212
#> SRR1044487 2 0.0424 0.74557 0.008 0.992 0.000
#> SRR1044488 2 0.6244 0.16703 0.000 0.560 0.440
#> SRR1044489 3 0.6309 0.00396 0.000 0.500 0.500
#> SRR1044490 1 0.6297 0.69213 0.756 0.184 0.060
#> SRR1044491 1 0.6204 0.40826 0.576 0.000 0.424
#> SRR1044492 1 0.5180 0.72540 0.812 0.156 0.032
#> SRR1044493 1 0.2318 0.76077 0.944 0.028 0.028
#> SRR1044494 2 0.0237 0.74593 0.004 0.996 0.000
#> SRR1044496 2 0.2280 0.73951 0.008 0.940 0.052
#> SRR1044495 2 0.0424 0.74557 0.008 0.992 0.000
#> SRR1044497 1 0.4883 0.75788 0.788 0.208 0.004
#> SRR1044499 3 0.5650 0.38650 0.000 0.312 0.688
#> SRR1044498 1 0.5988 0.72514 0.632 0.368 0.000
#> SRR1044500 2 0.5098 0.58423 0.000 0.752 0.248
#> SRR1044501 3 0.5968 0.33568 0.000 0.364 0.636
#> SRR1044502 2 0.8016 0.26712 0.156 0.656 0.188
#> SRR1044503 1 0.5178 0.75481 0.744 0.256 0.000
#> SRR1044504 1 0.5680 0.75548 0.764 0.212 0.024
#> SRR1044505 1 0.5843 0.74033 0.732 0.252 0.016
#> SRR1044506 1 0.5529 0.75421 0.704 0.296 0.000
#> SRR1044507 1 0.5650 0.73221 0.688 0.312 0.000
#> SRR1044508 1 0.6106 0.69420 0.756 0.200 0.044
#> SRR1044509 1 0.8297 0.54479 0.632 0.200 0.168
#> SRR1044510 3 0.2446 0.45905 0.052 0.012 0.936
#> SRR1044511 3 0.6510 0.38340 0.364 0.012 0.624
#> SRR1044512 3 0.6416 0.37907 0.376 0.008 0.616
#> SRR1044513 3 0.9083 0.32467 0.196 0.256 0.548
#> SRR1044514 3 0.6379 0.38159 0.368 0.008 0.624
#> SRR1044515 2 0.4137 0.65411 0.032 0.872 0.096
#> SRR1044516 3 0.6603 0.37390 0.020 0.332 0.648
#> SRR1044517 3 0.3966 0.44414 0.100 0.024 0.876
#> SRR1044518 3 0.6617 0.36902 0.388 0.012 0.600
#> SRR1044519 3 0.8780 0.34921 0.232 0.184 0.584
#> SRR1044520 3 0.8720 0.35423 0.252 0.164 0.584
#> SRR1044521 3 0.6796 0.32884 0.020 0.368 0.612
#> SRR1044522 2 0.2096 0.73856 0.004 0.944 0.052
#> SRR1044523 2 0.4966 0.60790 0.060 0.840 0.100
#> SRR1044524 2 0.9449 -0.16440 0.180 0.436 0.384
#> SRR1044525 1 0.4883 0.75788 0.788 0.208 0.004
#> SRR1044526 1 0.7044 0.56947 0.620 0.032 0.348
#> SRR1044527 2 0.0237 0.74593 0.004 0.996 0.000
#> SRR1044528 2 0.7059 0.37390 0.164 0.724 0.112
#> SRR1044529 2 0.4228 0.67261 0.008 0.844 0.148
#> SRR1044530 1 0.4636 0.74100 0.848 0.116 0.036
#> SRR1044531 1 0.3607 0.74152 0.880 0.008 0.112
#> SRR1044533 1 0.4544 0.74455 0.860 0.084 0.056
#> SRR1044532 1 0.3933 0.74887 0.880 0.092 0.028
#> SRR1044534 2 0.6421 0.21320 0.004 0.572 0.424
#> SRR1044535 3 0.9558 0.25939 0.200 0.356 0.444
#> SRR1044536 3 0.6204 0.21910 0.000 0.424 0.576
#> SRR1044537 1 0.6625 0.73844 0.660 0.316 0.024
#> SRR1044538 1 0.5635 0.72474 0.784 0.180 0.036
#> SRR1044539 1 0.4883 0.75788 0.788 0.208 0.004
#> SRR1044540 1 0.2492 0.75881 0.936 0.048 0.016
#> SRR1044541 3 0.5760 0.37376 0.000 0.328 0.672
#> SRR1044542 1 0.6719 0.77467 0.728 0.204 0.068
#> SRR1044543 1 0.4521 0.71821 0.816 0.004 0.180
#> SRR1044544 3 0.5650 0.38650 0.000 0.312 0.688
#> SRR1044545 1 0.5687 0.75287 0.756 0.224 0.020
#> SRR1044546 1 0.6066 0.77177 0.728 0.248 0.024
#> SRR1044547 1 0.5061 0.76391 0.784 0.208 0.008
#> SRR1044548 1 0.2982 0.75450 0.920 0.024 0.056
#> SRR1044549 2 0.1399 0.73752 0.004 0.968 0.028
#> SRR1044550 2 0.6192 0.18943 0.000 0.580 0.420
#> SRR1044551 2 0.0424 0.74622 0.000 0.992 0.008
#> SRR1044552 1 0.5325 0.74080 0.748 0.248 0.004
#> SRR1044553 1 0.5431 0.75295 0.716 0.284 0.000
#> SRR1044554 1 0.7844 0.63207 0.624 0.084 0.292
#> SRR1044555 3 0.6357 0.39540 0.020 0.296 0.684
#> SRR1044556 1 0.4931 0.75648 0.784 0.212 0.004
#> SRR1044557 1 0.4033 0.73818 0.856 0.008 0.136
#> SRR1044558 1 0.5450 0.75823 0.760 0.228 0.012
#> SRR1044559 1 0.5220 0.71830 0.780 0.208 0.012
#> SRR1044561 1 0.4883 0.75788 0.788 0.208 0.004
#> SRR1044560 3 0.5810 0.36645 0.000 0.336 0.664
#> SRR1044562 1 0.6497 0.72999 0.648 0.336 0.016
#> SRR1044563 1 0.6081 0.71973 0.652 0.344 0.004
#> SRR1044564 1 0.6398 0.72502 0.620 0.372 0.008
#> SRR1044565 2 0.0000 0.74711 0.000 1.000 0.000
#> SRR1044566 3 0.6026 0.31756 0.000 0.376 0.624
#> SRR1044567 1 0.3155 0.75279 0.916 0.044 0.040
#> SRR1044568 1 0.5926 0.64724 0.644 0.356 0.000
#> SRR1044569 1 0.8259 0.67140 0.632 0.152 0.216
#> SRR1044570 1 0.4209 0.74788 0.856 0.128 0.016
#> SRR1044571 1 0.5263 0.73294 0.828 0.084 0.088
#> SRR1044572 1 0.3207 0.73513 0.904 0.012 0.084
#> SRR1044573 1 0.5988 0.61341 0.688 0.008 0.304
#> SRR1044574 1 0.3415 0.74316 0.900 0.020 0.080
#> SRR1044575 1 0.5726 0.69807 0.760 0.024 0.216
#> SRR1044576 2 0.1860 0.74178 0.000 0.948 0.052
#> SRR1044577 2 0.0237 0.74737 0.004 0.996 0.000
#> SRR1044578 2 0.1711 0.74530 0.008 0.960 0.032
#> SRR1044579 1 0.4883 0.75788 0.788 0.208 0.004
#> SRR1044580 1 0.4110 0.78327 0.844 0.152 0.004
#> SRR1044581 1 0.4883 0.75788 0.788 0.208 0.004
#> SRR1044582 1 0.5581 0.74597 0.792 0.168 0.040
#> SRR1044583 1 0.5061 0.75759 0.784 0.208 0.008
#> SRR1044584 1 0.4233 0.77604 0.836 0.160 0.004
#> SRR1044585 1 0.4883 0.75788 0.788 0.208 0.004
#> SRR1044586 1 0.5012 0.77602 0.788 0.204 0.008
#> SRR1044587 1 0.6062 0.71717 0.616 0.384 0.000
#> SRR1044588 1 0.5201 0.74531 0.760 0.236 0.004
#> SRR1044589 1 0.4931 0.75970 0.768 0.232 0.000
#> SRR1044590 1 0.6008 0.69174 0.628 0.372 0.000
#> SRR1044591 1 0.4842 0.75836 0.776 0.224 0.000
#> SRR1044592 1 0.7633 0.61346 0.680 0.200 0.120
#> SRR1044593 1 0.5178 0.75890 0.744 0.256 0.000
#> SRR1044594 1 0.5926 0.67628 0.644 0.356 0.000
#> SRR1044595 1 0.9375 0.28662 0.496 0.196 0.308
#> SRR1044596 1 0.5733 0.72994 0.676 0.324 0.000
#> SRR1044597 3 0.9612 0.05998 0.372 0.204 0.424
#> SRR1044598 1 0.5503 0.72302 0.772 0.208 0.020
#> SRR1044599 1 0.4423 0.77745 0.864 0.088 0.048
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1044415 2 0.0188 0.847522 0.000 0.996 0.000 0.004
#> SRR1044416 4 0.5298 0.354843 0.000 0.372 0.016 0.612
#> SRR1044417 4 0.6437 0.590639 0.000 0.168 0.184 0.648
#> SRR1044418 4 0.6115 0.604617 0.000 0.148 0.172 0.680
#> SRR1044420 2 0.3649 0.694595 0.000 0.796 0.000 0.204
#> SRR1044419 2 0.0336 0.847394 0.000 0.992 0.000 0.008
#> SRR1044421 2 0.6936 0.321768 0.000 0.564 0.292 0.144
#> SRR1044422 2 0.0921 0.843151 0.000 0.972 0.000 0.028
#> SRR1044423 2 0.0804 0.845380 0.008 0.980 0.000 0.012
#> SRR1044424 2 0.4697 0.523791 0.008 0.696 0.000 0.296
#> SRR1044425 1 0.3583 0.687754 0.816 0.000 0.004 0.180
#> SRR1044426 1 0.2936 0.691428 0.900 0.040 0.004 0.056
#> SRR1044427 1 0.5568 0.673341 0.728 0.120 0.000 0.152
#> SRR1044428 1 0.5279 0.653104 0.744 0.008 0.196 0.052
#> SRR1044429 1 0.8363 0.562796 0.500 0.192 0.048 0.260
#> SRR1044430 1 0.8025 0.203977 0.508 0.068 0.332 0.092
#> SRR1044431 1 0.6430 0.699176 0.708 0.040 0.104 0.148
#> SRR1044433 3 0.2081 0.748587 0.000 0.000 0.916 0.084
#> SRR1044432 1 0.3920 0.684549 0.856 0.012 0.076 0.056
#> SRR1044434 1 0.4605 0.631836 0.664 0.000 0.000 0.336
#> SRR1044435 1 0.4967 0.456459 0.548 0.000 0.000 0.452
#> SRR1044436 1 0.4830 0.554810 0.608 0.000 0.000 0.392
#> SRR1044437 1 0.4855 0.562689 0.600 0.000 0.000 0.400
#> SRR1044439 1 0.4843 0.532106 0.604 0.000 0.000 0.396
#> SRR1044438 1 0.5060 0.521158 0.584 0.000 0.004 0.412
#> SRR1044440 1 0.4866 0.579312 0.596 0.000 0.000 0.404
#> SRR1044441 1 0.7272 0.540014 0.496 0.000 0.344 0.160
#> SRR1044442 3 0.5080 0.621546 0.092 0.000 0.764 0.144
#> SRR1044443 3 0.1557 0.757107 0.000 0.000 0.944 0.056
#> SRR1044444 1 0.3649 0.679313 0.796 0.000 0.000 0.204
#> SRR1044445 4 0.5954 0.000444 0.344 0.000 0.052 0.604
#> SRR1044446 3 0.0336 0.758749 0.000 0.000 0.992 0.008
#> SRR1044447 3 0.1174 0.760176 0.012 0.000 0.968 0.020
#> SRR1044449 3 0.7920 0.543046 0.160 0.140 0.604 0.096
#> SRR1044448 3 0.1411 0.753442 0.020 0.000 0.960 0.020
#> SRR1044450 3 0.0188 0.758535 0.000 0.000 0.996 0.004
#> SRR1044451 3 0.0817 0.757538 0.000 0.000 0.976 0.024
#> SRR1044452 2 0.5969 0.653880 0.052 0.748 0.120 0.080
#> SRR1044453 2 0.7411 0.529549 0.108 0.648 0.152 0.092
#> SRR1044454 2 0.5452 0.689062 0.048 0.780 0.108 0.064
#> SRR1044455 2 0.0524 0.843505 0.000 0.988 0.004 0.008
#> SRR1044456 4 0.6347 0.633793 0.048 0.132 0.100 0.720
#> SRR1044457 2 0.0336 0.847394 0.000 0.992 0.000 0.008
#> SRR1044458 2 0.0188 0.847522 0.000 0.996 0.000 0.004
#> SRR1044459 2 0.2888 0.771588 0.000 0.872 0.124 0.004
#> SRR1044460 2 0.0707 0.845464 0.000 0.980 0.000 0.020
#> SRR1044461 2 0.0336 0.847394 0.000 0.992 0.000 0.008
#> SRR1044462 1 0.8589 0.571969 0.492 0.068 0.180 0.260
#> SRR1044463 1 0.5288 0.639411 0.720 0.000 0.224 0.056
#> SRR1044464 1 0.7473 0.636305 0.580 0.020 0.220 0.180
#> SRR1044466 1 0.5898 0.567529 0.628 0.000 0.316 0.056
#> SRR1044465 1 0.6207 0.600830 0.616 0.004 0.316 0.064
#> SRR1044467 1 0.5543 0.682874 0.756 0.092 0.016 0.136
#> SRR1044468 2 0.3356 0.726974 0.000 0.824 0.000 0.176
#> SRR1044469 2 0.0336 0.845042 0.000 0.992 0.000 0.008
#> SRR1044470 1 0.6659 0.598668 0.632 0.024 0.272 0.072
#> SRR1044471 1 0.4687 0.688314 0.812 0.012 0.084 0.092
#> SRR1044472 1 0.2981 0.695090 0.904 0.016 0.032 0.048
#> SRR1044473 1 0.8172 0.581307 0.568 0.216 0.104 0.112
#> SRR1044474 4 0.6024 0.633304 0.008 0.160 0.124 0.708
#> SRR1044475 2 0.3987 0.765184 0.028 0.860 0.056 0.056
#> SRR1044476 2 0.0188 0.847522 0.000 0.996 0.000 0.004
#> SRR1044477 4 0.6190 0.635301 0.012 0.164 0.124 0.700
#> SRR1044478 2 0.3649 0.691247 0.000 0.796 0.000 0.204
#> SRR1044479 4 0.6194 0.625553 0.020 0.132 0.136 0.712
#> SRR1044480 1 0.4321 0.707926 0.796 0.004 0.024 0.176
#> SRR1044481 1 0.2179 0.697482 0.924 0.000 0.012 0.064
#> SRR1044482 4 0.4643 0.421917 0.000 0.344 0.000 0.656
#> SRR1044483 1 0.7674 0.594668 0.520 0.164 0.016 0.300
#> SRR1044484 1 0.4018 0.680949 0.772 0.004 0.000 0.224
#> SRR1044486 1 0.0937 0.695307 0.976 0.000 0.012 0.012
#> SRR1044485 2 0.4985 0.096636 0.000 0.532 0.000 0.468
#> SRR1044487 4 0.6410 0.637938 0.044 0.144 0.100 0.712
#> SRR1044488 2 0.2197 0.812048 0.000 0.916 0.004 0.080
#> SRR1044489 2 0.0817 0.843283 0.000 0.976 0.000 0.024
#> SRR1044490 1 0.6789 0.490179 0.572 0.012 0.336 0.080
#> SRR1044491 1 0.6104 0.463848 0.676 0.236 0.008 0.080
#> SRR1044492 1 0.5987 0.633146 0.680 0.012 0.248 0.060
#> SRR1044493 1 0.2021 0.694959 0.932 0.000 0.012 0.056
#> SRR1044494 4 0.6164 0.627399 0.012 0.144 0.140 0.704
#> SRR1044496 4 0.5832 0.602313 0.016 0.232 0.052 0.700
#> SRR1044495 4 0.6227 0.632029 0.016 0.148 0.132 0.704
#> SRR1044497 1 0.4605 0.631956 0.664 0.000 0.000 0.336
#> SRR1044499 2 0.0188 0.846272 0.000 0.996 0.000 0.004
#> SRR1044498 1 0.6409 0.603949 0.560 0.000 0.076 0.364
#> SRR1044500 2 0.4916 0.230785 0.000 0.576 0.000 0.424
#> SRR1044501 2 0.0188 0.847240 0.000 0.996 0.000 0.004
#> SRR1044502 3 0.5902 0.541706 0.000 0.160 0.700 0.140
#> SRR1044503 1 0.5050 0.538752 0.588 0.000 0.004 0.408
#> SRR1044504 1 0.5396 0.442981 0.524 0.012 0.000 0.464
#> SRR1044505 1 0.6863 0.641062 0.616 0.004 0.184 0.196
#> SRR1044506 4 0.6044 -0.235678 0.428 0.000 0.044 0.528
#> SRR1044507 3 0.5889 0.540642 0.116 0.000 0.696 0.188
#> SRR1044508 3 0.3962 0.698602 0.044 0.000 0.832 0.124
#> SRR1044509 3 0.3659 0.710902 0.024 0.000 0.840 0.136
#> SRR1044510 2 0.7293 0.227120 0.044 0.504 0.396 0.056
#> SRR1044511 3 0.6803 0.559615 0.272 0.012 0.612 0.104
#> SRR1044512 3 0.7402 0.563595 0.240 0.048 0.608 0.104
#> SRR1044513 3 0.1174 0.755517 0.000 0.012 0.968 0.020
#> SRR1044514 3 0.6752 0.552709 0.284 0.008 0.604 0.104
#> SRR1044515 3 0.5883 0.543263 0.000 0.128 0.700 0.172
#> SRR1044516 2 0.2245 0.832692 0.008 0.932 0.040 0.020
#> SRR1044517 2 0.8025 0.261655 0.068 0.508 0.332 0.092
#> SRR1044518 3 0.6426 0.562613 0.272 0.000 0.620 0.108
#> SRR1044519 3 0.2443 0.746839 0.060 0.000 0.916 0.024
#> SRR1044520 3 0.3128 0.731071 0.076 0.000 0.884 0.040
#> SRR1044521 2 0.1786 0.840026 0.008 0.948 0.008 0.036
#> SRR1044522 4 0.5803 0.626995 0.008 0.200 0.080 0.712
#> SRR1044523 3 0.7096 0.211455 0.000 0.144 0.524 0.332
#> SRR1044524 2 0.5924 0.199124 0.000 0.556 0.404 0.040
#> SRR1044525 1 0.4697 0.606497 0.644 0.000 0.000 0.356
#> SRR1044526 1 0.7386 0.524512 0.536 0.300 0.008 0.156
#> SRR1044527 4 0.6149 0.592854 0.004 0.132 0.176 0.688
#> SRR1044528 3 0.6745 0.409978 0.000 0.176 0.612 0.212
#> SRR1044529 4 0.5172 0.524548 0.016 0.284 0.008 0.692
#> SRR1044530 1 0.4094 0.693606 0.828 0.000 0.116 0.056
#> SRR1044531 1 0.4787 0.679821 0.820 0.044 0.056 0.080
#> SRR1044533 1 0.5035 0.651893 0.744 0.000 0.204 0.052
#> SRR1044532 1 0.4070 0.685100 0.824 0.000 0.132 0.044
#> SRR1044534 2 0.2647 0.780345 0.000 0.880 0.000 0.120
#> SRR1044535 3 0.5397 0.577956 0.004 0.244 0.708 0.044
#> SRR1044536 2 0.0469 0.846752 0.000 0.988 0.000 0.012
#> SRR1044537 1 0.5836 0.663880 0.700 0.000 0.112 0.188
#> SRR1044538 1 0.4990 0.668417 0.784 0.012 0.144 0.060
#> SRR1044539 1 0.4661 0.595552 0.652 0.000 0.000 0.348
#> SRR1044540 1 0.2797 0.697921 0.900 0.000 0.032 0.068
#> SRR1044541 2 0.0336 0.847394 0.000 0.992 0.000 0.008
#> SRR1044542 1 0.6021 0.693262 0.744 0.060 0.068 0.128
#> SRR1044543 1 0.3043 0.682358 0.876 0.004 0.008 0.112
#> SRR1044544 2 0.0000 0.847036 0.000 1.000 0.000 0.000
#> SRR1044545 1 0.5345 0.513896 0.560 0.012 0.000 0.428
#> SRR1044546 1 0.5281 0.700156 0.756 0.016 0.048 0.180
#> SRR1044547 1 0.4382 0.650891 0.704 0.000 0.000 0.296
#> SRR1044548 1 0.4537 0.704455 0.824 0.016 0.088 0.072
#> SRR1044549 4 0.7240 0.095028 0.000 0.144 0.400 0.456
#> SRR1044550 2 0.1637 0.825588 0.000 0.940 0.000 0.060
#> SRR1044551 4 0.6573 0.601934 0.004 0.208 0.144 0.644
#> SRR1044552 1 0.5158 0.413293 0.524 0.000 0.004 0.472
#> SRR1044553 1 0.5861 0.391997 0.492 0.000 0.032 0.476
#> SRR1044554 1 0.5680 0.642735 0.752 0.156 0.048 0.044
#> SRR1044555 2 0.0188 0.846900 0.000 0.996 0.004 0.000
#> SRR1044556 1 0.4941 0.513429 0.564 0.000 0.000 0.436
#> SRR1044557 1 0.3279 0.690000 0.888 0.028 0.016 0.068
#> SRR1044558 1 0.5080 0.582632 0.628 0.004 0.004 0.364
#> SRR1044559 1 0.6737 0.485558 0.532 0.000 0.368 0.100
#> SRR1044561 1 0.5004 0.613411 0.604 0.000 0.004 0.392
#> SRR1044560 2 0.0188 0.846272 0.000 0.996 0.000 0.004
#> SRR1044562 1 0.6242 0.569919 0.612 0.000 0.308 0.080
#> SRR1044563 4 0.6174 -0.393292 0.460 0.004 0.040 0.496
#> SRR1044564 1 0.6134 0.610779 0.660 0.000 0.104 0.236
#> SRR1044565 4 0.6323 0.639399 0.020 0.176 0.108 0.696
#> SRR1044566 2 0.0336 0.847415 0.000 0.992 0.000 0.008
#> SRR1044567 1 0.4296 0.701163 0.824 0.004 0.112 0.060
#> SRR1044568 4 0.5306 0.036555 0.348 0.000 0.020 0.632
#> SRR1044569 1 0.6878 0.600287 0.664 0.204 0.056 0.076
#> SRR1044570 1 0.4963 0.625499 0.696 0.000 0.284 0.020
#> SRR1044571 1 0.4958 0.686080 0.808 0.036 0.092 0.064
#> SRR1044572 1 0.3626 0.689936 0.872 0.012 0.056 0.060
#> SRR1044573 1 0.5574 0.668977 0.756 0.116 0.016 0.112
#> SRR1044574 1 0.4231 0.671883 0.824 0.000 0.080 0.096
#> SRR1044575 1 0.5713 0.682275 0.760 0.076 0.040 0.124
#> SRR1044576 4 0.6439 0.442518 0.000 0.340 0.084 0.576
#> SRR1044577 4 0.6296 0.639174 0.020 0.168 0.112 0.700
#> SRR1044578 4 0.5985 0.619465 0.016 0.216 0.068 0.700
#> SRR1044579 1 0.4661 0.611865 0.652 0.000 0.000 0.348
#> SRR1044580 1 0.4188 0.689962 0.752 0.000 0.004 0.244
#> SRR1044581 1 0.4643 0.596804 0.656 0.000 0.000 0.344
#> SRR1044582 1 0.3876 0.690144 0.856 0.008 0.068 0.068
#> SRR1044583 1 0.4477 0.643667 0.688 0.000 0.000 0.312
#> SRR1044584 1 0.4228 0.683541 0.760 0.000 0.008 0.232
#> SRR1044585 1 0.4500 0.621784 0.684 0.000 0.000 0.316
#> SRR1044586 1 0.4604 0.693260 0.756 0.008 0.012 0.224
#> SRR1044587 4 0.6756 0.193743 0.252 0.000 0.148 0.600
#> SRR1044588 4 0.4961 -0.224552 0.448 0.000 0.000 0.552
#> SRR1044589 1 0.4994 0.433304 0.520 0.000 0.000 0.480
#> SRR1044590 4 0.5478 0.086530 0.344 0.000 0.028 0.628
#> SRR1044591 4 0.5281 -0.284652 0.464 0.000 0.008 0.528
#> SRR1044592 3 0.3597 0.704908 0.016 0.000 0.836 0.148
#> SRR1044593 4 0.5466 -0.195885 0.436 0.000 0.016 0.548
#> SRR1044594 4 0.5254 0.220324 0.300 0.000 0.028 0.672
#> SRR1044595 3 0.1151 0.759449 0.008 0.000 0.968 0.024
#> SRR1044596 3 0.6013 0.526676 0.120 0.000 0.684 0.196
#> SRR1044597 3 0.2282 0.756429 0.052 0.000 0.924 0.024
#> SRR1044598 1 0.4711 0.679741 0.784 0.000 0.152 0.064
#> SRR1044599 1 0.3243 0.702962 0.876 0.000 0.036 0.088
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1044415 2 0.3143 0.3757 0.000 0.796 0.000 0.000 0.204
#> SRR1044416 2 0.4619 0.5322 0.008 0.776 0.008 0.116 0.092
#> SRR1044417 2 0.7744 0.3586 0.004 0.492 0.228 0.172 0.104
#> SRR1044418 2 0.8095 0.3383 0.008 0.448 0.220 0.216 0.108
#> SRR1044420 2 0.1082 0.5428 0.000 0.964 0.000 0.008 0.028
#> SRR1044419 2 0.2424 0.4629 0.000 0.868 0.000 0.000 0.132
#> SRR1044421 2 0.5038 0.4373 0.000 0.700 0.220 0.008 0.072
#> SRR1044422 2 0.1892 0.5064 0.000 0.916 0.000 0.004 0.080
#> SRR1044423 2 0.2338 0.4820 0.000 0.884 0.000 0.004 0.112
#> SRR1044424 2 0.2505 0.5444 0.000 0.888 0.000 0.092 0.020
#> SRR1044425 4 0.5697 0.5725 0.172 0.000 0.004 0.644 0.180
#> SRR1044426 1 0.5956 0.7313 0.644 0.020 0.000 0.188 0.148
#> SRR1044427 4 0.6550 0.5456 0.212 0.104 0.000 0.612 0.072
#> SRR1044428 1 0.6239 0.7677 0.680 0.008 0.096 0.124 0.092
#> SRR1044429 4 0.7478 0.4708 0.228 0.140 0.028 0.548 0.056
#> SRR1044430 1 0.6482 0.6913 0.680 0.044 0.120 0.052 0.104
#> SRR1044431 1 0.7266 0.3830 0.484 0.020 0.068 0.356 0.072
#> SRR1044433 3 0.0566 0.7417 0.004 0.000 0.984 0.012 0.000
#> SRR1044432 1 0.5208 0.7661 0.724 0.000 0.024 0.096 0.156
#> SRR1044434 4 0.3432 0.7681 0.132 0.000 0.000 0.828 0.040
#> SRR1044435 4 0.1412 0.7972 0.008 0.004 0.000 0.952 0.036
#> SRR1044436 4 0.0609 0.8000 0.020 0.000 0.000 0.980 0.000
#> SRR1044437 4 0.1725 0.8019 0.020 0.000 0.000 0.936 0.044
#> SRR1044439 4 0.1012 0.8020 0.020 0.000 0.000 0.968 0.012
#> SRR1044438 4 0.0865 0.7997 0.024 0.000 0.000 0.972 0.004
#> SRR1044440 4 0.1579 0.8063 0.032 0.000 0.000 0.944 0.024
#> SRR1044441 4 0.5938 0.3357 0.112 0.000 0.376 0.512 0.000
#> SRR1044442 3 0.1928 0.7162 0.004 0.000 0.920 0.072 0.004
#> SRR1044443 3 0.0290 0.7403 0.000 0.000 0.992 0.000 0.008
#> SRR1044444 4 0.3449 0.7276 0.164 0.000 0.000 0.812 0.024
#> SRR1044445 4 0.4069 0.7462 0.016 0.004 0.076 0.820 0.084
#> SRR1044446 3 0.0566 0.7367 0.012 0.000 0.984 0.000 0.004
#> SRR1044447 3 0.0740 0.7374 0.008 0.000 0.980 0.004 0.008
#> SRR1044449 5 0.5832 0.5109 0.088 0.040 0.160 0.012 0.700
#> SRR1044448 3 0.1251 0.7191 0.008 0.000 0.956 0.000 0.036
#> SRR1044450 3 0.0609 0.7326 0.000 0.000 0.980 0.000 0.020
#> SRR1044451 3 0.0960 0.7411 0.008 0.004 0.972 0.000 0.016
#> SRR1044452 5 0.4430 0.5452 0.000 0.360 0.000 0.012 0.628
#> SRR1044453 5 0.4415 0.5964 0.004 0.288 0.004 0.012 0.692
#> SRR1044454 5 0.4564 0.5117 0.004 0.388 0.000 0.008 0.600
#> SRR1044455 2 0.4126 -0.0395 0.000 0.620 0.000 0.000 0.380
#> SRR1044456 2 0.7866 0.3556 0.020 0.408 0.088 0.376 0.108
#> SRR1044457 2 0.1732 0.5052 0.000 0.920 0.000 0.000 0.080
#> SRR1044458 2 0.2732 0.4328 0.000 0.840 0.000 0.000 0.160
#> SRR1044459 2 0.4880 -0.0533 0.000 0.616 0.036 0.000 0.348
#> SRR1044460 2 0.1544 0.5119 0.000 0.932 0.000 0.000 0.068
#> SRR1044461 2 0.1792 0.5025 0.000 0.916 0.000 0.000 0.084
#> SRR1044462 4 0.7888 0.4376 0.168 0.072 0.180 0.536 0.044
#> SRR1044463 1 0.5811 0.7383 0.680 0.000 0.188 0.068 0.064
#> SRR1044464 4 0.7493 0.1427 0.344 0.008 0.144 0.448 0.056
#> SRR1044466 1 0.5392 0.6761 0.664 0.000 0.256 0.060 0.020
#> SRR1044465 1 0.7084 0.6593 0.548 0.000 0.212 0.176 0.064
#> SRR1044467 1 0.5657 0.7836 0.724 0.040 0.028 0.152 0.056
#> SRR1044468 2 0.0992 0.5419 0.000 0.968 0.000 0.008 0.024
#> SRR1044469 2 0.4150 -0.0699 0.000 0.612 0.000 0.000 0.388
#> SRR1044470 1 0.5344 0.7212 0.732 0.016 0.160 0.024 0.068
#> SRR1044471 1 0.5119 0.7879 0.744 0.000 0.048 0.140 0.068
#> SRR1044472 1 0.4596 0.7834 0.784 0.000 0.032 0.088 0.096
#> SRR1044473 1 0.8133 0.5638 0.520 0.088 0.088 0.220 0.084
#> SRR1044474 2 0.8109 0.3967 0.020 0.448 0.132 0.292 0.108
#> SRR1044475 5 0.4425 0.4029 0.000 0.452 0.000 0.004 0.544
#> SRR1044476 2 0.3274 0.3519 0.000 0.780 0.000 0.000 0.220
#> SRR1044477 2 0.8057 0.4025 0.020 0.452 0.124 0.296 0.108
#> SRR1044478 2 0.1300 0.5443 0.000 0.956 0.000 0.016 0.028
#> SRR1044479 2 0.8099 0.3712 0.020 0.420 0.120 0.332 0.108
#> SRR1044480 4 0.5466 0.4207 0.340 0.004 0.008 0.600 0.048
#> SRR1044481 1 0.6424 0.3313 0.444 0.000 0.000 0.380 0.176
#> SRR1044482 2 0.5428 0.5045 0.008 0.668 0.000 0.224 0.100
#> SRR1044483 4 0.7400 0.4639 0.224 0.116 0.012 0.552 0.096
#> SRR1044484 4 0.4557 0.6379 0.204 0.004 0.000 0.736 0.056
#> SRR1044486 1 0.5196 0.7658 0.700 0.000 0.004 0.160 0.136
#> SRR1044485 2 0.3397 0.5432 0.004 0.848 0.000 0.068 0.080
#> SRR1044487 2 0.7699 0.3802 0.020 0.428 0.072 0.372 0.108
#> SRR1044488 2 0.0740 0.5387 0.004 0.980 0.000 0.008 0.008
#> SRR1044489 2 0.0794 0.5282 0.000 0.972 0.000 0.000 0.028
#> SRR1044490 1 0.5125 0.6584 0.704 0.008 0.232 0.028 0.028
#> SRR1044491 1 0.4836 0.7417 0.748 0.028 0.000 0.056 0.168
#> SRR1044492 1 0.5805 0.7697 0.704 0.004 0.140 0.064 0.088
#> SRR1044493 1 0.5167 0.7628 0.696 0.000 0.004 0.192 0.108
#> SRR1044494 2 0.8138 0.3840 0.020 0.436 0.132 0.304 0.108
#> SRR1044496 2 0.6975 0.4531 0.024 0.524 0.024 0.320 0.108
#> SRR1044495 2 0.8149 0.3861 0.020 0.440 0.136 0.296 0.108
#> SRR1044497 4 0.3234 0.7840 0.084 0.000 0.000 0.852 0.064
#> SRR1044499 2 0.4171 -0.0959 0.000 0.604 0.000 0.000 0.396
#> SRR1044498 4 0.5802 0.5957 0.236 0.004 0.088 0.652 0.020
#> SRR1044500 2 0.2922 0.5450 0.000 0.872 0.000 0.056 0.072
#> SRR1044501 2 0.3074 0.3877 0.000 0.804 0.000 0.000 0.196
#> SRR1044502 3 0.5128 0.5754 0.004 0.184 0.716 0.008 0.088
#> SRR1044503 4 0.2032 0.8015 0.052 0.004 0.000 0.924 0.020
#> SRR1044504 4 0.2273 0.8006 0.024 0.024 0.000 0.920 0.032
#> SRR1044505 4 0.7334 -0.1154 0.380 0.000 0.160 0.408 0.052
#> SRR1044506 4 0.1772 0.7894 0.012 0.004 0.016 0.944 0.024
#> SRR1044507 3 0.4280 0.5582 0.004 0.004 0.744 0.224 0.024
#> SRR1044508 3 0.0960 0.7434 0.004 0.000 0.972 0.016 0.008
#> SRR1044509 3 0.1202 0.7384 0.004 0.000 0.960 0.032 0.004
#> SRR1044510 5 0.6233 0.6012 0.000 0.312 0.168 0.000 0.520
#> SRR1044511 5 0.6698 0.1523 0.060 0.020 0.436 0.032 0.452
#> SRR1044512 5 0.6393 0.3388 0.056 0.020 0.332 0.028 0.564
#> SRR1044513 3 0.1168 0.7380 0.000 0.008 0.960 0.000 0.032
#> SRR1044514 5 0.6450 0.2588 0.068 0.008 0.368 0.032 0.524
#> SRR1044515 3 0.4738 0.6313 0.004 0.120 0.772 0.020 0.084
#> SRR1044516 2 0.3639 0.4218 0.012 0.808 0.008 0.004 0.168
#> SRR1044517 5 0.6197 0.6056 0.004 0.328 0.100 0.012 0.556
#> SRR1044518 3 0.6454 -0.1930 0.060 0.004 0.460 0.040 0.436
#> SRR1044519 3 0.1970 0.6994 0.012 0.000 0.924 0.004 0.060
#> SRR1044520 3 0.3183 0.5832 0.016 0.000 0.828 0.000 0.156
#> SRR1044521 2 0.1443 0.5276 0.004 0.948 0.004 0.000 0.044
#> SRR1044522 2 0.7695 0.4346 0.032 0.480 0.064 0.320 0.104
#> SRR1044523 3 0.6022 0.2702 0.008 0.352 0.540 0.000 0.100
#> SRR1044524 2 0.5434 0.2385 0.004 0.580 0.356 0.000 0.060
#> SRR1044525 4 0.3862 0.7654 0.104 0.000 0.000 0.808 0.088
#> SRR1044526 4 0.7905 0.1563 0.304 0.196 0.016 0.428 0.056
#> SRR1044527 2 0.8306 0.2384 0.012 0.404 0.276 0.200 0.108
#> SRR1044528 3 0.5785 0.3886 0.012 0.320 0.596 0.004 0.068
#> SRR1044529 2 0.6225 0.4670 0.020 0.568 0.000 0.304 0.108
#> SRR1044530 1 0.4712 0.7741 0.784 0.000 0.076 0.064 0.076
#> SRR1044531 1 0.6161 0.7298 0.652 0.020 0.024 0.088 0.216
#> SRR1044533 1 0.6152 0.7826 0.672 0.000 0.092 0.128 0.108
#> SRR1044532 1 0.4935 0.7630 0.760 0.000 0.072 0.044 0.124
#> SRR1044534 2 0.1965 0.5312 0.000 0.924 0.000 0.024 0.052
#> SRR1044535 3 0.4117 0.6269 0.020 0.164 0.788 0.000 0.028
#> SRR1044536 2 0.1410 0.5147 0.000 0.940 0.000 0.000 0.060
#> SRR1044537 1 0.6396 0.6851 0.608 0.004 0.100 0.248 0.040
#> SRR1044538 1 0.5312 0.7885 0.740 0.000 0.088 0.104 0.068
#> SRR1044539 4 0.1893 0.8030 0.048 0.000 0.000 0.928 0.024
#> SRR1044540 1 0.4997 0.7828 0.740 0.000 0.024 0.156 0.080
#> SRR1044541 2 0.2516 0.4554 0.000 0.860 0.000 0.000 0.140
#> SRR1044542 1 0.5634 0.7830 0.720 0.020 0.044 0.160 0.056
#> SRR1044543 1 0.6113 0.7182 0.588 0.008 0.004 0.120 0.280
#> SRR1044544 2 0.3636 0.2538 0.000 0.728 0.000 0.000 0.272
#> SRR1044545 4 0.1471 0.8010 0.024 0.004 0.000 0.952 0.020
#> SRR1044546 1 0.6229 0.3070 0.476 0.000 0.024 0.424 0.076
#> SRR1044547 4 0.4671 0.6960 0.116 0.000 0.000 0.740 0.144
#> SRR1044548 1 0.5749 0.7734 0.692 0.004 0.040 0.176 0.088
#> SRR1044549 3 0.6538 0.0804 0.012 0.416 0.464 0.012 0.096
#> SRR1044550 2 0.0290 0.5354 0.000 0.992 0.000 0.000 0.008
#> SRR1044551 2 0.7732 0.3926 0.016 0.528 0.208 0.144 0.104
#> SRR1044552 4 0.2067 0.8022 0.044 0.004 0.000 0.924 0.028
#> SRR1044553 4 0.1605 0.7989 0.040 0.000 0.004 0.944 0.012
#> SRR1044554 1 0.7188 0.7468 0.632 0.088 0.064 0.128 0.088
#> SRR1044555 2 0.3689 0.2787 0.004 0.740 0.000 0.000 0.256
#> SRR1044556 4 0.1310 0.8027 0.020 0.000 0.000 0.956 0.024
#> SRR1044557 1 0.5320 0.7723 0.696 0.008 0.000 0.144 0.152
#> SRR1044558 4 0.1485 0.8033 0.032 0.000 0.000 0.948 0.020
#> SRR1044559 3 0.7227 -0.2527 0.316 0.008 0.440 0.220 0.016
#> SRR1044561 4 0.3697 0.7772 0.080 0.000 0.000 0.820 0.100
#> SRR1044560 2 0.3949 0.1048 0.000 0.668 0.000 0.000 0.332
#> SRR1044562 1 0.6649 0.6113 0.560 0.004 0.288 0.112 0.036
#> SRR1044563 4 0.3006 0.7868 0.056 0.008 0.020 0.888 0.028
#> SRR1044564 1 0.6658 0.5896 0.556 0.008 0.072 0.312 0.052
#> SRR1044565 2 0.7883 0.4255 0.020 0.472 0.104 0.296 0.108
#> SRR1044566 2 0.3336 0.3386 0.000 0.772 0.000 0.000 0.228
#> SRR1044567 1 0.4620 0.7747 0.788 0.000 0.048 0.080 0.084
#> SRR1044568 4 0.2766 0.7900 0.032 0.004 0.012 0.896 0.056
#> SRR1044569 1 0.6078 0.7177 0.704 0.128 0.036 0.092 0.040
#> SRR1044570 1 0.6570 0.7235 0.600 0.000 0.224 0.120 0.056
#> SRR1044571 1 0.5030 0.7787 0.764 0.004 0.052 0.068 0.112
#> SRR1044572 1 0.5406 0.7703 0.712 0.004 0.024 0.088 0.172
#> SRR1044573 1 0.6776 0.6627 0.576 0.048 0.000 0.204 0.172
#> SRR1044574 1 0.6805 0.6962 0.548 0.000 0.044 0.140 0.268
#> SRR1044575 1 0.7119 0.6610 0.584 0.080 0.016 0.220 0.100
#> SRR1044576 2 0.6665 0.5014 0.012 0.632 0.068 0.184 0.104
#> SRR1044577 2 0.8043 0.4114 0.020 0.464 0.128 0.280 0.108
#> SRR1044578 2 0.7187 0.4594 0.020 0.524 0.044 0.304 0.108
#> SRR1044579 4 0.2149 0.8023 0.036 0.000 0.000 0.916 0.048
#> SRR1044580 4 0.4668 0.5994 0.272 0.000 0.000 0.684 0.044
#> SRR1044581 4 0.1484 0.8011 0.048 0.000 0.000 0.944 0.008
#> SRR1044582 1 0.5101 0.7750 0.736 0.000 0.044 0.164 0.056
#> SRR1044583 4 0.3536 0.7738 0.084 0.000 0.000 0.832 0.084
#> SRR1044584 4 0.4918 0.6561 0.192 0.000 0.000 0.708 0.100
#> SRR1044585 4 0.2230 0.7985 0.044 0.000 0.000 0.912 0.044
#> SRR1044586 4 0.5217 0.3014 0.364 0.004 0.000 0.588 0.044
#> SRR1044587 4 0.3965 0.7164 0.020 0.012 0.108 0.828 0.032
#> SRR1044588 4 0.1026 0.7968 0.004 0.004 0.000 0.968 0.024
#> SRR1044589 4 0.1648 0.7997 0.020 0.000 0.000 0.940 0.040
#> SRR1044590 4 0.2029 0.7764 0.016 0.004 0.012 0.932 0.036
#> SRR1044591 4 0.1329 0.8004 0.008 0.000 0.004 0.956 0.032
#> SRR1044592 3 0.1731 0.7246 0.004 0.000 0.932 0.060 0.004
#> SRR1044593 4 0.0960 0.7951 0.004 0.000 0.008 0.972 0.016
#> SRR1044594 4 0.2472 0.7723 0.000 0.020 0.020 0.908 0.052
#> SRR1044595 3 0.0955 0.7363 0.028 0.000 0.968 0.000 0.004
#> SRR1044596 3 0.4616 0.4752 0.000 0.004 0.680 0.288 0.028
#> SRR1044597 3 0.2177 0.7047 0.080 0.000 0.908 0.004 0.008
#> SRR1044598 1 0.6754 0.6893 0.576 0.000 0.084 0.252 0.088
#> SRR1044599 1 0.5493 0.7552 0.664 0.000 0.008 0.220 0.108
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1044415 2 0.2896 0.46690 0.000 0.824 0.160 0.000 0.000 0.016
#> SRR1044416 2 0.4208 0.53371 0.000 0.772 0.000 0.092 0.024 0.112
#> SRR1044417 2 0.7040 0.28819 0.004 0.460 0.000 0.152 0.276 0.108
#> SRR1044418 2 0.7200 0.26497 0.000 0.412 0.000 0.208 0.268 0.112
#> SRR1044420 2 0.1226 0.56862 0.000 0.952 0.000 0.004 0.004 0.040
#> SRR1044419 2 0.2623 0.49459 0.000 0.852 0.132 0.000 0.000 0.016
#> SRR1044421 2 0.4612 0.44811 0.000 0.700 0.004 0.020 0.232 0.044
#> SRR1044422 2 0.2020 0.52666 0.000 0.896 0.096 0.000 0.000 0.008
#> SRR1044423 2 0.2162 0.53577 0.004 0.896 0.088 0.000 0.000 0.012
#> SRR1044424 2 0.3031 0.55027 0.000 0.844 0.004 0.108 0.000 0.044
#> SRR1044425 4 0.6095 0.39804 0.212 0.000 0.184 0.564 0.000 0.040
#> SRR1044426 1 0.7328 0.51189 0.384 0.008 0.176 0.104 0.000 0.328
#> SRR1044427 4 0.7008 0.42033 0.188 0.092 0.048 0.556 0.000 0.116
#> SRR1044428 1 0.6902 0.70644 0.512 0.004 0.016 0.136 0.068 0.264
#> SRR1044429 4 0.7457 0.28343 0.232 0.112 0.020 0.480 0.008 0.148
#> SRR1044430 1 0.6865 0.62144 0.456 0.020 0.068 0.024 0.052 0.380
#> SRR1044431 1 0.8132 0.50863 0.432 0.036 0.068 0.264 0.056 0.144
#> SRR1044433 5 0.1282 0.78500 0.004 0.000 0.024 0.004 0.956 0.012
#> SRR1044432 1 0.6817 0.59768 0.536 0.000 0.124 0.052 0.040 0.248
#> SRR1044434 4 0.3643 0.75138 0.080 0.000 0.052 0.824 0.000 0.044
#> SRR1044435 4 0.1434 0.77626 0.008 0.000 0.020 0.948 0.000 0.024
#> SRR1044436 4 0.0405 0.77446 0.000 0.000 0.004 0.988 0.000 0.008
#> SRR1044437 4 0.1738 0.77503 0.016 0.000 0.052 0.928 0.000 0.004
#> SRR1044439 4 0.0405 0.77524 0.000 0.000 0.004 0.988 0.000 0.008
#> SRR1044438 4 0.1036 0.77592 0.008 0.000 0.004 0.964 0.000 0.024
#> SRR1044440 4 0.1766 0.77915 0.028 0.000 0.016 0.936 0.004 0.016
#> SRR1044441 4 0.5971 0.19793 0.112 0.000 0.004 0.452 0.412 0.020
#> SRR1044442 5 0.0858 0.78532 0.000 0.000 0.000 0.028 0.968 0.004
#> SRR1044443 5 0.0405 0.78747 0.000 0.000 0.008 0.000 0.988 0.004
#> SRR1044444 4 0.3787 0.70160 0.104 0.000 0.072 0.804 0.000 0.020
#> SRR1044445 4 0.4257 0.70712 0.004 0.000 0.080 0.788 0.072 0.056
#> SRR1044446 5 0.1218 0.78117 0.028 0.000 0.012 0.000 0.956 0.004
#> SRR1044447 5 0.1381 0.78307 0.004 0.000 0.020 0.004 0.952 0.020
#> SRR1044449 3 0.6505 0.53729 0.060 0.032 0.616 0.008 0.116 0.168
#> SRR1044448 5 0.1493 0.77188 0.004 0.000 0.056 0.000 0.936 0.004
#> SRR1044450 5 0.1493 0.77275 0.004 0.000 0.056 0.000 0.936 0.004
#> SRR1044451 5 0.0520 0.78633 0.000 0.000 0.008 0.000 0.984 0.008
#> SRR1044452 3 0.3714 0.52278 0.000 0.340 0.656 0.000 0.000 0.004
#> SRR1044453 3 0.2994 0.63484 0.000 0.208 0.788 0.000 0.000 0.004
#> SRR1044454 3 0.4047 0.45936 0.000 0.384 0.604 0.000 0.000 0.012
#> SRR1044455 2 0.4954 0.14567 0.000 0.640 0.232 0.000 0.000 0.128
#> SRR1044456 4 0.6712 -0.17332 0.004 0.352 0.000 0.444 0.072 0.128
#> SRR1044457 2 0.1686 0.54237 0.000 0.924 0.064 0.000 0.000 0.012
#> SRR1044458 2 0.2704 0.48726 0.000 0.844 0.140 0.000 0.000 0.016
#> SRR1044459 2 0.5911 0.13760 0.000 0.624 0.176 0.000 0.112 0.088
#> SRR1044460 2 0.1141 0.55105 0.000 0.948 0.052 0.000 0.000 0.000
#> SRR1044461 2 0.2020 0.52661 0.000 0.896 0.096 0.000 0.000 0.008
#> SRR1044462 4 0.8137 0.23127 0.212 0.076 0.032 0.452 0.172 0.056
#> SRR1044463 1 0.5795 0.69596 0.660 0.000 0.032 0.040 0.176 0.092
#> SRR1044464 4 0.8240 0.00848 0.184 0.016 0.036 0.396 0.140 0.228
#> SRR1044466 1 0.4691 0.68725 0.720 0.000 0.008 0.048 0.196 0.028
#> SRR1044465 1 0.6822 0.70169 0.584 0.000 0.044 0.096 0.128 0.148
#> SRR1044467 1 0.5419 0.73755 0.720 0.036 0.036 0.080 0.008 0.120
#> SRR1044468 2 0.0922 0.56881 0.000 0.968 0.004 0.004 0.000 0.024
#> SRR1044469 2 0.4664 0.13914 0.000 0.644 0.280 0.000 0.000 0.076
#> SRR1044470 1 0.4318 0.70640 0.756 0.004 0.012 0.008 0.048 0.172
#> SRR1044471 1 0.5234 0.73313 0.676 0.000 0.020 0.080 0.016 0.208
#> SRR1044472 1 0.4584 0.73280 0.752 0.000 0.084 0.052 0.000 0.112
#> SRR1044473 1 0.7481 0.64136 0.496 0.052 0.024 0.128 0.044 0.256
#> SRR1044474 2 0.7203 0.36639 0.004 0.428 0.000 0.292 0.148 0.128
#> SRR1044475 3 0.4469 0.28338 0.000 0.468 0.504 0.000 0.000 0.028
#> SRR1044476 2 0.3156 0.43901 0.000 0.800 0.180 0.000 0.000 0.020
#> SRR1044477 2 0.7135 0.34920 0.004 0.416 0.000 0.324 0.128 0.128
#> SRR1044478 2 0.1534 0.57062 0.000 0.944 0.004 0.016 0.004 0.032
#> SRR1044479 2 0.7165 0.27563 0.004 0.376 0.000 0.364 0.132 0.124
#> SRR1044480 4 0.6270 -0.13948 0.416 0.004 0.048 0.444 0.004 0.084
#> SRR1044481 1 0.6763 0.31320 0.400 0.000 0.180 0.360 0.000 0.060
#> SRR1044482 2 0.5161 0.47799 0.000 0.640 0.000 0.236 0.012 0.112
#> SRR1044483 4 0.7124 0.10879 0.248 0.052 0.020 0.448 0.000 0.232
#> SRR1044484 4 0.5032 0.52710 0.236 0.004 0.056 0.672 0.000 0.032
#> SRR1044486 1 0.4734 0.73583 0.748 0.000 0.100 0.096 0.004 0.052
#> SRR1044485 2 0.2344 0.56351 0.000 0.892 0.000 0.028 0.004 0.076
#> SRR1044487 4 0.6633 -0.24355 0.004 0.388 0.000 0.420 0.064 0.124
#> SRR1044488 2 0.1453 0.56888 0.000 0.944 0.008 0.008 0.000 0.040
#> SRR1044489 2 0.0405 0.56442 0.000 0.988 0.008 0.000 0.000 0.004
#> SRR1044490 1 0.5323 0.67578 0.684 0.000 0.016 0.020 0.152 0.128
#> SRR1044491 1 0.6626 0.61704 0.520 0.024 0.144 0.028 0.004 0.280
#> SRR1044492 1 0.5059 0.73434 0.732 0.000 0.044 0.036 0.048 0.140
#> SRR1044493 1 0.6341 0.72994 0.604 0.000 0.132 0.136 0.008 0.120
#> SRR1044494 2 0.7324 0.32371 0.004 0.392 0.000 0.312 0.164 0.128
#> SRR1044496 2 0.6351 0.38242 0.004 0.480 0.000 0.348 0.044 0.124
#> SRR1044495 2 0.7312 0.33302 0.004 0.400 0.000 0.304 0.164 0.128
#> SRR1044497 4 0.3409 0.75155 0.064 0.000 0.060 0.840 0.000 0.036
#> SRR1044499 2 0.4049 0.12730 0.000 0.648 0.332 0.000 0.000 0.020
#> SRR1044498 4 0.4779 0.54813 0.300 0.000 0.004 0.644 0.028 0.024
#> SRR1044500 2 0.2687 0.56164 0.000 0.876 0.000 0.044 0.008 0.072
#> SRR1044501 2 0.2945 0.46765 0.000 0.824 0.156 0.000 0.000 0.020
#> SRR1044502 5 0.3549 0.68104 0.020 0.140 0.000 0.000 0.808 0.032
#> SRR1044503 4 0.1829 0.77617 0.028 0.000 0.008 0.928 0.000 0.036
#> SRR1044504 4 0.2755 0.76708 0.036 0.008 0.032 0.888 0.000 0.036
#> SRR1044505 1 0.7869 0.41739 0.416 0.008 0.036 0.276 0.112 0.152
#> SRR1044506 4 0.1511 0.77028 0.000 0.000 0.012 0.944 0.012 0.032
#> SRR1044507 5 0.2877 0.65609 0.000 0.000 0.000 0.168 0.820 0.012
#> SRR1044508 5 0.0964 0.78769 0.004 0.000 0.016 0.000 0.968 0.012
#> SRR1044509 5 0.1579 0.78414 0.004 0.000 0.024 0.020 0.944 0.008
#> SRR1044510 3 0.5476 0.64573 0.000 0.248 0.628 0.000 0.052 0.072
#> SRR1044511 3 0.4752 0.54310 0.000 0.008 0.708 0.012 0.196 0.076
#> SRR1044512 3 0.4395 0.56301 0.004 0.004 0.760 0.016 0.144 0.072
#> SRR1044513 5 0.0508 0.78443 0.000 0.004 0.000 0.000 0.984 0.012
#> SRR1044514 3 0.4517 0.54910 0.004 0.000 0.736 0.016 0.168 0.076
#> SRR1044515 5 0.4201 0.63639 0.000 0.164 0.000 0.032 0.760 0.044
#> SRR1044516 2 0.4013 0.43249 0.020 0.776 0.168 0.004 0.004 0.028
#> SRR1044517 3 0.5540 0.62806 0.004 0.280 0.608 0.000 0.040 0.068
#> SRR1044518 3 0.4708 0.50488 0.000 0.000 0.692 0.016 0.220 0.072
#> SRR1044519 5 0.2146 0.72539 0.004 0.000 0.116 0.000 0.880 0.000
#> SRR1044520 5 0.3274 0.59584 0.004 0.000 0.208 0.004 0.780 0.004
#> SRR1044521 2 0.1149 0.56762 0.000 0.960 0.008 0.000 0.008 0.024
#> SRR1044522 2 0.7019 0.34545 0.012 0.432 0.000 0.344 0.096 0.116
#> SRR1044523 5 0.5002 0.36279 0.004 0.340 0.000 0.012 0.596 0.048
#> SRR1044524 2 0.4805 0.17326 0.008 0.564 0.004 0.000 0.392 0.032
#> SRR1044525 4 0.3652 0.74136 0.080 0.000 0.084 0.816 0.000 0.020
#> SRR1044526 1 0.8114 0.21453 0.336 0.152 0.036 0.308 0.004 0.164
#> SRR1044527 2 0.7372 0.19806 0.004 0.388 0.000 0.184 0.300 0.124
#> SRR1044528 5 0.4528 0.43335 0.004 0.316 0.000 0.000 0.636 0.044
#> SRR1044529 2 0.5820 0.42822 0.000 0.536 0.000 0.320 0.024 0.120
#> SRR1044530 1 0.4068 0.73191 0.816 0.000 0.036 0.048 0.040 0.060
#> SRR1044531 1 0.7207 0.61092 0.512 0.012 0.216 0.048 0.032 0.180
#> SRR1044533 1 0.6911 0.70881 0.560 0.000 0.080 0.088 0.060 0.212
#> SRR1044532 1 0.5448 0.72522 0.692 0.000 0.116 0.028 0.028 0.136
#> SRR1044534 2 0.1528 0.56596 0.000 0.944 0.028 0.012 0.000 0.016
#> SRR1044535 5 0.3835 0.70020 0.048 0.120 0.004 0.000 0.804 0.024
#> SRR1044536 2 0.1644 0.54002 0.000 0.920 0.076 0.000 0.000 0.004
#> SRR1044537 1 0.5017 0.72763 0.728 0.004 0.012 0.152 0.044 0.060
#> SRR1044538 1 0.6071 0.74641 0.664 0.000 0.072 0.088 0.052 0.124
#> SRR1044539 4 0.1844 0.77255 0.040 0.000 0.016 0.928 0.000 0.016
#> SRR1044540 1 0.5566 0.74253 0.692 0.000 0.076 0.112 0.016 0.104
#> SRR1044541 2 0.2623 0.49459 0.000 0.852 0.132 0.000 0.000 0.016
#> SRR1044542 1 0.4761 0.74355 0.768 0.012 0.024 0.104 0.024 0.068
#> SRR1044543 1 0.6989 0.58116 0.404 0.000 0.196 0.080 0.000 0.320
#> SRR1044544 2 0.3679 0.38281 0.000 0.760 0.200 0.000 0.000 0.040
#> SRR1044545 4 0.0692 0.77579 0.020 0.000 0.000 0.976 0.000 0.004
#> SRR1044546 1 0.6588 0.47204 0.500 0.000 0.084 0.320 0.012 0.084
#> SRR1044547 4 0.5588 0.60674 0.088 0.000 0.172 0.656 0.000 0.084
#> SRR1044548 1 0.6906 0.70670 0.548 0.000 0.096 0.144 0.024 0.188
#> SRR1044549 5 0.5290 0.18323 0.000 0.392 0.000 0.008 0.520 0.080
#> SRR1044550 2 0.0363 0.56271 0.000 0.988 0.012 0.000 0.000 0.000
#> SRR1044551 2 0.6961 0.32497 0.004 0.484 0.000 0.140 0.256 0.116
#> SRR1044552 4 0.1148 0.77719 0.016 0.000 0.004 0.960 0.000 0.020
#> SRR1044553 4 0.1078 0.77537 0.012 0.000 0.008 0.964 0.000 0.016
#> SRR1044554 1 0.6998 0.71198 0.544 0.036 0.032 0.104 0.032 0.252
#> SRR1044555 2 0.3820 0.42296 0.004 0.780 0.144 0.000 0.000 0.072
#> SRR1044556 4 0.1232 0.77817 0.004 0.000 0.024 0.956 0.000 0.016
#> SRR1044557 1 0.6603 0.71491 0.580 0.008 0.136 0.104 0.004 0.168
#> SRR1044558 4 0.1332 0.77783 0.012 0.000 0.008 0.952 0.000 0.028
#> SRR1044559 5 0.6594 -0.12484 0.348 0.008 0.008 0.136 0.468 0.032
#> SRR1044561 4 0.3839 0.73067 0.040 0.000 0.132 0.796 0.000 0.032
#> SRR1044560 2 0.3876 0.26137 0.000 0.700 0.276 0.000 0.000 0.024
#> SRR1044562 1 0.5906 0.54492 0.556 0.008 0.004 0.076 0.324 0.032
#> SRR1044563 4 0.2699 0.76037 0.052 0.004 0.000 0.884 0.012 0.048
#> SRR1044564 1 0.6813 0.61721 0.508 0.004 0.008 0.260 0.064 0.156
#> SRR1044565 2 0.7064 0.39010 0.004 0.444 0.000 0.300 0.124 0.128
#> SRR1044566 2 0.3156 0.43910 0.000 0.800 0.180 0.000 0.000 0.020
#> SRR1044567 1 0.4971 0.72885 0.728 0.000 0.048 0.048 0.020 0.156
#> SRR1044568 4 0.4390 0.72161 0.072 0.004 0.056 0.792 0.012 0.064
#> SRR1044569 1 0.5496 0.71887 0.700 0.032 0.020 0.060 0.020 0.168
#> SRR1044570 1 0.6002 0.71439 0.664 0.000 0.076 0.068 0.144 0.048
#> SRR1044571 1 0.5138 0.72185 0.672 0.004 0.068 0.024 0.004 0.228
#> SRR1044572 1 0.5690 0.73098 0.672 0.000 0.136 0.068 0.012 0.112
#> SRR1044573 1 0.6097 0.68676 0.608 0.000 0.100 0.128 0.000 0.164
#> SRR1044574 1 0.6325 0.61223 0.512 0.000 0.320 0.044 0.008 0.116
#> SRR1044575 1 0.7057 0.61461 0.448 0.028 0.044 0.144 0.004 0.332
#> SRR1044576 2 0.5857 0.48228 0.000 0.624 0.000 0.192 0.084 0.100
#> SRR1044577 2 0.7146 0.37521 0.004 0.432 0.000 0.300 0.136 0.128
#> SRR1044578 2 0.6368 0.39767 0.000 0.484 0.000 0.336 0.060 0.120
#> SRR1044579 4 0.1932 0.77763 0.020 0.000 0.040 0.924 0.000 0.016
#> SRR1044580 4 0.5733 0.41950 0.272 0.000 0.040 0.596 0.004 0.088
#> SRR1044581 4 0.1857 0.77632 0.028 0.000 0.012 0.928 0.000 0.032
#> SRR1044582 1 0.4747 0.74389 0.768 0.004 0.056 0.104 0.028 0.040
#> SRR1044583 4 0.3075 0.75371 0.040 0.000 0.092 0.852 0.000 0.016
#> SRR1044584 4 0.5337 0.58537 0.180 0.000 0.128 0.660 0.000 0.032
#> SRR1044585 4 0.2466 0.76837 0.028 0.000 0.052 0.896 0.000 0.024
#> SRR1044586 4 0.6025 0.18931 0.324 0.000 0.068 0.532 0.000 0.076
#> SRR1044587 4 0.3174 0.71987 0.004 0.000 0.012 0.848 0.096 0.040
#> SRR1044588 4 0.1168 0.76894 0.000 0.000 0.016 0.956 0.000 0.028
#> SRR1044589 4 0.1257 0.77318 0.000 0.000 0.028 0.952 0.000 0.020
#> SRR1044590 4 0.1338 0.76249 0.004 0.000 0.004 0.952 0.008 0.032
#> SRR1044591 4 0.1789 0.76994 0.000 0.000 0.044 0.924 0.000 0.032
#> SRR1044592 5 0.1794 0.78348 0.008 0.000 0.020 0.024 0.936 0.012
#> SRR1044593 4 0.0790 0.76898 0.000 0.000 0.000 0.968 0.000 0.032
#> SRR1044594 4 0.1780 0.76945 0.000 0.000 0.028 0.932 0.012 0.028
#> SRR1044595 5 0.1251 0.78199 0.008 0.000 0.024 0.000 0.956 0.012
#> SRR1044596 5 0.3629 0.53116 0.000 0.000 0.000 0.260 0.724 0.016
#> SRR1044597 5 0.3574 0.73071 0.056 0.000 0.040 0.020 0.844 0.040
#> SRR1044598 1 0.7342 0.70738 0.532 0.004 0.092 0.196 0.060 0.116
#> SRR1044599 1 0.6247 0.72950 0.608 0.000 0.064 0.184 0.016 0.128
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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