Date: 2019-12-26 01:02:36 CET, cola version: 1.3.2
Document is loading...
All available functions which can be applied to this res_list object:
res_list
#> A 'ConsensusPartitionList' object with 24 methods.
#> On a matrix with 14431 rows and 191 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] 14431 191
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:skmeans | 4 | 1.000 | 0.996 | 0.995 | ** | 2,3 |
| SD:NMF | 3 | 1.000 | 0.995 | 0.988 | ** | 2 |
| CV:hclust | 3 | 1.000 | 1.000 | 1.000 | ** | 2 |
| CV:kmeans | 2 | 1.000 | 1.000 | 1.000 | ** | |
| CV:skmeans | 4 | 1.000 | 0.990 | 0.987 | ** | 2,3 |
| CV:pam | 3 | 1.000 | 1.000 | 1.000 | ** | 2 |
| CV:NMF | 3 | 1.000 | 0.983 | 0.969 | ** | 2 |
| MAD:hclust | 3 | 1.000 | 1.000 | 1.000 | ** | 2 |
| MAD:kmeans | 2 | 1.000 | 1.000 | 1.000 | ** | |
| MAD:skmeans | 4 | 1.000 | 0.999 | 0.997 | ** | 2,3 |
| MAD:NMF | 3 | 1.000 | 0.986 | 0.969 | ** | 2 |
| ATC:kmeans | 2 | 1.000 | 1.000 | 1.000 | ** | |
| ATC:NMF | 2 | 1.000 | 1.000 | 1.000 | ** | |
| CV:mclust | 5 | 0.987 | 0.954 | 0.972 | ** | 2,3,4 |
| MAD:mclust | 5 | 0.964 | 0.934 | 0.946 | ** | 2,3,4 |
| ATC:mclust | 4 | 0.961 | 0.955 | 0.978 | ** | 2 |
| SD:pam | 6 | 0.931 | 0.946 | 0.945 | * | 2,3,4 |
| ATC:hclust | 4 | 0.929 | 0.866 | 0.936 | * | 2 |
| ATC:skmeans | 6 | 0.928 | 0.902 | 0.914 | * | 2,3,4,5 |
| SD:mclust | 5 | 0.925 | 0.903 | 0.936 | * | 2,3,4 |
| ATC:pam | 6 | 0.924 | 0.925 | 0.930 | * | 2,3,4,5 |
| MAD:pam | 6 | 0.916 | 0.792 | 0.867 | * | 2,3,4,5 |
| SD:hclust | 6 | 0.912 | 0.929 | 0.921 | * | 2,3,5 |
**: 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 1 1 0.503 0.497 0.497
#> CV:NMF 2 1 1 1 0.503 0.497 0.497
#> MAD:NMF 2 1 1 1 0.503 0.497 0.497
#> ATC:NMF 2 1 1 1 0.503 0.497 0.497
#> SD:skmeans 2 1 1 1 0.503 0.497 0.497
#> CV:skmeans 2 1 1 1 0.503 0.497 0.497
#> MAD:skmeans 2 1 1 1 0.503 0.497 0.497
#> ATC:skmeans 2 1 1 1 0.503 0.497 0.497
#> SD:mclust 2 1 1 1 0.503 0.497 0.497
#> CV:mclust 2 1 1 1 0.503 0.497 0.497
#> MAD:mclust 2 1 1 1 0.503 0.497 0.497
#> ATC:mclust 2 1 1 1 0.503 0.497 0.497
#> SD:kmeans 2 1 1 1 0.503 0.497 0.497
#> CV:kmeans 2 1 1 1 0.503 0.497 0.497
#> MAD:kmeans 2 1 1 1 0.503 0.497 0.497
#> ATC:kmeans 2 1 1 1 0.503 0.497 0.497
#> SD:pam 2 1 1 1 0.503 0.497 0.497
#> CV:pam 2 1 1 1 0.503 0.497 0.497
#> MAD:pam 2 1 1 1 0.503 0.497 0.497
#> ATC:pam 2 1 1 1 0.503 0.497 0.497
#> SD:hclust 2 1 1 1 0.503 0.497 0.497
#> CV:hclust 2 1 1 1 0.503 0.497 0.497
#> MAD:hclust 2 1 1 1 0.503 0.497 0.497
#> ATC:hclust 2 1 1 1 0.503 0.497 0.497
get_stats(res_list, k = 3)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 3 1.000 0.995 0.988 0.2187 0.889 0.777
#> CV:NMF 3 1.000 0.983 0.969 0.2228 0.889 0.777
#> MAD:NMF 3 1.000 0.986 0.969 0.2173 0.889 0.777
#> ATC:NMF 3 0.889 0.938 0.934 0.0806 1.000 1.000
#> SD:skmeans 3 1.000 0.999 0.998 0.2207 0.889 0.777
#> CV:skmeans 3 1.000 0.998 0.997 0.2208 0.889 0.777
#> MAD:skmeans 3 1.000 0.998 0.997 0.2208 0.889 0.777
#> ATC:skmeans 3 1.000 0.996 0.993 0.2211 0.889 0.777
#> SD:mclust 3 1.000 1.000 1.000 0.2206 0.889 0.777
#> CV:mclust 3 1.000 1.000 1.000 0.2206 0.889 0.777
#> MAD:mclust 3 1.000 1.000 1.000 0.2206 0.889 0.777
#> ATC:mclust 3 0.718 0.860 0.887 0.2303 0.880 0.758
#> SD:kmeans 3 0.744 0.371 0.774 0.2345 0.980 0.959
#> CV:kmeans 3 0.746 0.500 0.733 0.2352 0.929 0.858
#> MAD:kmeans 3 0.762 0.486 0.736 0.2359 0.929 0.858
#> ATC:kmeans 3 0.762 0.450 0.590 0.2362 0.897 0.792
#> SD:pam 3 1.000 1.000 1.000 0.2206 0.889 0.777
#> CV:pam 3 1.000 1.000 1.000 0.2206 0.889 0.777
#> MAD:pam 3 1.000 1.000 1.000 0.2206 0.889 0.777
#> ATC:pam 3 1.000 1.000 1.000 0.2206 0.889 0.777
#> SD:hclust 3 1.000 1.000 1.000 0.2206 0.889 0.777
#> CV:hclust 3 1.000 1.000 1.000 0.2206 0.889 0.777
#> MAD:hclust 3 1.000 1.000 1.000 0.2206 0.889 0.777
#> ATC:hclust 3 0.894 0.952 0.962 0.2194 0.889 0.777
get_stats(res_list, k = 4)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 4 0.873 0.893 0.870 0.0783 1.000 1.000
#> CV:NMF 4 0.871 0.883 0.858 0.0921 1.000 1.000
#> MAD:NMF 4 0.876 0.893 0.890 0.0830 1.000 1.000
#> ATC:NMF 4 0.747 0.822 0.811 0.1383 0.879 0.756
#> SD:skmeans 4 1.000 0.996 0.995 0.2052 0.873 0.671
#> CV:skmeans 4 1.000 0.990 0.987 0.2038 0.873 0.671
#> MAD:skmeans 4 1.000 0.999 0.997 0.2055 0.873 0.671
#> ATC:skmeans 4 1.000 0.995 0.985 0.2015 0.873 0.671
#> SD:mclust 4 1.000 0.981 0.992 0.2056 0.874 0.674
#> CV:mclust 4 1.000 0.992 0.994 0.2049 0.873 0.671
#> MAD:mclust 4 1.000 1.000 1.000 0.2051 0.874 0.674
#> ATC:mclust 4 0.961 0.955 0.978 0.1843 0.884 0.694
#> SD:kmeans 4 0.658 0.877 0.801 0.1156 0.763 0.513
#> CV:kmeans 4 0.662 0.852 0.767 0.1116 0.776 0.508
#> MAD:kmeans 4 0.666 0.911 0.823 0.1179 0.776 0.508
#> ATC:kmeans 4 0.654 0.911 0.811 0.1185 0.757 0.458
#> SD:pam 4 1.000 0.994 0.997 0.2064 0.873 0.671
#> CV:pam 4 0.804 0.677 0.827 0.1478 0.905 0.753
#> MAD:pam 4 1.000 0.998 0.999 0.2065 0.873 0.671
#> ATC:pam 4 1.000 0.991 0.995 0.2061 0.873 0.671
#> SD:hclust 4 0.823 0.963 0.902 0.1742 0.873 0.671
#> CV:hclust 4 0.840 0.889 0.922 0.0927 0.951 0.874
#> MAD:hclust 4 0.821 0.897 0.851 0.1602 0.874 0.674
#> ATC:hclust 4 0.929 0.866 0.936 0.0784 0.946 0.861
get_stats(res_list, k = 5)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 5 0.821 0.970 0.835 0.0456 0.873 0.671
#> CV:NMF 5 0.846 0.946 0.899 0.0718 0.873 0.671
#> MAD:NMF 5 0.817 0.969 0.875 0.0425 0.873 0.671
#> ATC:NMF 5 0.702 0.891 0.811 0.0951 0.835 0.587
#> SD:skmeans 5 0.885 0.841 0.872 0.0604 1.000 1.000
#> CV:skmeans 5 0.880 0.893 0.881 0.0561 0.972 0.891
#> MAD:skmeans 5 0.885 0.945 0.912 0.0611 0.949 0.804
#> ATC:skmeans 5 0.955 0.939 0.937 0.0712 0.945 0.789
#> SD:mclust 5 0.925 0.903 0.936 0.0434 0.968 0.878
#> CV:mclust 5 0.987 0.954 0.972 0.0431 0.969 0.881
#> MAD:mclust 5 0.964 0.934 0.946 0.0456 0.968 0.878
#> ATC:mclust 5 0.885 0.893 0.927 0.0623 0.949 0.810
#> SD:kmeans 5 0.606 0.815 0.765 0.0704 1.000 1.000
#> CV:kmeans 5 0.640 0.812 0.780 0.0753 1.000 1.000
#> MAD:kmeans 5 0.596 0.839 0.785 0.0620 1.000 1.000
#> ATC:kmeans 5 0.593 0.855 0.787 0.0647 1.000 1.000
#> SD:pam 5 0.899 0.630 0.813 0.0559 0.920 0.704
#> CV:pam 5 0.831 0.861 0.920 0.1176 0.870 0.586
#> MAD:pam 5 0.928 0.961 0.948 0.0630 0.948 0.801
#> ATC:pam 5 0.995 0.969 0.985 0.0721 0.946 0.792
#> SD:hclust 5 0.960 0.951 0.961 0.0930 0.954 0.822
#> CV:hclust 5 0.870 0.888 0.936 0.1715 0.870 0.615
#> MAD:hclust 5 0.896 0.904 0.928 0.1009 0.934 0.754
#> ATC:hclust 5 0.781 0.784 0.884 0.1009 0.961 0.883
get_stats(res_list, k = 6)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 6 0.713 0.905 0.866 0.0603 1.000 1.000
#> CV:NMF 6 0.742 0.900 0.881 0.0354 1.000 1.000
#> MAD:NMF 6 0.680 0.920 0.874 0.0452 1.000 1.000
#> ATC:NMF 6 0.616 0.858 0.819 0.0537 1.000 1.000
#> SD:skmeans 6 0.860 0.860 0.864 0.0425 0.908 0.649
#> CV:skmeans 6 0.877 0.839 0.868 0.0381 0.909 0.629
#> MAD:skmeans 6 0.828 0.711 0.820 0.0384 0.976 0.886
#> ATC:skmeans 6 0.928 0.902 0.914 0.0281 0.987 0.935
#> SD:mclust 6 0.881 0.852 0.882 0.0431 0.959 0.819
#> CV:mclust 6 0.838 0.845 0.858 0.0467 1.000 1.000
#> MAD:mclust 6 0.857 0.770 0.866 0.0536 0.941 0.745
#> ATC:mclust 6 0.772 0.668 0.811 0.0388 0.925 0.687
#> SD:kmeans 6 0.639 0.509 0.649 0.0588 0.927 0.718
#> CV:kmeans 6 0.778 0.563 0.770 0.0566 0.968 0.878
#> MAD:kmeans 6 0.639 0.599 0.699 0.0555 0.957 0.833
#> ATC:kmeans 6 0.803 0.816 0.739 0.0629 0.946 0.792
#> SD:pam 6 0.931 0.946 0.945 0.0460 0.929 0.686
#> CV:pam 6 0.823 0.831 0.893 0.0355 0.970 0.856
#> MAD:pam 6 0.916 0.792 0.867 0.0304 0.969 0.858
#> ATC:pam 6 0.924 0.925 0.930 0.0236 0.989 0.948
#> SD:hclust 6 0.912 0.929 0.921 0.0310 0.972 0.868
#> CV:hclust 6 0.859 0.831 0.870 0.0306 1.000 1.000
#> MAD:hclust 6 0.860 0.859 0.873 0.0389 0.972 0.868
#> ATC:hclust 6 0.783 0.797 0.877 0.0238 0.987 0.955
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)
#> Error in valid.viewport(x, y, width, height, just, gp, clip, xscale, yscale, : invalid 'xscale' in viewport
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 = 1000, method = "euler")
top_rows_overlap(res_list, top_n = 2000, method = "euler")
top_rows_overlap(res_list, top_n = 3000, method = "euler")
top_rows_overlap(res_list, top_n = 4000, method = "euler")
top_rows_overlap(res_list, top_n = 5000, method = "euler")
Also visualize the correspondance of rankings between different top-row methods:
top_rows_overlap(res_list, top_n = 1000, method = "correspondance")
top_rows_overlap(res_list, top_n = 2000, method = "correspondance")
top_rows_overlap(res_list, top_n = 3000, method = "correspondance")
top_rows_overlap(res_list, top_n = 4000, method = "correspondance")
top_rows_overlap(res_list, top_n = 5000, method = "correspondance")
Heatmaps of the top rows:
top_rows_heatmap(res_list, top_n = 1000)
top_rows_heatmap(res_list, top_n = 2000)
top_rows_heatmap(res_list, top_n = 3000)
top_rows_heatmap(res_list, top_n = 4000)
top_rows_heatmap(res_list, top_n = 5000)
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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 6.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.503 0.497 0.497
#> 3 3 1.000 1.000 1.000 0.221 0.889 0.777
#> 4 4 0.823 0.963 0.902 0.174 0.873 0.671
#> 5 5 0.960 0.951 0.961 0.093 0.954 0.822
#> 6 6 0.912 0.929 0.921 0.031 0.972 0.868
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3 5
There is also optional best \(k\) = 2 3 5 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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0 1 0 1 0
#> SRR2001033 2 0 1 0 1 0
#> SRR2001034 2 0 1 0 1 0
#> SRR2001035 2 0 1 0 1 0
#> SRR2001204 1 0 1 1 0 0
#> SRR2001205 1 0 1 1 0 0
#> SRR2001206 1 0 1 1 0 0
#> SRR2001207 1 0 1 1 0 0
#> SRR2001200 1 0 1 1 0 0
#> SRR2001201 1 0 1 1 0 0
#> SRR2001202 1 0 1 1 0 0
#> SRR2001203 1 0 1 1 0 0
#> SRR2001196 1 0 1 1 0 0
#> SRR2001197 1 0 1 1 0 0
#> SRR2001198 1 0 1 1 0 0
#> SRR2001199 1 0 1 1 0 0
#> SRR2001192 3 0 1 0 0 1
#> SRR2001193 3 0 1 0 0 1
#> SRR2001194 3 0 1 0 0 1
#> SRR2001195 3 0 1 0 0 1
#> SRR2001188 1 0 1 1 0 0
#> SRR2001189 1 0 1 1 0 0
#> SRR2001190 1 0 1 1 0 0
#> SRR2001191 1 0 1 1 0 0
#> SRR2001184 3 0 1 0 0 1
#> SRR2001185 3 0 1 0 0 1
#> SRR2001186 3 0 1 0 0 1
#> SRR2001187 3 0 1 0 0 1
#> SRR2001180 1 0 1 1 0 0
#> SRR2001181 1 0 1 1 0 0
#> SRR2001182 1 0 1 1 0 0
#> SRR2001183 1 0 1 1 0 0
#> SRR2001176 3 0 1 0 0 1
#> SRR2001177 3 0 1 0 0 1
#> SRR2001178 3 0 1 0 0 1
#> SRR2001179 3 0 1 0 0 1
#> SRR2001172 3 0 1 0 0 1
#> SRR2001173 3 0 1 0 0 1
#> SRR2001174 3 0 1 0 0 1
#> SRR2001175 3 0 1 0 0 1
#> SRR2001168 1 0 1 1 0 0
#> SRR2001169 1 0 1 1 0 0
#> SRR2001170 1 0 1 1 0 0
#> SRR2001171 1 0 1 1 0 0
#> SRR2001164 1 0 1 1 0 0
#> SRR2001165 1 0 1 1 0 0
#> SRR2001166 1 0 1 1 0 0
#> SRR2001167 1 0 1 1 0 0
#> SRR2001160 1 0 1 1 0 0
#> SRR2001161 1 0 1 1 0 0
#> SRR2001162 1 0 1 1 0 0
#> SRR2001163 1 0 1 1 0 0
#> SRR2001156 1 0 1 1 0 0
#> SRR2001157 1 0 1 1 0 0
#> SRR2001158 1 0 1 1 0 0
#> SRR2001159 1 0 1 1 0 0
#> SRR2001152 1 0 1 1 0 0
#> SRR2001153 1 0 1 1 0 0
#> SRR2001154 1 0 1 1 0 0
#> SRR2001155 1 0 1 1 0 0
#> SRR2001148 3 0 1 0 0 1
#> SRR2001149 3 0 1 0 0 1
#> SRR2001150 3 0 1 0 0 1
#> SRR2001151 3 0 1 0 0 1
#> SRR2001144 1 0 1 1 0 0
#> SRR2001145 1 0 1 1 0 0
#> SRR2001146 1 0 1 1 0 0
#> SRR2001147 1 0 1 1 0 0
#> SRR2001140 1 0 1 1 0 0
#> SRR2001142 1 0 1 1 0 0
#> SRR2001143 1 0 1 1 0 0
#> SRR2001136 3 0 1 0 0 1
#> SRR2001137 3 0 1 0 0 1
#> SRR2001138 3 0 1 0 0 1
#> SRR2001139 3 0 1 0 0 1
#> SRR2001132 3 0 1 0 0 1
#> SRR2001133 3 0 1 0 0 1
#> SRR2001134 3 0 1 0 0 1
#> SRR2001135 3 0 1 0 0 1
#> SRR2001128 1 0 1 1 0 0
#> SRR2001129 1 0 1 1 0 0
#> SRR2001130 1 0 1 1 0 0
#> SRR2001131 1 0 1 1 0 0
#> SRR2001124 1 0 1 1 0 0
#> SRR2001125 1 0 1 1 0 0
#> SRR2001126 1 0 1 1 0 0
#> SRR2001127 1 0 1 1 0 0
#> SRR2001120 1 0 1 1 0 0
#> SRR2001121 1 0 1 1 0 0
#> SRR2001122 1 0 1 1 0 0
#> SRR2001123 1 0 1 1 0 0
#> SRR2001116 1 0 1 1 0 0
#> SRR2001117 1 0 1 1 0 0
#> SRR2001118 1 0 1 1 0 0
#> SRR2001119 1 0 1 1 0 0
#> SRR2001112 3 0 1 0 0 1
#> SRR2001113 3 0 1 0 0 1
#> SRR2001114 3 0 1 0 0 1
#> SRR2001115 3 0 1 0 0 1
#> SRR2001108 2 0 1 0 1 0
#> SRR2001109 2 0 1 0 1 0
#> SRR2001110 2 0 1 0 1 0
#> SRR2001111 2 0 1 0 1 0
#> SRR2001104 2 0 1 0 1 0
#> SRR2001105 2 0 1 0 1 0
#> SRR2001106 2 0 1 0 1 0
#> SRR2001107 2 0 1 0 1 0
#> SRR2001100 2 0 1 0 1 0
#> SRR2001101 2 0 1 0 1 0
#> SRR2001102 2 0 1 0 1 0
#> SRR2001103 2 0 1 0 1 0
#> SRR2001096 2 0 1 0 1 0
#> SRR2001097 2 0 1 0 1 0
#> SRR2001098 2 0 1 0 1 0
#> SRR2001099 2 0 1 0 1 0
#> SRR2001092 2 0 1 0 1 0
#> SRR2001093 2 0 1 0 1 0
#> SRR2001094 2 0 1 0 1 0
#> SRR2001095 2 0 1 0 1 0
#> SRR2001088 2 0 1 0 1 0
#> SRR2001089 2 0 1 0 1 0
#> SRR2001090 2 0 1 0 1 0
#> SRR2001091 2 0 1 0 1 0
#> SRR2001084 2 0 1 0 1 0
#> SRR2001085 2 0 1 0 1 0
#> SRR2001086 2 0 1 0 1 0
#> SRR2001087 2 0 1 0 1 0
#> SRR2001080 2 0 1 0 1 0
#> SRR2001081 2 0 1 0 1 0
#> SRR2001082 2 0 1 0 1 0
#> SRR2001083 2 0 1 0 1 0
#> SRR2001076 2 0 1 0 1 0
#> SRR2001077 2 0 1 0 1 0
#> SRR2001078 2 0 1 0 1 0
#> SRR2001079 2 0 1 0 1 0
#> SRR2001072 2 0 1 0 1 0
#> SRR2001073 2 0 1 0 1 0
#> SRR2001074 2 0 1 0 1 0
#> SRR2001075 2 0 1 0 1 0
#> SRR2001068 2 0 1 0 1 0
#> SRR2001069 2 0 1 0 1 0
#> SRR2001070 2 0 1 0 1 0
#> SRR2001071 2 0 1 0 1 0
#> SRR2001064 2 0 1 0 1 0
#> SRR2001065 2 0 1 0 1 0
#> SRR2001066 2 0 1 0 1 0
#> SRR2001067 2 0 1 0 1 0
#> SRR2001060 2 0 1 0 1 0
#> SRR2001061 2 0 1 0 1 0
#> SRR2001062 2 0 1 0 1 0
#> SRR2001063 2 0 1 0 1 0
#> SRR2001056 2 0 1 0 1 0
#> SRR2001057 2 0 1 0 1 0
#> SRR2001058 2 0 1 0 1 0
#> SRR2001059 2 0 1 0 1 0
#> SRR2001052 2 0 1 0 1 0
#> SRR2001053 2 0 1 0 1 0
#> SRR2001054 2 0 1 0 1 0
#> SRR2001055 2 0 1 0 1 0
#> SRR2001048 2 0 1 0 1 0
#> SRR2001049 2 0 1 0 1 0
#> SRR2001050 2 0 1 0 1 0
#> SRR2001051 2 0 1 0 1 0
#> SRR2001044 2 0 1 0 1 0
#> SRR2001045 2 0 1 0 1 0
#> SRR2001046 2 0 1 0 1 0
#> SRR2001047 2 0 1 0 1 0
#> SRR2001040 2 0 1 0 1 0
#> SRR2001041 2 0 1 0 1 0
#> SRR2001042 2 0 1 0 1 0
#> SRR2001043 2 0 1 0 1 0
#> SRR2001036 2 0 1 0 1 0
#> SRR2001037 2 0 1 0 1 0
#> SRR2001038 2 0 1 0 1 0
#> SRR2001039 2 0 1 0 1 0
#> SRR2001028 2 0 1 0 1 0
#> SRR2001029 2 0 1 0 1 0
#> SRR2001030 2 0 1 0 1 0
#> SRR2001031 2 0 1 0 1 0
#> SRR2001024 2 0 1 0 1 0
#> SRR2001025 2 0 1 0 1 0
#> SRR2001026 2 0 1 0 1 0
#> SRR2001027 2 0 1 0 1 0
#> SRR2001020 2 0 1 0 1 0
#> SRR2001021 2 0 1 0 1 0
#> SRR2001022 2 0 1 0 1 0
#> SRR2001023 2 0 1 0 1 0
#> SRR2001016 2 0 1 0 1 0
#> SRR2001017 2 0 1 0 1 0
#> SRR2001018 2 0 1 0 1 0
#> SRR2001019 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.4008 0.978 0.000 0.756 0 0.244
#> SRR2001033 2 0.4008 0.978 0.000 0.756 0 0.244
#> SRR2001034 2 0.4008 0.978 0.000 0.756 0 0.244
#> SRR2001035 2 0.4008 0.978 0.000 0.756 0 0.244
#> SRR2001204 1 0.3688 0.873 0.792 0.208 0 0.000
#> SRR2001205 1 0.3688 0.873 0.792 0.208 0 0.000
#> SRR2001206 1 0.3688 0.873 0.792 0.208 0 0.000
#> SRR2001207 1 0.3688 0.873 0.792 0.208 0 0.000
#> SRR2001200 1 0.1118 0.928 0.964 0.036 0 0.000
#> SRR2001201 1 0.1118 0.928 0.964 0.036 0 0.000
#> SRR2001202 1 0.1118 0.928 0.964 0.036 0 0.000
#> SRR2001203 1 0.1118 0.928 0.964 0.036 0 0.000
#> SRR2001196 1 0.1118 0.928 0.964 0.036 0 0.000
#> SRR2001197 1 0.1118 0.928 0.964 0.036 0 0.000
#> SRR2001198 1 0.1118 0.928 0.964 0.036 0 0.000
#> SRR2001199 1 0.1118 0.928 0.964 0.036 0 0.000
#> SRR2001192 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001193 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001194 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001195 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001188 1 0.0000 0.934 1.000 0.000 0 0.000
#> SRR2001189 1 0.0000 0.934 1.000 0.000 0 0.000
#> SRR2001190 1 0.0000 0.934 1.000 0.000 0 0.000
#> SRR2001191 1 0.0000 0.934 1.000 0.000 0 0.000
#> SRR2001184 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001185 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001186 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001187 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001180 1 0.0000 0.934 1.000 0.000 0 0.000
#> SRR2001181 1 0.0000 0.934 1.000 0.000 0 0.000
#> SRR2001182 1 0.0188 0.934 0.996 0.004 0 0.000
#> SRR2001183 1 0.0188 0.934 0.996 0.004 0 0.000
#> SRR2001176 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001177 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001178 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001179 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001172 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001173 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001174 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001175 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001168 1 0.3688 0.873 0.792 0.208 0 0.000
#> SRR2001169 1 0.3688 0.873 0.792 0.208 0 0.000
#> SRR2001170 1 0.3688 0.873 0.792 0.208 0 0.000
#> SRR2001171 1 0.3688 0.873 0.792 0.208 0 0.000
#> SRR2001164 1 0.1022 0.930 0.968 0.032 0 0.000
#> SRR2001165 1 0.1022 0.930 0.968 0.032 0 0.000
#> SRR2001166 1 0.1022 0.930 0.968 0.032 0 0.000
#> SRR2001167 1 0.1022 0.930 0.968 0.032 0 0.000
#> SRR2001160 1 0.0000 0.934 1.000 0.000 0 0.000
#> SRR2001161 1 0.0000 0.934 1.000 0.000 0 0.000
#> SRR2001162 1 0.0000 0.934 1.000 0.000 0 0.000
#> SRR2001163 1 0.0000 0.934 1.000 0.000 0 0.000
#> SRR2001156 1 0.1022 0.930 0.968 0.032 0 0.000
#> SRR2001157 1 0.1022 0.930 0.968 0.032 0 0.000
#> SRR2001158 1 0.1022 0.930 0.968 0.032 0 0.000
#> SRR2001159 1 0.1022 0.930 0.968 0.032 0 0.000
#> SRR2001152 1 0.1792 0.921 0.932 0.068 0 0.000
#> SRR2001153 1 0.1792 0.921 0.932 0.068 0 0.000
#> SRR2001154 1 0.1792 0.921 0.932 0.068 0 0.000
#> SRR2001155 1 0.1792 0.921 0.932 0.068 0 0.000
#> SRR2001148 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001149 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001150 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001151 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001144 1 0.3688 0.873 0.792 0.208 0 0.000
#> SRR2001145 1 0.3688 0.873 0.792 0.208 0 0.000
#> SRR2001146 1 0.3688 0.873 0.792 0.208 0 0.000
#> SRR2001147 1 0.3688 0.873 0.792 0.208 0 0.000
#> SRR2001140 1 0.3688 0.873 0.792 0.208 0 0.000
#> SRR2001142 1 0.3688 0.873 0.792 0.208 0 0.000
#> SRR2001143 1 0.3688 0.873 0.792 0.208 0 0.000
#> SRR2001136 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001137 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001138 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001139 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001132 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001133 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001134 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001135 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001128 1 0.0336 0.934 0.992 0.008 0 0.000
#> SRR2001129 1 0.0336 0.934 0.992 0.008 0 0.000
#> SRR2001130 1 0.0336 0.934 0.992 0.008 0 0.000
#> SRR2001131 1 0.0336 0.934 0.992 0.008 0 0.000
#> SRR2001124 1 0.1022 0.930 0.968 0.032 0 0.000
#> SRR2001125 1 0.1022 0.930 0.968 0.032 0 0.000
#> SRR2001126 1 0.1022 0.930 0.968 0.032 0 0.000
#> SRR2001127 1 0.1022 0.930 0.968 0.032 0 0.000
#> SRR2001120 1 0.3688 0.873 0.792 0.208 0 0.000
#> SRR2001121 1 0.3688 0.873 0.792 0.208 0 0.000
#> SRR2001122 1 0.3688 0.873 0.792 0.208 0 0.000
#> SRR2001123 1 0.3688 0.873 0.792 0.208 0 0.000
#> SRR2001116 1 0.0000 0.934 1.000 0.000 0 0.000
#> SRR2001117 1 0.0000 0.934 1.000 0.000 0 0.000
#> SRR2001118 1 0.0000 0.934 1.000 0.000 0 0.000
#> SRR2001119 1 0.0000 0.934 1.000 0.000 0 0.000
#> SRR2001112 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001113 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001114 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001115 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001108 4 0.0817 0.974 0.000 0.024 0 0.976
#> SRR2001109 4 0.0817 0.974 0.000 0.024 0 0.976
#> SRR2001110 4 0.0817 0.974 0.000 0.024 0 0.976
#> SRR2001111 4 0.0817 0.974 0.000 0.024 0 0.976
#> SRR2001104 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001105 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001106 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001107 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001100 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001101 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001102 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001103 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001096 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001097 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001098 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001099 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001092 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001093 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001094 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001095 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001088 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001089 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001090 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001091 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001084 4 0.0817 0.974 0.000 0.024 0 0.976
#> SRR2001085 4 0.0817 0.974 0.000 0.024 0 0.976
#> SRR2001086 4 0.0817 0.974 0.000 0.024 0 0.976
#> SRR2001087 4 0.0817 0.974 0.000 0.024 0 0.976
#> SRR2001080 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001081 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001082 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001083 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001076 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001077 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001078 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001079 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001072 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001073 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001074 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001075 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001068 2 0.4008 0.978 0.000 0.756 0 0.244
#> SRR2001069 2 0.4008 0.978 0.000 0.756 0 0.244
#> SRR2001070 2 0.4008 0.978 0.000 0.756 0 0.244
#> SRR2001071 2 0.4008 0.978 0.000 0.756 0 0.244
#> SRR2001064 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001065 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001066 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001067 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001060 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001061 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001062 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001063 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001056 4 0.0921 0.973 0.000 0.028 0 0.972
#> SRR2001057 4 0.0921 0.973 0.000 0.028 0 0.972
#> SRR2001058 4 0.0921 0.973 0.000 0.028 0 0.972
#> SRR2001059 4 0.0921 0.973 0.000 0.028 0 0.972
#> SRR2001052 2 0.4008 0.978 0.000 0.756 0 0.244
#> SRR2001053 2 0.4008 0.978 0.000 0.756 0 0.244
#> SRR2001054 2 0.4008 0.978 0.000 0.756 0 0.244
#> SRR2001055 2 0.4008 0.978 0.000 0.756 0 0.244
#> SRR2001048 2 0.4008 0.978 0.000 0.756 0 0.244
#> SRR2001049 2 0.4008 0.978 0.000 0.756 0 0.244
#> SRR2001050 2 0.4008 0.978 0.000 0.756 0 0.244
#> SRR2001051 2 0.4008 0.978 0.000 0.756 0 0.244
#> SRR2001044 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001045 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001046 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001047 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001040 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001041 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001042 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001043 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001036 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001037 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001038 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001039 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001028 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001029 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001030 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001031 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001024 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001025 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001026 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001027 4 0.0000 0.987 0.000 0.000 0 1.000
#> SRR2001020 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001021 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001022 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001023 2 0.4193 0.989 0.000 0.732 0 0.268
#> SRR2001016 4 0.1389 0.958 0.000 0.048 0 0.952
#> SRR2001017 4 0.1389 0.958 0.000 0.048 0 0.952
#> SRR2001018 4 0.1389 0.958 0.000 0.048 0 0.952
#> SRR2001019 4 0.1389 0.958 0.000 0.048 0 0.952
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.0510 0.980 0.000 0.984 0 0.000 0.016
#> SRR2001033 2 0.0510 0.980 0.000 0.984 0 0.000 0.016
#> SRR2001034 2 0.0510 0.980 0.000 0.984 0 0.000 0.016
#> SRR2001035 2 0.0510 0.980 0.000 0.984 0 0.000 0.016
#> SRR2001204 5 0.1043 0.989 0.040 0.000 0 0.000 0.960
#> SRR2001205 5 0.1043 0.989 0.040 0.000 0 0.000 0.960
#> SRR2001206 5 0.1043 0.989 0.040 0.000 0 0.000 0.960
#> SRR2001207 5 0.1043 0.989 0.040 0.000 0 0.000 0.960
#> SRR2001200 1 0.0703 0.883 0.976 0.000 0 0.000 0.024
#> SRR2001201 1 0.0703 0.883 0.976 0.000 0 0.000 0.024
#> SRR2001202 1 0.0703 0.883 0.976 0.000 0 0.000 0.024
#> SRR2001203 1 0.0703 0.883 0.976 0.000 0 0.000 0.024
#> SRR2001196 1 0.0703 0.883 0.976 0.000 0 0.000 0.024
#> SRR2001197 1 0.0703 0.883 0.976 0.000 0 0.000 0.024
#> SRR2001198 1 0.0703 0.883 0.976 0.000 0 0.000 0.024
#> SRR2001199 1 0.0703 0.883 0.976 0.000 0 0.000 0.024
#> SRR2001192 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001193 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001194 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001195 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001188 1 0.1341 0.901 0.944 0.000 0 0.000 0.056
#> SRR2001189 1 0.1851 0.897 0.912 0.000 0 0.000 0.088
#> SRR2001190 1 0.1732 0.899 0.920 0.000 0 0.000 0.080
#> SRR2001191 1 0.1851 0.897 0.912 0.000 0 0.000 0.088
#> SRR2001184 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001185 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001186 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001187 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001180 1 0.2280 0.883 0.880 0.000 0 0.000 0.120
#> SRR2001181 1 0.2179 0.889 0.888 0.000 0 0.000 0.112
#> SRR2001182 1 0.2329 0.882 0.876 0.000 0 0.000 0.124
#> SRR2001183 1 0.2329 0.882 0.876 0.000 0 0.000 0.124
#> SRR2001176 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001177 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001178 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001179 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001172 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001173 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001174 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001175 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001168 5 0.1043 0.989 0.040 0.000 0 0.000 0.960
#> SRR2001169 5 0.1043 0.989 0.040 0.000 0 0.000 0.960
#> SRR2001170 5 0.1043 0.989 0.040 0.000 0 0.000 0.960
#> SRR2001171 5 0.1043 0.989 0.040 0.000 0 0.000 0.960
#> SRR2001164 1 0.1608 0.898 0.928 0.000 0 0.000 0.072
#> SRR2001165 1 0.1410 0.900 0.940 0.000 0 0.000 0.060
#> SRR2001166 1 0.1608 0.898 0.928 0.000 0 0.000 0.072
#> SRR2001167 1 0.1608 0.898 0.928 0.000 0 0.000 0.072
#> SRR2001160 1 0.1270 0.901 0.948 0.000 0 0.000 0.052
#> SRR2001161 1 0.1270 0.901 0.948 0.000 0 0.000 0.052
#> SRR2001162 1 0.1270 0.901 0.948 0.000 0 0.000 0.052
#> SRR2001163 1 0.1270 0.901 0.948 0.000 0 0.000 0.052
#> SRR2001156 1 0.0000 0.894 1.000 0.000 0 0.000 0.000
#> SRR2001157 1 0.0000 0.894 1.000 0.000 0 0.000 0.000
#> SRR2001158 1 0.0000 0.894 1.000 0.000 0 0.000 0.000
#> SRR2001159 1 0.0000 0.894 1.000 0.000 0 0.000 0.000
#> SRR2001152 1 0.4219 0.421 0.584 0.000 0 0.000 0.416
#> SRR2001153 1 0.4227 0.413 0.580 0.000 0 0.000 0.420
#> SRR2001154 1 0.4192 0.430 0.596 0.000 0 0.000 0.404
#> SRR2001155 1 0.4192 0.430 0.596 0.000 0 0.000 0.404
#> SRR2001148 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001149 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001150 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001151 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001144 5 0.1341 0.984 0.056 0.000 0 0.000 0.944
#> SRR2001145 5 0.1410 0.981 0.060 0.000 0 0.000 0.940
#> SRR2001146 5 0.1410 0.981 0.060 0.000 0 0.000 0.940
#> SRR2001147 5 0.1410 0.981 0.060 0.000 0 0.000 0.940
#> SRR2001140 5 0.1851 0.948 0.088 0.000 0 0.000 0.912
#> SRR2001142 5 0.1270 0.986 0.052 0.000 0 0.000 0.948
#> SRR2001143 5 0.1270 0.986 0.052 0.000 0 0.000 0.948
#> SRR2001136 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001137 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001138 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001139 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001132 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001133 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001134 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001135 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001128 1 0.2280 0.884 0.880 0.000 0 0.000 0.120
#> SRR2001129 1 0.3003 0.834 0.812 0.000 0 0.000 0.188
#> SRR2001130 1 0.2179 0.888 0.888 0.000 0 0.000 0.112
#> SRR2001131 1 0.2179 0.888 0.888 0.000 0 0.000 0.112
#> SRR2001124 1 0.0162 0.895 0.996 0.000 0 0.000 0.004
#> SRR2001125 1 0.0162 0.895 0.996 0.000 0 0.000 0.004
#> SRR2001126 1 0.0162 0.895 0.996 0.000 0 0.000 0.004
#> SRR2001127 1 0.0162 0.895 0.996 0.000 0 0.000 0.004
#> SRR2001120 5 0.1043 0.989 0.040 0.000 0 0.000 0.960
#> SRR2001121 5 0.1043 0.989 0.040 0.000 0 0.000 0.960
#> SRR2001122 5 0.1043 0.989 0.040 0.000 0 0.000 0.960
#> SRR2001123 5 0.1270 0.986 0.052 0.000 0 0.000 0.948
#> SRR2001116 1 0.2561 0.864 0.856 0.000 0 0.000 0.144
#> SRR2001117 1 0.2852 0.845 0.828 0.000 0 0.000 0.172
#> SRR2001118 1 0.3395 0.781 0.764 0.000 0 0.000 0.236
#> SRR2001119 1 0.3395 0.781 0.764 0.000 0 0.000 0.236
#> SRR2001112 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001113 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001114 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001115 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001108 4 0.0807 0.973 0.000 0.012 0 0.976 0.012
#> SRR2001109 4 0.0807 0.973 0.000 0.012 0 0.976 0.012
#> SRR2001110 4 0.0807 0.973 0.000 0.012 0 0.976 0.012
#> SRR2001111 4 0.0807 0.973 0.000 0.012 0 0.976 0.012
#> SRR2001104 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001105 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001106 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001107 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001100 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001101 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001102 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001103 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001096 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001097 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001098 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001099 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001092 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001093 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001094 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001095 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001088 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001089 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001090 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001091 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001084 4 0.0807 0.973 0.000 0.012 0 0.976 0.012
#> SRR2001085 4 0.0807 0.973 0.000 0.012 0 0.976 0.012
#> SRR2001086 4 0.0807 0.973 0.000 0.012 0 0.976 0.012
#> SRR2001087 4 0.0807 0.973 0.000 0.012 0 0.976 0.012
#> SRR2001080 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001081 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001082 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001083 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001076 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001077 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001078 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001079 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001072 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001073 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001074 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001075 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001068 2 0.0510 0.980 0.000 0.984 0 0.000 0.016
#> SRR2001069 2 0.0510 0.980 0.000 0.984 0 0.000 0.016
#> SRR2001070 2 0.0510 0.980 0.000 0.984 0 0.000 0.016
#> SRR2001071 2 0.0510 0.980 0.000 0.984 0 0.000 0.016
#> SRR2001064 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001065 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001066 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001067 2 0.0404 0.988 0.000 0.988 0 0.012 0.000
#> SRR2001060 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001061 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001062 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001063 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001056 4 0.0912 0.971 0.000 0.012 0 0.972 0.016
#> SRR2001057 4 0.0912 0.971 0.000 0.012 0 0.972 0.016
#> SRR2001058 4 0.0912 0.971 0.000 0.012 0 0.972 0.016
#> SRR2001059 4 0.0912 0.971 0.000 0.012 0 0.972 0.016
#> SRR2001052 2 0.0510 0.980 0.000 0.984 0 0.000 0.016
#> SRR2001053 2 0.0510 0.980 0.000 0.984 0 0.000 0.016
#> SRR2001054 2 0.0510 0.980 0.000 0.984 0 0.000 0.016
#> SRR2001055 2 0.0510 0.980 0.000 0.984 0 0.000 0.016
#> SRR2001048 2 0.0510 0.980 0.000 0.984 0 0.000 0.016
#> SRR2001049 2 0.0510 0.980 0.000 0.984 0 0.000 0.016
#> SRR2001050 2 0.0510 0.980 0.000 0.984 0 0.000 0.016
#> SRR2001051 2 0.0510 0.980 0.000 0.984 0 0.000 0.016
#> SRR2001044 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001045 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001046 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001047 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001040 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001041 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001042 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001043 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001036 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001037 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001038 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001039 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001028 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001029 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001030 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001031 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001024 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001025 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001026 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001027 4 0.0000 0.983 0.000 0.000 0 1.000 0.000
#> SRR2001020 2 0.0963 0.970 0.000 0.964 0 0.036 0.000
#> SRR2001021 2 0.0963 0.970 0.000 0.964 0 0.036 0.000
#> SRR2001022 2 0.0963 0.970 0.000 0.964 0 0.036 0.000
#> SRR2001023 2 0.0963 0.970 0.000 0.964 0 0.036 0.000
#> SRR2001016 4 0.2573 0.881 0.000 0.104 0 0.880 0.016
#> SRR2001017 4 0.2573 0.881 0.000 0.104 0 0.880 0.016
#> SRR2001018 4 0.2573 0.881 0.000 0.104 0 0.880 0.016
#> SRR2001019 4 0.2573 0.881 0.000 0.104 0 0.880 0.016
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR2001033 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR2001034 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR2001035 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR2001204 6 0.0000 0.988 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001205 6 0.0000 0.988 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001206 6 0.0000 0.988 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001207 6 0.0000 0.988 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001200 1 0.0146 0.880 0.996 0.004 0.000 0.000 0.000 0.000
#> SRR2001201 1 0.0146 0.880 0.996 0.004 0.000 0.000 0.000 0.000
#> SRR2001202 1 0.0146 0.880 0.996 0.004 0.000 0.000 0.000 0.000
#> SRR2001203 1 0.0146 0.880 0.996 0.004 0.000 0.000 0.000 0.000
#> SRR2001196 1 0.0146 0.880 0.996 0.004 0.000 0.000 0.000 0.000
#> SRR2001197 1 0.0146 0.880 0.996 0.004 0.000 0.000 0.000 0.000
#> SRR2001198 1 0.0146 0.880 0.996 0.004 0.000 0.000 0.000 0.000
#> SRR2001199 1 0.0146 0.880 0.996 0.004 0.000 0.000 0.000 0.000
#> SRR2001192 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001193 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001194 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001195 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001188 1 0.1501 0.900 0.924 0.000 0.000 0.000 0.000 0.076
#> SRR2001189 1 0.2048 0.894 0.880 0.000 0.000 0.000 0.000 0.120
#> SRR2001190 1 0.1814 0.899 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR2001191 1 0.2048 0.895 0.880 0.000 0.000 0.000 0.000 0.120
#> SRR2001184 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001185 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001186 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001187 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001180 1 0.2340 0.882 0.852 0.000 0.000 0.000 0.000 0.148
#> SRR2001181 1 0.2260 0.887 0.860 0.000 0.000 0.000 0.000 0.140
#> SRR2001182 1 0.2378 0.881 0.848 0.000 0.000 0.000 0.000 0.152
#> SRR2001183 1 0.2378 0.881 0.848 0.000 0.000 0.000 0.000 0.152
#> SRR2001176 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001177 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001178 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001179 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001172 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001173 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001174 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001175 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001168 6 0.0000 0.988 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001169 6 0.0000 0.988 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001170 6 0.0000 0.988 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001171 6 0.0000 0.988 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001164 1 0.1714 0.897 0.908 0.000 0.000 0.000 0.000 0.092
#> SRR2001165 1 0.1714 0.899 0.908 0.000 0.000 0.000 0.000 0.092
#> SRR2001166 1 0.1714 0.897 0.908 0.000 0.000 0.000 0.000 0.092
#> SRR2001167 1 0.1714 0.897 0.908 0.000 0.000 0.000 0.000 0.092
#> SRR2001160 1 0.1556 0.899 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR2001161 1 0.1556 0.899 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR2001162 1 0.1556 0.899 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR2001163 1 0.1556 0.899 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR2001156 1 0.0713 0.893 0.972 0.000 0.000 0.000 0.000 0.028
#> SRR2001157 1 0.0713 0.893 0.972 0.000 0.000 0.000 0.000 0.028
#> SRR2001158 1 0.0713 0.893 0.972 0.000 0.000 0.000 0.000 0.028
#> SRR2001159 1 0.0713 0.893 0.972 0.000 0.000 0.000 0.000 0.028
#> SRR2001152 1 0.3838 0.423 0.552 0.000 0.000 0.000 0.000 0.448
#> SRR2001153 1 0.3843 0.415 0.548 0.000 0.000 0.000 0.000 0.452
#> SRR2001154 1 0.3823 0.432 0.564 0.000 0.000 0.000 0.000 0.436
#> SRR2001155 1 0.3823 0.432 0.564 0.000 0.000 0.000 0.000 0.436
#> SRR2001148 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001149 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001150 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001151 3 0.3023 0.914 0.000 0.232 0.768 0.000 0.000 0.000
#> SRR2001144 6 0.0547 0.981 0.020 0.000 0.000 0.000 0.000 0.980
#> SRR2001145 6 0.0632 0.978 0.024 0.000 0.000 0.000 0.000 0.976
#> SRR2001146 6 0.0632 0.978 0.024 0.000 0.000 0.000 0.000 0.976
#> SRR2001147 6 0.0632 0.978 0.024 0.000 0.000 0.000 0.000 0.976
#> SRR2001140 6 0.1075 0.949 0.048 0.000 0.000 0.000 0.000 0.952
#> SRR2001142 6 0.0363 0.985 0.012 0.000 0.000 0.000 0.000 0.988
#> SRR2001143 6 0.0363 0.985 0.012 0.000 0.000 0.000 0.000 0.988
#> SRR2001136 3 0.1327 0.831 0.000 0.064 0.936 0.000 0.000 0.000
#> SRR2001137 3 0.1327 0.831 0.000 0.064 0.936 0.000 0.000 0.000
#> SRR2001138 3 0.1327 0.831 0.000 0.064 0.936 0.000 0.000 0.000
#> SRR2001139 3 0.1327 0.831 0.000 0.064 0.936 0.000 0.000 0.000
#> SRR2001132 3 0.0000 0.855 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001133 3 0.0000 0.855 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001134 3 0.0000 0.855 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001135 3 0.0000 0.855 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001128 1 0.2260 0.886 0.860 0.000 0.000 0.000 0.000 0.140
#> SRR2001129 1 0.2941 0.831 0.780 0.000 0.000 0.000 0.000 0.220
#> SRR2001130 1 0.2300 0.885 0.856 0.000 0.000 0.000 0.000 0.144
#> SRR2001131 1 0.2300 0.885 0.856 0.000 0.000 0.000 0.000 0.144
#> SRR2001124 1 0.0790 0.894 0.968 0.000 0.000 0.000 0.000 0.032
#> SRR2001125 1 0.0790 0.894 0.968 0.000 0.000 0.000 0.000 0.032
#> SRR2001126 1 0.0790 0.894 0.968 0.000 0.000 0.000 0.000 0.032
#> SRR2001127 1 0.0790 0.894 0.968 0.000 0.000 0.000 0.000 0.032
#> SRR2001120 6 0.0000 0.988 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001121 6 0.0000 0.988 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001122 6 0.0000 0.988 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001123 6 0.0363 0.985 0.012 0.000 0.000 0.000 0.000 0.988
#> SRR2001116 1 0.2597 0.861 0.824 0.000 0.000 0.000 0.000 0.176
#> SRR2001117 1 0.2823 0.841 0.796 0.000 0.000 0.000 0.000 0.204
#> SRR2001118 1 0.3244 0.778 0.732 0.000 0.000 0.000 0.000 0.268
#> SRR2001119 1 0.3244 0.778 0.732 0.000 0.000 0.000 0.000 0.268
#> SRR2001112 3 0.1327 0.831 0.000 0.064 0.936 0.000 0.000 0.000
#> SRR2001113 3 0.1327 0.831 0.000 0.064 0.936 0.000 0.000 0.000
#> SRR2001114 3 0.1327 0.831 0.000 0.064 0.936 0.000 0.000 0.000
#> SRR2001115 3 0.1327 0.831 0.000 0.064 0.936 0.000 0.000 0.000
#> SRR2001108 4 0.0777 0.972 0.000 0.004 0.000 0.972 0.024 0.000
#> SRR2001109 4 0.0777 0.972 0.000 0.004 0.000 0.972 0.024 0.000
#> SRR2001110 4 0.0777 0.972 0.000 0.004 0.000 0.972 0.024 0.000
#> SRR2001111 4 0.0777 0.972 0.000 0.004 0.000 0.972 0.024 0.000
#> SRR2001104 2 0.3547 0.972 0.000 0.668 0.000 0.000 0.332 0.000
#> SRR2001105 2 0.3547 0.972 0.000 0.668 0.000 0.000 0.332 0.000
#> SRR2001106 2 0.3547 0.972 0.000 0.668 0.000 0.000 0.332 0.000
#> SRR2001107 2 0.3547 0.972 0.000 0.668 0.000 0.000 0.332 0.000
#> SRR2001100 2 0.3547 0.972 0.000 0.668 0.000 0.000 0.332 0.000
#> SRR2001101 2 0.3547 0.972 0.000 0.668 0.000 0.000 0.332 0.000
#> SRR2001102 2 0.3547 0.972 0.000 0.668 0.000 0.000 0.332 0.000
#> SRR2001103 2 0.3547 0.972 0.000 0.668 0.000 0.000 0.332 0.000
#> SRR2001096 2 0.3428 0.969 0.000 0.696 0.000 0.000 0.304 0.000
#> SRR2001097 2 0.3428 0.969 0.000 0.696 0.000 0.000 0.304 0.000
#> SRR2001098 2 0.3428 0.969 0.000 0.696 0.000 0.000 0.304 0.000
#> SRR2001099 2 0.3428 0.969 0.000 0.696 0.000 0.000 0.304 0.000
#> SRR2001092 2 0.3428 0.969 0.000 0.696 0.000 0.000 0.304 0.000
#> SRR2001093 2 0.3428 0.969 0.000 0.696 0.000 0.000 0.304 0.000
#> SRR2001094 2 0.3428 0.969 0.000 0.696 0.000 0.000 0.304 0.000
#> SRR2001095 2 0.3428 0.969 0.000 0.696 0.000 0.000 0.304 0.000
#> SRR2001088 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001089 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001090 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001091 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001084 4 0.0777 0.972 0.000 0.004 0.000 0.972 0.024 0.000
#> SRR2001085 4 0.0777 0.972 0.000 0.004 0.000 0.972 0.024 0.000
#> SRR2001086 4 0.0777 0.972 0.000 0.004 0.000 0.972 0.024 0.000
#> SRR2001087 4 0.0777 0.972 0.000 0.004 0.000 0.972 0.024 0.000
#> SRR2001080 2 0.3547 0.972 0.000 0.668 0.000 0.000 0.332 0.000
#> SRR2001081 2 0.3547 0.972 0.000 0.668 0.000 0.000 0.332 0.000
#> SRR2001082 2 0.3547 0.972 0.000 0.668 0.000 0.000 0.332 0.000
#> SRR2001083 2 0.3547 0.972 0.000 0.668 0.000 0.000 0.332 0.000
#> SRR2001076 2 0.3547 0.972 0.000 0.668 0.000 0.000 0.332 0.000
#> SRR2001077 2 0.3547 0.972 0.000 0.668 0.000 0.000 0.332 0.000
#> SRR2001078 2 0.3547 0.972 0.000 0.668 0.000 0.000 0.332 0.000
#> SRR2001079 2 0.3547 0.972 0.000 0.668 0.000 0.000 0.332 0.000
#> SRR2001072 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001073 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001074 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001075 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001068 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR2001069 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR2001070 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR2001071 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR2001064 2 0.3428 0.969 0.000 0.696 0.000 0.000 0.304 0.000
#> SRR2001065 2 0.3428 0.969 0.000 0.696 0.000 0.000 0.304 0.000
#> SRR2001066 2 0.3428 0.969 0.000 0.696 0.000 0.000 0.304 0.000
#> SRR2001067 2 0.3428 0.969 0.000 0.696 0.000 0.000 0.304 0.000
#> SRR2001060 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001061 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001062 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001063 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001056 4 0.0858 0.970 0.000 0.004 0.000 0.968 0.028 0.000
#> SRR2001057 4 0.0858 0.970 0.000 0.004 0.000 0.968 0.028 0.000
#> SRR2001058 4 0.0858 0.970 0.000 0.004 0.000 0.968 0.028 0.000
#> SRR2001059 4 0.0858 0.970 0.000 0.004 0.000 0.968 0.028 0.000
#> SRR2001052 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR2001053 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR2001054 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR2001055 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR2001048 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR2001049 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR2001050 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR2001051 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR2001044 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001045 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001046 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001047 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001040 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001041 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001042 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001043 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001036 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001037 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001038 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001039 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001028 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001029 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001030 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001031 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001024 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001025 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001026 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001027 4 0.0000 0.982 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001020 2 0.4028 0.921 0.000 0.668 0.000 0.024 0.308 0.000
#> SRR2001021 2 0.4028 0.921 0.000 0.668 0.000 0.024 0.308 0.000
#> SRR2001022 2 0.4028 0.921 0.000 0.668 0.000 0.024 0.308 0.000
#> SRR2001023 2 0.4028 0.921 0.000 0.668 0.000 0.024 0.308 0.000
#> SRR2001016 4 0.2191 0.876 0.000 0.004 0.000 0.876 0.120 0.000
#> SRR2001017 4 0.2191 0.876 0.000 0.004 0.000 0.876 0.120 0.000
#> SRR2001018 4 0.2191 0.876 0.000 0.004 0.000 0.876 0.120 0.000
#> SRR2001019 4 0.2191 0.876 0.000 0.004 0.000 0.876 0.120 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", "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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.5031 0.497 0.497
#> 3 3 0.744 0.371 0.774 0.2345 0.980 0.959
#> 4 4 0.658 0.877 0.801 0.1156 0.763 0.513
#> 5 5 0.606 0.815 0.765 0.0704 1.000 1.000
#> 6 6 0.639 0.509 0.649 0.0588 0.927 0.718
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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0.631 -0.874 0.000 0.508 0.492
#> SRR2001033 2 0.631 -0.874 0.000 0.508 0.492
#> SRR2001034 2 0.631 -0.890 0.000 0.504 0.496
#> SRR2001035 2 0.631 -0.890 0.000 0.504 0.496
#> SRR2001204 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001205 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001206 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001207 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001200 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001201 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001202 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001203 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001196 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001197 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001198 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001199 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001192 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001193 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001194 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001195 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001188 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001189 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001190 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001191 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001184 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001185 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001186 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001187 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001180 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001181 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001182 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001183 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001176 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001177 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001178 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001179 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001172 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001173 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001174 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001175 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001168 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001169 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001170 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001171 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001164 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001165 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001166 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001167 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001160 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001161 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001162 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001163 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001156 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001157 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001158 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001159 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001152 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001153 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001154 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001155 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001148 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001149 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001150 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001151 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001144 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001145 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001146 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001147 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001140 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001142 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001143 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001136 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001137 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001138 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001139 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001132 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001133 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001134 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001135 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001128 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001129 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001130 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001131 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001124 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001125 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001126 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001127 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001120 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001121 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001122 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001123 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001116 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001117 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001118 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001119 1 0.630 0.860 0.524 0.000 0.476
#> SRR2001112 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001113 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001114 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001115 1 0.000 0.695 1.000 0.000 0.000
#> SRR2001108 2 0.245 0.458 0.000 0.924 0.076
#> SRR2001109 2 0.245 0.458 0.000 0.924 0.076
#> SRR2001110 2 0.245 0.458 0.000 0.924 0.076
#> SRR2001111 2 0.245 0.458 0.000 0.924 0.076
#> SRR2001104 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001105 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001106 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001107 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001100 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001101 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001102 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001103 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001096 2 0.627 -0.708 0.000 0.548 0.452
#> SRR2001097 2 0.627 -0.708 0.000 0.548 0.452
#> SRR2001098 2 0.627 -0.708 0.000 0.548 0.452
#> SRR2001099 2 0.627 -0.708 0.000 0.548 0.452
#> SRR2001092 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001093 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001094 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001095 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001088 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001089 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001090 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001091 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001084 2 0.245 0.458 0.000 0.924 0.076
#> SRR2001085 2 0.245 0.458 0.000 0.924 0.076
#> SRR2001086 2 0.245 0.458 0.000 0.924 0.076
#> SRR2001087 2 0.245 0.458 0.000 0.924 0.076
#> SRR2001080 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001081 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001082 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001083 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001076 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001077 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001078 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001079 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001072 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001073 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001074 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001075 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001068 2 0.631 -0.874 0.000 0.508 0.492
#> SRR2001069 2 0.631 -0.874 0.000 0.508 0.492
#> SRR2001070 2 0.631 -0.874 0.000 0.508 0.492
#> SRR2001071 2 0.631 -0.874 0.000 0.508 0.492
#> SRR2001064 2 0.627 -0.708 0.000 0.548 0.452
#> SRR2001065 2 0.627 -0.708 0.000 0.548 0.452
#> SRR2001066 2 0.627 -0.708 0.000 0.548 0.452
#> SRR2001067 2 0.627 -0.708 0.000 0.548 0.452
#> SRR2001060 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001061 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001062 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001063 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001056 2 0.245 0.458 0.000 0.924 0.076
#> SRR2001057 2 0.245 0.458 0.000 0.924 0.076
#> SRR2001058 2 0.245 0.458 0.000 0.924 0.076
#> SRR2001059 2 0.245 0.458 0.000 0.924 0.076
#> SRR2001052 3 0.630 1.000 0.000 0.476 0.524
#> SRR2001053 3 0.630 1.000 0.000 0.476 0.524
#> SRR2001054 3 0.630 1.000 0.000 0.476 0.524
#> SRR2001055 3 0.630 1.000 0.000 0.476 0.524
#> SRR2001048 2 0.631 -0.874 0.000 0.508 0.492
#> SRR2001049 2 0.631 -0.874 0.000 0.508 0.492
#> SRR2001050 2 0.631 -0.874 0.000 0.508 0.492
#> SRR2001051 2 0.631 -0.874 0.000 0.508 0.492
#> SRR2001044 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001045 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001046 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001047 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001040 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001041 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001042 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001043 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001036 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001037 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001038 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001039 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001028 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001029 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001030 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001031 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001024 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001025 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001026 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001027 2 0.000 0.498 0.000 1.000 0.000
#> SRR2001020 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001021 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001022 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001023 2 0.626 -0.693 0.000 0.552 0.448
#> SRR2001016 2 0.245 0.458 0.000 0.924 0.076
#> SRR2001017 2 0.245 0.458 0.000 0.924 0.076
#> SRR2001018 2 0.245 0.458 0.000 0.924 0.076
#> SRR2001019 2 0.245 0.458 0.000 0.924 0.076
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.7185 0.745 0.000 0.540 0.176 0.284
#> SRR2001033 2 0.7185 0.745 0.000 0.540 0.176 0.284
#> SRR2001034 2 0.7166 0.749 0.000 0.544 0.176 0.280
#> SRR2001035 2 0.7185 0.745 0.000 0.540 0.176 0.284
#> SRR2001204 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001205 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001206 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001207 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001200 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001201 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001202 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001203 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001196 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001197 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001198 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001199 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001192 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001193 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001194 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001195 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001188 1 0.0921 0.911 0.972 0.028 0.000 0.000
#> SRR2001189 1 0.1118 0.913 0.964 0.036 0.000 0.000
#> SRR2001190 1 0.0921 0.911 0.972 0.028 0.000 0.000
#> SRR2001191 1 0.0921 0.911 0.972 0.028 0.000 0.000
#> SRR2001184 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001185 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001186 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001187 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001180 1 0.0188 0.913 0.996 0.004 0.000 0.000
#> SRR2001181 1 0.0469 0.913 0.988 0.012 0.000 0.000
#> SRR2001182 1 0.0188 0.913 0.996 0.004 0.000 0.000
#> SRR2001183 1 0.0188 0.913 0.996 0.004 0.000 0.000
#> SRR2001176 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001177 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001178 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001179 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001172 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001173 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001174 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001175 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001168 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001169 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001170 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001171 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001164 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001165 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001166 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001167 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001160 1 0.0469 0.913 0.988 0.012 0.000 0.000
#> SRR2001161 1 0.0469 0.913 0.988 0.012 0.000 0.000
#> SRR2001162 1 0.0469 0.913 0.988 0.012 0.000 0.000
#> SRR2001163 1 0.0469 0.913 0.988 0.012 0.000 0.000
#> SRR2001156 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001157 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001158 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001159 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001152 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001153 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001154 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001155 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001148 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001149 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001150 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001151 3 0.4356 0.968 0.292 0.000 0.708 0.000
#> SRR2001144 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001145 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001146 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001147 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001140 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001142 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001143 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001136 3 0.6329 0.946 0.292 0.092 0.616 0.000
#> SRR2001137 3 0.6329 0.946 0.292 0.092 0.616 0.000
#> SRR2001138 3 0.6329 0.946 0.292 0.092 0.616 0.000
#> SRR2001139 3 0.6329 0.946 0.292 0.092 0.616 0.000
#> SRR2001132 3 0.6329 0.946 0.292 0.092 0.616 0.000
#> SRR2001133 3 0.6329 0.946 0.292 0.092 0.616 0.000
#> SRR2001134 3 0.6329 0.946 0.292 0.092 0.616 0.000
#> SRR2001135 3 0.6329 0.946 0.292 0.092 0.616 0.000
#> SRR2001128 1 0.0188 0.914 0.996 0.004 0.000 0.000
#> SRR2001129 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001130 1 0.0592 0.913 0.984 0.016 0.000 0.000
#> SRR2001131 1 0.0469 0.913 0.988 0.012 0.000 0.000
#> SRR2001124 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001125 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001126 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001127 1 0.1211 0.908 0.960 0.040 0.000 0.000
#> SRR2001120 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001121 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001122 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001123 1 0.2973 0.874 0.856 0.144 0.000 0.000
#> SRR2001116 1 0.0188 0.913 0.996 0.004 0.000 0.000
#> SRR2001117 1 0.0336 0.913 0.992 0.008 0.000 0.000
#> SRR2001118 1 0.1022 0.910 0.968 0.032 0.000 0.000
#> SRR2001119 1 0.1022 0.910 0.968 0.032 0.000 0.000
#> SRR2001112 3 0.6329 0.946 0.292 0.092 0.616 0.000
#> SRR2001113 3 0.6329 0.946 0.292 0.092 0.616 0.000
#> SRR2001114 3 0.6329 0.946 0.292 0.092 0.616 0.000
#> SRR2001115 3 0.6329 0.946 0.292 0.092 0.616 0.000
#> SRR2001108 4 0.4706 0.777 0.000 0.072 0.140 0.788
#> SRR2001109 4 0.4706 0.777 0.000 0.072 0.140 0.788
#> SRR2001110 4 0.4706 0.777 0.000 0.072 0.140 0.788
#> SRR2001111 4 0.4706 0.777 0.000 0.072 0.140 0.788
#> SRR2001104 2 0.4855 0.878 0.000 0.644 0.004 0.352
#> SRR2001105 2 0.4855 0.878 0.000 0.644 0.004 0.352
#> SRR2001106 2 0.4855 0.878 0.000 0.644 0.004 0.352
#> SRR2001107 2 0.4855 0.878 0.000 0.644 0.004 0.352
#> SRR2001100 2 0.4855 0.878 0.000 0.644 0.004 0.352
#> SRR2001101 2 0.4855 0.878 0.000 0.644 0.004 0.352
#> SRR2001102 2 0.4855 0.878 0.000 0.644 0.004 0.352
#> SRR2001103 2 0.4855 0.878 0.000 0.644 0.004 0.352
#> SRR2001096 2 0.5386 0.875 0.000 0.632 0.024 0.344
#> SRR2001097 2 0.5386 0.875 0.000 0.632 0.024 0.344
#> SRR2001098 2 0.5386 0.875 0.000 0.632 0.024 0.344
#> SRR2001099 2 0.5386 0.875 0.000 0.632 0.024 0.344
#> SRR2001092 2 0.5323 0.873 0.000 0.628 0.020 0.352
#> SRR2001093 2 0.5323 0.873 0.000 0.628 0.020 0.352
#> SRR2001094 2 0.5323 0.873 0.000 0.628 0.020 0.352
#> SRR2001095 2 0.5323 0.873 0.000 0.628 0.020 0.352
#> SRR2001088 4 0.0817 0.883 0.000 0.000 0.024 0.976
#> SRR2001089 4 0.0817 0.883 0.000 0.000 0.024 0.976
#> SRR2001090 4 0.0817 0.883 0.000 0.000 0.024 0.976
#> SRR2001091 4 0.0817 0.883 0.000 0.000 0.024 0.976
#> SRR2001084 4 0.4706 0.777 0.000 0.072 0.140 0.788
#> SRR2001085 4 0.4706 0.777 0.000 0.072 0.140 0.788
#> SRR2001086 4 0.4706 0.777 0.000 0.072 0.140 0.788
#> SRR2001087 4 0.4706 0.777 0.000 0.072 0.140 0.788
#> SRR2001080 2 0.4679 0.877 0.000 0.648 0.000 0.352
#> SRR2001081 2 0.4679 0.877 0.000 0.648 0.000 0.352
#> SRR2001082 2 0.4679 0.877 0.000 0.648 0.000 0.352
#> SRR2001083 2 0.4679 0.877 0.000 0.648 0.000 0.352
#> SRR2001076 2 0.4679 0.877 0.000 0.648 0.000 0.352
#> SRR2001077 2 0.4679 0.877 0.000 0.648 0.000 0.352
#> SRR2001078 2 0.4679 0.877 0.000 0.648 0.000 0.352
#> SRR2001079 2 0.4679 0.877 0.000 0.648 0.000 0.352
#> SRR2001072 4 0.0817 0.883 0.000 0.000 0.024 0.976
#> SRR2001073 4 0.0817 0.883 0.000 0.000 0.024 0.976
#> SRR2001074 4 0.0817 0.883 0.000 0.000 0.024 0.976
#> SRR2001075 4 0.0817 0.883 0.000 0.000 0.024 0.976
#> SRR2001068 2 0.7216 0.744 0.000 0.536 0.180 0.284
#> SRR2001069 2 0.7216 0.744 0.000 0.536 0.180 0.284
#> SRR2001070 2 0.7216 0.744 0.000 0.536 0.180 0.284
#> SRR2001071 2 0.7216 0.744 0.000 0.536 0.180 0.284
#> SRR2001064 2 0.5403 0.875 0.000 0.628 0.024 0.348
#> SRR2001065 2 0.5403 0.875 0.000 0.628 0.024 0.348
#> SRR2001066 2 0.5403 0.875 0.000 0.628 0.024 0.348
#> SRR2001067 2 0.5403 0.875 0.000 0.628 0.024 0.348
#> SRR2001060 4 0.0817 0.883 0.000 0.000 0.024 0.976
#> SRR2001061 4 0.0817 0.883 0.000 0.000 0.024 0.976
#> SRR2001062 4 0.0817 0.883 0.000 0.000 0.024 0.976
#> SRR2001063 4 0.0817 0.883 0.000 0.000 0.024 0.976
#> SRR2001056 4 0.4706 0.777 0.000 0.072 0.140 0.788
#> SRR2001057 4 0.4706 0.777 0.000 0.072 0.140 0.788
#> SRR2001058 4 0.4706 0.777 0.000 0.072 0.140 0.788
#> SRR2001059 4 0.4706 0.777 0.000 0.072 0.140 0.788
#> SRR2001052 2 0.7044 0.771 0.000 0.560 0.164 0.276
#> SRR2001053 2 0.7044 0.771 0.000 0.560 0.164 0.276
#> SRR2001054 2 0.7044 0.771 0.000 0.560 0.164 0.276
#> SRR2001055 2 0.7044 0.771 0.000 0.560 0.164 0.276
#> SRR2001048 2 0.7216 0.744 0.000 0.536 0.180 0.284
#> SRR2001049 2 0.7216 0.744 0.000 0.536 0.180 0.284
#> SRR2001050 2 0.7216 0.744 0.000 0.536 0.180 0.284
#> SRR2001051 2 0.7216 0.744 0.000 0.536 0.180 0.284
#> SRR2001044 4 0.0000 0.883 0.000 0.000 0.000 1.000
#> SRR2001045 4 0.0000 0.883 0.000 0.000 0.000 1.000
#> SRR2001046 4 0.0000 0.883 0.000 0.000 0.000 1.000
#> SRR2001047 4 0.0000 0.883 0.000 0.000 0.000 1.000
#> SRR2001040 4 0.0707 0.883 0.000 0.000 0.020 0.980
#> SRR2001041 4 0.0707 0.883 0.000 0.000 0.020 0.980
#> SRR2001042 4 0.0707 0.883 0.000 0.000 0.020 0.980
#> SRR2001043 4 0.0707 0.883 0.000 0.000 0.020 0.980
#> SRR2001036 4 0.0376 0.882 0.000 0.004 0.004 0.992
#> SRR2001037 4 0.0376 0.882 0.000 0.004 0.004 0.992
#> SRR2001038 4 0.0376 0.882 0.000 0.004 0.004 0.992
#> SRR2001039 4 0.0376 0.882 0.000 0.004 0.004 0.992
#> SRR2001028 4 0.0000 0.883 0.000 0.000 0.000 1.000
#> SRR2001029 4 0.0000 0.883 0.000 0.000 0.000 1.000
#> SRR2001030 4 0.0000 0.883 0.000 0.000 0.000 1.000
#> SRR2001031 4 0.0000 0.883 0.000 0.000 0.000 1.000
#> SRR2001024 4 0.0817 0.883 0.000 0.000 0.024 0.976
#> SRR2001025 4 0.0817 0.883 0.000 0.000 0.024 0.976
#> SRR2001026 4 0.0817 0.883 0.000 0.000 0.024 0.976
#> SRR2001027 4 0.0817 0.883 0.000 0.000 0.024 0.976
#> SRR2001020 2 0.5682 0.871 0.000 0.612 0.036 0.352
#> SRR2001021 2 0.5682 0.871 0.000 0.612 0.036 0.352
#> SRR2001022 2 0.5682 0.871 0.000 0.612 0.036 0.352
#> SRR2001023 2 0.5682 0.871 0.000 0.612 0.036 0.352
#> SRR2001016 4 0.5566 0.685 0.000 0.072 0.224 0.704
#> SRR2001017 4 0.5566 0.685 0.000 0.072 0.224 0.704
#> SRR2001018 4 0.5566 0.685 0.000 0.072 0.224 0.704
#> SRR2001019 4 0.5566 0.685 0.000 0.072 0.224 0.704
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.5117 0.686 0.000 0.652 0.000 0.072 NA
#> SRR2001033 2 0.5117 0.686 0.000 0.652 0.000 0.072 NA
#> SRR2001034 2 0.5117 0.686 0.000 0.652 0.000 0.072 NA
#> SRR2001035 2 0.5117 0.686 0.000 0.652 0.000 0.072 NA
#> SRR2001204 1 0.1197 0.749 0.952 0.000 0.000 0.048 NA
#> SRR2001205 1 0.1197 0.749 0.952 0.000 0.000 0.048 NA
#> SRR2001206 1 0.1197 0.749 0.952 0.000 0.000 0.048 NA
#> SRR2001207 1 0.1197 0.749 0.952 0.000 0.000 0.048 NA
#> SRR2001200 1 0.4663 0.808 0.604 0.000 0.000 0.020 NA
#> SRR2001201 1 0.4734 0.808 0.604 0.000 0.000 0.024 NA
#> SRR2001202 1 0.4734 0.808 0.604 0.000 0.000 0.024 NA
#> SRR2001203 1 0.4663 0.808 0.604 0.000 0.000 0.020 NA
#> SRR2001196 1 0.4734 0.808 0.604 0.000 0.000 0.024 NA
#> SRR2001197 1 0.4663 0.808 0.604 0.000 0.000 0.020 NA
#> SRR2001198 1 0.4663 0.808 0.604 0.000 0.000 0.020 NA
#> SRR2001199 1 0.4663 0.808 0.604 0.000 0.000 0.020 NA
#> SRR2001192 3 0.3456 0.937 0.184 0.000 0.800 0.016 NA
#> SRR2001193 3 0.3456 0.937 0.184 0.000 0.800 0.016 NA
#> SRR2001194 3 0.3456 0.937 0.184 0.000 0.800 0.016 NA
#> SRR2001195 3 0.3456 0.937 0.184 0.000 0.800 0.016 NA
#> SRR2001188 1 0.4339 0.818 0.652 0.000 0.000 0.012 NA
#> SRR2001189 1 0.4047 0.823 0.676 0.000 0.000 0.004 NA
#> SRR2001190 1 0.4339 0.818 0.652 0.000 0.000 0.012 NA
#> SRR2001191 1 0.4252 0.818 0.652 0.000 0.000 0.008 NA
#> SRR2001184 3 0.3843 0.934 0.184 0.000 0.788 0.012 NA
#> SRR2001185 3 0.3943 0.934 0.184 0.000 0.784 0.016 NA
#> SRR2001186 3 0.3843 0.934 0.184 0.000 0.788 0.012 NA
#> SRR2001187 3 0.3843 0.934 0.184 0.000 0.788 0.012 NA
#> SRR2001180 1 0.3942 0.824 0.728 0.000 0.000 0.012 NA
#> SRR2001181 1 0.3807 0.823 0.748 0.000 0.000 0.012 NA
#> SRR2001182 1 0.3967 0.824 0.724 0.000 0.000 0.012 NA
#> SRR2001183 1 0.3942 0.824 0.728 0.000 0.000 0.012 NA
#> SRR2001176 3 0.3456 0.937 0.184 0.000 0.800 0.016 NA
#> SRR2001177 3 0.3355 0.937 0.184 0.000 0.804 0.012 NA
#> SRR2001178 3 0.3355 0.937 0.184 0.000 0.804 0.012 NA
#> SRR2001179 3 0.3456 0.937 0.184 0.000 0.800 0.016 NA
#> SRR2001172 3 0.3943 0.934 0.184 0.000 0.784 0.016 NA
#> SRR2001173 3 0.3943 0.934 0.184 0.000 0.784 0.016 NA
#> SRR2001174 3 0.3943 0.934 0.184 0.000 0.784 0.016 NA
#> SRR2001175 3 0.3943 0.934 0.184 0.000 0.784 0.016 NA
#> SRR2001168 1 0.1121 0.749 0.956 0.000 0.000 0.044 NA
#> SRR2001169 1 0.1121 0.749 0.956 0.000 0.000 0.044 NA
#> SRR2001170 1 0.1121 0.749 0.956 0.000 0.000 0.044 NA
#> SRR2001171 1 0.1121 0.749 0.956 0.000 0.000 0.044 NA
#> SRR2001164 1 0.4276 0.811 0.616 0.000 0.000 0.004 NA
#> SRR2001165 1 0.4367 0.812 0.620 0.000 0.000 0.008 NA
#> SRR2001166 1 0.4276 0.811 0.616 0.000 0.000 0.004 NA
#> SRR2001167 1 0.4276 0.811 0.616 0.000 0.000 0.004 NA
#> SRR2001160 1 0.4127 0.823 0.680 0.000 0.000 0.008 NA
#> SRR2001161 1 0.4009 0.823 0.684 0.000 0.000 0.004 NA
#> SRR2001162 1 0.4088 0.823 0.688 0.000 0.000 0.008 NA
#> SRR2001163 1 0.4108 0.823 0.684 0.000 0.000 0.008 NA
#> SRR2001156 1 0.4663 0.808 0.604 0.000 0.000 0.020 NA
#> SRR2001157 1 0.4663 0.808 0.604 0.000 0.000 0.020 NA
#> SRR2001158 1 0.4663 0.808 0.604 0.000 0.000 0.020 NA
#> SRR2001159 1 0.4663 0.808 0.604 0.000 0.000 0.020 NA
#> SRR2001152 1 0.0451 0.759 0.988 0.000 0.000 0.004 NA
#> SRR2001153 1 0.0693 0.760 0.980 0.000 0.000 0.008 NA
#> SRR2001154 1 0.0162 0.757 0.996 0.000 0.000 0.004 NA
#> SRR2001155 1 0.0162 0.757 0.996 0.000 0.000 0.004 NA
#> SRR2001148 3 0.3843 0.934 0.184 0.000 0.788 0.012 NA
#> SRR2001149 3 0.3843 0.934 0.184 0.000 0.788 0.012 NA
#> SRR2001150 3 0.3843 0.934 0.184 0.000 0.788 0.012 NA
#> SRR2001151 3 0.3843 0.934 0.184 0.000 0.788 0.012 NA
#> SRR2001144 1 0.0794 0.752 0.972 0.000 0.000 0.028 NA
#> SRR2001145 1 0.0880 0.752 0.968 0.000 0.000 0.032 NA
#> SRR2001146 1 0.0794 0.752 0.972 0.000 0.000 0.028 NA
#> SRR2001147 1 0.0794 0.752 0.972 0.000 0.000 0.028 NA
#> SRR2001140 1 0.1043 0.752 0.960 0.000 0.000 0.040 NA
#> SRR2001142 1 0.0963 0.751 0.964 0.000 0.000 0.036 NA
#> SRR2001143 1 0.0963 0.751 0.964 0.000 0.000 0.036 NA
#> SRR2001136 3 0.6119 0.907 0.184 0.000 0.656 0.056 NA
#> SRR2001137 3 0.6119 0.907 0.184 0.000 0.656 0.056 NA
#> SRR2001138 3 0.6119 0.907 0.184 0.000 0.656 0.056 NA
#> SRR2001139 3 0.6119 0.907 0.184 0.000 0.656 0.056 NA
#> SRR2001132 3 0.6145 0.908 0.184 0.000 0.656 0.064 NA
#> SRR2001133 3 0.6145 0.908 0.184 0.000 0.656 0.064 NA
#> SRR2001134 3 0.6145 0.908 0.184 0.000 0.656 0.064 NA
#> SRR2001135 3 0.6145 0.908 0.184 0.000 0.656 0.064 NA
#> SRR2001128 1 0.4063 0.826 0.708 0.000 0.000 0.012 NA
#> SRR2001129 1 0.2966 0.815 0.816 0.000 0.000 0.000 NA
#> SRR2001130 1 0.3579 0.824 0.756 0.000 0.000 0.004 NA
#> SRR2001131 1 0.3607 0.824 0.752 0.000 0.000 0.004 NA
#> SRR2001124 1 0.4415 0.809 0.604 0.000 0.000 0.008 NA
#> SRR2001125 1 0.4505 0.809 0.604 0.000 0.000 0.012 NA
#> SRR2001126 1 0.4171 0.810 0.604 0.000 0.000 0.000 NA
#> SRR2001127 1 0.4310 0.810 0.604 0.000 0.000 0.004 NA
#> SRR2001120 1 0.0963 0.751 0.964 0.000 0.000 0.036 NA
#> SRR2001121 1 0.0963 0.751 0.964 0.000 0.000 0.036 NA
#> SRR2001122 1 0.0963 0.751 0.964 0.000 0.000 0.036 NA
#> SRR2001123 1 0.0880 0.751 0.968 0.000 0.000 0.032 NA
#> SRR2001116 1 0.4014 0.824 0.728 0.000 0.000 0.016 NA
#> SRR2001117 1 0.3728 0.823 0.748 0.000 0.000 0.008 NA
#> SRR2001118 1 0.3353 0.818 0.796 0.000 0.000 0.008 NA
#> SRR2001119 1 0.3353 0.818 0.796 0.000 0.000 0.008 NA
#> SRR2001112 3 0.6119 0.907 0.184 0.000 0.656 0.056 NA
#> SRR2001113 3 0.6119 0.907 0.184 0.000 0.656 0.056 NA
#> SRR2001114 3 0.6119 0.907 0.184 0.000 0.656 0.056 NA
#> SRR2001115 3 0.6119 0.907 0.184 0.000 0.656 0.056 NA
#> SRR2001108 4 0.6575 0.737 0.000 0.172 0.044 0.600 NA
#> SRR2001109 4 0.6575 0.737 0.000 0.172 0.044 0.600 NA
#> SRR2001110 4 0.6575 0.737 0.000 0.172 0.044 0.600 NA
#> SRR2001111 4 0.6575 0.737 0.000 0.172 0.044 0.600 NA
#> SRR2001104 2 0.0000 0.842 0.000 1.000 0.000 0.000 NA
#> SRR2001105 2 0.0000 0.842 0.000 1.000 0.000 0.000 NA
#> SRR2001106 2 0.0000 0.842 0.000 1.000 0.000 0.000 NA
#> SRR2001107 2 0.0000 0.842 0.000 1.000 0.000 0.000 NA
#> SRR2001100 2 0.0000 0.842 0.000 1.000 0.000 0.000 NA
#> SRR2001101 2 0.0000 0.842 0.000 1.000 0.000 0.000 NA
#> SRR2001102 2 0.0000 0.842 0.000 1.000 0.000 0.000 NA
#> SRR2001103 2 0.0000 0.842 0.000 1.000 0.000 0.000 NA
#> SRR2001096 2 0.2863 0.820 0.000 0.876 0.064 0.000 NA
#> SRR2001097 2 0.2863 0.820 0.000 0.876 0.064 0.000 NA
#> SRR2001098 2 0.2863 0.820 0.000 0.876 0.064 0.000 NA
#> SRR2001099 2 0.2863 0.820 0.000 0.876 0.064 0.000 NA
#> SRR2001092 2 0.2230 0.828 0.000 0.912 0.044 0.000 NA
#> SRR2001093 2 0.2230 0.828 0.000 0.912 0.044 0.000 NA
#> SRR2001094 2 0.2230 0.828 0.000 0.912 0.044 0.000 NA
#> SRR2001095 2 0.2230 0.828 0.000 0.912 0.044 0.000 NA
#> SRR2001088 4 0.5493 0.845 0.000 0.220 0.052 0.684 NA
#> SRR2001089 4 0.5493 0.845 0.000 0.220 0.052 0.684 NA
#> SRR2001090 4 0.5493 0.845 0.000 0.220 0.052 0.684 NA
#> SRR2001091 4 0.5493 0.845 0.000 0.220 0.052 0.684 NA
#> SRR2001084 4 0.6632 0.736 0.000 0.172 0.044 0.592 NA
#> SRR2001085 4 0.6632 0.736 0.000 0.172 0.044 0.592 NA
#> SRR2001086 4 0.6632 0.736 0.000 0.172 0.044 0.592 NA
#> SRR2001087 4 0.6632 0.736 0.000 0.172 0.044 0.592 NA
#> SRR2001080 2 0.0000 0.842 0.000 1.000 0.000 0.000 NA
#> SRR2001081 2 0.0162 0.841 0.000 0.996 0.004 0.000 NA
#> SRR2001082 2 0.0162 0.841 0.000 0.996 0.004 0.000 NA
#> SRR2001083 2 0.0000 0.842 0.000 1.000 0.000 0.000 NA
#> SRR2001076 2 0.0000 0.842 0.000 1.000 0.000 0.000 NA
#> SRR2001077 2 0.0000 0.842 0.000 1.000 0.000 0.000 NA
#> SRR2001078 2 0.0000 0.842 0.000 1.000 0.000 0.000 NA
#> SRR2001079 2 0.0000 0.842 0.000 1.000 0.000 0.000 NA
#> SRR2001072 4 0.5556 0.844 0.000 0.220 0.056 0.680 NA
#> SRR2001073 4 0.5556 0.844 0.000 0.220 0.056 0.680 NA
#> SRR2001074 4 0.5556 0.844 0.000 0.220 0.056 0.680 NA
#> SRR2001075 4 0.5556 0.844 0.000 0.220 0.056 0.680 NA
#> SRR2001068 2 0.5159 0.683 0.000 0.644 0.000 0.072 NA
#> SRR2001069 2 0.5159 0.683 0.000 0.644 0.000 0.072 NA
#> SRR2001070 2 0.5159 0.683 0.000 0.644 0.000 0.072 NA
#> SRR2001071 2 0.5159 0.683 0.000 0.644 0.000 0.072 NA
#> SRR2001064 2 0.2863 0.820 0.000 0.876 0.064 0.000 NA
#> SRR2001065 2 0.2863 0.820 0.000 0.876 0.064 0.000 NA
#> SRR2001066 2 0.2863 0.820 0.000 0.876 0.064 0.000 NA
#> SRR2001067 2 0.2863 0.820 0.000 0.876 0.064 0.000 NA
#> SRR2001060 4 0.5556 0.844 0.000 0.220 0.056 0.680 NA
#> SRR2001061 4 0.5556 0.844 0.000 0.220 0.056 0.680 NA
#> SRR2001062 4 0.5556 0.844 0.000 0.220 0.056 0.680 NA
#> SRR2001063 4 0.5556 0.844 0.000 0.220 0.056 0.680 NA
#> SRR2001056 4 0.6575 0.737 0.000 0.172 0.044 0.600 NA
#> SRR2001057 4 0.6575 0.737 0.000 0.172 0.044 0.600 NA
#> SRR2001058 4 0.6575 0.737 0.000 0.172 0.044 0.600 NA
#> SRR2001059 4 0.6575 0.737 0.000 0.172 0.044 0.600 NA
#> SRR2001052 2 0.5110 0.729 0.000 0.668 0.012 0.048 NA
#> SRR2001053 2 0.5110 0.729 0.000 0.668 0.012 0.048 NA
#> SRR2001054 2 0.5110 0.729 0.000 0.668 0.012 0.048 NA
#> SRR2001055 2 0.5110 0.729 0.000 0.668 0.012 0.048 NA
#> SRR2001048 2 0.5159 0.683 0.000 0.644 0.000 0.072 NA
#> SRR2001049 2 0.5159 0.683 0.000 0.644 0.000 0.072 NA
#> SRR2001050 2 0.5159 0.683 0.000 0.644 0.000 0.072 NA
#> SRR2001051 2 0.5159 0.683 0.000 0.644 0.000 0.072 NA
#> SRR2001044 4 0.3707 0.845 0.000 0.220 0.004 0.768 NA
#> SRR2001045 4 0.3707 0.845 0.000 0.220 0.004 0.768 NA
#> SRR2001046 4 0.3707 0.845 0.000 0.220 0.004 0.768 NA
#> SRR2001047 4 0.3707 0.845 0.000 0.220 0.004 0.768 NA
#> SRR2001040 4 0.5000 0.845 0.000 0.220 0.032 0.712 NA
#> SRR2001041 4 0.5000 0.845 0.000 0.220 0.032 0.712 NA
#> SRR2001042 4 0.5000 0.845 0.000 0.220 0.032 0.712 NA
#> SRR2001043 4 0.5000 0.845 0.000 0.220 0.032 0.712 NA
#> SRR2001036 4 0.3274 0.847 0.000 0.220 0.000 0.780 NA
#> SRR2001037 4 0.3274 0.847 0.000 0.220 0.000 0.780 NA
#> SRR2001038 4 0.3274 0.847 0.000 0.220 0.000 0.780 NA
#> SRR2001039 4 0.3274 0.847 0.000 0.220 0.000 0.780 NA
#> SRR2001028 4 0.3707 0.845 0.000 0.220 0.004 0.768 NA
#> SRR2001029 4 0.3707 0.845 0.000 0.220 0.004 0.768 NA
#> SRR2001030 4 0.3707 0.845 0.000 0.220 0.004 0.768 NA
#> SRR2001031 4 0.3707 0.845 0.000 0.220 0.004 0.768 NA
#> SRR2001024 4 0.5219 0.845 0.000 0.220 0.044 0.700 NA
#> SRR2001025 4 0.5219 0.845 0.000 0.220 0.044 0.700 NA
#> SRR2001026 4 0.5219 0.845 0.000 0.220 0.044 0.700 NA
#> SRR2001027 4 0.5219 0.845 0.000 0.220 0.044 0.700 NA
#> SRR2001020 2 0.2221 0.829 0.000 0.912 0.036 0.000 NA
#> SRR2001021 2 0.2221 0.829 0.000 0.912 0.036 0.000 NA
#> SRR2001022 2 0.2221 0.829 0.000 0.912 0.036 0.000 NA
#> SRR2001023 2 0.2221 0.829 0.000 0.912 0.036 0.000 NA
#> SRR2001016 4 0.7212 0.642 0.000 0.172 0.052 0.496 NA
#> SRR2001017 4 0.7212 0.642 0.000 0.172 0.052 0.496 NA
#> SRR2001018 4 0.7212 0.642 0.000 0.172 0.052 0.496 NA
#> SRR2001019 4 0.7212 0.642 0.000 0.172 0.052 0.496 NA
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 2 0.1863 0.619 0.004 0.924 0.000 0.056 0.008 0.008
#> SRR2001033 2 0.1863 0.619 0.004 0.924 0.000 0.056 0.008 0.008
#> SRR2001034 2 0.1863 0.619 0.004 0.924 0.000 0.056 0.008 0.008
#> SRR2001035 2 0.1863 0.619 0.004 0.924 0.000 0.056 0.008 0.008
#> SRR2001204 6 0.2850 0.486 0.000 0.016 0.112 0.000 0.016 0.856
#> SRR2001205 6 0.2850 0.486 0.000 0.016 0.112 0.000 0.016 0.856
#> SRR2001206 6 0.2850 0.486 0.000 0.016 0.112 0.000 0.016 0.856
#> SRR2001207 6 0.2850 0.486 0.000 0.016 0.112 0.000 0.016 0.856
#> SRR2001200 6 0.7268 -0.625 0.348 0.004 0.112 0.000 0.168 0.368
#> SRR2001201 6 0.7268 -0.625 0.348 0.004 0.112 0.000 0.168 0.368
#> SRR2001202 6 0.7268 -0.625 0.348 0.004 0.112 0.000 0.168 0.368
#> SRR2001203 6 0.7145 -0.626 0.352 0.000 0.112 0.000 0.168 0.368
#> SRR2001196 6 0.7128 -0.631 0.356 0.000 0.112 0.000 0.164 0.368
#> SRR2001197 6 0.7128 -0.631 0.356 0.000 0.112 0.000 0.164 0.368
#> SRR2001198 6 0.7128 -0.631 0.356 0.000 0.112 0.000 0.164 0.368
#> SRR2001199 6 0.7128 -0.631 0.356 0.000 0.112 0.000 0.164 0.368
#> SRR2001192 3 0.0837 0.931 0.020 0.004 0.972 0.000 0.004 0.000
#> SRR2001193 3 0.0837 0.931 0.020 0.004 0.972 0.000 0.004 0.000
#> SRR2001194 3 0.0837 0.931 0.020 0.004 0.972 0.000 0.004 0.000
#> SRR2001195 3 0.0837 0.931 0.020 0.004 0.972 0.000 0.004 0.000
#> SRR2001188 1 0.5753 0.797 0.480 0.000 0.112 0.000 0.016 0.392
#> SRR2001189 1 0.5818 0.755 0.464 0.004 0.112 0.000 0.012 0.408
#> SRR2001190 1 0.5716 0.788 0.484 0.004 0.112 0.000 0.008 0.392
#> SRR2001191 1 0.5803 0.792 0.480 0.004 0.112 0.000 0.012 0.392
#> SRR2001184 3 0.0862 0.929 0.008 0.004 0.972 0.000 0.016 0.000
#> SRR2001185 3 0.0862 0.929 0.008 0.004 0.972 0.000 0.016 0.000
#> SRR2001186 3 0.0862 0.929 0.008 0.004 0.972 0.000 0.016 0.000
#> SRR2001187 3 0.0862 0.929 0.008 0.004 0.972 0.000 0.016 0.000
#> SRR2001180 6 0.5645 -0.589 0.428 0.004 0.112 0.000 0.004 0.452
#> SRR2001181 6 0.5631 -0.502 0.404 0.004 0.112 0.000 0.004 0.476
#> SRR2001182 6 0.5646 -0.606 0.432 0.004 0.112 0.000 0.004 0.448
#> SRR2001183 6 0.5645 -0.589 0.428 0.004 0.112 0.000 0.004 0.452
#> SRR2001176 3 0.0603 0.931 0.016 0.004 0.980 0.000 0.000 0.000
#> SRR2001177 3 0.0603 0.931 0.016 0.004 0.980 0.000 0.000 0.000
#> SRR2001178 3 0.0603 0.931 0.016 0.004 0.980 0.000 0.000 0.000
#> SRR2001179 3 0.0603 0.931 0.016 0.004 0.980 0.000 0.000 0.000
#> SRR2001172 3 0.0862 0.929 0.004 0.008 0.972 0.000 0.016 0.000
#> SRR2001173 3 0.0976 0.929 0.008 0.008 0.968 0.000 0.016 0.000
#> SRR2001174 3 0.0976 0.929 0.008 0.008 0.968 0.000 0.016 0.000
#> SRR2001175 3 0.0862 0.929 0.004 0.008 0.972 0.000 0.016 0.000
#> SRR2001168 6 0.2212 0.492 0.000 0.000 0.112 0.000 0.008 0.880
#> SRR2001169 6 0.2212 0.492 0.000 0.000 0.112 0.000 0.008 0.880
#> SRR2001170 6 0.2212 0.492 0.000 0.000 0.112 0.000 0.008 0.880
#> SRR2001171 6 0.2212 0.492 0.000 0.000 0.112 0.000 0.008 0.880
#> SRR2001164 1 0.6527 0.797 0.444 0.000 0.112 0.000 0.076 0.368
#> SRR2001165 1 0.6669 0.802 0.444 0.008 0.112 0.000 0.068 0.368
#> SRR2001166 1 0.6487 0.800 0.448 0.000 0.112 0.000 0.072 0.368
#> SRR2001167 1 0.6487 0.800 0.448 0.000 0.112 0.000 0.072 0.368
#> SRR2001160 1 0.5498 0.788 0.484 0.000 0.112 0.000 0.004 0.400
#> SRR2001161 1 0.5368 0.781 0.488 0.000 0.112 0.000 0.000 0.400
#> SRR2001162 1 0.5498 0.780 0.484 0.004 0.112 0.000 0.000 0.400
#> SRR2001163 1 0.5498 0.788 0.484 0.000 0.112 0.000 0.004 0.400
#> SRR2001156 6 0.7196 -0.642 0.364 0.004 0.112 0.000 0.152 0.368
#> SRR2001157 6 0.7196 -0.642 0.364 0.004 0.112 0.000 0.152 0.368
#> SRR2001158 6 0.7196 -0.642 0.364 0.004 0.112 0.000 0.152 0.368
#> SRR2001159 6 0.7196 -0.642 0.364 0.004 0.112 0.000 0.152 0.368
#> SRR2001152 6 0.4071 0.410 0.108 0.004 0.112 0.000 0.004 0.772
#> SRR2001153 6 0.4157 0.402 0.116 0.004 0.112 0.000 0.004 0.764
#> SRR2001154 6 0.3598 0.438 0.080 0.000 0.112 0.000 0.004 0.804
#> SRR2001155 6 0.3598 0.438 0.080 0.000 0.112 0.000 0.004 0.804
#> SRR2001148 3 0.0964 0.929 0.012 0.004 0.968 0.000 0.016 0.000
#> SRR2001149 3 0.0964 0.929 0.012 0.004 0.968 0.000 0.016 0.000
#> SRR2001150 3 0.0964 0.929 0.012 0.004 0.968 0.000 0.016 0.000
#> SRR2001151 3 0.0964 0.929 0.012 0.004 0.968 0.000 0.016 0.000
#> SRR2001144 6 0.1957 0.492 0.000 0.000 0.112 0.000 0.000 0.888
#> SRR2001145 6 0.2386 0.491 0.004 0.004 0.112 0.000 0.004 0.876
#> SRR2001146 6 0.1957 0.492 0.000 0.000 0.112 0.000 0.000 0.888
#> SRR2001147 6 0.2100 0.492 0.004 0.000 0.112 0.000 0.000 0.884
#> SRR2001140 6 0.2708 0.489 0.004 0.012 0.112 0.000 0.008 0.864
#> SRR2001142 6 0.2466 0.490 0.000 0.008 0.112 0.000 0.008 0.872
#> SRR2001143 6 0.2466 0.490 0.000 0.008 0.112 0.000 0.008 0.872
#> SRR2001136 3 0.3507 0.899 0.044 0.016 0.816 0.000 0.124 0.000
#> SRR2001137 3 0.3507 0.899 0.044 0.016 0.816 0.000 0.124 0.000
#> SRR2001138 3 0.3507 0.899 0.044 0.016 0.816 0.000 0.124 0.000
#> SRR2001139 3 0.3507 0.899 0.044 0.016 0.816 0.000 0.124 0.000
#> SRR2001132 3 0.3548 0.899 0.052 0.016 0.816 0.000 0.116 0.000
#> SRR2001133 3 0.3548 0.899 0.052 0.016 0.816 0.000 0.116 0.000
#> SRR2001134 3 0.3548 0.899 0.052 0.016 0.816 0.000 0.116 0.000
#> SRR2001135 3 0.3548 0.899 0.052 0.016 0.816 0.000 0.116 0.000
#> SRR2001128 6 0.5741 -0.607 0.424 0.004 0.112 0.000 0.008 0.452
#> SRR2001129 6 0.5462 -0.214 0.320 0.004 0.112 0.000 0.004 0.560
#> SRR2001130 6 0.5823 -0.525 0.400 0.008 0.112 0.000 0.008 0.472
#> SRR2001131 6 0.5819 -0.511 0.396 0.008 0.112 0.000 0.008 0.476
#> SRR2001124 1 0.6831 0.730 0.408 0.000 0.112 0.000 0.112 0.368
#> SRR2001125 1 0.6898 0.738 0.412 0.004 0.112 0.000 0.104 0.368
#> SRR2001126 1 0.6708 0.758 0.424 0.000 0.112 0.000 0.096 0.368
#> SRR2001127 1 0.6831 0.730 0.408 0.000 0.112 0.000 0.112 0.368
#> SRR2001120 6 0.2100 0.492 0.000 0.000 0.112 0.000 0.004 0.884
#> SRR2001121 6 0.2100 0.492 0.000 0.000 0.112 0.000 0.004 0.884
#> SRR2001122 6 0.2100 0.492 0.000 0.000 0.112 0.000 0.004 0.884
#> SRR2001123 6 0.2100 0.492 0.000 0.000 0.112 0.000 0.004 0.884
#> SRR2001116 6 0.5741 -0.580 0.424 0.004 0.112 0.000 0.008 0.452
#> SRR2001117 6 0.5826 -0.516 0.404 0.008 0.112 0.000 0.008 0.468
#> SRR2001118 6 0.5539 -0.299 0.348 0.004 0.112 0.000 0.004 0.532
#> SRR2001119 6 0.5539 -0.299 0.348 0.004 0.112 0.000 0.004 0.532
#> SRR2001112 3 0.3507 0.899 0.044 0.016 0.816 0.000 0.124 0.000
#> SRR2001113 3 0.3507 0.899 0.044 0.016 0.816 0.000 0.124 0.000
#> SRR2001114 3 0.3507 0.899 0.044 0.016 0.816 0.000 0.124 0.000
#> SRR2001115 3 0.3507 0.899 0.044 0.016 0.816 0.000 0.124 0.000
#> SRR2001108 4 0.5766 0.666 0.200 0.164 0.000 0.604 0.032 0.000
#> SRR2001109 4 0.5766 0.666 0.200 0.164 0.000 0.604 0.032 0.000
#> SRR2001110 4 0.5766 0.666 0.200 0.164 0.000 0.604 0.032 0.000
#> SRR2001111 4 0.5766 0.666 0.200 0.164 0.000 0.604 0.032 0.000
#> SRR2001104 2 0.6070 -0.738 0.032 0.436 0.000 0.100 0.428 0.004
#> SRR2001105 2 0.6070 -0.738 0.032 0.436 0.000 0.100 0.428 0.004
#> SRR2001106 2 0.6070 -0.738 0.032 0.436 0.000 0.100 0.428 0.004
#> SRR2001107 2 0.6070 -0.738 0.032 0.436 0.000 0.100 0.428 0.004
#> SRR2001100 2 0.6010 -0.736 0.028 0.440 0.000 0.100 0.428 0.004
#> SRR2001101 2 0.6010 -0.736 0.028 0.440 0.000 0.100 0.428 0.004
#> SRR2001102 2 0.6010 -0.736 0.028 0.440 0.000 0.100 0.428 0.004
#> SRR2001103 2 0.6010 -0.736 0.028 0.440 0.000 0.100 0.428 0.004
#> SRR2001096 5 0.6771 0.771 0.056 0.344 0.000 0.100 0.472 0.028
#> SRR2001097 5 0.6771 0.771 0.056 0.344 0.000 0.100 0.472 0.028
#> SRR2001098 5 0.6771 0.771 0.056 0.344 0.000 0.100 0.472 0.028
#> SRR2001099 5 0.6771 0.771 0.056 0.344 0.000 0.100 0.472 0.028
#> SRR2001092 5 0.5630 0.806 0.004 0.352 0.000 0.100 0.532 0.012
#> SRR2001093 5 0.5630 0.806 0.004 0.352 0.000 0.100 0.532 0.012
#> SRR2001094 5 0.5630 0.806 0.004 0.352 0.000 0.100 0.532 0.012
#> SRR2001095 5 0.5630 0.806 0.004 0.352 0.000 0.100 0.532 0.012
#> SRR2001088 4 0.3044 0.804 0.076 0.000 0.000 0.860 0.036 0.028
#> SRR2001089 4 0.3035 0.805 0.076 0.000 0.000 0.860 0.040 0.024
#> SRR2001090 4 0.3044 0.804 0.076 0.000 0.000 0.860 0.036 0.028
#> SRR2001091 4 0.3080 0.805 0.068 0.000 0.000 0.860 0.036 0.036
#> SRR2001084 4 0.5814 0.665 0.208 0.164 0.000 0.596 0.032 0.000
#> SRR2001085 4 0.5814 0.665 0.208 0.164 0.000 0.596 0.032 0.000
#> SRR2001086 4 0.5814 0.665 0.208 0.164 0.000 0.596 0.032 0.000
#> SRR2001087 4 0.5814 0.665 0.208 0.164 0.000 0.596 0.032 0.000
#> SRR2001080 5 0.5881 0.732 0.020 0.432 0.000 0.100 0.444 0.004
#> SRR2001081 5 0.5977 0.732 0.020 0.432 0.000 0.100 0.440 0.008
#> SRR2001082 5 0.5977 0.732 0.020 0.432 0.000 0.100 0.440 0.008
#> SRR2001083 5 0.5881 0.732 0.020 0.432 0.000 0.100 0.444 0.004
#> SRR2001076 5 0.5881 0.732 0.020 0.432 0.000 0.100 0.444 0.004
#> SRR2001077 5 0.5881 0.732 0.020 0.432 0.000 0.100 0.444 0.004
#> SRR2001078 5 0.5881 0.732 0.020 0.432 0.000 0.100 0.444 0.004
#> SRR2001079 5 0.5881 0.732 0.020 0.432 0.000 0.100 0.444 0.004
#> SRR2001072 4 0.3136 0.804 0.072 0.000 0.000 0.856 0.036 0.036
#> SRR2001073 4 0.3136 0.804 0.072 0.000 0.000 0.856 0.036 0.036
#> SRR2001074 4 0.3136 0.804 0.072 0.000 0.000 0.856 0.036 0.036
#> SRR2001075 4 0.3136 0.804 0.072 0.000 0.000 0.856 0.036 0.036
#> SRR2001068 2 0.1204 0.622 0.000 0.944 0.000 0.056 0.000 0.000
#> SRR2001069 2 0.1204 0.622 0.000 0.944 0.000 0.056 0.000 0.000
#> SRR2001070 2 0.1204 0.622 0.000 0.944 0.000 0.056 0.000 0.000
#> SRR2001071 2 0.1204 0.622 0.000 0.944 0.000 0.056 0.000 0.000
#> SRR2001064 5 0.6771 0.771 0.056 0.344 0.000 0.100 0.472 0.028
#> SRR2001065 5 0.6771 0.771 0.056 0.344 0.000 0.100 0.472 0.028
#> SRR2001066 5 0.6771 0.771 0.056 0.344 0.000 0.100 0.472 0.028
#> SRR2001067 5 0.6771 0.771 0.056 0.344 0.000 0.100 0.472 0.028
#> SRR2001060 4 0.3273 0.804 0.072 0.000 0.000 0.848 0.036 0.044
#> SRR2001061 4 0.3205 0.804 0.072 0.000 0.000 0.852 0.036 0.040
#> SRR2001062 4 0.3273 0.804 0.072 0.000 0.000 0.848 0.036 0.044
#> SRR2001063 4 0.3273 0.804 0.072 0.000 0.000 0.848 0.036 0.044
#> SRR2001056 4 0.5914 0.667 0.192 0.164 0.000 0.604 0.036 0.004
#> SRR2001057 4 0.5914 0.667 0.192 0.164 0.000 0.604 0.036 0.004
#> SRR2001058 4 0.5914 0.667 0.192 0.164 0.000 0.604 0.036 0.004
#> SRR2001059 4 0.5914 0.667 0.192 0.164 0.000 0.604 0.036 0.004
#> SRR2001052 2 0.3411 0.548 0.016 0.836 0.000 0.052 0.092 0.004
#> SRR2001053 2 0.3259 0.557 0.016 0.848 0.000 0.052 0.080 0.004
#> SRR2001054 2 0.3411 0.548 0.016 0.836 0.000 0.052 0.092 0.004
#> SRR2001055 2 0.3411 0.548 0.016 0.836 0.000 0.052 0.092 0.004
#> SRR2001048 2 0.1349 0.620 0.004 0.940 0.000 0.056 0.000 0.000
#> SRR2001049 2 0.1349 0.620 0.004 0.940 0.000 0.056 0.000 0.000
#> SRR2001050 2 0.1349 0.620 0.004 0.940 0.000 0.056 0.000 0.000
#> SRR2001051 2 0.1349 0.620 0.004 0.940 0.000 0.056 0.000 0.000
#> SRR2001044 4 0.1078 0.807 0.012 0.000 0.000 0.964 0.008 0.016
#> SRR2001045 4 0.0881 0.808 0.012 0.000 0.000 0.972 0.008 0.008
#> SRR2001046 4 0.1078 0.807 0.012 0.000 0.000 0.964 0.008 0.016
#> SRR2001047 4 0.0881 0.808 0.012 0.000 0.000 0.972 0.008 0.008
#> SRR2001040 4 0.1649 0.807 0.040 0.000 0.000 0.936 0.016 0.008
#> SRR2001041 4 0.1649 0.807 0.040 0.000 0.000 0.936 0.016 0.008
#> SRR2001042 4 0.1649 0.807 0.040 0.000 0.000 0.936 0.016 0.008
#> SRR2001043 4 0.1649 0.807 0.040 0.000 0.000 0.936 0.016 0.008
#> SRR2001036 4 0.1007 0.809 0.004 0.004 0.000 0.968 0.008 0.016
#> SRR2001037 4 0.1007 0.809 0.004 0.004 0.000 0.968 0.008 0.016
#> SRR2001038 4 0.0924 0.808 0.008 0.004 0.000 0.972 0.008 0.008
#> SRR2001039 4 0.1007 0.809 0.004 0.004 0.000 0.968 0.008 0.016
#> SRR2001028 4 0.0881 0.808 0.012 0.000 0.000 0.972 0.008 0.008
#> SRR2001029 4 0.0881 0.808 0.012 0.000 0.000 0.972 0.008 0.008
#> SRR2001030 4 0.0881 0.808 0.012 0.000 0.000 0.972 0.008 0.008
#> SRR2001031 4 0.0881 0.808 0.012 0.000 0.000 0.972 0.008 0.008
#> SRR2001024 4 0.2755 0.806 0.056 0.000 0.000 0.880 0.036 0.028
#> SRR2001025 4 0.2714 0.807 0.064 0.000 0.000 0.880 0.036 0.020
#> SRR2001026 4 0.2797 0.806 0.064 0.000 0.000 0.876 0.036 0.024
#> SRR2001027 4 0.2816 0.806 0.060 0.000 0.000 0.876 0.036 0.028
#> SRR2001020 5 0.6342 0.784 0.036 0.368 0.000 0.100 0.480 0.016
#> SRR2001021 5 0.6342 0.784 0.036 0.368 0.000 0.100 0.480 0.016
#> SRR2001022 5 0.6342 0.784 0.036 0.368 0.000 0.100 0.480 0.016
#> SRR2001023 5 0.6342 0.784 0.036 0.368 0.000 0.100 0.480 0.016
#> SRR2001016 4 0.6782 0.477 0.216 0.304 0.000 0.432 0.044 0.004
#> SRR2001017 4 0.6782 0.477 0.216 0.304 0.000 0.432 0.044 0.004
#> SRR2001018 4 0.6782 0.477 0.216 0.304 0.000 0.432 0.044 0.004
#> SRR2001019 4 0.6782 0.477 0.216 0.304 0.000 0.432 0.044 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["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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.5031 0.497 0.497
#> 3 3 1.000 0.999 0.998 0.2207 0.889 0.777
#> 4 4 1.000 0.996 0.995 0.2052 0.873 0.671
#> 5 5 0.885 0.841 0.872 0.0604 1.000 1.000
#> 6 6 0.860 0.860 0.864 0.0425 0.908 0.649
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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001033 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001034 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001035 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001204 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001205 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001206 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001207 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001200 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001201 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001202 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001203 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001196 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001197 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001198 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001199 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001192 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001193 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001194 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001195 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001188 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001189 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001190 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001191 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001184 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001185 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001186 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001187 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001180 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001181 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001182 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001183 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001176 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001177 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001178 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001179 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001172 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001173 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001174 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001175 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001168 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001169 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001170 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001171 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001164 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001165 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001166 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001167 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001160 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001161 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001162 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001163 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001156 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001157 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001158 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001159 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001152 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001153 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001154 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001155 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001148 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001149 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001150 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001151 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001144 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001145 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001146 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001147 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001140 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001142 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001143 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001136 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001137 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001138 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001139 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001132 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001133 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001134 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001135 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001128 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001129 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001130 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001131 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001124 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001125 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001126 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001127 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001120 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001121 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001122 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001123 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001116 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001117 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001118 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001119 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001112 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001113 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001114 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001115 3 0.0237 1.000 0.004 0.000 0.996
#> SRR2001108 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001109 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001110 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001111 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001104 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001105 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001106 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001107 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001100 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001101 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001102 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001103 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001096 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001097 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001098 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001099 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001092 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001093 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001094 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001095 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001088 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001089 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001090 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001091 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001084 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001085 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001086 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001087 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001080 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001081 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001082 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001083 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001076 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001077 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001078 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001079 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001072 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001073 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001074 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001075 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001068 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001069 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001070 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001071 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001064 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001065 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001066 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001067 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001060 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001061 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001062 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001063 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001056 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001057 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001058 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001059 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001052 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001053 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001054 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001055 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001048 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001049 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001050 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001051 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001044 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001045 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001046 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001047 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001040 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001041 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001042 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001043 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001036 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001037 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001038 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001039 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001028 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001029 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001030 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001031 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001024 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001025 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001026 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001027 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001020 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001021 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001022 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001023 2 0.0237 0.998 0.000 0.996 0.004
#> SRR2001016 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001017 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001018 2 0.0000 0.998 0.000 1.000 0.000
#> SRR2001019 2 0.0000 0.998 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.0592 0.990 0.000 0.984 0 0.016
#> SRR2001033 2 0.0592 0.990 0.000 0.984 0 0.016
#> SRR2001034 2 0.0592 0.990 0.000 0.984 0 0.016
#> SRR2001035 2 0.0592 0.990 0.000 0.984 0 0.016
#> SRR2001204 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001205 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001206 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001207 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001200 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001201 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001202 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001203 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001196 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001197 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001198 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001199 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001192 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001193 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001194 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001195 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001188 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001189 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001190 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001191 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001184 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001185 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001186 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001187 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001180 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001181 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001182 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001183 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001176 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001177 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001178 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001179 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001172 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001173 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001174 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001175 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001168 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001169 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001170 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001171 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001164 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001165 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001166 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001167 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001160 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001161 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001162 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001163 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001156 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001157 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001158 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001159 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001152 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001153 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001154 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001155 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001148 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001149 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001150 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001151 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001144 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001145 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001146 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001147 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001140 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001142 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001143 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001136 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001137 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001138 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001139 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001132 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001133 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001134 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001135 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001128 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001129 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001130 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001131 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001124 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001125 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001126 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001127 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001120 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001121 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001122 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001123 1 0.0336 0.996 0.992 0.000 0 0.008
#> SRR2001116 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001117 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001118 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001119 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001112 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001113 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001114 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001115 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001108 4 0.0336 0.994 0.000 0.008 0 0.992
#> SRR2001109 4 0.0336 0.994 0.000 0.008 0 0.992
#> SRR2001110 4 0.0336 0.994 0.000 0.008 0 0.992
#> SRR2001111 4 0.0336 0.994 0.000 0.008 0 0.992
#> SRR2001104 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001105 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001106 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001107 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001100 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001101 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001102 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001103 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001096 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001097 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001098 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001099 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001092 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001093 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001094 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001095 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001088 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001089 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001090 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001091 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001084 4 0.0336 0.994 0.000 0.008 0 0.992
#> SRR2001085 4 0.0336 0.994 0.000 0.008 0 0.992
#> SRR2001086 4 0.0336 0.994 0.000 0.008 0 0.992
#> SRR2001087 4 0.0336 0.994 0.000 0.008 0 0.992
#> SRR2001080 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001081 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001082 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001083 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001076 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001077 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001078 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001079 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001072 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001073 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001074 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001075 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001068 2 0.0592 0.990 0.000 0.984 0 0.016
#> SRR2001069 2 0.0592 0.990 0.000 0.984 0 0.016
#> SRR2001070 2 0.0592 0.990 0.000 0.984 0 0.016
#> SRR2001071 2 0.0592 0.990 0.000 0.984 0 0.016
#> SRR2001064 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001065 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001066 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001067 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001060 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001061 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001062 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001063 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001056 4 0.0336 0.994 0.000 0.008 0 0.992
#> SRR2001057 4 0.0336 0.994 0.000 0.008 0 0.992
#> SRR2001058 4 0.0336 0.994 0.000 0.008 0 0.992
#> SRR2001059 4 0.0336 0.994 0.000 0.008 0 0.992
#> SRR2001052 2 0.0336 0.992 0.000 0.992 0 0.008
#> SRR2001053 2 0.0336 0.992 0.000 0.992 0 0.008
#> SRR2001054 2 0.0336 0.992 0.000 0.992 0 0.008
#> SRR2001055 2 0.0336 0.992 0.000 0.992 0 0.008
#> SRR2001048 2 0.0592 0.990 0.000 0.984 0 0.016
#> SRR2001049 2 0.0592 0.990 0.000 0.984 0 0.016
#> SRR2001050 2 0.0592 0.990 0.000 0.984 0 0.016
#> SRR2001051 2 0.0592 0.990 0.000 0.984 0 0.016
#> SRR2001044 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001045 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001046 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001047 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001040 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001041 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001042 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001043 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001036 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001037 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001038 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001039 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001028 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001029 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001030 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001031 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001024 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001025 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001026 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001027 4 0.0592 0.997 0.000 0.016 0 0.984
#> SRR2001020 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001021 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001022 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001023 2 0.0000 0.996 0.000 1.000 0 0.000
#> SRR2001016 4 0.0336 0.994 0.000 0.008 0 0.992
#> SRR2001017 4 0.0336 0.994 0.000 0.008 0 0.992
#> SRR2001018 4 0.0336 0.994 0.000 0.008 0 0.992
#> SRR2001019 4 0.0336 0.994 0.000 0.008 0 0.992
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.4256 0.694 0.000 0.564 0 0.000 NA
#> SRR2001033 2 0.4256 0.694 0.000 0.564 0 0.000 NA
#> SRR2001034 2 0.4256 0.694 0.000 0.564 0 0.000 NA
#> SRR2001035 2 0.4256 0.694 0.000 0.564 0 0.000 NA
#> SRR2001204 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001205 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001206 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001207 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001200 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001201 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001202 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001203 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001196 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001197 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001198 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001199 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001192 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001193 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001194 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001195 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001188 1 0.0000 0.831 1.000 0.000 0 0.000 NA
#> SRR2001189 1 0.0162 0.832 0.996 0.000 0 0.000 NA
#> SRR2001190 1 0.0000 0.831 1.000 0.000 0 0.000 NA
#> SRR2001191 1 0.0000 0.831 1.000 0.000 0 0.000 NA
#> SRR2001184 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001185 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001186 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001187 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001180 1 0.0290 0.831 0.992 0.000 0 0.000 NA
#> SRR2001181 1 0.0510 0.831 0.984 0.000 0 0.000 NA
#> SRR2001182 1 0.0290 0.831 0.992 0.000 0 0.000 NA
#> SRR2001183 1 0.0404 0.831 0.988 0.000 0 0.000 NA
#> SRR2001176 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001177 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001178 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001179 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001172 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001173 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001174 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001175 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001168 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001169 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001170 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001171 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001164 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001165 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001166 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001167 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001160 1 0.0000 0.831 1.000 0.000 0 0.000 NA
#> SRR2001161 1 0.0162 0.831 0.996 0.000 0 0.000 NA
#> SRR2001162 1 0.0290 0.831 0.992 0.000 0 0.000 NA
#> SRR2001163 1 0.0290 0.831 0.992 0.000 0 0.000 NA
#> SRR2001156 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001157 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001158 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001159 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001152 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001153 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001154 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001155 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001148 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001149 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001150 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001151 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001144 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001145 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001146 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001147 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001140 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001142 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001143 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001136 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001137 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001138 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001139 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001132 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001133 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001134 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001135 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001128 1 0.0404 0.831 0.988 0.000 0 0.000 NA
#> SRR2001129 1 0.0510 0.831 0.984 0.000 0 0.000 NA
#> SRR2001130 1 0.0510 0.831 0.984 0.000 0 0.000 NA
#> SRR2001131 1 0.0510 0.831 0.984 0.000 0 0.000 NA
#> SRR2001124 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001125 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001126 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001127 1 0.0510 0.829 0.984 0.000 0 0.000 NA
#> SRR2001120 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001121 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001122 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001123 1 0.4305 0.694 0.512 0.000 0 0.000 NA
#> SRR2001116 1 0.0404 0.831 0.988 0.000 0 0.000 NA
#> SRR2001117 1 0.0404 0.831 0.988 0.000 0 0.000 NA
#> SRR2001118 1 0.0510 0.831 0.984 0.000 0 0.000 NA
#> SRR2001119 1 0.0510 0.831 0.984 0.000 0 0.000 NA
#> SRR2001112 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001113 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001114 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001115 3 0.0000 1.000 0.000 0.000 1 0.000 NA
#> SRR2001108 4 0.3796 0.780 0.000 0.000 0 0.700 NA
#> SRR2001109 4 0.3796 0.780 0.000 0.000 0 0.700 NA
#> SRR2001110 4 0.3796 0.780 0.000 0.000 0 0.700 NA
#> SRR2001111 4 0.3796 0.780 0.000 0.000 0 0.700 NA
#> SRR2001104 2 0.0000 0.870 0.000 1.000 0 0.000 NA
#> SRR2001105 2 0.0000 0.870 0.000 1.000 0 0.000 NA
#> SRR2001106 2 0.0000 0.870 0.000 1.000 0 0.000 NA
#> SRR2001107 2 0.0000 0.870 0.000 1.000 0 0.000 NA
#> SRR2001100 2 0.0000 0.870 0.000 1.000 0 0.000 NA
#> SRR2001101 2 0.0000 0.870 0.000 1.000 0 0.000 NA
#> SRR2001102 2 0.0000 0.870 0.000 1.000 0 0.000 NA
#> SRR2001103 2 0.0000 0.870 0.000 1.000 0 0.000 NA
#> SRR2001096 2 0.0162 0.869 0.000 0.996 0 0.000 NA
#> SRR2001097 2 0.0162 0.869 0.000 0.996 0 0.000 NA
#> SRR2001098 2 0.0162 0.869 0.000 0.996 0 0.000 NA
#> SRR2001099 2 0.0162 0.869 0.000 0.996 0 0.000 NA
#> SRR2001092 2 0.0162 0.869 0.000 0.996 0 0.000 NA
#> SRR2001093 2 0.0162 0.869 0.000 0.996 0 0.000 NA
#> SRR2001094 2 0.0162 0.869 0.000 0.996 0 0.000 NA
#> SRR2001095 2 0.0162 0.869 0.000 0.996 0 0.000 NA
#> SRR2001088 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001089 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001090 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001091 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001084 4 0.3796 0.780 0.000 0.000 0 0.700 NA
#> SRR2001085 4 0.3796 0.780 0.000 0.000 0 0.700 NA
#> SRR2001086 4 0.3796 0.780 0.000 0.000 0 0.700 NA
#> SRR2001087 4 0.3796 0.780 0.000 0.000 0 0.700 NA
#> SRR2001080 2 0.0000 0.870 0.000 1.000 0 0.000 NA
#> SRR2001081 2 0.0000 0.870 0.000 1.000 0 0.000 NA
#> SRR2001082 2 0.0000 0.870 0.000 1.000 0 0.000 NA
#> SRR2001083 2 0.0000 0.870 0.000 1.000 0 0.000 NA
#> SRR2001076 2 0.0000 0.870 0.000 1.000 0 0.000 NA
#> SRR2001077 2 0.0000 0.870 0.000 1.000 0 0.000 NA
#> SRR2001078 2 0.0000 0.870 0.000 1.000 0 0.000 NA
#> SRR2001079 2 0.0000 0.870 0.000 1.000 0 0.000 NA
#> SRR2001072 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001073 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001074 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001075 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001068 2 0.4256 0.694 0.000 0.564 0 0.000 NA
#> SRR2001069 2 0.4256 0.694 0.000 0.564 0 0.000 NA
#> SRR2001070 2 0.4256 0.694 0.000 0.564 0 0.000 NA
#> SRR2001071 2 0.4256 0.694 0.000 0.564 0 0.000 NA
#> SRR2001064 2 0.0162 0.869 0.000 0.996 0 0.000 NA
#> SRR2001065 2 0.0162 0.869 0.000 0.996 0 0.000 NA
#> SRR2001066 2 0.0162 0.869 0.000 0.996 0 0.000 NA
#> SRR2001067 2 0.0162 0.869 0.000 0.996 0 0.000 NA
#> SRR2001060 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001061 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001062 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001063 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001056 4 0.3796 0.780 0.000 0.000 0 0.700 NA
#> SRR2001057 4 0.3796 0.780 0.000 0.000 0 0.700 NA
#> SRR2001058 4 0.3796 0.780 0.000 0.000 0 0.700 NA
#> SRR2001059 4 0.3796 0.780 0.000 0.000 0 0.700 NA
#> SRR2001052 2 0.4171 0.717 0.000 0.604 0 0.000 NA
#> SRR2001053 2 0.4182 0.715 0.000 0.600 0 0.000 NA
#> SRR2001054 2 0.4171 0.717 0.000 0.604 0 0.000 NA
#> SRR2001055 2 0.4171 0.717 0.000 0.604 0 0.000 NA
#> SRR2001048 2 0.4256 0.694 0.000 0.564 0 0.000 NA
#> SRR2001049 2 0.4256 0.694 0.000 0.564 0 0.000 NA
#> SRR2001050 2 0.4256 0.694 0.000 0.564 0 0.000 NA
#> SRR2001051 2 0.4256 0.694 0.000 0.564 0 0.000 NA
#> SRR2001044 4 0.0290 0.896 0.000 0.000 0 0.992 NA
#> SRR2001045 4 0.0290 0.896 0.000 0.000 0 0.992 NA
#> SRR2001046 4 0.0290 0.896 0.000 0.000 0 0.992 NA
#> SRR2001047 4 0.0290 0.896 0.000 0.000 0 0.992 NA
#> SRR2001040 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001041 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001042 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001043 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001036 4 0.0290 0.896 0.000 0.000 0 0.992 NA
#> SRR2001037 4 0.0290 0.896 0.000 0.000 0 0.992 NA
#> SRR2001038 4 0.0290 0.896 0.000 0.000 0 0.992 NA
#> SRR2001039 4 0.0290 0.896 0.000 0.000 0 0.992 NA
#> SRR2001028 4 0.0290 0.896 0.000 0.000 0 0.992 NA
#> SRR2001029 4 0.0290 0.896 0.000 0.000 0 0.992 NA
#> SRR2001030 4 0.0290 0.896 0.000 0.000 0 0.992 NA
#> SRR2001031 4 0.0290 0.896 0.000 0.000 0 0.992 NA
#> SRR2001024 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001025 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001026 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001027 4 0.0000 0.896 0.000 0.000 0 1.000 NA
#> SRR2001020 2 0.0290 0.868 0.000 0.992 0 0.000 NA
#> SRR2001021 2 0.0290 0.868 0.000 0.992 0 0.000 NA
#> SRR2001022 2 0.0290 0.868 0.000 0.992 0 0.000 NA
#> SRR2001023 2 0.0290 0.868 0.000 0.992 0 0.000 NA
#> SRR2001016 4 0.4300 0.612 0.000 0.000 0 0.524 NA
#> SRR2001017 4 0.4300 0.612 0.000 0.000 0 0.524 NA
#> SRR2001018 4 0.4300 0.612 0.000 0.000 0 0.524 NA
#> SRR2001019 4 0.4300 0.612 0.000 0.000 0 0.524 NA
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 5 0.3266 0.820 0.000 0.272 0.000 0.000 0.728 0.000
#> SRR2001033 5 0.3266 0.820 0.000 0.272 0.000 0.000 0.728 0.000
#> SRR2001034 5 0.3266 0.820 0.000 0.272 0.000 0.000 0.728 0.000
#> SRR2001035 5 0.3266 0.820 0.000 0.272 0.000 0.000 0.728 0.000
#> SRR2001204 6 0.3043 0.993 0.200 0.000 0.000 0.000 0.008 0.792
#> SRR2001205 6 0.3043 0.993 0.200 0.000 0.000 0.000 0.008 0.792
#> SRR2001206 6 0.3043 0.993 0.200 0.000 0.000 0.000 0.008 0.792
#> SRR2001207 6 0.3043 0.993 0.200 0.000 0.000 0.000 0.008 0.792
#> SRR2001200 1 0.0363 0.920 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR2001201 1 0.0363 0.920 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR2001202 1 0.0363 0.920 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR2001203 1 0.0363 0.920 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR2001196 1 0.0363 0.920 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR2001197 1 0.0363 0.920 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR2001198 1 0.0363 0.920 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR2001199 1 0.0363 0.920 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR2001192 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001193 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001194 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001195 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001188 1 0.1141 0.915 0.948 0.000 0.000 0.000 0.000 0.052
#> SRR2001189 1 0.1610 0.903 0.916 0.000 0.000 0.000 0.000 0.084
#> SRR2001190 1 0.1204 0.914 0.944 0.000 0.000 0.000 0.000 0.056
#> SRR2001191 1 0.1141 0.915 0.948 0.000 0.000 0.000 0.000 0.052
#> SRR2001184 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001185 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001186 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001187 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001180 1 0.2135 0.871 0.872 0.000 0.000 0.000 0.000 0.128
#> SRR2001181 1 0.2378 0.845 0.848 0.000 0.000 0.000 0.000 0.152
#> SRR2001182 1 0.2003 0.882 0.884 0.000 0.000 0.000 0.000 0.116
#> SRR2001183 1 0.2092 0.875 0.876 0.000 0.000 0.000 0.000 0.124
#> SRR2001176 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001177 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001178 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001179 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001172 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001173 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001174 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001175 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001168 6 0.2933 0.994 0.200 0.000 0.000 0.000 0.004 0.796
#> SRR2001169 6 0.2933 0.994 0.200 0.000 0.000 0.000 0.004 0.796
#> SRR2001170 6 0.2933 0.994 0.200 0.000 0.000 0.000 0.004 0.796
#> SRR2001171 6 0.2933 0.994 0.200 0.000 0.000 0.000 0.004 0.796
#> SRR2001164 1 0.0000 0.920 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001165 1 0.0000 0.920 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001166 1 0.0000 0.920 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001167 1 0.0000 0.920 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001160 1 0.1204 0.914 0.944 0.000 0.000 0.000 0.000 0.056
#> SRR2001161 1 0.1556 0.905 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR2001162 1 0.1501 0.906 0.924 0.000 0.000 0.000 0.000 0.076
#> SRR2001163 1 0.1444 0.908 0.928 0.000 0.000 0.000 0.000 0.072
#> SRR2001156 1 0.0363 0.920 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR2001157 1 0.0363 0.920 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR2001158 1 0.0363 0.920 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR2001159 1 0.0363 0.920 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR2001152 6 0.2883 0.986 0.212 0.000 0.000 0.000 0.000 0.788
#> SRR2001153 6 0.2883 0.986 0.212 0.000 0.000 0.000 0.000 0.788
#> SRR2001154 6 0.2883 0.986 0.212 0.000 0.000 0.000 0.000 0.788
#> SRR2001155 6 0.2883 0.986 0.212 0.000 0.000 0.000 0.000 0.788
#> SRR2001148 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001149 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001150 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001151 3 0.0000 0.963 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001144 6 0.2793 0.995 0.200 0.000 0.000 0.000 0.000 0.800
#> SRR2001145 6 0.2793 0.995 0.200 0.000 0.000 0.000 0.000 0.800
#> SRR2001146 6 0.2793 0.995 0.200 0.000 0.000 0.000 0.000 0.800
#> SRR2001147 6 0.2793 0.995 0.200 0.000 0.000 0.000 0.000 0.800
#> SRR2001140 6 0.2793 0.995 0.200 0.000 0.000 0.000 0.000 0.800
#> SRR2001142 6 0.2793 0.995 0.200 0.000 0.000 0.000 0.000 0.800
#> SRR2001143 6 0.2793 0.995 0.200 0.000 0.000 0.000 0.000 0.800
#> SRR2001136 3 0.2433 0.938 0.000 0.000 0.884 0.000 0.072 0.044
#> SRR2001137 3 0.2433 0.938 0.000 0.000 0.884 0.000 0.072 0.044
#> SRR2001138 3 0.2433 0.938 0.000 0.000 0.884 0.000 0.072 0.044
#> SRR2001139 3 0.2433 0.938 0.000 0.000 0.884 0.000 0.072 0.044
#> SRR2001132 3 0.2433 0.938 0.000 0.000 0.884 0.000 0.072 0.044
#> SRR2001133 3 0.2433 0.938 0.000 0.000 0.884 0.000 0.072 0.044
#> SRR2001134 3 0.2433 0.938 0.000 0.000 0.884 0.000 0.072 0.044
#> SRR2001135 3 0.2433 0.938 0.000 0.000 0.884 0.000 0.072 0.044
#> SRR2001128 1 0.1765 0.896 0.904 0.000 0.000 0.000 0.000 0.096
#> SRR2001129 1 0.3050 0.708 0.764 0.000 0.000 0.000 0.000 0.236
#> SRR2001130 1 0.2219 0.864 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR2001131 1 0.2300 0.855 0.856 0.000 0.000 0.000 0.000 0.144
#> SRR2001124 1 0.0363 0.920 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR2001125 1 0.0363 0.920 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR2001126 1 0.0363 0.920 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR2001127 1 0.0363 0.920 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR2001120 6 0.2793 0.995 0.200 0.000 0.000 0.000 0.000 0.800
#> SRR2001121 6 0.2793 0.995 0.200 0.000 0.000 0.000 0.000 0.800
#> SRR2001122 6 0.2793 0.995 0.200 0.000 0.000 0.000 0.000 0.800
#> SRR2001123 6 0.2793 0.995 0.200 0.000 0.000 0.000 0.000 0.800
#> SRR2001116 1 0.2135 0.871 0.872 0.000 0.000 0.000 0.000 0.128
#> SRR2001117 1 0.2219 0.864 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR2001118 1 0.2854 0.761 0.792 0.000 0.000 0.000 0.000 0.208
#> SRR2001119 1 0.2883 0.755 0.788 0.000 0.000 0.000 0.000 0.212
#> SRR2001112 3 0.2488 0.936 0.000 0.000 0.880 0.000 0.076 0.044
#> SRR2001113 3 0.2488 0.936 0.000 0.000 0.880 0.000 0.076 0.044
#> SRR2001114 3 0.2488 0.936 0.000 0.000 0.880 0.000 0.076 0.044
#> SRR2001115 3 0.2488 0.936 0.000 0.000 0.880 0.000 0.076 0.044
#> SRR2001108 4 0.5654 0.334 0.000 0.000 0.000 0.444 0.404 0.152
#> SRR2001109 4 0.5654 0.334 0.000 0.000 0.000 0.444 0.404 0.152
#> SRR2001110 4 0.5654 0.334 0.000 0.000 0.000 0.444 0.404 0.152
#> SRR2001111 4 0.5654 0.334 0.000 0.000 0.000 0.444 0.404 0.152
#> SRR2001104 2 0.1075 0.962 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR2001105 2 0.1075 0.962 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR2001106 2 0.1075 0.962 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR2001107 2 0.1075 0.962 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR2001100 2 0.1075 0.962 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR2001101 2 0.1075 0.962 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR2001102 2 0.1075 0.962 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR2001103 2 0.1075 0.962 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR2001096 2 0.0260 0.959 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR2001097 2 0.0260 0.959 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR2001098 2 0.0260 0.959 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR2001099 2 0.0260 0.959 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR2001092 2 0.0000 0.961 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001093 2 0.0000 0.961 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001094 2 0.0000 0.961 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001095 2 0.0000 0.961 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001088 4 0.0508 0.829 0.000 0.000 0.000 0.984 0.012 0.004
#> SRR2001089 4 0.0508 0.829 0.000 0.000 0.000 0.984 0.012 0.004
#> SRR2001090 4 0.0508 0.829 0.000 0.000 0.000 0.984 0.012 0.004
#> SRR2001091 4 0.0363 0.829 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR2001084 4 0.5657 0.329 0.000 0.000 0.000 0.436 0.412 0.152
#> SRR2001085 4 0.5657 0.329 0.000 0.000 0.000 0.436 0.412 0.152
#> SRR2001086 4 0.5657 0.329 0.000 0.000 0.000 0.436 0.412 0.152
#> SRR2001087 4 0.5657 0.329 0.000 0.000 0.000 0.436 0.412 0.152
#> SRR2001080 2 0.1075 0.962 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR2001081 2 0.1075 0.962 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR2001082 2 0.1075 0.962 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR2001083 2 0.1075 0.962 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR2001076 2 0.1075 0.962 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR2001077 2 0.1075 0.962 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR2001078 2 0.1075 0.962 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR2001079 2 0.1075 0.962 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR2001072 4 0.0508 0.829 0.000 0.000 0.000 0.984 0.012 0.004
#> SRR2001073 4 0.0508 0.829 0.000 0.000 0.000 0.984 0.012 0.004
#> SRR2001074 4 0.0508 0.829 0.000 0.000 0.000 0.984 0.012 0.004
#> SRR2001075 4 0.0508 0.829 0.000 0.000 0.000 0.984 0.012 0.004
#> SRR2001068 5 0.3266 0.820 0.000 0.272 0.000 0.000 0.728 0.000
#> SRR2001069 5 0.3266 0.820 0.000 0.272 0.000 0.000 0.728 0.000
#> SRR2001070 5 0.3266 0.820 0.000 0.272 0.000 0.000 0.728 0.000
#> SRR2001071 5 0.3266 0.820 0.000 0.272 0.000 0.000 0.728 0.000
#> SRR2001064 2 0.0260 0.959 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR2001065 2 0.0260 0.959 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR2001066 2 0.0260 0.959 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR2001067 2 0.0260 0.959 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR2001060 4 0.0363 0.829 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR2001061 4 0.0363 0.829 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR2001062 4 0.0363 0.829 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR2001063 4 0.0363 0.829 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR2001056 4 0.5654 0.334 0.000 0.000 0.000 0.444 0.404 0.152
#> SRR2001057 4 0.5654 0.334 0.000 0.000 0.000 0.444 0.404 0.152
#> SRR2001058 4 0.5654 0.334 0.000 0.000 0.000 0.444 0.404 0.152
#> SRR2001059 4 0.5654 0.334 0.000 0.000 0.000 0.444 0.404 0.152
#> SRR2001052 5 0.3647 0.707 0.000 0.360 0.000 0.000 0.640 0.000
#> SRR2001053 5 0.3647 0.707 0.000 0.360 0.000 0.000 0.640 0.000
#> SRR2001054 5 0.3647 0.707 0.000 0.360 0.000 0.000 0.640 0.000
#> SRR2001055 5 0.3647 0.707 0.000 0.360 0.000 0.000 0.640 0.000
#> SRR2001048 5 0.3266 0.820 0.000 0.272 0.000 0.000 0.728 0.000
#> SRR2001049 5 0.3266 0.820 0.000 0.272 0.000 0.000 0.728 0.000
#> SRR2001050 5 0.3266 0.820 0.000 0.272 0.000 0.000 0.728 0.000
#> SRR2001051 5 0.3266 0.820 0.000 0.272 0.000 0.000 0.728 0.000
#> SRR2001044 4 0.0260 0.830 0.000 0.000 0.000 0.992 0.000 0.008
#> SRR2001045 4 0.0363 0.830 0.000 0.000 0.000 0.988 0.000 0.012
#> SRR2001046 4 0.0260 0.830 0.000 0.000 0.000 0.992 0.000 0.008
#> SRR2001047 4 0.0363 0.830 0.000 0.000 0.000 0.988 0.000 0.012
#> SRR2001040 4 0.0000 0.831 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001041 4 0.0000 0.831 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001042 4 0.0000 0.831 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001043 4 0.0000 0.831 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001036 4 0.0260 0.830 0.000 0.000 0.000 0.992 0.000 0.008
#> SRR2001037 4 0.0260 0.830 0.000 0.000 0.000 0.992 0.000 0.008
#> SRR2001038 4 0.0363 0.830 0.000 0.000 0.000 0.988 0.000 0.012
#> SRR2001039 4 0.0260 0.830 0.000 0.000 0.000 0.992 0.000 0.008
#> SRR2001028 4 0.0363 0.830 0.000 0.000 0.000 0.988 0.000 0.012
#> SRR2001029 4 0.0363 0.830 0.000 0.000 0.000 0.988 0.000 0.012
#> SRR2001030 4 0.0363 0.830 0.000 0.000 0.000 0.988 0.000 0.012
#> SRR2001031 4 0.0363 0.830 0.000 0.000 0.000 0.988 0.000 0.012
#> SRR2001024 4 0.0000 0.831 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001025 4 0.0000 0.831 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001026 4 0.0146 0.831 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR2001027 4 0.0000 0.831 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001020 2 0.0458 0.951 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR2001021 2 0.0458 0.951 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR2001022 2 0.0458 0.951 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR2001023 2 0.0458 0.951 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR2001016 5 0.4898 0.303 0.000 0.000 0.000 0.200 0.656 0.144
#> SRR2001017 5 0.4898 0.303 0.000 0.000 0.000 0.200 0.656 0.144
#> SRR2001018 5 0.4898 0.303 0.000 0.000 0.000 0.200 0.656 0.144
#> SRR2001019 5 0.4898 0.303 0.000 0.000 0.000 0.200 0.656 0.144
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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 6.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.5031 0.497 0.497
#> 3 3 1.000 1.000 1.000 0.2206 0.889 0.777
#> 4 4 1.000 0.994 0.997 0.2064 0.873 0.671
#> 5 5 0.899 0.630 0.813 0.0559 0.920 0.704
#> 6 6 0.931 0.946 0.945 0.0460 0.929 0.686
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3 4
There is also optional best \(k\) = 2 3 4 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0 1 0 1 0
#> SRR2001033 2 0 1 0 1 0
#> SRR2001034 2 0 1 0 1 0
#> SRR2001035 2 0 1 0 1 0
#> SRR2001204 1 0 1 1 0 0
#> SRR2001205 1 0 1 1 0 0
#> SRR2001206 1 0 1 1 0 0
#> SRR2001207 1 0 1 1 0 0
#> SRR2001200 1 0 1 1 0 0
#> SRR2001201 1 0 1 1 0 0
#> SRR2001202 1 0 1 1 0 0
#> SRR2001203 1 0 1 1 0 0
#> SRR2001196 1 0 1 1 0 0
#> SRR2001197 1 0 1 1 0 0
#> SRR2001198 1 0 1 1 0 0
#> SRR2001199 1 0 1 1 0 0
#> SRR2001192 3 0 1 0 0 1
#> SRR2001193 3 0 1 0 0 1
#> SRR2001194 3 0 1 0 0 1
#> SRR2001195 3 0 1 0 0 1
#> SRR2001188 1 0 1 1 0 0
#> SRR2001189 1 0 1 1 0 0
#> SRR2001190 1 0 1 1 0 0
#> SRR2001191 1 0 1 1 0 0
#> SRR2001184 3 0 1 0 0 1
#> SRR2001185 3 0 1 0 0 1
#> SRR2001186 3 0 1 0 0 1
#> SRR2001187 3 0 1 0 0 1
#> SRR2001180 1 0 1 1 0 0
#> SRR2001181 1 0 1 1 0 0
#> SRR2001182 1 0 1 1 0 0
#> SRR2001183 1 0 1 1 0 0
#> SRR2001176 3 0 1 0 0 1
#> SRR2001177 3 0 1 0 0 1
#> SRR2001178 3 0 1 0 0 1
#> SRR2001179 3 0 1 0 0 1
#> SRR2001172 3 0 1 0 0 1
#> SRR2001173 3 0 1 0 0 1
#> SRR2001174 3 0 1 0 0 1
#> SRR2001175 3 0 1 0 0 1
#> SRR2001168 1 0 1 1 0 0
#> SRR2001169 1 0 1 1 0 0
#> SRR2001170 1 0 1 1 0 0
#> SRR2001171 1 0 1 1 0 0
#> SRR2001164 1 0 1 1 0 0
#> SRR2001165 1 0 1 1 0 0
#> SRR2001166 1 0 1 1 0 0
#> SRR2001167 1 0 1 1 0 0
#> SRR2001160 1 0 1 1 0 0
#> SRR2001161 1 0 1 1 0 0
#> SRR2001162 1 0 1 1 0 0
#> SRR2001163 1 0 1 1 0 0
#> SRR2001156 1 0 1 1 0 0
#> SRR2001157 1 0 1 1 0 0
#> SRR2001158 1 0 1 1 0 0
#> SRR2001159 1 0 1 1 0 0
#> SRR2001152 1 0 1 1 0 0
#> SRR2001153 1 0 1 1 0 0
#> SRR2001154 1 0 1 1 0 0
#> SRR2001155 1 0 1 1 0 0
#> SRR2001148 3 0 1 0 0 1
#> SRR2001149 3 0 1 0 0 1
#> SRR2001150 3 0 1 0 0 1
#> SRR2001151 3 0 1 0 0 1
#> SRR2001144 1 0 1 1 0 0
#> SRR2001145 1 0 1 1 0 0
#> SRR2001146 1 0 1 1 0 0
#> SRR2001147 1 0 1 1 0 0
#> SRR2001140 1 0 1 1 0 0
#> SRR2001142 1 0 1 1 0 0
#> SRR2001143 1 0 1 1 0 0
#> SRR2001136 3 0 1 0 0 1
#> SRR2001137 3 0 1 0 0 1
#> SRR2001138 3 0 1 0 0 1
#> SRR2001139 3 0 1 0 0 1
#> SRR2001132 3 0 1 0 0 1
#> SRR2001133 3 0 1 0 0 1
#> SRR2001134 3 0 1 0 0 1
#> SRR2001135 3 0 1 0 0 1
#> SRR2001128 1 0 1 1 0 0
#> SRR2001129 1 0 1 1 0 0
#> SRR2001130 1 0 1 1 0 0
#> SRR2001131 1 0 1 1 0 0
#> SRR2001124 1 0 1 1 0 0
#> SRR2001125 1 0 1 1 0 0
#> SRR2001126 1 0 1 1 0 0
#> SRR2001127 1 0 1 1 0 0
#> SRR2001120 1 0 1 1 0 0
#> SRR2001121 1 0 1 1 0 0
#> SRR2001122 1 0 1 1 0 0
#> SRR2001123 1 0 1 1 0 0
#> SRR2001116 1 0 1 1 0 0
#> SRR2001117 1 0 1 1 0 0
#> SRR2001118 1 0 1 1 0 0
#> SRR2001119 1 0 1 1 0 0
#> SRR2001112 3 0 1 0 0 1
#> SRR2001113 3 0 1 0 0 1
#> SRR2001114 3 0 1 0 0 1
#> SRR2001115 3 0 1 0 0 1
#> SRR2001108 2 0 1 0 1 0
#> SRR2001109 2 0 1 0 1 0
#> SRR2001110 2 0 1 0 1 0
#> SRR2001111 2 0 1 0 1 0
#> SRR2001104 2 0 1 0 1 0
#> SRR2001105 2 0 1 0 1 0
#> SRR2001106 2 0 1 0 1 0
#> SRR2001107 2 0 1 0 1 0
#> SRR2001100 2 0 1 0 1 0
#> SRR2001101 2 0 1 0 1 0
#> SRR2001102 2 0 1 0 1 0
#> SRR2001103 2 0 1 0 1 0
#> SRR2001096 2 0 1 0 1 0
#> SRR2001097 2 0 1 0 1 0
#> SRR2001098 2 0 1 0 1 0
#> SRR2001099 2 0 1 0 1 0
#> SRR2001092 2 0 1 0 1 0
#> SRR2001093 2 0 1 0 1 0
#> SRR2001094 2 0 1 0 1 0
#> SRR2001095 2 0 1 0 1 0
#> SRR2001088 2 0 1 0 1 0
#> SRR2001089 2 0 1 0 1 0
#> SRR2001090 2 0 1 0 1 0
#> SRR2001091 2 0 1 0 1 0
#> SRR2001084 2 0 1 0 1 0
#> SRR2001085 2 0 1 0 1 0
#> SRR2001086 2 0 1 0 1 0
#> SRR2001087 2 0 1 0 1 0
#> SRR2001080 2 0 1 0 1 0
#> SRR2001081 2 0 1 0 1 0
#> SRR2001082 2 0 1 0 1 0
#> SRR2001083 2 0 1 0 1 0
#> SRR2001076 2 0 1 0 1 0
#> SRR2001077 2 0 1 0 1 0
#> SRR2001078 2 0 1 0 1 0
#> SRR2001079 2 0 1 0 1 0
#> SRR2001072 2 0 1 0 1 0
#> SRR2001073 2 0 1 0 1 0
#> SRR2001074 2 0 1 0 1 0
#> SRR2001075 2 0 1 0 1 0
#> SRR2001068 2 0 1 0 1 0
#> SRR2001069 2 0 1 0 1 0
#> SRR2001070 2 0 1 0 1 0
#> SRR2001071 2 0 1 0 1 0
#> SRR2001064 2 0 1 0 1 0
#> SRR2001065 2 0 1 0 1 0
#> SRR2001066 2 0 1 0 1 0
#> SRR2001067 2 0 1 0 1 0
#> SRR2001060 2 0 1 0 1 0
#> SRR2001061 2 0 1 0 1 0
#> SRR2001062 2 0 1 0 1 0
#> SRR2001063 2 0 1 0 1 0
#> SRR2001056 2 0 1 0 1 0
#> SRR2001057 2 0 1 0 1 0
#> SRR2001058 2 0 1 0 1 0
#> SRR2001059 2 0 1 0 1 0
#> SRR2001052 2 0 1 0 1 0
#> SRR2001053 2 0 1 0 1 0
#> SRR2001054 2 0 1 0 1 0
#> SRR2001055 2 0 1 0 1 0
#> SRR2001048 2 0 1 0 1 0
#> SRR2001049 2 0 1 0 1 0
#> SRR2001050 2 0 1 0 1 0
#> SRR2001051 2 0 1 0 1 0
#> SRR2001044 2 0 1 0 1 0
#> SRR2001045 2 0 1 0 1 0
#> SRR2001046 2 0 1 0 1 0
#> SRR2001047 2 0 1 0 1 0
#> SRR2001040 2 0 1 0 1 0
#> SRR2001041 2 0 1 0 1 0
#> SRR2001042 2 0 1 0 1 0
#> SRR2001043 2 0 1 0 1 0
#> SRR2001036 2 0 1 0 1 0
#> SRR2001037 2 0 1 0 1 0
#> SRR2001038 2 0 1 0 1 0
#> SRR2001039 2 0 1 0 1 0
#> SRR2001028 2 0 1 0 1 0
#> SRR2001029 2 0 1 0 1 0
#> SRR2001030 2 0 1 0 1 0
#> SRR2001031 2 0 1 0 1 0
#> SRR2001024 2 0 1 0 1 0
#> SRR2001025 2 0 1 0 1 0
#> SRR2001026 2 0 1 0 1 0
#> SRR2001027 2 0 1 0 1 0
#> SRR2001020 2 0 1 0 1 0
#> SRR2001021 2 0 1 0 1 0
#> SRR2001022 2 0 1 0 1 0
#> SRR2001023 2 0 1 0 1 0
#> SRR2001016 2 0 1 0 1 0
#> SRR2001017 2 0 1 0 1 0
#> SRR2001018 2 0 1 0 1 0
#> SRR2001019 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001033 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001034 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001035 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001204 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001205 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001206 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001207 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001200 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001201 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001202 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001203 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001196 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001197 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001198 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001199 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001192 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001193 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001194 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001195 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001188 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001189 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001190 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001191 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001184 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001185 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001186 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001187 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001180 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001181 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001182 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001183 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001176 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001177 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001178 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001179 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001172 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001173 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001174 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001175 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001168 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001169 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001170 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001171 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001164 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001165 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001166 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001167 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001160 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001161 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001162 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001163 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001156 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001157 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001158 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001159 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001152 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001153 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001154 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001155 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001148 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001149 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001150 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001151 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001144 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001145 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001146 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001147 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001140 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001142 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001143 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001136 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001137 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001138 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001139 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001132 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001133 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001134 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001135 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001128 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001129 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001130 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001131 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001124 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001125 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001126 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001127 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001120 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001121 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001122 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001123 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001116 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001117 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001118 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001119 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001112 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001113 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001114 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001115 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001108 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001109 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001110 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001111 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001104 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001105 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001106 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001107 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001100 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001101 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001102 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001103 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001096 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001097 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001098 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001099 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001092 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001093 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001094 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001095 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001088 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001089 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001090 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001091 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001084 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001085 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001086 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001087 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001080 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001081 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001082 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001083 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001076 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001077 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001078 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001079 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001072 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001073 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001074 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001075 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001068 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001069 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001070 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001071 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001064 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001065 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001066 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001067 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001060 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001061 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001062 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001063 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001056 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001057 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001058 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001059 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001052 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001053 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001054 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001055 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001048 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001049 2 0.0188 0.996 0 0.996 0 0.004
#> SRR2001050 2 0.0188 0.996 0 0.996 0 0.004
#> SRR2001051 2 0.0336 0.991 0 0.992 0 0.008
#> SRR2001044 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001045 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001046 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001047 4 0.2345 0.890 0 0.100 0 0.900
#> SRR2001040 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001041 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001042 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001043 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001036 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001037 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001038 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001039 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001028 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001029 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001030 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001031 4 0.0469 0.977 0 0.012 0 0.988
#> SRR2001024 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001025 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001026 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001027 4 0.0000 0.987 0 0.000 0 1.000
#> SRR2001020 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001021 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001022 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001023 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001016 4 0.3024 0.838 0 0.148 0 0.852
#> SRR2001017 4 0.2281 0.897 0 0.096 0 0.904
#> SRR2001018 4 0.2281 0.896 0 0.096 0 0.904
#> SRR2001019 4 0.2530 0.879 0 0.112 0 0.888
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.0290 0.972 0.000 0.992 0 0.000 0.008
#> SRR2001033 2 0.0162 0.974 0.000 0.996 0 0.000 0.004
#> SRR2001034 2 0.0609 0.967 0.000 0.980 0 0.000 0.020
#> SRR2001035 2 0.0162 0.974 0.000 0.996 0 0.000 0.004
#> SRR2001204 5 0.4307 -0.424 0.500 0.000 0 0.000 0.500
#> SRR2001205 1 0.4307 0.391 0.500 0.000 0 0.000 0.500
#> SRR2001206 1 0.4307 0.391 0.500 0.000 0 0.000 0.500
#> SRR2001207 5 0.4307 -0.424 0.500 0.000 0 0.000 0.500
#> SRR2001200 1 0.0000 0.639 1.000 0.000 0 0.000 0.000
#> SRR2001201 1 0.0000 0.639 1.000 0.000 0 0.000 0.000
#> SRR2001202 1 0.0000 0.639 1.000 0.000 0 0.000 0.000
#> SRR2001203 1 0.0000 0.639 1.000 0.000 0 0.000 0.000
#> SRR2001196 1 0.0000 0.639 1.000 0.000 0 0.000 0.000
#> SRR2001197 1 0.0000 0.639 1.000 0.000 0 0.000 0.000
#> SRR2001198 1 0.0000 0.639 1.000 0.000 0 0.000 0.000
#> SRR2001199 1 0.0000 0.639 1.000 0.000 0 0.000 0.000
#> SRR2001192 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001193 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001194 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001195 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001188 1 0.4227 0.457 0.580 0.000 0 0.000 0.420
#> SRR2001189 5 0.4307 -0.424 0.500 0.000 0 0.000 0.500
#> SRR2001190 5 0.4307 -0.424 0.500 0.000 0 0.000 0.500
#> SRR2001191 5 0.4307 -0.424 0.500 0.000 0 0.000 0.500
#> SRR2001184 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001185 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001186 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001187 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001180 1 0.4307 0.395 0.504 0.000 0 0.000 0.496
#> SRR2001181 5 0.4307 -0.424 0.500 0.000 0 0.000 0.500
#> SRR2001182 1 0.4306 0.399 0.508 0.000 0 0.000 0.492
#> SRR2001183 1 0.4307 0.395 0.504 0.000 0 0.000 0.496
#> SRR2001176 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001177 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001178 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001179 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001172 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001173 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001174 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001175 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001168 1 0.4307 0.391 0.500 0.000 0 0.000 0.500
#> SRR2001169 5 0.4307 -0.424 0.500 0.000 0 0.000 0.500
#> SRR2001170 1 0.4307 0.391 0.500 0.000 0 0.000 0.500
#> SRR2001171 1 0.4307 0.391 0.500 0.000 0 0.000 0.500
#> SRR2001164 1 0.0703 0.637 0.976 0.000 0 0.000 0.024
#> SRR2001165 1 0.0510 0.638 0.984 0.000 0 0.000 0.016
#> SRR2001166 1 0.2074 0.615 0.896 0.000 0 0.000 0.104
#> SRR2001167 1 0.0000 0.639 1.000 0.000 0 0.000 0.000
#> SRR2001160 1 0.0290 0.639 0.992 0.000 0 0.000 0.008
#> SRR2001161 1 0.0000 0.639 1.000 0.000 0 0.000 0.000
#> SRR2001162 1 0.1671 0.624 0.924 0.000 0 0.000 0.076
#> SRR2001163 1 0.3895 0.519 0.680 0.000 0 0.000 0.320
#> SRR2001156 1 0.0000 0.639 1.000 0.000 0 0.000 0.000
#> SRR2001157 1 0.0000 0.639 1.000 0.000 0 0.000 0.000
#> SRR2001158 1 0.0000 0.639 1.000 0.000 0 0.000 0.000
#> SRR2001159 1 0.0000 0.639 1.000 0.000 0 0.000 0.000
#> SRR2001152 1 0.4307 0.391 0.500 0.000 0 0.000 0.500
#> SRR2001153 1 0.4307 0.391 0.500 0.000 0 0.000 0.500
#> SRR2001154 5 0.4307 -0.424 0.500 0.000 0 0.000 0.500
#> SRR2001155 5 0.4307 -0.424 0.500 0.000 0 0.000 0.500
#> SRR2001148 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001149 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001150 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001151 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001144 5 0.4307 -0.424 0.500 0.000 0 0.000 0.500
#> SRR2001145 5 0.4307 -0.424 0.500 0.000 0 0.000 0.500
#> SRR2001146 1 0.4307 0.391 0.500 0.000 0 0.000 0.500
#> SRR2001147 1 0.4307 0.391 0.500 0.000 0 0.000 0.500
#> SRR2001140 5 0.4307 -0.424 0.500 0.000 0 0.000 0.500
#> SRR2001142 1 0.4307 0.391 0.500 0.000 0 0.000 0.500
#> SRR2001143 5 0.4307 -0.424 0.500 0.000 0 0.000 0.500
#> SRR2001136 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001137 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001138 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001139 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001132 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001133 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001134 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001135 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001128 1 0.4307 0.395 0.504 0.000 0 0.000 0.496
#> SRR2001129 1 0.4307 0.391 0.500 0.000 0 0.000 0.500
#> SRR2001130 5 0.4307 -0.424 0.500 0.000 0 0.000 0.500
#> SRR2001131 5 0.4307 -0.424 0.500 0.000 0 0.000 0.500
#> SRR2001124 1 0.0000 0.639 1.000 0.000 0 0.000 0.000
#> SRR2001125 1 0.0000 0.639 1.000 0.000 0 0.000 0.000
#> SRR2001126 1 0.0000 0.639 1.000 0.000 0 0.000 0.000
#> SRR2001127 1 0.0000 0.639 1.000 0.000 0 0.000 0.000
#> SRR2001120 1 0.4307 0.391 0.500 0.000 0 0.000 0.500
#> SRR2001121 1 0.4307 0.391 0.500 0.000 0 0.000 0.500
#> SRR2001122 5 0.4307 -0.424 0.500 0.000 0 0.000 0.500
#> SRR2001123 5 0.4307 -0.424 0.500 0.000 0 0.000 0.500
#> SRR2001116 5 0.4307 -0.424 0.500 0.000 0 0.000 0.500
#> SRR2001117 1 0.4307 0.391 0.500 0.000 0 0.000 0.500
#> SRR2001118 1 0.4307 0.391 0.500 0.000 0 0.000 0.500
#> SRR2001119 1 0.4307 0.391 0.500 0.000 0 0.000 0.500
#> SRR2001112 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001113 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001114 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001115 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001108 4 0.4304 0.405 0.000 0.000 0 0.516 0.484
#> SRR2001109 5 0.4307 -0.418 0.000 0.000 0 0.500 0.500
#> SRR2001110 5 0.4307 -0.418 0.000 0.000 0 0.500 0.500
#> SRR2001111 5 0.4307 -0.418 0.000 0.000 0 0.500 0.500
#> SRR2001104 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001105 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001106 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001107 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001100 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001101 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001102 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001103 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001096 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001097 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001098 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001099 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001092 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001093 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001094 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001095 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001088 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001089 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001090 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001091 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001084 5 0.4307 -0.418 0.000 0.000 0 0.500 0.500
#> SRR2001085 4 0.4307 0.380 0.000 0.000 0 0.500 0.500
#> SRR2001086 4 0.4307 0.380 0.000 0.000 0 0.500 0.500
#> SRR2001087 4 0.4307 0.380 0.000 0.000 0 0.500 0.500
#> SRR2001080 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001081 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001082 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001083 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001076 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001077 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001078 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001079 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001072 4 0.0794 0.919 0.000 0.000 0 0.972 0.028
#> SRR2001073 4 0.0162 0.935 0.000 0.000 0 0.996 0.004
#> SRR2001074 4 0.0963 0.913 0.000 0.000 0 0.964 0.036
#> SRR2001075 4 0.1851 0.870 0.000 0.000 0 0.912 0.088
#> SRR2001068 2 0.2516 0.889 0.000 0.860 0 0.000 0.140
#> SRR2001069 2 0.2605 0.883 0.000 0.852 0 0.000 0.148
#> SRR2001070 2 0.1270 0.951 0.000 0.948 0 0.000 0.052
#> SRR2001071 2 0.1671 0.936 0.000 0.924 0 0.000 0.076
#> SRR2001064 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001065 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001066 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001067 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001060 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001061 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001062 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001063 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001056 5 0.4307 -0.418 0.000 0.000 0 0.500 0.500
#> SRR2001057 5 0.4307 -0.418 0.000 0.000 0 0.500 0.500
#> SRR2001058 5 0.4307 -0.418 0.000 0.000 0 0.500 0.500
#> SRR2001059 5 0.4307 -0.418 0.000 0.000 0 0.500 0.500
#> SRR2001052 2 0.1043 0.957 0.000 0.960 0 0.000 0.040
#> SRR2001053 2 0.1410 0.946 0.000 0.940 0 0.000 0.060
#> SRR2001054 2 0.1197 0.953 0.000 0.952 0 0.000 0.048
#> SRR2001055 2 0.1410 0.946 0.000 0.940 0 0.000 0.060
#> SRR2001048 2 0.2929 0.856 0.000 0.820 0 0.000 0.180
#> SRR2001049 2 0.3039 0.844 0.000 0.808 0 0.000 0.192
#> SRR2001050 2 0.2690 0.877 0.000 0.844 0 0.000 0.156
#> SRR2001051 2 0.2966 0.852 0.000 0.816 0 0.000 0.184
#> SRR2001044 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001045 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001046 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001047 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001040 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001041 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001042 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001043 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001036 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001037 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001038 4 0.0609 0.924 0.000 0.000 0 0.980 0.020
#> SRR2001039 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001028 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001029 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001030 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001031 4 0.0510 0.923 0.000 0.016 0 0.984 0.000
#> SRR2001024 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001025 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001026 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001027 4 0.0000 0.937 0.000 0.000 0 1.000 0.000
#> SRR2001020 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001021 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001022 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001023 2 0.0000 0.975 0.000 1.000 0 0.000 0.000
#> SRR2001016 5 0.4659 -0.407 0.000 0.012 0 0.488 0.500
#> SRR2001017 5 0.4659 -0.407 0.000 0.012 0 0.488 0.500
#> SRR2001018 5 0.4659 -0.407 0.000 0.012 0 0.488 0.500
#> SRR2001019 5 0.4659 -0.407 0.000 0.012 0 0.488 0.500
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 2 0.1897 0.926 0.084 0.908 0.000 0.004 0.004 0.000
#> SRR2001033 2 0.1753 0.927 0.084 0.912 0.000 0.000 0.004 0.000
#> SRR2001034 2 0.2060 0.922 0.084 0.900 0.000 0.000 0.016 0.000
#> SRR2001035 2 0.1897 0.926 0.084 0.908 0.000 0.004 0.004 0.000
#> SRR2001204 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001205 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001206 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001207 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001200 1 0.1814 0.961 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR2001201 1 0.1814 0.961 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR2001202 1 0.1814 0.961 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR2001203 1 0.1814 0.961 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR2001196 1 0.1814 0.961 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR2001197 1 0.1814 0.961 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR2001198 1 0.1814 0.961 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR2001199 1 0.1814 0.961 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR2001192 3 0.0405 0.978 0.008 0.000 0.988 0.000 0.004 0.000
#> SRR2001193 3 0.0000 0.979 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001194 3 0.0520 0.977 0.008 0.000 0.984 0.000 0.008 0.000
#> SRR2001195 3 0.0000 0.979 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001188 6 0.2003 0.855 0.116 0.000 0.000 0.000 0.000 0.884
#> SRR2001189 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001190 6 0.1444 0.922 0.072 0.000 0.000 0.000 0.000 0.928
#> SRR2001191 6 0.0937 0.943 0.040 0.000 0.000 0.000 0.000 0.960
#> SRR2001184 3 0.0000 0.979 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001185 3 0.0000 0.979 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001186 3 0.0000 0.979 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001187 3 0.0000 0.979 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001180 6 0.1663 0.908 0.088 0.000 0.000 0.000 0.000 0.912
#> SRR2001181 6 0.0547 0.952 0.020 0.000 0.000 0.000 0.000 0.980
#> SRR2001182 6 0.1765 0.900 0.096 0.000 0.000 0.000 0.000 0.904
#> SRR2001183 6 0.1714 0.904 0.092 0.000 0.000 0.000 0.000 0.908
#> SRR2001176 3 0.0000 0.979 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001177 3 0.0000 0.979 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001178 3 0.0000 0.979 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001179 3 0.0000 0.979 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001172 3 0.0000 0.979 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001173 3 0.0000 0.979 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001174 3 0.0000 0.979 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001175 3 0.0000 0.979 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001168 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001169 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001170 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001171 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001164 1 0.2854 0.855 0.792 0.000 0.000 0.000 0.000 0.208
#> SRR2001165 1 0.2730 0.877 0.808 0.000 0.000 0.000 0.000 0.192
#> SRR2001166 1 0.3782 0.448 0.588 0.000 0.000 0.000 0.000 0.412
#> SRR2001167 1 0.2048 0.947 0.880 0.000 0.000 0.000 0.000 0.120
#> SRR2001160 1 0.1910 0.956 0.892 0.000 0.000 0.000 0.000 0.108
#> SRR2001161 1 0.1814 0.961 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR2001162 1 0.3198 0.796 0.740 0.000 0.000 0.000 0.000 0.260
#> SRR2001163 6 0.3843 0.018 0.452 0.000 0.000 0.000 0.000 0.548
#> SRR2001156 1 0.1814 0.961 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR2001157 1 0.1814 0.961 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR2001158 1 0.1814 0.961 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR2001159 1 0.1814 0.961 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR2001152 6 0.0363 0.955 0.012 0.000 0.000 0.000 0.000 0.988
#> SRR2001153 6 0.0363 0.955 0.012 0.000 0.000 0.000 0.000 0.988
#> SRR2001154 6 0.0363 0.955 0.012 0.000 0.000 0.000 0.000 0.988
#> SRR2001155 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001148 3 0.0000 0.979 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001149 3 0.0000 0.979 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001150 3 0.0000 0.979 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001151 3 0.0000 0.979 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001144 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001145 6 0.0632 0.951 0.024 0.000 0.000 0.000 0.000 0.976
#> SRR2001146 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001147 6 0.0146 0.957 0.004 0.000 0.000 0.000 0.000 0.996
#> SRR2001140 6 0.1327 0.927 0.064 0.000 0.000 0.000 0.000 0.936
#> SRR2001142 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001143 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001136 3 0.1500 0.967 0.012 0.000 0.936 0.000 0.052 0.000
#> SRR2001137 3 0.1500 0.967 0.012 0.000 0.936 0.000 0.052 0.000
#> SRR2001138 3 0.1500 0.967 0.012 0.000 0.936 0.000 0.052 0.000
#> SRR2001139 3 0.1500 0.967 0.012 0.000 0.936 0.000 0.052 0.000
#> SRR2001132 3 0.1500 0.967 0.012 0.000 0.936 0.000 0.052 0.000
#> SRR2001133 3 0.1434 0.968 0.012 0.000 0.940 0.000 0.048 0.000
#> SRR2001134 3 0.1500 0.967 0.012 0.000 0.936 0.000 0.052 0.000
#> SRR2001135 3 0.1500 0.967 0.012 0.000 0.936 0.000 0.052 0.000
#> SRR2001128 6 0.1714 0.905 0.092 0.000 0.000 0.000 0.000 0.908
#> SRR2001129 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001130 6 0.1444 0.922 0.072 0.000 0.000 0.000 0.000 0.928
#> SRR2001131 6 0.1501 0.919 0.076 0.000 0.000 0.000 0.000 0.924
#> SRR2001124 1 0.1814 0.961 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR2001125 1 0.1814 0.961 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR2001126 1 0.1814 0.961 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR2001127 1 0.1814 0.961 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR2001120 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001121 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001122 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001123 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001116 6 0.0713 0.949 0.028 0.000 0.000 0.000 0.000 0.972
#> SRR2001117 6 0.1444 0.922 0.072 0.000 0.000 0.000 0.000 0.928
#> SRR2001118 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001119 6 0.0000 0.958 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001112 3 0.1500 0.967 0.012 0.000 0.936 0.000 0.052 0.000
#> SRR2001113 3 0.1500 0.967 0.012 0.000 0.936 0.000 0.052 0.000
#> SRR2001114 3 0.1500 0.967 0.012 0.000 0.936 0.000 0.052 0.000
#> SRR2001115 3 0.1500 0.967 0.012 0.000 0.936 0.000 0.052 0.000
#> SRR2001108 5 0.1327 0.985 0.000 0.000 0.000 0.064 0.936 0.000
#> SRR2001109 5 0.1141 0.999 0.000 0.000 0.000 0.052 0.948 0.000
#> SRR2001110 5 0.1141 0.999 0.000 0.000 0.000 0.052 0.948 0.000
#> SRR2001111 5 0.1141 0.999 0.000 0.000 0.000 0.052 0.948 0.000
#> SRR2001104 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001105 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001106 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001107 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001100 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001101 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001102 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001103 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001096 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001097 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001098 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001099 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001092 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001093 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001094 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001095 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001088 4 0.0146 0.975 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR2001089 4 0.0000 0.976 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001090 4 0.0146 0.975 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR2001091 4 0.0000 0.976 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001084 5 0.1141 0.999 0.000 0.000 0.000 0.052 0.948 0.000
#> SRR2001085 5 0.1141 0.999 0.000 0.000 0.000 0.052 0.948 0.000
#> SRR2001086 5 0.1141 0.999 0.000 0.000 0.000 0.052 0.948 0.000
#> SRR2001087 5 0.1141 0.999 0.000 0.000 0.000 0.052 0.948 0.000
#> SRR2001080 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001081 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001082 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001083 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001076 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001077 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001078 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001079 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001072 4 0.1958 0.877 0.004 0.000 0.000 0.896 0.100 0.000
#> SRR2001073 4 0.0291 0.973 0.004 0.000 0.000 0.992 0.004 0.000
#> SRR2001074 4 0.2595 0.800 0.004 0.000 0.000 0.836 0.160 0.000
#> SRR2001075 4 0.3742 0.443 0.004 0.000 0.000 0.648 0.348 0.000
#> SRR2001068 2 0.3176 0.878 0.084 0.832 0.000 0.000 0.084 0.000
#> SRR2001069 2 0.3227 0.874 0.084 0.828 0.000 0.000 0.088 0.000
#> SRR2001070 2 0.2457 0.913 0.084 0.880 0.000 0.000 0.036 0.000
#> SRR2001071 2 0.2786 0.899 0.084 0.860 0.000 0.000 0.056 0.000
#> SRR2001064 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001065 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001066 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001067 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001060 4 0.0146 0.975 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR2001061 4 0.0146 0.975 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR2001062 4 0.0146 0.975 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR2001063 4 0.0146 0.975 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR2001056 5 0.1141 0.999 0.000 0.000 0.000 0.052 0.948 0.000
#> SRR2001057 5 0.1141 0.999 0.000 0.000 0.000 0.052 0.948 0.000
#> SRR2001058 5 0.1141 0.999 0.000 0.000 0.000 0.052 0.948 0.000
#> SRR2001059 5 0.1141 0.999 0.000 0.000 0.000 0.052 0.948 0.000
#> SRR2001052 2 0.2457 0.912 0.084 0.880 0.000 0.000 0.036 0.000
#> SRR2001053 2 0.2595 0.907 0.084 0.872 0.000 0.000 0.044 0.000
#> SRR2001054 2 0.2384 0.914 0.084 0.884 0.000 0.000 0.032 0.000
#> SRR2001055 2 0.2595 0.907 0.084 0.872 0.000 0.000 0.044 0.000
#> SRR2001048 2 0.3509 0.851 0.084 0.804 0.000 0.000 0.112 0.000
#> SRR2001049 2 0.3552 0.846 0.084 0.800 0.000 0.000 0.116 0.000
#> SRR2001050 2 0.3325 0.867 0.084 0.820 0.000 0.000 0.096 0.000
#> SRR2001051 2 0.3464 0.855 0.084 0.808 0.000 0.000 0.108 0.000
#> SRR2001044 4 0.0000 0.976 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001045 4 0.0000 0.976 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001046 4 0.0000 0.976 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001047 4 0.0000 0.976 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001040 4 0.0000 0.976 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001041 4 0.0000 0.976 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001042 4 0.0000 0.976 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001043 4 0.0000 0.976 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001036 4 0.0000 0.976 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001037 4 0.0000 0.976 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001038 4 0.0790 0.949 0.000 0.000 0.000 0.968 0.032 0.000
#> SRR2001039 4 0.0000 0.976 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001028 4 0.0000 0.976 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001029 4 0.0000 0.976 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001030 4 0.0000 0.976 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001031 4 0.0260 0.969 0.000 0.008 0.000 0.992 0.000 0.000
#> SRR2001024 4 0.0000 0.976 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001025 4 0.0146 0.975 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR2001026 4 0.0146 0.975 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR2001027 4 0.0000 0.976 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001020 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001021 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001022 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001023 2 0.0000 0.959 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001016 5 0.1141 0.999 0.000 0.000 0.000 0.052 0.948 0.000
#> SRR2001017 5 0.1141 0.999 0.000 0.000 0.000 0.052 0.948 0.000
#> SRR2001018 5 0.1141 0.999 0.000 0.000 0.000 0.052 0.948 0.000
#> SRR2001019 5 0.1141 0.999 0.000 0.000 0.000 0.052 0.948 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", "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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.5031 0.497 0.497
#> 3 3 1.000 1.000 1.000 0.2206 0.889 0.777
#> 4 4 1.000 0.981 0.992 0.2056 0.874 0.674
#> 5 5 0.925 0.903 0.936 0.0434 0.968 0.878
#> 6 6 0.881 0.852 0.882 0.0431 0.959 0.819
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3 4
There is also optional best \(k\) = 2 3 4 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0 1 0 1 0
#> SRR2001033 2 0 1 0 1 0
#> SRR2001034 2 0 1 0 1 0
#> SRR2001035 2 0 1 0 1 0
#> SRR2001204 1 0 1 1 0 0
#> SRR2001205 1 0 1 1 0 0
#> SRR2001206 1 0 1 1 0 0
#> SRR2001207 1 0 1 1 0 0
#> SRR2001200 1 0 1 1 0 0
#> SRR2001201 1 0 1 1 0 0
#> SRR2001202 1 0 1 1 0 0
#> SRR2001203 1 0 1 1 0 0
#> SRR2001196 1 0 1 1 0 0
#> SRR2001197 1 0 1 1 0 0
#> SRR2001198 1 0 1 1 0 0
#> SRR2001199 1 0 1 1 0 0
#> SRR2001192 3 0 1 0 0 1
#> SRR2001193 3 0 1 0 0 1
#> SRR2001194 3 0 1 0 0 1
#> SRR2001195 3 0 1 0 0 1
#> SRR2001188 1 0 1 1 0 0
#> SRR2001189 1 0 1 1 0 0
#> SRR2001190 1 0 1 1 0 0
#> SRR2001191 1 0 1 1 0 0
#> SRR2001184 3 0 1 0 0 1
#> SRR2001185 3 0 1 0 0 1
#> SRR2001186 3 0 1 0 0 1
#> SRR2001187 3 0 1 0 0 1
#> SRR2001180 1 0 1 1 0 0
#> SRR2001181 1 0 1 1 0 0
#> SRR2001182 1 0 1 1 0 0
#> SRR2001183 1 0 1 1 0 0
#> SRR2001176 3 0 1 0 0 1
#> SRR2001177 3 0 1 0 0 1
#> SRR2001178 3 0 1 0 0 1
#> SRR2001179 3 0 1 0 0 1
#> SRR2001172 3 0 1 0 0 1
#> SRR2001173 3 0 1 0 0 1
#> SRR2001174 3 0 1 0 0 1
#> SRR2001175 3 0 1 0 0 1
#> SRR2001168 1 0 1 1 0 0
#> SRR2001169 1 0 1 1 0 0
#> SRR2001170 1 0 1 1 0 0
#> SRR2001171 1 0 1 1 0 0
#> SRR2001164 1 0 1 1 0 0
#> SRR2001165 1 0 1 1 0 0
#> SRR2001166 1 0 1 1 0 0
#> SRR2001167 1 0 1 1 0 0
#> SRR2001160 1 0 1 1 0 0
#> SRR2001161 1 0 1 1 0 0
#> SRR2001162 1 0 1 1 0 0
#> SRR2001163 1 0 1 1 0 0
#> SRR2001156 1 0 1 1 0 0
#> SRR2001157 1 0 1 1 0 0
#> SRR2001158 1 0 1 1 0 0
#> SRR2001159 1 0 1 1 0 0
#> SRR2001152 1 0 1 1 0 0
#> SRR2001153 1 0 1 1 0 0
#> SRR2001154 1 0 1 1 0 0
#> SRR2001155 1 0 1 1 0 0
#> SRR2001148 3 0 1 0 0 1
#> SRR2001149 3 0 1 0 0 1
#> SRR2001150 3 0 1 0 0 1
#> SRR2001151 3 0 1 0 0 1
#> SRR2001144 1 0 1 1 0 0
#> SRR2001145 1 0 1 1 0 0
#> SRR2001146 1 0 1 1 0 0
#> SRR2001147 1 0 1 1 0 0
#> SRR2001140 1 0 1 1 0 0
#> SRR2001142 1 0 1 1 0 0
#> SRR2001143 1 0 1 1 0 0
#> SRR2001136 3 0 1 0 0 1
#> SRR2001137 3 0 1 0 0 1
#> SRR2001138 3 0 1 0 0 1
#> SRR2001139 3 0 1 0 0 1
#> SRR2001132 3 0 1 0 0 1
#> SRR2001133 3 0 1 0 0 1
#> SRR2001134 3 0 1 0 0 1
#> SRR2001135 3 0 1 0 0 1
#> SRR2001128 1 0 1 1 0 0
#> SRR2001129 1 0 1 1 0 0
#> SRR2001130 1 0 1 1 0 0
#> SRR2001131 1 0 1 1 0 0
#> SRR2001124 1 0 1 1 0 0
#> SRR2001125 1 0 1 1 0 0
#> SRR2001126 1 0 1 1 0 0
#> SRR2001127 1 0 1 1 0 0
#> SRR2001120 1 0 1 1 0 0
#> SRR2001121 1 0 1 1 0 0
#> SRR2001122 1 0 1 1 0 0
#> SRR2001123 1 0 1 1 0 0
#> SRR2001116 1 0 1 1 0 0
#> SRR2001117 1 0 1 1 0 0
#> SRR2001118 1 0 1 1 0 0
#> SRR2001119 1 0 1 1 0 0
#> SRR2001112 3 0 1 0 0 1
#> SRR2001113 3 0 1 0 0 1
#> SRR2001114 3 0 1 0 0 1
#> SRR2001115 3 0 1 0 0 1
#> SRR2001108 2 0 1 0 1 0
#> SRR2001109 2 0 1 0 1 0
#> SRR2001110 2 0 1 0 1 0
#> SRR2001111 2 0 1 0 1 0
#> SRR2001104 2 0 1 0 1 0
#> SRR2001105 2 0 1 0 1 0
#> SRR2001106 2 0 1 0 1 0
#> SRR2001107 2 0 1 0 1 0
#> SRR2001100 2 0 1 0 1 0
#> SRR2001101 2 0 1 0 1 0
#> SRR2001102 2 0 1 0 1 0
#> SRR2001103 2 0 1 0 1 0
#> SRR2001096 2 0 1 0 1 0
#> SRR2001097 2 0 1 0 1 0
#> SRR2001098 2 0 1 0 1 0
#> SRR2001099 2 0 1 0 1 0
#> SRR2001092 2 0 1 0 1 0
#> SRR2001093 2 0 1 0 1 0
#> SRR2001094 2 0 1 0 1 0
#> SRR2001095 2 0 1 0 1 0
#> SRR2001088 2 0 1 0 1 0
#> SRR2001089 2 0 1 0 1 0
#> SRR2001090 2 0 1 0 1 0
#> SRR2001091 2 0 1 0 1 0
#> SRR2001084 2 0 1 0 1 0
#> SRR2001085 2 0 1 0 1 0
#> SRR2001086 2 0 1 0 1 0
#> SRR2001087 2 0 1 0 1 0
#> SRR2001080 2 0 1 0 1 0
#> SRR2001081 2 0 1 0 1 0
#> SRR2001082 2 0 1 0 1 0
#> SRR2001083 2 0 1 0 1 0
#> SRR2001076 2 0 1 0 1 0
#> SRR2001077 2 0 1 0 1 0
#> SRR2001078 2 0 1 0 1 0
#> SRR2001079 2 0 1 0 1 0
#> SRR2001072 2 0 1 0 1 0
#> SRR2001073 2 0 1 0 1 0
#> SRR2001074 2 0 1 0 1 0
#> SRR2001075 2 0 1 0 1 0
#> SRR2001068 2 0 1 0 1 0
#> SRR2001069 2 0 1 0 1 0
#> SRR2001070 2 0 1 0 1 0
#> SRR2001071 2 0 1 0 1 0
#> SRR2001064 2 0 1 0 1 0
#> SRR2001065 2 0 1 0 1 0
#> SRR2001066 2 0 1 0 1 0
#> SRR2001067 2 0 1 0 1 0
#> SRR2001060 2 0 1 0 1 0
#> SRR2001061 2 0 1 0 1 0
#> SRR2001062 2 0 1 0 1 0
#> SRR2001063 2 0 1 0 1 0
#> SRR2001056 2 0 1 0 1 0
#> SRR2001057 2 0 1 0 1 0
#> SRR2001058 2 0 1 0 1 0
#> SRR2001059 2 0 1 0 1 0
#> SRR2001052 2 0 1 0 1 0
#> SRR2001053 2 0 1 0 1 0
#> SRR2001054 2 0 1 0 1 0
#> SRR2001055 2 0 1 0 1 0
#> SRR2001048 2 0 1 0 1 0
#> SRR2001049 2 0 1 0 1 0
#> SRR2001050 2 0 1 0 1 0
#> SRR2001051 2 0 1 0 1 0
#> SRR2001044 2 0 1 0 1 0
#> SRR2001045 2 0 1 0 1 0
#> SRR2001046 2 0 1 0 1 0
#> SRR2001047 2 0 1 0 1 0
#> SRR2001040 2 0 1 0 1 0
#> SRR2001041 2 0 1 0 1 0
#> SRR2001042 2 0 1 0 1 0
#> SRR2001043 2 0 1 0 1 0
#> SRR2001036 2 0 1 0 1 0
#> SRR2001037 2 0 1 0 1 0
#> SRR2001038 2 0 1 0 1 0
#> SRR2001039 2 0 1 0 1 0
#> SRR2001028 2 0 1 0 1 0
#> SRR2001029 2 0 1 0 1 0
#> SRR2001030 2 0 1 0 1 0
#> SRR2001031 2 0 1 0 1 0
#> SRR2001024 2 0 1 0 1 0
#> SRR2001025 2 0 1 0 1 0
#> SRR2001026 2 0 1 0 1 0
#> SRR2001027 2 0 1 0 1 0
#> SRR2001020 2 0 1 0 1 0
#> SRR2001021 2 0 1 0 1 0
#> SRR2001022 2 0 1 0 1 0
#> SRR2001023 2 0 1 0 1 0
#> SRR2001016 2 0 1 0 1 0
#> SRR2001017 2 0 1 0 1 0
#> SRR2001018 2 0 1 0 1 0
#> SRR2001019 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.0188 0.967 0 0.996 0 0.004
#> SRR2001033 2 0.0188 0.967 0 0.996 0 0.004
#> SRR2001034 2 0.0188 0.967 0 0.996 0 0.004
#> SRR2001035 2 0.0188 0.967 0 0.996 0 0.004
#> SRR2001204 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001205 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001206 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001207 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001200 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001201 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001202 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001203 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001196 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001197 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001198 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001199 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001192 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001193 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001194 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001195 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001188 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001189 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001190 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001191 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001184 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001185 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001186 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001187 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001180 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001181 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001182 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001183 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001176 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001177 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001178 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001179 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001172 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001173 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001174 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001175 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001168 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001169 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001170 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001171 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001164 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001165 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001166 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001167 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001160 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001161 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001162 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001163 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001156 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001157 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001158 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001159 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001152 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001153 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001154 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001155 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001148 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001149 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001150 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001151 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001144 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001145 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001146 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001147 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001140 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001142 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001143 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001136 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001137 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001138 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001139 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001132 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001133 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001134 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001135 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001128 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001129 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001130 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001131 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001124 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001125 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001126 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001127 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001120 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001121 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001122 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001123 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001116 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001117 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001118 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001119 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001112 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001113 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001114 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001115 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001108 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001109 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001110 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001111 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001104 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001105 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001106 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001107 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001100 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001101 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001102 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001103 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001096 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001097 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001098 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001099 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001092 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001093 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001094 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001095 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001088 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001089 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001090 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001091 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001084 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001085 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001086 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001087 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001080 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001081 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001082 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001083 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001076 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001077 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001078 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001079 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001072 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001073 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001074 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001075 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001068 2 0.0188 0.967 0 0.996 0 0.004
#> SRR2001069 2 0.0188 0.967 0 0.996 0 0.004
#> SRR2001070 2 0.0188 0.967 0 0.996 0 0.004
#> SRR2001071 2 0.0188 0.967 0 0.996 0 0.004
#> SRR2001064 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001065 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001066 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001067 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001060 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001061 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001062 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001063 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001056 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001057 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001058 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001059 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001052 2 0.0188 0.967 0 0.996 0 0.004
#> SRR2001053 2 0.0188 0.967 0 0.996 0 0.004
#> SRR2001054 2 0.0188 0.967 0 0.996 0 0.004
#> SRR2001055 2 0.0188 0.967 0 0.996 0 0.004
#> SRR2001048 2 0.0188 0.967 0 0.996 0 0.004
#> SRR2001049 2 0.0188 0.967 0 0.996 0 0.004
#> SRR2001050 2 0.0188 0.967 0 0.996 0 0.004
#> SRR2001051 2 0.0188 0.967 0 0.996 0 0.004
#> SRR2001044 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001045 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001046 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001047 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001040 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001041 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001042 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001043 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001036 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001037 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001038 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001039 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001028 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001029 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001030 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001031 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001024 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001025 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001026 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001027 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001020 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001021 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001022 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001023 2 0.0000 0.968 0 1.000 0 0.000
#> SRR2001016 2 0.4730 0.465 0 0.636 0 0.364
#> SRR2001017 2 0.4730 0.465 0 0.636 0 0.364
#> SRR2001018 2 0.4730 0.465 0 0.636 0 0.364
#> SRR2001019 2 0.4713 0.473 0 0.640 0 0.360
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.3242 0.709 0.000 0.784 0 0.000 0.216
#> SRR2001033 2 0.3242 0.709 0.000 0.784 0 0.000 0.216
#> SRR2001034 2 0.3242 0.709 0.000 0.784 0 0.000 0.216
#> SRR2001035 2 0.3242 0.709 0.000 0.784 0 0.000 0.216
#> SRR2001204 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001205 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001206 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001207 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001200 1 0.0703 0.987 0.976 0.000 0 0.000 0.024
#> SRR2001201 1 0.0703 0.987 0.976 0.000 0 0.000 0.024
#> SRR2001202 1 0.0703 0.987 0.976 0.000 0 0.000 0.024
#> SRR2001203 1 0.0703 0.987 0.976 0.000 0 0.000 0.024
#> SRR2001196 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001197 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001198 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001199 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001192 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001193 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001194 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001195 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001188 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001189 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001190 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001191 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001184 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001185 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001186 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001187 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001180 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001181 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001182 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001183 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001176 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001177 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001178 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001179 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001172 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001173 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001174 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001175 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001168 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001169 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001170 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001171 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001164 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001165 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001166 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001167 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001160 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001161 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001162 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001163 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001156 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001157 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001158 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001159 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001152 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001153 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001154 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001155 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001148 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001149 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001150 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001151 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001144 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001145 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001146 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001147 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001140 1 0.0794 0.984 0.972 0.000 0 0.000 0.028
#> SRR2001142 1 0.0794 0.984 0.972 0.000 0 0.000 0.028
#> SRR2001143 1 0.0609 0.989 0.980 0.000 0 0.000 0.020
#> SRR2001136 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001137 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001138 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001139 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001132 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001133 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001134 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001135 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001128 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001129 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001130 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001131 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001124 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001125 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001126 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001127 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001120 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001121 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001122 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001123 1 0.0000 0.994 1.000 0.000 0 0.000 0.000
#> SRR2001116 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001117 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001118 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001119 1 0.0404 0.993 0.988 0.000 0 0.000 0.012
#> SRR2001112 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001113 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001114 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001115 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001108 4 0.2605 0.872 0.000 0.000 0 0.852 0.148
#> SRR2001109 4 0.2605 0.872 0.000 0.000 0 0.852 0.148
#> SRR2001110 4 0.2605 0.872 0.000 0.000 0 0.852 0.148
#> SRR2001111 4 0.2605 0.872 0.000 0.000 0 0.852 0.148
#> SRR2001104 2 0.2813 0.613 0.000 0.832 0 0.000 0.168
#> SRR2001105 2 0.2813 0.613 0.000 0.832 0 0.000 0.168
#> SRR2001106 2 0.2813 0.613 0.000 0.832 0 0.000 0.168
#> SRR2001107 2 0.2813 0.613 0.000 0.832 0 0.000 0.168
#> SRR2001100 2 0.0000 0.724 0.000 1.000 0 0.000 0.000
#> SRR2001101 2 0.0000 0.724 0.000 1.000 0 0.000 0.000
#> SRR2001102 2 0.0000 0.724 0.000 1.000 0 0.000 0.000
#> SRR2001103 2 0.0000 0.724 0.000 1.000 0 0.000 0.000
#> SRR2001096 5 0.3612 0.915 0.000 0.268 0 0.000 0.732
#> SRR2001097 5 0.3612 0.915 0.000 0.268 0 0.000 0.732
#> SRR2001098 5 0.3612 0.915 0.000 0.268 0 0.000 0.732
#> SRR2001099 5 0.3612 0.915 0.000 0.268 0 0.000 0.732
#> SRR2001092 5 0.3612 0.915 0.000 0.268 0 0.000 0.732
#> SRR2001093 5 0.3612 0.915 0.000 0.268 0 0.000 0.732
#> SRR2001094 5 0.3612 0.915 0.000 0.268 0 0.000 0.732
#> SRR2001095 5 0.3612 0.915 0.000 0.268 0 0.000 0.732
#> SRR2001088 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001089 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001090 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001091 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001084 4 0.2605 0.872 0.000 0.000 0 0.852 0.148
#> SRR2001085 4 0.2605 0.872 0.000 0.000 0 0.852 0.148
#> SRR2001086 4 0.2605 0.872 0.000 0.000 0 0.852 0.148
#> SRR2001087 4 0.2605 0.872 0.000 0.000 0 0.852 0.148
#> SRR2001080 2 0.1908 0.680 0.000 0.908 0 0.000 0.092
#> SRR2001081 2 0.1544 0.695 0.000 0.932 0 0.000 0.068
#> SRR2001082 2 0.1410 0.699 0.000 0.940 0 0.000 0.060
#> SRR2001083 2 0.1908 0.680 0.000 0.908 0 0.000 0.092
#> SRR2001076 2 0.2813 0.613 0.000 0.832 0 0.000 0.168
#> SRR2001077 2 0.2813 0.613 0.000 0.832 0 0.000 0.168
#> SRR2001078 2 0.2813 0.613 0.000 0.832 0 0.000 0.168
#> SRR2001079 2 0.2813 0.613 0.000 0.832 0 0.000 0.168
#> SRR2001072 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001073 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001074 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001075 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001068 2 0.3274 0.707 0.000 0.780 0 0.000 0.220
#> SRR2001069 2 0.3274 0.707 0.000 0.780 0 0.000 0.220
#> SRR2001070 2 0.3274 0.707 0.000 0.780 0 0.000 0.220
#> SRR2001071 2 0.3274 0.707 0.000 0.780 0 0.000 0.220
#> SRR2001064 5 0.3612 0.915 0.000 0.268 0 0.000 0.732
#> SRR2001065 5 0.3636 0.910 0.000 0.272 0 0.000 0.728
#> SRR2001066 5 0.3612 0.915 0.000 0.268 0 0.000 0.732
#> SRR2001067 5 0.3612 0.915 0.000 0.268 0 0.000 0.732
#> SRR2001060 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001061 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001062 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001063 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001056 4 0.2605 0.872 0.000 0.000 0 0.852 0.148
#> SRR2001057 4 0.2605 0.872 0.000 0.000 0 0.852 0.148
#> SRR2001058 4 0.2605 0.872 0.000 0.000 0 0.852 0.148
#> SRR2001059 4 0.2605 0.872 0.000 0.000 0 0.852 0.148
#> SRR2001052 5 0.2605 0.728 0.000 0.148 0 0.000 0.852
#> SRR2001053 5 0.2605 0.728 0.000 0.148 0 0.000 0.852
#> SRR2001054 5 0.2605 0.728 0.000 0.148 0 0.000 0.852
#> SRR2001055 5 0.2605 0.728 0.000 0.148 0 0.000 0.852
#> SRR2001048 2 0.3242 0.709 0.000 0.784 0 0.000 0.216
#> SRR2001049 2 0.3242 0.709 0.000 0.784 0 0.000 0.216
#> SRR2001050 2 0.3242 0.709 0.000 0.784 0 0.000 0.216
#> SRR2001051 2 0.3242 0.709 0.000 0.784 0 0.000 0.216
#> SRR2001044 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001045 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001046 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001047 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001040 4 0.0000 0.951 0.000 0.000 0 1.000 0.000
#> SRR2001041 4 0.0000 0.951 0.000 0.000 0 1.000 0.000
#> SRR2001042 4 0.0000 0.951 0.000 0.000 0 1.000 0.000
#> SRR2001043 4 0.0000 0.951 0.000 0.000 0 1.000 0.000
#> SRR2001036 4 0.0000 0.951 0.000 0.000 0 1.000 0.000
#> SRR2001037 4 0.0000 0.951 0.000 0.000 0 1.000 0.000
#> SRR2001038 4 0.0000 0.951 0.000 0.000 0 1.000 0.000
#> SRR2001039 4 0.0000 0.951 0.000 0.000 0 1.000 0.000
#> SRR2001028 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001029 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001030 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001031 4 0.0404 0.951 0.000 0.000 0 0.988 0.012
#> SRR2001024 4 0.0000 0.951 0.000 0.000 0 1.000 0.000
#> SRR2001025 4 0.0000 0.951 0.000 0.000 0 1.000 0.000
#> SRR2001026 4 0.0000 0.951 0.000 0.000 0 1.000 0.000
#> SRR2001027 4 0.0000 0.951 0.000 0.000 0 1.000 0.000
#> SRR2001020 2 0.0000 0.724 0.000 1.000 0 0.000 0.000
#> SRR2001021 2 0.0000 0.724 0.000 1.000 0 0.000 0.000
#> SRR2001022 2 0.0000 0.724 0.000 1.000 0 0.000 0.000
#> SRR2001023 2 0.0000 0.724 0.000 1.000 0 0.000 0.000
#> SRR2001016 2 0.6334 0.286 0.000 0.452 0 0.388 0.160
#> SRR2001017 2 0.6334 0.286 0.000 0.452 0 0.388 0.160
#> SRR2001018 2 0.6334 0.286 0.000 0.452 0 0.388 0.160
#> SRR2001019 2 0.6334 0.286 0.000 0.452 0 0.388 0.160
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 2 0.3073 0.728 0.008 0.788 0 0.000 0.204 0.000
#> SRR2001033 2 0.3073 0.728 0.008 0.788 0 0.000 0.204 0.000
#> SRR2001034 2 0.3073 0.728 0.008 0.788 0 0.000 0.204 0.000
#> SRR2001035 2 0.3073 0.728 0.008 0.788 0 0.000 0.204 0.000
#> SRR2001204 6 0.0458 0.921 0.016 0.000 0 0.000 0.000 0.984
#> SRR2001205 6 0.0458 0.921 0.016 0.000 0 0.000 0.000 0.984
#> SRR2001206 6 0.0458 0.921 0.016 0.000 0 0.000 0.000 0.984
#> SRR2001207 6 0.0458 0.921 0.016 0.000 0 0.000 0.000 0.984
#> SRR2001200 1 0.3706 0.877 0.620 0.000 0 0.000 0.000 0.380
#> SRR2001201 1 0.3706 0.877 0.620 0.000 0 0.000 0.000 0.380
#> SRR2001202 1 0.3706 0.877 0.620 0.000 0 0.000 0.000 0.380
#> SRR2001203 1 0.3706 0.877 0.620 0.000 0 0.000 0.000 0.380
#> SRR2001196 1 0.3747 0.893 0.604 0.000 0 0.000 0.000 0.396
#> SRR2001197 1 0.3747 0.893 0.604 0.000 0 0.000 0.000 0.396
#> SRR2001198 1 0.3747 0.893 0.604 0.000 0 0.000 0.000 0.396
#> SRR2001199 1 0.3747 0.893 0.604 0.000 0 0.000 0.000 0.396
#> SRR2001192 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001193 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001194 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001195 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001188 6 0.0260 0.922 0.008 0.000 0 0.000 0.000 0.992
#> SRR2001189 6 0.0260 0.922 0.008 0.000 0 0.000 0.000 0.992
#> SRR2001190 6 0.0260 0.922 0.008 0.000 0 0.000 0.000 0.992
#> SRR2001191 6 0.0260 0.922 0.008 0.000 0 0.000 0.000 0.992
#> SRR2001184 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001185 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001186 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001187 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001180 6 0.0146 0.924 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001181 6 0.0146 0.924 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001182 6 0.0146 0.924 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001183 6 0.0000 0.923 0.000 0.000 0 0.000 0.000 1.000
#> SRR2001176 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001177 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001178 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001179 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001172 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001173 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001174 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001175 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001168 6 0.0632 0.917 0.024 0.000 0 0.000 0.000 0.976
#> SRR2001169 6 0.0632 0.917 0.024 0.000 0 0.000 0.000 0.976
#> SRR2001170 6 0.0632 0.917 0.024 0.000 0 0.000 0.000 0.976
#> SRR2001171 6 0.0632 0.917 0.024 0.000 0 0.000 0.000 0.976
#> SRR2001164 6 0.1075 0.870 0.048 0.000 0 0.000 0.000 0.952
#> SRR2001165 6 0.0146 0.923 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001166 6 0.0146 0.923 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001167 6 0.1075 0.870 0.048 0.000 0 0.000 0.000 0.952
#> SRR2001160 6 0.0146 0.924 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001161 6 0.0146 0.924 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001162 6 0.0146 0.924 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001163 6 0.0146 0.924 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001156 1 0.3866 0.880 0.516 0.000 0 0.000 0.000 0.484
#> SRR2001157 1 0.3866 0.880 0.516 0.000 0 0.000 0.000 0.484
#> SRR2001158 1 0.3866 0.880 0.516 0.000 0 0.000 0.000 0.484
#> SRR2001159 1 0.3866 0.880 0.516 0.000 0 0.000 0.000 0.484
#> SRR2001152 6 0.0146 0.924 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001153 6 0.0146 0.924 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001154 6 0.0146 0.924 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001155 6 0.0146 0.924 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001148 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001149 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001150 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001151 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001144 6 0.0547 0.920 0.020 0.000 0 0.000 0.000 0.980
#> SRR2001145 6 0.0547 0.920 0.020 0.000 0 0.000 0.000 0.980
#> SRR2001146 6 0.0632 0.917 0.024 0.000 0 0.000 0.000 0.976
#> SRR2001147 6 0.0547 0.920 0.020 0.000 0 0.000 0.000 0.980
#> SRR2001140 6 0.1007 0.888 0.044 0.000 0 0.000 0.000 0.956
#> SRR2001142 6 0.1007 0.888 0.044 0.000 0 0.000 0.000 0.956
#> SRR2001143 6 0.1007 0.888 0.044 0.000 0 0.000 0.000 0.956
#> SRR2001136 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001137 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001138 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001139 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001132 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001133 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001134 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001135 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001128 6 0.3515 -0.208 0.324 0.000 0 0.000 0.000 0.676
#> SRR2001129 6 0.3288 0.135 0.276 0.000 0 0.000 0.000 0.724
#> SRR2001130 6 0.3563 -0.237 0.336 0.000 0 0.000 0.000 0.664
#> SRR2001131 6 0.3563 -0.237 0.336 0.000 0 0.000 0.000 0.664
#> SRR2001124 1 0.3866 0.880 0.516 0.000 0 0.000 0.000 0.484
#> SRR2001125 1 0.3866 0.880 0.516 0.000 0 0.000 0.000 0.484
#> SRR2001126 1 0.3866 0.880 0.516 0.000 0 0.000 0.000 0.484
#> SRR2001127 1 0.3866 0.880 0.516 0.000 0 0.000 0.000 0.484
#> SRR2001120 6 0.0865 0.909 0.036 0.000 0 0.000 0.000 0.964
#> SRR2001121 6 0.0632 0.917 0.024 0.000 0 0.000 0.000 0.976
#> SRR2001122 6 0.0632 0.917 0.024 0.000 0 0.000 0.000 0.976
#> SRR2001123 6 0.0632 0.917 0.024 0.000 0 0.000 0.000 0.976
#> SRR2001116 6 0.0937 0.886 0.040 0.000 0 0.000 0.000 0.960
#> SRR2001117 6 0.0363 0.919 0.012 0.000 0 0.000 0.000 0.988
#> SRR2001118 6 0.0458 0.915 0.016 0.000 0 0.000 0.000 0.984
#> SRR2001119 6 0.0363 0.919 0.012 0.000 0 0.000 0.000 0.988
#> SRR2001112 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001113 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001114 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001115 3 0.0000 1.000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001108 4 0.3883 0.838 0.144 0.000 0 0.768 0.088 0.000
#> SRR2001109 4 0.3883 0.838 0.144 0.000 0 0.768 0.088 0.000
#> SRR2001110 4 0.3893 0.837 0.140 0.000 0 0.768 0.092 0.000
#> SRR2001111 4 0.3871 0.840 0.148 0.000 0 0.768 0.084 0.000
#> SRR2001104 2 0.2730 0.644 0.000 0.808 0 0.000 0.192 0.000
#> SRR2001105 2 0.2697 0.649 0.000 0.812 0 0.000 0.188 0.000
#> SRR2001106 2 0.2730 0.644 0.000 0.808 0 0.000 0.192 0.000
#> SRR2001107 2 0.2664 0.652 0.000 0.816 0 0.000 0.184 0.000
#> SRR2001100 2 0.0458 0.755 0.000 0.984 0 0.000 0.016 0.000
#> SRR2001101 2 0.0458 0.755 0.000 0.984 0 0.000 0.016 0.000
#> SRR2001102 2 0.0458 0.755 0.000 0.984 0 0.000 0.016 0.000
#> SRR2001103 2 0.0458 0.755 0.000 0.984 0 0.000 0.016 0.000
#> SRR2001096 5 0.2883 0.905 0.000 0.212 0 0.000 0.788 0.000
#> SRR2001097 5 0.2854 0.908 0.000 0.208 0 0.000 0.792 0.000
#> SRR2001098 5 0.2823 0.910 0.000 0.204 0 0.000 0.796 0.000
#> SRR2001099 5 0.2883 0.905 0.000 0.212 0 0.000 0.788 0.000
#> SRR2001092 5 0.2823 0.910 0.000 0.204 0 0.000 0.796 0.000
#> SRR2001093 5 0.2823 0.910 0.000 0.204 0 0.000 0.796 0.000
#> SRR2001094 5 0.2823 0.910 0.000 0.204 0 0.000 0.796 0.000
#> SRR2001095 5 0.2823 0.910 0.000 0.204 0 0.000 0.796 0.000
#> SRR2001088 4 0.0000 0.922 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001089 4 0.0000 0.922 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001090 4 0.0000 0.922 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001091 4 0.0000 0.922 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001084 4 0.3871 0.840 0.148 0.000 0 0.768 0.084 0.000
#> SRR2001085 4 0.3786 0.844 0.168 0.000 0 0.768 0.064 0.000
#> SRR2001086 4 0.3712 0.846 0.180 0.000 0 0.768 0.052 0.000
#> SRR2001087 4 0.3883 0.838 0.144 0.000 0 0.768 0.088 0.000
#> SRR2001080 2 0.1765 0.725 0.000 0.904 0 0.000 0.096 0.000
#> SRR2001081 2 0.1663 0.729 0.000 0.912 0 0.000 0.088 0.000
#> SRR2001082 2 0.1663 0.729 0.000 0.912 0 0.000 0.088 0.000
#> SRR2001083 2 0.1765 0.725 0.000 0.904 0 0.000 0.096 0.000
#> SRR2001076 2 0.2454 0.678 0.000 0.840 0 0.000 0.160 0.000
#> SRR2001077 2 0.2527 0.670 0.000 0.832 0 0.000 0.168 0.000
#> SRR2001078 2 0.2527 0.670 0.000 0.832 0 0.000 0.168 0.000
#> SRR2001079 2 0.2527 0.670 0.000 0.832 0 0.000 0.168 0.000
#> SRR2001072 4 0.0865 0.914 0.036 0.000 0 0.964 0.000 0.000
#> SRR2001073 4 0.0865 0.914 0.036 0.000 0 0.964 0.000 0.000
#> SRR2001074 4 0.0937 0.912 0.040 0.000 0 0.960 0.000 0.000
#> SRR2001075 4 0.0937 0.912 0.040 0.000 0 0.960 0.000 0.000
#> SRR2001068 2 0.3483 0.711 0.016 0.748 0 0.000 0.236 0.000
#> SRR2001069 2 0.3483 0.711 0.016 0.748 0 0.000 0.236 0.000
#> SRR2001070 2 0.3483 0.711 0.016 0.748 0 0.000 0.236 0.000
#> SRR2001071 2 0.3483 0.711 0.016 0.748 0 0.000 0.236 0.000
#> SRR2001064 5 0.2823 0.910 0.000 0.204 0 0.000 0.796 0.000
#> SRR2001065 5 0.2854 0.907 0.000 0.208 0 0.000 0.792 0.000
#> SRR2001066 5 0.2823 0.910 0.000 0.204 0 0.000 0.796 0.000
#> SRR2001067 5 0.2823 0.910 0.000 0.204 0 0.000 0.796 0.000
#> SRR2001060 4 0.0000 0.922 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001061 4 0.0000 0.922 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001062 4 0.0000 0.922 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001063 4 0.0000 0.922 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001056 4 0.3883 0.838 0.144 0.000 0 0.768 0.088 0.000
#> SRR2001057 4 0.3871 0.840 0.148 0.000 0 0.768 0.084 0.000
#> SRR2001058 4 0.3543 0.848 0.200 0.000 0 0.768 0.032 0.000
#> SRR2001059 4 0.3901 0.836 0.136 0.000 0 0.768 0.096 0.000
#> SRR2001052 5 0.1074 0.723 0.012 0.028 0 0.000 0.960 0.000
#> SRR2001053 5 0.1074 0.723 0.012 0.028 0 0.000 0.960 0.000
#> SRR2001054 5 0.1074 0.723 0.012 0.028 0 0.000 0.960 0.000
#> SRR2001055 5 0.1074 0.723 0.012 0.028 0 0.000 0.960 0.000
#> SRR2001048 2 0.3073 0.728 0.008 0.788 0 0.000 0.204 0.000
#> SRR2001049 2 0.3073 0.728 0.008 0.788 0 0.000 0.204 0.000
#> SRR2001050 2 0.3073 0.728 0.008 0.788 0 0.000 0.204 0.000
#> SRR2001051 2 0.3073 0.728 0.008 0.788 0 0.000 0.204 0.000
#> SRR2001044 4 0.0547 0.919 0.020 0.000 0 0.980 0.000 0.000
#> SRR2001045 4 0.0547 0.919 0.020 0.000 0 0.980 0.000 0.000
#> SRR2001046 4 0.0547 0.919 0.020 0.000 0 0.980 0.000 0.000
#> SRR2001047 4 0.0547 0.919 0.020 0.000 0 0.980 0.000 0.000
#> SRR2001040 4 0.1957 0.900 0.112 0.000 0 0.888 0.000 0.000
#> SRR2001041 4 0.1957 0.900 0.112 0.000 0 0.888 0.000 0.000
#> SRR2001042 4 0.1957 0.900 0.112 0.000 0 0.888 0.000 0.000
#> SRR2001043 4 0.1957 0.900 0.112 0.000 0 0.888 0.000 0.000
#> SRR2001036 4 0.2003 0.899 0.116 0.000 0 0.884 0.000 0.000
#> SRR2001037 4 0.1387 0.912 0.068 0.000 0 0.932 0.000 0.000
#> SRR2001038 4 0.0260 0.922 0.008 0.000 0 0.992 0.000 0.000
#> SRR2001039 4 0.1957 0.901 0.112 0.000 0 0.888 0.000 0.000
#> SRR2001028 4 0.0790 0.915 0.032 0.000 0 0.968 0.000 0.000
#> SRR2001029 4 0.0146 0.921 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001030 4 0.0865 0.914 0.036 0.000 0 0.964 0.000 0.000
#> SRR2001031 4 0.0790 0.915 0.032 0.000 0 0.968 0.000 0.000
#> SRR2001024 4 0.0260 0.921 0.008 0.000 0 0.992 0.000 0.000
#> SRR2001025 4 0.0000 0.922 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001026 4 0.0000 0.922 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001027 4 0.0146 0.922 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001020 2 0.0458 0.755 0.000 0.984 0 0.000 0.016 0.000
#> SRR2001021 2 0.0547 0.754 0.000 0.980 0 0.000 0.020 0.000
#> SRR2001022 2 0.0458 0.755 0.000 0.984 0 0.000 0.016 0.000
#> SRR2001023 2 0.0458 0.755 0.000 0.984 0 0.000 0.016 0.000
#> SRR2001016 2 0.7195 0.422 0.232 0.432 0 0.212 0.124 0.000
#> SRR2001017 2 0.7169 0.416 0.232 0.432 0 0.220 0.116 0.000
#> SRR2001018 2 0.7168 0.417 0.236 0.432 0 0.216 0.116 0.000
#> SRR2001019 2 0.7167 0.424 0.232 0.436 0 0.212 0.120 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", "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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.5031 0.497 0.497
#> 3 3 1.000 0.995 0.988 0.2187 0.889 0.777
#> 4 4 0.873 0.893 0.870 0.0783 1.000 1.000
#> 5 5 0.821 0.970 0.835 0.0456 0.873 0.671
#> 6 6 0.713 0.905 0.866 0.0603 1.000 1.000
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001033 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001034 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001035 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001204 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001205 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001206 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001207 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001200 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001201 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001202 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001203 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001196 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001197 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001198 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001199 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001192 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001193 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001194 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001195 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001188 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001189 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001190 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001191 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001184 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001185 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001186 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001187 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001180 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001181 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001182 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001183 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001176 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001177 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001178 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001179 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001172 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001173 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001174 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001175 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001168 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001169 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001170 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001171 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001164 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001165 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001166 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001167 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001160 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001161 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001162 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001163 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001156 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001157 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001158 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001159 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001152 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001153 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001154 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001155 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001148 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001149 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001150 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001151 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001144 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001145 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001146 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001147 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001140 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001142 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001143 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001136 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001137 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001138 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001139 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001132 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001133 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001134 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001135 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001128 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001129 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001130 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001131 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001124 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001125 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001126 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001127 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001120 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001121 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001122 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001123 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001116 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001117 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001118 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001119 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001112 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001113 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001114 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001115 3 0.1411 1.000 0.036 0.000 0.964
#> SRR2001108 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001109 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001110 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001111 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001104 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001105 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001106 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001107 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001100 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001101 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001102 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001103 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001096 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001097 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001098 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001099 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001092 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001093 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001094 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001095 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001088 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001089 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001090 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001091 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001084 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001085 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001086 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001087 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001080 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001081 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001082 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001083 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001076 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001077 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001078 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001079 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001072 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001073 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001074 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001075 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001068 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001069 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001070 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001071 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001064 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001065 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001066 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001067 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001060 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001061 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001062 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001063 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001056 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001057 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001058 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001059 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001052 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001053 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001054 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001055 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001048 2 0.0892 0.989 0.000 0.980 0.020
#> SRR2001049 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001050 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001051 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001044 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001045 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001046 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001047 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001040 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001041 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001042 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001043 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001036 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001037 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001038 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001039 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001028 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001029 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001030 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001031 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001024 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001025 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001026 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001027 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001020 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001021 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001022 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001023 2 0.1031 0.989 0.000 0.976 0.024
#> SRR2001016 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001017 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001018 2 0.0000 0.989 0.000 1.000 0.000
#> SRR2001019 2 0.0000 0.989 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.4830 0.802 0.000 0.608 0.392 NA
#> SRR2001033 2 0.4776 0.803 0.000 0.624 0.376 NA
#> SRR2001034 2 0.4830 0.802 0.000 0.608 0.392 NA
#> SRR2001035 2 0.4830 0.802 0.000 0.608 0.392 NA
#> SRR2001204 1 0.0524 0.983 0.988 0.000 0.008 NA
#> SRR2001205 1 0.0657 0.983 0.984 0.000 0.012 NA
#> SRR2001206 1 0.0657 0.983 0.984 0.000 0.012 NA
#> SRR2001207 1 0.0657 0.983 0.984 0.000 0.012 NA
#> SRR2001200 1 0.1557 0.958 0.944 0.000 0.056 NA
#> SRR2001201 1 0.1637 0.955 0.940 0.000 0.060 NA
#> SRR2001202 1 0.1557 0.958 0.944 0.000 0.056 NA
#> SRR2001203 1 0.1557 0.958 0.944 0.000 0.056 NA
#> SRR2001196 1 0.1557 0.960 0.944 0.000 0.056 NA
#> SRR2001197 1 0.1557 0.960 0.944 0.000 0.056 NA
#> SRR2001198 1 0.1637 0.957 0.940 0.000 0.060 NA
#> SRR2001199 1 0.1557 0.960 0.944 0.000 0.056 NA
#> SRR2001192 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001193 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001194 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001195 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001188 1 0.0188 0.982 0.996 0.000 0.004 NA
#> SRR2001189 1 0.0000 0.981 1.000 0.000 0.000 NA
#> SRR2001190 1 0.0000 0.981 1.000 0.000 0.000 NA
#> SRR2001191 1 0.0188 0.982 0.996 0.000 0.004 NA
#> SRR2001184 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001185 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001186 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001187 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001180 1 0.0188 0.981 0.996 0.000 0.000 NA
#> SRR2001181 1 0.0000 0.981 1.000 0.000 0.000 NA
#> SRR2001182 1 0.0188 0.981 0.996 0.000 0.000 NA
#> SRR2001183 1 0.0188 0.981 0.996 0.000 0.000 NA
#> SRR2001176 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001177 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001178 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001179 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001172 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001173 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001174 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001175 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001168 1 0.0657 0.980 0.984 0.000 0.012 NA
#> SRR2001169 1 0.0657 0.980 0.984 0.000 0.012 NA
#> SRR2001170 1 0.0657 0.980 0.984 0.000 0.012 NA
#> SRR2001171 1 0.0657 0.980 0.984 0.000 0.012 NA
#> SRR2001164 1 0.0707 0.979 0.980 0.000 0.020 NA
#> SRR2001165 1 0.0469 0.982 0.988 0.000 0.012 NA
#> SRR2001166 1 0.0592 0.981 0.984 0.000 0.016 NA
#> SRR2001167 1 0.0469 0.982 0.988 0.000 0.012 NA
#> SRR2001160 1 0.0188 0.982 0.996 0.000 0.004 NA
#> SRR2001161 1 0.0188 0.982 0.996 0.000 0.004 NA
#> SRR2001162 1 0.0188 0.982 0.996 0.000 0.004 NA
#> SRR2001163 1 0.0188 0.982 0.996 0.000 0.004 NA
#> SRR2001156 1 0.1557 0.960 0.944 0.000 0.056 NA
#> SRR2001157 1 0.1557 0.960 0.944 0.000 0.056 NA
#> SRR2001158 1 0.1389 0.964 0.952 0.000 0.048 NA
#> SRR2001159 1 0.1389 0.966 0.952 0.000 0.048 NA
#> SRR2001152 1 0.0376 0.979 0.992 0.000 0.004 NA
#> SRR2001153 1 0.0376 0.979 0.992 0.000 0.004 NA
#> SRR2001154 1 0.0188 0.981 0.996 0.000 0.000 NA
#> SRR2001155 1 0.0188 0.981 0.996 0.000 0.000 NA
#> SRR2001148 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001149 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001150 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001151 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001144 1 0.0657 0.982 0.984 0.000 0.012 NA
#> SRR2001145 1 0.0376 0.982 0.992 0.000 0.004 NA
#> SRR2001146 1 0.0376 0.982 0.992 0.000 0.004 NA
#> SRR2001147 1 0.0524 0.983 0.988 0.000 0.008 NA
#> SRR2001140 1 0.0376 0.982 0.992 0.000 0.004 NA
#> SRR2001142 1 0.0376 0.982 0.992 0.000 0.004 NA
#> SRR2001143 1 0.0376 0.982 0.992 0.000 0.004 NA
#> SRR2001136 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001137 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001138 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001139 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001132 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001133 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001134 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001135 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001128 1 0.0779 0.982 0.980 0.000 0.016 NA
#> SRR2001129 1 0.0657 0.983 0.984 0.000 0.012 NA
#> SRR2001130 1 0.0657 0.983 0.984 0.000 0.012 NA
#> SRR2001131 1 0.0657 0.983 0.984 0.000 0.012 NA
#> SRR2001124 1 0.1211 0.970 0.960 0.000 0.040 NA
#> SRR2001125 1 0.1302 0.968 0.956 0.000 0.044 NA
#> SRR2001126 1 0.1211 0.970 0.960 0.000 0.040 NA
#> SRR2001127 1 0.1302 0.968 0.956 0.000 0.044 NA
#> SRR2001120 1 0.0376 0.982 0.992 0.000 0.004 NA
#> SRR2001121 1 0.0524 0.982 0.988 0.000 0.008 NA
#> SRR2001122 1 0.0657 0.980 0.984 0.000 0.012 NA
#> SRR2001123 1 0.0524 0.982 0.988 0.000 0.008 NA
#> SRR2001116 1 0.0707 0.979 0.980 0.000 0.020 NA
#> SRR2001117 1 0.0336 0.982 0.992 0.000 0.008 NA
#> SRR2001118 1 0.0336 0.982 0.992 0.000 0.008 NA
#> SRR2001119 1 0.0469 0.982 0.988 0.000 0.012 NA
#> SRR2001112 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001113 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001114 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001115 3 0.5827 1.000 0.036 0.000 0.568 NA
#> SRR2001108 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001109 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001110 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001111 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001104 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001105 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001106 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001107 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001100 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001101 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001102 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001103 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001096 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001097 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001098 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001099 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001092 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001093 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001094 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001095 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001088 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001089 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001090 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001091 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001084 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001085 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001086 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001087 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001080 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001081 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001082 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001083 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001076 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001077 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001078 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001079 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001072 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001073 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001074 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001075 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001068 2 0.4817 0.803 0.000 0.612 0.388 NA
#> SRR2001069 2 0.4761 0.803 0.000 0.628 0.372 NA
#> SRR2001070 2 0.4817 0.803 0.000 0.612 0.388 NA
#> SRR2001071 2 0.4817 0.803 0.000 0.612 0.388 NA
#> SRR2001064 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001065 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001066 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001067 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001060 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001061 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001062 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001063 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001056 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001057 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001058 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001059 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001052 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001053 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001054 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001055 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001048 2 0.4679 0.803 0.000 0.648 0.352 NA
#> SRR2001049 2 0.4817 0.803 0.000 0.612 0.388 NA
#> SRR2001050 2 0.4817 0.803 0.000 0.612 0.388 NA
#> SRR2001051 2 0.4817 0.803 0.000 0.612 0.388 NA
#> SRR2001044 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001045 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001046 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001047 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001040 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001041 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001042 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001043 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001036 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001037 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001038 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001039 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001028 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001029 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001030 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001031 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001024 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001025 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001026 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001027 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001020 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001021 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001022 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001023 2 0.4843 0.802 0.000 0.604 0.396 NA
#> SRR2001016 2 0.0188 0.805 0.000 0.996 0.004 NA
#> SRR2001017 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001018 2 0.0000 0.805 0.000 1.000 0.000 NA
#> SRR2001019 2 0.0336 0.805 0.000 0.992 0.008 NA
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.0912 0.975 0.000 0.972 0.000 0.012 NA
#> SRR2001033 2 0.1211 0.963 0.000 0.960 0.000 0.024 NA
#> SRR2001034 2 0.0798 0.978 0.000 0.976 0.000 0.008 NA
#> SRR2001035 2 0.0912 0.975 0.000 0.972 0.000 0.012 NA
#> SRR2001204 1 0.1117 0.965 0.964 0.000 0.020 0.000 NA
#> SRR2001205 1 0.0912 0.967 0.972 0.000 0.016 0.000 NA
#> SRR2001206 1 0.0898 0.967 0.972 0.000 0.020 0.000 NA
#> SRR2001207 1 0.0898 0.968 0.972 0.000 0.020 0.000 NA
#> SRR2001200 1 0.2446 0.932 0.900 0.000 0.044 0.000 NA
#> SRR2001201 1 0.2230 0.940 0.912 0.000 0.044 0.000 NA
#> SRR2001202 1 0.2228 0.941 0.912 0.000 0.040 0.000 NA
#> SRR2001203 1 0.2304 0.938 0.908 0.000 0.044 0.000 NA
#> SRR2001196 1 0.1741 0.953 0.936 0.000 0.040 0.000 NA
#> SRR2001197 1 0.1741 0.953 0.936 0.000 0.040 0.000 NA
#> SRR2001198 1 0.1741 0.953 0.936 0.000 0.040 0.000 NA
#> SRR2001199 1 0.1741 0.953 0.936 0.000 0.040 0.000 NA
#> SRR2001192 3 0.1792 0.976 0.084 0.000 0.916 0.000 NA
#> SRR2001193 3 0.1851 0.976 0.088 0.000 0.912 0.000 NA
#> SRR2001194 3 0.1851 0.976 0.088 0.000 0.912 0.000 NA
#> SRR2001195 3 0.1851 0.976 0.088 0.000 0.912 0.000 NA
#> SRR2001188 1 0.0609 0.966 0.980 0.000 0.000 0.000 NA
#> SRR2001189 1 0.0703 0.965 0.976 0.000 0.000 0.000 NA
#> SRR2001190 1 0.0794 0.963 0.972 0.000 0.000 0.000 NA
#> SRR2001191 1 0.0609 0.966 0.980 0.000 0.000 0.000 NA
#> SRR2001184 3 0.2351 0.973 0.088 0.000 0.896 0.000 NA
#> SRR2001185 3 0.2351 0.973 0.088 0.000 0.896 0.000 NA
#> SRR2001186 3 0.2351 0.973 0.088 0.000 0.896 0.000 NA
#> SRR2001187 3 0.2351 0.973 0.088 0.000 0.896 0.000 NA
#> SRR2001180 1 0.0794 0.965 0.972 0.000 0.000 0.000 NA
#> SRR2001181 1 0.0703 0.967 0.976 0.000 0.000 0.000 NA
#> SRR2001182 1 0.0880 0.963 0.968 0.000 0.000 0.000 NA
#> SRR2001183 1 0.1043 0.960 0.960 0.000 0.000 0.000 NA
#> SRR2001176 3 0.1952 0.976 0.084 0.000 0.912 0.000 NA
#> SRR2001177 3 0.2011 0.976 0.088 0.000 0.908 0.000 NA
#> SRR2001178 3 0.1952 0.976 0.084 0.000 0.912 0.000 NA
#> SRR2001179 3 0.1952 0.976 0.084 0.000 0.912 0.000 NA
#> SRR2001172 3 0.2448 0.973 0.088 0.000 0.892 0.000 NA
#> SRR2001173 3 0.2448 0.973 0.088 0.000 0.892 0.000 NA
#> SRR2001174 3 0.2448 0.973 0.088 0.000 0.892 0.000 NA
#> SRR2001175 3 0.2448 0.973 0.088 0.000 0.892 0.000 NA
#> SRR2001168 1 0.2149 0.940 0.916 0.000 0.036 0.000 NA
#> SRR2001169 1 0.2304 0.933 0.908 0.000 0.044 0.000 NA
#> SRR2001170 1 0.2149 0.940 0.916 0.000 0.036 0.000 NA
#> SRR2001171 1 0.2221 0.937 0.912 0.000 0.036 0.000 NA
#> SRR2001164 1 0.1018 0.966 0.968 0.000 0.016 0.000 NA
#> SRR2001165 1 0.1018 0.967 0.968 0.000 0.016 0.000 NA
#> SRR2001166 1 0.0807 0.968 0.976 0.000 0.012 0.000 NA
#> SRR2001167 1 0.0807 0.968 0.976 0.000 0.012 0.000 NA
#> SRR2001160 1 0.0671 0.968 0.980 0.000 0.004 0.000 NA
#> SRR2001161 1 0.0451 0.969 0.988 0.000 0.004 0.000 NA
#> SRR2001162 1 0.0566 0.968 0.984 0.000 0.004 0.000 NA
#> SRR2001163 1 0.0566 0.968 0.984 0.000 0.004 0.000 NA
#> SRR2001156 1 0.1661 0.956 0.940 0.000 0.036 0.000 NA
#> SRR2001157 1 0.1741 0.953 0.936 0.000 0.040 0.000 NA
#> SRR2001158 1 0.1741 0.953 0.936 0.000 0.040 0.000 NA
#> SRR2001159 1 0.1661 0.956 0.940 0.000 0.036 0.000 NA
#> SRR2001152 1 0.0609 0.966 0.980 0.000 0.000 0.000 NA
#> SRR2001153 1 0.0609 0.966 0.980 0.000 0.000 0.000 NA
#> SRR2001154 1 0.0703 0.966 0.976 0.000 0.000 0.000 NA
#> SRR2001155 1 0.0510 0.967 0.984 0.000 0.000 0.000 NA
#> SRR2001148 3 0.2351 0.975 0.088 0.000 0.896 0.000 NA
#> SRR2001149 3 0.2408 0.974 0.092 0.000 0.892 0.000 NA
#> SRR2001150 3 0.2408 0.974 0.092 0.000 0.892 0.000 NA
#> SRR2001151 3 0.2408 0.974 0.092 0.000 0.892 0.000 NA
#> SRR2001144 1 0.1211 0.965 0.960 0.000 0.024 0.000 NA
#> SRR2001145 1 0.1211 0.965 0.960 0.000 0.024 0.000 NA
#> SRR2001146 1 0.1211 0.965 0.960 0.000 0.024 0.000 NA
#> SRR2001147 1 0.1117 0.964 0.964 0.000 0.020 0.000 NA
#> SRR2001140 1 0.0693 0.969 0.980 0.000 0.008 0.000 NA
#> SRR2001142 1 0.0671 0.967 0.980 0.000 0.004 0.000 NA
#> SRR2001143 1 0.0693 0.969 0.980 0.000 0.008 0.000 NA
#> SRR2001136 3 0.2830 0.968 0.080 0.000 0.876 0.000 NA
#> SRR2001137 3 0.2830 0.968 0.080 0.000 0.876 0.000 NA
#> SRR2001138 3 0.2830 0.968 0.080 0.000 0.876 0.000 NA
#> SRR2001139 3 0.2830 0.968 0.080 0.000 0.876 0.000 NA
#> SRR2001132 3 0.2511 0.972 0.080 0.000 0.892 0.000 NA
#> SRR2001133 3 0.2511 0.972 0.080 0.000 0.892 0.000 NA
#> SRR2001134 3 0.2676 0.970 0.080 0.000 0.884 0.000 NA
#> SRR2001135 3 0.2595 0.971 0.080 0.000 0.888 0.000 NA
#> SRR2001128 1 0.0798 0.969 0.976 0.000 0.008 0.000 NA
#> SRR2001129 1 0.0693 0.968 0.980 0.000 0.012 0.000 NA
#> SRR2001130 1 0.0912 0.969 0.972 0.000 0.012 0.000 NA
#> SRR2001131 1 0.0912 0.969 0.972 0.000 0.012 0.000 NA
#> SRR2001124 1 0.1106 0.965 0.964 0.000 0.024 0.000 NA
#> SRR2001125 1 0.1281 0.962 0.956 0.000 0.032 0.000 NA
#> SRR2001126 1 0.1082 0.965 0.964 0.000 0.028 0.000 NA
#> SRR2001127 1 0.1300 0.961 0.956 0.000 0.028 0.000 NA
#> SRR2001120 1 0.1668 0.958 0.940 0.000 0.028 0.000 NA
#> SRR2001121 1 0.1753 0.955 0.936 0.000 0.032 0.000 NA
#> SRR2001122 1 0.1579 0.957 0.944 0.000 0.024 0.000 NA
#> SRR2001123 1 0.1668 0.956 0.940 0.000 0.032 0.000 NA
#> SRR2001116 1 0.0693 0.969 0.980 0.000 0.008 0.000 NA
#> SRR2001117 1 0.0798 0.969 0.976 0.000 0.008 0.000 NA
#> SRR2001118 1 0.0566 0.969 0.984 0.000 0.004 0.000 NA
#> SRR2001119 1 0.0671 0.968 0.980 0.000 0.004 0.000 NA
#> SRR2001112 3 0.3644 0.947 0.080 0.000 0.824 0.000 NA
#> SRR2001113 3 0.3697 0.945 0.080 0.000 0.820 0.000 NA
#> SRR2001114 3 0.3644 0.947 0.080 0.000 0.824 0.000 NA
#> SRR2001115 3 0.3644 0.947 0.080 0.000 0.824 0.000 NA
#> SRR2001108 4 0.4251 0.984 0.000 0.372 0.000 0.624 NA
#> SRR2001109 4 0.4251 0.984 0.000 0.372 0.000 0.624 NA
#> SRR2001110 4 0.4367 0.983 0.000 0.372 0.000 0.620 NA
#> SRR2001111 4 0.4367 0.983 0.000 0.372 0.000 0.620 NA
#> SRR2001104 2 0.0162 0.983 0.000 0.996 0.000 0.000 NA
#> SRR2001105 2 0.0404 0.982 0.000 0.988 0.000 0.000 NA
#> SRR2001106 2 0.0000 0.982 0.000 1.000 0.000 0.000 NA
#> SRR2001107 2 0.0000 0.982 0.000 1.000 0.000 0.000 NA
#> SRR2001100 2 0.0451 0.982 0.000 0.988 0.000 0.008 NA
#> SRR2001101 2 0.0579 0.981 0.000 0.984 0.000 0.008 NA
#> SRR2001102 2 0.0451 0.982 0.000 0.988 0.000 0.008 NA
#> SRR2001103 2 0.0451 0.982 0.000 0.988 0.000 0.008 NA
#> SRR2001096 2 0.0290 0.978 0.000 0.992 0.000 0.000 NA
#> SRR2001097 2 0.0290 0.978 0.000 0.992 0.000 0.000 NA
#> SRR2001098 2 0.0290 0.978 0.000 0.992 0.000 0.000 NA
#> SRR2001099 2 0.0290 0.978 0.000 0.992 0.000 0.000 NA
#> SRR2001092 2 0.0162 0.981 0.000 0.996 0.000 0.000 NA
#> SRR2001093 2 0.0162 0.981 0.000 0.996 0.000 0.000 NA
#> SRR2001094 2 0.0162 0.981 0.000 0.996 0.000 0.000 NA
#> SRR2001095 2 0.0162 0.981 0.000 0.996 0.000 0.000 NA
#> SRR2001088 4 0.4114 0.984 0.000 0.376 0.000 0.624 NA
#> SRR2001089 4 0.4114 0.984 0.000 0.376 0.000 0.624 NA
#> SRR2001090 4 0.4264 0.983 0.000 0.376 0.000 0.620 NA
#> SRR2001091 4 0.4264 0.983 0.000 0.376 0.000 0.620 NA
#> SRR2001084 4 0.4251 0.984 0.000 0.372 0.000 0.624 NA
#> SRR2001085 4 0.4367 0.983 0.000 0.372 0.000 0.620 NA
#> SRR2001086 4 0.4367 0.983 0.000 0.372 0.000 0.620 NA
#> SRR2001087 4 0.4367 0.983 0.000 0.372 0.000 0.620 NA
#> SRR2001080 2 0.0566 0.982 0.000 0.984 0.000 0.004 NA
#> SRR2001081 2 0.0566 0.982 0.000 0.984 0.000 0.004 NA
#> SRR2001082 2 0.0451 0.983 0.000 0.988 0.000 0.004 NA
#> SRR2001083 2 0.0451 0.983 0.000 0.988 0.000 0.004 NA
#> SRR2001076 2 0.0000 0.982 0.000 1.000 0.000 0.000 NA
#> SRR2001077 2 0.0404 0.982 0.000 0.988 0.000 0.000 NA
#> SRR2001078 2 0.0000 0.982 0.000 1.000 0.000 0.000 NA
#> SRR2001079 2 0.0000 0.982 0.000 1.000 0.000 0.000 NA
#> SRR2001072 4 0.4276 0.980 0.000 0.380 0.000 0.616 NA
#> SRR2001073 4 0.4276 0.980 0.000 0.380 0.000 0.616 NA
#> SRR2001074 4 0.4276 0.980 0.000 0.380 0.000 0.616 NA
#> SRR2001075 4 0.4288 0.977 0.000 0.384 0.000 0.612 NA
#> SRR2001068 2 0.0693 0.979 0.000 0.980 0.000 0.008 NA
#> SRR2001069 2 0.1211 0.961 0.000 0.960 0.000 0.024 NA
#> SRR2001070 2 0.0693 0.979 0.000 0.980 0.000 0.008 NA
#> SRR2001071 2 0.0912 0.973 0.000 0.972 0.000 0.016 NA
#> SRR2001064 2 0.0290 0.978 0.000 0.992 0.000 0.000 NA
#> SRR2001065 2 0.0290 0.978 0.000 0.992 0.000 0.000 NA
#> SRR2001066 2 0.0290 0.978 0.000 0.992 0.000 0.000 NA
#> SRR2001067 2 0.0290 0.978 0.000 0.992 0.000 0.000 NA
#> SRR2001060 4 0.4264 0.983 0.000 0.376 0.000 0.620 NA
#> SRR2001061 4 0.4264 0.983 0.000 0.376 0.000 0.620 NA
#> SRR2001062 4 0.4264 0.983 0.000 0.376 0.000 0.620 NA
#> SRR2001063 4 0.4264 0.983 0.000 0.376 0.000 0.620 NA
#> SRR2001056 4 0.4367 0.983 0.000 0.372 0.000 0.620 NA
#> SRR2001057 4 0.4367 0.983 0.000 0.372 0.000 0.620 NA
#> SRR2001058 4 0.4367 0.983 0.000 0.372 0.000 0.620 NA
#> SRR2001059 4 0.4367 0.983 0.000 0.372 0.000 0.620 NA
#> SRR2001052 2 0.0290 0.982 0.000 0.992 0.000 0.000 NA
#> SRR2001053 2 0.0451 0.981 0.000 0.988 0.000 0.004 NA
#> SRR2001054 2 0.0290 0.982 0.000 0.992 0.000 0.000 NA
#> SRR2001055 2 0.0290 0.982 0.000 0.992 0.000 0.000 NA
#> SRR2001048 2 0.1469 0.943 0.000 0.948 0.000 0.036 NA
#> SRR2001049 2 0.1117 0.967 0.000 0.964 0.000 0.020 NA
#> SRR2001050 2 0.0912 0.975 0.000 0.972 0.000 0.012 NA
#> SRR2001051 2 0.0912 0.975 0.000 0.972 0.000 0.012 NA
#> SRR2001044 4 0.4264 0.983 0.000 0.376 0.000 0.620 NA
#> SRR2001045 4 0.4380 0.980 0.000 0.376 0.000 0.616 NA
#> SRR2001046 4 0.4101 0.984 0.000 0.372 0.000 0.628 NA
#> SRR2001047 4 0.4114 0.984 0.000 0.376 0.000 0.624 NA
#> SRR2001040 4 0.4088 0.982 0.000 0.368 0.000 0.632 NA
#> SRR2001041 4 0.4088 0.982 0.000 0.368 0.000 0.632 NA
#> SRR2001042 4 0.4088 0.982 0.000 0.368 0.000 0.632 NA
#> SRR2001043 4 0.4088 0.982 0.000 0.368 0.000 0.632 NA
#> SRR2001036 4 0.4101 0.984 0.000 0.372 0.000 0.628 NA
#> SRR2001037 4 0.4101 0.984 0.000 0.372 0.000 0.628 NA
#> SRR2001038 4 0.4101 0.984 0.000 0.372 0.000 0.628 NA
#> SRR2001039 4 0.4101 0.984 0.000 0.372 0.000 0.628 NA
#> SRR2001028 4 0.4138 0.978 0.000 0.384 0.000 0.616 NA
#> SRR2001029 4 0.4138 0.978 0.000 0.384 0.000 0.616 NA
#> SRR2001030 4 0.4126 0.982 0.000 0.380 0.000 0.620 NA
#> SRR2001031 4 0.4126 0.982 0.000 0.380 0.000 0.620 NA
#> SRR2001024 4 0.4101 0.984 0.000 0.372 0.000 0.628 NA
#> SRR2001025 4 0.4101 0.984 0.000 0.372 0.000 0.628 NA
#> SRR2001026 4 0.4101 0.984 0.000 0.372 0.000 0.628 NA
#> SRR2001027 4 0.4114 0.984 0.000 0.376 0.000 0.624 NA
#> SRR2001020 2 0.0671 0.973 0.000 0.980 0.000 0.016 NA
#> SRR2001021 2 0.0510 0.976 0.000 0.984 0.000 0.016 NA
#> SRR2001022 2 0.0404 0.979 0.000 0.988 0.000 0.012 NA
#> SRR2001023 2 0.0566 0.977 0.000 0.984 0.000 0.012 NA
#> SRR2001016 4 0.4489 0.919 0.000 0.420 0.000 0.572 NA
#> SRR2001017 4 0.4481 0.925 0.000 0.416 0.000 0.576 NA
#> SRR2001018 4 0.4489 0.919 0.000 0.420 0.000 0.572 NA
#> SRR2001019 4 0.4522 0.882 0.000 0.440 0.000 0.552 NA
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 2 0.4012 0.912 0.000 0.724 0.000 0.240 NA NA
#> SRR2001033 2 0.4107 0.903 0.000 0.708 0.000 0.256 NA NA
#> SRR2001034 2 0.4012 0.913 0.000 0.724 0.000 0.240 NA NA
#> SRR2001035 2 0.4012 0.912 0.000 0.724 0.000 0.240 NA NA
#> SRR2001204 1 0.3078 0.860 0.836 0.000 0.108 0.000 NA NA
#> SRR2001205 1 0.3176 0.864 0.840 0.000 0.100 0.000 NA NA
#> SRR2001206 1 0.3065 0.864 0.844 0.000 0.100 0.000 NA NA
#> SRR2001207 1 0.3079 0.867 0.848 0.000 0.092 0.000 NA NA
#> SRR2001200 1 0.3767 0.827 0.780 0.000 0.088 0.000 NA NA
#> SRR2001201 1 0.3686 0.833 0.788 0.000 0.088 0.000 NA NA
#> SRR2001202 1 0.3686 0.833 0.788 0.000 0.088 0.000 NA NA
#> SRR2001203 1 0.3686 0.833 0.788 0.000 0.088 0.000 NA NA
#> SRR2001196 1 0.3125 0.856 0.836 0.000 0.080 0.000 NA NA
#> SRR2001197 1 0.3175 0.853 0.832 0.000 0.080 0.000 NA NA
#> SRR2001198 1 0.3175 0.853 0.832 0.000 0.080 0.000 NA NA
#> SRR2001199 1 0.3175 0.853 0.832 0.000 0.080 0.000 NA NA
#> SRR2001192 3 0.2556 0.911 0.032 0.000 0.892 0.000 NA NA
#> SRR2001193 3 0.2490 0.911 0.032 0.000 0.896 0.000 NA NA
#> SRR2001194 3 0.2424 0.911 0.036 0.000 0.900 0.000 NA NA
#> SRR2001195 3 0.2342 0.912 0.040 0.000 0.904 0.000 NA NA
#> SRR2001188 1 0.1643 0.886 0.924 0.000 0.000 0.000 NA NA
#> SRR2001189 1 0.1728 0.886 0.924 0.000 0.004 0.000 NA NA
#> SRR2001190 1 0.1584 0.887 0.928 0.000 0.000 0.000 NA NA
#> SRR2001191 1 0.1471 0.887 0.932 0.000 0.000 0.000 NA NA
#> SRR2001184 3 0.2272 0.907 0.056 0.000 0.900 0.000 NA NA
#> SRR2001185 3 0.2325 0.905 0.060 0.000 0.892 0.000 NA NA
#> SRR2001186 3 0.2384 0.903 0.064 0.000 0.888 0.000 NA NA
#> SRR2001187 3 0.2384 0.903 0.064 0.000 0.888 0.000 NA NA
#> SRR2001180 1 0.1686 0.887 0.924 0.000 0.000 0.000 NA NA
#> SRR2001181 1 0.1606 0.888 0.932 0.000 0.004 0.000 NA NA
#> SRR2001182 1 0.1584 0.886 0.928 0.000 0.000 0.000 NA NA
#> SRR2001183 1 0.1807 0.887 0.920 0.000 0.000 0.000 NA NA
#> SRR2001176 3 0.2411 0.912 0.044 0.000 0.900 0.000 NA NA
#> SRR2001177 3 0.2342 0.914 0.040 0.000 0.904 0.000 NA NA
#> SRR2001178 3 0.2519 0.914 0.044 0.000 0.892 0.000 NA NA
#> SRR2001179 3 0.2450 0.913 0.040 0.000 0.896 0.000 NA NA
#> SRR2001172 3 0.2451 0.900 0.060 0.000 0.884 0.000 NA NA
#> SRR2001173 3 0.2390 0.900 0.056 0.000 0.888 0.000 NA NA
#> SRR2001174 3 0.2451 0.900 0.060 0.000 0.884 0.000 NA NA
#> SRR2001175 3 0.2451 0.900 0.060 0.000 0.884 0.000 NA NA
#> SRR2001168 1 0.4120 0.806 0.744 0.000 0.160 0.000 NA NA
#> SRR2001169 1 0.4085 0.809 0.748 0.000 0.156 0.000 NA NA
#> SRR2001170 1 0.4050 0.813 0.752 0.000 0.152 0.000 NA NA
#> SRR2001171 1 0.4085 0.809 0.748 0.000 0.156 0.000 NA NA
#> SRR2001164 1 0.1950 0.885 0.912 0.000 0.024 0.000 NA NA
#> SRR2001165 1 0.1686 0.888 0.924 0.000 0.012 0.000 NA NA
#> SRR2001166 1 0.1745 0.887 0.920 0.000 0.012 0.000 NA NA
#> SRR2001167 1 0.1867 0.886 0.916 0.000 0.020 0.000 NA NA
#> SRR2001160 1 0.1219 0.891 0.948 0.000 0.004 0.000 NA NA
#> SRR2001161 1 0.1364 0.891 0.944 0.000 0.004 0.000 NA NA
#> SRR2001162 1 0.1296 0.892 0.948 0.000 0.004 0.000 NA NA
#> SRR2001163 1 0.1364 0.891 0.944 0.000 0.004 0.000 NA NA
#> SRR2001156 1 0.3123 0.857 0.836 0.000 0.076 0.000 NA NA
#> SRR2001157 1 0.3017 0.860 0.844 0.000 0.072 0.000 NA NA
#> SRR2001158 1 0.3068 0.860 0.840 0.000 0.072 0.000 NA NA
#> SRR2001159 1 0.3013 0.862 0.844 0.000 0.068 0.000 NA NA
#> SRR2001152 1 0.2172 0.888 0.912 0.000 0.024 0.000 NA NA
#> SRR2001153 1 0.1861 0.889 0.928 0.000 0.016 0.000 NA NA
#> SRR2001154 1 0.1932 0.889 0.924 0.000 0.016 0.000 NA NA
#> SRR2001155 1 0.2152 0.887 0.912 0.000 0.036 0.000 NA NA
#> SRR2001148 3 0.2328 0.906 0.056 0.000 0.892 0.000 NA NA
#> SRR2001149 3 0.2258 0.906 0.060 0.000 0.896 0.000 NA NA
#> SRR2001150 3 0.2325 0.905 0.060 0.000 0.892 0.000 NA NA
#> SRR2001151 3 0.2258 0.904 0.060 0.000 0.896 0.000 NA NA
#> SRR2001144 1 0.3641 0.835 0.788 0.000 0.140 0.000 NA NA
#> SRR2001145 1 0.3522 0.841 0.800 0.000 0.128 0.000 NA NA
#> SRR2001146 1 0.3563 0.840 0.796 0.000 0.132 0.000 NA NA
#> SRR2001147 1 0.3616 0.838 0.792 0.000 0.132 0.000 NA NA
#> SRR2001140 1 0.2152 0.887 0.912 0.000 0.036 0.000 NA NA
#> SRR2001142 1 0.2314 0.883 0.900 0.000 0.056 0.000 NA NA
#> SRR2001143 1 0.2257 0.884 0.904 0.000 0.048 0.000 NA NA
#> SRR2001136 3 0.2897 0.888 0.060 0.000 0.852 0.000 NA NA
#> SRR2001137 3 0.2948 0.890 0.060 0.000 0.848 0.000 NA NA
#> SRR2001138 3 0.2956 0.888 0.064 0.000 0.848 0.000 NA NA
#> SRR2001139 3 0.2956 0.888 0.064 0.000 0.848 0.000 NA NA
#> SRR2001132 3 0.2731 0.901 0.044 0.000 0.876 0.000 NA NA
#> SRR2001133 3 0.2862 0.899 0.048 0.000 0.864 0.000 NA NA
#> SRR2001134 3 0.2728 0.900 0.040 0.000 0.872 0.000 NA NA
#> SRR2001135 3 0.2685 0.899 0.044 0.000 0.872 0.000 NA NA
#> SRR2001128 1 0.1773 0.894 0.932 0.000 0.016 0.000 NA NA
#> SRR2001129 1 0.2100 0.888 0.916 0.000 0.036 0.000 NA NA
#> SRR2001130 1 0.2116 0.890 0.916 0.000 0.024 0.000 NA NA
#> SRR2001131 1 0.1794 0.892 0.932 0.000 0.016 0.000 NA NA
#> SRR2001124 1 0.2389 0.878 0.888 0.000 0.052 0.000 NA NA
#> SRR2001125 1 0.2448 0.877 0.884 0.000 0.052 0.000 NA NA
#> SRR2001126 1 0.2129 0.885 0.904 0.000 0.040 0.000 NA NA
#> SRR2001127 1 0.2318 0.880 0.892 0.000 0.044 0.000 NA NA
#> SRR2001120 1 0.3784 0.828 0.776 0.000 0.144 0.000 NA NA
#> SRR2001121 1 0.3834 0.825 0.772 0.000 0.144 0.000 NA NA
#> SRR2001122 1 0.3834 0.825 0.772 0.000 0.144 0.000 NA NA
#> SRR2001123 1 0.3796 0.827 0.776 0.000 0.140 0.000 NA NA
#> SRR2001116 1 0.1196 0.893 0.952 0.000 0.008 0.000 NA NA
#> SRR2001117 1 0.1333 0.891 0.944 0.000 0.008 0.000 NA NA
#> SRR2001118 1 0.1082 0.891 0.956 0.000 0.004 0.000 NA NA
#> SRR2001119 1 0.1219 0.891 0.948 0.000 0.004 0.000 NA NA
#> SRR2001112 3 0.3752 0.855 0.064 0.000 0.772 0.000 NA NA
#> SRR2001113 3 0.3717 0.857 0.064 0.000 0.776 0.000 NA NA
#> SRR2001114 3 0.3660 0.855 0.060 0.000 0.780 0.000 NA NA
#> SRR2001115 3 0.3681 0.859 0.064 0.000 0.780 0.000 NA NA
#> SRR2001108 4 0.1230 0.950 0.000 0.028 0.000 0.956 NA NA
#> SRR2001109 4 0.1230 0.950 0.000 0.028 0.000 0.956 NA NA
#> SRR2001110 4 0.1332 0.948 0.000 0.028 0.000 0.952 NA NA
#> SRR2001111 4 0.1332 0.948 0.000 0.028 0.000 0.952 NA NA
#> SRR2001104 2 0.2810 0.933 0.000 0.832 0.000 0.156 NA NA
#> SRR2001105 2 0.3000 0.932 0.000 0.824 0.000 0.156 NA NA
#> SRR2001106 2 0.2810 0.933 0.000 0.832 0.000 0.156 NA NA
#> SRR2001107 2 0.2909 0.933 0.000 0.828 0.000 0.156 NA NA
#> SRR2001100 2 0.3488 0.930 0.000 0.764 0.000 0.216 NA NA
#> SRR2001101 2 0.3398 0.930 0.000 0.768 0.000 0.216 NA NA
#> SRR2001102 2 0.3243 0.933 0.000 0.780 0.000 0.208 NA NA
#> SRR2001103 2 0.3230 0.932 0.000 0.776 0.000 0.212 NA NA
#> SRR2001096 2 0.2593 0.929 0.000 0.844 0.000 0.148 NA NA
#> SRR2001097 2 0.2520 0.931 0.000 0.844 0.000 0.152 NA NA
#> SRR2001098 2 0.2593 0.929 0.000 0.844 0.000 0.148 NA NA
#> SRR2001099 2 0.2520 0.932 0.000 0.844 0.000 0.152 NA NA
#> SRR2001092 2 0.3166 0.929 0.000 0.816 0.000 0.156 NA NA
#> SRR2001093 2 0.3492 0.926 0.000 0.796 0.000 0.160 NA NA
#> SRR2001094 2 0.3102 0.930 0.000 0.816 0.000 0.156 NA NA
#> SRR2001095 2 0.3166 0.929 0.000 0.816 0.000 0.156 NA NA
#> SRR2001088 4 0.0891 0.954 0.000 0.024 0.000 0.968 NA NA
#> SRR2001089 4 0.0891 0.954 0.000 0.024 0.000 0.968 NA NA
#> SRR2001090 4 0.0972 0.955 0.000 0.028 0.000 0.964 NA NA
#> SRR2001091 4 0.1003 0.955 0.000 0.028 0.000 0.964 NA NA
#> SRR2001084 4 0.1251 0.949 0.000 0.024 0.000 0.956 NA NA
#> SRR2001085 4 0.1251 0.949 0.000 0.024 0.000 0.956 NA NA
#> SRR2001086 4 0.1353 0.948 0.000 0.024 0.000 0.952 NA NA
#> SRR2001087 4 0.1353 0.948 0.000 0.024 0.000 0.952 NA NA
#> SRR2001080 2 0.3393 0.937 0.000 0.784 0.000 0.192 NA NA
#> SRR2001081 2 0.3652 0.935 0.000 0.768 0.000 0.196 NA NA
#> SRR2001082 2 0.3823 0.933 0.000 0.760 0.000 0.192 NA NA
#> SRR2001083 2 0.3450 0.936 0.000 0.780 0.000 0.188 NA NA
#> SRR2001076 2 0.2778 0.938 0.000 0.824 0.000 0.168 NA NA
#> SRR2001077 2 0.3073 0.936 0.000 0.816 0.000 0.164 NA NA
#> SRR2001078 2 0.2706 0.936 0.000 0.832 0.000 0.160 NA NA
#> SRR2001079 2 0.2706 0.935 0.000 0.832 0.000 0.160 NA NA
#> SRR2001072 4 0.2371 0.929 0.000 0.052 0.000 0.900 NA NA
#> SRR2001073 4 0.2341 0.926 0.000 0.056 0.000 0.900 NA NA
#> SRR2001074 4 0.2414 0.926 0.000 0.056 0.000 0.896 NA NA
#> SRR2001075 4 0.2501 0.922 0.000 0.072 0.000 0.888 NA NA
#> SRR2001068 2 0.4293 0.901 0.000 0.704 0.000 0.248 NA NA
#> SRR2001069 2 0.4464 0.867 0.000 0.672 0.000 0.280 NA NA
#> SRR2001070 2 0.4290 0.892 0.000 0.696 0.000 0.260 NA NA
#> SRR2001071 2 0.4334 0.884 0.000 0.688 0.000 0.268 NA NA
#> SRR2001064 2 0.2778 0.937 0.000 0.824 0.000 0.168 NA NA
#> SRR2001065 2 0.2877 0.938 0.000 0.820 0.000 0.168 NA NA
#> SRR2001066 2 0.3122 0.939 0.000 0.804 0.000 0.176 NA NA
#> SRR2001067 2 0.2877 0.937 0.000 0.820 0.000 0.168 NA NA
#> SRR2001060 4 0.1332 0.952 0.000 0.028 0.000 0.952 NA NA
#> SRR2001061 4 0.1194 0.955 0.000 0.032 0.000 0.956 NA NA
#> SRR2001062 4 0.1523 0.949 0.000 0.044 0.000 0.940 NA NA
#> SRR2001063 4 0.1409 0.953 0.000 0.032 0.000 0.948 NA NA
#> SRR2001056 4 0.1332 0.948 0.000 0.028 0.000 0.952 NA NA
#> SRR2001057 4 0.1332 0.948 0.000 0.028 0.000 0.952 NA NA
#> SRR2001058 4 0.1434 0.947 0.000 0.028 0.000 0.948 NA NA
#> SRR2001059 4 0.1434 0.947 0.000 0.028 0.000 0.948 NA NA
#> SRR2001052 2 0.3504 0.930 0.000 0.776 0.000 0.196 NA NA
#> SRR2001053 2 0.3473 0.929 0.000 0.780 0.000 0.192 NA NA
#> SRR2001054 2 0.3550 0.928 0.000 0.780 0.000 0.188 NA NA
#> SRR2001055 2 0.3582 0.928 0.000 0.776 0.000 0.192 NA NA
#> SRR2001048 2 0.4327 0.867 0.000 0.676 0.000 0.284 NA NA
#> SRR2001049 2 0.4225 0.891 0.000 0.696 0.000 0.264 NA NA
#> SRR2001050 2 0.4268 0.896 0.000 0.700 0.000 0.256 NA NA
#> SRR2001051 2 0.4361 0.890 0.000 0.692 0.000 0.260 NA NA
#> SRR2001044 4 0.0935 0.958 0.000 0.032 0.000 0.964 NA NA
#> SRR2001045 4 0.1007 0.956 0.000 0.044 0.000 0.956 NA NA
#> SRR2001046 4 0.0937 0.956 0.000 0.040 0.000 0.960 NA NA
#> SRR2001047 4 0.1007 0.956 0.000 0.044 0.000 0.956 NA NA
#> SRR2001040 4 0.0603 0.950 0.000 0.016 0.000 0.980 NA NA
#> SRR2001041 4 0.0508 0.952 0.000 0.012 0.000 0.984 NA NA
#> SRR2001042 4 0.0508 0.952 0.000 0.012 0.000 0.984 NA NA
#> SRR2001043 4 0.0603 0.950 0.000 0.016 0.000 0.980 NA NA
#> SRR2001036 4 0.0146 0.951 0.000 0.000 0.000 0.996 NA NA
#> SRR2001037 4 0.0146 0.951 0.000 0.000 0.000 0.996 NA NA
#> SRR2001038 4 0.0000 0.951 0.000 0.000 0.000 1.000 NA NA
#> SRR2001039 4 0.0146 0.951 0.000 0.000 0.000 0.996 NA NA
#> SRR2001028 4 0.1007 0.956 0.000 0.044 0.000 0.956 NA NA
#> SRR2001029 4 0.1075 0.955 0.000 0.048 0.000 0.952 NA NA
#> SRR2001030 4 0.1007 0.955 0.000 0.044 0.000 0.956 NA NA
#> SRR2001031 4 0.1075 0.955 0.000 0.048 0.000 0.952 NA NA
#> SRR2001024 4 0.0632 0.957 0.000 0.024 0.000 0.976 NA NA
#> SRR2001025 4 0.0547 0.956 0.000 0.020 0.000 0.980 NA NA
#> SRR2001026 4 0.0547 0.955 0.000 0.020 0.000 0.980 NA NA
#> SRR2001027 4 0.0547 0.955 0.000 0.020 0.000 0.980 NA NA
#> SRR2001020 2 0.3964 0.908 0.000 0.724 0.000 0.232 NA NA
#> SRR2001021 2 0.3874 0.912 0.000 0.732 0.000 0.228 NA NA
#> SRR2001022 2 0.4051 0.912 0.000 0.728 0.000 0.224 NA NA
#> SRR2001023 2 0.3900 0.910 0.000 0.728 0.000 0.232 NA NA
#> SRR2001016 4 0.2786 0.867 0.000 0.100 0.000 0.864 NA NA
#> SRR2001017 4 0.2687 0.878 0.000 0.092 0.000 0.872 NA NA
#> SRR2001018 4 0.2786 0.867 0.000 0.100 0.000 0.864 NA NA
#> SRR2001019 4 0.2880 0.855 0.000 0.108 0.000 0.856 NA NA
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 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 1.000 1.000 0.5031 0.497 0.497
#> 3 3 1.000 1.000 1.000 0.2206 0.889 0.777
#> 4 4 0.840 0.889 0.922 0.0927 0.951 0.874
#> 5 5 0.870 0.888 0.936 0.1715 0.870 0.615
#> 6 6 0.859 0.831 0.870 0.0306 1.000 1.000
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0 1 0 1 0
#> SRR2001033 2 0 1 0 1 0
#> SRR2001034 2 0 1 0 1 0
#> SRR2001035 2 0 1 0 1 0
#> SRR2001204 1 0 1 1 0 0
#> SRR2001205 1 0 1 1 0 0
#> SRR2001206 1 0 1 1 0 0
#> SRR2001207 1 0 1 1 0 0
#> SRR2001200 1 0 1 1 0 0
#> SRR2001201 1 0 1 1 0 0
#> SRR2001202 1 0 1 1 0 0
#> SRR2001203 1 0 1 1 0 0
#> SRR2001196 1 0 1 1 0 0
#> SRR2001197 1 0 1 1 0 0
#> SRR2001198 1 0 1 1 0 0
#> SRR2001199 1 0 1 1 0 0
#> SRR2001192 3 0 1 0 0 1
#> SRR2001193 3 0 1 0 0 1
#> SRR2001194 3 0 1 0 0 1
#> SRR2001195 3 0 1 0 0 1
#> SRR2001188 1 0 1 1 0 0
#> SRR2001189 1 0 1 1 0 0
#> SRR2001190 1 0 1 1 0 0
#> SRR2001191 1 0 1 1 0 0
#> SRR2001184 3 0 1 0 0 1
#> SRR2001185 3 0 1 0 0 1
#> SRR2001186 3 0 1 0 0 1
#> SRR2001187 3 0 1 0 0 1
#> SRR2001180 1 0 1 1 0 0
#> SRR2001181 1 0 1 1 0 0
#> SRR2001182 1 0 1 1 0 0
#> SRR2001183 1 0 1 1 0 0
#> SRR2001176 3 0 1 0 0 1
#> SRR2001177 3 0 1 0 0 1
#> SRR2001178 3 0 1 0 0 1
#> SRR2001179 3 0 1 0 0 1
#> SRR2001172 3 0 1 0 0 1
#> SRR2001173 3 0 1 0 0 1
#> SRR2001174 3 0 1 0 0 1
#> SRR2001175 3 0 1 0 0 1
#> SRR2001168 1 0 1 1 0 0
#> SRR2001169 1 0 1 1 0 0
#> SRR2001170 1 0 1 1 0 0
#> SRR2001171 1 0 1 1 0 0
#> SRR2001164 1 0 1 1 0 0
#> SRR2001165 1 0 1 1 0 0
#> SRR2001166 1 0 1 1 0 0
#> SRR2001167 1 0 1 1 0 0
#> SRR2001160 1 0 1 1 0 0
#> SRR2001161 1 0 1 1 0 0
#> SRR2001162 1 0 1 1 0 0
#> SRR2001163 1 0 1 1 0 0
#> SRR2001156 1 0 1 1 0 0
#> SRR2001157 1 0 1 1 0 0
#> SRR2001158 1 0 1 1 0 0
#> SRR2001159 1 0 1 1 0 0
#> SRR2001152 1 0 1 1 0 0
#> SRR2001153 1 0 1 1 0 0
#> SRR2001154 1 0 1 1 0 0
#> SRR2001155 1 0 1 1 0 0
#> SRR2001148 3 0 1 0 0 1
#> SRR2001149 3 0 1 0 0 1
#> SRR2001150 3 0 1 0 0 1
#> SRR2001151 3 0 1 0 0 1
#> SRR2001144 1 0 1 1 0 0
#> SRR2001145 1 0 1 1 0 0
#> SRR2001146 1 0 1 1 0 0
#> SRR2001147 1 0 1 1 0 0
#> SRR2001140 1 0 1 1 0 0
#> SRR2001142 1 0 1 1 0 0
#> SRR2001143 1 0 1 1 0 0
#> SRR2001136 3 0 1 0 0 1
#> SRR2001137 3 0 1 0 0 1
#> SRR2001138 3 0 1 0 0 1
#> SRR2001139 3 0 1 0 0 1
#> SRR2001132 3 0 1 0 0 1
#> SRR2001133 3 0 1 0 0 1
#> SRR2001134 3 0 1 0 0 1
#> SRR2001135 3 0 1 0 0 1
#> SRR2001128 1 0 1 1 0 0
#> SRR2001129 1 0 1 1 0 0
#> SRR2001130 1 0 1 1 0 0
#> SRR2001131 1 0 1 1 0 0
#> SRR2001124 1 0 1 1 0 0
#> SRR2001125 1 0 1 1 0 0
#> SRR2001126 1 0 1 1 0 0
#> SRR2001127 1 0 1 1 0 0
#> SRR2001120 1 0 1 1 0 0
#> SRR2001121 1 0 1 1 0 0
#> SRR2001122 1 0 1 1 0 0
#> SRR2001123 1 0 1 1 0 0
#> SRR2001116 1 0 1 1 0 0
#> SRR2001117 1 0 1 1 0 0
#> SRR2001118 1 0 1 1 0 0
#> SRR2001119 1 0 1 1 0 0
#> SRR2001112 3 0 1 0 0 1
#> SRR2001113 3 0 1 0 0 1
#> SRR2001114 3 0 1 0 0 1
#> SRR2001115 3 0 1 0 0 1
#> SRR2001108 2 0 1 0 1 0
#> SRR2001109 2 0 1 0 1 0
#> SRR2001110 2 0 1 0 1 0
#> SRR2001111 2 0 1 0 1 0
#> SRR2001104 2 0 1 0 1 0
#> SRR2001105 2 0 1 0 1 0
#> SRR2001106 2 0 1 0 1 0
#> SRR2001107 2 0 1 0 1 0
#> SRR2001100 2 0 1 0 1 0
#> SRR2001101 2 0 1 0 1 0
#> SRR2001102 2 0 1 0 1 0
#> SRR2001103 2 0 1 0 1 0
#> SRR2001096 2 0 1 0 1 0
#> SRR2001097 2 0 1 0 1 0
#> SRR2001098 2 0 1 0 1 0
#> SRR2001099 2 0 1 0 1 0
#> SRR2001092 2 0 1 0 1 0
#> SRR2001093 2 0 1 0 1 0
#> SRR2001094 2 0 1 0 1 0
#> SRR2001095 2 0 1 0 1 0
#> SRR2001088 2 0 1 0 1 0
#> SRR2001089 2 0 1 0 1 0
#> SRR2001090 2 0 1 0 1 0
#> SRR2001091 2 0 1 0 1 0
#> SRR2001084 2 0 1 0 1 0
#> SRR2001085 2 0 1 0 1 0
#> SRR2001086 2 0 1 0 1 0
#> SRR2001087 2 0 1 0 1 0
#> SRR2001080 2 0 1 0 1 0
#> SRR2001081 2 0 1 0 1 0
#> SRR2001082 2 0 1 0 1 0
#> SRR2001083 2 0 1 0 1 0
#> SRR2001076 2 0 1 0 1 0
#> SRR2001077 2 0 1 0 1 0
#> SRR2001078 2 0 1 0 1 0
#> SRR2001079 2 0 1 0 1 0
#> SRR2001072 2 0 1 0 1 0
#> SRR2001073 2 0 1 0 1 0
#> SRR2001074 2 0 1 0 1 0
#> SRR2001075 2 0 1 0 1 0
#> SRR2001068 2 0 1 0 1 0
#> SRR2001069 2 0 1 0 1 0
#> SRR2001070 2 0 1 0 1 0
#> SRR2001071 2 0 1 0 1 0
#> SRR2001064 2 0 1 0 1 0
#> SRR2001065 2 0 1 0 1 0
#> SRR2001066 2 0 1 0 1 0
#> SRR2001067 2 0 1 0 1 0
#> SRR2001060 2 0 1 0 1 0
#> SRR2001061 2 0 1 0 1 0
#> SRR2001062 2 0 1 0 1 0
#> SRR2001063 2 0 1 0 1 0
#> SRR2001056 2 0 1 0 1 0
#> SRR2001057 2 0 1 0 1 0
#> SRR2001058 2 0 1 0 1 0
#> SRR2001059 2 0 1 0 1 0
#> SRR2001052 2 0 1 0 1 0
#> SRR2001053 2 0 1 0 1 0
#> SRR2001054 2 0 1 0 1 0
#> SRR2001055 2 0 1 0 1 0
#> SRR2001048 2 0 1 0 1 0
#> SRR2001049 2 0 1 0 1 0
#> SRR2001050 2 0 1 0 1 0
#> SRR2001051 2 0 1 0 1 0
#> SRR2001044 2 0 1 0 1 0
#> SRR2001045 2 0 1 0 1 0
#> SRR2001046 2 0 1 0 1 0
#> SRR2001047 2 0 1 0 1 0
#> SRR2001040 2 0 1 0 1 0
#> SRR2001041 2 0 1 0 1 0
#> SRR2001042 2 0 1 0 1 0
#> SRR2001043 2 0 1 0 1 0
#> SRR2001036 2 0 1 0 1 0
#> SRR2001037 2 0 1 0 1 0
#> SRR2001038 2 0 1 0 1 0
#> SRR2001039 2 0 1 0 1 0
#> SRR2001028 2 0 1 0 1 0
#> SRR2001029 2 0 1 0 1 0
#> SRR2001030 2 0 1 0 1 0
#> SRR2001031 2 0 1 0 1 0
#> SRR2001024 2 0 1 0 1 0
#> SRR2001025 2 0 1 0 1 0
#> SRR2001026 2 0 1 0 1 0
#> SRR2001027 2 0 1 0 1 0
#> SRR2001020 2 0 1 0 1 0
#> SRR2001021 2 0 1 0 1 0
#> SRR2001022 2 0 1 0 1 0
#> SRR2001023 2 0 1 0 1 0
#> SRR2001016 2 0 1 0 1 0
#> SRR2001017 2 0 1 0 1 0
#> SRR2001018 2 0 1 0 1 0
#> SRR2001019 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 4 0.0188 0.951 0.000 0.004 0 0.996
#> SRR2001033 4 0.0336 0.952 0.000 0.008 0 0.992
#> SRR2001034 4 0.0188 0.951 0.000 0.004 0 0.996
#> SRR2001035 4 0.0188 0.951 0.000 0.004 0 0.996
#> SRR2001204 2 0.2868 0.846 0.136 0.864 0 0.000
#> SRR2001205 2 0.2868 0.846 0.136 0.864 0 0.000
#> SRR2001206 2 0.2868 0.846 0.136 0.864 0 0.000
#> SRR2001207 2 0.2868 0.846 0.136 0.864 0 0.000
#> SRR2001200 1 0.0000 0.849 1.000 0.000 0 0.000
#> SRR2001201 1 0.0188 0.848 0.996 0.004 0 0.000
#> SRR2001202 1 0.0000 0.849 1.000 0.000 0 0.000
#> SRR2001203 1 0.0000 0.849 1.000 0.000 0 0.000
#> SRR2001196 1 0.0336 0.853 0.992 0.008 0 0.000
#> SRR2001197 1 0.0336 0.853 0.992 0.008 0 0.000
#> SRR2001198 1 0.0188 0.851 0.996 0.004 0 0.000
#> SRR2001199 1 0.0469 0.855 0.988 0.012 0 0.000
#> SRR2001192 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001193 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001194 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001195 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001188 1 0.2814 0.821 0.868 0.132 0 0.000
#> SRR2001189 1 0.2530 0.831 0.888 0.112 0 0.000
#> SRR2001190 1 0.2868 0.816 0.864 0.136 0 0.000
#> SRR2001191 1 0.3074 0.803 0.848 0.152 0 0.000
#> SRR2001184 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001185 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001186 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001187 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001180 1 0.2081 0.851 0.916 0.084 0 0.000
#> SRR2001181 1 0.2081 0.850 0.916 0.084 0 0.000
#> SRR2001182 1 0.2589 0.825 0.884 0.116 0 0.000
#> SRR2001183 1 0.3172 0.780 0.840 0.160 0 0.000
#> SRR2001176 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001177 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001178 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001179 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001172 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001173 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001174 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001175 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001168 2 0.2814 0.843 0.132 0.868 0 0.000
#> SRR2001169 2 0.2760 0.841 0.128 0.872 0 0.000
#> SRR2001170 2 0.2814 0.843 0.132 0.868 0 0.000
#> SRR2001171 2 0.2868 0.846 0.136 0.864 0 0.000
#> SRR2001164 1 0.1022 0.856 0.968 0.032 0 0.000
#> SRR2001165 1 0.1389 0.857 0.952 0.048 0 0.000
#> SRR2001166 1 0.1474 0.857 0.948 0.052 0 0.000
#> SRR2001167 1 0.1022 0.856 0.968 0.032 0 0.000
#> SRR2001160 1 0.2589 0.821 0.884 0.116 0 0.000
#> SRR2001161 1 0.2868 0.806 0.864 0.136 0 0.000
#> SRR2001162 1 0.2345 0.836 0.900 0.100 0 0.000
#> SRR2001163 1 0.3074 0.793 0.848 0.152 0 0.000
#> SRR2001156 1 0.0188 0.851 0.996 0.004 0 0.000
#> SRR2001157 1 0.0707 0.856 0.980 0.020 0 0.000
#> SRR2001158 1 0.0336 0.853 0.992 0.008 0 0.000
#> SRR2001159 1 0.0336 0.853 0.992 0.008 0 0.000
#> SRR2001152 2 0.4992 0.332 0.476 0.524 0 0.000
#> SRR2001153 1 0.4888 0.145 0.588 0.412 0 0.000
#> SRR2001154 1 0.4989 -0.172 0.528 0.472 0 0.000
#> SRR2001155 2 0.4888 0.535 0.412 0.588 0 0.000
#> SRR2001148 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001149 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001150 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001151 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001144 2 0.4103 0.789 0.256 0.744 0 0.000
#> SRR2001145 2 0.3801 0.813 0.220 0.780 0 0.000
#> SRR2001146 2 0.4605 0.680 0.336 0.664 0 0.000
#> SRR2001147 2 0.4304 0.763 0.284 0.716 0 0.000
#> SRR2001140 2 0.4898 0.532 0.416 0.584 0 0.000
#> SRR2001142 2 0.4776 0.618 0.376 0.624 0 0.000
#> SRR2001143 2 0.4933 0.474 0.432 0.568 0 0.000
#> SRR2001136 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001137 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001138 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001139 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001132 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001133 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001134 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001135 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001128 1 0.2216 0.846 0.908 0.092 0 0.000
#> SRR2001129 1 0.2530 0.833 0.888 0.112 0 0.000
#> SRR2001130 1 0.2760 0.823 0.872 0.128 0 0.000
#> SRR2001131 1 0.2973 0.806 0.856 0.144 0 0.000
#> SRR2001124 1 0.0592 0.855 0.984 0.016 0 0.000
#> SRR2001125 1 0.1637 0.853 0.940 0.060 0 0.000
#> SRR2001126 1 0.0707 0.856 0.980 0.020 0 0.000
#> SRR2001127 1 0.0592 0.855 0.984 0.016 0 0.000
#> SRR2001120 2 0.3172 0.841 0.160 0.840 0 0.000
#> SRR2001121 2 0.3123 0.845 0.156 0.844 0 0.000
#> SRR2001122 2 0.3074 0.846 0.152 0.848 0 0.000
#> SRR2001123 2 0.3024 0.844 0.148 0.852 0 0.000
#> SRR2001116 1 0.4888 0.144 0.588 0.412 0 0.000
#> SRR2001117 1 0.4898 0.116 0.584 0.416 0 0.000
#> SRR2001118 1 0.4776 0.275 0.624 0.376 0 0.000
#> SRR2001119 1 0.4804 0.241 0.616 0.384 0 0.000
#> SRR2001112 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001113 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001114 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001115 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001108 4 0.2011 0.953 0.000 0.080 0 0.920
#> SRR2001109 4 0.1940 0.953 0.000 0.076 0 0.924
#> SRR2001110 4 0.1940 0.953 0.000 0.076 0 0.924
#> SRR2001111 4 0.1940 0.953 0.000 0.076 0 0.924
#> SRR2001104 4 0.1022 0.945 0.000 0.032 0 0.968
#> SRR2001105 4 0.1022 0.945 0.000 0.032 0 0.968
#> SRR2001106 4 0.1022 0.945 0.000 0.032 0 0.968
#> SRR2001107 4 0.1022 0.945 0.000 0.032 0 0.968
#> SRR2001100 4 0.0592 0.949 0.000 0.016 0 0.984
#> SRR2001101 4 0.1022 0.945 0.000 0.032 0 0.968
#> SRR2001102 4 0.0592 0.949 0.000 0.016 0 0.984
#> SRR2001103 4 0.0921 0.946 0.000 0.028 0 0.972
#> SRR2001096 4 0.1118 0.944 0.000 0.036 0 0.964
#> SRR2001097 4 0.1118 0.944 0.000 0.036 0 0.964
#> SRR2001098 4 0.1118 0.944 0.000 0.036 0 0.964
#> SRR2001099 4 0.1118 0.944 0.000 0.036 0 0.964
#> SRR2001092 4 0.1118 0.944 0.000 0.036 0 0.964
#> SRR2001093 4 0.1022 0.945 0.000 0.032 0 0.968
#> SRR2001094 4 0.1022 0.945 0.000 0.032 0 0.968
#> SRR2001095 4 0.1022 0.945 0.000 0.032 0 0.968
#> SRR2001088 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001089 4 0.2081 0.951 0.000 0.084 0 0.916
#> SRR2001090 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001091 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001084 4 0.2081 0.952 0.000 0.084 0 0.916
#> SRR2001085 4 0.2011 0.953 0.000 0.080 0 0.920
#> SRR2001086 4 0.2081 0.952 0.000 0.084 0 0.916
#> SRR2001087 4 0.2081 0.952 0.000 0.084 0 0.916
#> SRR2001080 4 0.1022 0.945 0.000 0.032 0 0.968
#> SRR2001081 4 0.1022 0.945 0.000 0.032 0 0.968
#> SRR2001082 4 0.1022 0.945 0.000 0.032 0 0.968
#> SRR2001083 4 0.1022 0.945 0.000 0.032 0 0.968
#> SRR2001076 4 0.1118 0.944 0.000 0.036 0 0.964
#> SRR2001077 4 0.1022 0.945 0.000 0.032 0 0.968
#> SRR2001078 4 0.1022 0.945 0.000 0.032 0 0.968
#> SRR2001079 4 0.1022 0.945 0.000 0.032 0 0.968
#> SRR2001072 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001073 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001074 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001075 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001068 4 0.0188 0.951 0.000 0.004 0 0.996
#> SRR2001069 4 0.0188 0.951 0.000 0.004 0 0.996
#> SRR2001070 4 0.0188 0.951 0.000 0.004 0 0.996
#> SRR2001071 4 0.0188 0.951 0.000 0.004 0 0.996
#> SRR2001064 4 0.1118 0.944 0.000 0.036 0 0.964
#> SRR2001065 4 0.1118 0.944 0.000 0.036 0 0.964
#> SRR2001066 4 0.1118 0.944 0.000 0.036 0 0.964
#> SRR2001067 4 0.1118 0.944 0.000 0.036 0 0.964
#> SRR2001060 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001061 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001062 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001063 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001056 4 0.2081 0.952 0.000 0.084 0 0.916
#> SRR2001057 4 0.2081 0.952 0.000 0.084 0 0.916
#> SRR2001058 4 0.2081 0.952 0.000 0.084 0 0.916
#> SRR2001059 4 0.2149 0.951 0.000 0.088 0 0.912
#> SRR2001052 4 0.0188 0.951 0.000 0.004 0 0.996
#> SRR2001053 4 0.0469 0.950 0.000 0.012 0 0.988
#> SRR2001054 4 0.0188 0.951 0.000 0.004 0 0.996
#> SRR2001055 4 0.0188 0.951 0.000 0.004 0 0.996
#> SRR2001048 4 0.0188 0.951 0.000 0.004 0 0.996
#> SRR2001049 4 0.0188 0.951 0.000 0.004 0 0.996
#> SRR2001050 4 0.0188 0.951 0.000 0.004 0 0.996
#> SRR2001051 4 0.0188 0.951 0.000 0.004 0 0.996
#> SRR2001044 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001045 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001046 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001047 4 0.2081 0.951 0.000 0.084 0 0.916
#> SRR2001040 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001041 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001042 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001043 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001036 4 0.2081 0.951 0.000 0.084 0 0.916
#> SRR2001037 4 0.2011 0.952 0.000 0.080 0 0.920
#> SRR2001038 4 0.2149 0.951 0.000 0.088 0 0.912
#> SRR2001039 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001028 4 0.2081 0.951 0.000 0.084 0 0.916
#> SRR2001029 4 0.2281 0.950 0.000 0.096 0 0.904
#> SRR2001030 4 0.2408 0.950 0.000 0.104 0 0.896
#> SRR2001031 4 0.2216 0.951 0.000 0.092 0 0.908
#> SRR2001024 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001025 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001026 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001027 4 0.2149 0.950 0.000 0.088 0 0.912
#> SRR2001020 4 0.1022 0.945 0.000 0.032 0 0.968
#> SRR2001021 4 0.1022 0.945 0.000 0.032 0 0.968
#> SRR2001022 4 0.1022 0.945 0.000 0.032 0 0.968
#> SRR2001023 4 0.1022 0.945 0.000 0.032 0 0.968
#> SRR2001016 4 0.2081 0.952 0.000 0.084 0 0.916
#> SRR2001017 4 0.2011 0.952 0.000 0.080 0 0.920
#> SRR2001018 4 0.2011 0.952 0.000 0.080 0 0.920
#> SRR2001019 4 0.2011 0.952 0.000 0.080 0 0.920
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.2605 0.8772 0.000 0.852 0 0.148 0.000
#> SRR2001033 2 0.2891 0.8530 0.000 0.824 0 0.176 0.000
#> SRR2001034 2 0.2329 0.8907 0.000 0.876 0 0.124 0.000
#> SRR2001035 2 0.2605 0.8772 0.000 0.852 0 0.148 0.000
#> SRR2001204 5 0.0404 0.8263 0.012 0.000 0 0.000 0.988
#> SRR2001205 5 0.0404 0.8263 0.012 0.000 0 0.000 0.988
#> SRR2001206 5 0.0404 0.8263 0.012 0.000 0 0.000 0.988
#> SRR2001207 5 0.0404 0.8263 0.012 0.000 0 0.000 0.988
#> SRR2001200 1 0.0162 0.8573 0.996 0.004 0 0.000 0.000
#> SRR2001201 1 0.0324 0.8564 0.992 0.004 0 0.000 0.004
#> SRR2001202 1 0.0162 0.8573 0.996 0.004 0 0.000 0.000
#> SRR2001203 1 0.0000 0.8572 1.000 0.000 0 0.000 0.000
#> SRR2001196 1 0.0566 0.8624 0.984 0.004 0 0.000 0.012
#> SRR2001197 1 0.0566 0.8620 0.984 0.004 0 0.000 0.012
#> SRR2001198 1 0.0290 0.8610 0.992 0.000 0 0.000 0.008
#> SRR2001199 1 0.0671 0.8638 0.980 0.004 0 0.000 0.016
#> SRR2001192 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001193 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001194 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001195 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001188 1 0.2852 0.8085 0.828 0.000 0 0.000 0.172
#> SRR2001189 1 0.2806 0.8200 0.844 0.004 0 0.000 0.152
#> SRR2001190 1 0.2648 0.8255 0.848 0.000 0 0.000 0.152
#> SRR2001191 1 0.2891 0.8073 0.824 0.000 0 0.000 0.176
#> SRR2001184 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001185 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001186 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001187 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001180 1 0.2124 0.8594 0.900 0.004 0 0.000 0.096
#> SRR2001181 1 0.1952 0.8622 0.912 0.004 0 0.000 0.084
#> SRR2001182 1 0.2377 0.8354 0.872 0.000 0 0.000 0.128
#> SRR2001183 1 0.2891 0.7920 0.824 0.000 0 0.000 0.176
#> SRR2001176 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001177 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001178 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001179 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001172 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001173 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001174 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001175 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001168 5 0.0290 0.8238 0.008 0.000 0 0.000 0.992
#> SRR2001169 5 0.0162 0.8217 0.004 0.000 0 0.000 0.996
#> SRR2001170 5 0.0290 0.8238 0.008 0.000 0 0.000 0.992
#> SRR2001171 5 0.0404 0.8260 0.012 0.000 0 0.000 0.988
#> SRR2001164 1 0.0963 0.8650 0.964 0.000 0 0.000 0.036
#> SRR2001165 1 0.1410 0.8659 0.940 0.000 0 0.000 0.060
#> SRR2001166 1 0.1410 0.8659 0.940 0.000 0 0.000 0.060
#> SRR2001167 1 0.0963 0.8654 0.964 0.000 0 0.000 0.036
#> SRR2001160 1 0.2377 0.8313 0.872 0.000 0 0.000 0.128
#> SRR2001161 1 0.2648 0.8159 0.848 0.000 0 0.000 0.152
#> SRR2001162 1 0.2179 0.8448 0.888 0.000 0 0.000 0.112
#> SRR2001163 1 0.2813 0.8053 0.832 0.000 0 0.000 0.168
#> SRR2001156 1 0.0162 0.8591 0.996 0.000 0 0.000 0.004
#> SRR2001157 1 0.0794 0.8658 0.972 0.000 0 0.000 0.028
#> SRR2001158 1 0.0290 0.8614 0.992 0.000 0 0.000 0.008
#> SRR2001159 1 0.0404 0.8626 0.988 0.000 0 0.000 0.012
#> SRR2001152 5 0.4182 0.3639 0.400 0.000 0 0.000 0.600
#> SRR2001153 1 0.4283 0.1633 0.544 0.000 0 0.000 0.456
#> SRR2001154 5 0.4302 0.0839 0.480 0.000 0 0.000 0.520
#> SRR2001155 5 0.3949 0.5483 0.332 0.000 0 0.000 0.668
#> SRR2001148 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001149 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001150 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001151 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001144 5 0.2690 0.7744 0.156 0.000 0 0.000 0.844
#> SRR2001145 5 0.2280 0.7941 0.120 0.000 0 0.000 0.880
#> SRR2001146 5 0.3366 0.6972 0.232 0.000 0 0.000 0.768
#> SRR2001147 5 0.3210 0.7306 0.212 0.000 0 0.000 0.788
#> SRR2001140 5 0.3895 0.5761 0.320 0.000 0 0.000 0.680
#> SRR2001142 5 0.3752 0.6233 0.292 0.000 0 0.000 0.708
#> SRR2001143 5 0.3983 0.5236 0.340 0.000 0 0.000 0.660
#> SRR2001136 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001137 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001138 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001139 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001132 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001133 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001134 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001135 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001128 1 0.2074 0.8548 0.896 0.000 0 0.000 0.104
#> SRR2001129 1 0.2424 0.8383 0.868 0.000 0 0.000 0.132
#> SRR2001130 1 0.2648 0.8253 0.848 0.000 0 0.000 0.152
#> SRR2001131 1 0.2929 0.7981 0.820 0.000 0 0.000 0.180
#> SRR2001124 1 0.0671 0.8632 0.980 0.004 0 0.000 0.016
#> SRR2001125 1 0.1831 0.8597 0.920 0.004 0 0.000 0.076
#> SRR2001126 1 0.0703 0.8654 0.976 0.000 0 0.000 0.024
#> SRR2001127 1 0.0609 0.8645 0.980 0.000 0 0.000 0.020
#> SRR2001120 5 0.1121 0.8230 0.044 0.000 0 0.000 0.956
#> SRR2001121 5 0.1121 0.8244 0.044 0.000 0 0.000 0.956
#> SRR2001122 5 0.0880 0.8267 0.032 0.000 0 0.000 0.968
#> SRR2001123 5 0.0880 0.8247 0.032 0.000 0 0.000 0.968
#> SRR2001116 1 0.4278 0.1806 0.548 0.000 0 0.000 0.452
#> SRR2001117 1 0.4297 0.0979 0.528 0.000 0 0.000 0.472
#> SRR2001118 1 0.4249 0.2353 0.568 0.000 0 0.000 0.432
#> SRR2001119 1 0.4273 0.1800 0.552 0.000 0 0.000 0.448
#> SRR2001112 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001113 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001114 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001115 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001108 4 0.1043 0.9705 0.000 0.040 0 0.960 0.000
#> SRR2001109 4 0.1121 0.9670 0.000 0.044 0 0.956 0.000
#> SRR2001110 4 0.1121 0.9639 0.000 0.044 0 0.956 0.000
#> SRR2001111 4 0.0880 0.9734 0.000 0.032 0 0.968 0.000
#> SRR2001104 2 0.0510 0.9318 0.000 0.984 0 0.016 0.000
#> SRR2001105 2 0.0609 0.9325 0.000 0.980 0 0.020 0.000
#> SRR2001106 2 0.0703 0.9332 0.000 0.976 0 0.024 0.000
#> SRR2001107 2 0.0609 0.9325 0.000 0.980 0 0.020 0.000
#> SRR2001100 2 0.1478 0.9231 0.000 0.936 0 0.064 0.000
#> SRR2001101 2 0.1043 0.9288 0.000 0.960 0 0.040 0.000
#> SRR2001102 2 0.1478 0.9231 0.000 0.936 0 0.064 0.000
#> SRR2001103 2 0.1270 0.9267 0.000 0.948 0 0.052 0.000
#> SRR2001096 2 0.0162 0.9299 0.000 0.996 0 0.004 0.000
#> SRR2001097 2 0.0162 0.9299 0.000 0.996 0 0.004 0.000
#> SRR2001098 2 0.0162 0.9299 0.000 0.996 0 0.004 0.000
#> SRR2001099 2 0.0162 0.9299 0.000 0.996 0 0.004 0.000
#> SRR2001092 2 0.0404 0.9316 0.000 0.988 0 0.012 0.000
#> SRR2001093 2 0.0510 0.9318 0.000 0.984 0 0.016 0.000
#> SRR2001094 2 0.0510 0.9318 0.000 0.984 0 0.016 0.000
#> SRR2001095 2 0.0609 0.9325 0.000 0.980 0 0.020 0.000
#> SRR2001088 4 0.0162 0.9825 0.000 0.004 0 0.996 0.000
#> SRR2001089 4 0.0510 0.9822 0.000 0.016 0 0.984 0.000
#> SRR2001090 4 0.0290 0.9837 0.000 0.008 0 0.992 0.000
#> SRR2001091 4 0.0290 0.9837 0.000 0.008 0 0.992 0.000
#> SRR2001084 4 0.0609 0.9789 0.000 0.020 0 0.980 0.000
#> SRR2001085 4 0.0703 0.9782 0.000 0.024 0 0.976 0.000
#> SRR2001086 4 0.0703 0.9780 0.000 0.024 0 0.976 0.000
#> SRR2001087 4 0.0703 0.9780 0.000 0.024 0 0.976 0.000
#> SRR2001080 2 0.0703 0.9332 0.000 0.976 0 0.024 0.000
#> SRR2001081 2 0.0510 0.9318 0.000 0.984 0 0.016 0.000
#> SRR2001082 2 0.0703 0.9333 0.000 0.976 0 0.024 0.000
#> SRR2001083 2 0.0609 0.9325 0.000 0.980 0 0.020 0.000
#> SRR2001076 2 0.0510 0.9331 0.000 0.984 0 0.016 0.000
#> SRR2001077 2 0.0609 0.9325 0.000 0.980 0 0.020 0.000
#> SRR2001078 2 0.0510 0.9318 0.000 0.984 0 0.016 0.000
#> SRR2001079 2 0.0703 0.9332 0.000 0.976 0 0.024 0.000
#> SRR2001072 4 0.0290 0.9837 0.000 0.008 0 0.992 0.000
#> SRR2001073 4 0.0290 0.9837 0.000 0.008 0 0.992 0.000
#> SRR2001074 4 0.0290 0.9837 0.000 0.008 0 0.992 0.000
#> SRR2001075 4 0.0290 0.9837 0.000 0.008 0 0.992 0.000
#> SRR2001068 2 0.2852 0.8565 0.000 0.828 0 0.172 0.000
#> SRR2001069 2 0.2852 0.8565 0.000 0.828 0 0.172 0.000
#> SRR2001070 2 0.2648 0.8743 0.000 0.848 0 0.152 0.000
#> SRR2001071 2 0.2732 0.8681 0.000 0.840 0 0.160 0.000
#> SRR2001064 2 0.0162 0.9299 0.000 0.996 0 0.004 0.000
#> SRR2001065 2 0.0162 0.9299 0.000 0.996 0 0.004 0.000
#> SRR2001066 2 0.0290 0.9310 0.000 0.992 0 0.008 0.000
#> SRR2001067 2 0.0162 0.9299 0.000 0.996 0 0.004 0.000
#> SRR2001060 4 0.0290 0.9837 0.000 0.008 0 0.992 0.000
#> SRR2001061 4 0.0162 0.9825 0.000 0.004 0 0.996 0.000
#> SRR2001062 4 0.0290 0.9837 0.000 0.008 0 0.992 0.000
#> SRR2001063 4 0.0162 0.9834 0.000 0.004 0 0.996 0.000
#> SRR2001056 4 0.0609 0.9789 0.000 0.020 0 0.980 0.000
#> SRR2001057 4 0.0609 0.9789 0.000 0.020 0 0.980 0.000
#> SRR2001058 4 0.0609 0.9789 0.000 0.020 0 0.980 0.000
#> SRR2001059 4 0.0510 0.9791 0.000 0.016 0 0.984 0.000
#> SRR2001052 2 0.2561 0.8799 0.000 0.856 0 0.144 0.000
#> SRR2001053 2 0.2127 0.8981 0.000 0.892 0 0.108 0.000
#> SRR2001054 2 0.2561 0.8799 0.000 0.856 0 0.144 0.000
#> SRR2001055 2 0.2561 0.8799 0.000 0.856 0 0.144 0.000
#> SRR2001048 2 0.2813 0.8610 0.000 0.832 0 0.168 0.000
#> SRR2001049 2 0.2732 0.8697 0.000 0.840 0 0.160 0.000
#> SRR2001050 2 0.2690 0.8715 0.000 0.844 0 0.156 0.000
#> SRR2001051 2 0.2690 0.8715 0.000 0.844 0 0.156 0.000
#> SRR2001044 4 0.0404 0.9826 0.000 0.012 0 0.988 0.000
#> SRR2001045 4 0.0510 0.9809 0.000 0.016 0 0.984 0.000
#> SRR2001046 4 0.0404 0.9826 0.000 0.012 0 0.988 0.000
#> SRR2001047 4 0.0963 0.9677 0.000 0.036 0 0.964 0.000
#> SRR2001040 4 0.0290 0.9837 0.000 0.008 0 0.992 0.000
#> SRR2001041 4 0.0290 0.9837 0.000 0.008 0 0.992 0.000
#> SRR2001042 4 0.0290 0.9837 0.000 0.008 0 0.992 0.000
#> SRR2001043 4 0.0290 0.9837 0.000 0.008 0 0.992 0.000
#> SRR2001036 4 0.0162 0.9827 0.000 0.004 0 0.996 0.000
#> SRR2001037 4 0.0404 0.9818 0.000 0.012 0 0.988 0.000
#> SRR2001038 4 0.0510 0.9791 0.000 0.016 0 0.984 0.000
#> SRR2001039 4 0.0162 0.9834 0.000 0.004 0 0.996 0.000
#> SRR2001028 4 0.1043 0.9641 0.000 0.040 0 0.960 0.000
#> SRR2001029 4 0.0963 0.9671 0.000 0.036 0 0.964 0.000
#> SRR2001030 4 0.1544 0.9354 0.000 0.068 0 0.932 0.000
#> SRR2001031 4 0.1043 0.9645 0.000 0.040 0 0.960 0.000
#> SRR2001024 4 0.0290 0.9837 0.000 0.008 0 0.992 0.000
#> SRR2001025 4 0.0162 0.9825 0.000 0.004 0 0.996 0.000
#> SRR2001026 4 0.0162 0.9834 0.000 0.004 0 0.996 0.000
#> SRR2001027 4 0.0290 0.9837 0.000 0.008 0 0.992 0.000
#> SRR2001020 2 0.0609 0.9325 0.000 0.980 0 0.020 0.000
#> SRR2001021 2 0.0510 0.9318 0.000 0.984 0 0.016 0.000
#> SRR2001022 2 0.0609 0.9325 0.000 0.980 0 0.020 0.000
#> SRR2001023 2 0.0703 0.9332 0.000 0.976 0 0.024 0.000
#> SRR2001016 4 0.0609 0.9789 0.000 0.020 0 0.980 0.000
#> SRR2001017 4 0.0703 0.9780 0.000 0.024 0 0.976 0.000
#> SRR2001018 4 0.0703 0.9780 0.000 0.024 0 0.976 0.000
#> SRR2001019 4 0.0703 0.9780 0.000 0.024 0 0.976 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 2 0.4660 0.7102 0.000 0.600 0.000 0.056 NA 0.000
#> SRR2001033 2 0.4950 0.6902 0.000 0.576 0.000 0.080 NA 0.000
#> SRR2001034 2 0.4538 0.7224 0.000 0.624 0.000 0.052 NA 0.000
#> SRR2001035 2 0.4660 0.7102 0.000 0.600 0.000 0.056 NA 0.000
#> SRR2001204 6 0.0458 0.8102 0.000 0.000 0.000 0.000 NA 0.984
#> SRR2001205 6 0.0458 0.8102 0.000 0.000 0.000 0.000 NA 0.984
#> SRR2001206 6 0.0458 0.8102 0.000 0.000 0.000 0.000 NA 0.984
#> SRR2001207 6 0.0458 0.8102 0.000 0.000 0.000 0.000 NA 0.984
#> SRR2001200 1 0.1714 0.8039 0.908 0.000 0.000 0.000 NA 0.000
#> SRR2001201 1 0.1814 0.8075 0.900 0.000 0.000 0.000 NA 0.000
#> SRR2001202 1 0.1610 0.8036 0.916 0.000 0.000 0.000 NA 0.000
#> SRR2001203 1 0.1863 0.8049 0.896 0.000 0.000 0.000 NA 0.000
#> SRR2001196 1 0.2118 0.8067 0.888 0.000 0.000 0.000 NA 0.008
#> SRR2001197 1 0.2070 0.8046 0.892 0.000 0.000 0.000 NA 0.008
#> SRR2001198 1 0.1588 0.8145 0.924 0.000 0.000 0.000 NA 0.004
#> SRR2001199 1 0.2020 0.8083 0.896 0.000 0.000 0.000 NA 0.008
#> SRR2001192 3 0.0260 0.9713 0.000 0.000 0.992 0.000 NA 0.000
#> SRR2001193 3 0.0260 0.9713 0.000 0.000 0.992 0.000 NA 0.000
#> SRR2001194 3 0.0260 0.9713 0.000 0.000 0.992 0.000 NA 0.000
#> SRR2001195 3 0.0260 0.9713 0.000 0.000 0.992 0.000 NA 0.000
#> SRR2001188 1 0.4503 0.7382 0.684 0.000 0.000 0.000 NA 0.084
#> SRR2001189 1 0.4461 0.7446 0.704 0.000 0.000 0.000 NA 0.104
#> SRR2001190 1 0.4062 0.7672 0.744 0.000 0.000 0.000 NA 0.080
#> SRR2001191 1 0.4340 0.7491 0.720 0.000 0.000 0.000 NA 0.104
#> SRR2001184 3 0.0260 0.9705 0.000 0.000 0.992 0.000 NA 0.000
#> SRR2001185 3 0.0146 0.9710 0.000 0.000 0.996 0.000 NA 0.000
#> SRR2001186 3 0.0146 0.9710 0.000 0.000 0.996 0.000 NA 0.000
#> SRR2001187 3 0.0260 0.9705 0.000 0.000 0.992 0.000 NA 0.000
#> SRR2001180 1 0.3450 0.7956 0.780 0.000 0.000 0.000 NA 0.032
#> SRR2001181 1 0.3394 0.8020 0.776 0.000 0.000 0.000 NA 0.024
#> SRR2001182 1 0.3928 0.7672 0.760 0.000 0.000 0.000 NA 0.080
#> SRR2001183 1 0.4573 0.7215 0.692 0.000 0.000 0.000 NA 0.112
#> SRR2001176 3 0.0865 0.9695 0.000 0.000 0.964 0.000 NA 0.000
#> SRR2001177 3 0.0790 0.9685 0.000 0.000 0.968 0.000 NA 0.000
#> SRR2001178 3 0.0713 0.9692 0.000 0.000 0.972 0.000 NA 0.000
#> SRR2001179 3 0.0713 0.9692 0.000 0.000 0.972 0.000 NA 0.000
#> SRR2001172 3 0.0260 0.9705 0.000 0.000 0.992 0.000 NA 0.000
#> SRR2001173 3 0.0363 0.9707 0.000 0.000 0.988 0.000 NA 0.000
#> SRR2001174 3 0.0260 0.9705 0.000 0.000 0.992 0.000 NA 0.000
#> SRR2001175 3 0.0260 0.9705 0.000 0.000 0.992 0.000 NA 0.000
#> SRR2001168 6 0.0363 0.8084 0.000 0.000 0.000 0.000 NA 0.988
#> SRR2001169 6 0.0547 0.8067 0.000 0.000 0.000 0.000 NA 0.980
#> SRR2001170 6 0.0458 0.8072 0.000 0.000 0.000 0.000 NA 0.984
#> SRR2001171 6 0.0508 0.8096 0.004 0.000 0.000 0.000 NA 0.984
#> SRR2001164 1 0.1918 0.8154 0.904 0.000 0.000 0.000 NA 0.008
#> SRR2001165 1 0.2752 0.8159 0.856 0.000 0.000 0.000 NA 0.036
#> SRR2001166 1 0.2609 0.8176 0.868 0.000 0.000 0.000 NA 0.036
#> SRR2001167 1 0.1967 0.8159 0.904 0.000 0.000 0.000 NA 0.012
#> SRR2001160 1 0.3979 0.7627 0.752 0.000 0.000 0.000 NA 0.076
#> SRR2001161 1 0.4243 0.7511 0.732 0.000 0.000 0.000 NA 0.104
#> SRR2001162 1 0.3426 0.7924 0.808 0.000 0.000 0.000 NA 0.068
#> SRR2001163 1 0.4286 0.7468 0.728 0.000 0.000 0.000 NA 0.108
#> SRR2001156 1 0.1327 0.8132 0.936 0.000 0.000 0.000 NA 0.000
#> SRR2001157 1 0.1866 0.8160 0.908 0.000 0.000 0.000 NA 0.008
#> SRR2001158 1 0.1007 0.8130 0.956 0.000 0.000 0.000 NA 0.000
#> SRR2001159 1 0.1141 0.8140 0.948 0.000 0.000 0.000 NA 0.000
#> SRR2001152 6 0.5336 0.3498 0.332 0.000 0.000 0.000 NA 0.544
#> SRR2001153 1 0.5686 0.1134 0.456 0.000 0.000 0.000 NA 0.384
#> SRR2001154 6 0.5524 0.1123 0.404 0.000 0.000 0.000 NA 0.464
#> SRR2001155 6 0.5081 0.5480 0.256 0.000 0.000 0.000 NA 0.616
#> SRR2001148 3 0.0260 0.9718 0.000 0.000 0.992 0.000 NA 0.000
#> SRR2001149 3 0.0260 0.9718 0.000 0.000 0.992 0.000 NA 0.000
#> SRR2001150 3 0.0260 0.9718 0.000 0.000 0.992 0.000 NA 0.000
#> SRR2001151 3 0.0363 0.9716 0.000 0.000 0.988 0.000 NA 0.000
#> SRR2001144 6 0.3792 0.7552 0.108 0.000 0.000 0.000 NA 0.780
#> SRR2001145 6 0.3227 0.7807 0.088 0.000 0.000 0.000 NA 0.828
#> SRR2001146 6 0.4125 0.6810 0.184 0.000 0.000 0.000 NA 0.736
#> SRR2001147 6 0.4187 0.7165 0.168 0.000 0.000 0.000 NA 0.736
#> SRR2001140 6 0.5102 0.5614 0.240 0.000 0.000 0.000 NA 0.620
#> SRR2001142 6 0.4955 0.6029 0.220 0.000 0.000 0.000 NA 0.644
#> SRR2001143 6 0.5331 0.4882 0.268 0.000 0.000 0.000 NA 0.580
#> SRR2001136 3 0.1910 0.9432 0.000 0.000 0.892 0.000 NA 0.000
#> SRR2001137 3 0.1863 0.9451 0.000 0.000 0.896 0.000 NA 0.000
#> SRR2001138 3 0.1863 0.9437 0.000 0.000 0.896 0.000 NA 0.000
#> SRR2001139 3 0.1863 0.9437 0.000 0.000 0.896 0.000 NA 0.000
#> SRR2001132 3 0.0790 0.9683 0.000 0.000 0.968 0.000 NA 0.000
#> SRR2001133 3 0.0790 0.9683 0.000 0.000 0.968 0.000 NA 0.000
#> SRR2001134 3 0.0790 0.9683 0.000 0.000 0.968 0.000 NA 0.000
#> SRR2001135 3 0.0790 0.9683 0.000 0.000 0.968 0.000 NA 0.000
#> SRR2001128 1 0.3017 0.8058 0.840 0.000 0.000 0.000 NA 0.052
#> SRR2001129 1 0.3548 0.7880 0.796 0.000 0.000 0.000 NA 0.068
#> SRR2001130 1 0.3767 0.7775 0.780 0.000 0.000 0.000 NA 0.088
#> SRR2001131 1 0.4040 0.7580 0.756 0.000 0.000 0.000 NA 0.112
#> SRR2001124 1 0.2362 0.8062 0.860 0.000 0.000 0.000 NA 0.004
#> SRR2001125 1 0.3381 0.7980 0.800 0.000 0.000 0.000 NA 0.044
#> SRR2001126 1 0.1970 0.8143 0.900 0.000 0.000 0.000 NA 0.008
#> SRR2001127 1 0.1812 0.8159 0.912 0.000 0.000 0.000 NA 0.008
#> SRR2001120 6 0.2750 0.7893 0.020 0.000 0.000 0.000 NA 0.844
#> SRR2001121 6 0.1995 0.8064 0.036 0.000 0.000 0.000 NA 0.912
#> SRR2001122 6 0.1367 0.8112 0.012 0.000 0.000 0.000 NA 0.944
#> SRR2001123 6 0.1745 0.8067 0.020 0.000 0.000 0.000 NA 0.924
#> SRR2001116 1 0.5856 0.1188 0.436 0.000 0.000 0.000 NA 0.368
#> SRR2001117 1 0.5855 0.0343 0.412 0.000 0.000 0.000 NA 0.396
#> SRR2001118 1 0.5753 0.1861 0.460 0.000 0.000 0.000 NA 0.364
#> SRR2001119 1 0.5771 0.1321 0.444 0.000 0.000 0.000 NA 0.380
#> SRR2001112 3 0.1910 0.9432 0.000 0.000 0.892 0.000 NA 0.000
#> SRR2001113 3 0.1863 0.9451 0.000 0.000 0.896 0.000 NA 0.000
#> SRR2001114 3 0.1910 0.9432 0.000 0.000 0.892 0.000 NA 0.000
#> SRR2001115 3 0.1863 0.9451 0.000 0.000 0.896 0.000 NA 0.000
#> SRR2001108 4 0.2234 0.9116 0.000 0.004 0.000 0.872 NA 0.000
#> SRR2001109 4 0.2278 0.9085 0.000 0.004 0.000 0.868 NA 0.000
#> SRR2001110 4 0.2494 0.9029 0.000 0.016 0.000 0.864 NA 0.000
#> SRR2001111 4 0.2191 0.9122 0.000 0.004 0.000 0.876 NA 0.000
#> SRR2001104 2 0.0725 0.8540 0.000 0.976 0.000 0.012 NA 0.000
#> SRR2001105 2 0.1003 0.8540 0.000 0.964 0.000 0.016 NA 0.000
#> SRR2001106 2 0.0909 0.8540 0.000 0.968 0.000 0.020 NA 0.000
#> SRR2001107 2 0.0820 0.8543 0.000 0.972 0.000 0.016 NA 0.000
#> SRR2001100 2 0.1563 0.8413 0.000 0.932 0.000 0.056 NA 0.000
#> SRR2001101 2 0.1010 0.8497 0.000 0.960 0.000 0.036 NA 0.000
#> SRR2001102 2 0.1462 0.8419 0.000 0.936 0.000 0.056 NA 0.000
#> SRR2001103 2 0.1219 0.8457 0.000 0.948 0.000 0.048 NA 0.000
#> SRR2001096 2 0.1007 0.8386 0.000 0.956 0.000 0.000 NA 0.000
#> SRR2001097 2 0.1075 0.8368 0.000 0.952 0.000 0.000 NA 0.000
#> SRR2001098 2 0.1075 0.8368 0.000 0.952 0.000 0.000 NA 0.000
#> SRR2001099 2 0.1007 0.8386 0.000 0.956 0.000 0.000 NA 0.000
#> SRR2001092 2 0.0520 0.8519 0.000 0.984 0.000 0.008 NA 0.000
#> SRR2001093 2 0.0508 0.8529 0.000 0.984 0.000 0.012 NA 0.000
#> SRR2001094 2 0.0622 0.8525 0.000 0.980 0.000 0.012 NA 0.000
#> SRR2001095 2 0.0717 0.8526 0.000 0.976 0.000 0.016 NA 0.000
#> SRR2001088 4 0.0146 0.9527 0.000 0.004 0.000 0.996 NA 0.000
#> SRR2001089 4 0.0508 0.9528 0.000 0.012 0.000 0.984 NA 0.000
#> SRR2001090 4 0.0260 0.9528 0.000 0.008 0.000 0.992 NA 0.000
#> SRR2001091 4 0.0260 0.9528 0.000 0.008 0.000 0.992 NA 0.000
#> SRR2001084 4 0.1863 0.9243 0.000 0.000 0.000 0.896 NA 0.000
#> SRR2001085 4 0.1814 0.9268 0.000 0.000 0.000 0.900 NA 0.000
#> SRR2001086 4 0.1910 0.9223 0.000 0.000 0.000 0.892 NA 0.000
#> SRR2001087 4 0.1910 0.9223 0.000 0.000 0.000 0.892 NA 0.000
#> SRR2001080 2 0.0547 0.8533 0.000 0.980 0.000 0.020 NA 0.000
#> SRR2001081 2 0.0363 0.8533 0.000 0.988 0.000 0.012 NA 0.000
#> SRR2001082 2 0.0547 0.8537 0.000 0.980 0.000 0.020 NA 0.000
#> SRR2001083 2 0.0458 0.8532 0.000 0.984 0.000 0.016 NA 0.000
#> SRR2001076 2 0.0717 0.8543 0.000 0.976 0.000 0.008 NA 0.000
#> SRR2001077 2 0.0914 0.8542 0.000 0.968 0.000 0.016 NA 0.000
#> SRR2001078 2 0.0363 0.8533 0.000 0.988 0.000 0.012 NA 0.000
#> SRR2001079 2 0.0692 0.8537 0.000 0.976 0.000 0.020 NA 0.000
#> SRR2001072 4 0.0260 0.9528 0.000 0.008 0.000 0.992 NA 0.000
#> SRR2001073 4 0.0405 0.9535 0.000 0.008 0.000 0.988 NA 0.000
#> SRR2001074 4 0.0405 0.9535 0.000 0.008 0.000 0.988 NA 0.000
#> SRR2001075 4 0.0405 0.9535 0.000 0.008 0.000 0.988 NA 0.000
#> SRR2001068 2 0.4928 0.6880 0.000 0.572 0.000 0.076 NA 0.000
#> SRR2001069 2 0.4928 0.6891 0.000 0.572 0.000 0.076 NA 0.000
#> SRR2001070 2 0.4684 0.7050 0.000 0.592 0.000 0.056 NA 0.000
#> SRR2001071 2 0.4786 0.7003 0.000 0.584 0.000 0.064 NA 0.000
#> SRR2001064 2 0.1007 0.8386 0.000 0.956 0.000 0.000 NA 0.000
#> SRR2001065 2 0.1075 0.8368 0.000 0.952 0.000 0.000 NA 0.000
#> SRR2001066 2 0.1082 0.8406 0.000 0.956 0.000 0.004 NA 0.000
#> SRR2001067 2 0.1007 0.8386 0.000 0.956 0.000 0.000 NA 0.000
#> SRR2001060 4 0.0260 0.9528 0.000 0.008 0.000 0.992 NA 0.000
#> SRR2001061 4 0.0291 0.9530 0.000 0.004 0.000 0.992 NA 0.000
#> SRR2001062 4 0.0260 0.9528 0.000 0.008 0.000 0.992 NA 0.000
#> SRR2001063 4 0.0146 0.9534 0.000 0.004 0.000 0.996 NA 0.000
#> SRR2001056 4 0.1863 0.9243 0.000 0.000 0.000 0.896 NA 0.000
#> SRR2001057 4 0.1863 0.9243 0.000 0.000 0.000 0.896 NA 0.000
#> SRR2001058 4 0.1863 0.9243 0.000 0.000 0.000 0.896 NA 0.000
#> SRR2001059 4 0.1663 0.9308 0.000 0.000 0.000 0.912 NA 0.000
#> SRR2001052 2 0.4575 0.7108 0.000 0.600 0.000 0.048 NA 0.000
#> SRR2001053 2 0.4012 0.7259 0.000 0.640 0.000 0.016 NA 0.000
#> SRR2001054 2 0.4575 0.7108 0.000 0.600 0.000 0.048 NA 0.000
#> SRR2001055 2 0.4575 0.7108 0.000 0.600 0.000 0.048 NA 0.000
#> SRR2001048 2 0.4871 0.6960 0.000 0.580 0.000 0.072 NA 0.000
#> SRR2001049 2 0.4786 0.7018 0.000 0.584 0.000 0.064 NA 0.000
#> SRR2001050 2 0.4736 0.7032 0.000 0.588 0.000 0.060 NA 0.000
#> SRR2001051 2 0.4736 0.7032 0.000 0.588 0.000 0.060 NA 0.000
#> SRR2001044 4 0.0363 0.9520 0.000 0.012 0.000 0.988 NA 0.000
#> SRR2001045 4 0.0458 0.9505 0.000 0.016 0.000 0.984 NA 0.000
#> SRR2001046 4 0.0363 0.9520 0.000 0.012 0.000 0.988 NA 0.000
#> SRR2001047 4 0.0865 0.9396 0.000 0.036 0.000 0.964 NA 0.000
#> SRR2001040 4 0.0260 0.9528 0.000 0.008 0.000 0.992 NA 0.000
#> SRR2001041 4 0.0260 0.9528 0.000 0.008 0.000 0.992 NA 0.000
#> SRR2001042 4 0.0260 0.9528 0.000 0.008 0.000 0.992 NA 0.000
#> SRR2001043 4 0.0260 0.9528 0.000 0.008 0.000 0.992 NA 0.000
#> SRR2001036 4 0.0547 0.9509 0.000 0.000 0.000 0.980 NA 0.000
#> SRR2001037 4 0.0937 0.9465 0.000 0.000 0.000 0.960 NA 0.000
#> SRR2001038 4 0.1141 0.9425 0.000 0.000 0.000 0.948 NA 0.000
#> SRR2001039 4 0.0405 0.9535 0.000 0.004 0.000 0.988 NA 0.000
#> SRR2001028 4 0.0937 0.9368 0.000 0.040 0.000 0.960 NA 0.000
#> SRR2001029 4 0.0865 0.9422 0.000 0.036 0.000 0.964 NA 0.000
#> SRR2001030 4 0.1387 0.9201 0.000 0.068 0.000 0.932 NA 0.000
#> SRR2001031 4 0.0937 0.9395 0.000 0.040 0.000 0.960 NA 0.000
#> SRR2001024 4 0.0260 0.9528 0.000 0.008 0.000 0.992 NA 0.000
#> SRR2001025 4 0.0291 0.9530 0.000 0.004 0.000 0.992 NA 0.000
#> SRR2001026 4 0.0146 0.9534 0.000 0.004 0.000 0.996 NA 0.000
#> SRR2001027 4 0.0260 0.9528 0.000 0.008 0.000 0.992 NA 0.000
#> SRR2001020 2 0.0603 0.8528 0.000 0.980 0.000 0.016 NA 0.000
#> SRR2001021 2 0.0508 0.8529 0.000 0.984 0.000 0.012 NA 0.000
#> SRR2001022 2 0.0603 0.8528 0.000 0.980 0.000 0.016 NA 0.000
#> SRR2001023 2 0.0692 0.8537 0.000 0.976 0.000 0.020 NA 0.000
#> SRR2001016 4 0.1863 0.9243 0.000 0.000 0.000 0.896 NA 0.000
#> SRR2001017 4 0.2006 0.9227 0.000 0.004 0.000 0.892 NA 0.000
#> SRR2001018 4 0.2006 0.9227 0.000 0.004 0.000 0.892 NA 0.000
#> SRR2001019 4 0.2006 0.9227 0.000 0.004 0.000 0.892 NA 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.5031 0.497 0.497
#> 3 3 0.746 0.500 0.733 0.2352 0.929 0.858
#> 4 4 0.662 0.852 0.767 0.1116 0.776 0.508
#> 5 5 0.640 0.812 0.780 0.0753 1.000 1.000
#> 6 6 0.778 0.563 0.770 0.0566 0.968 0.878
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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 3 0.631 0.975 0.000 0.488 0.512
#> SRR2001033 3 0.631 0.966 0.000 0.492 0.508
#> SRR2001034 3 0.630 0.960 0.000 0.472 0.528
#> SRR2001035 3 0.630 0.973 0.000 0.484 0.516
#> SRR2001204 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001205 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001206 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001207 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001200 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001201 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001202 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001203 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001196 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001197 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001198 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001199 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001192 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001193 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001194 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001195 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001188 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001189 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001190 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001191 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001184 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001185 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001186 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001187 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001180 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001181 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001182 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001183 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001176 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001177 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001178 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001179 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001172 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001173 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001174 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001175 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001168 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001169 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001170 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001171 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001164 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001165 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001166 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001167 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001160 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001161 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001162 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001163 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001156 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001157 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001158 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001159 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001152 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001153 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001154 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001155 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001148 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001149 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001150 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001151 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001144 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001145 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001146 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001147 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001140 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001142 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001143 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001136 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001137 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001138 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001139 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001132 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001133 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001134 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001135 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001128 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001129 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001130 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001131 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001124 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001125 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001126 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001127 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001120 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001121 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001122 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001123 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001116 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001117 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001118 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001119 1 0.000 0.862 1.000 0.000 0.000
#> SRR2001112 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001113 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001114 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001115 1 0.629 0.701 0.532 0.000 0.468
#> SRR2001108 2 0.254 0.505 0.000 0.920 0.080
#> SRR2001109 2 0.254 0.505 0.000 0.920 0.080
#> SRR2001110 2 0.254 0.505 0.000 0.920 0.080
#> SRR2001111 2 0.254 0.505 0.000 0.920 0.080
#> SRR2001104 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001105 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001106 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001107 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001100 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001101 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001102 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001103 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001096 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001097 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001098 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001099 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001092 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001093 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001094 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001095 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001088 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001089 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001090 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001091 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001084 2 0.254 0.505 0.000 0.920 0.080
#> SRR2001085 2 0.254 0.505 0.000 0.920 0.080
#> SRR2001086 2 0.254 0.505 0.000 0.920 0.080
#> SRR2001087 2 0.254 0.505 0.000 0.920 0.080
#> SRR2001080 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001081 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001082 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001083 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001076 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001077 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001078 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001079 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001072 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001073 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001074 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001075 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001068 3 0.631 0.975 0.000 0.488 0.512
#> SRR2001069 3 0.631 0.941 0.000 0.500 0.500
#> SRR2001070 3 0.630 0.970 0.000 0.480 0.520
#> SRR2001071 3 0.631 0.975 0.000 0.488 0.512
#> SRR2001064 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001065 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001066 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001067 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001060 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001061 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001062 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001063 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001056 2 0.254 0.505 0.000 0.920 0.080
#> SRR2001057 2 0.254 0.505 0.000 0.920 0.080
#> SRR2001058 2 0.254 0.505 0.000 0.920 0.080
#> SRR2001059 2 0.254 0.505 0.000 0.920 0.080
#> SRR2001052 3 0.630 0.960 0.000 0.472 0.528
#> SRR2001053 3 0.630 0.960 0.000 0.472 0.528
#> SRR2001054 3 0.630 0.960 0.000 0.472 0.528
#> SRR2001055 3 0.630 0.960 0.000 0.472 0.528
#> SRR2001048 3 0.631 0.966 0.000 0.492 0.508
#> SRR2001049 3 0.631 0.975 0.000 0.488 0.512
#> SRR2001050 3 0.631 0.975 0.000 0.488 0.512
#> SRR2001051 3 0.631 0.975 0.000 0.488 0.512
#> SRR2001044 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001045 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001046 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001047 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001040 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001041 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001042 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001043 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001036 2 0.116 0.535 0.000 0.972 0.028
#> SRR2001037 2 0.153 0.529 0.000 0.960 0.040
#> SRR2001038 2 0.164 0.527 0.000 0.956 0.044
#> SRR2001039 2 0.141 0.531 0.000 0.964 0.036
#> SRR2001028 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001029 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001030 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001031 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001024 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001025 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001026 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001027 2 0.000 0.547 0.000 1.000 0.000
#> SRR2001020 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001021 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001022 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001023 2 0.627 -0.693 0.000 0.548 0.452
#> SRR2001016 2 0.254 0.505 0.000 0.920 0.080
#> SRR2001017 2 0.254 0.505 0.000 0.920 0.080
#> SRR2001018 2 0.254 0.505 0.000 0.920 0.080
#> SRR2001019 2 0.254 0.505 0.000 0.920 0.080
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.7657 0.652 0.280 0.464 0.000 0.256
#> SRR2001033 2 0.7674 0.647 0.280 0.460 0.000 0.260
#> SRR2001034 2 0.7640 0.656 0.280 0.468 0.000 0.252
#> SRR2001035 2 0.7657 0.652 0.280 0.464 0.000 0.256
#> SRR2001204 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001205 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001206 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001207 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001200 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001201 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001202 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001203 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001196 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001197 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001198 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001199 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001192 3 0.0188 0.975 0.000 0.004 0.996 0.000
#> SRR2001193 3 0.0188 0.975 0.000 0.004 0.996 0.000
#> SRR2001194 3 0.0188 0.975 0.000 0.004 0.996 0.000
#> SRR2001195 3 0.0188 0.975 0.000 0.004 0.996 0.000
#> SRR2001188 1 0.4730 0.903 0.636 0.000 0.364 0.000
#> SRR2001189 1 0.4730 0.903 0.636 0.000 0.364 0.000
#> SRR2001190 1 0.4730 0.903 0.636 0.000 0.364 0.000
#> SRR2001191 1 0.4730 0.903 0.636 0.000 0.364 0.000
#> SRR2001184 3 0.0188 0.974 0.000 0.004 0.996 0.000
#> SRR2001185 3 0.0336 0.974 0.000 0.008 0.992 0.000
#> SRR2001186 3 0.0188 0.974 0.000 0.004 0.996 0.000
#> SRR2001187 3 0.0188 0.974 0.000 0.004 0.996 0.000
#> SRR2001180 1 0.4730 0.903 0.636 0.000 0.364 0.000
#> SRR2001181 1 0.4730 0.903 0.636 0.000 0.364 0.000
#> SRR2001182 1 0.4730 0.903 0.636 0.000 0.364 0.000
#> SRR2001183 1 0.4905 0.903 0.632 0.004 0.364 0.000
#> SRR2001176 3 0.0336 0.974 0.000 0.008 0.992 0.000
#> SRR2001177 3 0.0469 0.974 0.000 0.012 0.988 0.000
#> SRR2001178 3 0.0336 0.974 0.000 0.008 0.992 0.000
#> SRR2001179 3 0.0336 0.974 0.000 0.008 0.992 0.000
#> SRR2001172 3 0.0336 0.974 0.000 0.008 0.992 0.000
#> SRR2001173 3 0.0336 0.975 0.000 0.008 0.992 0.000
#> SRR2001174 3 0.0336 0.974 0.000 0.008 0.992 0.000
#> SRR2001175 3 0.0469 0.973 0.000 0.012 0.988 0.000
#> SRR2001168 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001169 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001170 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001171 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001164 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001165 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001166 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001167 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001160 1 0.4730 0.903 0.636 0.000 0.364 0.000
#> SRR2001161 1 0.4730 0.903 0.636 0.000 0.364 0.000
#> SRR2001162 1 0.4730 0.903 0.636 0.000 0.364 0.000
#> SRR2001163 1 0.4730 0.903 0.636 0.000 0.364 0.000
#> SRR2001156 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001157 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001158 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001159 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001152 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001153 1 0.7318 0.854 0.476 0.160 0.364 0.000
#> SRR2001154 1 0.7318 0.854 0.476 0.160 0.364 0.000
#> SRR2001155 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001148 3 0.0336 0.974 0.000 0.008 0.992 0.000
#> SRR2001149 3 0.0336 0.974 0.000 0.008 0.992 0.000
#> SRR2001150 3 0.0336 0.974 0.000 0.008 0.992 0.000
#> SRR2001151 3 0.0000 0.975 0.000 0.000 1.000 0.000
#> SRR2001144 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001145 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001146 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001147 1 0.7318 0.854 0.476 0.160 0.364 0.000
#> SRR2001140 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001142 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001143 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001136 3 0.1716 0.959 0.000 0.064 0.936 0.000
#> SRR2001137 3 0.1716 0.959 0.000 0.064 0.936 0.000
#> SRR2001138 3 0.1716 0.959 0.000 0.064 0.936 0.000
#> SRR2001139 3 0.1716 0.959 0.000 0.064 0.936 0.000
#> SRR2001132 3 0.1557 0.962 0.000 0.056 0.944 0.000
#> SRR2001133 3 0.1557 0.962 0.000 0.056 0.944 0.000
#> SRR2001134 3 0.1637 0.961 0.000 0.060 0.940 0.000
#> SRR2001135 3 0.1557 0.962 0.000 0.056 0.944 0.000
#> SRR2001128 1 0.4730 0.903 0.636 0.000 0.364 0.000
#> SRR2001129 1 0.4730 0.903 0.636 0.000 0.364 0.000
#> SRR2001130 1 0.4730 0.903 0.636 0.000 0.364 0.000
#> SRR2001131 1 0.4730 0.903 0.636 0.000 0.364 0.000
#> SRR2001124 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001125 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001126 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001127 1 0.4905 0.902 0.632 0.004 0.364 0.000
#> SRR2001120 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001121 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001122 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001123 1 0.7436 0.847 0.460 0.176 0.364 0.000
#> SRR2001116 1 0.7073 0.865 0.504 0.132 0.364 0.000
#> SRR2001117 1 0.6773 0.875 0.532 0.104 0.364 0.000
#> SRR2001118 1 0.6028 0.891 0.584 0.052 0.364 0.000
#> SRR2001119 1 0.6290 0.887 0.568 0.068 0.364 0.000
#> SRR2001112 3 0.1637 0.960 0.000 0.060 0.940 0.000
#> SRR2001113 3 0.1637 0.961 0.000 0.060 0.940 0.000
#> SRR2001114 3 0.1637 0.960 0.000 0.060 0.940 0.000
#> SRR2001115 3 0.1637 0.960 0.000 0.060 0.940 0.000
#> SRR2001108 4 0.5363 0.717 0.216 0.064 0.000 0.720
#> SRR2001109 4 0.5328 0.720 0.212 0.064 0.000 0.724
#> SRR2001110 4 0.5363 0.717 0.216 0.064 0.000 0.720
#> SRR2001111 4 0.5292 0.723 0.208 0.064 0.000 0.728
#> SRR2001104 2 0.4677 0.844 0.004 0.680 0.000 0.316
#> SRR2001105 2 0.4677 0.844 0.004 0.680 0.000 0.316
#> SRR2001106 2 0.4677 0.844 0.004 0.680 0.000 0.316
#> SRR2001107 2 0.4677 0.844 0.004 0.680 0.000 0.316
#> SRR2001100 2 0.4677 0.844 0.004 0.680 0.000 0.316
#> SRR2001101 2 0.4677 0.844 0.004 0.680 0.000 0.316
#> SRR2001102 2 0.4677 0.844 0.004 0.680 0.000 0.316
#> SRR2001103 2 0.4677 0.844 0.004 0.680 0.000 0.316
#> SRR2001096 2 0.4936 0.842 0.012 0.672 0.000 0.316
#> SRR2001097 2 0.4936 0.842 0.012 0.672 0.000 0.316
#> SRR2001098 2 0.4936 0.842 0.012 0.672 0.000 0.316
#> SRR2001099 2 0.4936 0.842 0.012 0.672 0.000 0.316
#> SRR2001092 2 0.4814 0.842 0.008 0.676 0.000 0.316
#> SRR2001093 2 0.4814 0.842 0.008 0.676 0.000 0.316
#> SRR2001094 2 0.4814 0.842 0.008 0.676 0.000 0.316
#> SRR2001095 2 0.4814 0.842 0.008 0.676 0.000 0.316
#> SRR2001088 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001089 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001090 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001091 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001084 4 0.5363 0.717 0.216 0.064 0.000 0.720
#> SRR2001085 4 0.5292 0.723 0.208 0.064 0.000 0.728
#> SRR2001086 4 0.5328 0.720 0.212 0.064 0.000 0.724
#> SRR2001087 4 0.5328 0.720 0.212 0.064 0.000 0.724
#> SRR2001080 2 0.4500 0.844 0.000 0.684 0.000 0.316
#> SRR2001081 2 0.4500 0.844 0.000 0.684 0.000 0.316
#> SRR2001082 2 0.4500 0.844 0.000 0.684 0.000 0.316
#> SRR2001083 2 0.4500 0.844 0.000 0.684 0.000 0.316
#> SRR2001076 2 0.4500 0.844 0.000 0.684 0.000 0.316
#> SRR2001077 2 0.4500 0.844 0.000 0.684 0.000 0.316
#> SRR2001078 2 0.4500 0.844 0.000 0.684 0.000 0.316
#> SRR2001079 2 0.4500 0.844 0.000 0.684 0.000 0.316
#> SRR2001072 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001073 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001074 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001075 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001068 2 0.7702 0.641 0.288 0.452 0.000 0.260
#> SRR2001069 2 0.7732 0.628 0.288 0.444 0.000 0.268
#> SRR2001070 2 0.7685 0.646 0.288 0.456 0.000 0.256
#> SRR2001071 2 0.7702 0.641 0.288 0.452 0.000 0.260
#> SRR2001064 2 0.4936 0.842 0.012 0.672 0.000 0.316
#> SRR2001065 2 0.4936 0.842 0.012 0.672 0.000 0.316
#> SRR2001066 2 0.4936 0.842 0.012 0.672 0.000 0.316
#> SRR2001067 2 0.4936 0.842 0.012 0.672 0.000 0.316
#> SRR2001060 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001061 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001062 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001063 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001056 4 0.5328 0.720 0.212 0.064 0.000 0.724
#> SRR2001057 4 0.5363 0.717 0.216 0.064 0.000 0.720
#> SRR2001058 4 0.5363 0.717 0.216 0.064 0.000 0.720
#> SRR2001059 4 0.5363 0.717 0.216 0.064 0.000 0.720
#> SRR2001052 2 0.7640 0.658 0.280 0.468 0.000 0.252
#> SRR2001053 2 0.7625 0.661 0.276 0.472 0.000 0.252
#> SRR2001054 2 0.7625 0.661 0.276 0.472 0.000 0.252
#> SRR2001055 2 0.7625 0.661 0.276 0.472 0.000 0.252
#> SRR2001048 2 0.7702 0.641 0.288 0.452 0.000 0.260
#> SRR2001049 2 0.7702 0.641 0.288 0.452 0.000 0.260
#> SRR2001050 2 0.7702 0.641 0.288 0.452 0.000 0.260
#> SRR2001051 2 0.7702 0.641 0.288 0.452 0.000 0.260
#> SRR2001044 4 0.0188 0.862 0.004 0.000 0.000 0.996
#> SRR2001045 4 0.0188 0.862 0.004 0.000 0.000 0.996
#> SRR2001046 4 0.0188 0.862 0.004 0.000 0.000 0.996
#> SRR2001047 4 0.0188 0.862 0.004 0.000 0.000 0.996
#> SRR2001040 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001041 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001042 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001043 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001036 4 0.0469 0.860 0.000 0.012 0.000 0.988
#> SRR2001037 4 0.1022 0.850 0.000 0.032 0.000 0.968
#> SRR2001038 4 0.1004 0.853 0.004 0.024 0.000 0.972
#> SRR2001039 4 0.0707 0.856 0.000 0.020 0.000 0.980
#> SRR2001028 4 0.0188 0.862 0.004 0.000 0.000 0.996
#> SRR2001029 4 0.0188 0.862 0.004 0.000 0.000 0.996
#> SRR2001030 4 0.0188 0.862 0.004 0.000 0.000 0.996
#> SRR2001031 4 0.0188 0.862 0.004 0.000 0.000 0.996
#> SRR2001024 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001025 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001026 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001027 4 0.0469 0.863 0.012 0.000 0.000 0.988
#> SRR2001020 2 0.4814 0.842 0.008 0.676 0.000 0.316
#> SRR2001021 2 0.4814 0.842 0.008 0.676 0.000 0.316
#> SRR2001022 2 0.4814 0.842 0.008 0.676 0.000 0.316
#> SRR2001023 2 0.4814 0.842 0.008 0.676 0.000 0.316
#> SRR2001016 4 0.5619 0.679 0.248 0.064 0.000 0.688
#> SRR2001017 4 0.5619 0.679 0.248 0.064 0.000 0.688
#> SRR2001018 4 0.5619 0.679 0.248 0.064 0.000 0.688
#> SRR2001019 4 0.5619 0.679 0.248 0.064 0.000 0.688
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.7342 0.634 0.000 0.548 0.144 0.176 NA
#> SRR2001033 2 0.7397 0.623 0.000 0.540 0.144 0.184 NA
#> SRR2001034 2 0.7314 0.638 0.000 0.552 0.144 0.172 NA
#> SRR2001035 2 0.7342 0.634 0.000 0.548 0.144 0.176 NA
#> SRR2001204 1 0.4251 0.736 0.624 0.000 0.000 0.004 NA
#> SRR2001205 1 0.4251 0.736 0.624 0.000 0.000 0.004 NA
#> SRR2001206 1 0.4251 0.736 0.624 0.000 0.000 0.004 NA
#> SRR2001207 1 0.4251 0.736 0.624 0.000 0.000 0.004 NA
#> SRR2001200 1 0.0703 0.825 0.976 0.000 0.000 0.024 NA
#> SRR2001201 1 0.0510 0.825 0.984 0.000 0.000 0.016 NA
#> SRR2001202 1 0.0609 0.824 0.980 0.000 0.000 0.020 NA
#> SRR2001203 1 0.0609 0.824 0.980 0.000 0.000 0.020 NA
#> SRR2001196 1 0.0794 0.825 0.972 0.000 0.000 0.028 NA
#> SRR2001197 1 0.0794 0.826 0.972 0.000 0.000 0.028 NA
#> SRR2001198 1 0.0510 0.825 0.984 0.000 0.000 0.016 NA
#> SRR2001199 1 0.0880 0.826 0.968 0.000 0.000 0.032 NA
#> SRR2001192 3 0.3740 0.945 0.196 0.000 0.784 0.012 NA
#> SRR2001193 3 0.3740 0.945 0.196 0.000 0.784 0.012 NA
#> SRR2001194 3 0.3740 0.945 0.196 0.000 0.784 0.012 NA
#> SRR2001195 3 0.3948 0.945 0.196 0.000 0.776 0.012 NA
#> SRR2001188 1 0.0880 0.827 0.968 0.000 0.000 0.032 NA
#> SRR2001189 1 0.1364 0.828 0.952 0.000 0.000 0.036 NA
#> SRR2001190 1 0.1043 0.826 0.960 0.000 0.000 0.040 NA
#> SRR2001191 1 0.0794 0.827 0.972 0.000 0.000 0.028 NA
#> SRR2001184 3 0.3353 0.945 0.196 0.000 0.796 0.000 NA
#> SRR2001185 3 0.3387 0.946 0.196 0.000 0.796 0.004 NA
#> SRR2001186 3 0.3387 0.946 0.196 0.000 0.796 0.004 NA
#> SRR2001187 3 0.3387 0.946 0.196 0.000 0.796 0.004 NA
#> SRR2001180 1 0.1270 0.826 0.948 0.000 0.000 0.052 NA
#> SRR2001181 1 0.1341 0.826 0.944 0.000 0.000 0.056 NA
#> SRR2001182 1 0.1121 0.825 0.956 0.000 0.000 0.044 NA
#> SRR2001183 1 0.1557 0.826 0.940 0.000 0.000 0.052 NA
#> SRR2001176 3 0.4651 0.941 0.196 0.000 0.744 0.024 NA
#> SRR2001177 3 0.4323 0.944 0.196 0.000 0.760 0.020 NA
#> SRR2001178 3 0.3387 0.946 0.196 0.000 0.796 0.004 NA
#> SRR2001179 3 0.3387 0.946 0.196 0.000 0.796 0.004 NA
#> SRR2001172 3 0.3509 0.946 0.196 0.000 0.792 0.008 NA
#> SRR2001173 3 0.3631 0.947 0.196 0.000 0.788 0.008 NA
#> SRR2001174 3 0.3387 0.946 0.196 0.000 0.796 0.004 NA
#> SRR2001175 3 0.3509 0.946 0.196 0.000 0.792 0.008 NA
#> SRR2001168 1 0.4251 0.736 0.624 0.000 0.000 0.004 NA
#> SRR2001169 1 0.4251 0.736 0.624 0.000 0.000 0.004 NA
#> SRR2001170 1 0.4251 0.736 0.624 0.000 0.000 0.004 NA
#> SRR2001171 1 0.4251 0.736 0.624 0.000 0.000 0.004 NA
#> SRR2001164 1 0.0510 0.825 0.984 0.000 0.000 0.016 NA
#> SRR2001165 1 0.0794 0.826 0.972 0.000 0.000 0.028 NA
#> SRR2001166 1 0.0404 0.827 0.988 0.000 0.000 0.012 NA
#> SRR2001167 1 0.0510 0.826 0.984 0.000 0.000 0.016 NA
#> SRR2001160 1 0.1270 0.826 0.948 0.000 0.000 0.052 NA
#> SRR2001161 1 0.1197 0.826 0.952 0.000 0.000 0.048 NA
#> SRR2001162 1 0.1282 0.827 0.952 0.000 0.000 0.044 NA
#> SRR2001163 1 0.1197 0.826 0.952 0.000 0.000 0.048 NA
#> SRR2001156 1 0.0794 0.824 0.972 0.000 0.000 0.028 NA
#> SRR2001157 1 0.0880 0.824 0.968 0.000 0.000 0.032 NA
#> SRR2001158 1 0.0794 0.824 0.972 0.000 0.000 0.028 NA
#> SRR2001159 1 0.0794 0.824 0.972 0.000 0.000 0.028 NA
#> SRR2001152 1 0.4731 0.747 0.640 0.000 0.000 0.032 NA
#> SRR2001153 1 0.4713 0.762 0.676 0.000 0.000 0.044 NA
#> SRR2001154 1 0.4562 0.761 0.676 0.000 0.000 0.032 NA
#> SRR2001155 1 0.4585 0.740 0.628 0.000 0.000 0.020 NA
#> SRR2001148 3 0.3231 0.945 0.196 0.000 0.800 0.000 NA
#> SRR2001149 3 0.3387 0.946 0.196 0.000 0.796 0.004 NA
#> SRR2001150 3 0.3231 0.945 0.196 0.000 0.800 0.000 NA
#> SRR2001151 3 0.3387 0.946 0.196 0.000 0.796 0.004 NA
#> SRR2001144 1 0.4444 0.738 0.624 0.000 0.000 0.012 NA
#> SRR2001145 1 0.4444 0.738 0.624 0.000 0.000 0.012 NA
#> SRR2001146 1 0.4354 0.737 0.624 0.000 0.000 0.008 NA
#> SRR2001147 1 0.4608 0.747 0.640 0.000 0.000 0.024 NA
#> SRR2001140 1 0.4444 0.738 0.624 0.000 0.000 0.012 NA
#> SRR2001142 1 0.4444 0.738 0.624 0.000 0.000 0.012 NA
#> SRR2001143 1 0.4444 0.738 0.624 0.000 0.000 0.012 NA
#> SRR2001136 3 0.6194 0.914 0.196 0.000 0.644 0.052 NA
#> SRR2001137 3 0.6194 0.914 0.196 0.000 0.644 0.052 NA
#> SRR2001138 3 0.6103 0.917 0.196 0.000 0.652 0.052 NA
#> SRR2001139 3 0.6211 0.915 0.196 0.000 0.644 0.056 NA
#> SRR2001132 3 0.5857 0.923 0.196 0.000 0.668 0.040 NA
#> SRR2001133 3 0.5827 0.923 0.196 0.000 0.672 0.044 NA
#> SRR2001134 3 0.6299 0.913 0.196 0.000 0.636 0.056 NA
#> SRR2001135 3 0.6039 0.920 0.196 0.000 0.656 0.048 NA
#> SRR2001128 1 0.0794 0.827 0.972 0.000 0.000 0.028 NA
#> SRR2001129 1 0.1205 0.827 0.956 0.000 0.000 0.040 NA
#> SRR2001130 1 0.0771 0.828 0.976 0.000 0.000 0.020 NA
#> SRR2001131 1 0.0898 0.829 0.972 0.000 0.000 0.020 NA
#> SRR2001124 1 0.0880 0.824 0.968 0.000 0.000 0.032 NA
#> SRR2001125 1 0.1121 0.827 0.956 0.000 0.000 0.044 NA
#> SRR2001126 1 0.0794 0.824 0.972 0.000 0.000 0.028 NA
#> SRR2001127 1 0.0794 0.824 0.972 0.000 0.000 0.028 NA
#> SRR2001120 1 0.4251 0.737 0.624 0.000 0.000 0.004 NA
#> SRR2001121 1 0.4251 0.737 0.624 0.000 0.000 0.004 NA
#> SRR2001122 1 0.4251 0.736 0.624 0.000 0.000 0.004 NA
#> SRR2001123 1 0.4444 0.738 0.624 0.000 0.000 0.012 NA
#> SRR2001116 1 0.4455 0.771 0.704 0.000 0.000 0.036 NA
#> SRR2001117 1 0.4398 0.776 0.720 0.000 0.000 0.040 NA
#> SRR2001118 1 0.3267 0.810 0.844 0.000 0.000 0.044 NA
#> SRR2001119 1 0.3413 0.808 0.832 0.000 0.000 0.044 NA
#> SRR2001112 3 0.6281 0.913 0.196 0.000 0.636 0.052 NA
#> SRR2001113 3 0.6281 0.913 0.196 0.000 0.636 0.052 NA
#> SRR2001114 3 0.6281 0.913 0.196 0.000 0.636 0.052 NA
#> SRR2001115 3 0.6281 0.913 0.196 0.000 0.636 0.052 NA
#> SRR2001108 4 0.2732 0.722 0.000 0.160 0.000 0.840 NA
#> SRR2001109 4 0.2890 0.722 0.000 0.160 0.000 0.836 NA
#> SRR2001110 4 0.2890 0.719 0.000 0.160 0.000 0.836 NA
#> SRR2001111 4 0.2732 0.722 0.000 0.160 0.000 0.840 NA
#> SRR2001104 2 0.1012 0.826 0.000 0.968 0.012 0.000 NA
#> SRR2001105 2 0.1106 0.825 0.000 0.964 0.012 0.000 NA
#> SRR2001106 2 0.1012 0.826 0.000 0.968 0.012 0.000 NA
#> SRR2001107 2 0.1012 0.826 0.000 0.968 0.012 0.000 NA
#> SRR2001100 2 0.1018 0.826 0.000 0.968 0.016 0.000 NA
#> SRR2001101 2 0.0912 0.826 0.000 0.972 0.012 0.000 NA
#> SRR2001102 2 0.0912 0.826 0.000 0.972 0.012 0.000 NA
#> SRR2001103 2 0.0912 0.826 0.000 0.972 0.012 0.000 NA
#> SRR2001096 2 0.1469 0.816 0.000 0.948 0.016 0.000 NA
#> SRR2001097 2 0.1469 0.816 0.000 0.948 0.016 0.000 NA
#> SRR2001098 2 0.1469 0.816 0.000 0.948 0.016 0.000 NA
#> SRR2001099 2 0.1469 0.816 0.000 0.948 0.016 0.000 NA
#> SRR2001092 2 0.0451 0.824 0.000 0.988 0.004 0.000 NA
#> SRR2001093 2 0.0451 0.824 0.000 0.988 0.004 0.000 NA
#> SRR2001094 2 0.0566 0.823 0.000 0.984 0.004 0.000 NA
#> SRR2001095 2 0.0566 0.823 0.000 0.984 0.004 0.000 NA
#> SRR2001088 4 0.6430 0.857 0.000 0.192 0.000 0.480 NA
#> SRR2001089 4 0.6816 0.857 0.000 0.192 0.016 0.484 NA
#> SRR2001090 4 0.6554 0.856 0.000 0.192 0.004 0.484 NA
#> SRR2001091 4 0.6653 0.856 0.000 0.192 0.008 0.484 NA
#> SRR2001084 4 0.2732 0.722 0.000 0.160 0.000 0.840 NA
#> SRR2001085 4 0.3123 0.729 0.000 0.160 0.000 0.828 NA
#> SRR2001086 4 0.2732 0.722 0.000 0.160 0.000 0.840 NA
#> SRR2001087 4 0.2732 0.722 0.000 0.160 0.000 0.840 NA
#> SRR2001080 2 0.0162 0.827 0.000 0.996 0.004 0.000 NA
#> SRR2001081 2 0.0000 0.827 0.000 1.000 0.000 0.000 NA
#> SRR2001082 2 0.0162 0.827 0.000 0.996 0.004 0.000 NA
#> SRR2001083 2 0.0162 0.827 0.000 0.996 0.004 0.000 NA
#> SRR2001076 2 0.0324 0.827 0.000 0.992 0.004 0.000 NA
#> SRR2001077 2 0.0324 0.827 0.000 0.992 0.004 0.000 NA
#> SRR2001078 2 0.0324 0.827 0.000 0.992 0.004 0.000 NA
#> SRR2001079 2 0.0324 0.827 0.000 0.992 0.004 0.000 NA
#> SRR2001072 4 0.6816 0.855 0.000 0.192 0.016 0.484 NA
#> SRR2001073 4 0.6816 0.855 0.000 0.192 0.016 0.484 NA
#> SRR2001074 4 0.6816 0.855 0.000 0.192 0.016 0.484 NA
#> SRR2001075 4 0.6816 0.855 0.000 0.192 0.016 0.484 NA
#> SRR2001068 2 0.7367 0.630 0.000 0.544 0.148 0.180 NA
#> SRR2001069 2 0.7472 0.607 0.000 0.528 0.148 0.196 NA
#> SRR2001070 2 0.7311 0.638 0.000 0.552 0.148 0.172 NA
#> SRR2001071 2 0.7340 0.634 0.000 0.548 0.148 0.176 NA
#> SRR2001064 2 0.1469 0.816 0.000 0.948 0.016 0.000 NA
#> SRR2001065 2 0.1469 0.816 0.000 0.948 0.016 0.000 NA
#> SRR2001066 2 0.1364 0.817 0.000 0.952 0.012 0.000 NA
#> SRR2001067 2 0.1469 0.816 0.000 0.948 0.016 0.000 NA
#> SRR2001060 4 0.6816 0.855 0.000 0.192 0.016 0.484 NA
#> SRR2001061 4 0.6816 0.855 0.000 0.192 0.016 0.484 NA
#> SRR2001062 4 0.6816 0.855 0.000 0.192 0.016 0.484 NA
#> SRR2001063 4 0.6816 0.855 0.000 0.192 0.016 0.484 NA
#> SRR2001056 4 0.2890 0.722 0.000 0.160 0.000 0.836 NA
#> SRR2001057 4 0.2890 0.722 0.000 0.160 0.000 0.836 NA
#> SRR2001058 4 0.2890 0.722 0.000 0.160 0.000 0.836 NA
#> SRR2001059 4 0.2890 0.722 0.000 0.160 0.000 0.836 NA
#> SRR2001052 2 0.7222 0.647 0.000 0.564 0.152 0.156 NA
#> SRR2001053 2 0.7222 0.647 0.000 0.564 0.152 0.156 NA
#> SRR2001054 2 0.7222 0.647 0.000 0.564 0.152 0.156 NA
#> SRR2001055 2 0.7222 0.647 0.000 0.564 0.152 0.156 NA
#> SRR2001048 2 0.7340 0.634 0.000 0.548 0.148 0.176 NA
#> SRR2001049 2 0.7340 0.634 0.000 0.548 0.148 0.176 NA
#> SRR2001050 2 0.7340 0.634 0.000 0.548 0.148 0.176 NA
#> SRR2001051 2 0.7340 0.634 0.000 0.548 0.148 0.176 NA
#> SRR2001044 4 0.6649 0.858 0.000 0.192 0.012 0.512 NA
#> SRR2001045 4 0.6649 0.858 0.000 0.192 0.012 0.512 NA
#> SRR2001046 4 0.6649 0.858 0.000 0.192 0.012 0.512 NA
#> SRR2001047 4 0.6649 0.858 0.000 0.192 0.012 0.512 NA
#> SRR2001040 4 0.6420 0.857 0.000 0.192 0.000 0.484 NA
#> SRR2001041 4 0.6554 0.857 0.000 0.192 0.004 0.484 NA
#> SRR2001042 4 0.6420 0.857 0.000 0.192 0.000 0.484 NA
#> SRR2001043 4 0.6420 0.857 0.000 0.192 0.000 0.484 NA
#> SRR2001036 4 0.6649 0.858 0.000 0.192 0.012 0.512 NA
#> SRR2001037 4 0.6625 0.858 0.000 0.188 0.012 0.516 NA
#> SRR2001038 4 0.6578 0.855 0.000 0.188 0.012 0.528 NA
#> SRR2001039 4 0.6649 0.858 0.000 0.192 0.012 0.512 NA
#> SRR2001028 4 0.6649 0.858 0.000 0.192 0.012 0.512 NA
#> SRR2001029 4 0.6649 0.858 0.000 0.192 0.012 0.512 NA
#> SRR2001030 4 0.6649 0.858 0.000 0.192 0.012 0.512 NA
#> SRR2001031 4 0.6649 0.858 0.000 0.192 0.012 0.512 NA
#> SRR2001024 4 0.6410 0.857 0.000 0.192 0.000 0.488 NA
#> SRR2001025 4 0.6410 0.857 0.000 0.192 0.000 0.488 NA
#> SRR2001026 4 0.6554 0.856 0.000 0.192 0.004 0.484 NA
#> SRR2001027 4 0.6410 0.857 0.000 0.192 0.000 0.488 NA
#> SRR2001020 2 0.0000 0.827 0.000 1.000 0.000 0.000 NA
#> SRR2001021 2 0.0000 0.827 0.000 1.000 0.000 0.000 NA
#> SRR2001022 2 0.0000 0.827 0.000 1.000 0.000 0.000 NA
#> SRR2001023 2 0.0000 0.827 0.000 1.000 0.000 0.000 NA
#> SRR2001016 4 0.4065 0.678 0.000 0.160 0.016 0.792 NA
#> SRR2001017 4 0.4143 0.674 0.000 0.160 0.016 0.788 NA
#> SRR2001018 4 0.4143 0.674 0.000 0.160 0.016 0.788 NA
#> SRR2001019 4 0.4143 0.674 0.000 0.160 0.016 0.788 NA
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 5 0.1913 0.984 0.000 0.000 0.000 0.080 0.908 0.012
#> SRR2001033 5 0.2147 0.977 0.000 0.000 0.000 0.084 0.896 0.020
#> SRR2001034 5 0.2094 0.979 0.000 0.000 0.000 0.080 0.900 0.020
#> SRR2001035 5 0.1913 0.984 0.000 0.000 0.000 0.080 0.908 0.012
#> SRR2001204 1 0.4937 -0.879 0.492 0.028 0.000 0.000 0.020 0.460
#> SRR2001205 1 0.4937 -0.879 0.492 0.028 0.000 0.000 0.020 0.460
#> SRR2001206 1 0.4997 -0.882 0.492 0.032 0.000 0.000 0.020 0.456
#> SRR2001207 1 0.4997 -0.882 0.492 0.032 0.000 0.000 0.020 0.456
#> SRR2001200 1 0.1890 0.547 0.916 0.060 0.000 0.000 0.024 0.000
#> SRR2001201 1 0.1807 0.547 0.920 0.060 0.000 0.000 0.020 0.000
#> SRR2001202 1 0.1807 0.547 0.920 0.060 0.000 0.000 0.020 0.000
#> SRR2001203 1 0.1890 0.547 0.916 0.060 0.000 0.000 0.024 0.000
#> SRR2001196 1 0.1829 0.549 0.920 0.056 0.000 0.000 0.024 0.000
#> SRR2001197 1 0.1890 0.547 0.916 0.060 0.000 0.000 0.024 0.000
#> SRR2001198 1 0.1807 0.547 0.920 0.060 0.000 0.000 0.020 0.000
#> SRR2001199 1 0.1950 0.547 0.912 0.064 0.000 0.000 0.024 0.000
#> SRR2001192 3 0.2306 0.917 0.092 0.004 0.888 0.000 0.000 0.016
#> SRR2001193 3 0.2306 0.917 0.092 0.004 0.888 0.000 0.000 0.016
#> SRR2001194 3 0.2306 0.917 0.092 0.004 0.888 0.000 0.000 0.016
#> SRR2001195 3 0.2418 0.917 0.092 0.008 0.884 0.000 0.000 0.016
#> SRR2001188 1 0.1155 0.547 0.956 0.036 0.000 0.000 0.004 0.004
#> SRR2001189 1 0.1483 0.542 0.944 0.036 0.000 0.000 0.008 0.012
#> SRR2001190 1 0.0891 0.549 0.968 0.024 0.000 0.000 0.008 0.000
#> SRR2001191 1 0.0790 0.548 0.968 0.032 0.000 0.000 0.000 0.000
#> SRR2001184 3 0.2214 0.916 0.092 0.004 0.892 0.000 0.000 0.012
#> SRR2001185 3 0.2468 0.916 0.092 0.004 0.884 0.000 0.008 0.012
#> SRR2001186 3 0.2357 0.915 0.092 0.004 0.888 0.000 0.004 0.012
#> SRR2001187 3 0.2357 0.915 0.092 0.004 0.888 0.000 0.004 0.012
#> SRR2001180 1 0.2239 0.530 0.908 0.048 0.000 0.000 0.020 0.024
#> SRR2001181 1 0.1991 0.530 0.920 0.044 0.000 0.000 0.012 0.024
#> SRR2001182 1 0.2151 0.530 0.912 0.048 0.000 0.000 0.016 0.024
#> SRR2001183 1 0.2313 0.524 0.904 0.044 0.000 0.000 0.016 0.036
#> SRR2001176 3 0.3397 0.912 0.092 0.036 0.836 0.000 0.000 0.036
#> SRR2001177 3 0.3179 0.914 0.092 0.028 0.848 0.000 0.000 0.032
#> SRR2001178 3 0.2113 0.916 0.092 0.004 0.896 0.000 0.000 0.008
#> SRR2001179 3 0.2368 0.916 0.092 0.008 0.888 0.000 0.004 0.008
#> SRR2001172 3 0.2561 0.915 0.092 0.008 0.880 0.000 0.004 0.016
#> SRR2001173 3 0.2580 0.917 0.092 0.008 0.880 0.000 0.008 0.012
#> SRR2001174 3 0.2561 0.915 0.092 0.008 0.880 0.000 0.004 0.016
#> SRR2001175 3 0.2661 0.915 0.092 0.012 0.876 0.000 0.004 0.016
#> SRR2001168 1 0.4872 -0.884 0.492 0.020 0.000 0.000 0.024 0.464
#> SRR2001169 1 0.4937 -0.879 0.492 0.028 0.000 0.000 0.020 0.460
#> SRR2001170 1 0.4937 -0.879 0.492 0.028 0.000 0.000 0.020 0.460
#> SRR2001171 1 0.4872 -0.882 0.492 0.024 0.000 0.000 0.020 0.464
#> SRR2001164 1 0.1297 0.554 0.948 0.040 0.000 0.000 0.012 0.000
#> SRR2001165 1 0.1594 0.552 0.932 0.052 0.000 0.000 0.016 0.000
#> SRR2001166 1 0.0972 0.554 0.964 0.028 0.000 0.000 0.008 0.000
#> SRR2001167 1 0.0972 0.555 0.964 0.028 0.000 0.000 0.008 0.000
#> SRR2001160 1 0.2123 0.529 0.912 0.052 0.000 0.000 0.012 0.024
#> SRR2001161 1 0.2058 0.530 0.916 0.048 0.000 0.000 0.012 0.024
#> SRR2001162 1 0.2265 0.524 0.904 0.056 0.000 0.000 0.012 0.028
#> SRR2001163 1 0.2058 0.530 0.916 0.048 0.000 0.000 0.012 0.024
#> SRR2001156 1 0.1745 0.550 0.920 0.068 0.000 0.000 0.012 0.000
#> SRR2001157 1 0.1913 0.550 0.908 0.080 0.000 0.000 0.012 0.000
#> SRR2001158 1 0.1745 0.550 0.920 0.068 0.000 0.000 0.012 0.000
#> SRR2001159 1 0.1686 0.552 0.924 0.064 0.000 0.000 0.012 0.000
#> SRR2001152 1 0.4437 -0.819 0.540 0.020 0.000 0.000 0.004 0.436
#> SRR2001153 1 0.4570 -0.590 0.596 0.024 0.000 0.000 0.012 0.368
#> SRR2001154 1 0.4387 -0.662 0.584 0.016 0.000 0.000 0.008 0.392
#> SRR2001155 1 0.4374 -0.852 0.532 0.016 0.000 0.000 0.004 0.448
#> SRR2001148 3 0.2144 0.916 0.092 0.004 0.896 0.000 0.004 0.004
#> SRR2001149 3 0.2306 0.917 0.092 0.004 0.888 0.000 0.000 0.016
#> SRR2001150 3 0.2001 0.915 0.092 0.004 0.900 0.000 0.000 0.004
#> SRR2001151 3 0.2256 0.918 0.092 0.004 0.892 0.000 0.004 0.008
#> SRR2001144 1 0.4128 -0.979 0.500 0.004 0.000 0.000 0.004 0.492
#> SRR2001145 6 0.3999 0.000 0.496 0.004 0.000 0.000 0.000 0.500
#> SRR2001146 1 0.4227 -0.979 0.496 0.004 0.000 0.000 0.008 0.492
#> SRR2001147 1 0.4222 -0.914 0.516 0.008 0.000 0.000 0.004 0.472
#> SRR2001140 1 0.4314 -0.972 0.500 0.012 0.000 0.000 0.004 0.484
#> SRR2001142 1 0.4097 -0.979 0.500 0.008 0.000 0.000 0.000 0.492
#> SRR2001143 1 0.4184 -0.975 0.500 0.012 0.000 0.000 0.000 0.488
#> SRR2001136 3 0.5734 0.867 0.092 0.152 0.648 0.000 0.000 0.108
#> SRR2001137 3 0.5734 0.867 0.092 0.152 0.648 0.000 0.000 0.108
#> SRR2001138 3 0.5734 0.867 0.092 0.152 0.648 0.000 0.000 0.108
#> SRR2001139 3 0.5701 0.868 0.092 0.148 0.652 0.000 0.000 0.108
#> SRR2001132 3 0.5536 0.876 0.092 0.128 0.680 0.000 0.004 0.096
#> SRR2001133 3 0.5503 0.877 0.092 0.120 0.684 0.000 0.004 0.100
#> SRR2001134 3 0.5809 0.869 0.092 0.140 0.652 0.000 0.004 0.112
#> SRR2001135 3 0.5703 0.873 0.092 0.128 0.664 0.000 0.004 0.112
#> SRR2001128 1 0.1426 0.551 0.948 0.028 0.000 0.000 0.016 0.008
#> SRR2001129 1 0.1230 0.546 0.956 0.028 0.000 0.000 0.008 0.008
#> SRR2001130 1 0.0806 0.551 0.972 0.020 0.000 0.000 0.008 0.000
#> SRR2001131 1 0.1149 0.550 0.960 0.024 0.000 0.000 0.008 0.008
#> SRR2001124 1 0.1895 0.550 0.912 0.072 0.000 0.000 0.016 0.000
#> SRR2001125 1 0.2009 0.552 0.908 0.068 0.000 0.000 0.024 0.000
#> SRR2001126 1 0.1563 0.553 0.932 0.056 0.000 0.000 0.012 0.000
#> SRR2001127 1 0.1686 0.552 0.924 0.064 0.000 0.000 0.012 0.000
#> SRR2001120 1 0.4652 -0.947 0.496 0.020 0.000 0.000 0.012 0.472
#> SRR2001121 1 0.4579 -0.942 0.496 0.016 0.000 0.000 0.012 0.476
#> SRR2001122 1 0.4731 -0.921 0.492 0.016 0.000 0.000 0.020 0.472
#> SRR2001123 1 0.4658 -0.916 0.492 0.016 0.000 0.000 0.016 0.476
#> SRR2001116 1 0.4649 -0.403 0.632 0.028 0.000 0.000 0.020 0.320
#> SRR2001117 1 0.4638 -0.404 0.632 0.032 0.000 0.000 0.016 0.320
#> SRR2001118 1 0.3384 0.291 0.800 0.024 0.000 0.000 0.008 0.168
#> SRR2001119 1 0.3748 0.166 0.760 0.028 0.000 0.000 0.008 0.204
#> SRR2001112 3 0.5726 0.867 0.092 0.156 0.648 0.000 0.000 0.104
#> SRR2001113 3 0.5829 0.867 0.092 0.152 0.648 0.000 0.004 0.104
#> SRR2001114 3 0.5726 0.867 0.092 0.156 0.648 0.000 0.000 0.104
#> SRR2001115 3 0.5726 0.867 0.092 0.156 0.648 0.000 0.000 0.104
#> SRR2001108 4 0.6717 0.510 0.000 0.048 0.004 0.472 0.216 0.260
#> SRR2001109 4 0.6801 0.510 0.000 0.048 0.008 0.472 0.216 0.256
#> SRR2001110 4 0.6720 0.508 0.000 0.048 0.004 0.472 0.220 0.256
#> SRR2001111 4 0.6717 0.510 0.000 0.048 0.004 0.472 0.216 0.260
#> SRR2001104 2 0.5746 0.946 0.000 0.552 0.004 0.116 0.312 0.016
#> SRR2001105 2 0.5746 0.944 0.000 0.552 0.004 0.116 0.312 0.016
#> SRR2001106 2 0.5614 0.945 0.000 0.556 0.000 0.116 0.312 0.016
#> SRR2001107 2 0.5441 0.947 0.000 0.564 0.000 0.116 0.312 0.008
#> SRR2001100 2 0.5626 0.940 0.000 0.552 0.000 0.116 0.316 0.016
#> SRR2001101 2 0.5614 0.943 0.000 0.556 0.000 0.116 0.312 0.016
#> SRR2001102 2 0.5626 0.940 0.000 0.552 0.000 0.116 0.316 0.016
#> SRR2001103 2 0.5614 0.943 0.000 0.556 0.000 0.116 0.312 0.016
#> SRR2001096 2 0.6807 0.920 0.000 0.508 0.044 0.116 0.292 0.040
#> SRR2001097 2 0.6807 0.920 0.000 0.508 0.044 0.116 0.292 0.040
#> SRR2001098 2 0.6807 0.920 0.000 0.508 0.044 0.116 0.292 0.040
#> SRR2001099 2 0.6807 0.920 0.000 0.508 0.044 0.116 0.292 0.040
#> SRR2001092 2 0.5786 0.949 0.000 0.568 0.012 0.116 0.292 0.012
#> SRR2001093 2 0.5696 0.951 0.000 0.572 0.008 0.116 0.292 0.012
#> SRR2001094 2 0.5696 0.950 0.000 0.572 0.008 0.116 0.292 0.012
#> SRR2001095 2 0.5696 0.950 0.000 0.572 0.008 0.116 0.292 0.012
#> SRR2001088 4 0.1167 0.792 0.000 0.008 0.020 0.960 0.000 0.012
#> SRR2001089 4 0.1167 0.791 0.000 0.008 0.012 0.960 0.000 0.020
#> SRR2001090 4 0.1078 0.792 0.000 0.016 0.012 0.964 0.000 0.008
#> SRR2001091 4 0.1448 0.789 0.000 0.012 0.024 0.948 0.000 0.016
#> SRR2001084 4 0.6753 0.510 0.000 0.052 0.004 0.472 0.216 0.256
#> SRR2001085 4 0.6717 0.516 0.000 0.052 0.004 0.480 0.208 0.256
#> SRR2001086 4 0.6753 0.510 0.000 0.052 0.004 0.472 0.216 0.256
#> SRR2001087 4 0.6753 0.510 0.000 0.052 0.004 0.472 0.216 0.256
#> SRR2001080 2 0.5385 0.951 0.000 0.580 0.000 0.116 0.296 0.008
#> SRR2001081 2 0.5282 0.953 0.000 0.584 0.004 0.116 0.296 0.000
#> SRR2001082 2 0.5148 0.952 0.000 0.588 0.000 0.116 0.296 0.000
#> SRR2001083 2 0.5385 0.951 0.000 0.580 0.000 0.116 0.296 0.008
#> SRR2001076 2 0.5475 0.952 0.000 0.576 0.000 0.116 0.296 0.012
#> SRR2001077 2 0.5609 0.950 0.000 0.572 0.004 0.116 0.296 0.012
#> SRR2001078 2 0.5475 0.952 0.000 0.576 0.000 0.116 0.296 0.012
#> SRR2001079 2 0.5558 0.951 0.000 0.572 0.000 0.116 0.296 0.016
#> SRR2001072 4 0.0964 0.789 0.000 0.012 0.016 0.968 0.000 0.004
#> SRR2001073 4 0.1364 0.789 0.000 0.012 0.020 0.952 0.000 0.016
#> SRR2001074 4 0.1364 0.789 0.000 0.012 0.020 0.952 0.000 0.016
#> SRR2001075 4 0.1364 0.789 0.000 0.012 0.020 0.952 0.000 0.016
#> SRR2001068 5 0.1556 0.987 0.000 0.000 0.000 0.080 0.920 0.000
#> SRR2001069 5 0.1663 0.974 0.000 0.000 0.000 0.088 0.912 0.000
#> SRR2001070 5 0.1556 0.987 0.000 0.000 0.000 0.080 0.920 0.000
#> SRR2001071 5 0.1556 0.987 0.000 0.000 0.000 0.080 0.920 0.000
#> SRR2001064 2 0.6807 0.920 0.000 0.508 0.044 0.116 0.292 0.040
#> SRR2001065 2 0.6807 0.920 0.000 0.508 0.044 0.116 0.292 0.040
#> SRR2001066 2 0.6807 0.920 0.000 0.508 0.044 0.116 0.292 0.040
#> SRR2001067 2 0.6807 0.920 0.000 0.508 0.044 0.116 0.292 0.040
#> SRR2001060 4 0.1078 0.789 0.000 0.012 0.016 0.964 0.000 0.008
#> SRR2001061 4 0.1269 0.789 0.000 0.012 0.020 0.956 0.000 0.012
#> SRR2001062 4 0.1078 0.790 0.000 0.012 0.016 0.964 0.000 0.008
#> SRR2001063 4 0.1078 0.790 0.000 0.012 0.016 0.964 0.000 0.008
#> SRR2001056 4 0.6699 0.513 0.000 0.048 0.004 0.476 0.212 0.260
#> SRR2001057 4 0.6717 0.510 0.000 0.048 0.004 0.472 0.216 0.260
#> SRR2001058 4 0.6717 0.510 0.000 0.048 0.004 0.472 0.216 0.260
#> SRR2001059 4 0.6717 0.510 0.000 0.048 0.004 0.472 0.216 0.260
#> SRR2001052 5 0.2056 0.975 0.000 0.012 0.000 0.080 0.904 0.004
#> SRR2001053 5 0.2169 0.975 0.000 0.012 0.000 0.080 0.900 0.008
#> SRR2001054 5 0.2056 0.975 0.000 0.012 0.000 0.080 0.904 0.004
#> SRR2001055 5 0.2056 0.975 0.000 0.012 0.000 0.080 0.904 0.004
#> SRR2001048 5 0.1556 0.987 0.000 0.000 0.000 0.080 0.920 0.000
#> SRR2001049 5 0.1700 0.986 0.000 0.000 0.000 0.080 0.916 0.004
#> SRR2001050 5 0.1556 0.987 0.000 0.000 0.000 0.080 0.920 0.000
#> SRR2001051 5 0.1556 0.987 0.000 0.000 0.000 0.080 0.920 0.000
#> SRR2001044 4 0.1511 0.790 0.000 0.012 0.012 0.944 0.000 0.032
#> SRR2001045 4 0.1585 0.790 0.000 0.012 0.012 0.940 0.000 0.036
#> SRR2001046 4 0.1332 0.790 0.000 0.012 0.008 0.952 0.000 0.028
#> SRR2001047 4 0.1511 0.790 0.000 0.012 0.012 0.944 0.000 0.032
#> SRR2001040 4 0.0291 0.791 0.000 0.004 0.000 0.992 0.000 0.004
#> SRR2001041 4 0.0146 0.791 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR2001042 4 0.0146 0.791 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR2001043 4 0.0291 0.791 0.000 0.004 0.004 0.992 0.000 0.000
#> SRR2001036 4 0.1396 0.792 0.000 0.012 0.008 0.952 0.004 0.024
#> SRR2001037 4 0.1801 0.788 0.000 0.012 0.004 0.932 0.012 0.040
#> SRR2001038 4 0.2238 0.778 0.000 0.008 0.004 0.904 0.016 0.068
#> SRR2001039 4 0.1294 0.791 0.000 0.008 0.004 0.956 0.008 0.024
#> SRR2001028 4 0.1585 0.790 0.000 0.012 0.012 0.940 0.000 0.036
#> SRR2001029 4 0.1409 0.790 0.000 0.012 0.008 0.948 0.000 0.032
#> SRR2001030 4 0.1585 0.790 0.000 0.012 0.012 0.940 0.000 0.036
#> SRR2001031 4 0.1657 0.790 0.000 0.012 0.012 0.936 0.000 0.040
#> SRR2001024 4 0.0260 0.791 0.000 0.008 0.000 0.992 0.000 0.000
#> SRR2001025 4 0.0862 0.792 0.000 0.004 0.016 0.972 0.000 0.008
#> SRR2001026 4 0.1078 0.790 0.000 0.016 0.012 0.964 0.000 0.008
#> SRR2001027 4 0.0405 0.791 0.000 0.008 0.004 0.988 0.000 0.000
#> SRR2001020 2 0.5732 0.944 0.000 0.580 0.008 0.116 0.280 0.016
#> SRR2001021 2 0.5882 0.945 0.000 0.572 0.008 0.116 0.280 0.024
#> SRR2001022 2 0.5732 0.944 0.000 0.580 0.008 0.116 0.280 0.016
#> SRR2001023 2 0.5951 0.944 0.000 0.568 0.008 0.116 0.280 0.028
#> SRR2001016 4 0.6915 0.473 0.000 0.060 0.004 0.448 0.240 0.248
#> SRR2001017 4 0.6915 0.473 0.000 0.060 0.004 0.448 0.240 0.248
#> SRR2001018 4 0.6915 0.473 0.000 0.060 0.004 0.448 0.240 0.248
#> SRR2001019 4 0.6915 0.473 0.000 0.060 0.004 0.448 0.240 0.248
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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.5031 0.497 0.497
#> 3 3 1.000 0.998 0.997 0.2208 0.889 0.777
#> 4 4 1.000 0.990 0.987 0.2038 0.873 0.671
#> 5 5 0.880 0.893 0.881 0.0561 0.972 0.891
#> 6 6 0.877 0.839 0.868 0.0381 0.909 0.629
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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001033 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001034 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001035 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001204 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001205 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001206 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001207 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001200 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001201 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001202 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001203 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001196 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001197 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001198 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001199 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001192 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001193 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001194 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001195 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001188 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001189 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001190 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001191 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001184 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001185 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001186 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001187 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001180 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001181 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001182 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001183 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001176 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001177 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001178 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001179 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001172 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001173 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001174 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001175 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001168 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001169 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001170 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001171 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001164 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001165 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001166 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001167 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001160 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001161 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001162 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001163 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001156 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001157 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001158 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001159 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001152 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001153 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001154 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001155 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001148 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001149 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001150 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001151 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001144 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001145 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001146 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001147 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001140 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001142 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001143 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001136 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001137 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001138 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001139 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001132 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001133 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001134 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001135 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001128 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001129 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001130 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001131 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001124 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001125 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001126 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001127 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001120 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001121 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001122 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001123 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001116 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001117 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001118 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001119 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001112 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001113 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001114 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001115 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001108 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001109 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001110 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001111 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001104 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001105 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001106 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001107 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001100 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001101 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001102 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001103 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001096 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001097 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001098 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001099 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001092 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001093 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001094 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001095 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001088 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001089 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001090 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001091 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001084 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001085 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001086 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001087 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001080 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001081 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001082 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001083 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001076 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001077 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001078 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001079 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001072 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001073 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001074 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001075 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001068 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001069 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001070 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001071 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001064 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001065 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001066 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001067 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001060 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001061 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001062 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001063 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001056 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001057 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001058 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001059 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001052 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001053 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001054 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001055 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001048 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001049 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001050 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001051 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001044 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001045 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001046 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001047 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001040 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001041 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001042 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001043 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001036 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001037 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001038 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001039 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001028 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001029 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001030 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001031 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001024 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001025 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001026 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001027 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001020 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001021 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001022 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001023 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001016 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001017 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001018 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001019 2 0.0000 0.996 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.1211 0.972 0.000 0.960 0 0.040
#> SRR2001033 2 0.1637 0.957 0.000 0.940 0 0.060
#> SRR2001034 2 0.1118 0.974 0.000 0.964 0 0.036
#> SRR2001035 2 0.1211 0.972 0.000 0.960 0 0.040
#> SRR2001204 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001205 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001206 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001207 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001200 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001201 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001202 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001203 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001196 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001197 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001198 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001199 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001192 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001193 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001194 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001195 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001188 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001189 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001190 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001191 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001184 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001185 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001186 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001187 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001180 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001181 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001182 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001183 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001176 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001177 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001178 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001179 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001172 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001173 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001174 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001175 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001168 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001169 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001170 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001171 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001164 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001165 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001166 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001167 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001160 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001161 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001162 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001163 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001156 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001157 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001158 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001159 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001152 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001153 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001154 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001155 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001148 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001149 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001150 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001151 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001144 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001145 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001146 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001147 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001140 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001142 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001143 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001136 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001137 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001138 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001139 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001132 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001133 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001134 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001135 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001128 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001129 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001130 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001131 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001124 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001125 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001126 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001127 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001120 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001121 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001122 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001123 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001116 1 0.0592 0.992 0.984 0.000 0 0.016
#> SRR2001117 1 0.0188 0.994 0.996 0.000 0 0.004
#> SRR2001118 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001119 1 0.0000 0.995 1.000 0.000 0 0.000
#> SRR2001112 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001113 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001114 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001115 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001108 4 0.0592 0.983 0.000 0.016 0 0.984
#> SRR2001109 4 0.0592 0.983 0.000 0.016 0 0.984
#> SRR2001110 4 0.0592 0.983 0.000 0.016 0 0.984
#> SRR2001111 4 0.0592 0.983 0.000 0.016 0 0.984
#> SRR2001104 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001105 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001106 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001107 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001100 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001101 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001102 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001103 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001096 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001097 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001098 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001099 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001092 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001093 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001094 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001095 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001088 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001089 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001090 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001091 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001084 4 0.0592 0.983 0.000 0.016 0 0.984
#> SRR2001085 4 0.0592 0.983 0.000 0.016 0 0.984
#> SRR2001086 4 0.0592 0.983 0.000 0.016 0 0.984
#> SRR2001087 4 0.0592 0.983 0.000 0.016 0 0.984
#> SRR2001080 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001081 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001082 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001083 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001076 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001077 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001078 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001079 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001072 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001073 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001074 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001075 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001068 2 0.1302 0.970 0.000 0.956 0 0.044
#> SRR2001069 2 0.1940 0.942 0.000 0.924 0 0.076
#> SRR2001070 2 0.1118 0.974 0.000 0.964 0 0.036
#> SRR2001071 2 0.1211 0.972 0.000 0.960 0 0.040
#> SRR2001064 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001065 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001066 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001067 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001060 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001061 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001062 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001063 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001056 4 0.0592 0.983 0.000 0.016 0 0.984
#> SRR2001057 4 0.0592 0.983 0.000 0.016 0 0.984
#> SRR2001058 4 0.0592 0.983 0.000 0.016 0 0.984
#> SRR2001059 4 0.0592 0.983 0.000 0.016 0 0.984
#> SRR2001052 2 0.0817 0.976 0.000 0.976 0 0.024
#> SRR2001053 2 0.0921 0.976 0.000 0.972 0 0.028
#> SRR2001054 2 0.0817 0.976 0.000 0.976 0 0.024
#> SRR2001055 2 0.0817 0.976 0.000 0.976 0 0.024
#> SRR2001048 2 0.1302 0.970 0.000 0.956 0 0.044
#> SRR2001049 2 0.1302 0.970 0.000 0.956 0 0.044
#> SRR2001050 2 0.1211 0.972 0.000 0.960 0 0.040
#> SRR2001051 2 0.1211 0.972 0.000 0.960 0 0.040
#> SRR2001044 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001045 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001046 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001047 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001040 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001041 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001042 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001043 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001036 4 0.1022 0.988 0.000 0.032 0 0.968
#> SRR2001037 4 0.0707 0.985 0.000 0.020 0 0.980
#> SRR2001038 4 0.0921 0.987 0.000 0.028 0 0.972
#> SRR2001039 4 0.0921 0.987 0.000 0.028 0 0.972
#> SRR2001028 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001029 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001030 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001031 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001024 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001025 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001026 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001027 4 0.1211 0.990 0.000 0.040 0 0.960
#> SRR2001020 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001021 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001022 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001023 2 0.0000 0.988 0.000 1.000 0 0.000
#> SRR2001016 4 0.0592 0.983 0.000 0.016 0 0.984
#> SRR2001017 4 0.0592 0.983 0.000 0.016 0 0.984
#> SRR2001018 4 0.0592 0.983 0.000 0.016 0 0.984
#> SRR2001019 4 0.0592 0.983 0.000 0.016 0 0.984
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 5 0.4294 0.980 0.000 0.468 0.000 0.000 0.532
#> SRR2001033 5 0.4546 0.976 0.000 0.460 0.000 0.008 0.532
#> SRR2001034 5 0.4297 0.977 0.000 0.472 0.000 0.000 0.528
#> SRR2001035 5 0.4291 0.982 0.000 0.464 0.000 0.000 0.536
#> SRR2001204 1 0.4060 0.788 0.640 0.000 0.000 0.000 0.360
#> SRR2001205 1 0.4060 0.788 0.640 0.000 0.000 0.000 0.360
#> SRR2001206 1 0.4060 0.788 0.640 0.000 0.000 0.000 0.360
#> SRR2001207 1 0.4060 0.788 0.640 0.000 0.000 0.000 0.360
#> SRR2001200 1 0.0290 0.882 0.992 0.000 0.000 0.000 0.008
#> SRR2001201 1 0.0290 0.882 0.992 0.000 0.000 0.000 0.008
#> SRR2001202 1 0.0290 0.882 0.992 0.000 0.000 0.000 0.008
#> SRR2001203 1 0.0404 0.881 0.988 0.000 0.000 0.000 0.012
#> SRR2001196 1 0.0290 0.882 0.992 0.000 0.000 0.000 0.008
#> SRR2001197 1 0.0290 0.882 0.992 0.000 0.000 0.000 0.008
#> SRR2001198 1 0.0404 0.881 0.988 0.000 0.000 0.000 0.012
#> SRR2001199 1 0.0290 0.882 0.992 0.000 0.000 0.000 0.008
#> SRR2001192 3 0.0162 0.995 0.000 0.000 0.996 0.000 0.004
#> SRR2001193 3 0.0000 0.995 0.000 0.000 1.000 0.000 0.000
#> SRR2001194 3 0.0000 0.995 0.000 0.000 1.000 0.000 0.000
#> SRR2001195 3 0.0000 0.995 0.000 0.000 1.000 0.000 0.000
#> SRR2001188 1 0.0510 0.885 0.984 0.000 0.000 0.000 0.016
#> SRR2001189 1 0.0000 0.883 1.000 0.000 0.000 0.000 0.000
#> SRR2001190 1 0.0703 0.885 0.976 0.000 0.000 0.000 0.024
#> SRR2001191 1 0.0162 0.884 0.996 0.000 0.000 0.000 0.004
#> SRR2001184 3 0.0000 0.995 0.000 0.000 1.000 0.000 0.000
#> SRR2001185 3 0.0000 0.995 0.000 0.000 1.000 0.000 0.000
#> SRR2001186 3 0.0000 0.995 0.000 0.000 1.000 0.000 0.000
#> SRR2001187 3 0.0000 0.995 0.000 0.000 1.000 0.000 0.000
#> SRR2001180 1 0.0404 0.885 0.988 0.000 0.000 0.000 0.012
#> SRR2001181 1 0.0510 0.885 0.984 0.000 0.000 0.000 0.016
#> SRR2001182 1 0.0510 0.884 0.984 0.000 0.000 0.000 0.016
#> SRR2001183 1 0.0880 0.883 0.968 0.000 0.000 0.000 0.032
#> SRR2001176 3 0.0162 0.995 0.000 0.000 0.996 0.000 0.004
#> SRR2001177 3 0.0000 0.995 0.000 0.000 1.000 0.000 0.000
#> SRR2001178 3 0.0000 0.995 0.000 0.000 1.000 0.000 0.000
#> SRR2001179 3 0.0000 0.995 0.000 0.000 1.000 0.000 0.000
#> SRR2001172 3 0.0000 0.995 0.000 0.000 1.000 0.000 0.000
#> SRR2001173 3 0.0000 0.995 0.000 0.000 1.000 0.000 0.000
#> SRR2001174 3 0.0000 0.995 0.000 0.000 1.000 0.000 0.000
#> SRR2001175 3 0.0000 0.995 0.000 0.000 1.000 0.000 0.000
#> SRR2001168 1 0.4088 0.783 0.632 0.000 0.000 0.000 0.368
#> SRR2001169 1 0.4101 0.780 0.628 0.000 0.000 0.000 0.372
#> SRR2001170 1 0.4074 0.785 0.636 0.000 0.000 0.000 0.364
#> SRR2001171 1 0.4074 0.785 0.636 0.000 0.000 0.000 0.364
#> SRR2001164 1 0.0290 0.882 0.992 0.000 0.000 0.000 0.008
#> SRR2001165 1 0.0162 0.883 0.996 0.000 0.000 0.000 0.004
#> SRR2001166 1 0.0404 0.881 0.988 0.000 0.000 0.000 0.012
#> SRR2001167 1 0.0162 0.883 0.996 0.000 0.000 0.000 0.004
#> SRR2001160 1 0.0510 0.884 0.984 0.000 0.000 0.000 0.016
#> SRR2001161 1 0.0510 0.884 0.984 0.000 0.000 0.000 0.016
#> SRR2001162 1 0.0510 0.884 0.984 0.000 0.000 0.000 0.016
#> SRR2001163 1 0.0510 0.884 0.984 0.000 0.000 0.000 0.016
#> SRR2001156 1 0.0290 0.882 0.992 0.000 0.000 0.000 0.008
#> SRR2001157 1 0.0290 0.882 0.992 0.000 0.000 0.000 0.008
#> SRR2001158 1 0.0290 0.882 0.992 0.000 0.000 0.000 0.008
#> SRR2001159 1 0.0290 0.882 0.992 0.000 0.000 0.000 0.008
#> SRR2001152 1 0.3661 0.825 0.724 0.000 0.000 0.000 0.276
#> SRR2001153 1 0.3586 0.828 0.736 0.000 0.000 0.000 0.264
#> SRR2001154 1 0.3730 0.821 0.712 0.000 0.000 0.000 0.288
#> SRR2001155 1 0.3796 0.817 0.700 0.000 0.000 0.000 0.300
#> SRR2001148 3 0.0000 0.995 0.000 0.000 1.000 0.000 0.000
#> SRR2001149 3 0.0000 0.995 0.000 0.000 1.000 0.000 0.000
#> SRR2001150 3 0.0000 0.995 0.000 0.000 1.000 0.000 0.000
#> SRR2001151 3 0.0000 0.995 0.000 0.000 1.000 0.000 0.000
#> SRR2001144 1 0.3876 0.811 0.684 0.000 0.000 0.000 0.316
#> SRR2001145 1 0.3949 0.804 0.668 0.000 0.000 0.000 0.332
#> SRR2001146 1 0.3913 0.807 0.676 0.000 0.000 0.000 0.324
#> SRR2001147 1 0.3876 0.811 0.684 0.000 0.000 0.000 0.316
#> SRR2001140 1 0.3913 0.807 0.676 0.000 0.000 0.000 0.324
#> SRR2001142 1 0.3932 0.806 0.672 0.000 0.000 0.000 0.328
#> SRR2001143 1 0.3932 0.806 0.672 0.000 0.000 0.000 0.328
#> SRR2001136 3 0.0510 0.993 0.000 0.000 0.984 0.000 0.016
#> SRR2001137 3 0.0510 0.993 0.000 0.000 0.984 0.000 0.016
#> SRR2001138 3 0.0510 0.993 0.000 0.000 0.984 0.000 0.016
#> SRR2001139 3 0.0404 0.993 0.000 0.000 0.988 0.000 0.012
#> SRR2001132 3 0.0510 0.993 0.000 0.000 0.984 0.000 0.016
#> SRR2001133 3 0.0510 0.993 0.000 0.000 0.984 0.000 0.016
#> SRR2001134 3 0.0510 0.993 0.000 0.000 0.984 0.000 0.016
#> SRR2001135 3 0.0510 0.993 0.000 0.000 0.984 0.000 0.016
#> SRR2001128 1 0.0290 0.884 0.992 0.000 0.000 0.000 0.008
#> SRR2001129 1 0.0290 0.884 0.992 0.000 0.000 0.000 0.008
#> SRR2001130 1 0.0000 0.883 1.000 0.000 0.000 0.000 0.000
#> SRR2001131 1 0.0162 0.884 0.996 0.000 0.000 0.000 0.004
#> SRR2001124 1 0.0290 0.882 0.992 0.000 0.000 0.000 0.008
#> SRR2001125 1 0.0162 0.883 0.996 0.000 0.000 0.000 0.004
#> SRR2001126 1 0.0290 0.882 0.992 0.000 0.000 0.000 0.008
#> SRR2001127 1 0.0290 0.882 0.992 0.000 0.000 0.000 0.008
#> SRR2001120 1 0.3913 0.808 0.676 0.000 0.000 0.000 0.324
#> SRR2001121 1 0.3999 0.798 0.656 0.000 0.000 0.000 0.344
#> SRR2001122 1 0.4015 0.795 0.652 0.000 0.000 0.000 0.348
#> SRR2001123 1 0.3999 0.798 0.656 0.000 0.000 0.000 0.344
#> SRR2001116 1 0.2966 0.851 0.816 0.000 0.000 0.000 0.184
#> SRR2001117 1 0.2424 0.864 0.868 0.000 0.000 0.000 0.132
#> SRR2001118 1 0.1410 0.880 0.940 0.000 0.000 0.000 0.060
#> SRR2001119 1 0.1908 0.873 0.908 0.000 0.000 0.000 0.092
#> SRR2001112 3 0.0510 0.993 0.000 0.000 0.984 0.000 0.016
#> SRR2001113 3 0.0510 0.993 0.000 0.000 0.984 0.000 0.016
#> SRR2001114 3 0.0510 0.993 0.000 0.000 0.984 0.000 0.016
#> SRR2001115 3 0.0510 0.993 0.000 0.000 0.984 0.000 0.016
#> SRR2001108 4 0.4114 0.650 0.000 0.000 0.000 0.624 0.376
#> SRR2001109 4 0.4114 0.650 0.000 0.000 0.000 0.624 0.376
#> SRR2001110 4 0.4126 0.646 0.000 0.000 0.000 0.620 0.380
#> SRR2001111 4 0.4101 0.654 0.000 0.000 0.000 0.628 0.372
#> SRR2001104 2 0.0290 0.987 0.000 0.992 0.000 0.000 0.008
#> SRR2001105 2 0.0290 0.987 0.000 0.992 0.000 0.000 0.008
#> SRR2001106 2 0.0290 0.987 0.000 0.992 0.000 0.000 0.008
#> SRR2001107 2 0.0290 0.987 0.000 0.992 0.000 0.000 0.008
#> SRR2001100 2 0.0290 0.987 0.000 0.992 0.000 0.000 0.008
#> SRR2001101 2 0.0290 0.987 0.000 0.992 0.000 0.000 0.008
#> SRR2001102 2 0.0290 0.987 0.000 0.992 0.000 0.000 0.008
#> SRR2001103 2 0.0290 0.987 0.000 0.992 0.000 0.000 0.008
#> SRR2001096 2 0.0290 0.986 0.000 0.992 0.000 0.000 0.008
#> SRR2001097 2 0.0404 0.981 0.000 0.988 0.000 0.000 0.012
#> SRR2001098 2 0.0290 0.986 0.000 0.992 0.000 0.000 0.008
#> SRR2001099 2 0.0290 0.986 0.000 0.992 0.000 0.000 0.008
#> SRR2001092 2 0.0162 0.989 0.000 0.996 0.000 0.000 0.004
#> SRR2001093 2 0.0162 0.989 0.000 0.996 0.000 0.000 0.004
#> SRR2001094 2 0.0162 0.989 0.000 0.996 0.000 0.000 0.004
#> SRR2001095 2 0.0162 0.989 0.000 0.996 0.000 0.000 0.004
#> SRR2001088 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001089 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001090 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001091 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001084 4 0.4114 0.650 0.000 0.000 0.000 0.624 0.376
#> SRR2001085 4 0.4045 0.667 0.000 0.000 0.000 0.644 0.356
#> SRR2001086 4 0.4114 0.650 0.000 0.000 0.000 0.624 0.376
#> SRR2001087 4 0.4114 0.650 0.000 0.000 0.000 0.624 0.376
#> SRR2001080 2 0.0290 0.987 0.000 0.992 0.000 0.000 0.008
#> SRR2001081 2 0.0000 0.990 0.000 1.000 0.000 0.000 0.000
#> SRR2001082 2 0.0000 0.990 0.000 1.000 0.000 0.000 0.000
#> SRR2001083 2 0.0000 0.990 0.000 1.000 0.000 0.000 0.000
#> SRR2001076 2 0.0162 0.989 0.000 0.996 0.000 0.000 0.004
#> SRR2001077 2 0.0290 0.987 0.000 0.992 0.000 0.000 0.008
#> SRR2001078 2 0.0162 0.989 0.000 0.996 0.000 0.000 0.004
#> SRR2001079 2 0.0000 0.990 0.000 1.000 0.000 0.000 0.000
#> SRR2001072 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001073 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001074 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001075 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001068 5 0.4430 0.975 0.000 0.456 0.000 0.004 0.540
#> SRR2001069 5 0.4538 0.967 0.000 0.452 0.000 0.008 0.540
#> SRR2001070 5 0.4291 0.982 0.000 0.464 0.000 0.000 0.536
#> SRR2001071 5 0.4291 0.982 0.000 0.464 0.000 0.000 0.536
#> SRR2001064 2 0.0290 0.986 0.000 0.992 0.000 0.000 0.008
#> SRR2001065 2 0.0404 0.981 0.000 0.988 0.000 0.000 0.012
#> SRR2001066 2 0.0290 0.986 0.000 0.992 0.000 0.000 0.008
#> SRR2001067 2 0.0290 0.986 0.000 0.992 0.000 0.000 0.008
#> SRR2001060 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001061 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001062 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001063 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001056 4 0.4114 0.650 0.000 0.000 0.000 0.624 0.376
#> SRR2001057 4 0.4114 0.650 0.000 0.000 0.000 0.624 0.376
#> SRR2001058 4 0.4114 0.650 0.000 0.000 0.000 0.624 0.376
#> SRR2001059 4 0.4114 0.650 0.000 0.000 0.000 0.624 0.376
#> SRR2001052 5 0.4304 0.964 0.000 0.484 0.000 0.000 0.516
#> SRR2001053 5 0.4304 0.964 0.000 0.484 0.000 0.000 0.516
#> SRR2001054 5 0.4304 0.964 0.000 0.484 0.000 0.000 0.516
#> SRR2001055 5 0.4304 0.964 0.000 0.484 0.000 0.000 0.516
#> SRR2001048 5 0.4434 0.980 0.000 0.460 0.000 0.004 0.536
#> SRR2001049 5 0.4434 0.980 0.000 0.460 0.000 0.004 0.536
#> SRR2001050 5 0.4291 0.982 0.000 0.464 0.000 0.000 0.536
#> SRR2001051 5 0.4434 0.980 0.000 0.460 0.000 0.004 0.536
#> SRR2001044 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001045 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001046 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001047 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001040 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001041 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001042 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001043 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001036 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001037 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001038 4 0.0404 0.860 0.000 0.000 0.000 0.988 0.012
#> SRR2001039 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001028 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001029 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001030 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001031 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001024 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001025 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001026 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001027 4 0.0000 0.865 0.000 0.000 0.000 1.000 0.000
#> SRR2001020 2 0.0000 0.990 0.000 1.000 0.000 0.000 0.000
#> SRR2001021 2 0.0000 0.990 0.000 1.000 0.000 0.000 0.000
#> SRR2001022 2 0.0000 0.990 0.000 1.000 0.000 0.000 0.000
#> SRR2001023 2 0.0000 0.990 0.000 1.000 0.000 0.000 0.000
#> SRR2001016 4 0.4227 0.596 0.000 0.000 0.000 0.580 0.420
#> SRR2001017 4 0.4235 0.590 0.000 0.000 0.000 0.576 0.424
#> SRR2001018 4 0.4235 0.590 0.000 0.000 0.000 0.576 0.424
#> SRR2001019 4 0.4235 0.590 0.000 0.000 0.000 0.576 0.424
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 5 0.4905 0.533 0.000 0.284 0.000 0.000 0.620 0.096
#> SRR2001033 5 0.4851 0.543 0.000 0.272 0.000 0.000 0.632 0.096
#> SRR2001034 5 0.4939 0.523 0.000 0.292 0.000 0.000 0.612 0.096
#> SRR2001035 5 0.4905 0.533 0.000 0.284 0.000 0.000 0.620 0.096
#> SRR2001204 6 0.3508 0.878 0.292 0.000 0.000 0.000 0.004 0.704
#> SRR2001205 6 0.3528 0.880 0.296 0.000 0.000 0.000 0.004 0.700
#> SRR2001206 6 0.3528 0.880 0.296 0.000 0.000 0.000 0.004 0.700
#> SRR2001207 6 0.3508 0.878 0.292 0.000 0.000 0.000 0.004 0.704
#> SRR2001200 1 0.0622 0.887 0.980 0.000 0.000 0.000 0.012 0.008
#> SRR2001201 1 0.0622 0.887 0.980 0.000 0.000 0.000 0.012 0.008
#> SRR2001202 1 0.0622 0.887 0.980 0.000 0.000 0.000 0.012 0.008
#> SRR2001203 1 0.0622 0.887 0.980 0.000 0.000 0.000 0.012 0.008
#> SRR2001196 1 0.0405 0.891 0.988 0.000 0.000 0.000 0.008 0.004
#> SRR2001197 1 0.0260 0.893 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR2001198 1 0.0405 0.891 0.988 0.000 0.000 0.000 0.008 0.004
#> SRR2001199 1 0.0260 0.893 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR2001192 3 0.0405 0.982 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR2001193 3 0.0405 0.982 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR2001194 3 0.0405 0.982 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR2001195 3 0.0405 0.982 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR2001188 1 0.1010 0.891 0.960 0.000 0.000 0.000 0.004 0.036
#> SRR2001189 1 0.1700 0.845 0.916 0.000 0.000 0.000 0.004 0.080
#> SRR2001190 1 0.1082 0.888 0.956 0.000 0.000 0.000 0.004 0.040
#> SRR2001191 1 0.1152 0.889 0.952 0.000 0.000 0.000 0.004 0.044
#> SRR2001184 3 0.0000 0.982 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001185 3 0.0000 0.982 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001186 3 0.0000 0.982 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001187 3 0.0000 0.982 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001180 1 0.0972 0.893 0.964 0.000 0.000 0.000 0.008 0.028
#> SRR2001181 1 0.0935 0.893 0.964 0.000 0.000 0.000 0.004 0.032
#> SRR2001182 1 0.1333 0.879 0.944 0.000 0.000 0.000 0.008 0.048
#> SRR2001183 1 0.2266 0.798 0.880 0.000 0.000 0.000 0.012 0.108
#> SRR2001176 3 0.0622 0.982 0.000 0.000 0.980 0.000 0.008 0.012
#> SRR2001177 3 0.0146 0.983 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001178 3 0.0000 0.982 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001179 3 0.0146 0.983 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001172 3 0.0000 0.982 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001173 3 0.0405 0.982 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR2001174 3 0.0000 0.982 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001175 3 0.0000 0.982 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001168 6 0.3468 0.871 0.284 0.000 0.000 0.000 0.004 0.712
#> SRR2001169 6 0.3163 0.806 0.232 0.000 0.000 0.000 0.004 0.764
#> SRR2001170 6 0.3426 0.862 0.276 0.000 0.000 0.000 0.004 0.720
#> SRR2001171 6 0.3508 0.878 0.292 0.000 0.000 0.000 0.004 0.704
#> SRR2001164 1 0.0260 0.895 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR2001165 1 0.0806 0.891 0.972 0.000 0.000 0.000 0.008 0.020
#> SRR2001166 1 0.0405 0.895 0.988 0.000 0.000 0.000 0.008 0.004
#> SRR2001167 1 0.0260 0.895 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR2001160 1 0.1151 0.890 0.956 0.000 0.000 0.000 0.012 0.032
#> SRR2001161 1 0.0972 0.892 0.964 0.000 0.000 0.000 0.008 0.028
#> SRR2001162 1 0.1152 0.885 0.952 0.000 0.000 0.000 0.004 0.044
#> SRR2001163 1 0.1152 0.885 0.952 0.000 0.000 0.000 0.004 0.044
#> SRR2001156 1 0.0291 0.893 0.992 0.000 0.000 0.000 0.004 0.004
#> SRR2001157 1 0.0291 0.893 0.992 0.000 0.000 0.000 0.004 0.004
#> SRR2001158 1 0.0000 0.894 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001159 1 0.0000 0.894 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001152 6 0.3997 0.685 0.488 0.000 0.000 0.000 0.004 0.508
#> SRR2001153 1 0.3872 -0.288 0.604 0.000 0.000 0.000 0.004 0.392
#> SRR2001154 1 0.3864 -0.613 0.520 0.000 0.000 0.000 0.000 0.480
#> SRR2001155 6 0.4067 0.790 0.444 0.000 0.000 0.000 0.008 0.548
#> SRR2001148 3 0.0000 0.982 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001149 3 0.0000 0.982 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001150 3 0.0000 0.982 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001151 3 0.0405 0.982 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR2001144 6 0.3993 0.868 0.400 0.000 0.000 0.000 0.008 0.592
#> SRR2001145 6 0.3830 0.884 0.376 0.000 0.000 0.000 0.004 0.620
#> SRR2001146 6 0.3782 0.852 0.412 0.000 0.000 0.000 0.000 0.588
#> SRR2001147 6 0.4032 0.835 0.420 0.000 0.000 0.000 0.008 0.572
#> SRR2001140 6 0.3899 0.863 0.404 0.000 0.000 0.000 0.004 0.592
#> SRR2001142 6 0.3975 0.875 0.392 0.000 0.000 0.000 0.008 0.600
#> SRR2001143 6 0.3727 0.878 0.388 0.000 0.000 0.000 0.000 0.612
#> SRR2001136 3 0.1257 0.974 0.000 0.000 0.952 0.000 0.020 0.028
#> SRR2001137 3 0.1334 0.973 0.000 0.000 0.948 0.000 0.020 0.032
#> SRR2001138 3 0.1257 0.975 0.000 0.000 0.952 0.000 0.020 0.028
#> SRR2001139 3 0.1492 0.972 0.000 0.000 0.940 0.000 0.024 0.036
#> SRR2001132 3 0.1418 0.974 0.000 0.000 0.944 0.000 0.024 0.032
#> SRR2001133 3 0.1176 0.976 0.000 0.000 0.956 0.000 0.020 0.024
#> SRR2001134 3 0.1492 0.973 0.000 0.000 0.940 0.000 0.024 0.036
#> SRR2001135 3 0.1334 0.975 0.000 0.000 0.948 0.000 0.020 0.032
#> SRR2001128 1 0.0935 0.891 0.964 0.000 0.000 0.000 0.004 0.032
#> SRR2001129 1 0.1265 0.885 0.948 0.000 0.000 0.000 0.008 0.044
#> SRR2001130 1 0.1462 0.873 0.936 0.000 0.000 0.000 0.008 0.056
#> SRR2001131 1 0.1285 0.878 0.944 0.000 0.000 0.000 0.004 0.052
#> SRR2001124 1 0.0622 0.889 0.980 0.000 0.000 0.000 0.012 0.008
#> SRR2001125 1 0.0508 0.894 0.984 0.000 0.000 0.000 0.012 0.004
#> SRR2001126 1 0.0000 0.894 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001127 1 0.0000 0.894 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001120 6 0.4273 0.870 0.380 0.000 0.000 0.000 0.024 0.596
#> SRR2001121 6 0.3998 0.888 0.340 0.000 0.000 0.000 0.016 0.644
#> SRR2001122 6 0.3515 0.888 0.324 0.000 0.000 0.000 0.000 0.676
#> SRR2001123 6 0.4004 0.885 0.368 0.000 0.000 0.000 0.012 0.620
#> SRR2001116 1 0.3468 0.313 0.712 0.000 0.000 0.000 0.004 0.284
#> SRR2001117 1 0.3534 0.337 0.716 0.000 0.000 0.000 0.008 0.276
#> SRR2001118 1 0.2706 0.704 0.832 0.000 0.000 0.000 0.008 0.160
#> SRR2001119 1 0.3073 0.598 0.788 0.000 0.000 0.000 0.008 0.204
#> SRR2001112 3 0.1720 0.968 0.000 0.000 0.928 0.000 0.032 0.040
#> SRR2001113 3 0.1720 0.968 0.000 0.000 0.928 0.000 0.032 0.040
#> SRR2001114 3 0.1720 0.968 0.000 0.000 0.928 0.000 0.032 0.040
#> SRR2001115 3 0.1720 0.968 0.000 0.000 0.928 0.000 0.032 0.040
#> SRR2001108 5 0.3872 0.449 0.000 0.000 0.000 0.392 0.604 0.004
#> SRR2001109 5 0.3890 0.442 0.000 0.000 0.000 0.400 0.596 0.004
#> SRR2001110 5 0.3747 0.450 0.000 0.000 0.000 0.396 0.604 0.000
#> SRR2001111 5 0.3774 0.434 0.000 0.000 0.000 0.408 0.592 0.000
#> SRR2001104 2 0.0806 0.975 0.000 0.972 0.000 0.000 0.020 0.008
#> SRR2001105 2 0.0993 0.971 0.000 0.964 0.000 0.000 0.024 0.012
#> SRR2001106 2 0.0909 0.974 0.000 0.968 0.000 0.000 0.020 0.012
#> SRR2001107 2 0.0806 0.975 0.000 0.972 0.000 0.000 0.020 0.008
#> SRR2001100 2 0.0891 0.973 0.000 0.968 0.000 0.000 0.024 0.008
#> SRR2001101 2 0.0717 0.977 0.000 0.976 0.000 0.000 0.016 0.008
#> SRR2001102 2 0.0891 0.973 0.000 0.968 0.000 0.000 0.024 0.008
#> SRR2001103 2 0.0806 0.975 0.000 0.972 0.000 0.000 0.020 0.008
#> SRR2001096 2 0.0972 0.974 0.000 0.964 0.000 0.000 0.008 0.028
#> SRR2001097 2 0.1498 0.950 0.000 0.940 0.000 0.000 0.028 0.032
#> SRR2001098 2 0.0777 0.977 0.000 0.972 0.000 0.000 0.004 0.024
#> SRR2001099 2 0.0972 0.974 0.000 0.964 0.000 0.000 0.008 0.028
#> SRR2001092 2 0.0260 0.981 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR2001093 2 0.0405 0.980 0.000 0.988 0.000 0.000 0.004 0.008
#> SRR2001094 2 0.0000 0.980 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001095 2 0.0260 0.980 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR2001088 4 0.0405 0.978 0.000 0.000 0.000 0.988 0.008 0.004
#> SRR2001089 4 0.0508 0.979 0.000 0.000 0.000 0.984 0.012 0.004
#> SRR2001090 4 0.0146 0.980 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR2001091 4 0.0405 0.978 0.000 0.000 0.000 0.988 0.008 0.004
#> SRR2001084 5 0.3774 0.431 0.000 0.000 0.000 0.408 0.592 0.000
#> SRR2001085 5 0.3930 0.389 0.000 0.000 0.000 0.420 0.576 0.004
#> SRR2001086 5 0.3747 0.447 0.000 0.000 0.000 0.396 0.604 0.000
#> SRR2001087 5 0.3890 0.441 0.000 0.000 0.000 0.400 0.596 0.004
#> SRR2001080 2 0.0508 0.980 0.000 0.984 0.000 0.000 0.004 0.012
#> SRR2001081 2 0.0405 0.981 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR2001082 2 0.0000 0.980 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001083 2 0.0260 0.980 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR2001076 2 0.0291 0.980 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR2001077 2 0.0717 0.977 0.000 0.976 0.000 0.000 0.016 0.008
#> SRR2001078 2 0.0508 0.979 0.000 0.984 0.000 0.000 0.012 0.004
#> SRR2001079 2 0.0146 0.980 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR2001072 4 0.0405 0.978 0.000 0.000 0.000 0.988 0.008 0.004
#> SRR2001073 4 0.0405 0.978 0.000 0.000 0.000 0.988 0.008 0.004
#> SRR2001074 4 0.0405 0.978 0.000 0.000 0.000 0.988 0.008 0.004
#> SRR2001075 4 0.0405 0.978 0.000 0.000 0.000 0.988 0.008 0.004
#> SRR2001068 5 0.4789 0.547 0.000 0.268 0.000 0.000 0.640 0.092
#> SRR2001069 5 0.4749 0.549 0.000 0.260 0.000 0.000 0.648 0.092
#> SRR2001070 5 0.4827 0.543 0.000 0.276 0.000 0.000 0.632 0.092
#> SRR2001071 5 0.4869 0.540 0.000 0.276 0.000 0.000 0.628 0.096
#> SRR2001064 2 0.0858 0.973 0.000 0.968 0.000 0.000 0.004 0.028
#> SRR2001065 2 0.1074 0.972 0.000 0.960 0.000 0.000 0.012 0.028
#> SRR2001066 2 0.0777 0.975 0.000 0.972 0.000 0.000 0.004 0.024
#> SRR2001067 2 0.0858 0.973 0.000 0.968 0.000 0.000 0.004 0.028
#> SRR2001060 4 0.0291 0.979 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR2001061 4 0.0291 0.979 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR2001062 4 0.0405 0.978 0.000 0.000 0.000 0.988 0.008 0.004
#> SRR2001063 4 0.0291 0.979 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR2001056 5 0.3899 0.436 0.000 0.000 0.000 0.404 0.592 0.004
#> SRR2001057 5 0.4002 0.435 0.000 0.000 0.000 0.404 0.588 0.008
#> SRR2001058 5 0.3993 0.438 0.000 0.000 0.000 0.400 0.592 0.008
#> SRR2001059 5 0.3890 0.444 0.000 0.000 0.000 0.400 0.596 0.004
#> SRR2001052 5 0.4986 0.506 0.000 0.304 0.000 0.000 0.600 0.096
#> SRR2001053 5 0.5030 0.491 0.000 0.316 0.000 0.000 0.588 0.096
#> SRR2001054 5 0.4975 0.502 0.000 0.312 0.000 0.000 0.596 0.092
#> SRR2001055 5 0.5001 0.500 0.000 0.308 0.000 0.000 0.596 0.096
#> SRR2001048 5 0.4789 0.548 0.000 0.268 0.000 0.000 0.640 0.092
#> SRR2001049 5 0.4808 0.546 0.000 0.272 0.000 0.000 0.636 0.092
#> SRR2001050 5 0.4845 0.540 0.000 0.280 0.000 0.000 0.628 0.092
#> SRR2001051 5 0.4827 0.543 0.000 0.276 0.000 0.000 0.632 0.092
#> SRR2001044 4 0.1092 0.972 0.000 0.000 0.000 0.960 0.020 0.020
#> SRR2001045 4 0.1168 0.969 0.000 0.000 0.000 0.956 0.028 0.016
#> SRR2001046 4 0.1176 0.970 0.000 0.000 0.000 0.956 0.024 0.020
#> SRR2001047 4 0.1088 0.971 0.000 0.000 0.000 0.960 0.024 0.016
#> SRR2001040 4 0.0146 0.980 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR2001041 4 0.0260 0.980 0.000 0.000 0.000 0.992 0.000 0.008
#> SRR2001042 4 0.0260 0.980 0.000 0.000 0.000 0.992 0.000 0.008
#> SRR2001043 4 0.0260 0.979 0.000 0.000 0.000 0.992 0.000 0.008
#> SRR2001036 4 0.0891 0.973 0.000 0.000 0.000 0.968 0.024 0.008
#> SRR2001037 4 0.1124 0.967 0.000 0.000 0.000 0.956 0.036 0.008
#> SRR2001038 4 0.1333 0.950 0.000 0.000 0.000 0.944 0.048 0.008
#> SRR2001039 4 0.0972 0.969 0.000 0.000 0.000 0.964 0.028 0.008
#> SRR2001028 4 0.1168 0.969 0.000 0.000 0.000 0.956 0.028 0.016
#> SRR2001029 4 0.1257 0.967 0.000 0.000 0.000 0.952 0.028 0.020
#> SRR2001030 4 0.1168 0.969 0.000 0.000 0.000 0.956 0.028 0.016
#> SRR2001031 4 0.1168 0.969 0.000 0.000 0.000 0.956 0.028 0.016
#> SRR2001024 4 0.0405 0.980 0.000 0.000 0.000 0.988 0.004 0.008
#> SRR2001025 4 0.0146 0.980 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR2001026 4 0.0291 0.979 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR2001027 4 0.0146 0.979 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR2001020 2 0.0508 0.977 0.000 0.984 0.000 0.000 0.004 0.012
#> SRR2001021 2 0.0603 0.977 0.000 0.980 0.000 0.000 0.004 0.016
#> SRR2001022 2 0.0603 0.977 0.000 0.980 0.000 0.000 0.004 0.016
#> SRR2001023 2 0.0603 0.977 0.000 0.980 0.000 0.000 0.004 0.016
#> SRR2001016 5 0.3647 0.479 0.000 0.000 0.000 0.360 0.640 0.000
#> SRR2001017 5 0.3782 0.478 0.000 0.000 0.000 0.360 0.636 0.004
#> SRR2001018 5 0.3634 0.482 0.000 0.000 0.000 0.356 0.644 0.000
#> SRR2001019 5 0.3782 0.478 0.000 0.000 0.000 0.360 0.636 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["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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.5031 0.497 0.497
#> 3 3 1.000 1.000 1.000 0.2206 0.889 0.777
#> 4 4 0.804 0.677 0.827 0.1478 0.905 0.753
#> 5 5 0.831 0.861 0.920 0.1176 0.870 0.586
#> 6 6 0.823 0.831 0.893 0.0355 0.970 0.856
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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0 1 0 1 0
#> SRR2001033 2 0 1 0 1 0
#> SRR2001034 2 0 1 0 1 0
#> SRR2001035 2 0 1 0 1 0
#> SRR2001204 1 0 1 1 0 0
#> SRR2001205 1 0 1 1 0 0
#> SRR2001206 1 0 1 1 0 0
#> SRR2001207 1 0 1 1 0 0
#> SRR2001200 1 0 1 1 0 0
#> SRR2001201 1 0 1 1 0 0
#> SRR2001202 1 0 1 1 0 0
#> SRR2001203 1 0 1 1 0 0
#> SRR2001196 1 0 1 1 0 0
#> SRR2001197 1 0 1 1 0 0
#> SRR2001198 1 0 1 1 0 0
#> SRR2001199 1 0 1 1 0 0
#> SRR2001192 3 0 1 0 0 1
#> SRR2001193 3 0 1 0 0 1
#> SRR2001194 3 0 1 0 0 1
#> SRR2001195 3 0 1 0 0 1
#> SRR2001188 1 0 1 1 0 0
#> SRR2001189 1 0 1 1 0 0
#> SRR2001190 1 0 1 1 0 0
#> SRR2001191 1 0 1 1 0 0
#> SRR2001184 3 0 1 0 0 1
#> SRR2001185 3 0 1 0 0 1
#> SRR2001186 3 0 1 0 0 1
#> SRR2001187 3 0 1 0 0 1
#> SRR2001180 1 0 1 1 0 0
#> SRR2001181 1 0 1 1 0 0
#> SRR2001182 1 0 1 1 0 0
#> SRR2001183 1 0 1 1 0 0
#> SRR2001176 3 0 1 0 0 1
#> SRR2001177 3 0 1 0 0 1
#> SRR2001178 3 0 1 0 0 1
#> SRR2001179 3 0 1 0 0 1
#> SRR2001172 3 0 1 0 0 1
#> SRR2001173 3 0 1 0 0 1
#> SRR2001174 3 0 1 0 0 1
#> SRR2001175 3 0 1 0 0 1
#> SRR2001168 1 0 1 1 0 0
#> SRR2001169 1 0 1 1 0 0
#> SRR2001170 1 0 1 1 0 0
#> SRR2001171 1 0 1 1 0 0
#> SRR2001164 1 0 1 1 0 0
#> SRR2001165 1 0 1 1 0 0
#> SRR2001166 1 0 1 1 0 0
#> SRR2001167 1 0 1 1 0 0
#> SRR2001160 1 0 1 1 0 0
#> SRR2001161 1 0 1 1 0 0
#> SRR2001162 1 0 1 1 0 0
#> SRR2001163 1 0 1 1 0 0
#> SRR2001156 1 0 1 1 0 0
#> SRR2001157 1 0 1 1 0 0
#> SRR2001158 1 0 1 1 0 0
#> SRR2001159 1 0 1 1 0 0
#> SRR2001152 1 0 1 1 0 0
#> SRR2001153 1 0 1 1 0 0
#> SRR2001154 1 0 1 1 0 0
#> SRR2001155 1 0 1 1 0 0
#> SRR2001148 3 0 1 0 0 1
#> SRR2001149 3 0 1 0 0 1
#> SRR2001150 3 0 1 0 0 1
#> SRR2001151 3 0 1 0 0 1
#> SRR2001144 1 0 1 1 0 0
#> SRR2001145 1 0 1 1 0 0
#> SRR2001146 1 0 1 1 0 0
#> SRR2001147 1 0 1 1 0 0
#> SRR2001140 1 0 1 1 0 0
#> SRR2001142 1 0 1 1 0 0
#> SRR2001143 1 0 1 1 0 0
#> SRR2001136 3 0 1 0 0 1
#> SRR2001137 3 0 1 0 0 1
#> SRR2001138 3 0 1 0 0 1
#> SRR2001139 3 0 1 0 0 1
#> SRR2001132 3 0 1 0 0 1
#> SRR2001133 3 0 1 0 0 1
#> SRR2001134 3 0 1 0 0 1
#> SRR2001135 3 0 1 0 0 1
#> SRR2001128 1 0 1 1 0 0
#> SRR2001129 1 0 1 1 0 0
#> SRR2001130 1 0 1 1 0 0
#> SRR2001131 1 0 1 1 0 0
#> SRR2001124 1 0 1 1 0 0
#> SRR2001125 1 0 1 1 0 0
#> SRR2001126 1 0 1 1 0 0
#> SRR2001127 1 0 1 1 0 0
#> SRR2001120 1 0 1 1 0 0
#> SRR2001121 1 0 1 1 0 0
#> SRR2001122 1 0 1 1 0 0
#> SRR2001123 1 0 1 1 0 0
#> SRR2001116 1 0 1 1 0 0
#> SRR2001117 1 0 1 1 0 0
#> SRR2001118 1 0 1 1 0 0
#> SRR2001119 1 0 1 1 0 0
#> SRR2001112 3 0 1 0 0 1
#> SRR2001113 3 0 1 0 0 1
#> SRR2001114 3 0 1 0 0 1
#> SRR2001115 3 0 1 0 0 1
#> SRR2001108 2 0 1 0 1 0
#> SRR2001109 2 0 1 0 1 0
#> SRR2001110 2 0 1 0 1 0
#> SRR2001111 2 0 1 0 1 0
#> SRR2001104 2 0 1 0 1 0
#> SRR2001105 2 0 1 0 1 0
#> SRR2001106 2 0 1 0 1 0
#> SRR2001107 2 0 1 0 1 0
#> SRR2001100 2 0 1 0 1 0
#> SRR2001101 2 0 1 0 1 0
#> SRR2001102 2 0 1 0 1 0
#> SRR2001103 2 0 1 0 1 0
#> SRR2001096 2 0 1 0 1 0
#> SRR2001097 2 0 1 0 1 0
#> SRR2001098 2 0 1 0 1 0
#> SRR2001099 2 0 1 0 1 0
#> SRR2001092 2 0 1 0 1 0
#> SRR2001093 2 0 1 0 1 0
#> SRR2001094 2 0 1 0 1 0
#> SRR2001095 2 0 1 0 1 0
#> SRR2001088 2 0 1 0 1 0
#> SRR2001089 2 0 1 0 1 0
#> SRR2001090 2 0 1 0 1 0
#> SRR2001091 2 0 1 0 1 0
#> SRR2001084 2 0 1 0 1 0
#> SRR2001085 2 0 1 0 1 0
#> SRR2001086 2 0 1 0 1 0
#> SRR2001087 2 0 1 0 1 0
#> SRR2001080 2 0 1 0 1 0
#> SRR2001081 2 0 1 0 1 0
#> SRR2001082 2 0 1 0 1 0
#> SRR2001083 2 0 1 0 1 0
#> SRR2001076 2 0 1 0 1 0
#> SRR2001077 2 0 1 0 1 0
#> SRR2001078 2 0 1 0 1 0
#> SRR2001079 2 0 1 0 1 0
#> SRR2001072 2 0 1 0 1 0
#> SRR2001073 2 0 1 0 1 0
#> SRR2001074 2 0 1 0 1 0
#> SRR2001075 2 0 1 0 1 0
#> SRR2001068 2 0 1 0 1 0
#> SRR2001069 2 0 1 0 1 0
#> SRR2001070 2 0 1 0 1 0
#> SRR2001071 2 0 1 0 1 0
#> SRR2001064 2 0 1 0 1 0
#> SRR2001065 2 0 1 0 1 0
#> SRR2001066 2 0 1 0 1 0
#> SRR2001067 2 0 1 0 1 0
#> SRR2001060 2 0 1 0 1 0
#> SRR2001061 2 0 1 0 1 0
#> SRR2001062 2 0 1 0 1 0
#> SRR2001063 2 0 1 0 1 0
#> SRR2001056 2 0 1 0 1 0
#> SRR2001057 2 0 1 0 1 0
#> SRR2001058 2 0 1 0 1 0
#> SRR2001059 2 0 1 0 1 0
#> SRR2001052 2 0 1 0 1 0
#> SRR2001053 2 0 1 0 1 0
#> SRR2001054 2 0 1 0 1 0
#> SRR2001055 2 0 1 0 1 0
#> SRR2001048 2 0 1 0 1 0
#> SRR2001049 2 0 1 0 1 0
#> SRR2001050 2 0 1 0 1 0
#> SRR2001051 2 0 1 0 1 0
#> SRR2001044 2 0 1 0 1 0
#> SRR2001045 2 0 1 0 1 0
#> SRR2001046 2 0 1 0 1 0
#> SRR2001047 2 0 1 0 1 0
#> SRR2001040 2 0 1 0 1 0
#> SRR2001041 2 0 1 0 1 0
#> SRR2001042 2 0 1 0 1 0
#> SRR2001043 2 0 1 0 1 0
#> SRR2001036 2 0 1 0 1 0
#> SRR2001037 2 0 1 0 1 0
#> SRR2001038 2 0 1 0 1 0
#> SRR2001039 2 0 1 0 1 0
#> SRR2001028 2 0 1 0 1 0
#> SRR2001029 2 0 1 0 1 0
#> SRR2001030 2 0 1 0 1 0
#> SRR2001031 2 0 1 0 1 0
#> SRR2001024 2 0 1 0 1 0
#> SRR2001025 2 0 1 0 1 0
#> SRR2001026 2 0 1 0 1 0
#> SRR2001027 2 0 1 0 1 0
#> SRR2001020 2 0 1 0 1 0
#> SRR2001021 2 0 1 0 1 0
#> SRR2001022 2 0 1 0 1 0
#> SRR2001023 2 0 1 0 1 0
#> SRR2001016 2 0 1 0 1 0
#> SRR2001017 2 0 1 0 1 0
#> SRR2001018 2 0 1 0 1 0
#> SRR2001019 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.0188 0.7366 0.000 0.996 0 0.004
#> SRR2001033 2 0.0817 0.7216 0.000 0.976 0 0.024
#> SRR2001034 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001035 2 0.0707 0.7252 0.000 0.980 0 0.020
#> SRR2001204 1 0.0000 0.7632 1.000 0.000 0 0.000
#> SRR2001205 1 0.0000 0.7632 1.000 0.000 0 0.000
#> SRR2001206 1 0.0000 0.7632 1.000 0.000 0 0.000
#> SRR2001207 1 0.0000 0.7632 1.000 0.000 0 0.000
#> SRR2001200 1 0.4972 0.8322 0.544 0.000 0 0.456
#> SRR2001201 1 0.4972 0.8322 0.544 0.000 0 0.456
#> SRR2001202 1 0.4972 0.8322 0.544 0.000 0 0.456
#> SRR2001203 1 0.4967 0.8332 0.548 0.000 0 0.452
#> SRR2001196 1 0.4967 0.8331 0.548 0.000 0 0.452
#> SRR2001197 1 0.4972 0.8322 0.544 0.000 0 0.456
#> SRR2001198 1 0.4967 0.8332 0.548 0.000 0 0.452
#> SRR2001199 1 0.4972 0.8322 0.544 0.000 0 0.456
#> SRR2001192 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001193 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001194 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001195 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001188 1 0.4948 0.8356 0.560 0.000 0 0.440
#> SRR2001189 1 0.4925 0.8365 0.572 0.000 0 0.428
#> SRR2001190 1 0.4907 0.8365 0.580 0.000 0 0.420
#> SRR2001191 1 0.4898 0.8367 0.584 0.000 0 0.416
#> SRR2001184 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001185 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001186 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001187 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001180 1 0.4972 0.8322 0.544 0.000 0 0.456
#> SRR2001181 1 0.4967 0.8331 0.548 0.000 0 0.452
#> SRR2001182 1 0.4761 0.8322 0.628 0.000 0 0.372
#> SRR2001183 1 0.4855 0.8361 0.600 0.000 0 0.400
#> SRR2001176 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001177 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001178 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001179 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001172 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001173 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001174 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001175 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001168 1 0.0000 0.7632 1.000 0.000 0 0.000
#> SRR2001169 1 0.0000 0.7632 1.000 0.000 0 0.000
#> SRR2001170 1 0.0188 0.7643 0.996 0.000 0 0.004
#> SRR2001171 1 0.0000 0.7632 1.000 0.000 0 0.000
#> SRR2001164 1 0.4925 0.8364 0.572 0.000 0 0.428
#> SRR2001165 1 0.4941 0.8360 0.564 0.000 0 0.436
#> SRR2001166 1 0.4967 0.8333 0.548 0.000 0 0.452
#> SRR2001167 1 0.4933 0.8363 0.568 0.000 0 0.432
#> SRR2001160 1 0.4933 0.8367 0.568 0.000 0 0.432
#> SRR2001161 1 0.4955 0.8350 0.556 0.000 0 0.444
#> SRR2001162 1 0.4948 0.8355 0.560 0.000 0 0.440
#> SRR2001163 1 0.4888 0.8361 0.588 0.000 0 0.412
#> SRR2001156 1 0.4972 0.8322 0.544 0.000 0 0.456
#> SRR2001157 1 0.4972 0.8322 0.544 0.000 0 0.456
#> SRR2001158 1 0.4972 0.8322 0.544 0.000 0 0.456
#> SRR2001159 1 0.4972 0.8322 0.544 0.000 0 0.456
#> SRR2001152 1 0.3172 0.7994 0.840 0.000 0 0.160
#> SRR2001153 1 0.0592 0.7680 0.984 0.000 0 0.016
#> SRR2001154 1 0.0469 0.7680 0.988 0.000 0 0.012
#> SRR2001155 1 0.0921 0.7730 0.972 0.000 0 0.028
#> SRR2001148 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001149 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001150 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001151 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001144 1 0.0592 0.7688 0.984 0.000 0 0.016
#> SRR2001145 1 0.1118 0.7750 0.964 0.000 0 0.036
#> SRR2001146 1 0.1867 0.7829 0.928 0.000 0 0.072
#> SRR2001147 1 0.0336 0.7664 0.992 0.000 0 0.008
#> SRR2001140 1 0.0000 0.7632 1.000 0.000 0 0.000
#> SRR2001142 1 0.0000 0.7632 1.000 0.000 0 0.000
#> SRR2001143 1 0.0000 0.7632 1.000 0.000 0 0.000
#> SRR2001136 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001137 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001138 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001139 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001132 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001133 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001134 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001135 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001128 1 0.4898 0.8365 0.584 0.000 0 0.416
#> SRR2001129 1 0.4866 0.8360 0.596 0.000 0 0.404
#> SRR2001130 1 0.4907 0.8367 0.580 0.000 0 0.420
#> SRR2001131 1 0.4955 0.8349 0.556 0.000 0 0.444
#> SRR2001124 1 0.4972 0.8322 0.544 0.000 0 0.456
#> SRR2001125 1 0.4972 0.8322 0.544 0.000 0 0.456
#> SRR2001126 1 0.4972 0.8322 0.544 0.000 0 0.456
#> SRR2001127 1 0.4972 0.8322 0.544 0.000 0 0.456
#> SRR2001120 1 0.0188 0.7643 0.996 0.000 0 0.004
#> SRR2001121 1 0.0000 0.7632 1.000 0.000 0 0.000
#> SRR2001122 1 0.0000 0.7632 1.000 0.000 0 0.000
#> SRR2001123 1 0.0000 0.7632 1.000 0.000 0 0.000
#> SRR2001116 1 0.1302 0.7767 0.956 0.000 0 0.044
#> SRR2001117 1 0.0000 0.7632 1.000 0.000 0 0.000
#> SRR2001118 1 0.3569 0.8057 0.804 0.000 0 0.196
#> SRR2001119 1 0.0921 0.7731 0.972 0.000 0 0.028
#> SRR2001112 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001113 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001114 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001115 3 0.0000 1.0000 0.000 0.000 1 0.000
#> SRR2001108 4 0.4998 0.9362 0.000 0.488 0 0.512
#> SRR2001109 2 0.4643 -0.2687 0.000 0.656 0 0.344
#> SRR2001110 2 0.2149 0.6431 0.000 0.912 0 0.088
#> SRR2001111 2 0.2921 0.5501 0.000 0.860 0 0.140
#> SRR2001104 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001105 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001106 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001107 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001100 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001101 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001102 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001103 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001096 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001097 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001098 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001099 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001092 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001093 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001094 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001095 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001088 4 0.4981 0.9711 0.000 0.464 0 0.536
#> SRR2001089 4 0.4994 0.9613 0.000 0.480 0 0.520
#> SRR2001090 4 0.4992 0.9656 0.000 0.476 0 0.524
#> SRR2001091 4 0.4985 0.9722 0.000 0.468 0 0.532
#> SRR2001084 2 0.4992 -0.8211 0.000 0.524 0 0.476
#> SRR2001085 4 0.4994 0.9419 0.000 0.480 0 0.520
#> SRR2001086 2 0.4998 -0.8572 0.000 0.512 0 0.488
#> SRR2001087 4 0.4999 0.9148 0.000 0.492 0 0.508
#> SRR2001080 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001081 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001082 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001083 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001076 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001077 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001078 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001079 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001072 2 0.4916 -0.6699 0.000 0.576 0 0.424
#> SRR2001073 2 0.5000 -0.9192 0.000 0.500 0 0.500
#> SRR2001074 4 0.4981 0.9711 0.000 0.464 0 0.536
#> SRR2001075 2 0.4996 -0.8721 0.000 0.516 0 0.484
#> SRR2001068 2 0.1302 0.7042 0.000 0.956 0 0.044
#> SRR2001069 2 0.0469 0.7330 0.000 0.988 0 0.012
#> SRR2001070 2 0.0188 0.7366 0.000 0.996 0 0.004
#> SRR2001071 2 0.0188 0.7366 0.000 0.996 0 0.004
#> SRR2001064 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001065 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001066 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001067 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001060 2 0.4994 -0.8605 0.000 0.520 0 0.480
#> SRR2001061 2 0.4994 -0.8571 0.000 0.520 0 0.480
#> SRR2001062 2 0.4948 -0.7293 0.000 0.560 0 0.440
#> SRR2001063 2 0.4972 -0.7904 0.000 0.544 0 0.456
#> SRR2001056 4 0.4992 0.9482 0.000 0.476 0 0.524
#> SRR2001057 4 0.4972 0.9612 0.000 0.456 0 0.544
#> SRR2001058 2 0.4998 -0.8589 0.000 0.512 0 0.488
#> SRR2001059 2 0.4925 -0.6530 0.000 0.572 0 0.428
#> SRR2001052 2 0.0469 0.7306 0.000 0.988 0 0.012
#> SRR2001053 2 0.0188 0.7364 0.000 0.996 0 0.004
#> SRR2001054 2 0.0469 0.7306 0.000 0.988 0 0.012
#> SRR2001055 2 0.0469 0.7306 0.000 0.988 0 0.012
#> SRR2001048 2 0.2281 0.6290 0.000 0.904 0 0.096
#> SRR2001049 2 0.0592 0.7304 0.000 0.984 0 0.016
#> SRR2001050 2 0.0336 0.7338 0.000 0.992 0 0.008
#> SRR2001051 2 0.0592 0.7295 0.000 0.984 0 0.016
#> SRR2001044 2 0.4955 -0.7476 0.000 0.556 0 0.444
#> SRR2001045 2 0.4585 -0.2615 0.000 0.668 0 0.332
#> SRR2001046 2 0.5000 -0.9258 0.000 0.500 0 0.500
#> SRR2001047 2 0.4304 0.0132 0.000 0.716 0 0.284
#> SRR2001040 4 0.4985 0.9722 0.000 0.468 0 0.532
#> SRR2001041 4 0.4985 0.9722 0.000 0.468 0 0.532
#> SRR2001042 4 0.4985 0.9722 0.000 0.468 0 0.532
#> SRR2001043 4 0.4985 0.9722 0.000 0.468 0 0.532
#> SRR2001036 4 0.4985 0.9716 0.000 0.468 0 0.532
#> SRR2001037 4 0.4977 0.9672 0.000 0.460 0 0.540
#> SRR2001038 4 0.4996 0.9314 0.000 0.484 0 0.516
#> SRR2001039 4 0.4977 0.9636 0.000 0.460 0 0.540
#> SRR2001028 2 0.4977 -0.8022 0.000 0.540 0 0.460
#> SRR2001029 4 0.4994 0.9623 0.000 0.480 0 0.520
#> SRR2001030 4 0.4996 0.9561 0.000 0.484 0 0.516
#> SRR2001031 2 0.4804 -0.5075 0.000 0.616 0 0.384
#> SRR2001024 4 0.4989 0.9711 0.000 0.472 0 0.528
#> SRR2001025 4 0.4977 0.9671 0.000 0.460 0 0.540
#> SRR2001026 4 0.4985 0.9722 0.000 0.468 0 0.532
#> SRR2001027 4 0.4985 0.9722 0.000 0.468 0 0.532
#> SRR2001020 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001021 2 0.0336 0.7331 0.000 0.992 0 0.008
#> SRR2001022 2 0.1792 0.6628 0.000 0.932 0 0.068
#> SRR2001023 2 0.0000 0.7388 0.000 1.000 0 0.000
#> SRR2001016 2 0.4008 0.2506 0.000 0.756 0 0.244
#> SRR2001017 2 0.4543 -0.1811 0.000 0.676 0 0.324
#> SRR2001018 2 0.4746 -0.3889 0.000 0.632 0 0.368
#> SRR2001019 2 0.4477 -0.1092 0.000 0.688 0 0.312
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.0510 0.9362 0.000 0.984 0 0.000 0.016
#> SRR2001033 2 0.0912 0.9299 0.000 0.972 0 0.016 0.012
#> SRR2001034 2 0.0162 0.9398 0.000 0.996 0 0.000 0.004
#> SRR2001035 2 0.1300 0.9222 0.000 0.956 0 0.016 0.028
#> SRR2001204 5 0.1197 0.9354 0.048 0.000 0 0.000 0.952
#> SRR2001205 5 0.1121 0.9321 0.044 0.000 0 0.000 0.956
#> SRR2001206 5 0.0963 0.9327 0.036 0.000 0 0.000 0.964
#> SRR2001207 5 0.0963 0.9327 0.036 0.000 0 0.000 0.964
#> SRR2001200 1 0.0162 0.8471 0.996 0.000 0 0.000 0.004
#> SRR2001201 1 0.0404 0.8485 0.988 0.000 0 0.000 0.012
#> SRR2001202 1 0.0162 0.8470 0.996 0.000 0 0.000 0.004
#> SRR2001203 1 0.1965 0.8398 0.904 0.000 0 0.000 0.096
#> SRR2001196 1 0.1732 0.8534 0.920 0.000 0 0.000 0.080
#> SRR2001197 1 0.0963 0.8527 0.964 0.000 0 0.000 0.036
#> SRR2001198 1 0.1410 0.8488 0.940 0.000 0 0.000 0.060
#> SRR2001199 1 0.0162 0.8474 0.996 0.000 0 0.000 0.004
#> SRR2001192 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001193 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001194 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001195 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001188 1 0.2179 0.8455 0.888 0.000 0 0.000 0.112
#> SRR2001189 1 0.3636 0.7210 0.728 0.000 0 0.000 0.272
#> SRR2001190 1 0.3966 0.6277 0.664 0.000 0 0.000 0.336
#> SRR2001191 1 0.3774 0.6786 0.704 0.000 0 0.000 0.296
#> SRR2001184 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001185 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001186 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001187 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001180 1 0.1341 0.8551 0.944 0.000 0 0.000 0.056
#> SRR2001181 1 0.2690 0.8251 0.844 0.000 0 0.000 0.156
#> SRR2001182 1 0.3336 0.7445 0.772 0.000 0 0.000 0.228
#> SRR2001183 1 0.4126 0.5348 0.620 0.000 0 0.000 0.380
#> SRR2001176 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001177 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001178 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001179 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001172 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001173 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001174 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001175 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001168 5 0.1043 0.9333 0.040 0.000 0 0.000 0.960
#> SRR2001169 5 0.0963 0.9327 0.036 0.000 0 0.000 0.964
#> SRR2001170 5 0.1908 0.9205 0.092 0.000 0 0.000 0.908
#> SRR2001171 5 0.1270 0.9354 0.052 0.000 0 0.000 0.948
#> SRR2001164 1 0.3586 0.7263 0.736 0.000 0 0.000 0.264
#> SRR2001165 1 0.3586 0.7345 0.736 0.000 0 0.000 0.264
#> SRR2001166 1 0.1410 0.8551 0.940 0.000 0 0.000 0.060
#> SRR2001167 1 0.3074 0.7860 0.804 0.000 0 0.000 0.196
#> SRR2001160 1 0.2377 0.8361 0.872 0.000 0 0.000 0.128
#> SRR2001161 1 0.1478 0.8551 0.936 0.000 0 0.000 0.064
#> SRR2001162 1 0.2773 0.8198 0.836 0.000 0 0.000 0.164
#> SRR2001163 1 0.2929 0.8057 0.820 0.000 0 0.000 0.180
#> SRR2001156 1 0.1043 0.8534 0.960 0.000 0 0.000 0.040
#> SRR2001157 1 0.0510 0.8491 0.984 0.000 0 0.000 0.016
#> SRR2001158 1 0.0290 0.8480 0.992 0.000 0 0.000 0.008
#> SRR2001159 1 0.0404 0.8484 0.988 0.000 0 0.000 0.012
#> SRR2001152 5 0.3816 0.5722 0.304 0.000 0 0.000 0.696
#> SRR2001153 5 0.2852 0.8666 0.172 0.000 0 0.000 0.828
#> SRR2001154 5 0.2280 0.9095 0.120 0.000 0 0.000 0.880
#> SRR2001155 5 0.2179 0.9057 0.112 0.000 0 0.000 0.888
#> SRR2001148 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001149 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001150 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001151 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001144 5 0.2929 0.8407 0.180 0.000 0 0.000 0.820
#> SRR2001145 5 0.2230 0.9066 0.116 0.000 0 0.000 0.884
#> SRR2001146 5 0.2813 0.8432 0.168 0.000 0 0.000 0.832
#> SRR2001147 5 0.2020 0.9226 0.100 0.000 0 0.000 0.900
#> SRR2001140 5 0.1341 0.9355 0.056 0.000 0 0.000 0.944
#> SRR2001142 5 0.1478 0.9330 0.064 0.000 0 0.000 0.936
#> SRR2001143 5 0.1121 0.9333 0.044 0.000 0 0.000 0.956
#> SRR2001136 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001137 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001138 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001139 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001132 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001133 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001134 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001135 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001128 1 0.4210 0.4875 0.588 0.000 0 0.000 0.412
#> SRR2001129 1 0.3003 0.7933 0.812 0.000 0 0.000 0.188
#> SRR2001130 1 0.3966 0.6246 0.664 0.000 0 0.000 0.336
#> SRR2001131 1 0.2074 0.8476 0.896 0.000 0 0.000 0.104
#> SRR2001124 1 0.0404 0.8484 0.988 0.000 0 0.000 0.012
#> SRR2001125 1 0.0290 0.8490 0.992 0.000 0 0.000 0.008
#> SRR2001126 1 0.0162 0.8470 0.996 0.000 0 0.000 0.004
#> SRR2001127 1 0.0000 0.8462 1.000 0.000 0 0.000 0.000
#> SRR2001120 5 0.1121 0.9340 0.044 0.000 0 0.000 0.956
#> SRR2001121 5 0.1544 0.9325 0.068 0.000 0 0.000 0.932
#> SRR2001122 5 0.1341 0.9341 0.056 0.000 0 0.000 0.944
#> SRR2001123 5 0.0963 0.9327 0.036 0.000 0 0.000 0.964
#> SRR2001116 5 0.2329 0.9012 0.124 0.000 0 0.000 0.876
#> SRR2001117 5 0.1341 0.9360 0.056 0.000 0 0.000 0.944
#> SRR2001118 1 0.4304 0.0979 0.516 0.000 0 0.000 0.484
#> SRR2001119 5 0.2471 0.8889 0.136 0.000 0 0.000 0.864
#> SRR2001112 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001113 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001114 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001115 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000
#> SRR2001108 4 0.2722 0.8597 0.000 0.108 0 0.872 0.020
#> SRR2001109 4 0.4855 0.3388 0.000 0.424 0 0.552 0.024
#> SRR2001110 2 0.3182 0.8025 0.000 0.844 0 0.124 0.032
#> SRR2001111 2 0.3724 0.7170 0.000 0.788 0 0.184 0.028
#> SRR2001104 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001105 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001106 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001107 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001100 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001101 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001102 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001103 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001096 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001097 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001098 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001099 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001092 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001093 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001094 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001095 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001088 4 0.0162 0.8649 0.000 0.004 0 0.996 0.000
#> SRR2001089 4 0.0510 0.8695 0.000 0.016 0 0.984 0.000
#> SRR2001090 4 0.1121 0.8733 0.000 0.044 0 0.956 0.000
#> SRR2001091 4 0.0290 0.8663 0.000 0.008 0 0.992 0.000
#> SRR2001084 4 0.4021 0.7753 0.000 0.200 0 0.764 0.036
#> SRR2001085 4 0.2104 0.8709 0.000 0.060 0 0.916 0.024
#> SRR2001086 4 0.3531 0.8276 0.000 0.148 0 0.816 0.036
#> SRR2001087 4 0.3115 0.8525 0.000 0.112 0 0.852 0.036
#> SRR2001080 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001081 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001082 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001083 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001076 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001077 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001078 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001079 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001072 4 0.3816 0.6242 0.000 0.304 0 0.696 0.000
#> SRR2001073 4 0.1851 0.8712 0.000 0.088 0 0.912 0.000
#> SRR2001074 4 0.0162 0.8649 0.000 0.004 0 0.996 0.000
#> SRR2001075 4 0.1704 0.8717 0.000 0.068 0 0.928 0.004
#> SRR2001068 2 0.1893 0.8990 0.000 0.928 0 0.048 0.024
#> SRR2001069 2 0.0609 0.9348 0.000 0.980 0 0.000 0.020
#> SRR2001070 2 0.0510 0.9362 0.000 0.984 0 0.000 0.016
#> SRR2001071 2 0.0404 0.9374 0.000 0.988 0 0.000 0.012
#> SRR2001064 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001065 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001066 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001067 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001060 4 0.3242 0.7536 0.000 0.216 0 0.784 0.000
#> SRR2001061 4 0.1965 0.8569 0.000 0.096 0 0.904 0.000
#> SRR2001062 4 0.2230 0.8491 0.000 0.116 0 0.884 0.000
#> SRR2001063 4 0.2424 0.8454 0.000 0.132 0 0.868 0.000
#> SRR2001056 4 0.2074 0.8695 0.000 0.044 0 0.920 0.036
#> SRR2001057 4 0.1168 0.8654 0.000 0.008 0 0.960 0.032
#> SRR2001058 4 0.3489 0.8289 0.000 0.144 0 0.820 0.036
#> SRR2001059 4 0.3724 0.7950 0.000 0.184 0 0.788 0.028
#> SRR2001052 2 0.1124 0.9249 0.000 0.960 0 0.004 0.036
#> SRR2001053 2 0.0865 0.9311 0.000 0.972 0 0.004 0.024
#> SRR2001054 2 0.1124 0.9249 0.000 0.960 0 0.004 0.036
#> SRR2001055 2 0.1041 0.9272 0.000 0.964 0 0.004 0.032
#> SRR2001048 2 0.2676 0.8557 0.000 0.884 0 0.080 0.036
#> SRR2001049 2 0.1281 0.9231 0.000 0.956 0 0.012 0.032
#> SRR2001050 2 0.0609 0.9347 0.000 0.980 0 0.000 0.020
#> SRR2001051 2 0.1082 0.9273 0.000 0.964 0 0.008 0.028
#> SRR2001044 4 0.3003 0.8056 0.000 0.188 0 0.812 0.000
#> SRR2001045 2 0.4278 0.0437 0.000 0.548 0 0.452 0.000
#> SRR2001046 4 0.3143 0.7932 0.000 0.204 0 0.796 0.000
#> SRR2001047 2 0.4300 -0.0526 0.000 0.524 0 0.476 0.000
#> SRR2001040 4 0.0162 0.8649 0.000 0.004 0 0.996 0.000
#> SRR2001041 4 0.0162 0.8649 0.000 0.004 0 0.996 0.000
#> SRR2001042 4 0.0162 0.8649 0.000 0.004 0 0.996 0.000
#> SRR2001043 4 0.0162 0.8649 0.000 0.004 0 0.996 0.000
#> SRR2001036 4 0.0510 0.8691 0.000 0.016 0 0.984 0.000
#> SRR2001037 4 0.0162 0.8649 0.000 0.004 0 0.996 0.000
#> SRR2001038 4 0.1205 0.8731 0.000 0.040 0 0.956 0.004
#> SRR2001039 4 0.0290 0.8679 0.000 0.008 0 0.992 0.000
#> SRR2001028 4 0.2732 0.8338 0.000 0.160 0 0.840 0.000
#> SRR2001029 4 0.2179 0.8618 0.000 0.112 0 0.888 0.000
#> SRR2001030 4 0.2561 0.8430 0.000 0.144 0 0.856 0.000
#> SRR2001031 4 0.3932 0.6027 0.000 0.328 0 0.672 0.000
#> SRR2001024 4 0.0404 0.8683 0.000 0.012 0 0.988 0.000
#> SRR2001025 4 0.0000 0.8632 0.000 0.000 0 1.000 0.000
#> SRR2001026 4 0.0290 0.8665 0.000 0.008 0 0.992 0.000
#> SRR2001027 4 0.0290 0.8668 0.000 0.008 0 0.992 0.000
#> SRR2001020 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001021 2 0.0963 0.9168 0.000 0.964 0 0.036 0.000
#> SRR2001022 2 0.1965 0.8561 0.000 0.904 0 0.096 0.000
#> SRR2001023 2 0.0000 0.9410 0.000 1.000 0 0.000 0.000
#> SRR2001016 2 0.5010 0.2012 0.000 0.572 0 0.392 0.036
#> SRR2001017 2 0.5019 0.1806 0.000 0.568 0 0.396 0.036
#> SRR2001018 4 0.5052 0.3669 0.000 0.412 0 0.552 0.036
#> SRR2001019 4 0.5103 0.2485 0.000 0.452 0 0.512 0.036
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 2 0.0865 0.9078 0.000 0.964 0.000 0.000 0.036 0.000
#> SRR2001033 2 0.1196 0.9030 0.000 0.952 0.000 0.008 0.040 0.000
#> SRR2001034 2 0.0547 0.9150 0.000 0.980 0.000 0.000 0.020 0.000
#> SRR2001035 2 0.1802 0.8794 0.000 0.916 0.000 0.012 0.072 0.000
#> SRR2001204 6 0.1549 0.9170 0.020 0.000 0.000 0.000 0.044 0.936
#> SRR2001205 6 0.1461 0.9136 0.016 0.000 0.000 0.000 0.044 0.940
#> SRR2001206 6 0.1265 0.9145 0.008 0.000 0.000 0.000 0.044 0.948
#> SRR2001207 6 0.1265 0.9145 0.008 0.000 0.000 0.000 0.044 0.948
#> SRR2001200 1 0.0260 0.8433 0.992 0.000 0.000 0.000 0.000 0.008
#> SRR2001201 1 0.0777 0.8451 0.972 0.000 0.000 0.000 0.004 0.024
#> SRR2001202 1 0.0146 0.8420 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR2001203 1 0.2402 0.8259 0.868 0.000 0.000 0.000 0.012 0.120
#> SRR2001196 1 0.1913 0.8513 0.908 0.000 0.000 0.000 0.012 0.080
#> SRR2001197 1 0.1285 0.8480 0.944 0.000 0.000 0.000 0.004 0.052
#> SRR2001198 1 0.1866 0.8407 0.908 0.000 0.000 0.000 0.008 0.084
#> SRR2001199 1 0.0520 0.8443 0.984 0.000 0.000 0.000 0.008 0.008
#> SRR2001192 3 0.0713 0.9534 0.000 0.000 0.972 0.000 0.028 0.000
#> SRR2001193 3 0.0363 0.9557 0.000 0.000 0.988 0.000 0.012 0.000
#> SRR2001194 3 0.1075 0.9500 0.000 0.000 0.952 0.000 0.048 0.000
#> SRR2001195 3 0.0000 0.9559 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001188 1 0.2178 0.8413 0.868 0.000 0.000 0.000 0.000 0.132
#> SRR2001189 1 0.3489 0.7219 0.708 0.000 0.000 0.000 0.004 0.288
#> SRR2001190 1 0.4039 0.6237 0.632 0.000 0.000 0.000 0.016 0.352
#> SRR2001191 1 0.3784 0.6787 0.680 0.000 0.000 0.000 0.012 0.308
#> SRR2001184 3 0.0000 0.9559 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001185 3 0.0000 0.9559 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001186 3 0.0547 0.9549 0.000 0.000 0.980 0.000 0.020 0.000
#> SRR2001187 3 0.0146 0.9560 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001180 1 0.1387 0.8516 0.932 0.000 0.000 0.000 0.000 0.068
#> SRR2001181 1 0.2841 0.8255 0.824 0.000 0.000 0.000 0.012 0.164
#> SRR2001182 1 0.3081 0.7566 0.776 0.000 0.000 0.000 0.004 0.220
#> SRR2001183 1 0.4076 0.5289 0.592 0.000 0.000 0.000 0.012 0.396
#> SRR2001176 3 0.0260 0.9559 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR2001177 3 0.0000 0.9559 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001178 3 0.0000 0.9559 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001179 3 0.0000 0.9559 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001172 3 0.0000 0.9559 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001173 3 0.0000 0.9559 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001174 3 0.0146 0.9559 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001175 3 0.0000 0.9559 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001168 6 0.0717 0.9191 0.008 0.000 0.000 0.000 0.016 0.976
#> SRR2001169 6 0.0790 0.9167 0.000 0.000 0.000 0.000 0.032 0.968
#> SRR2001170 6 0.2488 0.9007 0.076 0.000 0.000 0.000 0.044 0.880
#> SRR2001171 6 0.1713 0.9187 0.028 0.000 0.000 0.000 0.044 0.928
#> SRR2001164 1 0.3650 0.7201 0.708 0.000 0.000 0.000 0.012 0.280
#> SRR2001165 1 0.3717 0.7224 0.708 0.000 0.000 0.000 0.016 0.276
#> SRR2001166 1 0.1838 0.8518 0.916 0.000 0.000 0.000 0.016 0.068
#> SRR2001167 1 0.3168 0.7901 0.792 0.000 0.000 0.000 0.016 0.192
#> SRR2001160 1 0.2278 0.8367 0.868 0.000 0.000 0.000 0.004 0.128
#> SRR2001161 1 0.1858 0.8515 0.912 0.000 0.000 0.000 0.012 0.076
#> SRR2001162 1 0.2703 0.8192 0.824 0.000 0.000 0.000 0.004 0.172
#> SRR2001163 1 0.2664 0.8049 0.816 0.000 0.000 0.000 0.000 0.184
#> SRR2001156 1 0.1219 0.8497 0.948 0.000 0.000 0.000 0.004 0.048
#> SRR2001157 1 0.0547 0.8444 0.980 0.000 0.000 0.000 0.000 0.020
#> SRR2001158 1 0.0363 0.8433 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR2001159 1 0.0458 0.8438 0.984 0.000 0.000 0.000 0.000 0.016
#> SRR2001152 6 0.3555 0.5599 0.280 0.000 0.000 0.000 0.008 0.712
#> SRR2001153 6 0.2988 0.8534 0.152 0.000 0.000 0.000 0.024 0.824
#> SRR2001154 6 0.2121 0.8969 0.096 0.000 0.000 0.000 0.012 0.892
#> SRR2001155 6 0.1701 0.8955 0.072 0.000 0.000 0.000 0.008 0.920
#> SRR2001148 3 0.0000 0.9559 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001149 3 0.0000 0.9559 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001150 3 0.0000 0.9559 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001151 3 0.0000 0.9559 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001144 6 0.2859 0.8187 0.156 0.000 0.000 0.000 0.016 0.828
#> SRR2001145 6 0.2176 0.8941 0.080 0.000 0.000 0.000 0.024 0.896
#> SRR2001146 6 0.2572 0.8330 0.136 0.000 0.000 0.000 0.012 0.852
#> SRR2001147 6 0.1913 0.9015 0.080 0.000 0.000 0.000 0.012 0.908
#> SRR2001140 6 0.1074 0.9206 0.012 0.000 0.000 0.000 0.028 0.960
#> SRR2001142 6 0.1865 0.9150 0.040 0.000 0.000 0.000 0.040 0.920
#> SRR2001143 6 0.0820 0.9190 0.012 0.000 0.000 0.000 0.016 0.972
#> SRR2001136 3 0.2454 0.9081 0.000 0.000 0.840 0.000 0.160 0.000
#> SRR2001137 3 0.2260 0.9170 0.000 0.000 0.860 0.000 0.140 0.000
#> SRR2001138 3 0.1075 0.9501 0.000 0.000 0.952 0.000 0.048 0.000
#> SRR2001139 3 0.1267 0.9470 0.000 0.000 0.940 0.000 0.060 0.000
#> SRR2001132 3 0.2562 0.9023 0.000 0.000 0.828 0.000 0.172 0.000
#> SRR2001133 3 0.2048 0.9263 0.000 0.000 0.880 0.000 0.120 0.000
#> SRR2001134 3 0.2562 0.9023 0.000 0.000 0.828 0.000 0.172 0.000
#> SRR2001135 3 0.1610 0.9397 0.000 0.000 0.916 0.000 0.084 0.000
#> SRR2001128 1 0.4234 0.4622 0.544 0.000 0.000 0.000 0.016 0.440
#> SRR2001129 1 0.3168 0.7932 0.792 0.000 0.000 0.000 0.016 0.192
#> SRR2001130 1 0.4039 0.6133 0.632 0.000 0.000 0.000 0.016 0.352
#> SRR2001131 1 0.2357 0.8440 0.872 0.000 0.000 0.000 0.012 0.116
#> SRR2001124 1 0.0363 0.8440 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR2001125 1 0.0508 0.8449 0.984 0.000 0.000 0.000 0.004 0.012
#> SRR2001126 1 0.0291 0.8431 0.992 0.000 0.000 0.000 0.004 0.004
#> SRR2001127 1 0.0146 0.8419 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR2001120 6 0.0363 0.9195 0.012 0.000 0.000 0.000 0.000 0.988
#> SRR2001121 6 0.0972 0.9173 0.028 0.000 0.000 0.000 0.008 0.964
#> SRR2001122 6 0.0713 0.9186 0.028 0.000 0.000 0.000 0.000 0.972
#> SRR2001123 6 0.0146 0.9176 0.000 0.000 0.000 0.000 0.004 0.996
#> SRR2001116 6 0.1863 0.8868 0.104 0.000 0.000 0.000 0.000 0.896
#> SRR2001117 6 0.1010 0.9215 0.036 0.000 0.000 0.000 0.004 0.960
#> SRR2001118 1 0.4534 0.0933 0.496 0.000 0.000 0.000 0.032 0.472
#> SRR2001119 6 0.2302 0.8697 0.120 0.000 0.000 0.000 0.008 0.872
#> SRR2001112 3 0.2562 0.9023 0.000 0.000 0.828 0.000 0.172 0.000
#> SRR2001113 3 0.2562 0.9023 0.000 0.000 0.828 0.000 0.172 0.000
#> SRR2001114 3 0.2562 0.9023 0.000 0.000 0.828 0.000 0.172 0.000
#> SRR2001115 3 0.2562 0.9023 0.000 0.000 0.828 0.000 0.172 0.000
#> SRR2001108 5 0.4335 0.4184 0.000 0.020 0.000 0.472 0.508 0.000
#> SRR2001109 5 0.5879 0.5131 0.000 0.220 0.000 0.316 0.464 0.000
#> SRR2001110 5 0.4835 0.4402 0.000 0.352 0.000 0.068 0.580 0.000
#> SRR2001111 2 0.4641 0.5462 0.000 0.664 0.000 0.088 0.248 0.000
#> SRR2001104 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001105 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001106 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001107 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001100 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001101 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001102 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001103 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001096 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001097 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001098 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001099 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001092 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001093 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001094 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001095 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001088 4 0.0000 0.8321 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001089 4 0.0458 0.8334 0.000 0.016 0.000 0.984 0.000 0.000
#> SRR2001090 4 0.0713 0.8315 0.000 0.028 0.000 0.972 0.000 0.000
#> SRR2001091 4 0.0000 0.8321 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001084 5 0.3403 0.8397 0.000 0.020 0.000 0.212 0.768 0.000
#> SRR2001085 5 0.3871 0.7533 0.000 0.016 0.000 0.308 0.676 0.000
#> SRR2001086 5 0.3217 0.8349 0.000 0.008 0.000 0.224 0.768 0.000
#> SRR2001087 5 0.3342 0.8365 0.000 0.012 0.000 0.228 0.760 0.000
#> SRR2001080 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001081 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001082 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001083 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001076 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001077 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001078 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001079 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001072 4 0.2823 0.6395 0.000 0.204 0.000 0.796 0.000 0.000
#> SRR2001073 4 0.2053 0.7739 0.000 0.108 0.000 0.888 0.004 0.000
#> SRR2001074 4 0.0632 0.8227 0.000 0.000 0.000 0.976 0.024 0.000
#> SRR2001075 4 0.2129 0.7930 0.000 0.056 0.000 0.904 0.040 0.000
#> SRR2001068 2 0.3509 0.6984 0.000 0.744 0.000 0.016 0.240 0.000
#> SRR2001069 2 0.1765 0.8670 0.000 0.904 0.000 0.000 0.096 0.000
#> SRR2001070 2 0.1007 0.9029 0.000 0.956 0.000 0.000 0.044 0.000
#> SRR2001071 2 0.0632 0.9140 0.000 0.976 0.000 0.000 0.024 0.000
#> SRR2001064 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001065 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001066 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001067 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001060 4 0.2092 0.7438 0.000 0.124 0.000 0.876 0.000 0.000
#> SRR2001061 4 0.0790 0.8289 0.000 0.032 0.000 0.968 0.000 0.000
#> SRR2001062 4 0.1141 0.8165 0.000 0.052 0.000 0.948 0.000 0.000
#> SRR2001063 4 0.1765 0.7855 0.000 0.096 0.000 0.904 0.000 0.000
#> SRR2001056 5 0.3050 0.8269 0.000 0.000 0.000 0.236 0.764 0.000
#> SRR2001057 5 0.3288 0.8015 0.000 0.000 0.000 0.276 0.724 0.000
#> SRR2001058 5 0.3376 0.8394 0.000 0.016 0.000 0.220 0.764 0.000
#> SRR2001059 5 0.3816 0.8295 0.000 0.032 0.000 0.240 0.728 0.000
#> SRR2001052 2 0.3782 0.3717 0.000 0.588 0.000 0.000 0.412 0.000
#> SRR2001053 2 0.3050 0.7157 0.000 0.764 0.000 0.000 0.236 0.000
#> SRR2001054 2 0.3266 0.6710 0.000 0.728 0.000 0.000 0.272 0.000
#> SRR2001055 2 0.3221 0.6771 0.000 0.736 0.000 0.000 0.264 0.000
#> SRR2001048 2 0.3314 0.6929 0.000 0.740 0.000 0.004 0.256 0.000
#> SRR2001049 2 0.2902 0.7719 0.000 0.800 0.000 0.004 0.196 0.000
#> SRR2001050 2 0.1765 0.8689 0.000 0.904 0.000 0.000 0.096 0.000
#> SRR2001051 2 0.2178 0.8388 0.000 0.868 0.000 0.000 0.132 0.000
#> SRR2001044 4 0.3428 0.4669 0.000 0.304 0.000 0.696 0.000 0.000
#> SRR2001045 2 0.3531 0.4921 0.000 0.672 0.000 0.328 0.000 0.000
#> SRR2001046 4 0.3175 0.5685 0.000 0.256 0.000 0.744 0.000 0.000
#> SRR2001047 2 0.3592 0.4501 0.000 0.656 0.000 0.344 0.000 0.000
#> SRR2001040 4 0.0000 0.8321 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001041 4 0.0000 0.8321 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001042 4 0.0000 0.8321 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001043 4 0.0000 0.8321 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001036 4 0.0405 0.8337 0.000 0.008 0.000 0.988 0.004 0.000
#> SRR2001037 4 0.0000 0.8321 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001038 4 0.2822 0.7197 0.000 0.040 0.000 0.852 0.108 0.000
#> SRR2001039 4 0.2003 0.7329 0.000 0.000 0.000 0.884 0.116 0.000
#> SRR2001028 4 0.2969 0.6202 0.000 0.224 0.000 0.776 0.000 0.000
#> SRR2001029 4 0.2902 0.6515 0.000 0.196 0.000 0.800 0.004 0.000
#> SRR2001030 4 0.2996 0.6025 0.000 0.228 0.000 0.772 0.000 0.000
#> SRR2001031 4 0.3868 0.0897 0.000 0.492 0.000 0.508 0.000 0.000
#> SRR2001024 4 0.0146 0.8333 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR2001025 4 0.0000 0.8321 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001026 4 0.0146 0.8332 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR2001027 4 0.0146 0.8334 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR2001020 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001021 2 0.0713 0.9047 0.000 0.972 0.000 0.028 0.000 0.000
#> SRR2001022 2 0.1007 0.8917 0.000 0.956 0.000 0.044 0.000 0.000
#> SRR2001023 2 0.0000 0.9226 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001016 5 0.3883 0.8003 0.000 0.088 0.000 0.144 0.768 0.000
#> SRR2001017 5 0.3842 0.7242 0.000 0.156 0.000 0.076 0.768 0.000
#> SRR2001018 5 0.3582 0.8373 0.000 0.036 0.000 0.196 0.768 0.000
#> SRR2001019 5 0.3739 0.8277 0.000 0.056 0.000 0.176 0.768 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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.5031 0.497 0.497
#> 3 3 1.000 1.000 1.000 0.2206 0.889 0.777
#> 4 4 1.000 0.992 0.994 0.2049 0.873 0.671
#> 5 5 0.987 0.954 0.972 0.0431 0.969 0.881
#> 6 6 0.838 0.845 0.858 0.0467 1.000 1.000
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3 4
There is also optional best \(k\) = 2 3 4 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0 1 0 1 0
#> SRR2001033 2 0 1 0 1 0
#> SRR2001034 2 0 1 0 1 0
#> SRR2001035 2 0 1 0 1 0
#> SRR2001204 1 0 1 1 0 0
#> SRR2001205 1 0 1 1 0 0
#> SRR2001206 1 0 1 1 0 0
#> SRR2001207 1 0 1 1 0 0
#> SRR2001200 1 0 1 1 0 0
#> SRR2001201 1 0 1 1 0 0
#> SRR2001202 1 0 1 1 0 0
#> SRR2001203 1 0 1 1 0 0
#> SRR2001196 1 0 1 1 0 0
#> SRR2001197 1 0 1 1 0 0
#> SRR2001198 1 0 1 1 0 0
#> SRR2001199 1 0 1 1 0 0
#> SRR2001192 3 0 1 0 0 1
#> SRR2001193 3 0 1 0 0 1
#> SRR2001194 3 0 1 0 0 1
#> SRR2001195 3 0 1 0 0 1
#> SRR2001188 1 0 1 1 0 0
#> SRR2001189 1 0 1 1 0 0
#> SRR2001190 1 0 1 1 0 0
#> SRR2001191 1 0 1 1 0 0
#> SRR2001184 3 0 1 0 0 1
#> SRR2001185 3 0 1 0 0 1
#> SRR2001186 3 0 1 0 0 1
#> SRR2001187 3 0 1 0 0 1
#> SRR2001180 1 0 1 1 0 0
#> SRR2001181 1 0 1 1 0 0
#> SRR2001182 1 0 1 1 0 0
#> SRR2001183 1 0 1 1 0 0
#> SRR2001176 3 0 1 0 0 1
#> SRR2001177 3 0 1 0 0 1
#> SRR2001178 3 0 1 0 0 1
#> SRR2001179 3 0 1 0 0 1
#> SRR2001172 3 0 1 0 0 1
#> SRR2001173 3 0 1 0 0 1
#> SRR2001174 3 0 1 0 0 1
#> SRR2001175 3 0 1 0 0 1
#> SRR2001168 1 0 1 1 0 0
#> SRR2001169 1 0 1 1 0 0
#> SRR2001170 1 0 1 1 0 0
#> SRR2001171 1 0 1 1 0 0
#> SRR2001164 1 0 1 1 0 0
#> SRR2001165 1 0 1 1 0 0
#> SRR2001166 1 0 1 1 0 0
#> SRR2001167 1 0 1 1 0 0
#> SRR2001160 1 0 1 1 0 0
#> SRR2001161 1 0 1 1 0 0
#> SRR2001162 1 0 1 1 0 0
#> SRR2001163 1 0 1 1 0 0
#> SRR2001156 1 0 1 1 0 0
#> SRR2001157 1 0 1 1 0 0
#> SRR2001158 1 0 1 1 0 0
#> SRR2001159 1 0 1 1 0 0
#> SRR2001152 1 0 1 1 0 0
#> SRR2001153 1 0 1 1 0 0
#> SRR2001154 1 0 1 1 0 0
#> SRR2001155 1 0 1 1 0 0
#> SRR2001148 3 0 1 0 0 1
#> SRR2001149 3 0 1 0 0 1
#> SRR2001150 3 0 1 0 0 1
#> SRR2001151 3 0 1 0 0 1
#> SRR2001144 1 0 1 1 0 0
#> SRR2001145 1 0 1 1 0 0
#> SRR2001146 1 0 1 1 0 0
#> SRR2001147 1 0 1 1 0 0
#> SRR2001140 1 0 1 1 0 0
#> SRR2001142 1 0 1 1 0 0
#> SRR2001143 1 0 1 1 0 0
#> SRR2001136 3 0 1 0 0 1
#> SRR2001137 3 0 1 0 0 1
#> SRR2001138 3 0 1 0 0 1
#> SRR2001139 3 0 1 0 0 1
#> SRR2001132 3 0 1 0 0 1
#> SRR2001133 3 0 1 0 0 1
#> SRR2001134 3 0 1 0 0 1
#> SRR2001135 3 0 1 0 0 1
#> SRR2001128 1 0 1 1 0 0
#> SRR2001129 1 0 1 1 0 0
#> SRR2001130 1 0 1 1 0 0
#> SRR2001131 1 0 1 1 0 0
#> SRR2001124 1 0 1 1 0 0
#> SRR2001125 1 0 1 1 0 0
#> SRR2001126 1 0 1 1 0 0
#> SRR2001127 1 0 1 1 0 0
#> SRR2001120 1 0 1 1 0 0
#> SRR2001121 1 0 1 1 0 0
#> SRR2001122 1 0 1 1 0 0
#> SRR2001123 1 0 1 1 0 0
#> SRR2001116 1 0 1 1 0 0
#> SRR2001117 1 0 1 1 0 0
#> SRR2001118 1 0 1 1 0 0
#> SRR2001119 1 0 1 1 0 0
#> SRR2001112 3 0 1 0 0 1
#> SRR2001113 3 0 1 0 0 1
#> SRR2001114 3 0 1 0 0 1
#> SRR2001115 3 0 1 0 0 1
#> SRR2001108 2 0 1 0 1 0
#> SRR2001109 2 0 1 0 1 0
#> SRR2001110 2 0 1 0 1 0
#> SRR2001111 2 0 1 0 1 0
#> SRR2001104 2 0 1 0 1 0
#> SRR2001105 2 0 1 0 1 0
#> SRR2001106 2 0 1 0 1 0
#> SRR2001107 2 0 1 0 1 0
#> SRR2001100 2 0 1 0 1 0
#> SRR2001101 2 0 1 0 1 0
#> SRR2001102 2 0 1 0 1 0
#> SRR2001103 2 0 1 0 1 0
#> SRR2001096 2 0 1 0 1 0
#> SRR2001097 2 0 1 0 1 0
#> SRR2001098 2 0 1 0 1 0
#> SRR2001099 2 0 1 0 1 0
#> SRR2001092 2 0 1 0 1 0
#> SRR2001093 2 0 1 0 1 0
#> SRR2001094 2 0 1 0 1 0
#> SRR2001095 2 0 1 0 1 0
#> SRR2001088 2 0 1 0 1 0
#> SRR2001089 2 0 1 0 1 0
#> SRR2001090 2 0 1 0 1 0
#> SRR2001091 2 0 1 0 1 0
#> SRR2001084 2 0 1 0 1 0
#> SRR2001085 2 0 1 0 1 0
#> SRR2001086 2 0 1 0 1 0
#> SRR2001087 2 0 1 0 1 0
#> SRR2001080 2 0 1 0 1 0
#> SRR2001081 2 0 1 0 1 0
#> SRR2001082 2 0 1 0 1 0
#> SRR2001083 2 0 1 0 1 0
#> SRR2001076 2 0 1 0 1 0
#> SRR2001077 2 0 1 0 1 0
#> SRR2001078 2 0 1 0 1 0
#> SRR2001079 2 0 1 0 1 0
#> SRR2001072 2 0 1 0 1 0
#> SRR2001073 2 0 1 0 1 0
#> SRR2001074 2 0 1 0 1 0
#> SRR2001075 2 0 1 0 1 0
#> SRR2001068 2 0 1 0 1 0
#> SRR2001069 2 0 1 0 1 0
#> SRR2001070 2 0 1 0 1 0
#> SRR2001071 2 0 1 0 1 0
#> SRR2001064 2 0 1 0 1 0
#> SRR2001065 2 0 1 0 1 0
#> SRR2001066 2 0 1 0 1 0
#> SRR2001067 2 0 1 0 1 0
#> SRR2001060 2 0 1 0 1 0
#> SRR2001061 2 0 1 0 1 0
#> SRR2001062 2 0 1 0 1 0
#> SRR2001063 2 0 1 0 1 0
#> SRR2001056 2 0 1 0 1 0
#> SRR2001057 2 0 1 0 1 0
#> SRR2001058 2 0 1 0 1 0
#> SRR2001059 2 0 1 0 1 0
#> SRR2001052 2 0 1 0 1 0
#> SRR2001053 2 0 1 0 1 0
#> SRR2001054 2 0 1 0 1 0
#> SRR2001055 2 0 1 0 1 0
#> SRR2001048 2 0 1 0 1 0
#> SRR2001049 2 0 1 0 1 0
#> SRR2001050 2 0 1 0 1 0
#> SRR2001051 2 0 1 0 1 0
#> SRR2001044 2 0 1 0 1 0
#> SRR2001045 2 0 1 0 1 0
#> SRR2001046 2 0 1 0 1 0
#> SRR2001047 2 0 1 0 1 0
#> SRR2001040 2 0 1 0 1 0
#> SRR2001041 2 0 1 0 1 0
#> SRR2001042 2 0 1 0 1 0
#> SRR2001043 2 0 1 0 1 0
#> SRR2001036 2 0 1 0 1 0
#> SRR2001037 2 0 1 0 1 0
#> SRR2001038 2 0 1 0 1 0
#> SRR2001039 2 0 1 0 1 0
#> SRR2001028 2 0 1 0 1 0
#> SRR2001029 2 0 1 0 1 0
#> SRR2001030 2 0 1 0 1 0
#> SRR2001031 2 0 1 0 1 0
#> SRR2001024 2 0 1 0 1 0
#> SRR2001025 2 0 1 0 1 0
#> SRR2001026 2 0 1 0 1 0
#> SRR2001027 2 0 1 0 1 0
#> SRR2001020 2 0 1 0 1 0
#> SRR2001021 2 0 1 0 1 0
#> SRR2001022 2 0 1 0 1 0
#> SRR2001023 2 0 1 0 1 0
#> SRR2001016 2 0 1 0 1 0
#> SRR2001017 2 0 1 0 1 0
#> SRR2001018 2 0 1 0 1 0
#> SRR2001019 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.1474 0.966 0 0.948 0 0.052
#> SRR2001033 2 0.1637 0.960 0 0.940 0 0.060
#> SRR2001034 2 0.1474 0.966 0 0.948 0 0.052
#> SRR2001035 2 0.1474 0.966 0 0.948 0 0.052
#> SRR2001204 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001205 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001206 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001207 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001200 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001201 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001202 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001203 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001196 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001197 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001198 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001199 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001192 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001193 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001194 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001195 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001188 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001189 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001190 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001191 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001184 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001185 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001186 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001187 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001180 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001181 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001182 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001183 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001176 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001177 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001178 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001179 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001172 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001173 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001174 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001175 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001168 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001169 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001170 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001171 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001164 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001165 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001166 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001167 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001160 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001161 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001162 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001163 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001156 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001157 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001158 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001159 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001152 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001153 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001154 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001155 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001148 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001149 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001150 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001151 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001144 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001145 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001146 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001147 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001140 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001142 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001143 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001136 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001137 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001138 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001139 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001132 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001133 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001134 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001135 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001128 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001129 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001130 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001131 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001124 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001125 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001126 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001127 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001120 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001121 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001122 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001123 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001116 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001117 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001118 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001119 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001112 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001113 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001114 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001115 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001108 4 0.0000 0.996 0 0.000 0 1.000
#> SRR2001109 4 0.0000 0.996 0 0.000 0 1.000
#> SRR2001110 4 0.0000 0.996 0 0.000 0 1.000
#> SRR2001111 4 0.0000 0.996 0 0.000 0 1.000
#> SRR2001104 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001105 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001106 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001107 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001100 2 0.1302 0.968 0 0.956 0 0.044
#> SRR2001101 2 0.1302 0.968 0 0.956 0 0.044
#> SRR2001102 2 0.1302 0.968 0 0.956 0 0.044
#> SRR2001103 2 0.0188 0.977 0 0.996 0 0.004
#> SRR2001096 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001097 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001098 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001099 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001092 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001093 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001094 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001095 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001088 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001089 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001090 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001091 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001084 4 0.0000 0.996 0 0.000 0 1.000
#> SRR2001085 4 0.0000 0.996 0 0.000 0 1.000
#> SRR2001086 4 0.0000 0.996 0 0.000 0 1.000
#> SRR2001087 4 0.0000 0.996 0 0.000 0 1.000
#> SRR2001080 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001081 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001082 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001083 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001076 2 0.0707 0.974 0 0.980 0 0.020
#> SRR2001077 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001078 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001079 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001072 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001073 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001074 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001075 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001068 2 0.1637 0.960 0 0.940 0 0.060
#> SRR2001069 2 0.1474 0.966 0 0.948 0 0.052
#> SRR2001070 2 0.1474 0.966 0 0.948 0 0.052
#> SRR2001071 2 0.1474 0.966 0 0.948 0 0.052
#> SRR2001064 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001065 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001066 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001067 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001060 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001061 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001062 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001063 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001056 4 0.0000 0.996 0 0.000 0 1.000
#> SRR2001057 4 0.0000 0.996 0 0.000 0 1.000
#> SRR2001058 4 0.0000 0.996 0 0.000 0 1.000
#> SRR2001059 4 0.0000 0.996 0 0.000 0 1.000
#> SRR2001052 2 0.1474 0.966 0 0.948 0 0.052
#> SRR2001053 2 0.1474 0.966 0 0.948 0 0.052
#> SRR2001054 2 0.1474 0.966 0 0.948 0 0.052
#> SRR2001055 2 0.1474 0.966 0 0.948 0 0.052
#> SRR2001048 2 0.1557 0.963 0 0.944 0 0.056
#> SRR2001049 2 0.1474 0.966 0 0.948 0 0.052
#> SRR2001050 2 0.1474 0.966 0 0.948 0 0.052
#> SRR2001051 2 0.1474 0.966 0 0.948 0 0.052
#> SRR2001044 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001045 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001046 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001047 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001040 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001041 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001042 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001043 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001036 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001037 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001038 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001039 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001028 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001029 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001030 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001031 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001024 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001025 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001026 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001027 4 0.0188 0.998 0 0.004 0 0.996
#> SRR2001020 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001021 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001022 2 0.0000 0.978 0 1.000 0 0.000
#> SRR2001023 2 0.0336 0.976 0 0.992 0 0.008
#> SRR2001016 4 0.0000 0.996 0 0.000 0 1.000
#> SRR2001017 4 0.0000 0.996 0 0.000 0 1.000
#> SRR2001018 4 0.0336 0.990 0 0.008 0 0.992
#> SRR2001019 4 0.0592 0.982 0 0.016 0 0.984
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 5 0.0510 0.875 0.000 0.016 0 0.000 0.984
#> SRR2001033 5 0.0798 0.871 0.000 0.016 0 0.008 0.976
#> SRR2001034 5 0.1851 0.833 0.000 0.088 0 0.000 0.912
#> SRR2001035 5 0.0510 0.875 0.000 0.016 0 0.000 0.984
#> SRR2001204 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001205 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001206 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001207 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001200 1 0.0290 0.995 0.992 0.000 0 0.000 0.008
#> SRR2001201 1 0.0162 0.996 0.996 0.000 0 0.000 0.004
#> SRR2001202 1 0.0290 0.995 0.992 0.000 0 0.000 0.008
#> SRR2001203 1 0.0290 0.995 0.992 0.000 0 0.000 0.008
#> SRR2001196 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001197 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001198 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001199 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001192 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001193 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001194 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001195 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001188 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001189 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001190 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001191 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001184 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001185 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001186 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001187 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001180 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001181 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001182 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001183 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001176 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001177 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001178 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001179 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001172 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001173 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001174 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001175 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001168 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001169 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001170 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001171 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001164 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001165 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001166 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001167 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001160 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001161 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001162 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001163 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001156 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001157 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001158 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001159 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001152 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001153 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001154 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001155 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001148 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001149 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001150 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001151 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001144 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001145 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001146 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001147 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001140 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001142 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001143 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001136 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001137 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001138 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001139 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001132 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001133 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001134 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001135 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001128 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001129 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001130 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001131 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001124 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001125 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001126 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001127 1 0.0162 0.998 0.996 0.000 0 0.000 0.004
#> SRR2001120 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001121 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001122 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001123 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001116 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001117 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001118 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001119 1 0.0000 0.998 1.000 0.000 0 0.000 0.000
#> SRR2001112 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001113 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001114 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001115 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001108 4 0.1270 0.961 0.000 0.000 0 0.948 0.052
#> SRR2001109 4 0.1270 0.961 0.000 0.000 0 0.948 0.052
#> SRR2001110 4 0.1341 0.958 0.000 0.000 0 0.944 0.056
#> SRR2001111 4 0.1197 0.963 0.000 0.000 0 0.952 0.048
#> SRR2001104 2 0.0404 0.913 0.000 0.988 0 0.000 0.012
#> SRR2001105 2 0.3480 0.641 0.000 0.752 0 0.000 0.248
#> SRR2001106 2 0.0404 0.913 0.000 0.988 0 0.000 0.012
#> SRR2001107 2 0.0510 0.913 0.000 0.984 0 0.000 0.016
#> SRR2001100 5 0.3336 0.790 0.000 0.228 0 0.000 0.772
#> SRR2001101 5 0.3519 0.796 0.000 0.216 0 0.008 0.776
#> SRR2001102 5 0.3143 0.806 0.000 0.204 0 0.000 0.796
#> SRR2001103 5 0.3534 0.766 0.000 0.256 0 0.000 0.744
#> SRR2001096 2 0.0000 0.915 0.000 1.000 0 0.000 0.000
#> SRR2001097 2 0.0000 0.915 0.000 1.000 0 0.000 0.000
#> SRR2001098 2 0.0000 0.915 0.000 1.000 0 0.000 0.000
#> SRR2001099 2 0.0000 0.915 0.000 1.000 0 0.000 0.000
#> SRR2001092 2 0.0162 0.914 0.000 0.996 0 0.000 0.004
#> SRR2001093 2 0.0000 0.915 0.000 1.000 0 0.000 0.000
#> SRR2001094 2 0.0000 0.915 0.000 1.000 0 0.000 0.000
#> SRR2001095 2 0.0000 0.915 0.000 1.000 0 0.000 0.000
#> SRR2001088 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001089 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001090 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001091 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001084 4 0.1270 0.961 0.000 0.000 0 0.948 0.052
#> SRR2001085 4 0.1043 0.967 0.000 0.000 0 0.960 0.040
#> SRR2001086 4 0.1197 0.963 0.000 0.000 0 0.952 0.048
#> SRR2001087 4 0.1270 0.961 0.000 0.000 0 0.948 0.052
#> SRR2001080 2 0.3039 0.734 0.000 0.808 0 0.000 0.192
#> SRR2001081 2 0.2561 0.798 0.000 0.856 0 0.000 0.144
#> SRR2001082 2 0.1965 0.855 0.000 0.904 0 0.000 0.096
#> SRR2001083 2 0.3395 0.664 0.000 0.764 0 0.000 0.236
#> SRR2001076 2 0.1671 0.881 0.000 0.924 0 0.000 0.076
#> SRR2001077 2 0.0404 0.913 0.000 0.988 0 0.000 0.012
#> SRR2001078 2 0.0510 0.912 0.000 0.984 0 0.000 0.016
#> SRR2001079 2 0.0609 0.911 0.000 0.980 0 0.000 0.020
#> SRR2001072 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001073 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001074 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001075 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001068 5 0.0609 0.875 0.000 0.020 0 0.000 0.980
#> SRR2001069 5 0.0609 0.875 0.000 0.020 0 0.000 0.980
#> SRR2001070 5 0.0510 0.875 0.000 0.016 0 0.000 0.984
#> SRR2001071 5 0.0510 0.875 0.000 0.016 0 0.000 0.984
#> SRR2001064 2 0.0000 0.915 0.000 1.000 0 0.000 0.000
#> SRR2001065 2 0.0000 0.915 0.000 1.000 0 0.000 0.000
#> SRR2001066 2 0.0000 0.915 0.000 1.000 0 0.000 0.000
#> SRR2001067 2 0.0000 0.915 0.000 1.000 0 0.000 0.000
#> SRR2001060 4 0.0162 0.980 0.000 0.000 0 0.996 0.004
#> SRR2001061 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001062 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001063 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001056 4 0.1270 0.961 0.000 0.000 0 0.948 0.052
#> SRR2001057 4 0.1197 0.963 0.000 0.000 0 0.952 0.048
#> SRR2001058 4 0.1270 0.961 0.000 0.000 0 0.948 0.052
#> SRR2001059 4 0.1270 0.961 0.000 0.000 0 0.948 0.052
#> SRR2001052 2 0.3274 0.732 0.000 0.780 0 0.000 0.220
#> SRR2001053 2 0.3210 0.741 0.000 0.788 0 0.000 0.212
#> SRR2001054 2 0.3274 0.732 0.000 0.780 0 0.000 0.220
#> SRR2001055 2 0.3210 0.741 0.000 0.788 0 0.000 0.212
#> SRR2001048 5 0.0771 0.873 0.000 0.020 0 0.004 0.976
#> SRR2001049 5 0.0510 0.875 0.000 0.016 0 0.000 0.984
#> SRR2001050 5 0.0510 0.875 0.000 0.016 0 0.000 0.984
#> SRR2001051 5 0.0794 0.873 0.000 0.028 0 0.000 0.972
#> SRR2001044 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001045 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001046 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001047 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001040 4 0.0162 0.980 0.000 0.000 0 0.996 0.004
#> SRR2001041 4 0.0000 0.979 0.000 0.000 0 1.000 0.000
#> SRR2001042 4 0.0162 0.980 0.000 0.000 0 0.996 0.004
#> SRR2001043 4 0.0162 0.980 0.000 0.000 0 0.996 0.004
#> SRR2001036 4 0.0000 0.979 0.000 0.000 0 1.000 0.000
#> SRR2001037 4 0.0162 0.979 0.000 0.000 0 0.996 0.004
#> SRR2001038 4 0.0000 0.979 0.000 0.000 0 1.000 0.000
#> SRR2001039 4 0.0000 0.979 0.000 0.000 0 1.000 0.000
#> SRR2001028 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001029 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001030 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001031 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001024 4 0.0000 0.979 0.000 0.000 0 1.000 0.000
#> SRR2001025 4 0.0000 0.979 0.000 0.000 0 1.000 0.000
#> SRR2001026 4 0.0290 0.980 0.000 0.000 0 0.992 0.008
#> SRR2001027 4 0.0162 0.980 0.000 0.000 0 0.996 0.004
#> SRR2001020 5 0.3586 0.759 0.000 0.264 0 0.000 0.736
#> SRR2001021 5 0.3586 0.759 0.000 0.264 0 0.000 0.736
#> SRR2001022 5 0.3586 0.759 0.000 0.264 0 0.000 0.736
#> SRR2001023 5 0.3508 0.772 0.000 0.252 0 0.000 0.748
#> SRR2001016 4 0.1341 0.958 0.000 0.000 0 0.944 0.056
#> SRR2001017 4 0.0880 0.970 0.000 0.000 0 0.968 0.032
#> SRR2001018 4 0.1410 0.955 0.000 0.000 0 0.940 0.060
#> SRR2001019 4 0.1410 0.956 0.000 0.000 0 0.940 0.060
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 6 0.0260 0.853 0.000 0.008 0 0.000 NA 0.992
#> SRR2001033 6 0.0000 0.850 0.000 0.000 0 0.000 NA 1.000
#> SRR2001034 6 0.0777 0.847 0.000 0.024 0 0.000 NA 0.972
#> SRR2001035 6 0.0260 0.853 0.000 0.008 0 0.000 NA 0.992
#> SRR2001204 1 0.2135 0.853 0.872 0.000 0 0.000 NA 0.000
#> SRR2001205 1 0.2135 0.853 0.872 0.000 0 0.000 NA 0.000
#> SRR2001206 1 0.2178 0.852 0.868 0.000 0 0.000 NA 0.000
#> SRR2001207 1 0.2260 0.851 0.860 0.000 0 0.000 NA 0.000
#> SRR2001200 1 0.3531 0.820 0.672 0.000 0 0.000 NA 0.000
#> SRR2001201 1 0.3531 0.820 0.672 0.000 0 0.000 NA 0.000
#> SRR2001202 1 0.3499 0.826 0.680 0.000 0 0.000 NA 0.000
#> SRR2001203 1 0.3531 0.820 0.672 0.000 0 0.000 NA 0.000
#> SRR2001196 1 0.3464 0.819 0.688 0.000 0 0.000 NA 0.000
#> SRR2001197 1 0.3464 0.819 0.688 0.000 0 0.000 NA 0.000
#> SRR2001198 1 0.3309 0.826 0.720 0.000 0 0.000 NA 0.000
#> SRR2001199 1 0.3221 0.828 0.736 0.000 0 0.000 NA 0.000
#> SRR2001192 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001193 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001194 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001195 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001188 1 0.0363 0.874 0.988 0.000 0 0.000 NA 0.000
#> SRR2001189 1 0.0632 0.875 0.976 0.000 0 0.000 NA 0.000
#> SRR2001190 1 0.0865 0.875 0.964 0.000 0 0.000 NA 0.000
#> SRR2001191 1 0.0713 0.874 0.972 0.000 0 0.000 NA 0.000
#> SRR2001184 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001185 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001186 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001187 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001180 1 0.0865 0.879 0.964 0.000 0 0.000 NA 0.000
#> SRR2001181 1 0.0547 0.876 0.980 0.000 0 0.000 NA 0.000
#> SRR2001182 1 0.0713 0.874 0.972 0.000 0 0.000 NA 0.000
#> SRR2001183 1 0.0713 0.877 0.972 0.000 0 0.000 NA 0.000
#> SRR2001176 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001177 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001178 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001179 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001172 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001173 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001174 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001175 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001168 1 0.2092 0.853 0.876 0.000 0 0.000 NA 0.000
#> SRR2001169 1 0.2092 0.853 0.876 0.000 0 0.000 NA 0.000
#> SRR2001170 1 0.2092 0.853 0.876 0.000 0 0.000 NA 0.000
#> SRR2001171 1 0.2092 0.853 0.876 0.000 0 0.000 NA 0.000
#> SRR2001164 1 0.2527 0.869 0.832 0.000 0 0.000 NA 0.000
#> SRR2001165 1 0.3198 0.847 0.740 0.000 0 0.000 NA 0.000
#> SRR2001166 1 0.1075 0.879 0.952 0.000 0 0.000 NA 0.000
#> SRR2001167 1 0.2527 0.871 0.832 0.000 0 0.000 NA 0.000
#> SRR2001160 1 0.0260 0.873 0.992 0.000 0 0.000 NA 0.000
#> SRR2001161 1 0.0260 0.873 0.992 0.000 0 0.000 NA 0.000
#> SRR2001162 1 0.0363 0.874 0.988 0.000 0 0.000 NA 0.000
#> SRR2001163 1 0.0363 0.874 0.988 0.000 0 0.000 NA 0.000
#> SRR2001156 1 0.3023 0.838 0.768 0.000 0 0.000 NA 0.000
#> SRR2001157 1 0.3023 0.838 0.768 0.000 0 0.000 NA 0.000
#> SRR2001158 1 0.2969 0.839 0.776 0.000 0 0.000 NA 0.000
#> SRR2001159 1 0.2996 0.839 0.772 0.000 0 0.000 NA 0.000
#> SRR2001152 1 0.0790 0.874 0.968 0.000 0 0.000 NA 0.000
#> SRR2001153 1 0.0937 0.878 0.960 0.000 0 0.000 NA 0.000
#> SRR2001154 1 0.0547 0.875 0.980 0.000 0 0.000 NA 0.000
#> SRR2001155 1 0.0458 0.876 0.984 0.000 0 0.000 NA 0.000
#> SRR2001148 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001149 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001150 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001151 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001144 1 0.2631 0.850 0.820 0.000 0 0.000 NA 0.000
#> SRR2001145 1 0.2597 0.849 0.824 0.000 0 0.000 NA 0.000
#> SRR2001146 1 0.2260 0.855 0.860 0.000 0 0.000 NA 0.000
#> SRR2001147 1 0.2135 0.862 0.872 0.000 0 0.000 NA 0.000
#> SRR2001140 1 0.3198 0.854 0.740 0.000 0 0.000 NA 0.000
#> SRR2001142 1 0.3221 0.848 0.736 0.000 0 0.000 NA 0.000
#> SRR2001143 1 0.3198 0.850 0.740 0.000 0 0.000 NA 0.000
#> SRR2001136 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001137 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001138 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001139 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001132 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001133 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001134 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001135 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001128 1 0.3175 0.835 0.744 0.000 0 0.000 NA 0.000
#> SRR2001129 1 0.2883 0.845 0.788 0.000 0 0.000 NA 0.000
#> SRR2001130 1 0.2996 0.839 0.772 0.000 0 0.000 NA 0.000
#> SRR2001131 1 0.2969 0.839 0.776 0.000 0 0.000 NA 0.000
#> SRR2001124 1 0.2969 0.840 0.776 0.000 0 0.000 NA 0.000
#> SRR2001125 1 0.2996 0.839 0.772 0.000 0 0.000 NA 0.000
#> SRR2001126 1 0.2969 0.839 0.776 0.000 0 0.000 NA 0.000
#> SRR2001127 1 0.2996 0.839 0.772 0.000 0 0.000 NA 0.000
#> SRR2001120 1 0.2178 0.852 0.868 0.000 0 0.000 NA 0.000
#> SRR2001121 1 0.2178 0.853 0.868 0.000 0 0.000 NA 0.000
#> SRR2001122 1 0.2092 0.853 0.876 0.000 0 0.000 NA 0.000
#> SRR2001123 1 0.2003 0.855 0.884 0.000 0 0.000 NA 0.000
#> SRR2001116 1 0.3221 0.850 0.736 0.000 0 0.000 NA 0.000
#> SRR2001117 1 0.3175 0.852 0.744 0.000 0 0.000 NA 0.000
#> SRR2001118 1 0.3076 0.853 0.760 0.000 0 0.000 NA 0.000
#> SRR2001119 1 0.3076 0.856 0.760 0.000 0 0.000 NA 0.000
#> SRR2001112 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001113 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001114 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001115 3 0.0000 1.000 0.000 0.000 1 0.000 NA 0.000
#> SRR2001108 4 0.1219 0.805 0.000 0.000 0 0.948 NA 0.004
#> SRR2001109 4 0.0146 0.789 0.000 0.000 0 0.996 NA 0.000
#> SRR2001110 4 0.1462 0.806 0.000 0.000 0 0.936 NA 0.008
#> SRR2001111 4 0.1124 0.802 0.000 0.000 0 0.956 NA 0.008
#> SRR2001104 2 0.1644 0.836 0.000 0.920 0 0.000 NA 0.076
#> SRR2001105 2 0.3950 0.154 0.000 0.564 0 0.000 NA 0.432
#> SRR2001106 2 0.1644 0.836 0.000 0.920 0 0.000 NA 0.076
#> SRR2001107 2 0.2191 0.803 0.000 0.876 0 0.000 NA 0.120
#> SRR2001100 6 0.3421 0.733 0.000 0.256 0 0.000 NA 0.736
#> SRR2001101 6 0.3337 0.732 0.000 0.260 0 0.000 NA 0.736
#> SRR2001102 6 0.3265 0.740 0.000 0.248 0 0.000 NA 0.748
#> SRR2001103 6 0.3426 0.715 0.000 0.276 0 0.000 NA 0.720
#> SRR2001096 2 0.0713 0.860 0.000 0.972 0 0.000 NA 0.000
#> SRR2001097 2 0.0713 0.860 0.000 0.972 0 0.000 NA 0.000
#> SRR2001098 2 0.0547 0.862 0.000 0.980 0 0.000 NA 0.000
#> SRR2001099 2 0.0547 0.862 0.000 0.980 0 0.000 NA 0.000
#> SRR2001092 2 0.0692 0.863 0.000 0.976 0 0.000 NA 0.004
#> SRR2001093 2 0.0547 0.862 0.000 0.980 0 0.000 NA 0.000
#> SRR2001094 2 0.0692 0.863 0.000 0.976 0 0.000 NA 0.004
#> SRR2001095 2 0.0692 0.863 0.000 0.976 0 0.000 NA 0.004
#> SRR2001088 4 0.3390 0.824 0.000 0.000 0 0.704 NA 0.000
#> SRR2001089 4 0.3578 0.823 0.000 0.000 0 0.660 NA 0.000
#> SRR2001090 4 0.3747 0.816 0.000 0.000 0 0.604 NA 0.000
#> SRR2001091 4 0.3804 0.811 0.000 0.000 0 0.576 NA 0.000
#> SRR2001084 4 0.0146 0.789 0.000 0.000 0 0.996 NA 0.000
#> SRR2001085 4 0.0363 0.790 0.000 0.000 0 0.988 NA 0.000
#> SRR2001086 4 0.1204 0.807 0.000 0.000 0 0.944 NA 0.000
#> SRR2001087 4 0.1398 0.804 0.000 0.000 0 0.940 NA 0.008
#> SRR2001080 2 0.3508 0.552 0.000 0.704 0 0.000 NA 0.292
#> SRR2001081 2 0.3383 0.595 0.000 0.728 0 0.000 NA 0.268
#> SRR2001082 2 0.2191 0.805 0.000 0.876 0 0.000 NA 0.120
#> SRR2001083 2 0.3915 0.217 0.000 0.584 0 0.000 NA 0.412
#> SRR2001076 2 0.2165 0.819 0.000 0.884 0 0.000 NA 0.108
#> SRR2001077 2 0.0632 0.858 0.000 0.976 0 0.000 NA 0.024
#> SRR2001078 2 0.0777 0.857 0.000 0.972 0 0.000 NA 0.024
#> SRR2001079 2 0.0858 0.857 0.000 0.968 0 0.000 NA 0.028
#> SRR2001072 4 0.3828 0.807 0.000 0.000 0 0.560 NA 0.000
#> SRR2001073 4 0.3857 0.799 0.000 0.000 0 0.532 NA 0.000
#> SRR2001074 4 0.3851 0.802 0.000 0.000 0 0.540 NA 0.000
#> SRR2001075 4 0.3860 0.797 0.000 0.000 0 0.528 NA 0.000
#> SRR2001068 6 0.0260 0.853 0.000 0.008 0 0.000 NA 0.992
#> SRR2001069 6 0.0146 0.852 0.000 0.004 0 0.000 NA 0.996
#> SRR2001070 6 0.0260 0.853 0.000 0.008 0 0.000 NA 0.992
#> SRR2001071 6 0.0146 0.849 0.000 0.004 0 0.000 NA 0.996
#> SRR2001064 2 0.0363 0.862 0.000 0.988 0 0.000 NA 0.000
#> SRR2001065 2 0.0260 0.862 0.000 0.992 0 0.000 NA 0.000
#> SRR2001066 2 0.0260 0.862 0.000 0.992 0 0.000 NA 0.000
#> SRR2001067 2 0.0547 0.862 0.000 0.980 0 0.000 NA 0.000
#> SRR2001060 4 0.3695 0.816 0.000 0.000 0 0.624 NA 0.000
#> SRR2001061 4 0.3797 0.811 0.000 0.000 0 0.580 NA 0.000
#> SRR2001062 4 0.3823 0.808 0.000 0.000 0 0.564 NA 0.000
#> SRR2001063 4 0.3857 0.798 0.000 0.000 0 0.532 NA 0.000
#> SRR2001056 4 0.0000 0.791 0.000 0.000 0 1.000 NA 0.000
#> SRR2001057 4 0.0146 0.789 0.000 0.000 0 0.996 NA 0.000
#> SRR2001058 4 0.0260 0.788 0.000 0.000 0 0.992 NA 0.000
#> SRR2001059 4 0.0713 0.798 0.000 0.000 0 0.972 NA 0.000
#> SRR2001052 2 0.3240 0.670 0.000 0.752 0 0.000 NA 0.244
#> SRR2001053 2 0.3189 0.680 0.000 0.760 0 0.000 NA 0.236
#> SRR2001054 2 0.3163 0.684 0.000 0.764 0 0.000 NA 0.232
#> SRR2001055 2 0.3215 0.674 0.000 0.756 0 0.000 NA 0.240
#> SRR2001048 6 0.0000 0.850 0.000 0.000 0 0.000 NA 1.000
#> SRR2001049 6 0.0000 0.850 0.000 0.000 0 0.000 NA 1.000
#> SRR2001050 6 0.0260 0.853 0.000 0.008 0 0.000 NA 0.992
#> SRR2001051 6 0.0000 0.850 0.000 0.000 0 0.000 NA 1.000
#> SRR2001044 4 0.3838 0.805 0.000 0.000 0 0.552 NA 0.000
#> SRR2001045 4 0.3851 0.802 0.000 0.000 0 0.540 NA 0.000
#> SRR2001046 4 0.3854 0.800 0.000 0.000 0 0.536 NA 0.000
#> SRR2001047 4 0.3854 0.800 0.000 0.000 0 0.536 NA 0.000
#> SRR2001040 4 0.1714 0.804 0.000 0.000 0 0.908 NA 0.000
#> SRR2001041 4 0.1863 0.801 0.000 0.000 0 0.896 NA 0.000
#> SRR2001042 4 0.2416 0.813 0.000 0.000 0 0.844 NA 0.000
#> SRR2001043 4 0.1910 0.801 0.000 0.000 0 0.892 NA 0.000
#> SRR2001036 4 0.1204 0.793 0.000 0.000 0 0.944 NA 0.000
#> SRR2001037 4 0.0790 0.780 0.000 0.000 0 0.968 NA 0.000
#> SRR2001038 4 0.1957 0.820 0.000 0.000 0 0.888 NA 0.000
#> SRR2001039 4 0.1714 0.814 0.000 0.000 0 0.908 NA 0.000
#> SRR2001028 4 0.3860 0.797 0.000 0.000 0 0.528 NA 0.000
#> SRR2001029 4 0.3860 0.797 0.000 0.000 0 0.528 NA 0.000
#> SRR2001030 4 0.3860 0.797 0.000 0.000 0 0.528 NA 0.000
#> SRR2001031 4 0.3860 0.797 0.000 0.000 0 0.528 NA 0.000
#> SRR2001024 4 0.2092 0.812 0.000 0.000 0 0.876 NA 0.000
#> SRR2001025 4 0.1957 0.815 0.000 0.000 0 0.888 NA 0.000
#> SRR2001026 4 0.3198 0.821 0.000 0.000 0 0.740 NA 0.000
#> SRR2001027 4 0.2823 0.821 0.000 0.000 0 0.796 NA 0.000
#> SRR2001020 6 0.3330 0.708 0.000 0.284 0 0.000 NA 0.716
#> SRR2001021 6 0.3448 0.711 0.000 0.280 0 0.000 NA 0.716
#> SRR2001022 6 0.3468 0.706 0.000 0.284 0 0.000 NA 0.712
#> SRR2001023 6 0.3426 0.716 0.000 0.276 0 0.000 NA 0.720
#> SRR2001016 4 0.4252 0.775 0.000 0.000 0 0.604 NA 0.024
#> SRR2001017 4 0.3953 0.780 0.000 0.000 0 0.656 NA 0.016
#> SRR2001018 4 0.4563 0.764 0.000 0.000 0 0.588 NA 0.044
#> SRR2001019 4 0.4378 0.772 0.000 0.000 0 0.600 NA 0.032
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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 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 1.000 1.000 0.5031 0.497 0.497
#> 3 3 1.000 0.983 0.969 0.2228 0.889 0.777
#> 4 4 0.871 0.883 0.858 0.0921 1.000 1.000
#> 5 5 0.846 0.946 0.899 0.0718 0.873 0.671
#> 6 6 0.742 0.900 0.881 0.0354 1.000 1.000
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0.0592 0.966 0.000 0.988 0.012
#> SRR2001033 2 0.0000 0.967 0.000 1.000 0.000
#> SRR2001034 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001035 2 0.0592 0.966 0.000 0.988 0.012
#> SRR2001204 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001205 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001206 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001207 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001200 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001201 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001202 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001203 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001196 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001197 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001198 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001199 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001192 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001193 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001194 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001195 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001188 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001189 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001190 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001191 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001184 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001185 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001186 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001187 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001180 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001181 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001182 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001183 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001176 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001177 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001178 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001179 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001172 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001173 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001174 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001175 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001168 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001169 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001170 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001171 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001164 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001165 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001166 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001167 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001160 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001161 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001162 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001163 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001156 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001157 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001158 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001159 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001152 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001153 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001154 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001155 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001148 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001149 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001150 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001151 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001144 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001145 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001146 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001147 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001140 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001142 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001143 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001136 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001137 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001138 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001139 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001132 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001133 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001134 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001135 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001128 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001129 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001130 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001131 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001124 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001125 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001126 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001127 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001120 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001121 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001122 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001123 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001116 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001117 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001118 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001119 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001112 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001113 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001114 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001115 3 0.2448 1.000 0.076 0.000 0.924
#> SRR2001108 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001109 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001110 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001111 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001104 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001105 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001106 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001107 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001100 2 0.0424 0.967 0.000 0.992 0.008
#> SRR2001101 2 0.0592 0.966 0.000 0.988 0.012
#> SRR2001102 2 0.0592 0.966 0.000 0.988 0.012
#> SRR2001103 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001096 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001097 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001098 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001099 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001092 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001093 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001094 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001095 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001088 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001089 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001090 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001091 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001084 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001085 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001086 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001087 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001080 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001081 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001082 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001083 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001076 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001077 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001078 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001079 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001072 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001073 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001074 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001075 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001068 2 0.0237 0.967 0.000 0.996 0.004
#> SRR2001069 2 0.0237 0.967 0.000 0.996 0.004
#> SRR2001070 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001071 2 0.0237 0.967 0.000 0.996 0.004
#> SRR2001064 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001065 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001066 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001067 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001060 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001061 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001062 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001063 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001056 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001057 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001058 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001059 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001052 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001053 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001054 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001055 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001048 2 0.0237 0.967 0.000 0.996 0.004
#> SRR2001049 2 0.0592 0.966 0.000 0.988 0.012
#> SRR2001050 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001051 2 0.0424 0.967 0.000 0.992 0.008
#> SRR2001044 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001045 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001046 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001047 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001040 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001041 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001042 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001043 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001036 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001037 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001038 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001039 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001028 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001029 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001030 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001031 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001024 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001025 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001026 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001027 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001020 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001021 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001022 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001023 2 0.0747 0.966 0.000 0.984 0.016
#> SRR2001016 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001017 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001018 2 0.2066 0.968 0.000 0.940 0.060
#> SRR2001019 2 0.2066 0.968 0.000 0.940 0.060
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.4898 0.776 0.000 0.584 0.000 0.416
#> SRR2001033 2 0.4761 0.779 0.000 0.628 0.000 0.372
#> SRR2001034 2 0.4967 0.768 0.000 0.548 0.000 0.452
#> SRR2001035 2 0.4855 0.777 0.000 0.600 0.000 0.400
#> SRR2001204 1 0.0657 0.989 0.984 0.000 0.004 0.012
#> SRR2001205 1 0.0469 0.989 0.988 0.000 0.000 0.012
#> SRR2001206 1 0.0524 0.989 0.988 0.000 0.004 0.008
#> SRR2001207 1 0.0336 0.990 0.992 0.000 0.000 0.008
#> SRR2001200 1 0.1388 0.975 0.960 0.000 0.012 0.028
#> SRR2001201 1 0.1388 0.975 0.960 0.000 0.012 0.028
#> SRR2001202 1 0.1488 0.974 0.956 0.000 0.012 0.032
#> SRR2001203 1 0.1388 0.975 0.960 0.000 0.012 0.028
#> SRR2001196 1 0.0804 0.986 0.980 0.000 0.012 0.008
#> SRR2001197 1 0.1059 0.982 0.972 0.000 0.012 0.016
#> SRR2001198 1 0.0804 0.986 0.980 0.000 0.012 0.008
#> SRR2001199 1 0.0804 0.986 0.980 0.000 0.012 0.008
#> SRR2001192 3 0.0657 0.996 0.012 0.000 0.984 0.004
#> SRR2001193 3 0.0657 0.996 0.012 0.000 0.984 0.004
#> SRR2001194 3 0.0657 0.996 0.012 0.000 0.984 0.004
#> SRR2001195 3 0.0657 0.996 0.012 0.000 0.984 0.004
#> SRR2001188 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001189 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001190 1 0.0188 0.989 0.996 0.000 0.000 0.004
#> SRR2001191 1 0.0524 0.989 0.988 0.000 0.004 0.008
#> SRR2001184 3 0.0804 0.995 0.012 0.000 0.980 0.008
#> SRR2001185 3 0.0804 0.995 0.012 0.000 0.980 0.008
#> SRR2001186 3 0.0804 0.995 0.012 0.000 0.980 0.008
#> SRR2001187 3 0.0804 0.995 0.012 0.000 0.980 0.008
#> SRR2001180 1 0.0188 0.989 0.996 0.000 0.000 0.004
#> SRR2001181 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001182 1 0.0336 0.989 0.992 0.000 0.000 0.008
#> SRR2001183 1 0.0592 0.988 0.984 0.000 0.000 0.016
#> SRR2001176 3 0.0657 0.996 0.012 0.000 0.984 0.004
#> SRR2001177 3 0.0469 0.996 0.012 0.000 0.988 0.000
#> SRR2001178 3 0.0469 0.996 0.012 0.000 0.988 0.000
#> SRR2001179 3 0.0657 0.996 0.012 0.000 0.984 0.004
#> SRR2001172 3 0.1059 0.993 0.012 0.000 0.972 0.016
#> SRR2001173 3 0.1059 0.993 0.012 0.000 0.972 0.016
#> SRR2001174 3 0.1059 0.993 0.012 0.000 0.972 0.016
#> SRR2001175 3 0.1059 0.993 0.012 0.000 0.972 0.016
#> SRR2001168 1 0.0657 0.987 0.984 0.000 0.004 0.012
#> SRR2001169 1 0.0779 0.985 0.980 0.000 0.004 0.016
#> SRR2001170 1 0.0895 0.983 0.976 0.000 0.004 0.020
#> SRR2001171 1 0.0469 0.989 0.988 0.000 0.000 0.012
#> SRR2001164 1 0.1042 0.984 0.972 0.000 0.008 0.020
#> SRR2001165 1 0.0657 0.988 0.984 0.000 0.004 0.012
#> SRR2001166 1 0.0524 0.989 0.988 0.000 0.004 0.008
#> SRR2001167 1 0.0672 0.988 0.984 0.000 0.008 0.008
#> SRR2001160 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001161 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001162 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001163 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001156 1 0.0937 0.984 0.976 0.000 0.012 0.012
#> SRR2001157 1 0.0804 0.986 0.980 0.000 0.012 0.008
#> SRR2001158 1 0.0804 0.986 0.980 0.000 0.012 0.008
#> SRR2001159 1 0.0657 0.986 0.984 0.000 0.012 0.004
#> SRR2001152 1 0.0336 0.990 0.992 0.000 0.000 0.008
#> SRR2001153 1 0.0336 0.990 0.992 0.000 0.000 0.008
#> SRR2001154 1 0.0336 0.990 0.992 0.000 0.000 0.008
#> SRR2001155 1 0.0469 0.989 0.988 0.000 0.000 0.012
#> SRR2001148 3 0.0804 0.995 0.012 0.000 0.980 0.008
#> SRR2001149 3 0.0804 0.995 0.012 0.000 0.980 0.008
#> SRR2001150 3 0.0804 0.995 0.012 0.000 0.980 0.008
#> SRR2001151 3 0.0657 0.996 0.012 0.000 0.984 0.004
#> SRR2001144 1 0.0336 0.990 0.992 0.000 0.000 0.008
#> SRR2001145 1 0.0336 0.990 0.992 0.000 0.000 0.008
#> SRR2001146 1 0.0336 0.990 0.992 0.000 0.000 0.008
#> SRR2001147 1 0.0336 0.990 0.992 0.000 0.000 0.008
#> SRR2001140 1 0.0469 0.989 0.988 0.000 0.000 0.012
#> SRR2001142 1 0.0469 0.989 0.988 0.000 0.000 0.012
#> SRR2001143 1 0.0469 0.989 0.988 0.000 0.000 0.012
#> SRR2001136 3 0.0469 0.996 0.012 0.000 0.988 0.000
#> SRR2001137 3 0.0657 0.996 0.012 0.000 0.984 0.004
#> SRR2001138 3 0.0469 0.996 0.012 0.000 0.988 0.000
#> SRR2001139 3 0.0657 0.996 0.012 0.000 0.984 0.004
#> SRR2001132 3 0.0657 0.996 0.012 0.000 0.984 0.004
#> SRR2001133 3 0.0657 0.996 0.012 0.000 0.984 0.004
#> SRR2001134 3 0.0657 0.996 0.012 0.000 0.984 0.004
#> SRR2001135 3 0.0657 0.996 0.012 0.000 0.984 0.004
#> SRR2001128 1 0.0188 0.990 0.996 0.000 0.004 0.000
#> SRR2001129 1 0.0188 0.990 0.996 0.000 0.004 0.000
#> SRR2001130 1 0.0188 0.990 0.996 0.000 0.004 0.000
#> SRR2001131 1 0.0188 0.990 0.996 0.000 0.004 0.000
#> SRR2001124 1 0.0804 0.986 0.980 0.000 0.012 0.008
#> SRR2001125 1 0.0657 0.986 0.984 0.000 0.012 0.004
#> SRR2001126 1 0.0524 0.988 0.988 0.000 0.008 0.004
#> SRR2001127 1 0.0804 0.986 0.980 0.000 0.012 0.008
#> SRR2001120 1 0.0336 0.990 0.992 0.000 0.000 0.008
#> SRR2001121 1 0.0336 0.990 0.992 0.000 0.000 0.008
#> SRR2001122 1 0.0336 0.990 0.992 0.000 0.000 0.008
#> SRR2001123 1 0.0336 0.990 0.992 0.000 0.000 0.008
#> SRR2001116 1 0.0376 0.990 0.992 0.000 0.004 0.004
#> SRR2001117 1 0.0524 0.990 0.988 0.000 0.004 0.008
#> SRR2001118 1 0.0188 0.990 0.996 0.000 0.004 0.000
#> SRR2001119 1 0.0376 0.990 0.992 0.000 0.004 0.004
#> SRR2001112 3 0.0937 0.993 0.012 0.000 0.976 0.012
#> SRR2001113 3 0.1059 0.992 0.012 0.000 0.972 0.016
#> SRR2001114 3 0.0937 0.993 0.012 0.000 0.976 0.012
#> SRR2001115 3 0.0937 0.993 0.012 0.000 0.976 0.012
#> SRR2001108 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001109 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001110 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001111 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001104 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001105 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001106 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001107 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001100 2 0.4898 0.776 0.000 0.584 0.000 0.416
#> SRR2001101 2 0.4907 0.775 0.000 0.580 0.000 0.420
#> SRR2001102 2 0.4933 0.773 0.000 0.568 0.000 0.432
#> SRR2001103 2 0.4925 0.774 0.000 0.572 0.000 0.428
#> SRR2001096 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001097 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001098 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001099 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001092 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001093 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001094 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001095 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001088 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001089 2 0.0188 0.784 0.000 0.996 0.000 0.004
#> SRR2001090 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001091 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001084 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001085 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001086 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001087 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001080 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001081 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001082 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001083 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001076 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001077 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001078 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001079 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001072 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001073 2 0.0336 0.784 0.000 0.992 0.000 0.008
#> SRR2001074 2 0.0817 0.784 0.000 0.976 0.000 0.024
#> SRR2001075 2 0.0188 0.784 0.000 0.996 0.000 0.004
#> SRR2001068 2 0.4804 0.778 0.000 0.616 0.000 0.384
#> SRR2001069 2 0.4643 0.779 0.000 0.656 0.000 0.344
#> SRR2001070 2 0.4916 0.774 0.000 0.576 0.000 0.424
#> SRR2001071 2 0.4830 0.778 0.000 0.608 0.000 0.392
#> SRR2001064 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001065 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001066 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001067 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001060 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001061 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001062 2 0.0188 0.783 0.000 0.996 0.000 0.004
#> SRR2001063 2 0.0188 0.784 0.000 0.996 0.000 0.004
#> SRR2001056 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001057 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001058 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001059 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001052 2 0.4967 0.768 0.000 0.548 0.000 0.452
#> SRR2001053 2 0.4967 0.768 0.000 0.548 0.000 0.452
#> SRR2001054 2 0.4961 0.769 0.000 0.552 0.000 0.448
#> SRR2001055 2 0.4972 0.767 0.000 0.544 0.000 0.456
#> SRR2001048 2 0.4761 0.779 0.000 0.628 0.000 0.372
#> SRR2001049 2 0.4898 0.776 0.000 0.584 0.000 0.416
#> SRR2001050 2 0.4877 0.777 0.000 0.592 0.000 0.408
#> SRR2001051 2 0.4888 0.776 0.000 0.588 0.000 0.412
#> SRR2001044 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001045 2 0.0817 0.784 0.000 0.976 0.000 0.024
#> SRR2001046 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001047 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001040 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001041 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001042 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001043 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001036 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001037 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001038 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001039 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001028 2 0.0336 0.784 0.000 0.992 0.000 0.008
#> SRR2001029 2 0.0188 0.784 0.000 0.996 0.000 0.004
#> SRR2001030 2 0.0592 0.784 0.000 0.984 0.000 0.016
#> SRR2001031 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001024 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001025 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001026 2 0.0188 0.784 0.000 0.996 0.000 0.004
#> SRR2001027 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001020 2 0.4967 0.768 0.000 0.548 0.000 0.452
#> SRR2001021 2 0.4961 0.769 0.000 0.552 0.000 0.448
#> SRR2001022 2 0.4967 0.768 0.000 0.548 0.000 0.452
#> SRR2001023 2 0.4948 0.771 0.000 0.560 0.000 0.440
#> SRR2001016 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001017 2 0.0000 0.783 0.000 1.000 0.000 0.000
#> SRR2001018 2 0.0469 0.784 0.000 0.988 0.000 0.012
#> SRR2001019 2 0.0188 0.784 0.000 0.996 0.000 0.004
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.2712 0.890 0.000 0.880 0.000 0.088 NA
#> SRR2001033 2 0.3531 0.810 0.000 0.816 0.000 0.148 NA
#> SRR2001034 2 0.2036 0.916 0.000 0.920 0.000 0.056 NA
#> SRR2001035 2 0.3002 0.862 0.000 0.856 0.000 0.116 NA
#> SRR2001204 1 0.2172 0.945 0.908 0.000 0.016 0.000 NA
#> SRR2001205 1 0.2233 0.941 0.904 0.000 0.016 0.000 NA
#> SRR2001206 1 0.2110 0.946 0.912 0.000 0.016 0.000 NA
#> SRR2001207 1 0.2046 0.947 0.916 0.000 0.016 0.000 NA
#> SRR2001200 1 0.1877 0.945 0.924 0.000 0.012 0.000 NA
#> SRR2001201 1 0.1845 0.949 0.928 0.000 0.016 0.000 NA
#> SRR2001202 1 0.1740 0.950 0.932 0.000 0.012 0.000 NA
#> SRR2001203 1 0.1740 0.950 0.932 0.000 0.012 0.000 NA
#> SRR2001196 1 0.1012 0.967 0.968 0.000 0.012 0.000 NA
#> SRR2001197 1 0.1117 0.966 0.964 0.000 0.016 0.000 NA
#> SRR2001198 1 0.0912 0.967 0.972 0.000 0.012 0.000 NA
#> SRR2001199 1 0.0912 0.967 0.972 0.000 0.012 0.000 NA
#> SRR2001192 3 0.0290 0.980 0.000 0.000 0.992 0.000 NA
#> SRR2001193 3 0.0324 0.981 0.000 0.000 0.992 0.004 NA
#> SRR2001194 3 0.0771 0.979 0.000 0.000 0.976 0.004 NA
#> SRR2001195 3 0.0566 0.980 0.000 0.000 0.984 0.004 NA
#> SRR2001188 1 0.0162 0.972 0.996 0.000 0.000 0.000 NA
#> SRR2001189 1 0.0404 0.972 0.988 0.000 0.000 0.000 NA
#> SRR2001190 1 0.0162 0.972 0.996 0.000 0.000 0.000 NA
#> SRR2001191 1 0.0162 0.972 0.996 0.000 0.000 0.000 NA
#> SRR2001184 3 0.0404 0.980 0.000 0.000 0.988 0.000 NA
#> SRR2001185 3 0.0510 0.980 0.000 0.000 0.984 0.000 NA
#> SRR2001186 3 0.0510 0.979 0.000 0.000 0.984 0.000 NA
#> SRR2001187 3 0.0510 0.979 0.000 0.000 0.984 0.000 NA
#> SRR2001180 1 0.0162 0.972 0.996 0.000 0.000 0.000 NA
#> SRR2001181 1 0.0162 0.972 0.996 0.000 0.000 0.000 NA
#> SRR2001182 1 0.0162 0.972 0.996 0.000 0.000 0.000 NA
#> SRR2001183 1 0.0162 0.972 0.996 0.000 0.000 0.000 NA
#> SRR2001176 3 0.0290 0.981 0.000 0.000 0.992 0.000 NA
#> SRR2001177 3 0.0290 0.980 0.000 0.000 0.992 0.000 NA
#> SRR2001178 3 0.0000 0.981 0.000 0.000 1.000 0.000 NA
#> SRR2001179 3 0.0162 0.980 0.000 0.000 0.996 0.000 NA
#> SRR2001172 3 0.1952 0.951 0.004 0.000 0.912 0.000 NA
#> SRR2001173 3 0.1768 0.957 0.004 0.000 0.924 0.000 NA
#> SRR2001174 3 0.1892 0.954 0.004 0.000 0.916 0.000 NA
#> SRR2001175 3 0.1892 0.953 0.004 0.000 0.916 0.000 NA
#> SRR2001168 1 0.2233 0.941 0.904 0.000 0.016 0.000 NA
#> SRR2001169 1 0.2784 0.920 0.872 0.000 0.016 0.004 NA
#> SRR2001170 1 0.2677 0.920 0.872 0.000 0.016 0.000 NA
#> SRR2001171 1 0.2573 0.925 0.880 0.000 0.016 0.000 NA
#> SRR2001164 1 0.0510 0.970 0.984 0.000 0.000 0.000 NA
#> SRR2001165 1 0.0671 0.969 0.980 0.000 0.004 0.000 NA
#> SRR2001166 1 0.0404 0.971 0.988 0.000 0.000 0.000 NA
#> SRR2001167 1 0.0510 0.970 0.984 0.000 0.000 0.000 NA
#> SRR2001160 1 0.0162 0.972 0.996 0.000 0.000 0.000 NA
#> SRR2001161 1 0.0162 0.972 0.996 0.000 0.000 0.000 NA
#> SRR2001162 1 0.0290 0.972 0.992 0.000 0.000 0.000 NA
#> SRR2001163 1 0.0000 0.972 1.000 0.000 0.000 0.000 NA
#> SRR2001156 1 0.1012 0.966 0.968 0.000 0.012 0.000 NA
#> SRR2001157 1 0.0912 0.967 0.972 0.000 0.012 0.000 NA
#> SRR2001158 1 0.1012 0.966 0.968 0.000 0.012 0.000 NA
#> SRR2001159 1 0.1012 0.968 0.968 0.000 0.012 0.000 NA
#> SRR2001152 1 0.0794 0.969 0.972 0.000 0.000 0.000 NA
#> SRR2001153 1 0.0794 0.969 0.972 0.000 0.000 0.000 NA
#> SRR2001154 1 0.0703 0.970 0.976 0.000 0.000 0.000 NA
#> SRR2001155 1 0.0880 0.968 0.968 0.000 0.000 0.000 NA
#> SRR2001148 3 0.0566 0.979 0.004 0.000 0.984 0.000 NA
#> SRR2001149 3 0.0404 0.980 0.000 0.000 0.988 0.000 NA
#> SRR2001150 3 0.0703 0.978 0.000 0.000 0.976 0.000 NA
#> SRR2001151 3 0.0404 0.980 0.000 0.000 0.988 0.000 NA
#> SRR2001144 1 0.1717 0.958 0.936 0.000 0.008 0.004 NA
#> SRR2001145 1 0.1557 0.960 0.940 0.000 0.008 0.000 NA
#> SRR2001146 1 0.1502 0.959 0.940 0.000 0.004 0.000 NA
#> SRR2001147 1 0.1430 0.961 0.944 0.000 0.004 0.000 NA
#> SRR2001140 1 0.0880 0.968 0.968 0.000 0.000 0.000 NA
#> SRR2001142 1 0.0955 0.968 0.968 0.000 0.004 0.000 NA
#> SRR2001143 1 0.1365 0.964 0.952 0.000 0.004 0.004 NA
#> SRR2001136 3 0.0510 0.980 0.000 0.000 0.984 0.000 NA
#> SRR2001137 3 0.0865 0.979 0.004 0.000 0.972 0.000 NA
#> SRR2001138 3 0.0404 0.981 0.000 0.000 0.988 0.000 NA
#> SRR2001139 3 0.0566 0.980 0.004 0.000 0.984 0.000 NA
#> SRR2001132 3 0.0794 0.977 0.000 0.000 0.972 0.000 NA
#> SRR2001133 3 0.0703 0.978 0.000 0.000 0.976 0.000 NA
#> SRR2001134 3 0.0703 0.979 0.000 0.000 0.976 0.000 NA
#> SRR2001135 3 0.0794 0.978 0.000 0.000 0.972 0.000 NA
#> SRR2001128 1 0.0000 0.972 1.000 0.000 0.000 0.000 NA
#> SRR2001129 1 0.0290 0.972 0.992 0.000 0.000 0.000 NA
#> SRR2001130 1 0.0162 0.972 0.996 0.000 0.000 0.000 NA
#> SRR2001131 1 0.0451 0.972 0.988 0.000 0.000 0.004 NA
#> SRR2001124 1 0.1106 0.965 0.964 0.000 0.012 0.000 NA
#> SRR2001125 1 0.0898 0.968 0.972 0.000 0.008 0.000 NA
#> SRR2001126 1 0.0898 0.967 0.972 0.000 0.008 0.000 NA
#> SRR2001127 1 0.1012 0.966 0.968 0.000 0.012 0.000 NA
#> SRR2001120 1 0.1597 0.959 0.940 0.000 0.012 0.000 NA
#> SRR2001121 1 0.1857 0.954 0.928 0.000 0.008 0.004 NA
#> SRR2001122 1 0.1628 0.957 0.936 0.000 0.008 0.000 NA
#> SRR2001123 1 0.1518 0.961 0.944 0.000 0.004 0.004 NA
#> SRR2001116 1 0.0290 0.972 0.992 0.000 0.000 0.000 NA
#> SRR2001117 1 0.0451 0.972 0.988 0.000 0.004 0.000 NA
#> SRR2001118 1 0.0290 0.972 0.992 0.000 0.000 0.000 NA
#> SRR2001119 1 0.0290 0.972 0.992 0.000 0.000 0.000 NA
#> SRR2001112 3 0.1792 0.956 0.000 0.000 0.916 0.000 NA
#> SRR2001113 3 0.1792 0.956 0.000 0.000 0.916 0.000 NA
#> SRR2001114 3 0.1732 0.958 0.000 0.000 0.920 0.000 NA
#> SRR2001115 3 0.1792 0.956 0.000 0.000 0.916 0.000 NA
#> SRR2001108 4 0.4058 0.957 0.000 0.236 0.000 0.740 NA
#> SRR2001109 4 0.4113 0.955 0.000 0.232 0.000 0.740 NA
#> SRR2001110 4 0.4169 0.954 0.000 0.240 0.000 0.732 NA
#> SRR2001111 4 0.4141 0.955 0.000 0.236 0.000 0.736 NA
#> SRR2001104 2 0.0162 0.927 0.000 0.996 0.000 0.004 NA
#> SRR2001105 2 0.0771 0.929 0.000 0.976 0.000 0.020 NA
#> SRR2001106 2 0.0162 0.927 0.000 0.996 0.000 0.004 NA
#> SRR2001107 2 0.0162 0.927 0.000 0.996 0.000 0.004 NA
#> SRR2001100 2 0.2293 0.899 0.000 0.900 0.000 0.084 NA
#> SRR2001101 2 0.2540 0.896 0.000 0.888 0.000 0.088 NA
#> SRR2001102 2 0.1845 0.917 0.000 0.928 0.000 0.056 NA
#> SRR2001103 2 0.1408 0.924 0.000 0.948 0.000 0.044 NA
#> SRR2001096 2 0.0404 0.918 0.000 0.988 0.000 0.012 NA
#> SRR2001097 2 0.0566 0.917 0.000 0.984 0.000 0.012 NA
#> SRR2001098 2 0.0404 0.918 0.000 0.988 0.000 0.012 NA
#> SRR2001099 2 0.0898 0.923 0.000 0.972 0.000 0.020 NA
#> SRR2001092 2 0.0693 0.920 0.000 0.980 0.000 0.008 NA
#> SRR2001093 2 0.1364 0.911 0.000 0.952 0.000 0.012 NA
#> SRR2001094 2 0.0693 0.918 0.000 0.980 0.000 0.012 NA
#> SRR2001095 2 0.0992 0.918 0.000 0.968 0.000 0.008 NA
#> SRR2001088 4 0.3999 0.955 0.000 0.240 0.000 0.740 NA
#> SRR2001089 4 0.3878 0.955 0.000 0.236 0.000 0.748 NA
#> SRR2001090 4 0.4167 0.948 0.000 0.252 0.000 0.724 NA
#> SRR2001091 4 0.4250 0.947 0.000 0.252 0.000 0.720 NA
#> SRR2001084 4 0.4113 0.954 0.000 0.232 0.000 0.740 NA
#> SRR2001085 4 0.4000 0.955 0.000 0.228 0.000 0.748 NA
#> SRR2001086 4 0.4197 0.951 0.000 0.244 0.000 0.728 NA
#> SRR2001087 4 0.4169 0.954 0.000 0.240 0.000 0.732 NA
#> SRR2001080 2 0.1893 0.920 0.000 0.928 0.000 0.024 NA
#> SRR2001081 2 0.1281 0.925 0.000 0.956 0.000 0.012 NA
#> SRR2001082 2 0.1012 0.929 0.000 0.968 0.000 0.020 NA
#> SRR2001083 2 0.1493 0.927 0.000 0.948 0.000 0.024 NA
#> SRR2001076 2 0.0671 0.929 0.000 0.980 0.000 0.016 NA
#> SRR2001077 2 0.0162 0.927 0.000 0.996 0.000 0.004 NA
#> SRR2001078 2 0.0290 0.927 0.000 0.992 0.000 0.008 NA
#> SRR2001079 2 0.0162 0.927 0.000 0.996 0.000 0.004 NA
#> SRR2001072 4 0.4777 0.916 0.000 0.268 0.000 0.680 NA
#> SRR2001073 4 0.4863 0.914 0.000 0.272 0.000 0.672 NA
#> SRR2001074 4 0.4797 0.896 0.000 0.296 0.000 0.660 NA
#> SRR2001075 4 0.4576 0.931 0.000 0.268 0.000 0.692 NA
#> SRR2001068 2 0.3238 0.836 0.000 0.836 0.000 0.136 NA
#> SRR2001069 2 0.3724 0.748 0.000 0.788 0.000 0.184 NA
#> SRR2001070 2 0.2685 0.889 0.000 0.880 0.000 0.092 NA
#> SRR2001071 2 0.3193 0.842 0.000 0.840 0.000 0.132 NA
#> SRR2001064 2 0.1082 0.917 0.000 0.964 0.000 0.008 NA
#> SRR2001065 2 0.0510 0.925 0.000 0.984 0.000 0.000 NA
#> SRR2001066 2 0.1124 0.921 0.000 0.960 0.000 0.004 NA
#> SRR2001067 2 0.0579 0.925 0.000 0.984 0.000 0.008 NA
#> SRR2001060 4 0.4712 0.921 0.000 0.268 0.000 0.684 NA
#> SRR2001061 4 0.4645 0.923 0.000 0.268 0.000 0.688 NA
#> SRR2001062 4 0.4597 0.932 0.000 0.260 0.000 0.696 NA
#> SRR2001063 4 0.4823 0.913 0.000 0.276 0.000 0.672 NA
#> SRR2001056 4 0.4083 0.954 0.000 0.228 0.000 0.744 NA
#> SRR2001057 4 0.4113 0.955 0.000 0.232 0.000 0.740 NA
#> SRR2001058 4 0.4058 0.957 0.000 0.236 0.000 0.740 NA
#> SRR2001059 4 0.3970 0.958 0.000 0.236 0.000 0.744 NA
#> SRR2001052 2 0.1836 0.923 0.000 0.932 0.000 0.032 NA
#> SRR2001053 2 0.1750 0.923 0.000 0.936 0.000 0.028 NA
#> SRR2001054 2 0.1753 0.924 0.000 0.936 0.000 0.032 NA
#> SRR2001055 2 0.1485 0.925 0.000 0.948 0.000 0.020 NA
#> SRR2001048 2 0.3370 0.818 0.000 0.824 0.000 0.148 NA
#> SRR2001049 2 0.2795 0.881 0.000 0.872 0.000 0.100 NA
#> SRR2001050 2 0.2848 0.876 0.000 0.868 0.000 0.104 NA
#> SRR2001051 2 0.3051 0.857 0.000 0.852 0.000 0.120 NA
#> SRR2001044 4 0.3579 0.960 0.000 0.240 0.000 0.756 NA
#> SRR2001045 4 0.3728 0.960 0.000 0.244 0.000 0.748 NA
#> SRR2001046 4 0.3635 0.959 0.000 0.248 0.000 0.748 NA
#> SRR2001047 4 0.3916 0.955 0.000 0.256 0.000 0.732 NA
#> SRR2001040 4 0.3551 0.954 0.000 0.220 0.000 0.772 NA
#> SRR2001041 4 0.3274 0.954 0.000 0.220 0.000 0.780 NA
#> SRR2001042 4 0.3461 0.955 0.000 0.224 0.000 0.772 NA
#> SRR2001043 4 0.3551 0.953 0.000 0.220 0.000 0.772 NA
#> SRR2001036 4 0.3430 0.954 0.000 0.220 0.000 0.776 NA
#> SRR2001037 4 0.3519 0.952 0.000 0.216 0.000 0.776 NA
#> SRR2001038 4 0.3659 0.954 0.000 0.220 0.000 0.768 NA
#> SRR2001039 4 0.3551 0.954 0.000 0.220 0.000 0.772 NA
#> SRR2001028 4 0.3861 0.951 0.000 0.264 0.000 0.728 NA
#> SRR2001029 4 0.3635 0.959 0.000 0.248 0.000 0.748 NA
#> SRR2001030 4 0.3835 0.954 0.000 0.260 0.000 0.732 NA
#> SRR2001031 4 0.3700 0.960 0.000 0.240 0.000 0.752 NA
#> SRR2001024 4 0.3521 0.959 0.000 0.232 0.000 0.764 NA
#> SRR2001025 4 0.3642 0.958 0.000 0.232 0.000 0.760 NA
#> SRR2001026 4 0.3700 0.960 0.000 0.240 0.000 0.752 NA
#> SRR2001027 4 0.3579 0.958 0.000 0.240 0.000 0.756 NA
#> SRR2001020 2 0.2378 0.914 0.000 0.904 0.000 0.048 NA
#> SRR2001021 2 0.2592 0.905 0.000 0.892 0.000 0.052 NA
#> SRR2001022 2 0.1915 0.923 0.000 0.928 0.000 0.040 NA
#> SRR2001023 2 0.2592 0.908 0.000 0.892 0.000 0.056 NA
#> SRR2001016 4 0.4276 0.945 0.000 0.256 0.000 0.716 NA
#> SRR2001017 4 0.4250 0.947 0.000 0.252 0.000 0.720 NA
#> SRR2001018 4 0.4326 0.937 0.000 0.264 0.000 0.708 NA
#> SRR2001019 4 0.4326 0.937 0.000 0.264 0.000 0.708 NA
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 2 0.4405 0.804 0.000 0.688 0.000 0.240 NA NA
#> SRR2001033 2 0.4751 0.708 0.000 0.616 0.000 0.312 NA NA
#> SRR2001034 2 0.4011 0.839 0.000 0.736 0.000 0.204 NA NA
#> SRR2001035 2 0.4544 0.784 0.000 0.668 0.000 0.256 NA NA
#> SRR2001204 1 0.3053 0.883 0.812 0.000 0.020 0.000 NA NA
#> SRR2001205 1 0.3409 0.859 0.780 0.000 0.028 0.000 NA NA
#> SRR2001206 1 0.3279 0.871 0.796 0.000 0.028 0.000 NA NA
#> SRR2001207 1 0.2805 0.890 0.828 0.000 0.012 0.000 NA NA
#> SRR2001200 1 0.2883 0.884 0.844 0.000 0.012 0.000 NA NA
#> SRR2001201 1 0.3062 0.889 0.844 0.000 0.016 0.000 NA NA
#> SRR2001202 1 0.2588 0.893 0.860 0.000 0.012 0.000 NA NA
#> SRR2001203 1 0.2618 0.895 0.860 0.000 0.024 0.000 NA NA
#> SRR2001196 1 0.1605 0.931 0.936 0.000 0.004 0.000 NA NA
#> SRR2001197 1 0.2147 0.916 0.896 0.000 0.020 0.000 NA NA
#> SRR2001198 1 0.1802 0.923 0.916 0.000 0.012 0.000 NA NA
#> SRR2001199 1 0.1829 0.925 0.920 0.000 0.012 0.000 NA NA
#> SRR2001192 3 0.1194 0.961 0.008 0.000 0.956 0.000 NA NA
#> SRR2001193 3 0.1148 0.960 0.004 0.000 0.960 0.000 NA NA
#> SRR2001194 3 0.1194 0.961 0.004 0.000 0.956 0.000 NA NA
#> SRR2001195 3 0.0748 0.962 0.004 0.000 0.976 0.000 NA NA
#> SRR2001188 1 0.0837 0.937 0.972 0.000 0.004 0.000 NA NA
#> SRR2001189 1 0.1082 0.937 0.956 0.000 0.004 0.000 NA NA
#> SRR2001190 1 0.0767 0.936 0.976 0.000 0.004 0.000 NA NA
#> SRR2001191 1 0.0717 0.936 0.976 0.000 0.000 0.000 NA NA
#> SRR2001184 3 0.1296 0.960 0.004 0.000 0.952 0.000 NA NA
#> SRR2001185 3 0.1606 0.956 0.004 0.000 0.932 0.000 NA NA
#> SRR2001186 3 0.1542 0.957 0.004 0.000 0.936 0.000 NA NA
#> SRR2001187 3 0.1511 0.958 0.004 0.000 0.940 0.000 NA NA
#> SRR2001180 1 0.1065 0.935 0.964 0.000 0.008 0.000 NA NA
#> SRR2001181 1 0.0603 0.937 0.980 0.000 0.000 0.000 NA NA
#> SRR2001182 1 0.0862 0.934 0.972 0.000 0.004 0.000 NA NA
#> SRR2001183 1 0.1124 0.937 0.956 0.000 0.000 0.000 NA NA
#> SRR2001176 3 0.1074 0.960 0.012 0.000 0.960 0.000 NA NA
#> SRR2001177 3 0.0976 0.963 0.008 0.000 0.968 0.000 NA NA
#> SRR2001178 3 0.0951 0.962 0.004 0.000 0.968 0.000 NA NA
#> SRR2001179 3 0.0436 0.961 0.004 0.000 0.988 0.000 NA NA
#> SRR2001172 3 0.2308 0.934 0.008 0.000 0.880 0.000 NA NA
#> SRR2001173 3 0.1918 0.942 0.008 0.000 0.904 0.000 NA NA
#> SRR2001174 3 0.2165 0.935 0.008 0.000 0.884 0.000 NA NA
#> SRR2001175 3 0.2165 0.936 0.008 0.000 0.884 0.000 NA NA
#> SRR2001168 1 0.3483 0.847 0.764 0.000 0.024 0.000 NA NA
#> SRR2001169 1 0.4099 0.802 0.708 0.000 0.048 0.000 NA NA
#> SRR2001170 1 0.4014 0.807 0.716 0.000 0.044 0.000 NA NA
#> SRR2001171 1 0.3884 0.815 0.724 0.000 0.036 0.000 NA NA
#> SRR2001164 1 0.1477 0.928 0.940 0.000 0.004 0.000 NA NA
#> SRR2001165 1 0.1245 0.933 0.952 0.000 0.000 0.000 NA NA
#> SRR2001166 1 0.1218 0.932 0.956 0.000 0.004 0.000 NA NA
#> SRR2001167 1 0.1442 0.929 0.944 0.000 0.004 0.000 NA NA
#> SRR2001160 1 0.0964 0.936 0.968 0.000 0.004 0.000 NA NA
#> SRR2001161 1 0.0767 0.935 0.976 0.000 0.004 0.000 NA NA
#> SRR2001162 1 0.0767 0.937 0.976 0.000 0.004 0.000 NA NA
#> SRR2001163 1 0.0767 0.935 0.976 0.000 0.004 0.000 NA NA
#> SRR2001156 1 0.2019 0.914 0.900 0.000 0.012 0.000 NA NA
#> SRR2001157 1 0.1787 0.923 0.920 0.000 0.008 0.000 NA NA
#> SRR2001158 1 0.2095 0.920 0.904 0.000 0.016 0.000 NA NA
#> SRR2001159 1 0.1732 0.923 0.920 0.000 0.004 0.000 NA NA
#> SRR2001152 1 0.1411 0.929 0.936 0.000 0.004 0.000 NA NA
#> SRR2001153 1 0.1082 0.934 0.956 0.000 0.004 0.000 NA NA
#> SRR2001154 1 0.1524 0.930 0.932 0.000 0.008 0.000 NA NA
#> SRR2001155 1 0.1411 0.930 0.936 0.000 0.004 0.000 NA NA
#> SRR2001148 3 0.1194 0.960 0.004 0.000 0.956 0.000 NA NA
#> SRR2001149 3 0.0858 0.961 0.004 0.000 0.968 0.000 NA NA
#> SRR2001150 3 0.1226 0.960 0.004 0.000 0.952 0.000 NA NA
#> SRR2001151 3 0.1296 0.961 0.004 0.000 0.952 0.000 NA NA
#> SRR2001144 1 0.2402 0.911 0.868 0.000 0.012 0.000 NA NA
#> SRR2001145 1 0.2404 0.913 0.872 0.000 0.016 0.000 NA NA
#> SRR2001146 1 0.2538 0.908 0.860 0.000 0.016 0.000 NA NA
#> SRR2001147 1 0.2266 0.915 0.880 0.000 0.012 0.000 NA NA
#> SRR2001140 1 0.1866 0.922 0.908 0.000 0.008 0.000 NA NA
#> SRR2001142 1 0.2218 0.916 0.884 0.000 0.012 0.000 NA NA
#> SRR2001143 1 0.1970 0.920 0.900 0.000 0.008 0.000 NA NA
#> SRR2001136 3 0.1523 0.958 0.008 0.000 0.940 0.000 NA NA
#> SRR2001137 3 0.1477 0.957 0.008 0.000 0.940 0.000 NA NA
#> SRR2001138 3 0.1268 0.960 0.008 0.000 0.952 0.000 NA NA
#> SRR2001139 3 0.1477 0.958 0.008 0.000 0.940 0.000 NA NA
#> SRR2001132 3 0.1194 0.959 0.004 0.000 0.956 0.000 NA NA
#> SRR2001133 3 0.1268 0.958 0.008 0.000 0.952 0.000 NA NA
#> SRR2001134 3 0.1340 0.958 0.008 0.000 0.948 0.000 NA NA
#> SRR2001135 3 0.1477 0.956 0.008 0.000 0.940 0.000 NA NA
#> SRR2001128 1 0.0837 0.937 0.972 0.000 0.004 0.000 NA NA
#> SRR2001129 1 0.1194 0.936 0.956 0.000 0.008 0.000 NA NA
#> SRR2001130 1 0.0862 0.937 0.972 0.000 0.008 0.000 NA NA
#> SRR2001131 1 0.0922 0.937 0.968 0.000 0.004 0.000 NA NA
#> SRR2001124 1 0.1524 0.929 0.932 0.000 0.000 0.000 NA NA
#> SRR2001125 1 0.1409 0.934 0.948 0.000 0.012 0.000 NA NA
#> SRR2001126 1 0.1624 0.929 0.936 0.000 0.008 0.000 NA NA
#> SRR2001127 1 0.1555 0.926 0.932 0.000 0.004 0.000 NA NA
#> SRR2001120 1 0.2404 0.912 0.872 0.000 0.016 0.000 NA NA
#> SRR2001121 1 0.2750 0.904 0.844 0.000 0.020 0.000 NA NA
#> SRR2001122 1 0.2740 0.904 0.852 0.000 0.028 0.000 NA NA
#> SRR2001123 1 0.2664 0.902 0.848 0.000 0.016 0.000 NA NA
#> SRR2001116 1 0.0777 0.936 0.972 0.000 0.004 0.000 NA NA
#> SRR2001117 1 0.0858 0.937 0.968 0.000 0.004 0.000 NA NA
#> SRR2001118 1 0.0363 0.935 0.988 0.000 0.000 0.000 NA NA
#> SRR2001119 1 0.0692 0.937 0.976 0.000 0.000 0.000 NA NA
#> SRR2001112 3 0.3147 0.901 0.016 0.000 0.816 0.000 NA NA
#> SRR2001113 3 0.2925 0.909 0.016 0.000 0.832 0.000 NA NA
#> SRR2001114 3 0.2925 0.911 0.016 0.000 0.832 0.000 NA NA
#> SRR2001115 3 0.2963 0.908 0.016 0.000 0.828 0.000 NA NA
#> SRR2001108 4 0.2237 0.896 0.000 0.036 0.000 0.896 NA NA
#> SRR2001109 4 0.2164 0.897 0.000 0.032 0.000 0.900 NA NA
#> SRR2001110 4 0.2433 0.892 0.000 0.044 0.000 0.884 NA NA
#> SRR2001111 4 0.2499 0.892 0.000 0.048 0.000 0.880 NA NA
#> SRR2001104 2 0.1863 0.888 0.000 0.896 0.000 0.104 NA NA
#> SRR2001105 2 0.2748 0.890 0.000 0.848 0.000 0.128 NA NA
#> SRR2001106 2 0.2149 0.888 0.000 0.888 0.000 0.104 NA NA
#> SRR2001107 2 0.2587 0.887 0.000 0.868 0.000 0.108 NA NA
#> SRR2001100 2 0.3245 0.878 0.000 0.800 0.000 0.172 NA NA
#> SRR2001101 2 0.3947 0.846 0.000 0.732 0.000 0.220 NA NA
#> SRR2001102 2 0.2981 0.881 0.000 0.820 0.000 0.160 NA NA
#> SRR2001103 2 0.3168 0.880 0.000 0.804 0.000 0.172 NA NA
#> SRR2001096 2 0.1858 0.884 0.000 0.904 0.000 0.092 NA NA
#> SRR2001097 2 0.1858 0.884 0.000 0.904 0.000 0.092 NA NA
#> SRR2001098 2 0.1908 0.886 0.000 0.900 0.000 0.096 NA NA
#> SRR2001099 2 0.2121 0.886 0.000 0.892 0.000 0.096 NA NA
#> SRR2001092 2 0.2821 0.877 0.000 0.860 0.000 0.096 NA NA
#> SRR2001093 2 0.3410 0.864 0.000 0.820 0.000 0.100 NA NA
#> SRR2001094 2 0.2679 0.881 0.000 0.868 0.000 0.096 NA NA
#> SRR2001095 2 0.2772 0.877 0.000 0.864 0.000 0.092 NA NA
#> SRR2001088 4 0.2732 0.894 0.000 0.056 0.000 0.880 NA NA
#> SRR2001089 4 0.2147 0.903 0.000 0.044 0.000 0.912 NA NA
#> SRR2001090 4 0.2295 0.906 0.000 0.052 0.000 0.904 NA NA
#> SRR2001091 4 0.2713 0.892 0.000 0.052 0.000 0.880 NA NA
#> SRR2001084 4 0.2106 0.899 0.000 0.032 0.000 0.904 NA NA
#> SRR2001085 4 0.2164 0.897 0.000 0.032 0.000 0.900 NA NA
#> SRR2001086 4 0.2571 0.889 0.000 0.060 0.000 0.876 NA NA
#> SRR2001087 4 0.2308 0.896 0.000 0.040 0.000 0.892 NA NA
#> SRR2001080 2 0.3416 0.884 0.000 0.804 0.000 0.140 NA NA
#> SRR2001081 2 0.3649 0.877 0.000 0.796 0.000 0.132 NA NA
#> SRR2001082 2 0.2956 0.887 0.000 0.840 0.000 0.120 NA NA
#> SRR2001083 2 0.3633 0.878 0.000 0.796 0.000 0.136 NA NA
#> SRR2001076 2 0.2680 0.889 0.000 0.860 0.000 0.108 NA NA
#> SRR2001077 2 0.2213 0.887 0.000 0.888 0.000 0.100 NA NA
#> SRR2001078 2 0.2100 0.889 0.000 0.884 0.000 0.112 NA NA
#> SRR2001079 2 0.2358 0.888 0.000 0.876 0.000 0.108 NA NA
#> SRR2001072 4 0.3169 0.872 0.000 0.084 0.000 0.848 NA NA
#> SRR2001073 4 0.3341 0.858 0.000 0.088 0.000 0.836 NA NA
#> SRR2001074 4 0.3380 0.860 0.000 0.096 0.000 0.832 NA NA
#> SRR2001075 4 0.3053 0.879 0.000 0.080 0.000 0.856 NA NA
#> SRR2001068 2 0.4507 0.776 0.000 0.664 0.000 0.268 NA NA
#> SRR2001069 2 0.4855 0.671 0.000 0.596 0.000 0.328 NA NA
#> SRR2001070 2 0.4466 0.787 0.000 0.672 0.000 0.260 NA NA
#> SRR2001071 2 0.4557 0.772 0.000 0.660 0.000 0.268 NA NA
#> SRR2001064 2 0.2586 0.886 0.000 0.868 0.000 0.100 NA NA
#> SRR2001065 2 0.2558 0.885 0.000 0.868 0.000 0.104 NA NA
#> SRR2001066 2 0.3127 0.880 0.000 0.840 0.000 0.100 NA NA
#> SRR2001067 2 0.2383 0.885 0.000 0.880 0.000 0.096 NA NA
#> SRR2001060 4 0.2973 0.871 0.000 0.084 0.000 0.860 NA NA
#> SRR2001061 4 0.3157 0.870 0.000 0.088 0.000 0.848 NA NA
#> SRR2001062 4 0.3178 0.871 0.000 0.080 0.000 0.848 NA NA
#> SRR2001063 4 0.3520 0.849 0.000 0.108 0.000 0.820 NA NA
#> SRR2001056 4 0.2119 0.901 0.000 0.036 0.000 0.904 NA NA
#> SRR2001057 4 0.2164 0.897 0.000 0.032 0.000 0.900 NA NA
#> SRR2001058 4 0.2237 0.898 0.000 0.036 0.000 0.896 NA NA
#> SRR2001059 4 0.2237 0.898 0.000 0.036 0.000 0.896 NA NA
#> SRR2001052 2 0.3763 0.860 0.000 0.768 0.000 0.172 NA NA
#> SRR2001053 2 0.3912 0.863 0.000 0.776 0.000 0.148 NA NA
#> SRR2001054 2 0.3796 0.858 0.000 0.764 0.000 0.176 NA NA
#> SRR2001055 2 0.3821 0.864 0.000 0.776 0.000 0.156 NA NA
#> SRR2001048 2 0.4616 0.756 0.000 0.648 0.000 0.280 NA NA
#> SRR2001049 2 0.4544 0.782 0.000 0.668 0.000 0.256 NA NA
#> SRR2001050 2 0.4428 0.798 0.000 0.684 0.000 0.244 NA NA
#> SRR2001051 2 0.4500 0.792 0.000 0.676 0.000 0.248 NA NA
#> SRR2001044 4 0.1429 0.917 0.000 0.052 0.000 0.940 NA NA
#> SRR2001045 4 0.1584 0.914 0.000 0.064 0.000 0.928 NA NA
#> SRR2001046 4 0.1728 0.917 0.000 0.064 0.000 0.924 NA NA
#> SRR2001047 4 0.1901 0.909 0.000 0.076 0.000 0.912 NA NA
#> SRR2001040 4 0.1149 0.905 0.000 0.008 0.000 0.960 NA NA
#> SRR2001041 4 0.1078 0.908 0.000 0.012 0.000 0.964 NA NA
#> SRR2001042 4 0.1078 0.909 0.000 0.016 0.000 0.964 NA NA
#> SRR2001043 4 0.1262 0.908 0.000 0.020 0.000 0.956 NA NA
#> SRR2001036 4 0.0964 0.912 0.000 0.012 0.000 0.968 NA NA
#> SRR2001037 4 0.0806 0.911 0.000 0.008 0.000 0.972 NA NA
#> SRR2001038 4 0.0993 0.912 0.000 0.012 0.000 0.964 NA NA
#> SRR2001039 4 0.1088 0.913 0.000 0.016 0.000 0.960 NA NA
#> SRR2001028 4 0.1588 0.912 0.000 0.072 0.000 0.924 NA NA
#> SRR2001029 4 0.1625 0.916 0.000 0.060 0.000 0.928 NA NA
#> SRR2001030 4 0.1643 0.913 0.000 0.068 0.000 0.924 NA NA
#> SRR2001031 4 0.1285 0.917 0.000 0.052 0.000 0.944 NA NA
#> SRR2001024 4 0.0951 0.915 0.000 0.020 0.000 0.968 NA NA
#> SRR2001025 4 0.1149 0.916 0.000 0.024 0.000 0.960 NA NA
#> SRR2001026 4 0.1410 0.917 0.000 0.044 0.000 0.944 NA NA
#> SRR2001027 4 0.1155 0.917 0.000 0.036 0.000 0.956 NA NA
#> SRR2001020 2 0.4218 0.854 0.000 0.740 0.000 0.184 NA NA
#> SRR2001021 2 0.4585 0.831 0.000 0.708 0.000 0.200 NA NA
#> SRR2001022 2 0.4023 0.860 0.000 0.752 0.000 0.188 NA NA
#> SRR2001023 2 0.4199 0.851 0.000 0.736 0.000 0.196 NA NA
#> SRR2001016 4 0.3020 0.869 0.000 0.080 0.000 0.844 NA NA
#> SRR2001017 4 0.2857 0.878 0.000 0.072 0.000 0.856 NA NA
#> SRR2001018 4 0.3215 0.850 0.000 0.100 0.000 0.828 NA NA
#> SRR2001019 4 0.3167 0.854 0.000 0.096 0.000 0.832 NA NA
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 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 1.000 1.000 0.5031 0.497 0.497
#> 3 3 1.000 1.000 1.000 0.2206 0.889 0.777
#> 4 4 0.821 0.897 0.851 0.1602 0.874 0.674
#> 5 5 0.896 0.904 0.928 0.1009 0.934 0.754
#> 6 6 0.860 0.859 0.873 0.0389 0.972 0.868
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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0 1 0 1 0
#> SRR2001033 2 0 1 0 1 0
#> SRR2001034 2 0 1 0 1 0
#> SRR2001035 2 0 1 0 1 0
#> SRR2001204 1 0 1 1 0 0
#> SRR2001205 1 0 1 1 0 0
#> SRR2001206 1 0 1 1 0 0
#> SRR2001207 1 0 1 1 0 0
#> SRR2001200 1 0 1 1 0 0
#> SRR2001201 1 0 1 1 0 0
#> SRR2001202 1 0 1 1 0 0
#> SRR2001203 1 0 1 1 0 0
#> SRR2001196 1 0 1 1 0 0
#> SRR2001197 1 0 1 1 0 0
#> SRR2001198 1 0 1 1 0 0
#> SRR2001199 1 0 1 1 0 0
#> SRR2001192 3 0 1 0 0 1
#> SRR2001193 3 0 1 0 0 1
#> SRR2001194 3 0 1 0 0 1
#> SRR2001195 3 0 1 0 0 1
#> SRR2001188 1 0 1 1 0 0
#> SRR2001189 1 0 1 1 0 0
#> SRR2001190 1 0 1 1 0 0
#> SRR2001191 1 0 1 1 0 0
#> SRR2001184 3 0 1 0 0 1
#> SRR2001185 3 0 1 0 0 1
#> SRR2001186 3 0 1 0 0 1
#> SRR2001187 3 0 1 0 0 1
#> SRR2001180 1 0 1 1 0 0
#> SRR2001181 1 0 1 1 0 0
#> SRR2001182 1 0 1 1 0 0
#> SRR2001183 1 0 1 1 0 0
#> SRR2001176 3 0 1 0 0 1
#> SRR2001177 3 0 1 0 0 1
#> SRR2001178 3 0 1 0 0 1
#> SRR2001179 3 0 1 0 0 1
#> SRR2001172 3 0 1 0 0 1
#> SRR2001173 3 0 1 0 0 1
#> SRR2001174 3 0 1 0 0 1
#> SRR2001175 3 0 1 0 0 1
#> SRR2001168 1 0 1 1 0 0
#> SRR2001169 1 0 1 1 0 0
#> SRR2001170 1 0 1 1 0 0
#> SRR2001171 1 0 1 1 0 0
#> SRR2001164 1 0 1 1 0 0
#> SRR2001165 1 0 1 1 0 0
#> SRR2001166 1 0 1 1 0 0
#> SRR2001167 1 0 1 1 0 0
#> SRR2001160 1 0 1 1 0 0
#> SRR2001161 1 0 1 1 0 0
#> SRR2001162 1 0 1 1 0 0
#> SRR2001163 1 0 1 1 0 0
#> SRR2001156 1 0 1 1 0 0
#> SRR2001157 1 0 1 1 0 0
#> SRR2001158 1 0 1 1 0 0
#> SRR2001159 1 0 1 1 0 0
#> SRR2001152 1 0 1 1 0 0
#> SRR2001153 1 0 1 1 0 0
#> SRR2001154 1 0 1 1 0 0
#> SRR2001155 1 0 1 1 0 0
#> SRR2001148 3 0 1 0 0 1
#> SRR2001149 3 0 1 0 0 1
#> SRR2001150 3 0 1 0 0 1
#> SRR2001151 3 0 1 0 0 1
#> SRR2001144 1 0 1 1 0 0
#> SRR2001145 1 0 1 1 0 0
#> SRR2001146 1 0 1 1 0 0
#> SRR2001147 1 0 1 1 0 0
#> SRR2001140 1 0 1 1 0 0
#> SRR2001142 1 0 1 1 0 0
#> SRR2001143 1 0 1 1 0 0
#> SRR2001136 3 0 1 0 0 1
#> SRR2001137 3 0 1 0 0 1
#> SRR2001138 3 0 1 0 0 1
#> SRR2001139 3 0 1 0 0 1
#> SRR2001132 3 0 1 0 0 1
#> SRR2001133 3 0 1 0 0 1
#> SRR2001134 3 0 1 0 0 1
#> SRR2001135 3 0 1 0 0 1
#> SRR2001128 1 0 1 1 0 0
#> SRR2001129 1 0 1 1 0 0
#> SRR2001130 1 0 1 1 0 0
#> SRR2001131 1 0 1 1 0 0
#> SRR2001124 1 0 1 1 0 0
#> SRR2001125 1 0 1 1 0 0
#> SRR2001126 1 0 1 1 0 0
#> SRR2001127 1 0 1 1 0 0
#> SRR2001120 1 0 1 1 0 0
#> SRR2001121 1 0 1 1 0 0
#> SRR2001122 1 0 1 1 0 0
#> SRR2001123 1 0 1 1 0 0
#> SRR2001116 1 0 1 1 0 0
#> SRR2001117 1 0 1 1 0 0
#> SRR2001118 1 0 1 1 0 0
#> SRR2001119 1 0 1 1 0 0
#> SRR2001112 3 0 1 0 0 1
#> SRR2001113 3 0 1 0 0 1
#> SRR2001114 3 0 1 0 0 1
#> SRR2001115 3 0 1 0 0 1
#> SRR2001108 2 0 1 0 1 0
#> SRR2001109 2 0 1 0 1 0
#> SRR2001110 2 0 1 0 1 0
#> SRR2001111 2 0 1 0 1 0
#> SRR2001104 2 0 1 0 1 0
#> SRR2001105 2 0 1 0 1 0
#> SRR2001106 2 0 1 0 1 0
#> SRR2001107 2 0 1 0 1 0
#> SRR2001100 2 0 1 0 1 0
#> SRR2001101 2 0 1 0 1 0
#> SRR2001102 2 0 1 0 1 0
#> SRR2001103 2 0 1 0 1 0
#> SRR2001096 2 0 1 0 1 0
#> SRR2001097 2 0 1 0 1 0
#> SRR2001098 2 0 1 0 1 0
#> SRR2001099 2 0 1 0 1 0
#> SRR2001092 2 0 1 0 1 0
#> SRR2001093 2 0 1 0 1 0
#> SRR2001094 2 0 1 0 1 0
#> SRR2001095 2 0 1 0 1 0
#> SRR2001088 2 0 1 0 1 0
#> SRR2001089 2 0 1 0 1 0
#> SRR2001090 2 0 1 0 1 0
#> SRR2001091 2 0 1 0 1 0
#> SRR2001084 2 0 1 0 1 0
#> SRR2001085 2 0 1 0 1 0
#> SRR2001086 2 0 1 0 1 0
#> SRR2001087 2 0 1 0 1 0
#> SRR2001080 2 0 1 0 1 0
#> SRR2001081 2 0 1 0 1 0
#> SRR2001082 2 0 1 0 1 0
#> SRR2001083 2 0 1 0 1 0
#> SRR2001076 2 0 1 0 1 0
#> SRR2001077 2 0 1 0 1 0
#> SRR2001078 2 0 1 0 1 0
#> SRR2001079 2 0 1 0 1 0
#> SRR2001072 2 0 1 0 1 0
#> SRR2001073 2 0 1 0 1 0
#> SRR2001074 2 0 1 0 1 0
#> SRR2001075 2 0 1 0 1 0
#> SRR2001068 2 0 1 0 1 0
#> SRR2001069 2 0 1 0 1 0
#> SRR2001070 2 0 1 0 1 0
#> SRR2001071 2 0 1 0 1 0
#> SRR2001064 2 0 1 0 1 0
#> SRR2001065 2 0 1 0 1 0
#> SRR2001066 2 0 1 0 1 0
#> SRR2001067 2 0 1 0 1 0
#> SRR2001060 2 0 1 0 1 0
#> SRR2001061 2 0 1 0 1 0
#> SRR2001062 2 0 1 0 1 0
#> SRR2001063 2 0 1 0 1 0
#> SRR2001056 2 0 1 0 1 0
#> SRR2001057 2 0 1 0 1 0
#> SRR2001058 2 0 1 0 1 0
#> SRR2001059 2 0 1 0 1 0
#> SRR2001052 2 0 1 0 1 0
#> SRR2001053 2 0 1 0 1 0
#> SRR2001054 2 0 1 0 1 0
#> SRR2001055 2 0 1 0 1 0
#> SRR2001048 2 0 1 0 1 0
#> SRR2001049 2 0 1 0 1 0
#> SRR2001050 2 0 1 0 1 0
#> SRR2001051 2 0 1 0 1 0
#> SRR2001044 2 0 1 0 1 0
#> SRR2001045 2 0 1 0 1 0
#> SRR2001046 2 0 1 0 1 0
#> SRR2001047 2 0 1 0 1 0
#> SRR2001040 2 0 1 0 1 0
#> SRR2001041 2 0 1 0 1 0
#> SRR2001042 2 0 1 0 1 0
#> SRR2001043 2 0 1 0 1 0
#> SRR2001036 2 0 1 0 1 0
#> SRR2001037 2 0 1 0 1 0
#> SRR2001038 2 0 1 0 1 0
#> SRR2001039 2 0 1 0 1 0
#> SRR2001028 2 0 1 0 1 0
#> SRR2001029 2 0 1 0 1 0
#> SRR2001030 2 0 1 0 1 0
#> SRR2001031 2 0 1 0 1 0
#> SRR2001024 2 0 1 0 1 0
#> SRR2001025 2 0 1 0 1 0
#> SRR2001026 2 0 1 0 1 0
#> SRR2001027 2 0 1 0 1 0
#> SRR2001020 2 0 1 0 1 0
#> SRR2001021 2 0 1 0 1 0
#> SRR2001022 2 0 1 0 1 0
#> SRR2001023 2 0 1 0 1 0
#> SRR2001016 2 0 1 0 1 0
#> SRR2001017 2 0 1 0 1 0
#> SRR2001018 2 0 1 0 1 0
#> SRR2001019 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.1474 0.890 0.000 0.948 0 0.052
#> SRR2001033 2 0.1474 0.890 0.000 0.948 0 0.052
#> SRR2001034 2 0.1474 0.890 0.000 0.948 0 0.052
#> SRR2001035 2 0.1474 0.890 0.000 0.948 0 0.052
#> SRR2001204 1 0.4193 0.829 0.732 0.000 0 0.268
#> SRR2001205 1 0.4193 0.829 0.732 0.000 0 0.268
#> SRR2001206 1 0.4193 0.829 0.732 0.000 0 0.268
#> SRR2001207 1 0.4193 0.829 0.732 0.000 0 0.268
#> SRR2001200 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001201 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001202 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001203 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001196 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001197 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001198 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001199 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001192 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001193 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001194 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001195 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001188 1 0.0336 0.900 0.992 0.000 0 0.008
#> SRR2001189 1 0.0336 0.900 0.992 0.000 0 0.008
#> SRR2001190 1 0.0336 0.900 0.992 0.000 0 0.008
#> SRR2001191 1 0.0336 0.900 0.992 0.000 0 0.008
#> SRR2001184 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001185 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001186 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001187 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001180 1 0.0336 0.901 0.992 0.000 0 0.008
#> SRR2001181 1 0.0336 0.901 0.992 0.000 0 0.008
#> SRR2001182 1 0.0336 0.901 0.992 0.000 0 0.008
#> SRR2001183 1 0.0336 0.901 0.992 0.000 0 0.008
#> SRR2001176 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001177 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001178 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001179 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001172 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001173 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001174 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001175 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001168 1 0.4193 0.829 0.732 0.000 0 0.268
#> SRR2001169 1 0.4193 0.829 0.732 0.000 0 0.268
#> SRR2001170 1 0.4193 0.829 0.732 0.000 0 0.268
#> SRR2001171 1 0.4193 0.829 0.732 0.000 0 0.268
#> SRR2001164 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001165 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001166 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001167 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001160 1 0.0000 0.901 1.000 0.000 0 0.000
#> SRR2001161 1 0.0000 0.901 1.000 0.000 0 0.000
#> SRR2001162 1 0.0000 0.901 1.000 0.000 0 0.000
#> SRR2001163 1 0.0000 0.901 1.000 0.000 0 0.000
#> SRR2001156 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001157 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001158 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001159 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001152 1 0.1867 0.894 0.928 0.000 0 0.072
#> SRR2001153 1 0.1867 0.894 0.928 0.000 0 0.072
#> SRR2001154 1 0.1867 0.894 0.928 0.000 0 0.072
#> SRR2001155 1 0.1867 0.894 0.928 0.000 0 0.072
#> SRR2001148 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001149 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001150 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001151 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001144 1 0.4193 0.829 0.732 0.000 0 0.268
#> SRR2001145 1 0.4193 0.829 0.732 0.000 0 0.268
#> SRR2001146 1 0.4193 0.829 0.732 0.000 0 0.268
#> SRR2001147 1 0.4193 0.829 0.732 0.000 0 0.268
#> SRR2001140 1 0.4072 0.836 0.748 0.000 0 0.252
#> SRR2001142 1 0.4072 0.836 0.748 0.000 0 0.252
#> SRR2001143 1 0.4072 0.836 0.748 0.000 0 0.252
#> SRR2001136 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001137 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001138 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001139 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001132 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001133 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001134 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001135 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001128 1 0.0000 0.901 1.000 0.000 0 0.000
#> SRR2001129 1 0.0000 0.901 1.000 0.000 0 0.000
#> SRR2001130 1 0.0000 0.901 1.000 0.000 0 0.000
#> SRR2001131 1 0.0000 0.901 1.000 0.000 0 0.000
#> SRR2001124 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001125 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001126 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001127 1 0.2081 0.887 0.916 0.000 0 0.084
#> SRR2001120 1 0.4193 0.829 0.732 0.000 0 0.268
#> SRR2001121 1 0.4193 0.829 0.732 0.000 0 0.268
#> SRR2001122 1 0.4193 0.829 0.732 0.000 0 0.268
#> SRR2001123 1 0.4193 0.829 0.732 0.000 0 0.268
#> SRR2001116 1 0.1867 0.894 0.928 0.000 0 0.072
#> SRR2001117 1 0.1867 0.894 0.928 0.000 0 0.072
#> SRR2001118 1 0.1867 0.894 0.928 0.000 0 0.072
#> SRR2001119 1 0.1867 0.894 0.928 0.000 0 0.072
#> SRR2001112 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001113 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001114 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001115 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001108 4 0.4730 0.969 0.000 0.364 0 0.636
#> SRR2001109 4 0.4730 0.969 0.000 0.364 0 0.636
#> SRR2001110 4 0.4730 0.969 0.000 0.364 0 0.636
#> SRR2001111 4 0.4730 0.969 0.000 0.364 0 0.636
#> SRR2001104 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001105 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001106 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001107 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001100 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001101 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001102 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001103 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001096 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001097 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001098 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001099 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001092 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001093 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001094 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001095 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001088 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001089 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001090 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001091 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001084 4 0.4730 0.969 0.000 0.364 0 0.636
#> SRR2001085 4 0.4730 0.969 0.000 0.364 0 0.636
#> SRR2001086 4 0.4730 0.969 0.000 0.364 0 0.636
#> SRR2001087 4 0.4730 0.969 0.000 0.364 0 0.636
#> SRR2001080 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001081 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001082 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001083 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001076 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001077 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001078 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001079 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001072 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001073 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001074 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001075 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001068 2 0.1474 0.890 0.000 0.948 0 0.052
#> SRR2001069 2 0.1474 0.890 0.000 0.948 0 0.052
#> SRR2001070 2 0.1474 0.890 0.000 0.948 0 0.052
#> SRR2001071 2 0.1474 0.890 0.000 0.948 0 0.052
#> SRR2001064 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001065 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001066 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001067 2 0.0000 0.919 0.000 1.000 0 0.000
#> SRR2001060 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001061 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001062 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001063 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001056 4 0.4730 0.969 0.000 0.364 0 0.636
#> SRR2001057 4 0.4730 0.969 0.000 0.364 0 0.636
#> SRR2001058 4 0.4730 0.969 0.000 0.364 0 0.636
#> SRR2001059 4 0.4730 0.969 0.000 0.364 0 0.636
#> SRR2001052 2 0.0592 0.908 0.000 0.984 0 0.016
#> SRR2001053 2 0.0592 0.908 0.000 0.984 0 0.016
#> SRR2001054 2 0.0592 0.908 0.000 0.984 0 0.016
#> SRR2001055 2 0.0592 0.908 0.000 0.984 0 0.016
#> SRR2001048 2 0.1474 0.890 0.000 0.948 0 0.052
#> SRR2001049 2 0.1474 0.890 0.000 0.948 0 0.052
#> SRR2001050 2 0.1474 0.890 0.000 0.948 0 0.052
#> SRR2001051 2 0.1474 0.890 0.000 0.948 0 0.052
#> SRR2001044 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001045 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001046 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001047 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001040 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001041 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001042 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001043 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001036 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001037 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001038 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001039 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001028 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001029 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001030 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001031 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001024 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001025 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001026 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001027 4 0.4746 0.989 0.000 0.368 0 0.632
#> SRR2001020 2 0.0592 0.907 0.000 0.984 0 0.016
#> SRR2001021 2 0.0592 0.907 0.000 0.984 0 0.016
#> SRR2001022 2 0.0592 0.907 0.000 0.984 0 0.016
#> SRR2001023 2 0.0592 0.907 0.000 0.984 0 0.016
#> SRR2001016 2 0.4998 -0.659 0.000 0.512 0 0.488
#> SRR2001017 2 0.4998 -0.659 0.000 0.512 0 0.488
#> SRR2001018 2 0.4998 -0.659 0.000 0.512 0 0.488
#> SRR2001019 2 0.4998 -0.659 0.000 0.512 0 0.488
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.3601 0.895 0.000 0.820 0 0.052 0.128
#> SRR2001033 2 0.3601 0.895 0.000 0.820 0 0.052 0.128
#> SRR2001034 2 0.3601 0.895 0.000 0.820 0 0.052 0.128
#> SRR2001035 2 0.3601 0.895 0.000 0.820 0 0.052 0.128
#> SRR2001204 5 0.2929 0.985 0.180 0.000 0 0.000 0.820
#> SRR2001205 5 0.2929 0.985 0.180 0.000 0 0.000 0.820
#> SRR2001206 5 0.2929 0.985 0.180 0.000 0 0.000 0.820
#> SRR2001207 5 0.2929 0.985 0.180 0.000 0 0.000 0.820
#> SRR2001200 1 0.0000 0.874 1.000 0.000 0 0.000 0.000
#> SRR2001201 1 0.0000 0.874 1.000 0.000 0 0.000 0.000
#> SRR2001202 1 0.0000 0.874 1.000 0.000 0 0.000 0.000
#> SRR2001203 1 0.0000 0.874 1.000 0.000 0 0.000 0.000
#> SRR2001196 1 0.0000 0.874 1.000 0.000 0 0.000 0.000
#> SRR2001197 1 0.0000 0.874 1.000 0.000 0 0.000 0.000
#> SRR2001198 1 0.0000 0.874 1.000 0.000 0 0.000 0.000
#> SRR2001199 1 0.0000 0.874 1.000 0.000 0 0.000 0.000
#> SRR2001192 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001193 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001194 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001195 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001188 1 0.1851 0.870 0.912 0.000 0 0.000 0.088
#> SRR2001189 1 0.1851 0.870 0.912 0.000 0 0.000 0.088
#> SRR2001190 1 0.1851 0.870 0.912 0.000 0 0.000 0.088
#> SRR2001191 1 0.1851 0.870 0.912 0.000 0 0.000 0.088
#> SRR2001184 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001185 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001186 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001187 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001180 1 0.2280 0.855 0.880 0.000 0 0.000 0.120
#> SRR2001181 1 0.2280 0.855 0.880 0.000 0 0.000 0.120
#> SRR2001182 1 0.2280 0.855 0.880 0.000 0 0.000 0.120
#> SRR2001183 1 0.2280 0.855 0.880 0.000 0 0.000 0.120
#> SRR2001176 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001177 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001178 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001179 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001172 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001173 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001174 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001175 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001168 5 0.2929 0.985 0.180 0.000 0 0.000 0.820
#> SRR2001169 5 0.2929 0.985 0.180 0.000 0 0.000 0.820
#> SRR2001170 5 0.2929 0.985 0.180 0.000 0 0.000 0.820
#> SRR2001171 5 0.2929 0.985 0.180 0.000 0 0.000 0.820
#> SRR2001164 1 0.0162 0.875 0.996 0.000 0 0.000 0.004
#> SRR2001165 1 0.0162 0.875 0.996 0.000 0 0.000 0.004
#> SRR2001166 1 0.0162 0.875 0.996 0.000 0 0.000 0.004
#> SRR2001167 1 0.0162 0.875 0.996 0.000 0 0.000 0.004
#> SRR2001160 1 0.2074 0.866 0.896 0.000 0 0.000 0.104
#> SRR2001161 1 0.2074 0.866 0.896 0.000 0 0.000 0.104
#> SRR2001162 1 0.2074 0.866 0.896 0.000 0 0.000 0.104
#> SRR2001163 1 0.2074 0.866 0.896 0.000 0 0.000 0.104
#> SRR2001156 1 0.0000 0.874 1.000 0.000 0 0.000 0.000
#> SRR2001157 1 0.0000 0.874 1.000 0.000 0 0.000 0.000
#> SRR2001158 1 0.0000 0.874 1.000 0.000 0 0.000 0.000
#> SRR2001159 1 0.0000 0.874 1.000 0.000 0 0.000 0.000
#> SRR2001152 1 0.4182 0.293 0.600 0.000 0 0.000 0.400
#> SRR2001153 1 0.4182 0.293 0.600 0.000 0 0.000 0.400
#> SRR2001154 1 0.4182 0.293 0.600 0.000 0 0.000 0.400
#> SRR2001155 1 0.4171 0.308 0.604 0.000 0 0.000 0.396
#> SRR2001148 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001149 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001150 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001151 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001144 5 0.3210 0.961 0.212 0.000 0 0.000 0.788
#> SRR2001145 5 0.3177 0.965 0.208 0.000 0 0.000 0.792
#> SRR2001146 5 0.3177 0.965 0.208 0.000 0 0.000 0.792
#> SRR2001147 5 0.3177 0.965 0.208 0.000 0 0.000 0.792
#> SRR2001140 5 0.3109 0.973 0.200 0.000 0 0.000 0.800
#> SRR2001142 5 0.3109 0.973 0.200 0.000 0 0.000 0.800
#> SRR2001143 5 0.3109 0.973 0.200 0.000 0 0.000 0.800
#> SRR2001136 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001137 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001138 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001139 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001132 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001133 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001134 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001135 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001128 1 0.2074 0.866 0.896 0.000 0 0.000 0.104
#> SRR2001129 1 0.2074 0.866 0.896 0.000 0 0.000 0.104
#> SRR2001130 1 0.2074 0.866 0.896 0.000 0 0.000 0.104
#> SRR2001131 1 0.2074 0.866 0.896 0.000 0 0.000 0.104
#> SRR2001124 1 0.0000 0.874 1.000 0.000 0 0.000 0.000
#> SRR2001125 1 0.0000 0.874 1.000 0.000 0 0.000 0.000
#> SRR2001126 1 0.0000 0.874 1.000 0.000 0 0.000 0.000
#> SRR2001127 1 0.0000 0.874 1.000 0.000 0 0.000 0.000
#> SRR2001120 5 0.2929 0.985 0.180 0.000 0 0.000 0.820
#> SRR2001121 5 0.2929 0.985 0.180 0.000 0 0.000 0.820
#> SRR2001122 5 0.2929 0.985 0.180 0.000 0 0.000 0.820
#> SRR2001123 5 0.2929 0.985 0.180 0.000 0 0.000 0.820
#> SRR2001116 1 0.3452 0.705 0.756 0.000 0 0.000 0.244
#> SRR2001117 1 0.3480 0.699 0.752 0.000 0 0.000 0.248
#> SRR2001118 1 0.3452 0.705 0.756 0.000 0 0.000 0.244
#> SRR2001119 1 0.3452 0.705 0.756 0.000 0 0.000 0.244
#> SRR2001112 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001113 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001114 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001115 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001108 4 0.1121 0.932 0.000 0.000 0 0.956 0.044
#> SRR2001109 4 0.1121 0.932 0.000 0.000 0 0.956 0.044
#> SRR2001110 4 0.1121 0.932 0.000 0.000 0 0.956 0.044
#> SRR2001111 4 0.1121 0.932 0.000 0.000 0 0.956 0.044
#> SRR2001104 2 0.0510 0.939 0.000 0.984 0 0.016 0.000
#> SRR2001105 2 0.0510 0.939 0.000 0.984 0 0.016 0.000
#> SRR2001106 2 0.0510 0.939 0.000 0.984 0 0.016 0.000
#> SRR2001107 2 0.0510 0.939 0.000 0.984 0 0.016 0.000
#> SRR2001100 2 0.0510 0.939 0.000 0.984 0 0.016 0.000
#> SRR2001101 2 0.0510 0.939 0.000 0.984 0 0.016 0.000
#> SRR2001102 2 0.0510 0.939 0.000 0.984 0 0.016 0.000
#> SRR2001103 2 0.0510 0.939 0.000 0.984 0 0.016 0.000
#> SRR2001096 2 0.0000 0.935 0.000 1.000 0 0.000 0.000
#> SRR2001097 2 0.0000 0.935 0.000 1.000 0 0.000 0.000
#> SRR2001098 2 0.0000 0.935 0.000 1.000 0 0.000 0.000
#> SRR2001099 2 0.0000 0.935 0.000 1.000 0 0.000 0.000
#> SRR2001092 2 0.0000 0.935 0.000 1.000 0 0.000 0.000
#> SRR2001093 2 0.0000 0.935 0.000 1.000 0 0.000 0.000
#> SRR2001094 2 0.0000 0.935 0.000 1.000 0 0.000 0.000
#> SRR2001095 2 0.0000 0.935 0.000 1.000 0 0.000 0.000
#> SRR2001088 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001089 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001090 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001091 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001084 4 0.1121 0.932 0.000 0.000 0 0.956 0.044
#> SRR2001085 4 0.1121 0.932 0.000 0.000 0 0.956 0.044
#> SRR2001086 4 0.1121 0.932 0.000 0.000 0 0.956 0.044
#> SRR2001087 4 0.1121 0.932 0.000 0.000 0 0.956 0.044
#> SRR2001080 2 0.0510 0.939 0.000 0.984 0 0.016 0.000
#> SRR2001081 2 0.0510 0.939 0.000 0.984 0 0.016 0.000
#> SRR2001082 2 0.0510 0.939 0.000 0.984 0 0.016 0.000
#> SRR2001083 2 0.0510 0.939 0.000 0.984 0 0.016 0.000
#> SRR2001076 2 0.0510 0.939 0.000 0.984 0 0.016 0.000
#> SRR2001077 2 0.0510 0.939 0.000 0.984 0 0.016 0.000
#> SRR2001078 2 0.0510 0.939 0.000 0.984 0 0.016 0.000
#> SRR2001079 2 0.0510 0.939 0.000 0.984 0 0.016 0.000
#> SRR2001072 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001073 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001074 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001075 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001068 2 0.3601 0.895 0.000 0.820 0 0.052 0.128
#> SRR2001069 2 0.3601 0.895 0.000 0.820 0 0.052 0.128
#> SRR2001070 2 0.3601 0.895 0.000 0.820 0 0.052 0.128
#> SRR2001071 2 0.3601 0.895 0.000 0.820 0 0.052 0.128
#> SRR2001064 2 0.0000 0.935 0.000 1.000 0 0.000 0.000
#> SRR2001065 2 0.0000 0.935 0.000 1.000 0 0.000 0.000
#> SRR2001066 2 0.0000 0.935 0.000 1.000 0 0.000 0.000
#> SRR2001067 2 0.0000 0.935 0.000 1.000 0 0.000 0.000
#> SRR2001060 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001061 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001062 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001063 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001056 4 0.1121 0.932 0.000 0.000 0 0.956 0.044
#> SRR2001057 4 0.1121 0.932 0.000 0.000 0 0.956 0.044
#> SRR2001058 4 0.1121 0.932 0.000 0.000 0 0.956 0.044
#> SRR2001059 4 0.1121 0.932 0.000 0.000 0 0.956 0.044
#> SRR2001052 2 0.2773 0.893 0.000 0.836 0 0.000 0.164
#> SRR2001053 2 0.2773 0.893 0.000 0.836 0 0.000 0.164
#> SRR2001054 2 0.2773 0.893 0.000 0.836 0 0.000 0.164
#> SRR2001055 2 0.2773 0.893 0.000 0.836 0 0.000 0.164
#> SRR2001048 2 0.3601 0.895 0.000 0.820 0 0.052 0.128
#> SRR2001049 2 0.3601 0.895 0.000 0.820 0 0.052 0.128
#> SRR2001050 2 0.3601 0.895 0.000 0.820 0 0.052 0.128
#> SRR2001051 2 0.3601 0.895 0.000 0.820 0 0.052 0.128
#> SRR2001044 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001045 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001046 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001047 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001040 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001041 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001042 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001043 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001036 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001037 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001038 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001039 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001028 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001029 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001030 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001031 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001024 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001025 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001026 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001027 4 0.0000 0.948 0.000 0.000 0 1.000 0.000
#> SRR2001020 2 0.2735 0.889 0.000 0.880 0 0.084 0.036
#> SRR2001021 2 0.2735 0.889 0.000 0.880 0 0.084 0.036
#> SRR2001022 2 0.2735 0.889 0.000 0.880 0 0.084 0.036
#> SRR2001023 2 0.2735 0.889 0.000 0.880 0 0.084 0.036
#> SRR2001016 4 0.5793 0.266 0.000 0.364 0 0.536 0.100
#> SRR2001017 4 0.5793 0.266 0.000 0.364 0 0.536 0.100
#> SRR2001018 4 0.5793 0.266 0.000 0.364 0 0.536 0.100
#> SRR2001019 4 0.5793 0.266 0.000 0.364 0 0.536 0.100
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 5 0.3965 0.962 0.000 0.388 0.000 0.008 0.604 0.000
#> SRR2001033 5 0.3965 0.962 0.000 0.388 0.000 0.008 0.604 0.000
#> SRR2001034 5 0.3965 0.962 0.000 0.388 0.000 0.008 0.604 0.000
#> SRR2001035 5 0.3965 0.962 0.000 0.388 0.000 0.008 0.604 0.000
#> SRR2001204 6 0.1957 0.983 0.112 0.000 0.000 0.000 0.000 0.888
#> SRR2001205 6 0.1957 0.983 0.112 0.000 0.000 0.000 0.000 0.888
#> SRR2001206 6 0.1957 0.983 0.112 0.000 0.000 0.000 0.000 0.888
#> SRR2001207 6 0.1957 0.983 0.112 0.000 0.000 0.000 0.000 0.888
#> SRR2001200 1 0.0000 0.878 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001201 1 0.0000 0.878 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001202 1 0.0000 0.878 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001203 1 0.0000 0.878 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001196 1 0.0000 0.878 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001197 1 0.0000 0.878 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001198 1 0.0000 0.878 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001199 1 0.0000 0.878 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001192 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001193 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001194 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001195 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001188 1 0.1714 0.874 0.908 0.000 0.000 0.000 0.000 0.092
#> SRR2001189 1 0.1714 0.874 0.908 0.000 0.000 0.000 0.000 0.092
#> SRR2001190 1 0.1714 0.874 0.908 0.000 0.000 0.000 0.000 0.092
#> SRR2001191 1 0.1714 0.874 0.908 0.000 0.000 0.000 0.000 0.092
#> SRR2001184 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001185 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001186 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001187 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001180 1 0.2092 0.860 0.876 0.000 0.000 0.000 0.000 0.124
#> SRR2001181 1 0.2092 0.860 0.876 0.000 0.000 0.000 0.000 0.124
#> SRR2001182 1 0.2092 0.860 0.876 0.000 0.000 0.000 0.000 0.124
#> SRR2001183 1 0.2092 0.860 0.876 0.000 0.000 0.000 0.000 0.124
#> SRR2001176 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001177 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001178 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001179 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001172 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001173 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001174 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001175 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001168 6 0.1957 0.983 0.112 0.000 0.000 0.000 0.000 0.888
#> SRR2001169 6 0.1957 0.983 0.112 0.000 0.000 0.000 0.000 0.888
#> SRR2001170 6 0.1957 0.983 0.112 0.000 0.000 0.000 0.000 0.888
#> SRR2001171 6 0.1957 0.983 0.112 0.000 0.000 0.000 0.000 0.888
#> SRR2001164 1 0.0146 0.879 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR2001165 1 0.0146 0.879 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR2001166 1 0.0146 0.879 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR2001167 1 0.0146 0.879 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR2001160 1 0.1863 0.871 0.896 0.000 0.000 0.000 0.000 0.104
#> SRR2001161 1 0.1863 0.871 0.896 0.000 0.000 0.000 0.000 0.104
#> SRR2001162 1 0.1863 0.871 0.896 0.000 0.000 0.000 0.000 0.104
#> SRR2001163 1 0.1863 0.871 0.896 0.000 0.000 0.000 0.000 0.104
#> SRR2001156 1 0.0000 0.878 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001157 1 0.0000 0.878 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001158 1 0.0000 0.878 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001159 1 0.0000 0.878 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001152 1 0.3810 0.303 0.572 0.000 0.000 0.000 0.000 0.428
#> SRR2001153 1 0.3810 0.303 0.572 0.000 0.000 0.000 0.000 0.428
#> SRR2001154 1 0.3810 0.303 0.572 0.000 0.000 0.000 0.000 0.428
#> SRR2001155 1 0.3804 0.317 0.576 0.000 0.000 0.000 0.000 0.424
#> SRR2001148 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001149 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001150 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001151 3 0.0000 0.971 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001144 6 0.2527 0.931 0.168 0.000 0.000 0.000 0.000 0.832
#> SRR2001145 6 0.2340 0.957 0.148 0.000 0.000 0.000 0.000 0.852
#> SRR2001146 6 0.2340 0.957 0.148 0.000 0.000 0.000 0.000 0.852
#> SRR2001147 6 0.2340 0.957 0.148 0.000 0.000 0.000 0.000 0.852
#> SRR2001140 6 0.2178 0.972 0.132 0.000 0.000 0.000 0.000 0.868
#> SRR2001142 6 0.2178 0.972 0.132 0.000 0.000 0.000 0.000 0.868
#> SRR2001143 6 0.2178 0.972 0.132 0.000 0.000 0.000 0.000 0.868
#> SRR2001136 3 0.1714 0.951 0.000 0.000 0.908 0.000 0.092 0.000
#> SRR2001137 3 0.1714 0.951 0.000 0.000 0.908 0.000 0.092 0.000
#> SRR2001138 3 0.1714 0.951 0.000 0.000 0.908 0.000 0.092 0.000
#> SRR2001139 3 0.1714 0.951 0.000 0.000 0.908 0.000 0.092 0.000
#> SRR2001132 3 0.1714 0.951 0.000 0.000 0.908 0.000 0.092 0.000
#> SRR2001133 3 0.1714 0.951 0.000 0.000 0.908 0.000 0.092 0.000
#> SRR2001134 3 0.1714 0.951 0.000 0.000 0.908 0.000 0.092 0.000
#> SRR2001135 3 0.1714 0.951 0.000 0.000 0.908 0.000 0.092 0.000
#> SRR2001128 1 0.1957 0.868 0.888 0.000 0.000 0.000 0.000 0.112
#> SRR2001129 1 0.2003 0.866 0.884 0.000 0.000 0.000 0.000 0.116
#> SRR2001130 1 0.1957 0.868 0.888 0.000 0.000 0.000 0.000 0.112
#> SRR2001131 1 0.1957 0.868 0.888 0.000 0.000 0.000 0.000 0.112
#> SRR2001124 1 0.0000 0.878 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001125 1 0.0000 0.878 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001126 1 0.0000 0.878 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001127 1 0.0000 0.878 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001120 6 0.1957 0.983 0.112 0.000 0.000 0.000 0.000 0.888
#> SRR2001121 6 0.1957 0.983 0.112 0.000 0.000 0.000 0.000 0.888
#> SRR2001122 6 0.1957 0.983 0.112 0.000 0.000 0.000 0.000 0.888
#> SRR2001123 6 0.1957 0.983 0.112 0.000 0.000 0.000 0.000 0.888
#> SRR2001116 1 0.3151 0.721 0.748 0.000 0.000 0.000 0.000 0.252
#> SRR2001117 1 0.3198 0.709 0.740 0.000 0.000 0.000 0.000 0.260
#> SRR2001118 1 0.3175 0.715 0.744 0.000 0.000 0.000 0.000 0.256
#> SRR2001119 1 0.3175 0.715 0.744 0.000 0.000 0.000 0.000 0.256
#> SRR2001112 3 0.1714 0.951 0.000 0.000 0.908 0.000 0.092 0.000
#> SRR2001113 3 0.1714 0.951 0.000 0.000 0.908 0.000 0.092 0.000
#> SRR2001114 3 0.1714 0.951 0.000 0.000 0.908 0.000 0.092 0.000
#> SRR2001115 3 0.1714 0.951 0.000 0.000 0.908 0.000 0.092 0.000
#> SRR2001108 4 0.2511 0.886 0.000 0.000 0.000 0.880 0.064 0.056
#> SRR2001109 4 0.2511 0.886 0.000 0.000 0.000 0.880 0.064 0.056
#> SRR2001110 4 0.2511 0.886 0.000 0.000 0.000 0.880 0.064 0.056
#> SRR2001111 4 0.2511 0.886 0.000 0.000 0.000 0.880 0.064 0.056
#> SRR2001104 2 0.0260 0.749 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR2001105 2 0.0260 0.749 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR2001106 2 0.0260 0.749 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR2001107 2 0.0260 0.749 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR2001100 2 0.0260 0.749 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR2001101 2 0.0260 0.749 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR2001102 2 0.0260 0.749 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR2001103 2 0.0260 0.749 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR2001096 2 0.3390 0.714 0.000 0.704 0.000 0.000 0.296 0.000
#> SRR2001097 2 0.3390 0.714 0.000 0.704 0.000 0.000 0.296 0.000
#> SRR2001098 2 0.3390 0.714 0.000 0.704 0.000 0.000 0.296 0.000
#> SRR2001099 2 0.3390 0.714 0.000 0.704 0.000 0.000 0.296 0.000
#> SRR2001092 2 0.2631 0.746 0.000 0.820 0.000 0.000 0.180 0.000
#> SRR2001093 2 0.2631 0.746 0.000 0.820 0.000 0.000 0.180 0.000
#> SRR2001094 2 0.2631 0.746 0.000 0.820 0.000 0.000 0.180 0.000
#> SRR2001095 2 0.2631 0.746 0.000 0.820 0.000 0.000 0.180 0.000
#> SRR2001088 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001089 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001090 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001091 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001084 4 0.2511 0.886 0.000 0.000 0.000 0.880 0.064 0.056
#> SRR2001085 4 0.2511 0.886 0.000 0.000 0.000 0.880 0.064 0.056
#> SRR2001086 4 0.2511 0.886 0.000 0.000 0.000 0.880 0.064 0.056
#> SRR2001087 4 0.2511 0.886 0.000 0.000 0.000 0.880 0.064 0.056
#> SRR2001080 2 0.0260 0.749 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR2001081 2 0.0405 0.749 0.000 0.988 0.000 0.008 0.004 0.000
#> SRR2001082 2 0.0260 0.749 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR2001083 2 0.0260 0.749 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR2001076 2 0.0260 0.749 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR2001077 2 0.0260 0.749 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR2001078 2 0.0260 0.749 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR2001079 2 0.0260 0.749 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR2001072 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001073 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001074 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001075 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001068 5 0.3955 0.961 0.000 0.384 0.000 0.008 0.608 0.000
#> SRR2001069 5 0.3955 0.961 0.000 0.384 0.000 0.008 0.608 0.000
#> SRR2001070 5 0.3955 0.961 0.000 0.384 0.000 0.008 0.608 0.000
#> SRR2001071 5 0.3955 0.961 0.000 0.384 0.000 0.008 0.608 0.000
#> SRR2001064 2 0.3390 0.714 0.000 0.704 0.000 0.000 0.296 0.000
#> SRR2001065 2 0.3390 0.714 0.000 0.704 0.000 0.000 0.296 0.000
#> SRR2001066 2 0.3390 0.714 0.000 0.704 0.000 0.000 0.296 0.000
#> SRR2001067 2 0.3390 0.714 0.000 0.704 0.000 0.000 0.296 0.000
#> SRR2001060 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001061 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001062 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001063 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001056 4 0.2511 0.886 0.000 0.000 0.000 0.880 0.064 0.056
#> SRR2001057 4 0.2511 0.886 0.000 0.000 0.000 0.880 0.064 0.056
#> SRR2001058 4 0.2511 0.886 0.000 0.000 0.000 0.880 0.064 0.056
#> SRR2001059 4 0.2511 0.886 0.000 0.000 0.000 0.880 0.064 0.056
#> SRR2001052 5 0.4684 0.889 0.000 0.352 0.000 0.000 0.592 0.056
#> SRR2001053 5 0.4684 0.889 0.000 0.352 0.000 0.000 0.592 0.056
#> SRR2001054 5 0.4684 0.889 0.000 0.352 0.000 0.000 0.592 0.056
#> SRR2001055 5 0.4684 0.889 0.000 0.352 0.000 0.000 0.592 0.056
#> SRR2001048 5 0.3965 0.962 0.000 0.388 0.000 0.008 0.604 0.000
#> SRR2001049 5 0.3965 0.962 0.000 0.388 0.000 0.008 0.604 0.000
#> SRR2001050 5 0.3965 0.962 0.000 0.388 0.000 0.008 0.604 0.000
#> SRR2001051 5 0.3965 0.962 0.000 0.388 0.000 0.008 0.604 0.000
#> SRR2001044 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001045 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001046 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001047 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001040 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001041 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001042 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001043 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001036 4 0.0291 0.930 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR2001037 4 0.0291 0.930 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR2001038 4 0.0291 0.930 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR2001039 4 0.0291 0.930 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR2001028 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001029 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001030 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001031 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001024 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001025 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001026 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001027 4 0.0000 0.932 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001020 2 0.5859 0.415 0.000 0.452 0.000 0.084 0.428 0.036
#> SRR2001021 2 0.5859 0.415 0.000 0.452 0.000 0.084 0.428 0.036
#> SRR2001022 2 0.5859 0.415 0.000 0.452 0.000 0.084 0.428 0.036
#> SRR2001023 2 0.5859 0.415 0.000 0.452 0.000 0.084 0.428 0.036
#> SRR2001016 4 0.6256 0.321 0.000 0.056 0.000 0.496 0.336 0.112
#> SRR2001017 4 0.6256 0.321 0.000 0.056 0.000 0.496 0.336 0.112
#> SRR2001018 4 0.6256 0.321 0.000 0.056 0.000 0.496 0.336 0.112
#> SRR2001019 4 0.6256 0.321 0.000 0.056 0.000 0.496 0.336 0.112
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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.5031 0.497 0.497
#> 3 3 0.762 0.486 0.736 0.2359 0.929 0.858
#> 4 4 0.666 0.911 0.823 0.1179 0.776 0.508
#> 5 5 0.596 0.839 0.785 0.0620 1.000 1.000
#> 6 6 0.639 0.599 0.699 0.0555 0.957 0.833
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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 3 0.6295 1.000 0.000 0.472 0.528
#> SRR2001033 3 0.6295 1.000 0.000 0.472 0.528
#> SRR2001034 3 0.6295 1.000 0.000 0.472 0.528
#> SRR2001035 3 0.6295 1.000 0.000 0.472 0.528
#> SRR2001204 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001205 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001206 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001207 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001200 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001201 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001202 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001203 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001196 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001197 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001198 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001199 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001192 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001193 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001194 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001195 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001188 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001189 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001190 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001191 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001184 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001185 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001186 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001187 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001180 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001181 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001182 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001183 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001176 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001177 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001178 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001179 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001172 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001173 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001174 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001175 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001168 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001169 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001170 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001171 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001164 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001165 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001166 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001167 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001160 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001161 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001162 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001163 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001156 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001157 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001158 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001159 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001152 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001153 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001154 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001155 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001148 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001149 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001150 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001151 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001144 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001145 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001146 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001147 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001140 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001142 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001143 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001136 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001137 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001138 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001139 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001132 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001133 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001134 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001135 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001128 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001129 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001130 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001131 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001124 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001125 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001126 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001127 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001120 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001121 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001122 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001123 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001116 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001117 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001118 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001119 1 0.0000 0.862 1.000 0.000 0.000
#> SRR2001112 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001113 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001114 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001115 1 0.6295 0.701 0.528 0.000 0.472
#> SRR2001108 2 0.1643 0.557 0.000 0.956 0.044
#> SRR2001109 2 0.1643 0.557 0.000 0.956 0.044
#> SRR2001110 2 0.1643 0.557 0.000 0.956 0.044
#> SRR2001111 2 0.1643 0.557 0.000 0.956 0.044
#> SRR2001104 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001105 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001106 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001107 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001100 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001101 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001102 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001103 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001096 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001097 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001098 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001099 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001092 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001093 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001094 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001095 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001088 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001089 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001090 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001091 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001084 2 0.1643 0.557 0.000 0.956 0.044
#> SRR2001085 2 0.1643 0.557 0.000 0.956 0.044
#> SRR2001086 2 0.1643 0.557 0.000 0.956 0.044
#> SRR2001087 2 0.1643 0.557 0.000 0.956 0.044
#> SRR2001080 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001081 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001082 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001083 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001076 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001077 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001078 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001079 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001072 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001073 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001074 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001075 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001068 3 0.6295 1.000 0.000 0.472 0.528
#> SRR2001069 3 0.6295 1.000 0.000 0.472 0.528
#> SRR2001070 3 0.6295 1.000 0.000 0.472 0.528
#> SRR2001071 3 0.6295 1.000 0.000 0.472 0.528
#> SRR2001064 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001065 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001066 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001067 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001060 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001061 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001062 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001063 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001056 2 0.1643 0.557 0.000 0.956 0.044
#> SRR2001057 2 0.1643 0.557 0.000 0.956 0.044
#> SRR2001058 2 0.1643 0.557 0.000 0.956 0.044
#> SRR2001059 2 0.1643 0.557 0.000 0.956 0.044
#> SRR2001052 3 0.6295 1.000 0.000 0.472 0.528
#> SRR2001053 3 0.6295 1.000 0.000 0.472 0.528
#> SRR2001054 3 0.6295 1.000 0.000 0.472 0.528
#> SRR2001055 3 0.6295 1.000 0.000 0.472 0.528
#> SRR2001048 3 0.6295 1.000 0.000 0.472 0.528
#> SRR2001049 3 0.6295 1.000 0.000 0.472 0.528
#> SRR2001050 3 0.6295 1.000 0.000 0.472 0.528
#> SRR2001051 3 0.6295 1.000 0.000 0.472 0.528
#> SRR2001044 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001045 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001046 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001047 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001040 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001041 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001042 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001043 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001036 2 0.0237 0.576 0.000 0.996 0.004
#> SRR2001037 2 0.0237 0.576 0.000 0.996 0.004
#> SRR2001038 2 0.0237 0.576 0.000 0.996 0.004
#> SRR2001039 2 0.0237 0.576 0.000 0.996 0.004
#> SRR2001028 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001029 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001030 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001031 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001024 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001025 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001026 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001027 2 0.0000 0.578 0.000 1.000 0.000
#> SRR2001020 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001021 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001022 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001023 2 0.6305 -0.852 0.000 0.516 0.484
#> SRR2001016 2 0.1643 0.557 0.000 0.956 0.044
#> SRR2001017 2 0.1643 0.557 0.000 0.956 0.044
#> SRR2001018 2 0.1643 0.557 0.000 0.956 0.044
#> SRR2001019 2 0.1643 0.557 0.000 0.956 0.044
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.6606 0.838 0.000 0.624 0.152 0.224
#> SRR2001033 2 0.6606 0.838 0.000 0.624 0.152 0.224
#> SRR2001034 2 0.6606 0.838 0.000 0.624 0.152 0.224
#> SRR2001035 2 0.6606 0.838 0.000 0.624 0.152 0.224
#> SRR2001204 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001205 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001206 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001207 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001200 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001201 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001202 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001203 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001196 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001197 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001198 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001199 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001192 3 0.4543 0.975 0.324 0.000 0.676 0.000
#> SRR2001193 3 0.4543 0.975 0.324 0.000 0.676 0.000
#> SRR2001194 3 0.4543 0.975 0.324 0.000 0.676 0.000
#> SRR2001195 3 0.4543 0.975 0.324 0.000 0.676 0.000
#> SRR2001188 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001189 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001190 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001191 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001184 3 0.4857 0.975 0.324 0.008 0.668 0.000
#> SRR2001185 3 0.4857 0.975 0.324 0.008 0.668 0.000
#> SRR2001186 3 0.4857 0.975 0.324 0.008 0.668 0.000
#> SRR2001187 3 0.4857 0.975 0.324 0.008 0.668 0.000
#> SRR2001180 1 0.0000 0.923 1.000 0.000 0.000 0.000
#> SRR2001181 1 0.0000 0.923 1.000 0.000 0.000 0.000
#> SRR2001182 1 0.0000 0.923 1.000 0.000 0.000 0.000
#> SRR2001183 1 0.0000 0.923 1.000 0.000 0.000 0.000
#> SRR2001176 3 0.4543 0.975 0.324 0.000 0.676 0.000
#> SRR2001177 3 0.4543 0.975 0.324 0.000 0.676 0.000
#> SRR2001178 3 0.4543 0.975 0.324 0.000 0.676 0.000
#> SRR2001179 3 0.4543 0.975 0.324 0.000 0.676 0.000
#> SRR2001172 3 0.4857 0.975 0.324 0.008 0.668 0.000
#> SRR2001173 3 0.4857 0.975 0.324 0.008 0.668 0.000
#> SRR2001174 3 0.4857 0.975 0.324 0.008 0.668 0.000
#> SRR2001175 3 0.4857 0.975 0.324 0.008 0.668 0.000
#> SRR2001168 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001169 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001170 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001171 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001164 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001165 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001166 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001167 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001160 1 0.0000 0.923 1.000 0.000 0.000 0.000
#> SRR2001161 1 0.0000 0.923 1.000 0.000 0.000 0.000
#> SRR2001162 1 0.0000 0.923 1.000 0.000 0.000 0.000
#> SRR2001163 1 0.0000 0.923 1.000 0.000 0.000 0.000
#> SRR2001156 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001157 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001158 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001159 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001152 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001153 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001154 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001155 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001148 3 0.4857 0.975 0.324 0.008 0.668 0.000
#> SRR2001149 3 0.4857 0.975 0.324 0.008 0.668 0.000
#> SRR2001150 3 0.4857 0.975 0.324 0.008 0.668 0.000
#> SRR2001151 3 0.4857 0.975 0.324 0.008 0.668 0.000
#> SRR2001144 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001145 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001146 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001147 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001140 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001142 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001143 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001136 3 0.6005 0.962 0.324 0.060 0.616 0.000
#> SRR2001137 3 0.6005 0.962 0.324 0.060 0.616 0.000
#> SRR2001138 3 0.6005 0.962 0.324 0.060 0.616 0.000
#> SRR2001139 3 0.6005 0.962 0.324 0.060 0.616 0.000
#> SRR2001132 3 0.6005 0.962 0.324 0.060 0.616 0.000
#> SRR2001133 3 0.6005 0.962 0.324 0.060 0.616 0.000
#> SRR2001134 3 0.6005 0.962 0.324 0.060 0.616 0.000
#> SRR2001135 3 0.6005 0.962 0.324 0.060 0.616 0.000
#> SRR2001128 1 0.0000 0.923 1.000 0.000 0.000 0.000
#> SRR2001129 1 0.0000 0.923 1.000 0.000 0.000 0.000
#> SRR2001130 1 0.0000 0.923 1.000 0.000 0.000 0.000
#> SRR2001131 1 0.0000 0.923 1.000 0.000 0.000 0.000
#> SRR2001124 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001125 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001126 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001127 1 0.1302 0.916 0.956 0.044 0.000 0.000
#> SRR2001120 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001121 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001122 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001123 1 0.2530 0.894 0.888 0.112 0.000 0.000
#> SRR2001116 1 0.1022 0.918 0.968 0.032 0.000 0.000
#> SRR2001117 1 0.1022 0.918 0.968 0.032 0.000 0.000
#> SRR2001118 1 0.1022 0.918 0.968 0.032 0.000 0.000
#> SRR2001119 1 0.1022 0.918 0.968 0.032 0.000 0.000
#> SRR2001112 3 0.6005 0.962 0.324 0.060 0.616 0.000
#> SRR2001113 3 0.6005 0.962 0.324 0.060 0.616 0.000
#> SRR2001114 3 0.6005 0.962 0.324 0.060 0.616 0.000
#> SRR2001115 3 0.6005 0.962 0.324 0.060 0.616 0.000
#> SRR2001108 4 0.3647 0.869 0.000 0.040 0.108 0.852
#> SRR2001109 4 0.3647 0.869 0.000 0.040 0.108 0.852
#> SRR2001110 4 0.3647 0.869 0.000 0.040 0.108 0.852
#> SRR2001111 4 0.3647 0.869 0.000 0.040 0.108 0.852
#> SRR2001104 2 0.4164 0.910 0.000 0.736 0.000 0.264
#> SRR2001105 2 0.4164 0.910 0.000 0.736 0.000 0.264
#> SRR2001106 2 0.4164 0.910 0.000 0.736 0.000 0.264
#> SRR2001107 2 0.4164 0.910 0.000 0.736 0.000 0.264
#> SRR2001100 2 0.4482 0.910 0.000 0.728 0.008 0.264
#> SRR2001101 2 0.4482 0.910 0.000 0.728 0.008 0.264
#> SRR2001102 2 0.4482 0.910 0.000 0.728 0.008 0.264
#> SRR2001103 2 0.4482 0.910 0.000 0.728 0.008 0.264
#> SRR2001096 2 0.5799 0.902 0.000 0.668 0.068 0.264
#> SRR2001097 2 0.5799 0.902 0.000 0.668 0.068 0.264
#> SRR2001098 2 0.5799 0.902 0.000 0.668 0.068 0.264
#> SRR2001099 2 0.5799 0.902 0.000 0.668 0.068 0.264
#> SRR2001092 2 0.5592 0.903 0.000 0.680 0.056 0.264
#> SRR2001093 2 0.5592 0.903 0.000 0.680 0.056 0.264
#> SRR2001094 2 0.5592 0.903 0.000 0.680 0.056 0.264
#> SRR2001095 2 0.5592 0.903 0.000 0.680 0.056 0.264
#> SRR2001088 4 0.0469 0.929 0.000 0.000 0.012 0.988
#> SRR2001089 4 0.0469 0.929 0.000 0.000 0.012 0.988
#> SRR2001090 4 0.0469 0.929 0.000 0.000 0.012 0.988
#> SRR2001091 4 0.0469 0.929 0.000 0.000 0.012 0.988
#> SRR2001084 4 0.3706 0.869 0.000 0.040 0.112 0.848
#> SRR2001085 4 0.3706 0.869 0.000 0.040 0.112 0.848
#> SRR2001086 4 0.3706 0.869 0.000 0.040 0.112 0.848
#> SRR2001087 4 0.3706 0.869 0.000 0.040 0.112 0.848
#> SRR2001080 2 0.4482 0.909 0.000 0.728 0.008 0.264
#> SRR2001081 2 0.4482 0.909 0.000 0.728 0.008 0.264
#> SRR2001082 2 0.4482 0.909 0.000 0.728 0.008 0.264
#> SRR2001083 2 0.4482 0.909 0.000 0.728 0.008 0.264
#> SRR2001076 2 0.4482 0.909 0.000 0.728 0.008 0.264
#> SRR2001077 2 0.4482 0.909 0.000 0.728 0.008 0.264
#> SRR2001078 2 0.4482 0.909 0.000 0.728 0.008 0.264
#> SRR2001079 2 0.4482 0.909 0.000 0.728 0.008 0.264
#> SRR2001072 4 0.0592 0.928 0.000 0.000 0.016 0.984
#> SRR2001073 4 0.0592 0.928 0.000 0.000 0.016 0.984
#> SRR2001074 4 0.0592 0.928 0.000 0.000 0.016 0.984
#> SRR2001075 4 0.0592 0.928 0.000 0.000 0.016 0.984
#> SRR2001068 2 0.6685 0.836 0.000 0.616 0.160 0.224
#> SRR2001069 2 0.6685 0.836 0.000 0.616 0.160 0.224
#> SRR2001070 2 0.6685 0.836 0.000 0.616 0.160 0.224
#> SRR2001071 2 0.6685 0.836 0.000 0.616 0.160 0.224
#> SRR2001064 2 0.5799 0.902 0.000 0.668 0.068 0.264
#> SRR2001065 2 0.5799 0.902 0.000 0.668 0.068 0.264
#> SRR2001066 2 0.5799 0.902 0.000 0.668 0.068 0.264
#> SRR2001067 2 0.5799 0.902 0.000 0.668 0.068 0.264
#> SRR2001060 4 0.0469 0.929 0.000 0.000 0.012 0.988
#> SRR2001061 4 0.0469 0.929 0.000 0.000 0.012 0.988
#> SRR2001062 4 0.0469 0.929 0.000 0.000 0.012 0.988
#> SRR2001063 4 0.0469 0.929 0.000 0.000 0.012 0.988
#> SRR2001056 4 0.3647 0.869 0.000 0.040 0.108 0.852
#> SRR2001057 4 0.3647 0.869 0.000 0.040 0.108 0.852
#> SRR2001058 4 0.3647 0.869 0.000 0.040 0.108 0.852
#> SRR2001059 4 0.3647 0.869 0.000 0.040 0.108 0.852
#> SRR2001052 2 0.6606 0.863 0.000 0.624 0.152 0.224
#> SRR2001053 2 0.6606 0.863 0.000 0.624 0.152 0.224
#> SRR2001054 2 0.6606 0.863 0.000 0.624 0.152 0.224
#> SRR2001055 2 0.6606 0.863 0.000 0.624 0.152 0.224
#> SRR2001048 2 0.6646 0.836 0.000 0.620 0.156 0.224
#> SRR2001049 2 0.6646 0.836 0.000 0.620 0.156 0.224
#> SRR2001050 2 0.6646 0.836 0.000 0.620 0.156 0.224
#> SRR2001051 2 0.6646 0.836 0.000 0.620 0.156 0.224
#> SRR2001044 4 0.0336 0.929 0.000 0.000 0.008 0.992
#> SRR2001045 4 0.0336 0.929 0.000 0.000 0.008 0.992
#> SRR2001046 4 0.0336 0.929 0.000 0.000 0.008 0.992
#> SRR2001047 4 0.0336 0.929 0.000 0.000 0.008 0.992
#> SRR2001040 4 0.0336 0.929 0.000 0.000 0.008 0.992
#> SRR2001041 4 0.0336 0.929 0.000 0.000 0.008 0.992
#> SRR2001042 4 0.0336 0.929 0.000 0.000 0.008 0.992
#> SRR2001043 4 0.0336 0.929 0.000 0.000 0.008 0.992
#> SRR2001036 4 0.0524 0.928 0.000 0.008 0.004 0.988
#> SRR2001037 4 0.0524 0.928 0.000 0.008 0.004 0.988
#> SRR2001038 4 0.0524 0.928 0.000 0.008 0.004 0.988
#> SRR2001039 4 0.0524 0.928 0.000 0.008 0.004 0.988
#> SRR2001028 4 0.0336 0.929 0.000 0.000 0.008 0.992
#> SRR2001029 4 0.0336 0.929 0.000 0.000 0.008 0.992
#> SRR2001030 4 0.0336 0.929 0.000 0.000 0.008 0.992
#> SRR2001031 4 0.0336 0.929 0.000 0.000 0.008 0.992
#> SRR2001024 4 0.0469 0.929 0.000 0.000 0.012 0.988
#> SRR2001025 4 0.0469 0.929 0.000 0.000 0.012 0.988
#> SRR2001026 4 0.0469 0.929 0.000 0.000 0.012 0.988
#> SRR2001027 4 0.0469 0.929 0.000 0.000 0.012 0.988
#> SRR2001020 2 0.6164 0.895 0.000 0.644 0.092 0.264
#> SRR2001021 2 0.6164 0.895 0.000 0.644 0.092 0.264
#> SRR2001022 2 0.6164 0.895 0.000 0.644 0.092 0.264
#> SRR2001023 2 0.6164 0.895 0.000 0.644 0.092 0.264
#> SRR2001016 4 0.4831 0.779 0.000 0.040 0.208 0.752
#> SRR2001017 4 0.4831 0.779 0.000 0.040 0.208 0.752
#> SRR2001018 4 0.4831 0.779 0.000 0.040 0.208 0.752
#> SRR2001019 4 0.4831 0.779 0.000 0.040 0.208 0.752
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.4591 0.808 0.000 0.776 0.072 0.024 NA
#> SRR2001033 2 0.4591 0.808 0.000 0.776 0.072 0.024 NA
#> SRR2001034 2 0.4591 0.808 0.000 0.776 0.072 0.024 NA
#> SRR2001035 2 0.4591 0.808 0.000 0.776 0.072 0.024 NA
#> SRR2001204 1 0.4909 0.727 0.588 0.000 0.000 0.032 NA
#> SRR2001205 1 0.4909 0.727 0.588 0.000 0.000 0.032 NA
#> SRR2001206 1 0.4909 0.727 0.588 0.000 0.000 0.032 NA
#> SRR2001207 1 0.4909 0.727 0.588 0.000 0.000 0.032 NA
#> SRR2001200 1 0.1768 0.796 0.924 0.000 0.000 0.072 NA
#> SRR2001201 1 0.1768 0.796 0.924 0.000 0.000 0.072 NA
#> SRR2001202 1 0.1768 0.796 0.924 0.000 0.000 0.072 NA
#> SRR2001203 1 0.1768 0.796 0.924 0.000 0.000 0.072 NA
#> SRR2001196 1 0.1638 0.797 0.932 0.000 0.000 0.064 NA
#> SRR2001197 1 0.1638 0.797 0.932 0.000 0.000 0.064 NA
#> SRR2001198 1 0.1638 0.797 0.932 0.000 0.000 0.064 NA
#> SRR2001199 1 0.1638 0.797 0.932 0.000 0.000 0.064 NA
#> SRR2001192 3 0.3760 0.946 0.188 0.000 0.784 0.000 NA
#> SRR2001193 3 0.3760 0.946 0.188 0.000 0.784 0.000 NA
#> SRR2001194 3 0.3760 0.946 0.188 0.000 0.784 0.000 NA
#> SRR2001195 3 0.3760 0.946 0.188 0.000 0.784 0.000 NA
#> SRR2001188 1 0.0290 0.804 0.992 0.000 0.000 0.000 NA
#> SRR2001189 1 0.0290 0.806 0.992 0.000 0.000 0.000 NA
#> SRR2001190 1 0.0162 0.805 0.996 0.000 0.000 0.000 NA
#> SRR2001191 1 0.0162 0.805 0.996 0.000 0.000 0.000 NA
#> SRR2001184 3 0.3548 0.945 0.188 0.000 0.796 0.012 NA
#> SRR2001185 3 0.3548 0.945 0.188 0.000 0.796 0.012 NA
#> SRR2001186 3 0.3548 0.945 0.188 0.000 0.796 0.012 NA
#> SRR2001187 3 0.3548 0.945 0.188 0.000 0.796 0.012 NA
#> SRR2001180 1 0.1792 0.816 0.916 0.000 0.000 0.000 NA
#> SRR2001181 1 0.1851 0.816 0.912 0.000 0.000 0.000 NA
#> SRR2001182 1 0.1732 0.816 0.920 0.000 0.000 0.000 NA
#> SRR2001183 1 0.1851 0.816 0.912 0.000 0.000 0.000 NA
#> SRR2001176 3 0.3760 0.946 0.188 0.000 0.784 0.000 NA
#> SRR2001177 3 0.3760 0.946 0.188 0.000 0.784 0.000 NA
#> SRR2001178 3 0.3760 0.946 0.188 0.000 0.784 0.000 NA
#> SRR2001179 3 0.3760 0.946 0.188 0.000 0.784 0.000 NA
#> SRR2001172 3 0.3670 0.944 0.188 0.000 0.792 0.012 NA
#> SRR2001173 3 0.3670 0.944 0.188 0.000 0.792 0.012 NA
#> SRR2001174 3 0.3670 0.944 0.188 0.000 0.792 0.012 NA
#> SRR2001175 3 0.3670 0.944 0.188 0.000 0.792 0.012 NA
#> SRR2001168 1 0.4455 0.728 0.588 0.000 0.000 0.008 NA
#> SRR2001169 1 0.4455 0.728 0.588 0.000 0.000 0.008 NA
#> SRR2001170 1 0.4455 0.728 0.588 0.000 0.000 0.008 NA
#> SRR2001171 1 0.4455 0.728 0.588 0.000 0.000 0.008 NA
#> SRR2001164 1 0.1041 0.801 0.964 0.000 0.000 0.032 NA
#> SRR2001165 1 0.0955 0.801 0.968 0.000 0.000 0.028 NA
#> SRR2001166 1 0.1041 0.801 0.964 0.000 0.000 0.032 NA
#> SRR2001167 1 0.0955 0.801 0.968 0.000 0.000 0.028 NA
#> SRR2001160 1 0.1544 0.816 0.932 0.000 0.000 0.000 NA
#> SRR2001161 1 0.1544 0.816 0.932 0.000 0.000 0.000 NA
#> SRR2001162 1 0.1608 0.816 0.928 0.000 0.000 0.000 NA
#> SRR2001163 1 0.1544 0.816 0.932 0.000 0.000 0.000 NA
#> SRR2001156 1 0.1638 0.797 0.932 0.000 0.000 0.064 NA
#> SRR2001157 1 0.1638 0.797 0.932 0.000 0.000 0.064 NA
#> SRR2001158 1 0.1638 0.797 0.932 0.000 0.000 0.064 NA
#> SRR2001159 1 0.1638 0.797 0.932 0.000 0.000 0.064 NA
#> SRR2001152 1 0.4060 0.741 0.640 0.000 0.000 0.000 NA
#> SRR2001153 1 0.4060 0.741 0.640 0.000 0.000 0.000 NA
#> SRR2001154 1 0.4114 0.737 0.624 0.000 0.000 0.000 NA
#> SRR2001155 1 0.4114 0.737 0.624 0.000 0.000 0.000 NA
#> SRR2001148 3 0.3548 0.945 0.188 0.000 0.796 0.012 NA
#> SRR2001149 3 0.3548 0.945 0.188 0.000 0.796 0.012 NA
#> SRR2001150 3 0.3548 0.945 0.188 0.000 0.796 0.012 NA
#> SRR2001151 3 0.3548 0.945 0.188 0.000 0.796 0.012 NA
#> SRR2001144 1 0.4201 0.730 0.592 0.000 0.000 0.000 NA
#> SRR2001145 1 0.4201 0.730 0.592 0.000 0.000 0.000 NA
#> SRR2001146 1 0.4201 0.730 0.592 0.000 0.000 0.000 NA
#> SRR2001147 1 0.4201 0.730 0.592 0.000 0.000 0.000 NA
#> SRR2001140 1 0.4697 0.730 0.592 0.000 0.000 0.020 NA
#> SRR2001142 1 0.4697 0.730 0.592 0.000 0.000 0.020 NA
#> SRR2001143 1 0.4697 0.730 0.592 0.000 0.000 0.020 NA
#> SRR2001136 3 0.5908 0.922 0.188 0.000 0.672 0.084 NA
#> SRR2001137 3 0.5908 0.922 0.188 0.000 0.672 0.084 NA
#> SRR2001138 3 0.5908 0.922 0.188 0.000 0.672 0.084 NA
#> SRR2001139 3 0.5908 0.922 0.188 0.000 0.672 0.084 NA
#> SRR2001132 3 0.5925 0.924 0.188 0.000 0.672 0.068 NA
#> SRR2001133 3 0.5925 0.924 0.188 0.000 0.672 0.068 NA
#> SRR2001134 3 0.5925 0.924 0.188 0.000 0.672 0.068 NA
#> SRR2001135 3 0.5925 0.924 0.188 0.000 0.672 0.068 NA
#> SRR2001128 1 0.1851 0.816 0.912 0.000 0.000 0.000 NA
#> SRR2001129 1 0.1908 0.816 0.908 0.000 0.000 0.000 NA
#> SRR2001130 1 0.1908 0.816 0.908 0.000 0.000 0.000 NA
#> SRR2001131 1 0.1908 0.816 0.908 0.000 0.000 0.000 NA
#> SRR2001124 1 0.1205 0.800 0.956 0.000 0.000 0.040 NA
#> SRR2001125 1 0.1041 0.801 0.964 0.000 0.000 0.032 NA
#> SRR2001126 1 0.1041 0.801 0.964 0.000 0.000 0.032 NA
#> SRR2001127 1 0.1041 0.801 0.964 0.000 0.000 0.032 NA
#> SRR2001120 1 0.4201 0.730 0.592 0.000 0.000 0.000 NA
#> SRR2001121 1 0.4201 0.730 0.592 0.000 0.000 0.000 NA
#> SRR2001122 1 0.4201 0.730 0.592 0.000 0.000 0.000 NA
#> SRR2001123 1 0.4201 0.730 0.592 0.000 0.000 0.000 NA
#> SRR2001116 1 0.2612 0.812 0.868 0.000 0.000 0.008 NA
#> SRR2001117 1 0.2707 0.810 0.860 0.000 0.000 0.008 NA
#> SRR2001118 1 0.2513 0.813 0.876 0.000 0.000 0.008 NA
#> SRR2001119 1 0.2513 0.813 0.876 0.000 0.000 0.008 NA
#> SRR2001112 3 0.5916 0.922 0.188 0.000 0.672 0.080 NA
#> SRR2001113 3 0.5916 0.922 0.188 0.000 0.672 0.080 NA
#> SRR2001114 3 0.5916 0.922 0.188 0.000 0.672 0.080 NA
#> SRR2001115 3 0.5916 0.922 0.188 0.000 0.672 0.080 NA
#> SRR2001108 4 0.5848 0.810 0.000 0.200 0.000 0.608 NA
#> SRR2001109 4 0.5848 0.810 0.000 0.200 0.000 0.608 NA
#> SRR2001110 4 0.5848 0.810 0.000 0.200 0.000 0.608 NA
#> SRR2001111 4 0.5848 0.810 0.000 0.200 0.000 0.608 NA
#> SRR2001104 2 0.0162 0.878 0.000 0.996 0.000 0.000 NA
#> SRR2001105 2 0.0162 0.878 0.000 0.996 0.000 0.000 NA
#> SRR2001106 2 0.0162 0.878 0.000 0.996 0.000 0.000 NA
#> SRR2001107 2 0.0162 0.878 0.000 0.996 0.000 0.000 NA
#> SRR2001100 2 0.0451 0.878 0.000 0.988 0.004 0.000 NA
#> SRR2001101 2 0.0451 0.878 0.000 0.988 0.004 0.000 NA
#> SRR2001102 2 0.0451 0.878 0.000 0.988 0.004 0.000 NA
#> SRR2001103 2 0.0451 0.878 0.000 0.988 0.004 0.000 NA
#> SRR2001096 2 0.3181 0.855 0.000 0.856 0.072 0.000 NA
#> SRR2001097 2 0.3181 0.855 0.000 0.856 0.072 0.000 NA
#> SRR2001098 2 0.3181 0.855 0.000 0.856 0.072 0.000 NA
#> SRR2001099 2 0.3181 0.855 0.000 0.856 0.072 0.000 NA
#> SRR2001092 2 0.2795 0.860 0.000 0.880 0.056 0.000 NA
#> SRR2001093 2 0.2795 0.860 0.000 0.880 0.056 0.000 NA
#> SRR2001094 2 0.2795 0.860 0.000 0.880 0.056 0.000 NA
#> SRR2001095 2 0.2795 0.860 0.000 0.880 0.056 0.000 NA
#> SRR2001088 4 0.5684 0.873 0.000 0.220 0.032 0.668 NA
#> SRR2001089 4 0.5684 0.873 0.000 0.220 0.032 0.668 NA
#> SRR2001090 4 0.5684 0.873 0.000 0.220 0.032 0.668 NA
#> SRR2001091 4 0.5684 0.873 0.000 0.220 0.032 0.668 NA
#> SRR2001084 4 0.6008 0.806 0.000 0.200 0.000 0.584 NA
#> SRR2001085 4 0.5983 0.807 0.000 0.200 0.000 0.588 NA
#> SRR2001086 4 0.6008 0.806 0.000 0.200 0.000 0.584 NA
#> SRR2001087 4 0.6008 0.806 0.000 0.200 0.000 0.584 NA
#> SRR2001080 2 0.0000 0.878 0.000 1.000 0.000 0.000 NA
#> SRR2001081 2 0.0000 0.878 0.000 1.000 0.000 0.000 NA
#> SRR2001082 2 0.0000 0.878 0.000 1.000 0.000 0.000 NA
#> SRR2001083 2 0.0000 0.878 0.000 1.000 0.000 0.000 NA
#> SRR2001076 2 0.0000 0.878 0.000 1.000 0.000 0.000 NA
#> SRR2001077 2 0.0000 0.878 0.000 1.000 0.000 0.000 NA
#> SRR2001078 2 0.0000 0.878 0.000 1.000 0.000 0.000 NA
#> SRR2001079 2 0.0000 0.878 0.000 1.000 0.000 0.000 NA
#> SRR2001072 4 0.5885 0.867 0.000 0.220 0.032 0.652 NA
#> SRR2001073 4 0.5885 0.867 0.000 0.220 0.032 0.652 NA
#> SRR2001074 4 0.5885 0.867 0.000 0.220 0.032 0.652 NA
#> SRR2001075 4 0.5885 0.867 0.000 0.220 0.032 0.652 NA
#> SRR2001068 2 0.4804 0.801 0.000 0.756 0.072 0.024 NA
#> SRR2001069 2 0.4804 0.801 0.000 0.756 0.072 0.024 NA
#> SRR2001070 2 0.4804 0.801 0.000 0.756 0.072 0.024 NA
#> SRR2001071 2 0.4804 0.801 0.000 0.756 0.072 0.024 NA
#> SRR2001064 2 0.3181 0.855 0.000 0.856 0.072 0.000 NA
#> SRR2001065 2 0.3181 0.855 0.000 0.856 0.072 0.000 NA
#> SRR2001066 2 0.3181 0.855 0.000 0.856 0.072 0.000 NA
#> SRR2001067 2 0.3181 0.855 0.000 0.856 0.072 0.000 NA
#> SRR2001060 4 0.5684 0.873 0.000 0.220 0.032 0.668 NA
#> SRR2001061 4 0.5684 0.873 0.000 0.220 0.032 0.668 NA
#> SRR2001062 4 0.5684 0.873 0.000 0.220 0.032 0.668 NA
#> SRR2001063 4 0.5684 0.873 0.000 0.220 0.032 0.668 NA
#> SRR2001056 4 0.5819 0.811 0.000 0.200 0.000 0.612 NA
#> SRR2001057 4 0.5819 0.811 0.000 0.200 0.000 0.612 NA
#> SRR2001058 4 0.5819 0.811 0.000 0.200 0.000 0.612 NA
#> SRR2001059 4 0.5819 0.811 0.000 0.200 0.000 0.612 NA
#> SRR2001052 2 0.5018 0.826 0.000 0.736 0.088 0.020 NA
#> SRR2001053 2 0.5018 0.826 0.000 0.736 0.088 0.020 NA
#> SRR2001054 2 0.5018 0.826 0.000 0.736 0.088 0.020 NA
#> SRR2001055 2 0.5018 0.826 0.000 0.736 0.088 0.020 NA
#> SRR2001048 2 0.4804 0.801 0.000 0.756 0.072 0.024 NA
#> SRR2001049 2 0.4804 0.801 0.000 0.756 0.072 0.024 NA
#> SRR2001050 2 0.4804 0.801 0.000 0.756 0.072 0.024 NA
#> SRR2001051 2 0.4804 0.801 0.000 0.756 0.072 0.024 NA
#> SRR2001044 4 0.3274 0.881 0.000 0.220 0.000 0.780 NA
#> SRR2001045 4 0.3274 0.881 0.000 0.220 0.000 0.780 NA
#> SRR2001046 4 0.3274 0.881 0.000 0.220 0.000 0.780 NA
#> SRR2001047 4 0.3274 0.881 0.000 0.220 0.000 0.780 NA
#> SRR2001040 4 0.4529 0.877 0.000 0.220 0.008 0.732 NA
#> SRR2001041 4 0.4529 0.877 0.000 0.220 0.008 0.732 NA
#> SRR2001042 4 0.4529 0.877 0.000 0.220 0.008 0.732 NA
#> SRR2001043 4 0.4529 0.877 0.000 0.220 0.008 0.732 NA
#> SRR2001036 4 0.3274 0.881 0.000 0.220 0.000 0.780 NA
#> SRR2001037 4 0.3274 0.881 0.000 0.220 0.000 0.780 NA
#> SRR2001038 4 0.3274 0.881 0.000 0.220 0.000 0.780 NA
#> SRR2001039 4 0.3274 0.881 0.000 0.220 0.000 0.780 NA
#> SRR2001028 4 0.3430 0.881 0.000 0.220 0.004 0.776 NA
#> SRR2001029 4 0.3430 0.881 0.000 0.220 0.004 0.776 NA
#> SRR2001030 4 0.3430 0.881 0.000 0.220 0.004 0.776 NA
#> SRR2001031 4 0.3430 0.881 0.000 0.220 0.004 0.776 NA
#> SRR2001024 4 0.5133 0.874 0.000 0.220 0.028 0.704 NA
#> SRR2001025 4 0.5133 0.874 0.000 0.220 0.028 0.704 NA
#> SRR2001026 4 0.5133 0.874 0.000 0.220 0.028 0.704 NA
#> SRR2001027 4 0.5133 0.874 0.000 0.220 0.028 0.704 NA
#> SRR2001020 2 0.3262 0.846 0.000 0.840 0.036 0.000 NA
#> SRR2001021 2 0.3262 0.846 0.000 0.840 0.036 0.000 NA
#> SRR2001022 2 0.3262 0.846 0.000 0.840 0.036 0.000 NA
#> SRR2001023 2 0.3262 0.846 0.000 0.840 0.036 0.000 NA
#> SRR2001016 4 0.6598 0.716 0.000 0.200 0.004 0.476 NA
#> SRR2001017 4 0.6598 0.716 0.000 0.200 0.004 0.476 NA
#> SRR2001018 4 0.6598 0.716 0.000 0.200 0.004 0.476 NA
#> SRR2001019 4 0.6598 0.716 0.000 0.200 0.004 0.476 NA
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 2 0.5301 0.693 0.000 0.668 0.032 0.016 0.224 0.060
#> SRR2001033 2 0.5301 0.693 0.000 0.668 0.032 0.016 0.224 0.060
#> SRR2001034 2 0.5301 0.693 0.000 0.668 0.032 0.016 0.224 0.060
#> SRR2001035 2 0.5301 0.693 0.000 0.668 0.032 0.016 0.224 0.060
#> SRR2001204 1 0.5059 -0.899 0.480 0.000 0.000 0.036 0.020 0.464
#> SRR2001205 1 0.5059 -0.899 0.480 0.000 0.000 0.036 0.020 0.464
#> SRR2001206 1 0.5059 -0.899 0.480 0.000 0.000 0.036 0.020 0.464
#> SRR2001207 1 0.5059 -0.899 0.480 0.000 0.000 0.036 0.020 0.464
#> SRR2001200 1 0.2859 0.612 0.828 0.000 0.000 0.016 0.156 0.000
#> SRR2001201 1 0.2859 0.612 0.828 0.000 0.000 0.016 0.156 0.000
#> SRR2001202 1 0.2859 0.612 0.828 0.000 0.000 0.016 0.156 0.000
#> SRR2001203 1 0.2859 0.612 0.828 0.000 0.000 0.016 0.156 0.000
#> SRR2001196 1 0.2768 0.615 0.832 0.000 0.000 0.012 0.156 0.000
#> SRR2001197 1 0.2768 0.615 0.832 0.000 0.000 0.012 0.156 0.000
#> SRR2001198 1 0.2768 0.615 0.832 0.000 0.000 0.012 0.156 0.000
#> SRR2001199 1 0.2768 0.615 0.832 0.000 0.000 0.012 0.156 0.000
#> SRR2001192 3 0.2890 0.901 0.128 0.000 0.844 0.004 0.000 0.024
#> SRR2001193 3 0.2890 0.901 0.128 0.000 0.844 0.004 0.000 0.024
#> SRR2001194 3 0.2890 0.901 0.128 0.000 0.844 0.004 0.000 0.024
#> SRR2001195 3 0.2890 0.901 0.128 0.000 0.844 0.004 0.000 0.024
#> SRR2001188 1 0.0520 0.646 0.984 0.000 0.000 0.000 0.008 0.008
#> SRR2001189 1 0.0622 0.645 0.980 0.000 0.000 0.000 0.008 0.012
#> SRR2001190 1 0.0622 0.645 0.980 0.000 0.000 0.000 0.008 0.012
#> SRR2001191 1 0.0520 0.646 0.984 0.000 0.000 0.000 0.008 0.008
#> SRR2001184 3 0.3333 0.898 0.128 0.000 0.828 0.004 0.024 0.016
#> SRR2001185 3 0.3418 0.898 0.128 0.000 0.824 0.004 0.024 0.020
#> SRR2001186 3 0.3333 0.898 0.128 0.000 0.828 0.004 0.024 0.016
#> SRR2001187 3 0.3333 0.898 0.128 0.000 0.828 0.004 0.024 0.016
#> SRR2001180 1 0.1471 0.618 0.932 0.000 0.000 0.000 0.004 0.064
#> SRR2001181 1 0.1471 0.618 0.932 0.000 0.000 0.000 0.004 0.064
#> SRR2001182 1 0.1471 0.618 0.932 0.000 0.000 0.000 0.004 0.064
#> SRR2001183 1 0.1471 0.618 0.932 0.000 0.000 0.000 0.004 0.064
#> SRR2001176 3 0.2809 0.901 0.128 0.000 0.848 0.004 0.000 0.020
#> SRR2001177 3 0.2809 0.901 0.128 0.000 0.848 0.004 0.000 0.020
#> SRR2001178 3 0.2809 0.901 0.128 0.000 0.848 0.004 0.000 0.020
#> SRR2001179 3 0.2809 0.901 0.128 0.000 0.848 0.004 0.000 0.020
#> SRR2001172 3 0.3333 0.898 0.128 0.000 0.828 0.004 0.024 0.016
#> SRR2001173 3 0.3333 0.898 0.128 0.000 0.828 0.004 0.024 0.016
#> SRR2001174 3 0.3333 0.898 0.128 0.000 0.828 0.004 0.024 0.016
#> SRR2001175 3 0.3333 0.898 0.128 0.000 0.828 0.004 0.024 0.016
#> SRR2001168 6 0.4390 0.955 0.472 0.000 0.000 0.016 0.004 0.508
#> SRR2001169 6 0.4390 0.955 0.472 0.000 0.000 0.016 0.004 0.508
#> SRR2001170 6 0.4390 0.955 0.472 0.000 0.000 0.016 0.004 0.508
#> SRR2001171 6 0.4390 0.955 0.472 0.000 0.000 0.016 0.004 0.508
#> SRR2001164 1 0.1700 0.649 0.916 0.000 0.000 0.004 0.080 0.000
#> SRR2001165 1 0.1753 0.648 0.912 0.000 0.000 0.004 0.084 0.000
#> SRR2001166 1 0.1700 0.649 0.916 0.000 0.000 0.004 0.080 0.000
#> SRR2001167 1 0.1644 0.650 0.920 0.000 0.000 0.004 0.076 0.000
#> SRR2001160 1 0.1333 0.632 0.944 0.000 0.000 0.000 0.008 0.048
#> SRR2001161 1 0.1333 0.632 0.944 0.000 0.000 0.000 0.008 0.048
#> SRR2001162 1 0.1333 0.632 0.944 0.000 0.000 0.000 0.008 0.048
#> SRR2001163 1 0.1333 0.632 0.944 0.000 0.000 0.000 0.008 0.048
#> SRR2001156 1 0.2416 0.623 0.844 0.000 0.000 0.000 0.156 0.000
#> SRR2001157 1 0.2416 0.623 0.844 0.000 0.000 0.000 0.156 0.000
#> SRR2001158 1 0.2416 0.623 0.844 0.000 0.000 0.000 0.156 0.000
#> SRR2001159 1 0.2416 0.623 0.844 0.000 0.000 0.000 0.156 0.000
#> SRR2001152 1 0.4082 -0.784 0.560 0.000 0.000 0.004 0.004 0.432
#> SRR2001153 1 0.4088 -0.794 0.556 0.000 0.000 0.004 0.004 0.436
#> SRR2001154 1 0.4093 -0.805 0.552 0.000 0.000 0.004 0.004 0.440
#> SRR2001155 1 0.4093 -0.805 0.552 0.000 0.000 0.004 0.004 0.440
#> SRR2001148 3 0.3242 0.898 0.128 0.000 0.832 0.004 0.024 0.012
#> SRR2001149 3 0.3242 0.898 0.128 0.000 0.832 0.004 0.024 0.012
#> SRR2001150 3 0.3242 0.898 0.128 0.000 0.832 0.004 0.024 0.012
#> SRR2001151 3 0.3242 0.898 0.128 0.000 0.832 0.004 0.024 0.012
#> SRR2001144 6 0.3866 0.975 0.484 0.000 0.000 0.000 0.000 0.516
#> SRR2001145 6 0.3866 0.975 0.484 0.000 0.000 0.000 0.000 0.516
#> SRR2001146 6 0.3866 0.975 0.484 0.000 0.000 0.000 0.000 0.516
#> SRR2001147 6 0.3866 0.975 0.484 0.000 0.000 0.000 0.000 0.516
#> SRR2001140 1 0.4700 -0.925 0.488 0.000 0.000 0.028 0.008 0.476
#> SRR2001142 1 0.4700 -0.925 0.488 0.000 0.000 0.028 0.008 0.476
#> SRR2001143 1 0.4700 -0.925 0.488 0.000 0.000 0.028 0.008 0.476
#> SRR2001136 3 0.6164 0.855 0.128 0.000 0.632 0.028 0.156 0.056
#> SRR2001137 3 0.6164 0.855 0.128 0.000 0.632 0.028 0.156 0.056
#> SRR2001138 3 0.6164 0.855 0.128 0.000 0.632 0.028 0.156 0.056
#> SRR2001139 3 0.6164 0.855 0.128 0.000 0.632 0.028 0.156 0.056
#> SRR2001132 3 0.6186 0.855 0.128 0.000 0.632 0.028 0.152 0.060
#> SRR2001133 3 0.6186 0.855 0.128 0.000 0.632 0.028 0.152 0.060
#> SRR2001134 3 0.6186 0.855 0.128 0.000 0.632 0.028 0.152 0.060
#> SRR2001135 3 0.6186 0.855 0.128 0.000 0.632 0.028 0.152 0.060
#> SRR2001128 1 0.1471 0.618 0.932 0.000 0.000 0.000 0.004 0.064
#> SRR2001129 1 0.1471 0.618 0.932 0.000 0.000 0.000 0.004 0.064
#> SRR2001130 1 0.1471 0.618 0.932 0.000 0.000 0.000 0.004 0.064
#> SRR2001131 1 0.1471 0.618 0.932 0.000 0.000 0.000 0.004 0.064
#> SRR2001124 1 0.1610 0.649 0.916 0.000 0.000 0.000 0.084 0.000
#> SRR2001125 1 0.1610 0.649 0.916 0.000 0.000 0.000 0.084 0.000
#> SRR2001126 1 0.1556 0.649 0.920 0.000 0.000 0.000 0.080 0.000
#> SRR2001127 1 0.1610 0.649 0.916 0.000 0.000 0.000 0.084 0.000
#> SRR2001120 6 0.3996 0.975 0.484 0.000 0.000 0.004 0.000 0.512
#> SRR2001121 6 0.3996 0.975 0.484 0.000 0.000 0.004 0.000 0.512
#> SRR2001122 6 0.3996 0.975 0.484 0.000 0.000 0.004 0.000 0.512
#> SRR2001123 6 0.3996 0.975 0.484 0.000 0.000 0.004 0.000 0.512
#> SRR2001116 1 0.2243 0.537 0.880 0.000 0.000 0.004 0.004 0.112
#> SRR2001117 1 0.2288 0.528 0.876 0.000 0.000 0.004 0.004 0.116
#> SRR2001118 1 0.2243 0.537 0.880 0.000 0.000 0.004 0.004 0.112
#> SRR2001119 1 0.2243 0.537 0.880 0.000 0.000 0.004 0.004 0.112
#> SRR2001112 3 0.6164 0.855 0.128 0.000 0.632 0.028 0.156 0.056
#> SRR2001113 3 0.6164 0.855 0.128 0.000 0.632 0.028 0.156 0.056
#> SRR2001114 3 0.6164 0.855 0.128 0.000 0.632 0.028 0.156 0.056
#> SRR2001115 3 0.6164 0.855 0.128 0.000 0.632 0.028 0.156 0.056
#> SRR2001108 4 0.5078 -0.161 0.000 0.084 0.000 0.584 0.328 0.004
#> SRR2001109 4 0.5078 -0.161 0.000 0.084 0.000 0.584 0.328 0.004
#> SRR2001110 4 0.5078 -0.161 0.000 0.084 0.000 0.584 0.328 0.004
#> SRR2001111 4 0.5078 -0.161 0.000 0.084 0.000 0.584 0.328 0.004
#> SRR2001104 2 0.0508 0.806 0.000 0.984 0.012 0.000 0.000 0.004
#> SRR2001105 2 0.0508 0.806 0.000 0.984 0.012 0.000 0.000 0.004
#> SRR2001106 2 0.0508 0.806 0.000 0.984 0.012 0.000 0.000 0.004
#> SRR2001107 2 0.0508 0.806 0.000 0.984 0.012 0.000 0.000 0.004
#> SRR2001100 2 0.0951 0.805 0.000 0.968 0.004 0.000 0.020 0.008
#> SRR2001101 2 0.0951 0.805 0.000 0.968 0.004 0.000 0.020 0.008
#> SRR2001102 2 0.0951 0.805 0.000 0.968 0.004 0.000 0.020 0.008
#> SRR2001103 2 0.0951 0.805 0.000 0.968 0.004 0.000 0.020 0.008
#> SRR2001096 2 0.3806 0.768 0.000 0.752 0.000 0.000 0.048 0.200
#> SRR2001097 2 0.3806 0.768 0.000 0.752 0.000 0.000 0.048 0.200
#> SRR2001098 2 0.3806 0.768 0.000 0.752 0.000 0.000 0.048 0.200
#> SRR2001099 2 0.3806 0.768 0.000 0.752 0.000 0.000 0.048 0.200
#> SRR2001092 2 0.2887 0.784 0.000 0.844 0.000 0.000 0.036 0.120
#> SRR2001093 2 0.2887 0.784 0.000 0.844 0.000 0.000 0.036 0.120
#> SRR2001094 2 0.2887 0.784 0.000 0.844 0.000 0.000 0.036 0.120
#> SRR2001095 2 0.2887 0.784 0.000 0.844 0.000 0.000 0.036 0.120
#> SRR2001088 4 0.4633 0.663 0.000 0.108 0.040 0.768 0.024 0.060
#> SRR2001089 4 0.4576 0.665 0.000 0.108 0.040 0.772 0.024 0.056
#> SRR2001090 4 0.4633 0.663 0.000 0.108 0.040 0.768 0.024 0.060
#> SRR2001091 4 0.4633 0.663 0.000 0.108 0.040 0.768 0.024 0.060
#> SRR2001084 4 0.5168 -0.249 0.000 0.084 0.000 0.552 0.360 0.004
#> SRR2001085 4 0.5168 -0.249 0.000 0.084 0.000 0.552 0.360 0.004
#> SRR2001086 4 0.5168 -0.249 0.000 0.084 0.000 0.552 0.360 0.004
#> SRR2001087 4 0.5168 -0.249 0.000 0.084 0.000 0.552 0.360 0.004
#> SRR2001080 2 0.0508 0.805 0.000 0.984 0.000 0.000 0.004 0.012
#> SRR2001081 2 0.0603 0.804 0.000 0.980 0.000 0.000 0.004 0.016
#> SRR2001082 2 0.0508 0.805 0.000 0.984 0.000 0.000 0.004 0.012
#> SRR2001083 2 0.0508 0.805 0.000 0.984 0.000 0.000 0.004 0.012
#> SRR2001076 2 0.0653 0.804 0.000 0.980 0.004 0.000 0.004 0.012
#> SRR2001077 2 0.0653 0.804 0.000 0.980 0.004 0.000 0.004 0.012
#> SRR2001078 2 0.0653 0.804 0.000 0.980 0.004 0.000 0.004 0.012
#> SRR2001079 2 0.0653 0.804 0.000 0.980 0.004 0.000 0.004 0.012
#> SRR2001072 4 0.5147 0.637 0.000 0.108 0.052 0.736 0.036 0.068
#> SRR2001073 4 0.5147 0.637 0.000 0.108 0.052 0.736 0.036 0.068
#> SRR2001074 4 0.5147 0.637 0.000 0.108 0.052 0.736 0.036 0.068
#> SRR2001075 4 0.5147 0.637 0.000 0.108 0.052 0.736 0.036 0.068
#> SRR2001068 2 0.5522 0.680 0.000 0.636 0.028 0.016 0.248 0.072
#> SRR2001069 2 0.5522 0.680 0.000 0.636 0.028 0.016 0.248 0.072
#> SRR2001070 2 0.5522 0.680 0.000 0.636 0.028 0.016 0.248 0.072
#> SRR2001071 2 0.5522 0.680 0.000 0.636 0.028 0.016 0.248 0.072
#> SRR2001064 2 0.3776 0.769 0.000 0.756 0.000 0.000 0.048 0.196
#> SRR2001065 2 0.3776 0.769 0.000 0.756 0.000 0.000 0.048 0.196
#> SRR2001066 2 0.3776 0.769 0.000 0.756 0.000 0.000 0.048 0.196
#> SRR2001067 2 0.3776 0.769 0.000 0.756 0.000 0.000 0.048 0.196
#> SRR2001060 4 0.4817 0.656 0.000 0.108 0.048 0.756 0.024 0.064
#> SRR2001061 4 0.4817 0.656 0.000 0.108 0.048 0.756 0.024 0.064
#> SRR2001062 4 0.4817 0.656 0.000 0.108 0.048 0.756 0.024 0.064
#> SRR2001063 4 0.4817 0.656 0.000 0.108 0.048 0.756 0.024 0.064
#> SRR2001056 4 0.4957 -0.164 0.000 0.084 0.000 0.584 0.332 0.000
#> SRR2001057 4 0.4957 -0.164 0.000 0.084 0.000 0.584 0.332 0.000
#> SRR2001058 4 0.4957 -0.164 0.000 0.084 0.000 0.584 0.332 0.000
#> SRR2001059 4 0.4957 -0.164 0.000 0.084 0.000 0.584 0.332 0.000
#> SRR2001052 2 0.6108 0.703 0.000 0.588 0.028 0.016 0.220 0.148
#> SRR2001053 2 0.6045 0.705 0.000 0.596 0.028 0.016 0.220 0.140
#> SRR2001054 2 0.6108 0.703 0.000 0.588 0.028 0.016 0.220 0.148
#> SRR2001055 2 0.6108 0.703 0.000 0.588 0.028 0.016 0.220 0.148
#> SRR2001048 2 0.5548 0.680 0.000 0.636 0.028 0.016 0.244 0.076
#> SRR2001049 2 0.5548 0.680 0.000 0.636 0.028 0.016 0.244 0.076
#> SRR2001050 2 0.5548 0.680 0.000 0.636 0.028 0.016 0.244 0.076
#> SRR2001051 2 0.5548 0.680 0.000 0.636 0.028 0.016 0.244 0.076
#> SRR2001044 4 0.3266 0.674 0.000 0.108 0.004 0.840 0.032 0.016
#> SRR2001045 4 0.3266 0.674 0.000 0.108 0.004 0.840 0.032 0.016
#> SRR2001046 4 0.3266 0.674 0.000 0.108 0.004 0.840 0.032 0.016
#> SRR2001047 4 0.3266 0.674 0.000 0.108 0.004 0.840 0.032 0.016
#> SRR2001040 4 0.2308 0.687 0.000 0.108 0.008 0.880 0.000 0.004
#> SRR2001041 4 0.2308 0.687 0.000 0.108 0.008 0.880 0.000 0.004
#> SRR2001042 4 0.2308 0.687 0.000 0.108 0.008 0.880 0.000 0.004
#> SRR2001043 4 0.2308 0.687 0.000 0.108 0.008 0.880 0.000 0.004
#> SRR2001036 4 0.2586 0.675 0.000 0.100 0.000 0.868 0.032 0.000
#> SRR2001037 4 0.2586 0.675 0.000 0.100 0.000 0.868 0.032 0.000
#> SRR2001038 4 0.2586 0.675 0.000 0.100 0.000 0.868 0.032 0.000
#> SRR2001039 4 0.2586 0.675 0.000 0.100 0.000 0.868 0.032 0.000
#> SRR2001028 4 0.3266 0.674 0.000 0.108 0.004 0.840 0.032 0.016
#> SRR2001029 4 0.3266 0.674 0.000 0.108 0.004 0.840 0.032 0.016
#> SRR2001030 4 0.3266 0.674 0.000 0.108 0.004 0.840 0.032 0.016
#> SRR2001031 4 0.3266 0.674 0.000 0.108 0.004 0.840 0.032 0.016
#> SRR2001024 4 0.3482 0.682 0.000 0.108 0.020 0.824 0.000 0.048
#> SRR2001025 4 0.3482 0.682 0.000 0.108 0.020 0.824 0.000 0.048
#> SRR2001026 4 0.3482 0.682 0.000 0.108 0.020 0.824 0.000 0.048
#> SRR2001027 4 0.3482 0.682 0.000 0.108 0.020 0.824 0.000 0.048
#> SRR2001020 2 0.4510 0.750 0.000 0.744 0.024 0.000 0.104 0.128
#> SRR2001021 2 0.4510 0.750 0.000 0.744 0.024 0.000 0.104 0.128
#> SRR2001022 2 0.4510 0.750 0.000 0.744 0.024 0.000 0.104 0.128
#> SRR2001023 2 0.4510 0.750 0.000 0.744 0.024 0.000 0.104 0.128
#> SRR2001016 5 0.5873 1.000 0.000 0.084 0.020 0.380 0.504 0.012
#> SRR2001017 5 0.5873 1.000 0.000 0.084 0.020 0.380 0.504 0.012
#> SRR2001018 5 0.5873 1.000 0.000 0.084 0.020 0.380 0.504 0.012
#> SRR2001019 5 0.5873 1.000 0.000 0.084 0.020 0.380 0.504 0.012
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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.5031 0.497 0.497
#> 3 3 1.000 0.998 0.997 0.2208 0.889 0.777
#> 4 4 1.000 0.999 0.997 0.2055 0.873 0.671
#> 5 5 0.885 0.945 0.912 0.0611 0.949 0.804
#> 6 6 0.828 0.711 0.820 0.0384 0.976 0.886
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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001033 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001034 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001035 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001204 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001205 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001206 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001207 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001200 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001201 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001202 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001203 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001196 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001197 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001198 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001199 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001192 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001193 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001194 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001195 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001188 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001189 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001190 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001191 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001184 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001185 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001186 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001187 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001180 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001181 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001182 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001183 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001176 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001177 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001178 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001179 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001172 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001173 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001174 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001175 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001168 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001169 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001170 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001171 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001164 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001165 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001166 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001167 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001160 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001161 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001162 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001163 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001156 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001157 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001158 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001159 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001152 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001153 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001154 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001155 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001148 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001149 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001150 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001151 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001144 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001145 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001146 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001147 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001140 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001142 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001143 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001136 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001137 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001138 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001139 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001132 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001133 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001134 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001135 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001128 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001129 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001130 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001131 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001124 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001125 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001126 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001127 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001120 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001121 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001122 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001123 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001116 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001117 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001118 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001119 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001112 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001113 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001114 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001115 3 0.0424 1.000 0.008 0.000 0.992
#> SRR2001108 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001109 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001110 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001111 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001104 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001105 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001106 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001107 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001100 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001101 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001102 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001103 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001096 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001097 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001098 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001099 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001092 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001093 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001094 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001095 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001088 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001089 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001090 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001091 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001084 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001085 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001086 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001087 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001080 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001081 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001082 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001083 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001076 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001077 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001078 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001079 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001072 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001073 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001074 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001075 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001068 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001069 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001070 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001071 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001064 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001065 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001066 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001067 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001060 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001061 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001062 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001063 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001056 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001057 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001058 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001059 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001052 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001053 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001054 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001055 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001048 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001049 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001050 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001051 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001044 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001045 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001046 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001047 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001040 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001041 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001042 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001043 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001036 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001037 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001038 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001039 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001028 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001029 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001030 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001031 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001024 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001025 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001026 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001027 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001020 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001021 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001022 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001023 2 0.0000 0.996 0.000 1.000 0.000
#> SRR2001016 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001017 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001018 2 0.0424 0.996 0.000 0.992 0.008
#> SRR2001019 2 0.0424 0.996 0.000 0.992 0.008
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001033 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001034 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001035 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001204 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001205 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001206 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001207 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001200 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001201 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001202 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001203 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001196 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001197 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001198 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001199 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001192 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001193 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001194 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001195 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001188 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001189 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001190 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001191 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001184 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001185 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001186 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001187 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001180 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001181 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001182 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001183 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001176 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001177 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001178 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001179 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001172 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001173 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001174 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001175 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001168 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001169 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001170 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001171 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001164 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001165 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001166 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001167 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001160 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001161 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001162 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001163 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001156 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001157 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001158 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001159 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001152 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001153 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001154 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001155 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001148 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001149 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001150 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001151 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001144 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001145 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001146 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001147 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001140 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001142 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001143 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001136 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001137 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001138 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001139 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001132 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001133 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001134 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001135 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001128 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001129 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001130 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001131 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001124 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001125 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001126 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001127 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001120 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001121 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001122 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001123 1 0.0336 0.996 0.992 0.008 0 0.000
#> SRR2001116 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001117 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001118 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001119 1 0.0000 0.998 1.000 0.000 0 0.000
#> SRR2001112 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001113 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001114 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001115 3 0.0000 1.000 0.000 0.000 1 0.000
#> SRR2001108 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001109 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001110 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001111 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001104 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001105 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001106 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001107 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001100 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001101 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001102 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001103 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001096 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001097 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001098 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001099 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001092 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001093 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001094 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001095 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001088 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001089 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001090 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001091 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001084 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001085 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001086 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001087 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001080 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001081 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001082 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001083 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001076 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001077 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001078 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001079 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001072 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001073 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001074 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001075 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001068 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001069 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001070 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001071 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001064 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001065 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001066 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001067 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001060 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001061 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001062 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001063 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001056 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001057 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001058 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001059 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001052 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001053 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001054 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001055 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001048 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001049 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001050 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001051 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001044 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001045 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001046 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001047 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001040 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001041 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001042 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001043 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001036 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001037 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001038 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001039 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001028 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001029 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001030 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001031 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001024 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001025 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001026 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001027 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001020 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001021 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001022 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001023 2 0.0336 1.000 0.000 0.992 0 0.008
#> SRR2001016 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001017 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001018 4 0.0000 1.000 0.000 0.000 0 1.000
#> SRR2001019 4 0.0000 1.000 0.000 0.000 0 1.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.3395 0.843 0.000 0.764 0.000 0.00 0.236
#> SRR2001033 2 0.3395 0.843 0.000 0.764 0.000 0.00 0.236
#> SRR2001034 2 0.3395 0.843 0.000 0.764 0.000 0.00 0.236
#> SRR2001035 2 0.3395 0.843 0.000 0.764 0.000 0.00 0.236
#> SRR2001204 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001205 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001206 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001207 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001200 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001201 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001202 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001203 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001196 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001197 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001198 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001199 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001192 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001193 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001194 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001195 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001188 1 0.0162 0.972 0.996 0.000 0.000 0.00 0.004
#> SRR2001189 1 0.0404 0.971 0.988 0.000 0.000 0.00 0.012
#> SRR2001190 1 0.0404 0.971 0.988 0.000 0.000 0.00 0.012
#> SRR2001191 1 0.0404 0.971 0.988 0.000 0.000 0.00 0.012
#> SRR2001184 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001185 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001186 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001187 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001180 1 0.1043 0.959 0.960 0.000 0.000 0.00 0.040
#> SRR2001181 1 0.1197 0.951 0.952 0.000 0.000 0.00 0.048
#> SRR2001182 1 0.1043 0.959 0.960 0.000 0.000 0.00 0.040
#> SRR2001183 1 0.1197 0.951 0.952 0.000 0.000 0.00 0.048
#> SRR2001176 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001177 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001178 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001179 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001172 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001173 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001174 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001175 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001168 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001169 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001170 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001171 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001164 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001165 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001166 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001167 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001160 1 0.1043 0.959 0.960 0.000 0.000 0.00 0.040
#> SRR2001161 1 0.1043 0.959 0.960 0.000 0.000 0.00 0.040
#> SRR2001162 1 0.1043 0.959 0.960 0.000 0.000 0.00 0.040
#> SRR2001163 1 0.1043 0.959 0.960 0.000 0.000 0.00 0.040
#> SRR2001156 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001157 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001158 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001159 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001152 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001153 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001154 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001155 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001148 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001149 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001150 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001151 3 0.0000 0.999 0.000 0.000 1.000 0.00 0.000
#> SRR2001144 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001145 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001146 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001147 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001140 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001142 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001143 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001136 3 0.0162 0.998 0.000 0.000 0.996 0.00 0.004
#> SRR2001137 3 0.0162 0.998 0.000 0.000 0.996 0.00 0.004
#> SRR2001138 3 0.0162 0.998 0.000 0.000 0.996 0.00 0.004
#> SRR2001139 3 0.0162 0.998 0.000 0.000 0.996 0.00 0.004
#> SRR2001132 3 0.0162 0.998 0.000 0.000 0.996 0.00 0.004
#> SRR2001133 3 0.0162 0.998 0.000 0.000 0.996 0.00 0.004
#> SRR2001134 3 0.0162 0.998 0.000 0.000 0.996 0.00 0.004
#> SRR2001135 3 0.0162 0.998 0.000 0.000 0.996 0.00 0.004
#> SRR2001128 1 0.1121 0.955 0.956 0.000 0.000 0.00 0.044
#> SRR2001129 1 0.1197 0.951 0.952 0.000 0.000 0.00 0.048
#> SRR2001130 1 0.1197 0.951 0.952 0.000 0.000 0.00 0.048
#> SRR2001131 1 0.1197 0.951 0.952 0.000 0.000 0.00 0.048
#> SRR2001124 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001125 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001126 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001127 1 0.0000 0.972 1.000 0.000 0.000 0.00 0.000
#> SRR2001120 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001121 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001122 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001123 5 0.4060 1.000 0.360 0.000 0.000 0.00 0.640
#> SRR2001116 1 0.1043 0.959 0.960 0.000 0.000 0.00 0.040
#> SRR2001117 1 0.1121 0.955 0.956 0.000 0.000 0.00 0.044
#> SRR2001118 1 0.0880 0.964 0.968 0.000 0.000 0.00 0.032
#> SRR2001119 1 0.0880 0.964 0.968 0.000 0.000 0.00 0.032
#> SRR2001112 3 0.0162 0.998 0.000 0.000 0.996 0.00 0.004
#> SRR2001113 3 0.0162 0.998 0.000 0.000 0.996 0.00 0.004
#> SRR2001114 3 0.0162 0.998 0.000 0.000 0.996 0.00 0.004
#> SRR2001115 3 0.0162 0.998 0.000 0.000 0.996 0.00 0.004
#> SRR2001108 4 0.2929 0.880 0.000 0.000 0.000 0.82 0.180
#> SRR2001109 4 0.2929 0.880 0.000 0.000 0.000 0.82 0.180
#> SRR2001110 4 0.2929 0.880 0.000 0.000 0.000 0.82 0.180
#> SRR2001111 4 0.2929 0.880 0.000 0.000 0.000 0.82 0.180
#> SRR2001104 2 0.0000 0.924 0.000 1.000 0.000 0.00 0.000
#> SRR2001105 2 0.0000 0.924 0.000 1.000 0.000 0.00 0.000
#> SRR2001106 2 0.0000 0.924 0.000 1.000 0.000 0.00 0.000
#> SRR2001107 2 0.0000 0.924 0.000 1.000 0.000 0.00 0.000
#> SRR2001100 2 0.0000 0.924 0.000 1.000 0.000 0.00 0.000
#> SRR2001101 2 0.0000 0.924 0.000 1.000 0.000 0.00 0.000
#> SRR2001102 2 0.0000 0.924 0.000 1.000 0.000 0.00 0.000
#> SRR2001103 2 0.0000 0.924 0.000 1.000 0.000 0.00 0.000
#> SRR2001096 2 0.1121 0.920 0.000 0.956 0.000 0.00 0.044
#> SRR2001097 2 0.1121 0.920 0.000 0.956 0.000 0.00 0.044
#> SRR2001098 2 0.1121 0.920 0.000 0.956 0.000 0.00 0.044
#> SRR2001099 2 0.1121 0.920 0.000 0.956 0.000 0.00 0.044
#> SRR2001092 2 0.1043 0.921 0.000 0.960 0.000 0.00 0.040
#> SRR2001093 2 0.1043 0.921 0.000 0.960 0.000 0.00 0.040
#> SRR2001094 2 0.1043 0.921 0.000 0.960 0.000 0.00 0.040
#> SRR2001095 2 0.1043 0.921 0.000 0.960 0.000 0.00 0.040
#> SRR2001088 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001089 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001090 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001091 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001084 4 0.2929 0.880 0.000 0.000 0.000 0.82 0.180
#> SRR2001085 4 0.2929 0.880 0.000 0.000 0.000 0.82 0.180
#> SRR2001086 4 0.2929 0.880 0.000 0.000 0.000 0.82 0.180
#> SRR2001087 4 0.2929 0.880 0.000 0.000 0.000 0.82 0.180
#> SRR2001080 2 0.0000 0.924 0.000 1.000 0.000 0.00 0.000
#> SRR2001081 2 0.0000 0.924 0.000 1.000 0.000 0.00 0.000
#> SRR2001082 2 0.0000 0.924 0.000 1.000 0.000 0.00 0.000
#> SRR2001083 2 0.0000 0.924 0.000 1.000 0.000 0.00 0.000
#> SRR2001076 2 0.0000 0.924 0.000 1.000 0.000 0.00 0.000
#> SRR2001077 2 0.0000 0.924 0.000 1.000 0.000 0.00 0.000
#> SRR2001078 2 0.0000 0.924 0.000 1.000 0.000 0.00 0.000
#> SRR2001079 2 0.0000 0.924 0.000 1.000 0.000 0.00 0.000
#> SRR2001072 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001073 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001074 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001075 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001068 2 0.3395 0.843 0.000 0.764 0.000 0.00 0.236
#> SRR2001069 2 0.3424 0.841 0.000 0.760 0.000 0.00 0.240
#> SRR2001070 2 0.3424 0.841 0.000 0.760 0.000 0.00 0.240
#> SRR2001071 2 0.3424 0.841 0.000 0.760 0.000 0.00 0.240
#> SRR2001064 2 0.1121 0.920 0.000 0.956 0.000 0.00 0.044
#> SRR2001065 2 0.1121 0.920 0.000 0.956 0.000 0.00 0.044
#> SRR2001066 2 0.1121 0.920 0.000 0.956 0.000 0.00 0.044
#> SRR2001067 2 0.1121 0.920 0.000 0.956 0.000 0.00 0.044
#> SRR2001060 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001061 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001062 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001063 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001056 4 0.2929 0.880 0.000 0.000 0.000 0.82 0.180
#> SRR2001057 4 0.2929 0.880 0.000 0.000 0.000 0.82 0.180
#> SRR2001058 4 0.2929 0.880 0.000 0.000 0.000 0.82 0.180
#> SRR2001059 4 0.2929 0.880 0.000 0.000 0.000 0.82 0.180
#> SRR2001052 2 0.3074 0.877 0.000 0.804 0.000 0.00 0.196
#> SRR2001053 2 0.3074 0.877 0.000 0.804 0.000 0.00 0.196
#> SRR2001054 2 0.3074 0.877 0.000 0.804 0.000 0.00 0.196
#> SRR2001055 2 0.3074 0.877 0.000 0.804 0.000 0.00 0.196
#> SRR2001048 2 0.3424 0.841 0.000 0.760 0.000 0.00 0.240
#> SRR2001049 2 0.3424 0.841 0.000 0.760 0.000 0.00 0.240
#> SRR2001050 2 0.3424 0.841 0.000 0.760 0.000 0.00 0.240
#> SRR2001051 2 0.3424 0.841 0.000 0.760 0.000 0.00 0.240
#> SRR2001044 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001045 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001046 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001047 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001040 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001041 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001042 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001043 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001036 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001037 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001038 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001039 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001028 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001029 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001030 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001031 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001024 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001025 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001026 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001027 4 0.0000 0.940 0.000 0.000 0.000 1.00 0.000
#> SRR2001020 2 0.1121 0.920 0.000 0.956 0.000 0.00 0.044
#> SRR2001021 2 0.1121 0.920 0.000 0.956 0.000 0.00 0.044
#> SRR2001022 2 0.1121 0.920 0.000 0.956 0.000 0.00 0.044
#> SRR2001023 2 0.1121 0.920 0.000 0.956 0.000 0.00 0.044
#> SRR2001016 4 0.3796 0.790 0.000 0.000 0.000 0.70 0.300
#> SRR2001017 4 0.3796 0.790 0.000 0.000 0.000 0.70 0.300
#> SRR2001018 4 0.3796 0.790 0.000 0.000 0.000 0.70 0.300
#> SRR2001019 4 0.3796 0.790 0.000 0.000 0.000 0.70 0.300
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 2 0.2442 0.410 0.000 0.852 0.000 0.000 0.144 0.004
#> SRR2001033 2 0.2442 0.410 0.000 0.852 0.000 0.000 0.144 0.004
#> SRR2001034 2 0.2442 0.410 0.000 0.852 0.000 0.000 0.144 0.004
#> SRR2001035 2 0.2442 0.410 0.000 0.852 0.000 0.000 0.144 0.004
#> SRR2001204 6 0.2668 0.997 0.168 0.000 0.000 0.000 0.004 0.828
#> SRR2001205 6 0.2668 0.997 0.168 0.000 0.000 0.000 0.004 0.828
#> SRR2001206 6 0.2668 0.997 0.168 0.000 0.000 0.000 0.004 0.828
#> SRR2001207 6 0.2668 0.997 0.168 0.000 0.000 0.000 0.004 0.828
#> SRR2001200 1 0.0146 0.923 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001201 1 0.0146 0.923 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001202 1 0.0146 0.923 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001203 1 0.0146 0.923 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001196 1 0.0146 0.923 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001197 1 0.0146 0.923 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001198 1 0.0146 0.923 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001199 1 0.0146 0.923 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001192 3 0.0000 0.962 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001193 3 0.0000 0.962 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001194 3 0.0000 0.962 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001195 3 0.0000 0.962 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001188 1 0.0935 0.921 0.964 0.000 0.000 0.000 0.004 0.032
#> SRR2001189 1 0.1285 0.917 0.944 0.000 0.000 0.000 0.004 0.052
#> SRR2001190 1 0.1152 0.919 0.952 0.000 0.000 0.000 0.004 0.044
#> SRR2001191 1 0.1152 0.919 0.952 0.000 0.000 0.000 0.004 0.044
#> SRR2001184 3 0.0146 0.962 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001185 3 0.0146 0.962 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001186 3 0.0146 0.962 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001187 3 0.0146 0.962 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001180 1 0.2362 0.883 0.860 0.000 0.000 0.000 0.004 0.136
#> SRR2001181 1 0.2362 0.883 0.860 0.000 0.000 0.000 0.004 0.136
#> SRR2001182 1 0.2320 0.886 0.864 0.000 0.000 0.000 0.004 0.132
#> SRR2001183 1 0.2362 0.883 0.860 0.000 0.000 0.000 0.004 0.136
#> SRR2001176 3 0.0260 0.961 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR2001177 3 0.0260 0.961 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR2001178 3 0.0146 0.962 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001179 3 0.0146 0.962 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001172 3 0.0146 0.962 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001173 3 0.0146 0.962 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001174 3 0.0146 0.962 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001175 3 0.0146 0.962 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001168 6 0.2668 0.997 0.168 0.000 0.000 0.000 0.004 0.828
#> SRR2001169 6 0.2668 0.997 0.168 0.000 0.000 0.000 0.004 0.828
#> SRR2001170 6 0.2668 0.997 0.168 0.000 0.000 0.000 0.004 0.828
#> SRR2001171 6 0.2668 0.997 0.168 0.000 0.000 0.000 0.004 0.828
#> SRR2001164 1 0.0000 0.924 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001165 1 0.0000 0.924 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001166 1 0.0000 0.924 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001167 1 0.0000 0.924 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001160 1 0.2146 0.895 0.880 0.000 0.000 0.000 0.004 0.116
#> SRR2001161 1 0.2146 0.895 0.880 0.000 0.000 0.000 0.004 0.116
#> SRR2001162 1 0.2146 0.895 0.880 0.000 0.000 0.000 0.004 0.116
#> SRR2001163 1 0.2100 0.897 0.884 0.000 0.000 0.000 0.004 0.112
#> SRR2001156 1 0.0146 0.923 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001157 1 0.0146 0.923 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001158 1 0.0146 0.923 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001159 1 0.0146 0.923 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001152 6 0.2527 0.998 0.168 0.000 0.000 0.000 0.000 0.832
#> SRR2001153 6 0.2668 0.994 0.168 0.000 0.000 0.000 0.004 0.828
#> SRR2001154 6 0.2527 0.998 0.168 0.000 0.000 0.000 0.000 0.832
#> SRR2001155 6 0.2527 0.998 0.168 0.000 0.000 0.000 0.000 0.832
#> SRR2001148 3 0.0146 0.962 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001149 3 0.0146 0.962 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001150 3 0.0146 0.962 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001151 3 0.0146 0.962 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001144 6 0.2527 0.998 0.168 0.000 0.000 0.000 0.000 0.832
#> SRR2001145 6 0.2527 0.998 0.168 0.000 0.000 0.000 0.000 0.832
#> SRR2001146 6 0.2527 0.998 0.168 0.000 0.000 0.000 0.000 0.832
#> SRR2001147 6 0.2527 0.998 0.168 0.000 0.000 0.000 0.000 0.832
#> SRR2001140 6 0.2527 0.998 0.168 0.000 0.000 0.000 0.000 0.832
#> SRR2001142 6 0.2527 0.998 0.168 0.000 0.000 0.000 0.000 0.832
#> SRR2001143 6 0.2527 0.998 0.168 0.000 0.000 0.000 0.000 0.832
#> SRR2001136 3 0.2358 0.938 0.000 0.000 0.876 0.000 0.108 0.016
#> SRR2001137 3 0.2358 0.938 0.000 0.000 0.876 0.000 0.108 0.016
#> SRR2001138 3 0.2358 0.938 0.000 0.000 0.876 0.000 0.108 0.016
#> SRR2001139 3 0.2358 0.938 0.000 0.000 0.876 0.000 0.108 0.016
#> SRR2001132 3 0.2358 0.938 0.000 0.000 0.876 0.000 0.108 0.016
#> SRR2001133 3 0.2358 0.938 0.000 0.000 0.876 0.000 0.108 0.016
#> SRR2001134 3 0.2358 0.938 0.000 0.000 0.876 0.000 0.108 0.016
#> SRR2001135 3 0.2358 0.938 0.000 0.000 0.876 0.000 0.108 0.016
#> SRR2001128 1 0.2278 0.888 0.868 0.000 0.000 0.000 0.004 0.128
#> SRR2001129 1 0.2402 0.880 0.856 0.000 0.000 0.000 0.004 0.140
#> SRR2001130 1 0.2402 0.880 0.856 0.000 0.000 0.000 0.004 0.140
#> SRR2001131 1 0.2402 0.880 0.856 0.000 0.000 0.000 0.004 0.140
#> SRR2001124 1 0.0000 0.924 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001125 1 0.0000 0.924 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001126 1 0.0000 0.924 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001127 1 0.0000 0.924 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001120 6 0.2527 0.998 0.168 0.000 0.000 0.000 0.000 0.832
#> SRR2001121 6 0.2527 0.998 0.168 0.000 0.000 0.000 0.000 0.832
#> SRR2001122 6 0.2527 0.998 0.168 0.000 0.000 0.000 0.000 0.832
#> SRR2001123 6 0.2527 0.998 0.168 0.000 0.000 0.000 0.000 0.832
#> SRR2001116 1 0.2482 0.871 0.848 0.000 0.000 0.000 0.004 0.148
#> SRR2001117 1 0.2632 0.851 0.832 0.000 0.000 0.000 0.004 0.164
#> SRR2001118 1 0.2442 0.875 0.852 0.000 0.000 0.000 0.004 0.144
#> SRR2001119 1 0.2482 0.871 0.848 0.000 0.000 0.000 0.004 0.148
#> SRR2001112 3 0.2358 0.938 0.000 0.000 0.876 0.000 0.108 0.016
#> SRR2001113 3 0.2358 0.938 0.000 0.000 0.876 0.000 0.108 0.016
#> SRR2001114 3 0.2358 0.938 0.000 0.000 0.876 0.000 0.108 0.016
#> SRR2001115 3 0.2358 0.938 0.000 0.000 0.876 0.000 0.108 0.016
#> SRR2001108 4 0.5464 0.703 0.000 0.012 0.000 0.584 0.284 0.120
#> SRR2001109 4 0.5464 0.703 0.000 0.012 0.000 0.584 0.284 0.120
#> SRR2001110 4 0.5464 0.703 0.000 0.012 0.000 0.584 0.284 0.120
#> SRR2001111 4 0.5464 0.703 0.000 0.012 0.000 0.584 0.284 0.120
#> SRR2001104 2 0.3923 -0.319 0.000 0.620 0.000 0.000 0.372 0.008
#> SRR2001105 2 0.3923 -0.319 0.000 0.620 0.000 0.000 0.372 0.008
#> SRR2001106 2 0.3923 -0.319 0.000 0.620 0.000 0.000 0.372 0.008
#> SRR2001107 2 0.3923 -0.319 0.000 0.620 0.000 0.000 0.372 0.008
#> SRR2001100 2 0.3911 -0.313 0.000 0.624 0.000 0.000 0.368 0.008
#> SRR2001101 2 0.3911 -0.313 0.000 0.624 0.000 0.000 0.368 0.008
#> SRR2001102 2 0.3911 -0.313 0.000 0.624 0.000 0.000 0.368 0.008
#> SRR2001103 2 0.3911 -0.313 0.000 0.624 0.000 0.000 0.368 0.008
#> SRR2001096 5 0.4183 0.915 0.000 0.480 0.000 0.000 0.508 0.012
#> SRR2001097 5 0.4183 0.915 0.000 0.480 0.000 0.000 0.508 0.012
#> SRR2001098 5 0.4183 0.915 0.000 0.480 0.000 0.000 0.508 0.012
#> SRR2001099 5 0.4183 0.915 0.000 0.480 0.000 0.000 0.508 0.012
#> SRR2001092 2 0.3862 -0.737 0.000 0.524 0.000 0.000 0.476 0.000
#> SRR2001093 2 0.3862 -0.737 0.000 0.524 0.000 0.000 0.476 0.000
#> SRR2001094 2 0.3862 -0.737 0.000 0.524 0.000 0.000 0.476 0.000
#> SRR2001095 2 0.3862 -0.737 0.000 0.524 0.000 0.000 0.476 0.000
#> SRR2001088 4 0.0458 0.851 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR2001089 4 0.0458 0.851 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR2001090 4 0.0458 0.851 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR2001091 4 0.0458 0.851 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR2001084 4 0.5511 0.700 0.000 0.012 0.000 0.572 0.296 0.120
#> SRR2001085 4 0.5511 0.700 0.000 0.012 0.000 0.572 0.296 0.120
#> SRR2001086 4 0.5511 0.700 0.000 0.012 0.000 0.572 0.296 0.120
#> SRR2001087 4 0.5511 0.700 0.000 0.012 0.000 0.572 0.296 0.120
#> SRR2001080 2 0.3923 -0.319 0.000 0.620 0.000 0.000 0.372 0.008
#> SRR2001081 2 0.3923 -0.319 0.000 0.620 0.000 0.000 0.372 0.008
#> SRR2001082 2 0.3923 -0.319 0.000 0.620 0.000 0.000 0.372 0.008
#> SRR2001083 2 0.3923 -0.319 0.000 0.620 0.000 0.000 0.372 0.008
#> SRR2001076 2 0.3923 -0.319 0.000 0.620 0.000 0.000 0.372 0.008
#> SRR2001077 2 0.3923 -0.319 0.000 0.620 0.000 0.000 0.372 0.008
#> SRR2001078 2 0.3923 -0.319 0.000 0.620 0.000 0.000 0.372 0.008
#> SRR2001079 2 0.3923 -0.319 0.000 0.620 0.000 0.000 0.372 0.008
#> SRR2001072 4 0.0632 0.851 0.000 0.000 0.000 0.976 0.024 0.000
#> SRR2001073 4 0.0632 0.851 0.000 0.000 0.000 0.976 0.024 0.000
#> SRR2001074 4 0.0632 0.851 0.000 0.000 0.000 0.976 0.024 0.000
#> SRR2001075 4 0.0632 0.851 0.000 0.000 0.000 0.976 0.024 0.000
#> SRR2001068 2 0.2234 0.411 0.000 0.872 0.000 0.000 0.124 0.004
#> SRR2001069 2 0.2234 0.411 0.000 0.872 0.000 0.000 0.124 0.004
#> SRR2001070 2 0.2234 0.411 0.000 0.872 0.000 0.000 0.124 0.004
#> SRR2001071 2 0.2234 0.411 0.000 0.872 0.000 0.000 0.124 0.004
#> SRR2001064 5 0.4183 0.915 0.000 0.480 0.000 0.000 0.508 0.012
#> SRR2001065 5 0.4183 0.915 0.000 0.480 0.000 0.000 0.508 0.012
#> SRR2001066 5 0.4183 0.915 0.000 0.480 0.000 0.000 0.508 0.012
#> SRR2001067 5 0.4183 0.915 0.000 0.480 0.000 0.000 0.508 0.012
#> SRR2001060 4 0.0458 0.851 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR2001061 4 0.0458 0.851 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR2001062 4 0.0458 0.851 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR2001063 4 0.0458 0.851 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR2001056 4 0.5464 0.703 0.000 0.012 0.000 0.584 0.284 0.120
#> SRR2001057 4 0.5464 0.703 0.000 0.012 0.000 0.584 0.284 0.120
#> SRR2001058 4 0.5464 0.703 0.000 0.012 0.000 0.584 0.284 0.120
#> SRR2001059 4 0.5464 0.703 0.000 0.012 0.000 0.584 0.284 0.120
#> SRR2001052 2 0.1075 0.305 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR2001053 2 0.1007 0.308 0.000 0.956 0.000 0.000 0.044 0.000
#> SRR2001054 2 0.1075 0.305 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR2001055 2 0.1075 0.305 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR2001048 2 0.2234 0.411 0.000 0.872 0.000 0.000 0.124 0.004
#> SRR2001049 2 0.2234 0.411 0.000 0.872 0.000 0.000 0.124 0.004
#> SRR2001050 2 0.2234 0.411 0.000 0.872 0.000 0.000 0.124 0.004
#> SRR2001051 2 0.2234 0.411 0.000 0.872 0.000 0.000 0.124 0.004
#> SRR2001044 4 0.1003 0.852 0.000 0.000 0.000 0.964 0.016 0.020
#> SRR2001045 4 0.1003 0.852 0.000 0.000 0.000 0.964 0.016 0.020
#> SRR2001046 4 0.1003 0.852 0.000 0.000 0.000 0.964 0.016 0.020
#> SRR2001047 4 0.1003 0.852 0.000 0.000 0.000 0.964 0.016 0.020
#> SRR2001040 4 0.0000 0.852 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001041 4 0.0000 0.852 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001042 4 0.0000 0.852 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001043 4 0.0000 0.852 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001036 4 0.0909 0.853 0.000 0.000 0.000 0.968 0.012 0.020
#> SRR2001037 4 0.0909 0.853 0.000 0.000 0.000 0.968 0.012 0.020
#> SRR2001038 4 0.0909 0.853 0.000 0.000 0.000 0.968 0.012 0.020
#> SRR2001039 4 0.0909 0.853 0.000 0.000 0.000 0.968 0.012 0.020
#> SRR2001028 4 0.1003 0.852 0.000 0.000 0.000 0.964 0.016 0.020
#> SRR2001029 4 0.1003 0.852 0.000 0.000 0.000 0.964 0.016 0.020
#> SRR2001030 4 0.1003 0.852 0.000 0.000 0.000 0.964 0.016 0.020
#> SRR2001031 4 0.1003 0.852 0.000 0.000 0.000 0.964 0.016 0.020
#> SRR2001024 4 0.0000 0.852 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001025 4 0.0000 0.852 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001026 4 0.0000 0.852 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001027 4 0.0000 0.852 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001020 5 0.4097 0.815 0.000 0.492 0.000 0.000 0.500 0.008
#> SRR2001021 5 0.4097 0.815 0.000 0.492 0.000 0.000 0.500 0.008
#> SRR2001022 5 0.4097 0.815 0.000 0.492 0.000 0.000 0.500 0.008
#> SRR2001023 5 0.4097 0.815 0.000 0.492 0.000 0.000 0.500 0.008
#> SRR2001016 4 0.7290 0.445 0.000 0.220 0.000 0.344 0.328 0.108
#> SRR2001017 4 0.7290 0.445 0.000 0.220 0.000 0.344 0.328 0.108
#> SRR2001018 4 0.7290 0.445 0.000 0.220 0.000 0.344 0.328 0.108
#> SRR2001019 4 0.7290 0.445 0.000 0.220 0.000 0.344 0.328 0.108
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 6.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.5031 0.497 0.497
#> 3 3 1.000 1.000 1.000 0.2206 0.889 0.777
#> 4 4 1.000 0.998 0.999 0.2065 0.873 0.671
#> 5 5 0.928 0.961 0.948 0.0630 0.948 0.801
#> 6 6 0.916 0.792 0.867 0.0304 0.969 0.858
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3 4 5
There is also optional best \(k\) = 2 3 4 5 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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0 1 0 1 0
#> SRR2001033 2 0 1 0 1 0
#> SRR2001034 2 0 1 0 1 0
#> SRR2001035 2 0 1 0 1 0
#> SRR2001204 1 0 1 1 0 0
#> SRR2001205 1 0 1 1 0 0
#> SRR2001206 1 0 1 1 0 0
#> SRR2001207 1 0 1 1 0 0
#> SRR2001200 1 0 1 1 0 0
#> SRR2001201 1 0 1 1 0 0
#> SRR2001202 1 0 1 1 0 0
#> SRR2001203 1 0 1 1 0 0
#> SRR2001196 1 0 1 1 0 0
#> SRR2001197 1 0 1 1 0 0
#> SRR2001198 1 0 1 1 0 0
#> SRR2001199 1 0 1 1 0 0
#> SRR2001192 3 0 1 0 0 1
#> SRR2001193 3 0 1 0 0 1
#> SRR2001194 3 0 1 0 0 1
#> SRR2001195 3 0 1 0 0 1
#> SRR2001188 1 0 1 1 0 0
#> SRR2001189 1 0 1 1 0 0
#> SRR2001190 1 0 1 1 0 0
#> SRR2001191 1 0 1 1 0 0
#> SRR2001184 3 0 1 0 0 1
#> SRR2001185 3 0 1 0 0 1
#> SRR2001186 3 0 1 0 0 1
#> SRR2001187 3 0 1 0 0 1
#> SRR2001180 1 0 1 1 0 0
#> SRR2001181 1 0 1 1 0 0
#> SRR2001182 1 0 1 1 0 0
#> SRR2001183 1 0 1 1 0 0
#> SRR2001176 3 0 1 0 0 1
#> SRR2001177 3 0 1 0 0 1
#> SRR2001178 3 0 1 0 0 1
#> SRR2001179 3 0 1 0 0 1
#> SRR2001172 3 0 1 0 0 1
#> SRR2001173 3 0 1 0 0 1
#> SRR2001174 3 0 1 0 0 1
#> SRR2001175 3 0 1 0 0 1
#> SRR2001168 1 0 1 1 0 0
#> SRR2001169 1 0 1 1 0 0
#> SRR2001170 1 0 1 1 0 0
#> SRR2001171 1 0 1 1 0 0
#> SRR2001164 1 0 1 1 0 0
#> SRR2001165 1 0 1 1 0 0
#> SRR2001166 1 0 1 1 0 0
#> SRR2001167 1 0 1 1 0 0
#> SRR2001160 1 0 1 1 0 0
#> SRR2001161 1 0 1 1 0 0
#> SRR2001162 1 0 1 1 0 0
#> SRR2001163 1 0 1 1 0 0
#> SRR2001156 1 0 1 1 0 0
#> SRR2001157 1 0 1 1 0 0
#> SRR2001158 1 0 1 1 0 0
#> SRR2001159 1 0 1 1 0 0
#> SRR2001152 1 0 1 1 0 0
#> SRR2001153 1 0 1 1 0 0
#> SRR2001154 1 0 1 1 0 0
#> SRR2001155 1 0 1 1 0 0
#> SRR2001148 3 0 1 0 0 1
#> SRR2001149 3 0 1 0 0 1
#> SRR2001150 3 0 1 0 0 1
#> SRR2001151 3 0 1 0 0 1
#> SRR2001144 1 0 1 1 0 0
#> SRR2001145 1 0 1 1 0 0
#> SRR2001146 1 0 1 1 0 0
#> SRR2001147 1 0 1 1 0 0
#> SRR2001140 1 0 1 1 0 0
#> SRR2001142 1 0 1 1 0 0
#> SRR2001143 1 0 1 1 0 0
#> SRR2001136 3 0 1 0 0 1
#> SRR2001137 3 0 1 0 0 1
#> SRR2001138 3 0 1 0 0 1
#> SRR2001139 3 0 1 0 0 1
#> SRR2001132 3 0 1 0 0 1
#> SRR2001133 3 0 1 0 0 1
#> SRR2001134 3 0 1 0 0 1
#> SRR2001135 3 0 1 0 0 1
#> SRR2001128 1 0 1 1 0 0
#> SRR2001129 1 0 1 1 0 0
#> SRR2001130 1 0 1 1 0 0
#> SRR2001131 1 0 1 1 0 0
#> SRR2001124 1 0 1 1 0 0
#> SRR2001125 1 0 1 1 0 0
#> SRR2001126 1 0 1 1 0 0
#> SRR2001127 1 0 1 1 0 0
#> SRR2001120 1 0 1 1 0 0
#> SRR2001121 1 0 1 1 0 0
#> SRR2001122 1 0 1 1 0 0
#> SRR2001123 1 0 1 1 0 0
#> SRR2001116 1 0 1 1 0 0
#> SRR2001117 1 0 1 1 0 0
#> SRR2001118 1 0 1 1 0 0
#> SRR2001119 1 0 1 1 0 0
#> SRR2001112 3 0 1 0 0 1
#> SRR2001113 3 0 1 0 0 1
#> SRR2001114 3 0 1 0 0 1
#> SRR2001115 3 0 1 0 0 1
#> SRR2001108 2 0 1 0 1 0
#> SRR2001109 2 0 1 0 1 0
#> SRR2001110 2 0 1 0 1 0
#> SRR2001111 2 0 1 0 1 0
#> SRR2001104 2 0 1 0 1 0
#> SRR2001105 2 0 1 0 1 0
#> SRR2001106 2 0 1 0 1 0
#> SRR2001107 2 0 1 0 1 0
#> SRR2001100 2 0 1 0 1 0
#> SRR2001101 2 0 1 0 1 0
#> SRR2001102 2 0 1 0 1 0
#> SRR2001103 2 0 1 0 1 0
#> SRR2001096 2 0 1 0 1 0
#> SRR2001097 2 0 1 0 1 0
#> SRR2001098 2 0 1 0 1 0
#> SRR2001099 2 0 1 0 1 0
#> SRR2001092 2 0 1 0 1 0
#> SRR2001093 2 0 1 0 1 0
#> SRR2001094 2 0 1 0 1 0
#> SRR2001095 2 0 1 0 1 0
#> SRR2001088 2 0 1 0 1 0
#> SRR2001089 2 0 1 0 1 0
#> SRR2001090 2 0 1 0 1 0
#> SRR2001091 2 0 1 0 1 0
#> SRR2001084 2 0 1 0 1 0
#> SRR2001085 2 0 1 0 1 0
#> SRR2001086 2 0 1 0 1 0
#> SRR2001087 2 0 1 0 1 0
#> SRR2001080 2 0 1 0 1 0
#> SRR2001081 2 0 1 0 1 0
#> SRR2001082 2 0 1 0 1 0
#> SRR2001083 2 0 1 0 1 0
#> SRR2001076 2 0 1 0 1 0
#> SRR2001077 2 0 1 0 1 0
#> SRR2001078 2 0 1 0 1 0
#> SRR2001079 2 0 1 0 1 0
#> SRR2001072 2 0 1 0 1 0
#> SRR2001073 2 0 1 0 1 0
#> SRR2001074 2 0 1 0 1 0
#> SRR2001075 2 0 1 0 1 0
#> SRR2001068 2 0 1 0 1 0
#> SRR2001069 2 0 1 0 1 0
#> SRR2001070 2 0 1 0 1 0
#> SRR2001071 2 0 1 0 1 0
#> SRR2001064 2 0 1 0 1 0
#> SRR2001065 2 0 1 0 1 0
#> SRR2001066 2 0 1 0 1 0
#> SRR2001067 2 0 1 0 1 0
#> SRR2001060 2 0 1 0 1 0
#> SRR2001061 2 0 1 0 1 0
#> SRR2001062 2 0 1 0 1 0
#> SRR2001063 2 0 1 0 1 0
#> SRR2001056 2 0 1 0 1 0
#> SRR2001057 2 0 1 0 1 0
#> SRR2001058 2 0 1 0 1 0
#> SRR2001059 2 0 1 0 1 0
#> SRR2001052 2 0 1 0 1 0
#> SRR2001053 2 0 1 0 1 0
#> SRR2001054 2 0 1 0 1 0
#> SRR2001055 2 0 1 0 1 0
#> SRR2001048 2 0 1 0 1 0
#> SRR2001049 2 0 1 0 1 0
#> SRR2001050 2 0 1 0 1 0
#> SRR2001051 2 0 1 0 1 0
#> SRR2001044 2 0 1 0 1 0
#> SRR2001045 2 0 1 0 1 0
#> SRR2001046 2 0 1 0 1 0
#> SRR2001047 2 0 1 0 1 0
#> SRR2001040 2 0 1 0 1 0
#> SRR2001041 2 0 1 0 1 0
#> SRR2001042 2 0 1 0 1 0
#> SRR2001043 2 0 1 0 1 0
#> SRR2001036 2 0 1 0 1 0
#> SRR2001037 2 0 1 0 1 0
#> SRR2001038 2 0 1 0 1 0
#> SRR2001039 2 0 1 0 1 0
#> SRR2001028 2 0 1 0 1 0
#> SRR2001029 2 0 1 0 1 0
#> SRR2001030 2 0 1 0 1 0
#> SRR2001031 2 0 1 0 1 0
#> SRR2001024 2 0 1 0 1 0
#> SRR2001025 2 0 1 0 1 0
#> SRR2001026 2 0 1 0 1 0
#> SRR2001027 2 0 1 0 1 0
#> SRR2001020 2 0 1 0 1 0
#> SRR2001021 2 0 1 0 1 0
#> SRR2001022 2 0 1 0 1 0
#> SRR2001023 2 0 1 0 1 0
#> SRR2001016 2 0 1 0 1 0
#> SRR2001017 2 0 1 0 1 0
#> SRR2001018 2 0 1 0 1 0
#> SRR2001019 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001033 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001034 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001035 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001204 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001205 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001206 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001207 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001200 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001201 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001202 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001203 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001196 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001197 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001198 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001199 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001192 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001193 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001194 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001195 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001188 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001189 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001190 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001191 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001184 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001185 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001186 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001187 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001180 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001181 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001182 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001183 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001176 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001177 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001178 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001179 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001172 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001173 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001174 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001175 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001168 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001169 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001170 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001171 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001164 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001165 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001166 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001167 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001160 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001161 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001162 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001163 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001156 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001157 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001158 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001159 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001152 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001153 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001154 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001155 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001148 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001149 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001150 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001151 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001144 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001145 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001146 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001147 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001140 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001142 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001143 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001136 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001137 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001138 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001139 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001132 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001133 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001134 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001135 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001128 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001129 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001130 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001131 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001124 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001125 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001126 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001127 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001120 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001121 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001122 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001123 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001116 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001117 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001118 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001119 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001112 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001113 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001114 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001115 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001108 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001109 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001110 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001111 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001104 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001105 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001106 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001107 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001100 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001101 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001102 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001103 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001096 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001097 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001098 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001099 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001092 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001093 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001094 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001095 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001088 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001089 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001090 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001091 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001084 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001085 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001086 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001087 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001080 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001081 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001082 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001083 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001076 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001077 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001078 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001079 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001072 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001073 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001074 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001075 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001068 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001069 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001070 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001071 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001064 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001065 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001066 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001067 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001060 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001061 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001062 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001063 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001056 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001057 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001058 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001059 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001052 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001053 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001054 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001055 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001048 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001049 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001050 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001051 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001044 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001045 4 0.0469 0.984 0 0.012 0 0.988
#> SRR2001046 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001047 4 0.1716 0.932 0 0.064 0 0.936
#> SRR2001040 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001041 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001042 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001043 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001036 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001037 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001038 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001039 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001028 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001029 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001030 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001031 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001024 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001025 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001026 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001027 4 0.0000 0.995 0 0.000 0 1.000
#> SRR2001020 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001021 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001022 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001023 2 0.0000 1.000 0 1.000 0 0.000
#> SRR2001016 4 0.1716 0.932 0 0.064 0 0.936
#> SRR2001017 4 0.0817 0.974 0 0.024 0 0.976
#> SRR2001018 4 0.0817 0.974 0 0.024 0 0.976
#> SRR2001019 4 0.1211 0.958 0 0.040 0 0.960
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001033 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001034 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001035 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001204 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001205 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001206 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001207 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001200 5 0.0000 0.970 0.000 0.000 0 0.000 1.000
#> SRR2001201 5 0.0000 0.970 0.000 0.000 0 0.000 1.000
#> SRR2001202 5 0.0000 0.970 0.000 0.000 0 0.000 1.000
#> SRR2001203 5 0.0000 0.970 0.000 0.000 0 0.000 1.000
#> SRR2001196 5 0.0000 0.970 0.000 0.000 0 0.000 1.000
#> SRR2001197 5 0.0000 0.970 0.000 0.000 0 0.000 1.000
#> SRR2001198 5 0.0000 0.970 0.000 0.000 0 0.000 1.000
#> SRR2001199 5 0.0000 0.970 0.000 0.000 0 0.000 1.000
#> SRR2001192 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001193 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001194 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001195 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001188 5 0.3876 0.329 0.316 0.000 0 0.000 0.684
#> SRR2001189 1 0.4150 0.725 0.612 0.000 0 0.000 0.388
#> SRR2001190 1 0.3305 0.971 0.776 0.000 0 0.000 0.224
#> SRR2001191 1 0.3305 0.970 0.776 0.000 0 0.000 0.224
#> SRR2001184 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001185 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001186 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001187 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001180 1 0.3480 0.947 0.752 0.000 0 0.000 0.248
#> SRR2001181 1 0.3305 0.971 0.776 0.000 0 0.000 0.224
#> SRR2001182 1 0.3366 0.964 0.768 0.000 0 0.000 0.232
#> SRR2001183 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001176 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001177 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001178 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001179 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001172 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001173 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001174 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001175 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001168 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001169 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001170 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001171 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001164 5 0.0609 0.955 0.020 0.000 0 0.000 0.980
#> SRR2001165 5 0.0404 0.962 0.012 0.000 0 0.000 0.988
#> SRR2001166 5 0.0880 0.941 0.032 0.000 0 0.000 0.968
#> SRR2001167 5 0.0162 0.968 0.004 0.000 0 0.000 0.996
#> SRR2001160 5 0.0510 0.958 0.016 0.000 0 0.000 0.984
#> SRR2001161 5 0.0404 0.962 0.012 0.000 0 0.000 0.988
#> SRR2001162 5 0.2230 0.817 0.116 0.000 0 0.000 0.884
#> SRR2001163 1 0.4219 0.661 0.584 0.000 0 0.000 0.416
#> SRR2001156 5 0.0000 0.970 0.000 0.000 0 0.000 1.000
#> SRR2001157 5 0.0000 0.970 0.000 0.000 0 0.000 1.000
#> SRR2001158 5 0.0000 0.970 0.000 0.000 0 0.000 1.000
#> SRR2001159 5 0.0000 0.970 0.000 0.000 0 0.000 1.000
#> SRR2001152 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001153 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001154 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001155 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001148 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001149 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001150 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001151 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001144 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001145 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001146 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001147 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001140 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001142 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001143 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001136 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001137 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001138 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001139 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001132 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001133 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001134 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001135 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001128 1 0.3336 0.967 0.772 0.000 0 0.000 0.228
#> SRR2001129 1 0.3242 0.975 0.784 0.000 0 0.000 0.216
#> SRR2001130 1 0.3305 0.970 0.776 0.000 0 0.000 0.224
#> SRR2001131 1 0.3305 0.970 0.776 0.000 0 0.000 0.224
#> SRR2001124 5 0.0000 0.970 0.000 0.000 0 0.000 1.000
#> SRR2001125 5 0.0000 0.970 0.000 0.000 0 0.000 1.000
#> SRR2001126 5 0.0000 0.970 0.000 0.000 0 0.000 1.000
#> SRR2001127 5 0.0000 0.970 0.000 0.000 0 0.000 1.000
#> SRR2001120 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001121 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001122 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001123 1 0.3210 0.977 0.788 0.000 0 0.000 0.212
#> SRR2001116 1 0.3242 0.975 0.784 0.000 0 0.000 0.216
#> SRR2001117 1 0.3508 0.944 0.748 0.000 0 0.000 0.252
#> SRR2001118 1 0.3730 0.898 0.712 0.000 0 0.000 0.288
#> SRR2001119 1 0.3586 0.925 0.736 0.000 0 0.000 0.264
#> SRR2001112 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001113 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001114 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001115 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001108 4 0.3210 0.873 0.212 0.000 0 0.788 0.000
#> SRR2001109 4 0.3210 0.873 0.212 0.000 0 0.788 0.000
#> SRR2001110 4 0.3210 0.873 0.212 0.000 0 0.788 0.000
#> SRR2001111 4 0.3210 0.873 0.212 0.000 0 0.788 0.000
#> SRR2001104 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001105 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001106 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001107 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001100 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001101 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001102 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001103 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001096 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001097 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001098 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001099 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001092 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001093 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001094 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001095 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001088 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001089 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001090 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001091 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001084 4 0.3210 0.873 0.212 0.000 0 0.788 0.000
#> SRR2001085 4 0.3210 0.873 0.212 0.000 0 0.788 0.000
#> SRR2001086 4 0.3210 0.873 0.212 0.000 0 0.788 0.000
#> SRR2001087 4 0.3210 0.873 0.212 0.000 0 0.788 0.000
#> SRR2001080 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001081 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001082 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001083 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001076 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001077 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001078 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001079 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001072 4 0.0290 0.937 0.008 0.000 0 0.992 0.000
#> SRR2001073 4 0.0290 0.937 0.008 0.000 0 0.992 0.000
#> SRR2001074 4 0.0290 0.937 0.008 0.000 0 0.992 0.000
#> SRR2001075 4 0.0290 0.937 0.008 0.000 0 0.992 0.000
#> SRR2001068 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001069 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001070 2 0.0162 0.996 0.004 0.996 0 0.000 0.000
#> SRR2001071 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001064 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001065 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001066 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001067 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001060 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001061 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001062 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001063 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001056 4 0.3210 0.873 0.212 0.000 0 0.788 0.000
#> SRR2001057 4 0.3210 0.873 0.212 0.000 0 0.788 0.000
#> SRR2001058 4 0.3210 0.873 0.212 0.000 0 0.788 0.000
#> SRR2001059 4 0.3210 0.873 0.212 0.000 0 0.788 0.000
#> SRR2001052 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001053 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001054 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001055 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001048 2 0.0510 0.986 0.016 0.984 0 0.000 0.000
#> SRR2001049 2 0.0290 0.992 0.008 0.992 0 0.000 0.000
#> SRR2001050 2 0.0510 0.986 0.016 0.984 0 0.000 0.000
#> SRR2001051 2 0.0794 0.975 0.028 0.972 0 0.000 0.000
#> SRR2001044 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001045 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001046 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001047 4 0.0404 0.933 0.000 0.012 0 0.988 0.000
#> SRR2001040 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001041 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001042 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001043 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001036 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001037 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001038 4 0.0162 0.937 0.004 0.000 0 0.996 0.000
#> SRR2001039 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001028 4 0.0404 0.933 0.000 0.012 0 0.988 0.000
#> SRR2001029 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001030 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001031 4 0.0290 0.935 0.000 0.008 0 0.992 0.000
#> SRR2001024 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001025 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001026 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001027 4 0.0000 0.938 0.000 0.000 0 1.000 0.000
#> SRR2001020 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001021 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001022 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001023 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR2001016 4 0.3366 0.871 0.212 0.004 0 0.784 0.000
#> SRR2001017 4 0.3366 0.871 0.212 0.004 0 0.784 0.000
#> SRR2001018 4 0.3366 0.871 0.212 0.004 0 0.784 0.000
#> SRR2001019 4 0.3366 0.871 0.212 0.004 0 0.784 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 2 0.1444 0.9557 0.000 0.928 0.000 0.000 NA 0.000
#> SRR2001033 2 0.1444 0.9557 0.000 0.928 0.000 0.000 NA 0.000
#> SRR2001034 2 0.1444 0.9557 0.000 0.928 0.000 0.000 NA 0.000
#> SRR2001035 2 0.1444 0.9557 0.000 0.928 0.000 0.000 NA 0.000
#> SRR2001204 6 0.0000 0.9419 0.000 0.000 0.000 0.000 NA 1.000
#> SRR2001205 6 0.0000 0.9419 0.000 0.000 0.000 0.000 NA 1.000
#> SRR2001206 6 0.0000 0.9419 0.000 0.000 0.000 0.000 NA 1.000
#> SRR2001207 6 0.0000 0.9419 0.000 0.000 0.000 0.000 NA 1.000
#> SRR2001200 1 0.5201 0.6990 0.500 0.000 0.000 0.000 NA 0.092
#> SRR2001201 1 0.5201 0.6990 0.500 0.000 0.000 0.000 NA 0.092
#> SRR2001202 1 0.5201 0.6990 0.500 0.000 0.000 0.000 NA 0.092
#> SRR2001203 1 0.5201 0.6990 0.500 0.000 0.000 0.000 NA 0.092
#> SRR2001196 1 0.5201 0.6990 0.500 0.000 0.000 0.000 NA 0.092
#> SRR2001197 1 0.5201 0.6990 0.500 0.000 0.000 0.000 NA 0.092
#> SRR2001198 1 0.5201 0.6990 0.500 0.000 0.000 0.000 NA 0.092
#> SRR2001199 1 0.5201 0.6990 0.500 0.000 0.000 0.000 NA 0.092
#> SRR2001192 3 0.3175 0.8020 0.000 0.000 0.744 0.000 NA 0.000
#> SRR2001193 3 0.3371 0.7977 0.000 0.000 0.708 0.000 NA 0.000
#> SRR2001194 3 0.3499 0.7931 0.000 0.000 0.680 0.000 NA 0.000
#> SRR2001195 3 0.0260 0.8246 0.000 0.000 0.992 0.000 NA 0.000
#> SRR2001188 6 0.5934 -0.0655 0.328 0.000 0.000 0.000 NA 0.444
#> SRR2001189 6 0.3570 0.7560 0.064 0.000 0.000 0.000 NA 0.792
#> SRR2001190 6 0.1753 0.9064 0.004 0.000 0.000 0.000 NA 0.912
#> SRR2001191 6 0.0858 0.9353 0.004 0.000 0.000 0.000 NA 0.968
#> SRR2001184 3 0.0000 0.8248 0.000 0.000 1.000 0.000 NA 0.000
#> SRR2001185 3 0.0000 0.8248 0.000 0.000 1.000 0.000 NA 0.000
#> SRR2001186 3 0.0000 0.8248 0.000 0.000 1.000 0.000 NA 0.000
#> SRR2001187 3 0.0000 0.8248 0.000 0.000 1.000 0.000 NA 0.000
#> SRR2001180 6 0.2263 0.8839 0.016 0.000 0.000 0.000 NA 0.884
#> SRR2001181 6 0.1501 0.9156 0.000 0.000 0.000 0.000 NA 0.924
#> SRR2001182 6 0.1967 0.9008 0.012 0.000 0.000 0.000 NA 0.904
#> SRR2001183 6 0.1444 0.9153 0.000 0.000 0.000 0.000 NA 0.928
#> SRR2001176 3 0.0363 0.8244 0.000 0.000 0.988 0.000 NA 0.000
#> SRR2001177 3 0.0000 0.8248 0.000 0.000 1.000 0.000 NA 0.000
#> SRR2001178 3 0.0000 0.8248 0.000 0.000 1.000 0.000 NA 0.000
#> SRR2001179 3 0.0000 0.8248 0.000 0.000 1.000 0.000 NA 0.000
#> SRR2001172 3 0.0000 0.8248 0.000 0.000 1.000 0.000 NA 0.000
#> SRR2001173 3 0.0000 0.8248 0.000 0.000 1.000 0.000 NA 0.000
#> SRR2001174 3 0.0000 0.8248 0.000 0.000 1.000 0.000 NA 0.000
#> SRR2001175 3 0.0000 0.8248 0.000 0.000 1.000 0.000 NA 0.000
#> SRR2001168 6 0.0000 0.9419 0.000 0.000 0.000 0.000 NA 1.000
#> SRR2001169 6 0.0000 0.9419 0.000 0.000 0.000 0.000 NA 1.000
#> SRR2001170 6 0.0000 0.9419 0.000 0.000 0.000 0.000 NA 1.000
#> SRR2001171 6 0.0000 0.9419 0.000 0.000 0.000 0.000 NA 1.000
#> SRR2001164 1 0.5386 0.6794 0.496 0.000 0.000 0.000 NA 0.116
#> SRR2001165 1 0.5325 0.6872 0.500 0.000 0.000 0.000 NA 0.108
#> SRR2001166 1 0.5544 0.6497 0.500 0.000 0.000 0.000 NA 0.144
#> SRR2001167 1 0.5265 0.6938 0.500 0.000 0.000 0.000 NA 0.100
#> SRR2001160 1 0.5343 0.6871 0.484 0.000 0.000 0.000 NA 0.108
#> SRR2001161 1 0.5300 0.6906 0.496 0.000 0.000 0.000 NA 0.104
#> SRR2001162 1 0.6029 0.5095 0.396 0.000 0.000 0.000 NA 0.248
#> SRR2001163 6 0.4662 0.6060 0.140 0.000 0.000 0.000 NA 0.688
#> SRR2001156 1 0.5201 0.6990 0.500 0.000 0.000 0.000 NA 0.092
#> SRR2001157 1 0.5201 0.6990 0.500 0.000 0.000 0.000 NA 0.092
#> SRR2001158 1 0.5201 0.6990 0.500 0.000 0.000 0.000 NA 0.092
#> SRR2001159 1 0.5201 0.6990 0.500 0.000 0.000 0.000 NA 0.092
#> SRR2001152 6 0.0260 0.9412 0.000 0.000 0.000 0.000 NA 0.992
#> SRR2001153 6 0.0363 0.9403 0.000 0.000 0.000 0.000 NA 0.988
#> SRR2001154 6 0.0000 0.9419 0.000 0.000 0.000 0.000 NA 1.000
#> SRR2001155 6 0.0260 0.9412 0.000 0.000 0.000 0.000 NA 0.992
#> SRR2001148 3 0.0000 0.8248 0.000 0.000 1.000 0.000 NA 0.000
#> SRR2001149 3 0.0000 0.8248 0.000 0.000 1.000 0.000 NA 0.000
#> SRR2001150 3 0.0000 0.8248 0.000 0.000 1.000 0.000 NA 0.000
#> SRR2001151 3 0.0000 0.8248 0.000 0.000 1.000 0.000 NA 0.000
#> SRR2001144 6 0.0000 0.9419 0.000 0.000 0.000 0.000 NA 1.000
#> SRR2001145 6 0.0000 0.9419 0.000 0.000 0.000 0.000 NA 1.000
#> SRR2001146 6 0.0000 0.9419 0.000 0.000 0.000 0.000 NA 1.000
#> SRR2001147 6 0.0000 0.9419 0.000 0.000 0.000 0.000 NA 1.000
#> SRR2001140 6 0.1267 0.9209 0.000 0.000 0.000 0.000 NA 0.940
#> SRR2001142 6 0.0000 0.9419 0.000 0.000 0.000 0.000 NA 1.000
#> SRR2001143 6 0.0146 0.9416 0.000 0.000 0.000 0.000 NA 0.996
#> SRR2001136 3 0.3868 0.7597 0.000 0.000 0.508 0.000 NA 0.000
#> SRR2001137 3 0.3868 0.7597 0.000 0.000 0.508 0.000 NA 0.000
#> SRR2001138 3 0.3868 0.7597 0.000 0.000 0.508 0.000 NA 0.000
#> SRR2001139 3 0.3868 0.7597 0.000 0.000 0.508 0.000 NA 0.000
#> SRR2001132 3 0.3868 0.7597 0.000 0.000 0.508 0.000 NA 0.000
#> SRR2001133 3 0.3864 0.7625 0.000 0.000 0.520 0.000 NA 0.000
#> SRR2001134 3 0.3867 0.7607 0.000 0.000 0.512 0.000 NA 0.000
#> SRR2001135 3 0.3868 0.7597 0.000 0.000 0.508 0.000 NA 0.000
#> SRR2001128 6 0.1970 0.8980 0.008 0.000 0.000 0.000 NA 0.900
#> SRR2001129 6 0.0458 0.9397 0.000 0.000 0.000 0.000 NA 0.984
#> SRR2001130 6 0.1757 0.9084 0.008 0.000 0.000 0.000 NA 0.916
#> SRR2001131 6 0.0935 0.9339 0.004 0.000 0.000 0.000 NA 0.964
#> SRR2001124 1 0.5201 0.6990 0.500 0.000 0.000 0.000 NA 0.092
#> SRR2001125 1 0.5201 0.6990 0.500 0.000 0.000 0.000 NA 0.092
#> SRR2001126 1 0.5201 0.6990 0.500 0.000 0.000 0.000 NA 0.092
#> SRR2001127 1 0.5201 0.6990 0.500 0.000 0.000 0.000 NA 0.092
#> SRR2001120 6 0.0000 0.9419 0.000 0.000 0.000 0.000 NA 1.000
#> SRR2001121 6 0.0000 0.9419 0.000 0.000 0.000 0.000 NA 1.000
#> SRR2001122 6 0.0000 0.9419 0.000 0.000 0.000 0.000 NA 1.000
#> SRR2001123 6 0.0000 0.9419 0.000 0.000 0.000 0.000 NA 1.000
#> SRR2001116 6 0.0632 0.9385 0.000 0.000 0.000 0.000 NA 0.976
#> SRR2001117 6 0.2333 0.8843 0.024 0.000 0.000 0.000 NA 0.884
#> SRR2001118 6 0.1970 0.9003 0.060 0.000 0.000 0.000 NA 0.912
#> SRR2001119 6 0.1471 0.9121 0.004 0.000 0.000 0.000 NA 0.932
#> SRR2001112 3 0.3868 0.7597 0.000 0.000 0.508 0.000 NA 0.000
#> SRR2001113 3 0.3868 0.7597 0.000 0.000 0.508 0.000 NA 0.000
#> SRR2001114 3 0.3868 0.7597 0.000 0.000 0.508 0.000 NA 0.000
#> SRR2001115 3 0.3868 0.7597 0.000 0.000 0.508 0.000 NA 0.000
#> SRR2001108 1 0.3869 -0.5064 0.500 0.000 0.000 0.500 NA 0.000
#> SRR2001109 1 0.3869 -0.5064 0.500 0.000 0.000 0.500 NA 0.000
#> SRR2001110 4 0.3869 0.4768 0.500 0.000 0.000 0.500 NA 0.000
#> SRR2001111 1 0.3869 -0.5064 0.500 0.000 0.000 0.500 NA 0.000
#> SRR2001104 2 0.0000 0.9755 0.000 1.000 0.000 0.000 NA 0.000
#> SRR2001105 2 0.0000 0.9755 0.000 1.000 0.000 0.000 NA 0.000
#> SRR2001106 2 0.0000 0.9755 0.000 1.000 0.000 0.000 NA 0.000
#> SRR2001107 2 0.0000 0.9755 0.000 1.000 0.000 0.000 NA 0.000
#> SRR2001100 2 0.0000 0.9755 0.000 1.000 0.000 0.000 NA 0.000
#> SRR2001101 2 0.0000 0.9755 0.000 1.000 0.000 0.000 NA 0.000
#> SRR2001102 2 0.0000 0.9755 0.000 1.000 0.000 0.000 NA 0.000
#> SRR2001103 2 0.0000 0.9755 0.000 1.000 0.000 0.000 NA 0.000
#> SRR2001096 2 0.0458 0.9723 0.000 0.984 0.000 0.000 NA 0.000
#> SRR2001097 2 0.0458 0.9723 0.000 0.984 0.000 0.000 NA 0.000
#> SRR2001098 2 0.0458 0.9723 0.000 0.984 0.000 0.000 NA 0.000
#> SRR2001099 2 0.0458 0.9723 0.000 0.984 0.000 0.000 NA 0.000
#> SRR2001092 2 0.0260 0.9743 0.000 0.992 0.000 0.000 NA 0.000
#> SRR2001093 2 0.0146 0.9749 0.000 0.996 0.000 0.000 NA 0.000
#> SRR2001094 2 0.0458 0.9723 0.000 0.984 0.000 0.000 NA 0.000
#> SRR2001095 2 0.0458 0.9723 0.000 0.984 0.000 0.000 NA 0.000
#> SRR2001088 4 0.0363 0.8802 0.000 0.000 0.000 0.988 NA 0.000
#> SRR2001089 4 0.0000 0.8807 0.000 0.000 0.000 1.000 NA 0.000
#> SRR2001090 4 0.0260 0.8789 0.008 0.000 0.000 0.992 NA 0.000
#> SRR2001091 4 0.0146 0.8808 0.000 0.000 0.000 0.996 NA 0.000
#> SRR2001084 4 0.3869 0.4768 0.500 0.000 0.000 0.500 NA 0.000
#> SRR2001085 4 0.3869 0.4768 0.500 0.000 0.000 0.500 NA 0.000
#> SRR2001086 4 0.3869 0.4768 0.500 0.000 0.000 0.500 NA 0.000
#> SRR2001087 1 0.3869 -0.5064 0.500 0.000 0.000 0.500 NA 0.000
#> SRR2001080 2 0.0000 0.9755 0.000 1.000 0.000 0.000 NA 0.000
#> SRR2001081 2 0.0000 0.9755 0.000 1.000 0.000 0.000 NA 0.000
#> SRR2001082 2 0.0000 0.9755 0.000 1.000 0.000 0.000 NA 0.000
#> SRR2001083 2 0.0000 0.9755 0.000 1.000 0.000 0.000 NA 0.000
#> SRR2001076 2 0.0000 0.9755 0.000 1.000 0.000 0.000 NA 0.000
#> SRR2001077 2 0.0000 0.9755 0.000 1.000 0.000 0.000 NA 0.000
#> SRR2001078 2 0.0000 0.9755 0.000 1.000 0.000 0.000 NA 0.000
#> SRR2001079 2 0.0000 0.9755 0.000 1.000 0.000 0.000 NA 0.000
#> SRR2001072 4 0.1327 0.8505 0.064 0.000 0.000 0.936 NA 0.000
#> SRR2001073 4 0.0937 0.8640 0.040 0.000 0.000 0.960 NA 0.000
#> SRR2001074 4 0.2092 0.8121 0.124 0.000 0.000 0.876 NA 0.000
#> SRR2001075 4 0.2135 0.8093 0.128 0.000 0.000 0.872 NA 0.000
#> SRR2001068 2 0.1444 0.9557 0.000 0.928 0.000 0.000 NA 0.000
#> SRR2001069 2 0.1444 0.9557 0.000 0.928 0.000 0.000 NA 0.000
#> SRR2001070 2 0.1588 0.9540 0.004 0.924 0.000 0.000 NA 0.000
#> SRR2001071 2 0.1444 0.9557 0.000 0.928 0.000 0.000 NA 0.000
#> SRR2001064 2 0.0458 0.9723 0.000 0.984 0.000 0.000 NA 0.000
#> SRR2001065 2 0.0458 0.9723 0.000 0.984 0.000 0.000 NA 0.000
#> SRR2001066 2 0.0458 0.9723 0.000 0.984 0.000 0.000 NA 0.000
#> SRR2001067 2 0.0458 0.9723 0.000 0.984 0.000 0.000 NA 0.000
#> SRR2001060 4 0.0000 0.8807 0.000 0.000 0.000 1.000 NA 0.000
#> SRR2001061 4 0.0000 0.8807 0.000 0.000 0.000 1.000 NA 0.000
#> SRR2001062 4 0.0000 0.8807 0.000 0.000 0.000 1.000 NA 0.000
#> SRR2001063 4 0.0000 0.8807 0.000 0.000 0.000 1.000 NA 0.000
#> SRR2001056 4 0.3869 0.4768 0.500 0.000 0.000 0.500 NA 0.000
#> SRR2001057 4 0.3869 0.4768 0.500 0.000 0.000 0.500 NA 0.000
#> SRR2001058 1 0.3869 -0.5064 0.500 0.000 0.000 0.500 NA 0.000
#> SRR2001059 1 0.3869 -0.5064 0.500 0.000 0.000 0.500 NA 0.000
#> SRR2001052 2 0.1444 0.9557 0.000 0.928 0.000 0.000 NA 0.000
#> SRR2001053 2 0.1501 0.9556 0.000 0.924 0.000 0.000 NA 0.000
#> SRR2001054 2 0.1501 0.9553 0.000 0.924 0.000 0.000 NA 0.000
#> SRR2001055 2 0.1501 0.9556 0.000 0.924 0.000 0.000 NA 0.000
#> SRR2001048 2 0.1701 0.9521 0.008 0.920 0.000 0.000 NA 0.000
#> SRR2001049 2 0.1444 0.9557 0.000 0.928 0.000 0.000 NA 0.000
#> SRR2001050 2 0.1701 0.9519 0.008 0.920 0.000 0.000 NA 0.000
#> SRR2001051 2 0.1701 0.9520 0.008 0.920 0.000 0.000 NA 0.000
#> SRR2001044 4 0.0363 0.8802 0.000 0.000 0.000 0.988 NA 0.000
#> SRR2001045 4 0.0363 0.8802 0.000 0.000 0.000 0.988 NA 0.000
#> SRR2001046 4 0.0363 0.8802 0.000 0.000 0.000 0.988 NA 0.000
#> SRR2001047 4 0.0725 0.8746 0.000 0.012 0.000 0.976 NA 0.000
#> SRR2001040 4 0.0146 0.8808 0.000 0.000 0.000 0.996 NA 0.000
#> SRR2001041 4 0.0000 0.8807 0.000 0.000 0.000 1.000 NA 0.000
#> SRR2001042 4 0.0000 0.8807 0.000 0.000 0.000 1.000 NA 0.000
#> SRR2001043 4 0.0000 0.8807 0.000 0.000 0.000 1.000 NA 0.000
#> SRR2001036 4 0.0363 0.8802 0.000 0.000 0.000 0.988 NA 0.000
#> SRR2001037 4 0.0363 0.8802 0.000 0.000 0.000 0.988 NA 0.000
#> SRR2001038 4 0.0508 0.8798 0.004 0.000 0.000 0.984 NA 0.000
#> SRR2001039 4 0.0363 0.8802 0.000 0.000 0.000 0.988 NA 0.000
#> SRR2001028 4 0.0820 0.8715 0.000 0.016 0.000 0.972 NA 0.000
#> SRR2001029 4 0.0363 0.8802 0.000 0.000 0.000 0.988 NA 0.000
#> SRR2001030 4 0.0363 0.8802 0.000 0.000 0.000 0.988 NA 0.000
#> SRR2001031 4 0.0622 0.8768 0.000 0.008 0.000 0.980 NA 0.000
#> SRR2001024 4 0.0000 0.8807 0.000 0.000 0.000 1.000 NA 0.000
#> SRR2001025 4 0.0146 0.8808 0.000 0.000 0.000 0.996 NA 0.000
#> SRR2001026 4 0.0000 0.8807 0.000 0.000 0.000 1.000 NA 0.000
#> SRR2001027 4 0.0000 0.8807 0.000 0.000 0.000 1.000 NA 0.000
#> SRR2001020 2 0.0000 0.9755 0.000 1.000 0.000 0.000 NA 0.000
#> SRR2001021 2 0.0260 0.9743 0.000 0.992 0.000 0.000 NA 0.000
#> SRR2001022 2 0.0260 0.9743 0.000 0.992 0.000 0.000 NA 0.000
#> SRR2001023 2 0.0146 0.9750 0.000 0.996 0.000 0.000 NA 0.000
#> SRR2001016 1 0.3869 -0.5064 0.500 0.000 0.000 0.500 NA 0.000
#> SRR2001017 4 0.3869 0.4768 0.500 0.000 0.000 0.500 NA 0.000
#> SRR2001018 4 0.3869 0.4768 0.500 0.000 0.000 0.500 NA 0.000
#> SRR2001019 1 0.3869 -0.5064 0.500 0.000 0.000 0.500 NA 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.5031 0.497 0.497
#> 3 3 1.000 1.000 1.000 0.2206 0.889 0.777
#> 4 4 1.000 1.000 1.000 0.2051 0.874 0.674
#> 5 5 0.964 0.934 0.946 0.0456 0.968 0.878
#> 6 6 0.857 0.770 0.866 0.0536 0.941 0.745
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3 4
There is also optional best \(k\) = 2 3 4 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0 1 0 1 0
#> SRR2001033 2 0 1 0 1 0
#> SRR2001034 2 0 1 0 1 0
#> SRR2001035 2 0 1 0 1 0
#> SRR2001204 1 0 1 1 0 0
#> SRR2001205 1 0 1 1 0 0
#> SRR2001206 1 0 1 1 0 0
#> SRR2001207 1 0 1 1 0 0
#> SRR2001200 1 0 1 1 0 0
#> SRR2001201 1 0 1 1 0 0
#> SRR2001202 1 0 1 1 0 0
#> SRR2001203 1 0 1 1 0 0
#> SRR2001196 1 0 1 1 0 0
#> SRR2001197 1 0 1 1 0 0
#> SRR2001198 1 0 1 1 0 0
#> SRR2001199 1 0 1 1 0 0
#> SRR2001192 3 0 1 0 0 1
#> SRR2001193 3 0 1 0 0 1
#> SRR2001194 3 0 1 0 0 1
#> SRR2001195 3 0 1 0 0 1
#> SRR2001188 1 0 1 1 0 0
#> SRR2001189 1 0 1 1 0 0
#> SRR2001190 1 0 1 1 0 0
#> SRR2001191 1 0 1 1 0 0
#> SRR2001184 3 0 1 0 0 1
#> SRR2001185 3 0 1 0 0 1
#> SRR2001186 3 0 1 0 0 1
#> SRR2001187 3 0 1 0 0 1
#> SRR2001180 1 0 1 1 0 0
#> SRR2001181 1 0 1 1 0 0
#> SRR2001182 1 0 1 1 0 0
#> SRR2001183 1 0 1 1 0 0
#> SRR2001176 3 0 1 0 0 1
#> SRR2001177 3 0 1 0 0 1
#> SRR2001178 3 0 1 0 0 1
#> SRR2001179 3 0 1 0 0 1
#> SRR2001172 3 0 1 0 0 1
#> SRR2001173 3 0 1 0 0 1
#> SRR2001174 3 0 1 0 0 1
#> SRR2001175 3 0 1 0 0 1
#> SRR2001168 1 0 1 1 0 0
#> SRR2001169 1 0 1 1 0 0
#> SRR2001170 1 0 1 1 0 0
#> SRR2001171 1 0 1 1 0 0
#> SRR2001164 1 0 1 1 0 0
#> SRR2001165 1 0 1 1 0 0
#> SRR2001166 1 0 1 1 0 0
#> SRR2001167 1 0 1 1 0 0
#> SRR2001160 1 0 1 1 0 0
#> SRR2001161 1 0 1 1 0 0
#> SRR2001162 1 0 1 1 0 0
#> SRR2001163 1 0 1 1 0 0
#> SRR2001156 1 0 1 1 0 0
#> SRR2001157 1 0 1 1 0 0
#> SRR2001158 1 0 1 1 0 0
#> SRR2001159 1 0 1 1 0 0
#> SRR2001152 1 0 1 1 0 0
#> SRR2001153 1 0 1 1 0 0
#> SRR2001154 1 0 1 1 0 0
#> SRR2001155 1 0 1 1 0 0
#> SRR2001148 3 0 1 0 0 1
#> SRR2001149 3 0 1 0 0 1
#> SRR2001150 3 0 1 0 0 1
#> SRR2001151 3 0 1 0 0 1
#> SRR2001144 1 0 1 1 0 0
#> SRR2001145 1 0 1 1 0 0
#> SRR2001146 1 0 1 1 0 0
#> SRR2001147 1 0 1 1 0 0
#> SRR2001140 1 0 1 1 0 0
#> SRR2001142 1 0 1 1 0 0
#> SRR2001143 1 0 1 1 0 0
#> SRR2001136 3 0 1 0 0 1
#> SRR2001137 3 0 1 0 0 1
#> SRR2001138 3 0 1 0 0 1
#> SRR2001139 3 0 1 0 0 1
#> SRR2001132 3 0 1 0 0 1
#> SRR2001133 3 0 1 0 0 1
#> SRR2001134 3 0 1 0 0 1
#> SRR2001135 3 0 1 0 0 1
#> SRR2001128 1 0 1 1 0 0
#> SRR2001129 1 0 1 1 0 0
#> SRR2001130 1 0 1 1 0 0
#> SRR2001131 1 0 1 1 0 0
#> SRR2001124 1 0 1 1 0 0
#> SRR2001125 1 0 1 1 0 0
#> SRR2001126 1 0 1 1 0 0
#> SRR2001127 1 0 1 1 0 0
#> SRR2001120 1 0 1 1 0 0
#> SRR2001121 1 0 1 1 0 0
#> SRR2001122 1 0 1 1 0 0
#> SRR2001123 1 0 1 1 0 0
#> SRR2001116 1 0 1 1 0 0
#> SRR2001117 1 0 1 1 0 0
#> SRR2001118 1 0 1 1 0 0
#> SRR2001119 1 0 1 1 0 0
#> SRR2001112 3 0 1 0 0 1
#> SRR2001113 3 0 1 0 0 1
#> SRR2001114 3 0 1 0 0 1
#> SRR2001115 3 0 1 0 0 1
#> SRR2001108 2 0 1 0 1 0
#> SRR2001109 2 0 1 0 1 0
#> SRR2001110 2 0 1 0 1 0
#> SRR2001111 2 0 1 0 1 0
#> SRR2001104 2 0 1 0 1 0
#> SRR2001105 2 0 1 0 1 0
#> SRR2001106 2 0 1 0 1 0
#> SRR2001107 2 0 1 0 1 0
#> SRR2001100 2 0 1 0 1 0
#> SRR2001101 2 0 1 0 1 0
#> SRR2001102 2 0 1 0 1 0
#> SRR2001103 2 0 1 0 1 0
#> SRR2001096 2 0 1 0 1 0
#> SRR2001097 2 0 1 0 1 0
#> SRR2001098 2 0 1 0 1 0
#> SRR2001099 2 0 1 0 1 0
#> SRR2001092 2 0 1 0 1 0
#> SRR2001093 2 0 1 0 1 0
#> SRR2001094 2 0 1 0 1 0
#> SRR2001095 2 0 1 0 1 0
#> SRR2001088 2 0 1 0 1 0
#> SRR2001089 2 0 1 0 1 0
#> SRR2001090 2 0 1 0 1 0
#> SRR2001091 2 0 1 0 1 0
#> SRR2001084 2 0 1 0 1 0
#> SRR2001085 2 0 1 0 1 0
#> SRR2001086 2 0 1 0 1 0
#> SRR2001087 2 0 1 0 1 0
#> SRR2001080 2 0 1 0 1 0
#> SRR2001081 2 0 1 0 1 0
#> SRR2001082 2 0 1 0 1 0
#> SRR2001083 2 0 1 0 1 0
#> SRR2001076 2 0 1 0 1 0
#> SRR2001077 2 0 1 0 1 0
#> SRR2001078 2 0 1 0 1 0
#> SRR2001079 2 0 1 0 1 0
#> SRR2001072 2 0 1 0 1 0
#> SRR2001073 2 0 1 0 1 0
#> SRR2001074 2 0 1 0 1 0
#> SRR2001075 2 0 1 0 1 0
#> SRR2001068 2 0 1 0 1 0
#> SRR2001069 2 0 1 0 1 0
#> SRR2001070 2 0 1 0 1 0
#> SRR2001071 2 0 1 0 1 0
#> SRR2001064 2 0 1 0 1 0
#> SRR2001065 2 0 1 0 1 0
#> SRR2001066 2 0 1 0 1 0
#> SRR2001067 2 0 1 0 1 0
#> SRR2001060 2 0 1 0 1 0
#> SRR2001061 2 0 1 0 1 0
#> SRR2001062 2 0 1 0 1 0
#> SRR2001063 2 0 1 0 1 0
#> SRR2001056 2 0 1 0 1 0
#> SRR2001057 2 0 1 0 1 0
#> SRR2001058 2 0 1 0 1 0
#> SRR2001059 2 0 1 0 1 0
#> SRR2001052 2 0 1 0 1 0
#> SRR2001053 2 0 1 0 1 0
#> SRR2001054 2 0 1 0 1 0
#> SRR2001055 2 0 1 0 1 0
#> SRR2001048 2 0 1 0 1 0
#> SRR2001049 2 0 1 0 1 0
#> SRR2001050 2 0 1 0 1 0
#> SRR2001051 2 0 1 0 1 0
#> SRR2001044 2 0 1 0 1 0
#> SRR2001045 2 0 1 0 1 0
#> SRR2001046 2 0 1 0 1 0
#> SRR2001047 2 0 1 0 1 0
#> SRR2001040 2 0 1 0 1 0
#> SRR2001041 2 0 1 0 1 0
#> SRR2001042 2 0 1 0 1 0
#> SRR2001043 2 0 1 0 1 0
#> SRR2001036 2 0 1 0 1 0
#> SRR2001037 2 0 1 0 1 0
#> SRR2001038 2 0 1 0 1 0
#> SRR2001039 2 0 1 0 1 0
#> SRR2001028 2 0 1 0 1 0
#> SRR2001029 2 0 1 0 1 0
#> SRR2001030 2 0 1 0 1 0
#> SRR2001031 2 0 1 0 1 0
#> SRR2001024 2 0 1 0 1 0
#> SRR2001025 2 0 1 0 1 0
#> SRR2001026 2 0 1 0 1 0
#> SRR2001027 2 0 1 0 1 0
#> SRR2001020 2 0 1 0 1 0
#> SRR2001021 2 0 1 0 1 0
#> SRR2001022 2 0 1 0 1 0
#> SRR2001023 2 0 1 0 1 0
#> SRR2001016 2 0 1 0 1 0
#> SRR2001017 2 0 1 0 1 0
#> SRR2001018 2 0 1 0 1 0
#> SRR2001019 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001033 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001034 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001035 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001204 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001205 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001206 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001207 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001200 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001201 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001202 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001203 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001196 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001197 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001198 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001199 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001192 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001193 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001194 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001195 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001188 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001189 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001190 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001191 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001184 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001185 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001186 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001187 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001180 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001181 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001182 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001183 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001176 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001177 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001178 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001179 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001172 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001173 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001174 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001175 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001168 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001169 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001170 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001171 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001164 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001165 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001166 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001167 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001160 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001161 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001162 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001163 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001156 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001157 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001158 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001159 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001152 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001153 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001154 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001155 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001148 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001149 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001150 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001151 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001144 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001145 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001146 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001147 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001140 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001142 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001143 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001136 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001137 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001138 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001139 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001132 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001133 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001134 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001135 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001128 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001129 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001130 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001131 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001124 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001125 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001126 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001127 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001120 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001121 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001122 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001123 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001116 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001117 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001118 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001119 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001112 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001113 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001114 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001115 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001108 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001109 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001110 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001111 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001104 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001105 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001106 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001107 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001100 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001101 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001102 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001103 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001096 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001097 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001098 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001099 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001092 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001093 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001094 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001095 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001088 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001089 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001090 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001091 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001084 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001085 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001086 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001087 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001080 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001081 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001082 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001083 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001076 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001077 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001078 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001079 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001072 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001073 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001074 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001075 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001068 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001069 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001070 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001071 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001064 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001065 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001066 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001067 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001060 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001061 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001062 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001063 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001056 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001057 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001058 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001059 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001052 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001053 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001054 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001055 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001048 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001049 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001050 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001051 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001044 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001045 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001046 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001047 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001040 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001041 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001042 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001043 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001036 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001037 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001038 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001039 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001028 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001029 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001030 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001031 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001024 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001025 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001026 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001027 4 0.0000 1.000 0 0.000 0 1.000
#> SRR2001020 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001021 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001022 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001023 2 0.0000 0.999 0 1.000 0 0.000
#> SRR2001016 2 0.0336 0.992 0 0.992 0 0.008
#> SRR2001017 2 0.0336 0.992 0 0.992 0 0.008
#> SRR2001018 2 0.0336 0.992 0 0.992 0 0.008
#> SRR2001019 2 0.0336 0.992 0 0.992 0 0.008
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.000 0.805 0.000 1.000 0 0.000 0.000
#> SRR2001033 2 0.000 0.805 0.000 1.000 0 0.000 0.000
#> SRR2001034 2 0.000 0.805 0.000 1.000 0 0.000 0.000
#> SRR2001035 2 0.000 0.805 0.000 1.000 0 0.000 0.000
#> SRR2001204 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001205 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001206 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001207 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001200 1 0.196 0.933 0.904 0.000 0 0.000 0.096
#> SRR2001201 1 0.196 0.933 0.904 0.000 0 0.000 0.096
#> SRR2001202 1 0.196 0.933 0.904 0.000 0 0.000 0.096
#> SRR2001203 1 0.196 0.933 0.904 0.000 0 0.000 0.096
#> SRR2001196 1 0.196 0.933 0.904 0.000 0 0.000 0.096
#> SRR2001197 1 0.196 0.933 0.904 0.000 0 0.000 0.096
#> SRR2001198 1 0.196 0.933 0.904 0.000 0 0.000 0.096
#> SRR2001199 1 0.196 0.933 0.904 0.000 0 0.000 0.096
#> SRR2001192 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001193 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001194 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001195 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001188 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001189 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001190 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001191 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001184 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001185 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001186 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001187 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001180 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001181 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001182 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001183 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001176 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001177 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001178 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001179 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001172 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001173 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001174 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001175 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001168 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001169 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001170 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001171 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001164 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001165 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001166 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001167 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001160 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001161 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001162 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001163 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001156 1 0.196 0.933 0.904 0.000 0 0.000 0.096
#> SRR2001157 1 0.196 0.933 0.904 0.000 0 0.000 0.096
#> SRR2001158 1 0.196 0.933 0.904 0.000 0 0.000 0.096
#> SRR2001159 1 0.196 0.933 0.904 0.000 0 0.000 0.096
#> SRR2001152 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001153 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001154 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001155 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001148 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001149 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001150 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001151 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001144 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001145 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001146 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001147 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001140 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001142 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001143 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001136 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001137 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001138 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001139 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001132 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001133 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001134 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001135 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001128 1 0.051 0.971 0.984 0.000 0 0.000 0.016
#> SRR2001129 1 0.051 0.971 0.984 0.000 0 0.000 0.016
#> SRR2001130 1 0.051 0.971 0.984 0.000 0 0.000 0.016
#> SRR2001131 1 0.051 0.971 0.984 0.000 0 0.000 0.016
#> SRR2001124 1 0.196 0.933 0.904 0.000 0 0.000 0.096
#> SRR2001125 1 0.196 0.933 0.904 0.000 0 0.000 0.096
#> SRR2001126 1 0.196 0.933 0.904 0.000 0 0.000 0.096
#> SRR2001127 1 0.196 0.933 0.904 0.000 0 0.000 0.096
#> SRR2001120 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001121 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001122 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001123 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001116 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001117 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001118 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001119 1 0.000 0.977 1.000 0.000 0 0.000 0.000
#> SRR2001112 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001113 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001114 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001115 3 0.000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001108 4 0.141 0.952 0.000 0.060 0 0.940 0.000
#> SRR2001109 4 0.141 0.952 0.000 0.060 0 0.940 0.000
#> SRR2001110 4 0.141 0.952 0.000 0.060 0 0.940 0.000
#> SRR2001111 4 0.141 0.952 0.000 0.060 0 0.940 0.000
#> SRR2001104 2 0.364 0.767 0.000 0.728 0 0.000 0.272
#> SRR2001105 2 0.368 0.760 0.000 0.720 0 0.000 0.280
#> SRR2001106 2 0.353 0.779 0.000 0.744 0 0.000 0.256
#> SRR2001107 2 0.366 0.763 0.000 0.724 0 0.000 0.276
#> SRR2001100 2 0.281 0.838 0.000 0.832 0 0.000 0.168
#> SRR2001101 2 0.281 0.838 0.000 0.832 0 0.000 0.168
#> SRR2001102 2 0.281 0.838 0.000 0.832 0 0.000 0.168
#> SRR2001103 2 0.281 0.838 0.000 0.832 0 0.000 0.168
#> SRR2001096 5 0.238 0.919 0.000 0.128 0 0.000 0.872
#> SRR2001097 5 0.242 0.917 0.000 0.132 0 0.000 0.868
#> SRR2001098 5 0.238 0.919 0.000 0.128 0 0.000 0.872
#> SRR2001099 5 0.238 0.919 0.000 0.128 0 0.000 0.872
#> SRR2001092 5 0.196 0.914 0.000 0.096 0 0.000 0.904
#> SRR2001093 5 0.196 0.914 0.000 0.096 0 0.000 0.904
#> SRR2001094 5 0.196 0.914 0.000 0.096 0 0.000 0.904
#> SRR2001095 5 0.196 0.914 0.000 0.096 0 0.000 0.904
#> SRR2001088 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001089 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001090 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001091 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001084 4 0.141 0.952 0.000 0.060 0 0.940 0.000
#> SRR2001085 4 0.141 0.952 0.000 0.060 0 0.940 0.000
#> SRR2001086 4 0.141 0.952 0.000 0.060 0 0.940 0.000
#> SRR2001087 4 0.141 0.952 0.000 0.060 0 0.940 0.000
#> SRR2001080 2 0.300 0.830 0.000 0.812 0 0.000 0.188
#> SRR2001081 2 0.289 0.836 0.000 0.824 0 0.000 0.176
#> SRR2001082 2 0.289 0.836 0.000 0.824 0 0.000 0.176
#> SRR2001083 2 0.300 0.830 0.000 0.812 0 0.000 0.188
#> SRR2001076 2 0.337 0.807 0.000 0.768 0 0.000 0.232
#> SRR2001077 2 0.337 0.806 0.000 0.768 0 0.000 0.232
#> SRR2001078 2 0.342 0.802 0.000 0.760 0 0.000 0.240
#> SRR2001079 2 0.356 0.783 0.000 0.740 0 0.000 0.260
#> SRR2001072 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001073 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001074 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001075 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001068 2 0.273 0.663 0.000 0.840 0 0.000 0.160
#> SRR2001069 2 0.273 0.663 0.000 0.840 0 0.000 0.160
#> SRR2001070 2 0.273 0.663 0.000 0.840 0 0.000 0.160
#> SRR2001071 2 0.273 0.663 0.000 0.840 0 0.000 0.160
#> SRR2001064 5 0.265 0.899 0.000 0.152 0 0.000 0.848
#> SRR2001065 5 0.228 0.919 0.000 0.120 0 0.000 0.880
#> SRR2001066 5 0.256 0.908 0.000 0.144 0 0.000 0.856
#> SRR2001067 5 0.238 0.919 0.000 0.128 0 0.000 0.872
#> SRR2001060 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001061 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001062 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001063 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001056 4 0.141 0.952 0.000 0.060 0 0.940 0.000
#> SRR2001057 4 0.141 0.952 0.000 0.060 0 0.940 0.000
#> SRR2001058 4 0.141 0.952 0.000 0.060 0 0.940 0.000
#> SRR2001059 4 0.141 0.952 0.000 0.060 0 0.940 0.000
#> SRR2001052 5 0.359 0.810 0.000 0.264 0 0.000 0.736
#> SRR2001053 5 0.359 0.810 0.000 0.264 0 0.000 0.736
#> SRR2001054 5 0.359 0.810 0.000 0.264 0 0.000 0.736
#> SRR2001055 5 0.359 0.810 0.000 0.264 0 0.000 0.736
#> SRR2001048 2 0.000 0.805 0.000 1.000 0 0.000 0.000
#> SRR2001049 2 0.000 0.805 0.000 1.000 0 0.000 0.000
#> SRR2001050 2 0.029 0.804 0.000 0.992 0 0.000 0.008
#> SRR2001051 2 0.029 0.804 0.000 0.992 0 0.000 0.008
#> SRR2001044 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001045 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001046 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001047 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001040 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001041 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001042 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001043 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001036 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001037 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001038 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001039 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001028 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001029 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001030 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001031 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001024 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001025 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001026 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001027 4 0.000 0.982 0.000 0.000 0 1.000 0.000
#> SRR2001020 2 0.281 0.838 0.000 0.832 0 0.000 0.168
#> SRR2001021 2 0.281 0.838 0.000 0.832 0 0.000 0.168
#> SRR2001022 2 0.281 0.838 0.000 0.832 0 0.000 0.168
#> SRR2001023 2 0.281 0.838 0.000 0.832 0 0.000 0.168
#> SRR2001016 2 0.167 0.761 0.000 0.924 0 0.076 0.000
#> SRR2001017 2 0.167 0.761 0.000 0.924 0 0.076 0.000
#> SRR2001018 2 0.167 0.761 0.000 0.924 0 0.076 0.000
#> SRR2001019 2 0.167 0.761 0.000 0.924 0 0.076 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 2 0.4425 0.7466 0.152 0.716 0 0.000 0.132 0.000
#> SRR2001033 2 0.4425 0.7466 0.152 0.716 0 0.000 0.132 0.000
#> SRR2001034 2 0.4425 0.7466 0.152 0.716 0 0.000 0.132 0.000
#> SRR2001035 2 0.4425 0.7466 0.152 0.716 0 0.000 0.132 0.000
#> SRR2001204 6 0.0146 0.7131 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001205 6 0.0146 0.7131 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001206 6 0.0146 0.7131 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001207 6 0.0146 0.7131 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001200 1 0.3050 0.8306 0.764 0.000 0 0.000 0.000 0.236
#> SRR2001201 1 0.3050 0.8306 0.764 0.000 0 0.000 0.000 0.236
#> SRR2001202 1 0.3050 0.8306 0.764 0.000 0 0.000 0.000 0.236
#> SRR2001203 1 0.3050 0.8306 0.764 0.000 0 0.000 0.000 0.236
#> SRR2001196 1 0.3023 0.8298 0.768 0.000 0 0.000 0.000 0.232
#> SRR2001197 1 0.3023 0.8298 0.768 0.000 0 0.000 0.000 0.232
#> SRR2001198 1 0.3023 0.8298 0.768 0.000 0 0.000 0.000 0.232
#> SRR2001199 1 0.3023 0.8298 0.768 0.000 0 0.000 0.000 0.232
#> SRR2001192 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001193 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001194 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001195 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001188 6 0.2883 0.5441 0.212 0.000 0 0.000 0.000 0.788
#> SRR2001189 6 0.2562 0.5997 0.172 0.000 0 0.000 0.000 0.828
#> SRR2001190 6 0.2597 0.5944 0.176 0.000 0 0.000 0.000 0.824
#> SRR2001191 6 0.2631 0.5892 0.180 0.000 0 0.000 0.000 0.820
#> SRR2001184 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001185 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001186 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001187 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001180 6 0.3620 0.2718 0.352 0.000 0 0.000 0.000 0.648
#> SRR2001181 6 0.3563 0.3146 0.336 0.000 0 0.000 0.000 0.664
#> SRR2001182 6 0.3659 0.2311 0.364 0.000 0 0.000 0.000 0.636
#> SRR2001183 6 0.3737 0.1140 0.392 0.000 0 0.000 0.000 0.608
#> SRR2001176 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001177 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001178 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001179 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001172 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001173 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001174 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001175 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001168 6 0.0146 0.7131 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001169 6 0.0146 0.7131 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001170 6 0.0146 0.7131 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001171 6 0.0146 0.7131 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001164 6 0.3869 -0.4237 0.500 0.000 0 0.000 0.000 0.500
#> SRR2001165 1 0.3867 0.4134 0.512 0.000 0 0.000 0.000 0.488
#> SRR2001166 1 0.3868 0.3826 0.504 0.000 0 0.000 0.000 0.496
#> SRR2001167 1 0.3868 0.3901 0.504 0.000 0 0.000 0.000 0.496
#> SRR2001160 6 0.3620 0.2710 0.352 0.000 0 0.000 0.000 0.648
#> SRR2001161 6 0.3607 0.2833 0.348 0.000 0 0.000 0.000 0.652
#> SRR2001162 6 0.3659 0.2311 0.364 0.000 0 0.000 0.000 0.636
#> SRR2001163 6 0.3647 0.2451 0.360 0.000 0 0.000 0.000 0.640
#> SRR2001156 1 0.3330 0.8434 0.716 0.000 0 0.000 0.000 0.284
#> SRR2001157 1 0.3330 0.8434 0.716 0.000 0 0.000 0.000 0.284
#> SRR2001158 1 0.3330 0.8434 0.716 0.000 0 0.000 0.000 0.284
#> SRR2001159 1 0.3330 0.8434 0.716 0.000 0 0.000 0.000 0.284
#> SRR2001152 6 0.3659 0.2302 0.364 0.000 0 0.000 0.000 0.636
#> SRR2001153 6 0.3607 0.2828 0.348 0.000 0 0.000 0.000 0.652
#> SRR2001154 6 0.3578 0.3047 0.340 0.000 0 0.000 0.000 0.660
#> SRR2001155 6 0.3756 0.0745 0.400 0.000 0 0.000 0.000 0.600
#> SRR2001148 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001149 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001150 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001151 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001144 6 0.0260 0.7117 0.008 0.000 0 0.000 0.000 0.992
#> SRR2001145 6 0.0260 0.7117 0.008 0.000 0 0.000 0.000 0.992
#> SRR2001146 6 0.0260 0.7117 0.008 0.000 0 0.000 0.000 0.992
#> SRR2001147 6 0.0260 0.7117 0.008 0.000 0 0.000 0.000 0.992
#> SRR2001140 6 0.0363 0.7091 0.012 0.000 0 0.000 0.000 0.988
#> SRR2001142 6 0.0363 0.7091 0.012 0.000 0 0.000 0.000 0.988
#> SRR2001143 6 0.0363 0.7091 0.012 0.000 0 0.000 0.000 0.988
#> SRR2001136 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001137 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001138 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001139 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001132 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001133 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001134 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001135 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001128 1 0.3862 0.4510 0.524 0.000 0 0.000 0.000 0.476
#> SRR2001129 6 0.3857 -0.2973 0.468 0.000 0 0.000 0.000 0.532
#> SRR2001130 1 0.3860 0.4672 0.528 0.000 0 0.000 0.000 0.472
#> SRR2001131 6 0.3864 -0.3345 0.480 0.000 0 0.000 0.000 0.520
#> SRR2001124 1 0.3330 0.8434 0.716 0.000 0 0.000 0.000 0.284
#> SRR2001125 1 0.3330 0.8434 0.716 0.000 0 0.000 0.000 0.284
#> SRR2001126 1 0.3351 0.8409 0.712 0.000 0 0.000 0.000 0.288
#> SRR2001127 1 0.3330 0.8434 0.716 0.000 0 0.000 0.000 0.284
#> SRR2001120 6 0.0000 0.7120 0.000 0.000 0 0.000 0.000 1.000
#> SRR2001121 6 0.0146 0.7131 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001122 6 0.0146 0.7131 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001123 6 0.0146 0.7131 0.004 0.000 0 0.000 0.000 0.996
#> SRR2001116 6 0.1387 0.6921 0.068 0.000 0 0.000 0.000 0.932
#> SRR2001117 6 0.1501 0.6876 0.076 0.000 0 0.000 0.000 0.924
#> SRR2001118 6 0.1327 0.6940 0.064 0.000 0 0.000 0.000 0.936
#> SRR2001119 6 0.2854 0.5645 0.208 0.000 0 0.000 0.000 0.792
#> SRR2001112 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001113 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001114 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001115 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001108 4 0.3065 0.8577 0.152 0.000 0 0.820 0.028 0.000
#> SRR2001109 4 0.3065 0.8577 0.152 0.000 0 0.820 0.028 0.000
#> SRR2001110 4 0.3065 0.8577 0.152 0.000 0 0.820 0.028 0.000
#> SRR2001111 4 0.3065 0.8577 0.152 0.000 0 0.820 0.028 0.000
#> SRR2001104 2 0.1219 0.8118 0.004 0.948 0 0.000 0.048 0.000
#> SRR2001105 2 0.1411 0.8101 0.004 0.936 0 0.000 0.060 0.000
#> SRR2001106 2 0.1141 0.8107 0.000 0.948 0 0.000 0.052 0.000
#> SRR2001107 2 0.1411 0.8101 0.004 0.936 0 0.000 0.060 0.000
#> SRR2001100 2 0.0937 0.8313 0.040 0.960 0 0.000 0.000 0.000
#> SRR2001101 2 0.0937 0.8313 0.040 0.960 0 0.000 0.000 0.000
#> SRR2001102 2 0.0937 0.8313 0.040 0.960 0 0.000 0.000 0.000
#> SRR2001103 2 0.0937 0.8313 0.040 0.960 0 0.000 0.000 0.000
#> SRR2001096 5 0.2883 0.7927 0.000 0.212 0 0.000 0.788 0.000
#> SRR2001097 5 0.2883 0.7927 0.000 0.212 0 0.000 0.788 0.000
#> SRR2001098 5 0.2632 0.7986 0.004 0.164 0 0.000 0.832 0.000
#> SRR2001099 5 0.2883 0.7927 0.000 0.212 0 0.000 0.788 0.000
#> SRR2001092 5 0.2278 0.7982 0.004 0.128 0 0.000 0.868 0.000
#> SRR2001093 5 0.2278 0.7982 0.004 0.128 0 0.000 0.868 0.000
#> SRR2001094 5 0.2278 0.7982 0.004 0.128 0 0.000 0.868 0.000
#> SRR2001095 5 0.2278 0.7982 0.004 0.128 0 0.000 0.868 0.000
#> SRR2001088 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001089 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001090 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001091 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001084 4 0.3065 0.8577 0.152 0.000 0 0.820 0.028 0.000
#> SRR2001085 4 0.3065 0.8577 0.152 0.000 0 0.820 0.028 0.000
#> SRR2001086 4 0.3065 0.8577 0.152 0.000 0 0.820 0.028 0.000
#> SRR2001087 4 0.3065 0.8577 0.152 0.000 0 0.820 0.028 0.000
#> SRR2001080 2 0.0458 0.8270 0.000 0.984 0 0.000 0.016 0.000
#> SRR2001081 2 0.0260 0.8301 0.000 0.992 0 0.000 0.008 0.000
#> SRR2001082 2 0.0363 0.8288 0.000 0.988 0 0.000 0.012 0.000
#> SRR2001083 2 0.0363 0.8288 0.000 0.988 0 0.000 0.012 0.000
#> SRR2001076 2 0.1219 0.8130 0.004 0.948 0 0.000 0.048 0.000
#> SRR2001077 2 0.0865 0.8198 0.000 0.964 0 0.000 0.036 0.000
#> SRR2001078 2 0.1267 0.8022 0.000 0.940 0 0.000 0.060 0.000
#> SRR2001079 2 0.1663 0.7739 0.000 0.912 0 0.000 0.088 0.000
#> SRR2001072 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001073 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001074 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001075 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001068 5 0.5487 0.2143 0.148 0.320 0 0.000 0.532 0.000
#> SRR2001069 5 0.5504 0.2174 0.152 0.316 0 0.000 0.532 0.000
#> SRR2001070 5 0.5515 0.2110 0.152 0.320 0 0.000 0.528 0.000
#> SRR2001071 5 0.5531 0.2153 0.156 0.316 0 0.000 0.528 0.000
#> SRR2001064 5 0.2996 0.7861 0.000 0.228 0 0.000 0.772 0.000
#> SRR2001065 5 0.2912 0.7920 0.000 0.216 0 0.000 0.784 0.000
#> SRR2001066 5 0.2969 0.7887 0.000 0.224 0 0.000 0.776 0.000
#> SRR2001067 5 0.2969 0.7887 0.000 0.224 0 0.000 0.776 0.000
#> SRR2001060 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001061 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001062 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001063 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001056 4 0.3065 0.8577 0.152 0.000 0 0.820 0.028 0.000
#> SRR2001057 4 0.3065 0.8577 0.152 0.000 0 0.820 0.028 0.000
#> SRR2001058 4 0.3065 0.8577 0.152 0.000 0 0.820 0.028 0.000
#> SRR2001059 4 0.3065 0.8577 0.152 0.000 0 0.820 0.028 0.000
#> SRR2001052 5 0.1563 0.7474 0.012 0.056 0 0.000 0.932 0.000
#> SRR2001053 5 0.1563 0.7474 0.012 0.056 0 0.000 0.932 0.000
#> SRR2001054 5 0.1563 0.7474 0.012 0.056 0 0.000 0.932 0.000
#> SRR2001055 5 0.1563 0.7474 0.012 0.056 0 0.000 0.932 0.000
#> SRR2001048 2 0.4425 0.7466 0.152 0.716 0 0.000 0.132 0.000
#> SRR2001049 2 0.4425 0.7466 0.152 0.716 0 0.000 0.132 0.000
#> SRR2001050 2 0.4499 0.7424 0.152 0.708 0 0.000 0.140 0.000
#> SRR2001051 2 0.4535 0.7401 0.152 0.704 0 0.000 0.144 0.000
#> SRR2001044 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001045 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001046 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001047 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001040 4 0.0000 0.9490 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001041 4 0.0000 0.9490 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001042 4 0.0000 0.9490 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001043 4 0.0000 0.9490 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001036 4 0.0000 0.9490 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001037 4 0.0000 0.9490 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001038 4 0.0000 0.9490 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001039 4 0.0000 0.9490 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001028 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001029 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001030 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001031 4 0.0146 0.9494 0.004 0.000 0 0.996 0.000 0.000
#> SRR2001024 4 0.0000 0.9490 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001025 4 0.0000 0.9490 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001026 4 0.0000 0.9490 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001027 4 0.0000 0.9490 0.000 0.000 0 1.000 0.000 0.000
#> SRR2001020 2 0.0000 0.8319 0.000 1.000 0 0.000 0.000 0.000
#> SRR2001021 2 0.0000 0.8319 0.000 1.000 0 0.000 0.000 0.000
#> SRR2001022 2 0.0000 0.8319 0.000 1.000 0 0.000 0.000 0.000
#> SRR2001023 2 0.0000 0.8319 0.000 1.000 0 0.000 0.000 0.000
#> SRR2001016 2 0.4971 0.7231 0.200 0.684 0 0.024 0.092 0.000
#> SRR2001017 2 0.4971 0.7231 0.200 0.684 0 0.024 0.092 0.000
#> SRR2001018 2 0.4971 0.7231 0.200 0.684 0 0.024 0.092 0.000
#> SRR2001019 2 0.4971 0.7231 0.200 0.684 0 0.024 0.092 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", "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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 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 1.000 1.000 0.5031 0.497 0.497
#> 3 3 1.000 0.986 0.969 0.2173 0.889 0.777
#> 4 4 0.876 0.893 0.890 0.0830 1.000 1.000
#> 5 5 0.817 0.969 0.875 0.0425 0.873 0.671
#> 6 6 0.680 0.920 0.874 0.0452 1.000 1.000
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001033 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001034 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001035 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001204 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001205 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001206 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001207 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001200 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001201 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001202 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001203 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001196 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001197 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001198 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001199 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001192 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001193 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001194 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001195 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001188 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001189 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001190 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001191 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001184 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001185 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001186 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001187 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001180 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001181 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001182 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001183 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001176 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001177 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001178 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001179 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001172 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001173 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001174 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001175 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001168 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001169 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001170 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001171 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001164 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001165 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001166 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001167 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001160 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001161 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001162 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001163 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001156 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001157 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001158 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001159 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001152 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001153 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001154 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001155 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001148 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001149 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001150 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001151 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001144 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001145 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001146 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001147 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001140 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001142 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001143 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001136 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001137 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001138 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001139 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001132 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001133 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001134 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001135 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001128 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001129 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001130 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001131 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001124 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001125 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001126 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001127 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001120 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001121 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001122 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001123 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001116 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001117 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001118 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001119 1 0.000 1.000 1.000 0.000 0.000
#> SRR2001112 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001113 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001114 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001115 3 0.271 1.000 0.088 0.000 0.912
#> SRR2001108 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001109 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001110 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001111 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001104 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001105 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001106 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001107 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001100 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001101 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001102 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001103 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001096 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001097 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001098 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001099 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001092 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001093 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001094 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001095 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001088 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001089 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001090 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001091 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001084 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001085 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001086 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001087 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001080 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001081 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001082 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001083 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001076 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001077 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001078 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001079 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001072 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001073 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001074 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001075 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001068 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001069 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001070 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001071 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001064 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001065 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001066 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001067 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001060 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001061 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001062 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001063 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001056 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001057 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001058 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001059 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001052 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001053 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001054 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001055 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001048 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001049 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001050 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001051 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001044 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001045 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001046 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001047 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001040 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001041 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001042 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001043 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001036 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001037 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001038 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001039 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001028 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001029 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001030 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001031 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001024 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001025 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001026 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001027 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001020 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001021 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001022 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001023 2 0.000 0.971 0.000 1.000 0.000
#> SRR2001016 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001017 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001018 2 0.216 0.971 0.000 0.936 0.064
#> SRR2001019 2 0.216 0.971 0.000 0.936 0.064
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001033 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001034 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001035 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001204 1 0.0188 0.990 0.996 0.000 0.000 0.004
#> SRR2001205 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001206 1 0.0188 0.990 0.996 0.000 0.000 0.004
#> SRR2001207 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001200 1 0.1576 0.956 0.948 0.000 0.048 0.004
#> SRR2001201 1 0.1576 0.956 0.948 0.000 0.048 0.004
#> SRR2001202 1 0.1576 0.956 0.948 0.000 0.048 0.004
#> SRR2001203 1 0.1576 0.956 0.948 0.000 0.048 0.004
#> SRR2001196 1 0.1022 0.973 0.968 0.000 0.032 0.000
#> SRR2001197 1 0.1022 0.973 0.968 0.000 0.032 0.000
#> SRR2001198 1 0.1022 0.973 0.968 0.000 0.032 0.000
#> SRR2001199 1 0.1022 0.973 0.968 0.000 0.032 0.000
#> SRR2001192 3 0.0921 0.998 0.028 0.000 0.972 0.000
#> SRR2001193 3 0.0921 0.998 0.028 0.000 0.972 0.000
#> SRR2001194 3 0.0921 0.998 0.028 0.000 0.972 0.000
#> SRR2001195 3 0.0921 0.998 0.028 0.000 0.972 0.000
#> SRR2001188 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001189 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001190 1 0.0188 0.990 0.996 0.000 0.000 0.004
#> SRR2001191 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001184 3 0.1109 0.997 0.028 0.000 0.968 0.004
#> SRR2001185 3 0.1109 0.997 0.028 0.000 0.968 0.004
#> SRR2001186 3 0.1109 0.997 0.028 0.000 0.968 0.004
#> SRR2001187 3 0.1109 0.997 0.028 0.000 0.968 0.004
#> SRR2001180 1 0.0188 0.990 0.996 0.000 0.000 0.004
#> SRR2001181 1 0.0188 0.990 0.996 0.000 0.000 0.004
#> SRR2001182 1 0.0188 0.990 0.996 0.000 0.000 0.004
#> SRR2001183 1 0.0188 0.990 0.996 0.000 0.000 0.004
#> SRR2001176 3 0.1109 0.997 0.028 0.000 0.968 0.004
#> SRR2001177 3 0.0921 0.998 0.028 0.000 0.972 0.000
#> SRR2001178 3 0.1109 0.997 0.028 0.000 0.968 0.004
#> SRR2001179 3 0.1109 0.997 0.028 0.000 0.968 0.004
#> SRR2001172 3 0.1256 0.996 0.028 0.000 0.964 0.008
#> SRR2001173 3 0.1256 0.996 0.028 0.000 0.964 0.008
#> SRR2001174 3 0.1256 0.996 0.028 0.000 0.964 0.008
#> SRR2001175 3 0.1256 0.996 0.028 0.000 0.964 0.008
#> SRR2001168 1 0.0469 0.987 0.988 0.000 0.000 0.012
#> SRR2001169 1 0.0469 0.987 0.988 0.000 0.000 0.012
#> SRR2001170 1 0.0469 0.987 0.988 0.000 0.000 0.012
#> SRR2001171 1 0.0469 0.987 0.988 0.000 0.000 0.012
#> SRR2001164 1 0.0336 0.988 0.992 0.000 0.008 0.000
#> SRR2001165 1 0.0336 0.988 0.992 0.000 0.008 0.000
#> SRR2001166 1 0.0336 0.988 0.992 0.000 0.008 0.000
#> SRR2001167 1 0.0336 0.988 0.992 0.000 0.008 0.000
#> SRR2001160 1 0.0188 0.990 0.996 0.000 0.000 0.004
#> SRR2001161 1 0.0188 0.990 0.996 0.000 0.000 0.004
#> SRR2001162 1 0.0188 0.990 0.996 0.000 0.000 0.004
#> SRR2001163 1 0.0188 0.990 0.996 0.000 0.000 0.004
#> SRR2001156 1 0.0707 0.981 0.980 0.000 0.020 0.000
#> SRR2001157 1 0.0707 0.981 0.980 0.000 0.020 0.000
#> SRR2001158 1 0.0707 0.981 0.980 0.000 0.020 0.000
#> SRR2001159 1 0.0707 0.981 0.980 0.000 0.020 0.000
#> SRR2001152 1 0.0188 0.990 0.996 0.000 0.000 0.004
#> SRR2001153 1 0.0188 0.990 0.996 0.000 0.000 0.004
#> SRR2001154 1 0.0188 0.990 0.996 0.000 0.000 0.004
#> SRR2001155 1 0.0188 0.990 0.996 0.000 0.000 0.004
#> SRR2001148 3 0.0921 0.998 0.028 0.000 0.972 0.000
#> SRR2001149 3 0.1109 0.997 0.028 0.000 0.968 0.004
#> SRR2001150 3 0.1109 0.997 0.028 0.000 0.968 0.004
#> SRR2001151 3 0.0921 0.998 0.028 0.000 0.972 0.000
#> SRR2001144 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001145 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001146 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001147 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001140 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001142 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001143 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001136 3 0.1109 0.997 0.028 0.000 0.968 0.004
#> SRR2001137 3 0.1109 0.997 0.028 0.000 0.968 0.004
#> SRR2001138 3 0.1109 0.997 0.028 0.000 0.968 0.004
#> SRR2001139 3 0.1109 0.997 0.028 0.000 0.968 0.004
#> SRR2001132 3 0.0921 0.998 0.028 0.000 0.972 0.000
#> SRR2001133 3 0.0921 0.998 0.028 0.000 0.972 0.000
#> SRR2001134 3 0.1109 0.997 0.028 0.000 0.968 0.004
#> SRR2001135 3 0.1109 0.997 0.028 0.000 0.968 0.004
#> SRR2001128 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001129 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001130 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001131 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001124 1 0.0469 0.986 0.988 0.000 0.012 0.000
#> SRR2001125 1 0.0469 0.986 0.988 0.000 0.012 0.000
#> SRR2001126 1 0.0469 0.986 0.988 0.000 0.012 0.000
#> SRR2001127 1 0.0469 0.986 0.988 0.000 0.012 0.000
#> SRR2001120 1 0.0336 0.989 0.992 0.000 0.000 0.008
#> SRR2001121 1 0.0336 0.989 0.992 0.000 0.000 0.008
#> SRR2001122 1 0.0336 0.989 0.992 0.000 0.000 0.008
#> SRR2001123 1 0.0188 0.990 0.996 0.000 0.000 0.004
#> SRR2001116 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001117 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001118 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001119 1 0.0000 0.990 1.000 0.000 0.000 0.000
#> SRR2001112 3 0.1256 0.996 0.028 0.000 0.964 0.008
#> SRR2001113 3 0.1256 0.996 0.028 0.000 0.964 0.008
#> SRR2001114 3 0.1256 0.996 0.028 0.000 0.964 0.008
#> SRR2001115 3 0.1256 0.996 0.028 0.000 0.964 0.008
#> SRR2001108 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001109 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001110 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001111 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001104 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001105 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001106 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001107 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001100 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001101 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001102 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001103 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001096 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001097 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001098 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001099 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001092 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001093 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001094 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001095 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001088 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001089 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001090 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001091 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001084 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001085 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001086 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001087 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001080 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001081 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001082 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001083 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001076 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001077 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001078 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001079 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001072 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001073 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001074 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001075 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001068 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001069 2 0.4855 0.797 0.000 0.600 0.000 0.400
#> SRR2001070 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001071 2 0.4855 0.797 0.000 0.600 0.000 0.400
#> SRR2001064 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001065 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001066 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001067 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001060 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001061 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001062 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001063 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001056 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001057 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001058 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001059 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001052 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001053 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001054 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001055 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001048 2 0.4855 0.797 0.000 0.600 0.000 0.400
#> SRR2001049 2 0.4855 0.797 0.000 0.600 0.000 0.400
#> SRR2001050 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001051 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001044 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001045 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001046 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001047 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001040 2 0.0188 0.794 0.000 0.996 0.000 0.004
#> SRR2001041 2 0.0188 0.794 0.000 0.996 0.000 0.004
#> SRR2001042 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001043 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001036 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001037 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001038 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001039 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001028 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001029 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001030 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001031 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001024 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001025 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001026 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001027 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001020 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001021 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001022 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001023 2 0.4866 0.797 0.000 0.596 0.000 0.404
#> SRR2001016 2 0.0188 0.797 0.000 0.996 0.000 0.004
#> SRR2001017 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001018 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR2001019 2 0.0188 0.797 0.000 0.996 0.000 0.004
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.0703 0.966 0.000 0.976 0.000 0.024 NA
#> SRR2001033 2 0.0880 0.959 0.000 0.968 0.000 0.032 NA
#> SRR2001034 2 0.0703 0.966 0.000 0.976 0.000 0.024 NA
#> SRR2001035 2 0.0703 0.966 0.000 0.976 0.000 0.024 NA
#> SRR2001204 1 0.0960 0.963 0.972 0.000 0.008 0.004 NA
#> SRR2001205 1 0.1179 0.964 0.964 0.000 0.016 0.004 NA
#> SRR2001206 1 0.1074 0.965 0.968 0.000 0.012 0.004 NA
#> SRR2001207 1 0.0912 0.966 0.972 0.000 0.012 0.000 NA
#> SRR2001200 1 0.2378 0.936 0.904 0.000 0.048 0.000 NA
#> SRR2001201 1 0.2228 0.942 0.912 0.000 0.040 0.000 NA
#> SRR2001202 1 0.2228 0.942 0.912 0.000 0.040 0.000 NA
#> SRR2001203 1 0.2304 0.939 0.908 0.000 0.044 0.000 NA
#> SRR2001196 1 0.1741 0.954 0.936 0.000 0.040 0.000 NA
#> SRR2001197 1 0.1741 0.954 0.936 0.000 0.040 0.000 NA
#> SRR2001198 1 0.1830 0.952 0.932 0.000 0.040 0.000 NA
#> SRR2001199 1 0.1915 0.950 0.928 0.000 0.040 0.000 NA
#> SRR2001192 3 0.1608 0.977 0.072 0.000 0.928 0.000 NA
#> SRR2001193 3 0.1608 0.977 0.072 0.000 0.928 0.000 NA
#> SRR2001194 3 0.1608 0.977 0.072 0.000 0.928 0.000 NA
#> SRR2001195 3 0.1608 0.977 0.072 0.000 0.928 0.000 NA
#> SRR2001188 1 0.0693 0.968 0.980 0.000 0.008 0.000 NA
#> SRR2001189 1 0.0451 0.968 0.988 0.000 0.004 0.000 NA
#> SRR2001190 1 0.0451 0.968 0.988 0.000 0.004 0.000 NA
#> SRR2001191 1 0.0693 0.968 0.980 0.000 0.008 0.000 NA
#> SRR2001184 3 0.2136 0.975 0.088 0.000 0.904 0.000 NA
#> SRR2001185 3 0.2248 0.974 0.088 0.000 0.900 0.000 NA
#> SRR2001186 3 0.2305 0.972 0.092 0.000 0.896 0.000 NA
#> SRR2001187 3 0.2136 0.975 0.088 0.000 0.904 0.000 NA
#> SRR2001180 1 0.0451 0.968 0.988 0.000 0.004 0.000 NA
#> SRR2001181 1 0.0162 0.969 0.996 0.000 0.004 0.000 NA
#> SRR2001182 1 0.0290 0.967 0.992 0.000 0.000 0.000 NA
#> SRR2001183 1 0.0000 0.968 1.000 0.000 0.000 0.000 NA
#> SRR2001176 3 0.1831 0.978 0.076 0.000 0.920 0.004 NA
#> SRR2001177 3 0.1892 0.977 0.080 0.000 0.916 0.004 NA
#> SRR2001178 3 0.1831 0.978 0.076 0.000 0.920 0.004 NA
#> SRR2001179 3 0.1892 0.977 0.080 0.000 0.916 0.004 NA
#> SRR2001172 3 0.2505 0.970 0.092 0.000 0.888 0.000 NA
#> SRR2001173 3 0.2408 0.971 0.092 0.000 0.892 0.000 NA
#> SRR2001174 3 0.2720 0.966 0.096 0.000 0.880 0.004 NA
#> SRR2001175 3 0.2505 0.970 0.092 0.000 0.888 0.000 NA
#> SRR2001168 1 0.2437 0.926 0.904 0.000 0.060 0.004 NA
#> SRR2001169 1 0.2632 0.913 0.892 0.000 0.072 0.004 NA
#> SRR2001170 1 0.2437 0.922 0.904 0.000 0.060 0.004 NA
#> SRR2001171 1 0.2437 0.923 0.904 0.000 0.060 0.004 NA
#> SRR2001164 1 0.1211 0.965 0.960 0.000 0.016 0.000 NA
#> SRR2001165 1 0.1106 0.966 0.964 0.000 0.012 0.000 NA
#> SRR2001166 1 0.1117 0.966 0.964 0.000 0.016 0.000 NA
#> SRR2001167 1 0.1211 0.965 0.960 0.000 0.016 0.000 NA
#> SRR2001160 1 0.0162 0.968 0.996 0.000 0.000 0.000 NA
#> SRR2001161 1 0.0451 0.969 0.988 0.000 0.004 0.000 NA
#> SRR2001162 1 0.0162 0.968 0.996 0.000 0.000 0.000 NA
#> SRR2001163 1 0.0162 0.968 0.996 0.000 0.000 0.000 NA
#> SRR2001156 1 0.1579 0.960 0.944 0.000 0.024 0.000 NA
#> SRR2001157 1 0.1668 0.957 0.940 0.000 0.032 0.000 NA
#> SRR2001158 1 0.1668 0.958 0.940 0.000 0.028 0.000 NA
#> SRR2001159 1 0.1668 0.958 0.940 0.000 0.028 0.000 NA
#> SRR2001152 1 0.0290 0.967 0.992 0.000 0.000 0.000 NA
#> SRR2001153 1 0.0290 0.967 0.992 0.000 0.000 0.000 NA
#> SRR2001154 1 0.0404 0.967 0.988 0.000 0.000 0.000 NA
#> SRR2001155 1 0.0290 0.967 0.992 0.000 0.000 0.000 NA
#> SRR2001148 3 0.2361 0.971 0.096 0.000 0.892 0.000 NA
#> SRR2001149 3 0.2361 0.971 0.096 0.000 0.892 0.000 NA
#> SRR2001150 3 0.2361 0.971 0.096 0.000 0.892 0.000 NA
#> SRR2001151 3 0.2361 0.971 0.096 0.000 0.892 0.000 NA
#> SRR2001144 1 0.1646 0.958 0.944 0.000 0.032 0.004 NA
#> SRR2001145 1 0.1377 0.961 0.956 0.000 0.020 0.004 NA
#> SRR2001146 1 0.1560 0.957 0.948 0.000 0.028 0.004 NA
#> SRR2001147 1 0.1471 0.959 0.952 0.000 0.024 0.004 NA
#> SRR2001140 1 0.0290 0.967 0.992 0.000 0.000 0.000 NA
#> SRR2001142 1 0.0566 0.966 0.984 0.000 0.004 0.000 NA
#> SRR2001143 1 0.0404 0.966 0.988 0.000 0.000 0.000 NA
#> SRR2001136 3 0.2046 0.974 0.068 0.000 0.916 0.000 NA
#> SRR2001137 3 0.2110 0.975 0.072 0.000 0.912 0.000 NA
#> SRR2001138 3 0.2110 0.975 0.072 0.000 0.912 0.000 NA
#> SRR2001139 3 0.2110 0.975 0.072 0.000 0.912 0.000 NA
#> SRR2001132 3 0.1990 0.975 0.068 0.000 0.920 0.004 NA
#> SRR2001133 3 0.1990 0.975 0.068 0.000 0.920 0.004 NA
#> SRR2001134 3 0.1983 0.969 0.060 0.000 0.924 0.008 NA
#> SRR2001135 3 0.2050 0.972 0.064 0.000 0.920 0.008 NA
#> SRR2001128 1 0.0671 0.969 0.980 0.000 0.016 0.000 NA
#> SRR2001129 1 0.0566 0.969 0.984 0.000 0.012 0.000 NA
#> SRR2001130 1 0.0671 0.969 0.980 0.000 0.016 0.000 NA
#> SRR2001131 1 0.0566 0.969 0.984 0.000 0.012 0.000 NA
#> SRR2001124 1 0.1403 0.963 0.952 0.000 0.024 0.000 NA
#> SRR2001125 1 0.1106 0.966 0.964 0.000 0.024 0.000 NA
#> SRR2001126 1 0.1106 0.966 0.964 0.000 0.024 0.000 NA
#> SRR2001127 1 0.1012 0.967 0.968 0.000 0.020 0.000 NA
#> SRR2001120 1 0.1743 0.951 0.940 0.000 0.028 0.004 NA
#> SRR2001121 1 0.1990 0.943 0.928 0.000 0.040 0.004 NA
#> SRR2001122 1 0.1996 0.945 0.928 0.000 0.032 0.004 NA
#> SRR2001123 1 0.1990 0.946 0.928 0.000 0.040 0.004 NA
#> SRR2001116 1 0.0404 0.969 0.988 0.000 0.012 0.000 NA
#> SRR2001117 1 0.0566 0.969 0.984 0.000 0.012 0.000 NA
#> SRR2001118 1 0.0290 0.969 0.992 0.000 0.008 0.000 NA
#> SRR2001119 1 0.0451 0.969 0.988 0.000 0.008 0.000 NA
#> SRR2001112 3 0.2797 0.953 0.060 0.000 0.880 0.000 NA
#> SRR2001113 3 0.2927 0.949 0.060 0.000 0.872 0.000 NA
#> SRR2001114 3 0.2797 0.953 0.060 0.000 0.880 0.000 NA
#> SRR2001115 3 0.2797 0.953 0.060 0.000 0.880 0.000 NA
#> SRR2001108 4 0.4088 0.988 0.000 0.368 0.000 0.632 NA
#> SRR2001109 4 0.4074 0.988 0.000 0.364 0.000 0.636 NA
#> SRR2001110 4 0.4101 0.988 0.000 0.372 0.000 0.628 NA
#> SRR2001111 4 0.4088 0.988 0.000 0.368 0.000 0.632 NA
#> SRR2001104 2 0.0000 0.973 0.000 1.000 0.000 0.000 NA
#> SRR2001105 2 0.0162 0.974 0.000 0.996 0.000 0.004 NA
#> SRR2001106 2 0.0000 0.973 0.000 1.000 0.000 0.000 NA
#> SRR2001107 2 0.0000 0.973 0.000 1.000 0.000 0.000 NA
#> SRR2001100 2 0.0510 0.971 0.000 0.984 0.000 0.016 NA
#> SRR2001101 2 0.0510 0.971 0.000 0.984 0.000 0.016 NA
#> SRR2001102 2 0.0404 0.973 0.000 0.988 0.000 0.012 NA
#> SRR2001103 2 0.0404 0.973 0.000 0.988 0.000 0.012 NA
#> SRR2001096 2 0.0510 0.964 0.000 0.984 0.000 0.016 NA
#> SRR2001097 2 0.0510 0.964 0.000 0.984 0.000 0.016 NA
#> SRR2001098 2 0.0510 0.964 0.000 0.984 0.000 0.016 NA
#> SRR2001099 2 0.0510 0.964 0.000 0.984 0.000 0.016 NA
#> SRR2001092 2 0.0510 0.964 0.000 0.984 0.000 0.016 NA
#> SRR2001093 2 0.0510 0.964 0.000 0.984 0.000 0.016 NA
#> SRR2001094 2 0.0510 0.964 0.000 0.984 0.000 0.016 NA
#> SRR2001095 2 0.0510 0.964 0.000 0.984 0.000 0.016 NA
#> SRR2001088 4 0.4088 0.990 0.000 0.368 0.000 0.632 NA
#> SRR2001089 4 0.4088 0.990 0.000 0.368 0.000 0.632 NA
#> SRR2001090 4 0.4088 0.990 0.000 0.368 0.000 0.632 NA
#> SRR2001091 4 0.4088 0.990 0.000 0.368 0.000 0.632 NA
#> SRR2001084 4 0.4074 0.988 0.000 0.364 0.000 0.636 NA
#> SRR2001085 4 0.4074 0.988 0.000 0.364 0.000 0.636 NA
#> SRR2001086 4 0.4088 0.990 0.000 0.368 0.000 0.632 NA
#> SRR2001087 4 0.4088 0.990 0.000 0.368 0.000 0.632 NA
#> SRR2001080 2 0.0290 0.974 0.000 0.992 0.000 0.008 NA
#> SRR2001081 2 0.0404 0.973 0.000 0.988 0.000 0.012 NA
#> SRR2001082 2 0.0290 0.974 0.000 0.992 0.000 0.008 NA
#> SRR2001083 2 0.0290 0.974 0.000 0.992 0.000 0.008 NA
#> SRR2001076 2 0.0162 0.974 0.000 0.996 0.000 0.004 NA
#> SRR2001077 2 0.0162 0.974 0.000 0.996 0.000 0.004 NA
#> SRR2001078 2 0.0162 0.974 0.000 0.996 0.000 0.004 NA
#> SRR2001079 2 0.0162 0.974 0.000 0.996 0.000 0.004 NA
#> SRR2001072 4 0.4276 0.976 0.000 0.380 0.000 0.616 NA
#> SRR2001073 4 0.4251 0.985 0.000 0.372 0.000 0.624 NA
#> SRR2001074 4 0.4392 0.972 0.000 0.380 0.000 0.612 NA
#> SRR2001075 4 0.4367 0.982 0.000 0.372 0.000 0.620 NA
#> SRR2001068 2 0.0880 0.958 0.000 0.968 0.000 0.032 NA
#> SRR2001069 2 0.1121 0.944 0.000 0.956 0.000 0.044 NA
#> SRR2001070 2 0.0963 0.954 0.000 0.964 0.000 0.036 NA
#> SRR2001071 2 0.1043 0.949 0.000 0.960 0.000 0.040 NA
#> SRR2001064 2 0.0798 0.961 0.000 0.976 0.000 0.016 NA
#> SRR2001065 2 0.0693 0.965 0.000 0.980 0.000 0.012 NA
#> SRR2001066 2 0.0798 0.961 0.000 0.976 0.000 0.016 NA
#> SRR2001067 2 0.0798 0.961 0.000 0.976 0.000 0.016 NA
#> SRR2001060 4 0.4088 0.990 0.000 0.368 0.000 0.632 NA
#> SRR2001061 4 0.4088 0.990 0.000 0.368 0.000 0.632 NA
#> SRR2001062 4 0.4088 0.990 0.000 0.368 0.000 0.632 NA
#> SRR2001063 4 0.4101 0.987 0.000 0.372 0.000 0.628 NA
#> SRR2001056 4 0.4074 0.988 0.000 0.364 0.000 0.636 NA
#> SRR2001057 4 0.4101 0.988 0.000 0.372 0.000 0.628 NA
#> SRR2001058 4 0.4088 0.990 0.000 0.368 0.000 0.632 NA
#> SRR2001059 4 0.4088 0.990 0.000 0.368 0.000 0.632 NA
#> SRR2001052 2 0.0290 0.969 0.000 0.992 0.000 0.008 NA
#> SRR2001053 2 0.0290 0.973 0.000 0.992 0.000 0.008 NA
#> SRR2001054 2 0.0404 0.967 0.000 0.988 0.000 0.012 NA
#> SRR2001055 2 0.0290 0.969 0.000 0.992 0.000 0.008 NA
#> SRR2001048 2 0.1197 0.938 0.000 0.952 0.000 0.048 NA
#> SRR2001049 2 0.1121 0.944 0.000 0.956 0.000 0.044 NA
#> SRR2001050 2 0.1043 0.949 0.000 0.960 0.000 0.040 NA
#> SRR2001051 2 0.1043 0.949 0.000 0.960 0.000 0.040 NA
#> SRR2001044 4 0.4101 0.988 0.000 0.372 0.000 0.628 NA
#> SRR2001045 4 0.4101 0.988 0.000 0.372 0.000 0.628 NA
#> SRR2001046 4 0.4101 0.988 0.000 0.372 0.000 0.628 NA
#> SRR2001047 4 0.4101 0.988 0.000 0.372 0.000 0.628 NA
#> SRR2001040 4 0.4060 0.984 0.000 0.360 0.000 0.640 NA
#> SRR2001041 4 0.4060 0.984 0.000 0.360 0.000 0.640 NA
#> SRR2001042 4 0.4060 0.984 0.000 0.360 0.000 0.640 NA
#> SRR2001043 4 0.4060 0.984 0.000 0.360 0.000 0.640 NA
#> SRR2001036 4 0.4060 0.984 0.000 0.360 0.000 0.640 NA
#> SRR2001037 4 0.4060 0.984 0.000 0.360 0.000 0.640 NA
#> SRR2001038 4 0.4060 0.984 0.000 0.360 0.000 0.640 NA
#> SRR2001039 4 0.4060 0.984 0.000 0.360 0.000 0.640 NA
#> SRR2001028 4 0.4101 0.988 0.000 0.372 0.000 0.628 NA
#> SRR2001029 4 0.4101 0.988 0.000 0.372 0.000 0.628 NA
#> SRR2001030 4 0.4101 0.988 0.000 0.372 0.000 0.628 NA
#> SRR2001031 4 0.4101 0.988 0.000 0.372 0.000 0.628 NA
#> SRR2001024 4 0.4088 0.990 0.000 0.368 0.000 0.632 NA
#> SRR2001025 4 0.4088 0.990 0.000 0.368 0.000 0.632 NA
#> SRR2001026 4 0.4088 0.990 0.000 0.368 0.000 0.632 NA
#> SRR2001027 4 0.4088 0.990 0.000 0.368 0.000 0.632 NA
#> SRR2001020 2 0.0671 0.971 0.000 0.980 0.000 0.016 NA
#> SRR2001021 2 0.0798 0.970 0.000 0.976 0.000 0.016 NA
#> SRR2001022 2 0.0798 0.970 0.000 0.976 0.000 0.016 NA
#> SRR2001023 2 0.0771 0.968 0.000 0.976 0.000 0.020 NA
#> SRR2001016 4 0.4192 0.944 0.000 0.404 0.000 0.596 NA
#> SRR2001017 4 0.4171 0.956 0.000 0.396 0.000 0.604 NA
#> SRR2001018 4 0.4161 0.962 0.000 0.392 0.000 0.608 NA
#> SRR2001019 4 0.4201 0.937 0.000 0.408 0.000 0.592 NA
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 2 0.2617 0.918 0.000 0.876 0.000 0.080 NA NA
#> SRR2001033 2 0.2702 0.914 0.000 0.868 0.000 0.092 NA NA
#> SRR2001034 2 0.2600 0.918 0.000 0.876 0.000 0.084 NA NA
#> SRR2001035 2 0.2600 0.918 0.000 0.876 0.000 0.084 NA NA
#> SRR2001204 1 0.2448 0.899 0.884 0.000 0.064 0.000 NA NA
#> SRR2001205 1 0.2448 0.899 0.884 0.000 0.064 0.000 NA NA
#> SRR2001206 1 0.2389 0.900 0.888 0.000 0.060 0.000 NA NA
#> SRR2001207 1 0.2325 0.901 0.892 0.000 0.060 0.000 NA NA
#> SRR2001200 1 0.3408 0.859 0.832 0.000 0.080 0.000 NA NA
#> SRR2001201 1 0.3355 0.863 0.836 0.000 0.076 0.000 NA NA
#> SRR2001202 1 0.3460 0.855 0.828 0.000 0.084 0.000 NA NA
#> SRR2001203 1 0.3405 0.859 0.832 0.000 0.084 0.000 NA NA
#> SRR2001196 1 0.2632 0.890 0.880 0.000 0.076 0.000 NA NA
#> SRR2001197 1 0.2739 0.883 0.872 0.000 0.084 0.000 NA NA
#> SRR2001198 1 0.2739 0.886 0.872 0.000 0.084 0.000 NA NA
#> SRR2001199 1 0.2632 0.888 0.880 0.000 0.076 0.000 NA NA
#> SRR2001192 3 0.2766 0.927 0.092 0.000 0.868 0.000 NA NA
#> SRR2001193 3 0.2687 0.928 0.092 0.000 0.872 0.000 NA NA
#> SRR2001194 3 0.2687 0.927 0.092 0.000 0.872 0.000 NA NA
#> SRR2001195 3 0.2796 0.929 0.100 0.000 0.864 0.000 NA NA
#> SRR2001188 1 0.1528 0.915 0.936 0.000 0.000 0.000 NA NA
#> SRR2001189 1 0.1528 0.915 0.936 0.000 0.000 0.000 NA NA
#> SRR2001190 1 0.1461 0.916 0.940 0.000 0.000 0.000 NA NA
#> SRR2001191 1 0.1225 0.918 0.952 0.000 0.000 0.000 NA NA
#> SRR2001184 3 0.3190 0.919 0.136 0.000 0.820 0.000 NA NA
#> SRR2001185 3 0.3190 0.919 0.136 0.000 0.820 0.000 NA NA
#> SRR2001186 3 0.3190 0.919 0.136 0.000 0.820 0.000 NA NA
#> SRR2001187 3 0.3190 0.919 0.136 0.000 0.820 0.000 NA NA
#> SRR2001180 1 0.1297 0.917 0.948 0.000 0.000 0.000 NA NA
#> SRR2001181 1 0.1367 0.918 0.944 0.000 0.000 0.000 NA NA
#> SRR2001182 1 0.1802 0.904 0.916 0.000 0.000 0.000 NA NA
#> SRR2001183 1 0.1719 0.911 0.924 0.000 0.000 0.000 NA NA
#> SRR2001176 3 0.2575 0.929 0.100 0.000 0.872 0.000 NA NA
#> SRR2001177 3 0.2527 0.930 0.108 0.000 0.868 0.000 NA NA
#> SRR2001178 3 0.2653 0.929 0.100 0.000 0.868 0.000 NA NA
#> SRR2001179 3 0.2605 0.930 0.108 0.000 0.864 0.000 NA NA
#> SRR2001172 3 0.3570 0.908 0.144 0.000 0.792 0.000 NA NA
#> SRR2001173 3 0.3513 0.910 0.144 0.000 0.796 0.000 NA NA
#> SRR2001174 3 0.3710 0.907 0.144 0.000 0.788 0.000 NA NA
#> SRR2001175 3 0.3626 0.906 0.144 0.000 0.788 0.000 NA NA
#> SRR2001168 1 0.3479 0.862 0.820 0.000 0.084 0.000 NA NA
#> SRR2001169 1 0.3626 0.850 0.808 0.000 0.096 0.000 NA NA
#> SRR2001170 1 0.3578 0.856 0.812 0.000 0.088 0.000 NA NA
#> SRR2001171 1 0.3479 0.862 0.820 0.000 0.084 0.000 NA NA
#> SRR2001164 1 0.1693 0.913 0.932 0.000 0.020 0.000 NA NA
#> SRR2001165 1 0.1605 0.914 0.936 0.000 0.016 0.000 NA NA
#> SRR2001166 1 0.1693 0.913 0.932 0.000 0.020 0.000 NA NA
#> SRR2001167 1 0.1693 0.913 0.932 0.000 0.020 0.000 NA NA
#> SRR2001160 1 0.1333 0.914 0.944 0.000 0.000 0.000 NA NA
#> SRR2001161 1 0.1477 0.916 0.940 0.000 0.004 0.000 NA NA
#> SRR2001162 1 0.1511 0.916 0.940 0.000 0.004 0.000 NA NA
#> SRR2001163 1 0.1477 0.916 0.940 0.000 0.004 0.000 NA NA
#> SRR2001156 1 0.2485 0.900 0.892 0.000 0.056 0.000 NA NA
#> SRR2001157 1 0.2402 0.902 0.896 0.000 0.060 0.000 NA NA
#> SRR2001158 1 0.2278 0.905 0.904 0.000 0.052 0.000 NA NA
#> SRR2001159 1 0.2621 0.899 0.884 0.000 0.052 0.000 NA NA
#> SRR2001152 1 0.1480 0.917 0.940 0.000 0.020 0.000 NA NA
#> SRR2001153 1 0.1434 0.917 0.940 0.000 0.012 0.000 NA NA
#> SRR2001154 1 0.1633 0.916 0.932 0.000 0.024 0.000 NA NA
#> SRR2001155 1 0.1391 0.918 0.944 0.000 0.016 0.000 NA NA
#> SRR2001148 3 0.3190 0.919 0.136 0.000 0.820 0.000 NA NA
#> SRR2001149 3 0.3123 0.920 0.136 0.000 0.824 0.000 NA NA
#> SRR2001150 3 0.3190 0.919 0.136 0.000 0.820 0.000 NA NA
#> SRR2001151 3 0.3123 0.920 0.136 0.000 0.824 0.000 NA NA
#> SRR2001144 1 0.2511 0.901 0.880 0.000 0.056 0.000 NA NA
#> SRR2001145 1 0.2325 0.904 0.892 0.000 0.048 0.000 NA NA
#> SRR2001146 1 0.2389 0.902 0.888 0.000 0.052 0.000 NA NA
#> SRR2001147 1 0.2389 0.902 0.888 0.000 0.052 0.000 NA NA
#> SRR2001140 1 0.1549 0.916 0.936 0.000 0.020 0.000 NA NA
#> SRR2001142 1 0.1549 0.917 0.936 0.000 0.020 0.000 NA NA
#> SRR2001143 1 0.1633 0.915 0.932 0.000 0.024 0.000 NA NA
#> SRR2001136 3 0.3195 0.906 0.116 0.000 0.836 0.000 NA NA
#> SRR2001137 3 0.3252 0.909 0.128 0.000 0.828 0.000 NA NA
#> SRR2001138 3 0.3167 0.913 0.120 0.000 0.836 0.000 NA NA
#> SRR2001139 3 0.3210 0.911 0.124 0.000 0.832 0.000 NA NA
#> SRR2001132 3 0.2790 0.916 0.080 0.000 0.872 0.000 NA NA
#> SRR2001133 3 0.2790 0.919 0.080 0.000 0.872 0.000 NA NA
#> SRR2001134 3 0.2831 0.915 0.084 0.000 0.868 0.000 NA NA
#> SRR2001135 3 0.2807 0.919 0.088 0.000 0.868 0.000 NA NA
#> SRR2001128 1 0.1503 0.924 0.944 0.000 0.032 0.000 NA NA
#> SRR2001129 1 0.1257 0.918 0.952 0.000 0.020 0.000 NA NA
#> SRR2001130 1 0.1421 0.921 0.944 0.000 0.028 0.000 NA NA
#> SRR2001131 1 0.1261 0.921 0.952 0.000 0.024 0.000 NA NA
#> SRR2001124 1 0.1901 0.913 0.924 0.000 0.040 0.000 NA NA
#> SRR2001125 1 0.1693 0.915 0.932 0.000 0.044 0.000 NA NA
#> SRR2001126 1 0.1624 0.916 0.936 0.000 0.040 0.000 NA NA
#> SRR2001127 1 0.1624 0.916 0.936 0.000 0.040 0.000 NA NA
#> SRR2001120 1 0.2745 0.889 0.864 0.000 0.068 0.000 NA NA
#> SRR2001121 1 0.2688 0.889 0.868 0.000 0.068 0.000 NA NA
#> SRR2001122 1 0.2745 0.889 0.864 0.000 0.068 0.000 NA NA
#> SRR2001123 1 0.2744 0.886 0.864 0.000 0.072 0.000 NA NA
#> SRR2001116 1 0.0964 0.923 0.968 0.000 0.012 0.000 NA NA
#> SRR2001117 1 0.0653 0.921 0.980 0.000 0.004 0.000 NA NA
#> SRR2001118 1 0.0767 0.921 0.976 0.000 0.008 0.000 NA NA
#> SRR2001119 1 0.0767 0.921 0.976 0.000 0.008 0.000 NA NA
#> SRR2001112 3 0.4092 0.872 0.112 0.000 0.776 0.000 NA NA
#> SRR2001113 3 0.4223 0.864 0.108 0.000 0.768 0.000 NA NA
#> SRR2001114 3 0.4092 0.872 0.112 0.000 0.776 0.000 NA NA
#> SRR2001115 3 0.4176 0.870 0.112 0.000 0.772 0.000 NA NA
#> SRR2001108 4 0.3318 0.947 0.000 0.172 0.000 0.796 NA NA
#> SRR2001109 4 0.3102 0.948 0.000 0.156 0.000 0.816 NA NA
#> SRR2001110 4 0.3352 0.945 0.000 0.176 0.000 0.792 NA NA
#> SRR2001111 4 0.3318 0.947 0.000 0.172 0.000 0.796 NA NA
#> SRR2001104 2 0.0291 0.937 0.000 0.992 0.000 0.004 NA NA
#> SRR2001105 2 0.0717 0.940 0.000 0.976 0.000 0.016 NA NA
#> SRR2001106 2 0.0405 0.936 0.000 0.988 0.000 0.008 NA NA
#> SRR2001107 2 0.0508 0.939 0.000 0.984 0.000 0.012 NA NA
#> SRR2001100 2 0.1555 0.937 0.000 0.932 0.000 0.060 NA NA
#> SRR2001101 2 0.1615 0.935 0.000 0.928 0.000 0.064 NA NA
#> SRR2001102 2 0.1364 0.941 0.000 0.944 0.000 0.048 NA NA
#> SRR2001103 2 0.1285 0.941 0.000 0.944 0.000 0.052 NA NA
#> SRR2001096 2 0.0603 0.931 0.000 0.980 0.000 0.004 NA NA
#> SRR2001097 2 0.0820 0.937 0.000 0.972 0.000 0.012 NA NA
#> SRR2001098 2 0.0717 0.934 0.000 0.976 0.000 0.008 NA NA
#> SRR2001099 2 0.0820 0.937 0.000 0.972 0.000 0.012 NA NA
#> SRR2001092 2 0.0146 0.938 0.000 0.996 0.000 0.004 NA NA
#> SRR2001093 2 0.0405 0.939 0.000 0.988 0.000 0.008 NA NA
#> SRR2001094 2 0.0146 0.935 0.000 0.996 0.000 0.000 NA NA
#> SRR2001095 2 0.0508 0.939 0.000 0.984 0.000 0.012 NA NA
#> SRR2001088 4 0.2946 0.951 0.000 0.184 0.000 0.808 NA NA
#> SRR2001089 4 0.2979 0.951 0.000 0.188 0.000 0.804 NA NA
#> SRR2001090 4 0.3011 0.952 0.000 0.192 0.000 0.800 NA NA
#> SRR2001091 4 0.2946 0.954 0.000 0.184 0.000 0.808 NA NA
#> SRR2001084 4 0.3280 0.944 0.000 0.152 0.000 0.812 NA NA
#> SRR2001085 4 0.3139 0.944 0.000 0.152 0.000 0.816 NA NA
#> SRR2001086 4 0.3317 0.946 0.000 0.156 0.000 0.808 NA NA
#> SRR2001087 4 0.3317 0.946 0.000 0.156 0.000 0.808 NA NA
#> SRR2001080 2 0.0935 0.943 0.000 0.964 0.000 0.032 NA NA
#> SRR2001081 2 0.1340 0.941 0.000 0.948 0.000 0.040 NA NA
#> SRR2001082 2 0.1370 0.942 0.000 0.948 0.000 0.036 NA NA
#> SRR2001083 2 0.1155 0.942 0.000 0.956 0.000 0.036 NA NA
#> SRR2001076 2 0.0692 0.943 0.000 0.976 0.000 0.020 NA NA
#> SRR2001077 2 0.0777 0.942 0.000 0.972 0.000 0.024 NA NA
#> SRR2001078 2 0.0777 0.942 0.000 0.972 0.000 0.024 NA NA
#> SRR2001079 2 0.0692 0.943 0.000 0.976 0.000 0.020 NA NA
#> SRR2001072 4 0.3281 0.949 0.000 0.200 0.000 0.784 NA NA
#> SRR2001073 4 0.3074 0.950 0.000 0.200 0.000 0.792 NA NA
#> SRR2001074 4 0.3183 0.949 0.000 0.200 0.000 0.788 NA NA
#> SRR2001075 4 0.3074 0.950 0.000 0.200 0.000 0.792 NA NA
#> SRR2001068 2 0.2821 0.907 0.000 0.860 0.000 0.096 NA NA
#> SRR2001069 2 0.2917 0.901 0.000 0.852 0.000 0.104 NA NA
#> SRR2001070 2 0.2870 0.904 0.000 0.856 0.000 0.100 NA NA
#> SRR2001071 2 0.2984 0.897 0.000 0.848 0.000 0.104 NA NA
#> SRR2001064 2 0.0806 0.941 0.000 0.972 0.000 0.020 NA NA
#> SRR2001065 2 0.0717 0.940 0.000 0.976 0.000 0.016 NA NA
#> SRR2001066 2 0.0806 0.941 0.000 0.972 0.000 0.020 NA NA
#> SRR2001067 2 0.0717 0.940 0.000 0.976 0.000 0.016 NA NA
#> SRR2001060 4 0.3089 0.953 0.000 0.188 0.000 0.800 NA NA
#> SRR2001061 4 0.2979 0.953 0.000 0.188 0.000 0.804 NA NA
#> SRR2001062 4 0.3089 0.953 0.000 0.188 0.000 0.800 NA NA
#> SRR2001063 4 0.3121 0.951 0.000 0.192 0.000 0.796 NA NA
#> SRR2001056 4 0.3213 0.946 0.000 0.160 0.000 0.808 NA NA
#> SRR2001057 4 0.3284 0.946 0.000 0.168 0.000 0.800 NA NA
#> SRR2001058 4 0.3213 0.946 0.000 0.160 0.000 0.808 NA NA
#> SRR2001059 4 0.3318 0.946 0.000 0.172 0.000 0.796 NA NA
#> SRR2001052 2 0.1708 0.936 0.000 0.932 0.000 0.040 NA NA
#> SRR2001053 2 0.1777 0.934 0.000 0.928 0.000 0.044 NA NA
#> SRR2001054 2 0.1777 0.934 0.000 0.928 0.000 0.044 NA NA
#> SRR2001055 2 0.1844 0.935 0.000 0.924 0.000 0.048 NA NA
#> SRR2001048 2 0.2964 0.895 0.000 0.848 0.000 0.108 NA NA
#> SRR2001049 2 0.3076 0.887 0.000 0.840 0.000 0.112 NA NA
#> SRR2001050 2 0.2821 0.906 0.000 0.860 0.000 0.096 NA NA
#> SRR2001051 2 0.2821 0.906 0.000 0.860 0.000 0.096 NA NA
#> SRR2001044 4 0.3323 0.947 0.000 0.204 0.000 0.780 NA NA
#> SRR2001045 4 0.3352 0.944 0.000 0.208 0.000 0.776 NA NA
#> SRR2001046 4 0.3213 0.947 0.000 0.204 0.000 0.784 NA NA
#> SRR2001047 4 0.3074 0.951 0.000 0.200 0.000 0.792 NA NA
#> SRR2001040 4 0.2442 0.944 0.000 0.144 0.000 0.852 NA NA
#> SRR2001041 4 0.2402 0.942 0.000 0.140 0.000 0.856 NA NA
#> SRR2001042 4 0.2482 0.945 0.000 0.148 0.000 0.848 NA NA
#> SRR2001043 4 0.2662 0.944 0.000 0.152 0.000 0.840 NA NA
#> SRR2001036 4 0.2442 0.945 0.000 0.144 0.000 0.852 NA NA
#> SRR2001037 4 0.2584 0.945 0.000 0.144 0.000 0.848 NA NA
#> SRR2001038 4 0.2544 0.942 0.000 0.140 0.000 0.852 NA NA
#> SRR2001039 4 0.2300 0.946 0.000 0.144 0.000 0.856 NA NA
#> SRR2001028 4 0.3261 0.946 0.000 0.204 0.000 0.780 NA NA
#> SRR2001029 4 0.3261 0.945 0.000 0.204 0.000 0.780 NA NA
#> SRR2001030 4 0.3261 0.945 0.000 0.204 0.000 0.780 NA NA
#> SRR2001031 4 0.3284 0.947 0.000 0.196 0.000 0.784 NA NA
#> SRR2001024 4 0.2668 0.955 0.000 0.168 0.000 0.828 NA NA
#> SRR2001025 4 0.2703 0.955 0.000 0.172 0.000 0.824 NA NA
#> SRR2001026 4 0.2703 0.955 0.000 0.172 0.000 0.824 NA NA
#> SRR2001027 4 0.2773 0.954 0.000 0.164 0.000 0.828 NA NA
#> SRR2001020 2 0.2445 0.884 0.000 0.872 0.000 0.108 NA NA
#> SRR2001021 2 0.2587 0.882 0.000 0.868 0.000 0.108 NA NA
#> SRR2001022 2 0.2699 0.883 0.000 0.864 0.000 0.108 NA NA
#> SRR2001023 2 0.2678 0.884 0.000 0.860 0.000 0.116 NA NA
#> SRR2001016 4 0.4127 0.879 0.000 0.236 0.000 0.716 NA NA
#> SRR2001017 4 0.4077 0.890 0.000 0.228 0.000 0.724 NA NA
#> SRR2001018 4 0.4024 0.900 0.000 0.220 0.000 0.732 NA NA
#> SRR2001019 4 0.4127 0.879 0.000 0.236 0.000 0.716 NA NA
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.5031 0.497 0.497
#> 3 3 0.894 0.952 0.962 0.2194 0.889 0.777
#> 4 4 0.929 0.866 0.936 0.0784 0.946 0.861
#> 5 5 0.781 0.784 0.884 0.1009 0.961 0.883
#> 6 6 0.783 0.797 0.877 0.0238 0.987 0.955
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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0.0000 1.000 0.000 1 0.000
#> SRR2001033 2 0.0000 1.000 0.000 1 0.000
#> SRR2001034 2 0.0000 1.000 0.000 1 0.000
#> SRR2001035 2 0.0000 1.000 0.000 1 0.000
#> SRR2001204 1 0.0000 0.934 1.000 0 0.000
#> SRR2001205 1 0.0000 0.934 1.000 0 0.000
#> SRR2001206 1 0.0000 0.934 1.000 0 0.000
#> SRR2001207 1 0.0000 0.934 1.000 0 0.000
#> SRR2001200 1 0.4399 0.841 0.812 0 0.188
#> SRR2001201 1 0.4399 0.841 0.812 0 0.188
#> SRR2001202 1 0.4399 0.841 0.812 0 0.188
#> SRR2001203 1 0.4399 0.841 0.812 0 0.188
#> SRR2001196 1 0.4399 0.841 0.812 0 0.188
#> SRR2001197 1 0.4399 0.841 0.812 0 0.188
#> SRR2001198 1 0.4399 0.841 0.812 0 0.188
#> SRR2001199 1 0.4399 0.841 0.812 0 0.188
#> SRR2001192 3 0.4399 0.914 0.188 0 0.812
#> SRR2001193 3 0.4399 0.914 0.188 0 0.812
#> SRR2001194 3 0.4399 0.914 0.188 0 0.812
#> SRR2001195 3 0.4399 0.914 0.188 0 0.812
#> SRR2001188 1 0.0000 0.934 1.000 0 0.000
#> SRR2001189 1 0.0000 0.934 1.000 0 0.000
#> SRR2001190 1 0.0000 0.934 1.000 0 0.000
#> SRR2001191 1 0.0000 0.934 1.000 0 0.000
#> SRR2001184 3 0.4399 0.914 0.188 0 0.812
#> SRR2001185 3 0.4399 0.914 0.188 0 0.812
#> SRR2001186 3 0.4399 0.914 0.188 0 0.812
#> SRR2001187 3 0.4399 0.914 0.188 0 0.812
#> SRR2001180 1 0.0000 0.934 1.000 0 0.000
#> SRR2001181 1 0.0000 0.934 1.000 0 0.000
#> SRR2001182 1 0.0000 0.934 1.000 0 0.000
#> SRR2001183 1 0.0000 0.934 1.000 0 0.000
#> SRR2001176 3 0.4399 0.914 0.188 0 0.812
#> SRR2001177 3 0.4399 0.914 0.188 0 0.812
#> SRR2001178 3 0.4399 0.914 0.188 0 0.812
#> SRR2001179 3 0.4399 0.914 0.188 0 0.812
#> SRR2001172 3 0.4399 0.914 0.188 0 0.812
#> SRR2001173 3 0.4399 0.914 0.188 0 0.812
#> SRR2001174 3 0.4399 0.914 0.188 0 0.812
#> SRR2001175 3 0.4399 0.914 0.188 0 0.812
#> SRR2001168 1 0.0000 0.934 1.000 0 0.000
#> SRR2001169 1 0.0000 0.934 1.000 0 0.000
#> SRR2001170 1 0.0000 0.934 1.000 0 0.000
#> SRR2001171 1 0.0000 0.934 1.000 0 0.000
#> SRR2001164 1 0.4235 0.851 0.824 0 0.176
#> SRR2001165 1 0.4235 0.851 0.824 0 0.176
#> SRR2001166 1 0.4235 0.851 0.824 0 0.176
#> SRR2001167 1 0.4235 0.851 0.824 0 0.176
#> SRR2001160 1 0.0237 0.933 0.996 0 0.004
#> SRR2001161 1 0.0237 0.933 0.996 0 0.004
#> SRR2001162 1 0.0237 0.933 0.996 0 0.004
#> SRR2001163 1 0.0237 0.933 0.996 0 0.004
#> SRR2001156 1 0.3816 0.870 0.852 0 0.148
#> SRR2001157 1 0.3816 0.870 0.852 0 0.148
#> SRR2001158 1 0.3816 0.870 0.852 0 0.148
#> SRR2001159 1 0.3816 0.870 0.852 0 0.148
#> SRR2001152 1 0.0000 0.934 1.000 0 0.000
#> SRR2001153 1 0.0000 0.934 1.000 0 0.000
#> SRR2001154 1 0.0000 0.934 1.000 0 0.000
#> SRR2001155 1 0.0000 0.934 1.000 0 0.000
#> SRR2001148 3 0.4399 0.914 0.188 0 0.812
#> SRR2001149 3 0.4399 0.914 0.188 0 0.812
#> SRR2001150 3 0.4399 0.914 0.188 0 0.812
#> SRR2001151 3 0.4399 0.914 0.188 0 0.812
#> SRR2001144 1 0.0000 0.934 1.000 0 0.000
#> SRR2001145 1 0.0000 0.934 1.000 0 0.000
#> SRR2001146 1 0.0000 0.934 1.000 0 0.000
#> SRR2001147 1 0.0000 0.934 1.000 0 0.000
#> SRR2001140 1 0.0000 0.934 1.000 0 0.000
#> SRR2001142 1 0.0000 0.934 1.000 0 0.000
#> SRR2001143 1 0.0000 0.934 1.000 0 0.000
#> SRR2001136 3 0.0000 0.864 0.000 0 1.000
#> SRR2001137 3 0.0000 0.864 0.000 0 1.000
#> SRR2001138 3 0.0000 0.864 0.000 0 1.000
#> SRR2001139 3 0.0000 0.864 0.000 0 1.000
#> SRR2001132 3 0.0000 0.864 0.000 0 1.000
#> SRR2001133 3 0.0000 0.864 0.000 0 1.000
#> SRR2001134 3 0.0000 0.864 0.000 0 1.000
#> SRR2001135 3 0.0000 0.864 0.000 0 1.000
#> SRR2001128 1 0.0000 0.934 1.000 0 0.000
#> SRR2001129 1 0.0000 0.934 1.000 0 0.000
#> SRR2001130 1 0.0000 0.934 1.000 0 0.000
#> SRR2001131 1 0.0000 0.934 1.000 0 0.000
#> SRR2001124 1 0.3816 0.870 0.852 0 0.148
#> SRR2001125 1 0.3816 0.870 0.852 0 0.148
#> SRR2001126 1 0.3816 0.870 0.852 0 0.148
#> SRR2001127 1 0.3816 0.870 0.852 0 0.148
#> SRR2001120 1 0.0000 0.934 1.000 0 0.000
#> SRR2001121 1 0.0000 0.934 1.000 0 0.000
#> SRR2001122 1 0.0000 0.934 1.000 0 0.000
#> SRR2001123 1 0.0000 0.934 1.000 0 0.000
#> SRR2001116 1 0.1289 0.924 0.968 0 0.032
#> SRR2001117 1 0.1289 0.924 0.968 0 0.032
#> SRR2001118 1 0.1289 0.924 0.968 0 0.032
#> SRR2001119 1 0.1289 0.924 0.968 0 0.032
#> SRR2001112 3 0.0000 0.864 0.000 0 1.000
#> SRR2001113 3 0.0000 0.864 0.000 0 1.000
#> SRR2001114 3 0.0000 0.864 0.000 0 1.000
#> SRR2001115 3 0.0000 0.864 0.000 0 1.000
#> SRR2001108 2 0.0000 1.000 0.000 1 0.000
#> SRR2001109 2 0.0000 1.000 0.000 1 0.000
#> SRR2001110 2 0.0000 1.000 0.000 1 0.000
#> SRR2001111 2 0.0000 1.000 0.000 1 0.000
#> SRR2001104 2 0.0000 1.000 0.000 1 0.000
#> SRR2001105 2 0.0000 1.000 0.000 1 0.000
#> SRR2001106 2 0.0000 1.000 0.000 1 0.000
#> SRR2001107 2 0.0000 1.000 0.000 1 0.000
#> SRR2001100 2 0.0000 1.000 0.000 1 0.000
#> SRR2001101 2 0.0000 1.000 0.000 1 0.000
#> SRR2001102 2 0.0000 1.000 0.000 1 0.000
#> SRR2001103 2 0.0000 1.000 0.000 1 0.000
#> SRR2001096 2 0.0000 1.000 0.000 1 0.000
#> SRR2001097 2 0.0000 1.000 0.000 1 0.000
#> SRR2001098 2 0.0000 1.000 0.000 1 0.000
#> SRR2001099 2 0.0000 1.000 0.000 1 0.000
#> SRR2001092 2 0.0000 1.000 0.000 1 0.000
#> SRR2001093 2 0.0000 1.000 0.000 1 0.000
#> SRR2001094 2 0.0000 1.000 0.000 1 0.000
#> SRR2001095 2 0.0000 1.000 0.000 1 0.000
#> SRR2001088 2 0.0000 1.000 0.000 1 0.000
#> SRR2001089 2 0.0000 1.000 0.000 1 0.000
#> SRR2001090 2 0.0000 1.000 0.000 1 0.000
#> SRR2001091 2 0.0000 1.000 0.000 1 0.000
#> SRR2001084 2 0.0000 1.000 0.000 1 0.000
#> SRR2001085 2 0.0000 1.000 0.000 1 0.000
#> SRR2001086 2 0.0000 1.000 0.000 1 0.000
#> SRR2001087 2 0.0000 1.000 0.000 1 0.000
#> SRR2001080 2 0.0000 1.000 0.000 1 0.000
#> SRR2001081 2 0.0000 1.000 0.000 1 0.000
#> SRR2001082 2 0.0000 1.000 0.000 1 0.000
#> SRR2001083 2 0.0000 1.000 0.000 1 0.000
#> SRR2001076 2 0.0000 1.000 0.000 1 0.000
#> SRR2001077 2 0.0000 1.000 0.000 1 0.000
#> SRR2001078 2 0.0000 1.000 0.000 1 0.000
#> SRR2001079 2 0.0000 1.000 0.000 1 0.000
#> SRR2001072 2 0.0000 1.000 0.000 1 0.000
#> SRR2001073 2 0.0000 1.000 0.000 1 0.000
#> SRR2001074 2 0.0000 1.000 0.000 1 0.000
#> SRR2001075 2 0.0000 1.000 0.000 1 0.000
#> SRR2001068 2 0.0000 1.000 0.000 1 0.000
#> SRR2001069 2 0.0000 1.000 0.000 1 0.000
#> SRR2001070 2 0.0000 1.000 0.000 1 0.000
#> SRR2001071 2 0.0000 1.000 0.000 1 0.000
#> SRR2001064 2 0.0000 1.000 0.000 1 0.000
#> SRR2001065 2 0.0000 1.000 0.000 1 0.000
#> SRR2001066 2 0.0000 1.000 0.000 1 0.000
#> SRR2001067 2 0.0000 1.000 0.000 1 0.000
#> SRR2001060 2 0.0000 1.000 0.000 1 0.000
#> SRR2001061 2 0.0000 1.000 0.000 1 0.000
#> SRR2001062 2 0.0000 1.000 0.000 1 0.000
#> SRR2001063 2 0.0000 1.000 0.000 1 0.000
#> SRR2001056 2 0.0000 1.000 0.000 1 0.000
#> SRR2001057 2 0.0000 1.000 0.000 1 0.000
#> SRR2001058 2 0.0000 1.000 0.000 1 0.000
#> SRR2001059 2 0.0000 1.000 0.000 1 0.000
#> SRR2001052 2 0.0000 1.000 0.000 1 0.000
#> SRR2001053 2 0.0000 1.000 0.000 1 0.000
#> SRR2001054 2 0.0000 1.000 0.000 1 0.000
#> SRR2001055 2 0.0000 1.000 0.000 1 0.000
#> SRR2001048 2 0.0000 1.000 0.000 1 0.000
#> SRR2001049 2 0.0000 1.000 0.000 1 0.000
#> SRR2001050 2 0.0000 1.000 0.000 1 0.000
#> SRR2001051 2 0.0000 1.000 0.000 1 0.000
#> SRR2001044 2 0.0000 1.000 0.000 1 0.000
#> SRR2001045 2 0.0000 1.000 0.000 1 0.000
#> SRR2001046 2 0.0000 1.000 0.000 1 0.000
#> SRR2001047 2 0.0000 1.000 0.000 1 0.000
#> SRR2001040 2 0.0000 1.000 0.000 1 0.000
#> SRR2001041 2 0.0000 1.000 0.000 1 0.000
#> SRR2001042 2 0.0000 1.000 0.000 1 0.000
#> SRR2001043 2 0.0000 1.000 0.000 1 0.000
#> SRR2001036 2 0.0000 1.000 0.000 1 0.000
#> SRR2001037 2 0.0000 1.000 0.000 1 0.000
#> SRR2001038 2 0.0000 1.000 0.000 1 0.000
#> SRR2001039 2 0.0000 1.000 0.000 1 0.000
#> SRR2001028 2 0.0000 1.000 0.000 1 0.000
#> SRR2001029 2 0.0000 1.000 0.000 1 0.000
#> SRR2001030 2 0.0000 1.000 0.000 1 0.000
#> SRR2001031 2 0.0000 1.000 0.000 1 0.000
#> SRR2001024 2 0.0000 1.000 0.000 1 0.000
#> SRR2001025 2 0.0000 1.000 0.000 1 0.000
#> SRR2001026 2 0.0000 1.000 0.000 1 0.000
#> SRR2001027 2 0.0000 1.000 0.000 1 0.000
#> SRR2001020 2 0.0000 1.000 0.000 1 0.000
#> SRR2001021 2 0.0000 1.000 0.000 1 0.000
#> SRR2001022 2 0.0000 1.000 0.000 1 0.000
#> SRR2001023 2 0.0000 1.000 0.000 1 0.000
#> SRR2001016 2 0.0000 1.000 0.000 1 0.000
#> SRR2001017 2 0.0000 1.000 0.000 1 0.000
#> SRR2001018 2 0.0000 1.000 0.000 1 0.000
#> SRR2001019 2 0.0000 1.000 0.000 1 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001033 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001034 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001035 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001204 2 0.0817 0.7818 0.024 0.976 0.000 0
#> SRR2001205 2 0.0817 0.7818 0.024 0.976 0.000 0
#> SRR2001206 2 0.0817 0.7818 0.024 0.976 0.000 0
#> SRR2001207 2 0.0817 0.7818 0.024 0.976 0.000 0
#> SRR2001200 1 0.0000 0.7740 1.000 0.000 0.000 0
#> SRR2001201 1 0.0000 0.7740 1.000 0.000 0.000 0
#> SRR2001202 1 0.0000 0.7740 1.000 0.000 0.000 0
#> SRR2001203 1 0.0000 0.7740 1.000 0.000 0.000 0
#> SRR2001196 1 0.0000 0.7740 1.000 0.000 0.000 0
#> SRR2001197 1 0.0000 0.7740 1.000 0.000 0.000 0
#> SRR2001198 1 0.0000 0.7740 1.000 0.000 0.000 0
#> SRR2001199 1 0.0000 0.7740 1.000 0.000 0.000 0
#> SRR2001192 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001193 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001194 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001195 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001188 1 0.4713 0.5392 0.640 0.360 0.000 0
#> SRR2001189 1 0.4713 0.5392 0.640 0.360 0.000 0
#> SRR2001190 1 0.4713 0.5392 0.640 0.360 0.000 0
#> SRR2001191 1 0.4713 0.5392 0.640 0.360 0.000 0
#> SRR2001184 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001185 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001186 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001187 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001180 1 0.4746 0.5388 0.632 0.368 0.000 0
#> SRR2001181 1 0.4746 0.5388 0.632 0.368 0.000 0
#> SRR2001182 1 0.4746 0.5388 0.632 0.368 0.000 0
#> SRR2001183 1 0.4746 0.5388 0.632 0.368 0.000 0
#> SRR2001176 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001177 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001178 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001179 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001172 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001173 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001174 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001175 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001168 2 0.0000 0.7839 0.000 1.000 0.000 0
#> SRR2001169 2 0.0000 0.7839 0.000 1.000 0.000 0
#> SRR2001170 2 0.0000 0.7839 0.000 1.000 0.000 0
#> SRR2001171 2 0.0000 0.7839 0.000 1.000 0.000 0
#> SRR2001164 1 0.0469 0.7799 0.988 0.012 0.000 0
#> SRR2001165 1 0.0469 0.7799 0.988 0.012 0.000 0
#> SRR2001166 1 0.0469 0.7799 0.988 0.012 0.000 0
#> SRR2001167 1 0.0469 0.7799 0.988 0.012 0.000 0
#> SRR2001160 1 0.4331 0.6666 0.712 0.288 0.000 0
#> SRR2001161 1 0.4331 0.6666 0.712 0.288 0.000 0
#> SRR2001162 1 0.4331 0.6666 0.712 0.288 0.000 0
#> SRR2001163 1 0.4331 0.6666 0.712 0.288 0.000 0
#> SRR2001156 1 0.1792 0.7927 0.932 0.068 0.000 0
#> SRR2001157 1 0.1792 0.7927 0.932 0.068 0.000 0
#> SRR2001158 1 0.1792 0.7927 0.932 0.068 0.000 0
#> SRR2001159 1 0.1792 0.7927 0.932 0.068 0.000 0
#> SRR2001152 2 0.4925 0.1425 0.428 0.572 0.000 0
#> SRR2001153 2 0.4925 0.1425 0.428 0.572 0.000 0
#> SRR2001154 2 0.4925 0.1425 0.428 0.572 0.000 0
#> SRR2001155 2 0.4925 0.1425 0.428 0.572 0.000 0
#> SRR2001148 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001149 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001150 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001151 3 0.0000 0.9295 0.000 0.000 1.000 0
#> SRR2001144 2 0.0336 0.7853 0.008 0.992 0.000 0
#> SRR2001145 2 0.0336 0.7853 0.008 0.992 0.000 0
#> SRR2001146 2 0.0336 0.7853 0.008 0.992 0.000 0
#> SRR2001147 2 0.0336 0.7853 0.008 0.992 0.000 0
#> SRR2001140 2 0.2011 0.7486 0.080 0.920 0.000 0
#> SRR2001142 2 0.2011 0.7486 0.080 0.920 0.000 0
#> SRR2001143 2 0.2011 0.7486 0.080 0.920 0.000 0
#> SRR2001136 3 0.3486 0.8766 0.188 0.000 0.812 0
#> SRR2001137 3 0.3486 0.8766 0.188 0.000 0.812 0
#> SRR2001138 3 0.3486 0.8766 0.188 0.000 0.812 0
#> SRR2001139 3 0.3486 0.8766 0.188 0.000 0.812 0
#> SRR2001132 3 0.3486 0.8766 0.188 0.000 0.812 0
#> SRR2001133 3 0.3486 0.8766 0.188 0.000 0.812 0
#> SRR2001134 3 0.3486 0.8766 0.188 0.000 0.812 0
#> SRR2001135 3 0.3486 0.8766 0.188 0.000 0.812 0
#> SRR2001128 2 0.4999 -0.0965 0.492 0.508 0.000 0
#> SRR2001129 2 0.4999 -0.0965 0.492 0.508 0.000 0
#> SRR2001130 2 0.4999 -0.0965 0.492 0.508 0.000 0
#> SRR2001131 2 0.4999 -0.0965 0.492 0.508 0.000 0
#> SRR2001124 1 0.1792 0.7927 0.932 0.068 0.000 0
#> SRR2001125 1 0.1792 0.7927 0.932 0.068 0.000 0
#> SRR2001126 1 0.1792 0.7927 0.932 0.068 0.000 0
#> SRR2001127 1 0.1792 0.7927 0.932 0.068 0.000 0
#> SRR2001120 2 0.0000 0.7839 0.000 1.000 0.000 0
#> SRR2001121 2 0.0000 0.7839 0.000 1.000 0.000 0
#> SRR2001122 2 0.0000 0.7839 0.000 1.000 0.000 0
#> SRR2001123 2 0.0000 0.7839 0.000 1.000 0.000 0
#> SRR2001116 1 0.4164 0.6932 0.736 0.264 0.000 0
#> SRR2001117 1 0.4164 0.6932 0.736 0.264 0.000 0
#> SRR2001118 1 0.4164 0.6932 0.736 0.264 0.000 0
#> SRR2001119 1 0.4164 0.6932 0.736 0.264 0.000 0
#> SRR2001112 3 0.3486 0.8766 0.188 0.000 0.812 0
#> SRR2001113 3 0.3486 0.8766 0.188 0.000 0.812 0
#> SRR2001114 3 0.3486 0.8766 0.188 0.000 0.812 0
#> SRR2001115 3 0.3486 0.8766 0.188 0.000 0.812 0
#> SRR2001108 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001109 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001110 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001111 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001104 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001105 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001106 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001107 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001100 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001101 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001102 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001103 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001096 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001097 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001098 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001099 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001092 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001093 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001094 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001095 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001088 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001089 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001090 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001091 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001084 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001085 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001086 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001087 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001080 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001081 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001082 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001083 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001076 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001077 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001078 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001079 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001072 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001073 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001074 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001075 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001068 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001069 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001070 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001071 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001064 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001065 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001066 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001067 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001060 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001061 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001062 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001063 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001056 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001057 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001058 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001059 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001052 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001053 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001054 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001055 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001048 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001049 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001050 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001051 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001044 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001045 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001046 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001047 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001040 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001041 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001042 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001043 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001036 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001037 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001038 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001039 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001028 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001029 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001030 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001031 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001024 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001025 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001026 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001027 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001020 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001021 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001022 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001023 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001016 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001017 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001018 4 0.0000 1.0000 0.000 0.000 0.000 1
#> SRR2001019 4 0.0000 1.0000 0.000 0.000 0.000 1
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 4 0.2605 0.8392 0.000 0.148 0.000 0.852 0.000
#> SRR2001033 4 0.2605 0.8392 0.000 0.148 0.000 0.852 0.000
#> SRR2001034 4 0.2605 0.8392 0.000 0.148 0.000 0.852 0.000
#> SRR2001035 4 0.2605 0.8392 0.000 0.148 0.000 0.852 0.000
#> SRR2001204 5 0.0703 0.7818 0.024 0.000 0.000 0.000 0.976
#> SRR2001205 5 0.0703 0.7818 0.024 0.000 0.000 0.000 0.976
#> SRR2001206 5 0.0703 0.7818 0.024 0.000 0.000 0.000 0.976
#> SRR2001207 5 0.0703 0.7818 0.024 0.000 0.000 0.000 0.976
#> SRR2001200 1 0.0000 0.7740 1.000 0.000 0.000 0.000 0.000
#> SRR2001201 1 0.0000 0.7740 1.000 0.000 0.000 0.000 0.000
#> SRR2001202 1 0.0000 0.7740 1.000 0.000 0.000 0.000 0.000
#> SRR2001203 1 0.0000 0.7740 1.000 0.000 0.000 0.000 0.000
#> SRR2001196 1 0.0000 0.7740 1.000 0.000 0.000 0.000 0.000
#> SRR2001197 1 0.0000 0.7740 1.000 0.000 0.000 0.000 0.000
#> SRR2001198 1 0.0000 0.7740 1.000 0.000 0.000 0.000 0.000
#> SRR2001199 1 0.0000 0.7740 1.000 0.000 0.000 0.000 0.000
#> SRR2001192 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001193 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001194 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001195 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001188 1 0.4060 0.5392 0.640 0.000 0.000 0.000 0.360
#> SRR2001189 1 0.4060 0.5392 0.640 0.000 0.000 0.000 0.360
#> SRR2001190 1 0.4060 0.5392 0.640 0.000 0.000 0.000 0.360
#> SRR2001191 1 0.4060 0.5392 0.640 0.000 0.000 0.000 0.360
#> SRR2001184 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001185 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001186 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001187 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001180 1 0.4088 0.5388 0.632 0.000 0.000 0.000 0.368
#> SRR2001181 1 0.4088 0.5388 0.632 0.000 0.000 0.000 0.368
#> SRR2001182 1 0.4088 0.5388 0.632 0.000 0.000 0.000 0.368
#> SRR2001183 1 0.4088 0.5388 0.632 0.000 0.000 0.000 0.368
#> SRR2001176 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001177 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001178 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001179 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001172 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001173 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001174 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001175 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001168 5 0.0000 0.7839 0.000 0.000 0.000 0.000 1.000
#> SRR2001169 5 0.0000 0.7839 0.000 0.000 0.000 0.000 1.000
#> SRR2001170 5 0.0000 0.7839 0.000 0.000 0.000 0.000 1.000
#> SRR2001171 5 0.0000 0.7839 0.000 0.000 0.000 0.000 1.000
#> SRR2001164 1 0.0404 0.7799 0.988 0.000 0.000 0.000 0.012
#> SRR2001165 1 0.0404 0.7799 0.988 0.000 0.000 0.000 0.012
#> SRR2001166 1 0.0404 0.7799 0.988 0.000 0.000 0.000 0.012
#> SRR2001167 1 0.0404 0.7799 0.988 0.000 0.000 0.000 0.012
#> SRR2001160 1 0.3730 0.6666 0.712 0.000 0.000 0.000 0.288
#> SRR2001161 1 0.3730 0.6666 0.712 0.000 0.000 0.000 0.288
#> SRR2001162 1 0.3730 0.6666 0.712 0.000 0.000 0.000 0.288
#> SRR2001163 1 0.3730 0.6666 0.712 0.000 0.000 0.000 0.288
#> SRR2001156 1 0.1544 0.7927 0.932 0.000 0.000 0.000 0.068
#> SRR2001157 1 0.1544 0.7927 0.932 0.000 0.000 0.000 0.068
#> SRR2001158 1 0.1544 0.7927 0.932 0.000 0.000 0.000 0.068
#> SRR2001159 1 0.1544 0.7927 0.932 0.000 0.000 0.000 0.068
#> SRR2001152 5 0.4242 0.1425 0.428 0.000 0.000 0.000 0.572
#> SRR2001153 5 0.4242 0.1425 0.428 0.000 0.000 0.000 0.572
#> SRR2001154 5 0.4242 0.1425 0.428 0.000 0.000 0.000 0.572
#> SRR2001155 5 0.4242 0.1425 0.428 0.000 0.000 0.000 0.572
#> SRR2001148 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001149 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001150 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001151 3 0.0000 0.9172 0.000 0.000 1.000 0.000 0.000
#> SRR2001144 5 0.0290 0.7853 0.008 0.000 0.000 0.000 0.992
#> SRR2001145 5 0.0290 0.7853 0.008 0.000 0.000 0.000 0.992
#> SRR2001146 5 0.0290 0.7853 0.008 0.000 0.000 0.000 0.992
#> SRR2001147 5 0.0290 0.7853 0.008 0.000 0.000 0.000 0.992
#> SRR2001140 5 0.1732 0.7486 0.080 0.000 0.000 0.000 0.920
#> SRR2001142 5 0.1732 0.7486 0.080 0.000 0.000 0.000 0.920
#> SRR2001143 5 0.1732 0.7486 0.080 0.000 0.000 0.000 0.920
#> SRR2001136 3 0.3160 0.8578 0.188 0.004 0.808 0.000 0.000
#> SRR2001137 3 0.3160 0.8578 0.188 0.004 0.808 0.000 0.000
#> SRR2001138 3 0.3160 0.8578 0.188 0.004 0.808 0.000 0.000
#> SRR2001139 3 0.3160 0.8578 0.188 0.004 0.808 0.000 0.000
#> SRR2001132 3 0.3160 0.8578 0.188 0.004 0.808 0.000 0.000
#> SRR2001133 3 0.3160 0.8578 0.188 0.004 0.808 0.000 0.000
#> SRR2001134 3 0.3160 0.8578 0.188 0.004 0.808 0.000 0.000
#> SRR2001135 3 0.3160 0.8578 0.188 0.004 0.808 0.000 0.000
#> SRR2001128 5 0.4306 -0.0965 0.492 0.000 0.000 0.000 0.508
#> SRR2001129 5 0.4306 -0.0965 0.492 0.000 0.000 0.000 0.508
#> SRR2001130 5 0.4306 -0.0965 0.492 0.000 0.000 0.000 0.508
#> SRR2001131 5 0.4306 -0.0965 0.492 0.000 0.000 0.000 0.508
#> SRR2001124 1 0.1544 0.7927 0.932 0.000 0.000 0.000 0.068
#> SRR2001125 1 0.1544 0.7927 0.932 0.000 0.000 0.000 0.068
#> SRR2001126 1 0.1544 0.7927 0.932 0.000 0.000 0.000 0.068
#> SRR2001127 1 0.1544 0.7927 0.932 0.000 0.000 0.000 0.068
#> SRR2001120 5 0.0000 0.7839 0.000 0.000 0.000 0.000 1.000
#> SRR2001121 5 0.0000 0.7839 0.000 0.000 0.000 0.000 1.000
#> SRR2001122 5 0.0000 0.7839 0.000 0.000 0.000 0.000 1.000
#> SRR2001123 5 0.0000 0.7839 0.000 0.000 0.000 0.000 1.000
#> SRR2001116 1 0.3586 0.6932 0.736 0.000 0.000 0.000 0.264
#> SRR2001117 1 0.3586 0.6932 0.736 0.000 0.000 0.000 0.264
#> SRR2001118 1 0.3586 0.6932 0.736 0.000 0.000 0.000 0.264
#> SRR2001119 1 0.3586 0.6932 0.736 0.000 0.000 0.000 0.264
#> SRR2001112 3 0.3160 0.8578 0.188 0.004 0.808 0.000 0.000
#> SRR2001113 3 0.3160 0.8578 0.188 0.004 0.808 0.000 0.000
#> SRR2001114 3 0.3160 0.8578 0.188 0.004 0.808 0.000 0.000
#> SRR2001115 3 0.3160 0.8578 0.188 0.004 0.808 0.000 0.000
#> SRR2001108 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001109 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001110 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001111 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001104 4 0.3999 0.6697 0.000 0.344 0.000 0.656 0.000
#> SRR2001105 4 0.3999 0.6697 0.000 0.344 0.000 0.656 0.000
#> SRR2001106 4 0.3999 0.6697 0.000 0.344 0.000 0.656 0.000
#> SRR2001107 4 0.3999 0.6697 0.000 0.344 0.000 0.656 0.000
#> SRR2001100 4 0.3837 0.6928 0.000 0.308 0.000 0.692 0.000
#> SRR2001101 4 0.3837 0.6928 0.000 0.308 0.000 0.692 0.000
#> SRR2001102 4 0.3837 0.6928 0.000 0.308 0.000 0.692 0.000
#> SRR2001103 4 0.3837 0.6928 0.000 0.308 0.000 0.692 0.000
#> SRR2001096 2 0.0162 1.0000 0.000 0.996 0.000 0.004 0.000
#> SRR2001097 2 0.0162 1.0000 0.000 0.996 0.000 0.004 0.000
#> SRR2001098 2 0.0162 1.0000 0.000 0.996 0.000 0.004 0.000
#> SRR2001099 2 0.0162 1.0000 0.000 0.996 0.000 0.004 0.000
#> SRR2001092 4 0.3039 0.8145 0.000 0.192 0.000 0.808 0.000
#> SRR2001093 4 0.3039 0.8145 0.000 0.192 0.000 0.808 0.000
#> SRR2001094 4 0.3039 0.8145 0.000 0.192 0.000 0.808 0.000
#> SRR2001095 4 0.3039 0.8145 0.000 0.192 0.000 0.808 0.000
#> SRR2001088 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001089 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001090 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001091 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001084 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001085 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001086 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001087 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001080 4 0.2605 0.8393 0.000 0.148 0.000 0.852 0.000
#> SRR2001081 4 0.2605 0.8393 0.000 0.148 0.000 0.852 0.000
#> SRR2001082 4 0.2605 0.8393 0.000 0.148 0.000 0.852 0.000
#> SRR2001083 4 0.2605 0.8393 0.000 0.148 0.000 0.852 0.000
#> SRR2001076 4 0.3913 0.6965 0.000 0.324 0.000 0.676 0.000
#> SRR2001077 4 0.3913 0.6965 0.000 0.324 0.000 0.676 0.000
#> SRR2001078 4 0.3913 0.6965 0.000 0.324 0.000 0.676 0.000
#> SRR2001079 4 0.3913 0.6965 0.000 0.324 0.000 0.676 0.000
#> SRR2001072 4 0.0162 0.8826 0.000 0.004 0.000 0.996 0.000
#> SRR2001073 4 0.0162 0.8826 0.000 0.004 0.000 0.996 0.000
#> SRR2001074 4 0.0162 0.8826 0.000 0.004 0.000 0.996 0.000
#> SRR2001075 4 0.0162 0.8826 0.000 0.004 0.000 0.996 0.000
#> SRR2001068 4 0.3876 0.6867 0.000 0.316 0.000 0.684 0.000
#> SRR2001069 4 0.3876 0.6867 0.000 0.316 0.000 0.684 0.000
#> SRR2001070 4 0.3876 0.6867 0.000 0.316 0.000 0.684 0.000
#> SRR2001071 4 0.3876 0.6867 0.000 0.316 0.000 0.684 0.000
#> SRR2001064 2 0.0162 1.0000 0.000 0.996 0.000 0.004 0.000
#> SRR2001065 2 0.0162 1.0000 0.000 0.996 0.000 0.004 0.000
#> SRR2001066 2 0.0162 1.0000 0.000 0.996 0.000 0.004 0.000
#> SRR2001067 2 0.0162 1.0000 0.000 0.996 0.000 0.004 0.000
#> SRR2001060 4 0.0162 0.8826 0.000 0.004 0.000 0.996 0.000
#> SRR2001061 4 0.0162 0.8826 0.000 0.004 0.000 0.996 0.000
#> SRR2001062 4 0.0162 0.8826 0.000 0.004 0.000 0.996 0.000
#> SRR2001063 4 0.0162 0.8826 0.000 0.004 0.000 0.996 0.000
#> SRR2001056 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001057 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001058 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001059 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001052 4 0.3336 0.7911 0.000 0.228 0.000 0.772 0.000
#> SRR2001053 4 0.3336 0.7911 0.000 0.228 0.000 0.772 0.000
#> SRR2001054 4 0.3336 0.7911 0.000 0.228 0.000 0.772 0.000
#> SRR2001055 4 0.3336 0.7911 0.000 0.228 0.000 0.772 0.000
#> SRR2001048 4 0.3876 0.6861 0.000 0.316 0.000 0.684 0.000
#> SRR2001049 4 0.3876 0.6861 0.000 0.316 0.000 0.684 0.000
#> SRR2001050 4 0.3876 0.6861 0.000 0.316 0.000 0.684 0.000
#> SRR2001051 4 0.3876 0.6861 0.000 0.316 0.000 0.684 0.000
#> SRR2001044 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001045 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001046 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001047 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001040 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001041 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001042 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001043 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001036 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001037 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001038 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001039 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001028 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001029 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001030 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001031 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001024 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001025 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001026 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001027 4 0.0000 0.8828 0.000 0.000 0.000 1.000 0.000
#> SRR2001020 4 0.1908 0.8592 0.000 0.092 0.000 0.908 0.000
#> SRR2001021 4 0.1908 0.8592 0.000 0.092 0.000 0.908 0.000
#> SRR2001022 4 0.1908 0.8592 0.000 0.092 0.000 0.908 0.000
#> SRR2001023 4 0.1908 0.8592 0.000 0.092 0.000 0.908 0.000
#> SRR2001016 4 0.0963 0.8776 0.000 0.036 0.000 0.964 0.000
#> SRR2001017 4 0.0963 0.8776 0.000 0.036 0.000 0.964 0.000
#> SRR2001018 4 0.0963 0.8776 0.000 0.036 0.000 0.964 0.000
#> SRR2001019 4 0.0963 0.8776 0.000 0.036 0.000 0.964 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 4 0.3122 0.815 0.000 0.020 0.000 0.804 0.176 0.000
#> SRR2001033 4 0.3122 0.815 0.000 0.020 0.000 0.804 0.176 0.000
#> SRR2001034 4 0.3122 0.815 0.000 0.020 0.000 0.804 0.176 0.000
#> SRR2001035 4 0.3122 0.815 0.000 0.020 0.000 0.804 0.176 0.000
#> SRR2001204 6 0.0632 0.781 0.024 0.000 0.000 0.000 0.000 0.976
#> SRR2001205 6 0.0632 0.781 0.024 0.000 0.000 0.000 0.000 0.976
#> SRR2001206 6 0.0632 0.781 0.024 0.000 0.000 0.000 0.000 0.976
#> SRR2001207 6 0.0632 0.781 0.024 0.000 0.000 0.000 0.000 0.976
#> SRR2001200 1 0.0000 0.780 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001201 1 0.0000 0.780 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001202 1 0.0000 0.780 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001203 1 0.0000 0.780 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001196 1 0.0000 0.780 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001197 1 0.0000 0.780 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001198 1 0.0000 0.780 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001199 1 0.0000 0.780 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001192 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001193 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001194 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001195 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001188 1 0.3647 0.551 0.640 0.000 0.000 0.000 0.000 0.360
#> SRR2001189 1 0.3647 0.551 0.640 0.000 0.000 0.000 0.000 0.360
#> SRR2001190 1 0.3647 0.551 0.640 0.000 0.000 0.000 0.000 0.360
#> SRR2001191 1 0.3647 0.551 0.640 0.000 0.000 0.000 0.000 0.360
#> SRR2001184 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001185 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001186 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001187 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001180 1 0.3672 0.550 0.632 0.000 0.000 0.000 0.000 0.368
#> SRR2001181 1 0.3672 0.550 0.632 0.000 0.000 0.000 0.000 0.368
#> SRR2001182 1 0.3672 0.550 0.632 0.000 0.000 0.000 0.000 0.368
#> SRR2001183 1 0.3672 0.550 0.632 0.000 0.000 0.000 0.000 0.368
#> SRR2001176 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001177 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001178 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001179 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001172 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001173 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001174 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001175 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001168 6 0.0000 0.783 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001169 6 0.0000 0.783 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001170 6 0.0000 0.783 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001171 6 0.0000 0.783 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001164 1 0.0363 0.786 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR2001165 1 0.0363 0.786 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR2001166 1 0.0363 0.786 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR2001167 1 0.0363 0.786 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR2001160 1 0.3351 0.679 0.712 0.000 0.000 0.000 0.000 0.288
#> SRR2001161 1 0.3351 0.679 0.712 0.000 0.000 0.000 0.000 0.288
#> SRR2001162 1 0.3351 0.679 0.712 0.000 0.000 0.000 0.000 0.288
#> SRR2001163 1 0.3351 0.679 0.712 0.000 0.000 0.000 0.000 0.288
#> SRR2001156 1 0.1387 0.798 0.932 0.000 0.000 0.000 0.000 0.068
#> SRR2001157 1 0.1387 0.798 0.932 0.000 0.000 0.000 0.000 0.068
#> SRR2001158 1 0.1387 0.798 0.932 0.000 0.000 0.000 0.000 0.068
#> SRR2001159 1 0.1387 0.798 0.932 0.000 0.000 0.000 0.000 0.068
#> SRR2001152 6 0.3810 0.134 0.428 0.000 0.000 0.000 0.000 0.572
#> SRR2001153 6 0.3810 0.134 0.428 0.000 0.000 0.000 0.000 0.572
#> SRR2001154 6 0.3810 0.134 0.428 0.000 0.000 0.000 0.000 0.572
#> SRR2001155 6 0.3810 0.134 0.428 0.000 0.000 0.000 0.000 0.572
#> SRR2001148 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001149 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001150 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001151 3 0.0000 1.000 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001144 6 0.0260 0.785 0.008 0.000 0.000 0.000 0.000 0.992
#> SRR2001145 6 0.0260 0.785 0.008 0.000 0.000 0.000 0.000 0.992
#> SRR2001146 6 0.0260 0.785 0.008 0.000 0.000 0.000 0.000 0.992
#> SRR2001147 6 0.0260 0.785 0.008 0.000 0.000 0.000 0.000 0.992
#> SRR2001140 6 0.1556 0.748 0.080 0.000 0.000 0.000 0.000 0.920
#> SRR2001142 6 0.1556 0.748 0.080 0.000 0.000 0.000 0.000 0.920
#> SRR2001143 6 0.1556 0.748 0.080 0.000 0.000 0.000 0.000 0.920
#> SRR2001136 5 0.2597 0.998 0.000 0.000 0.176 0.000 0.824 0.000
#> SRR2001137 5 0.2597 0.998 0.000 0.000 0.176 0.000 0.824 0.000
#> SRR2001138 5 0.2597 0.998 0.000 0.000 0.176 0.000 0.824 0.000
#> SRR2001139 5 0.2597 0.998 0.000 0.000 0.176 0.000 0.824 0.000
#> SRR2001132 5 0.2631 0.996 0.000 0.000 0.180 0.000 0.820 0.000
#> SRR2001133 5 0.2631 0.996 0.000 0.000 0.180 0.000 0.820 0.000
#> SRR2001134 5 0.2631 0.996 0.000 0.000 0.180 0.000 0.820 0.000
#> SRR2001135 5 0.2631 0.996 0.000 0.000 0.180 0.000 0.820 0.000
#> SRR2001128 6 0.3868 -0.108 0.492 0.000 0.000 0.000 0.000 0.508
#> SRR2001129 6 0.3868 -0.108 0.492 0.000 0.000 0.000 0.000 0.508
#> SRR2001130 6 0.3868 -0.108 0.492 0.000 0.000 0.000 0.000 0.508
#> SRR2001131 6 0.3868 -0.108 0.492 0.000 0.000 0.000 0.000 0.508
#> SRR2001124 1 0.1387 0.798 0.932 0.000 0.000 0.000 0.000 0.068
#> SRR2001125 1 0.1387 0.798 0.932 0.000 0.000 0.000 0.000 0.068
#> SRR2001126 1 0.1387 0.798 0.932 0.000 0.000 0.000 0.000 0.068
#> SRR2001127 1 0.1387 0.798 0.932 0.000 0.000 0.000 0.000 0.068
#> SRR2001120 6 0.0000 0.783 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001121 6 0.0000 0.783 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001122 6 0.0000 0.783 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001123 6 0.0000 0.783 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001116 1 0.3221 0.703 0.736 0.000 0.000 0.000 0.000 0.264
#> SRR2001117 1 0.3221 0.703 0.736 0.000 0.000 0.000 0.000 0.264
#> SRR2001118 1 0.3221 0.703 0.736 0.000 0.000 0.000 0.000 0.264
#> SRR2001119 1 0.3221 0.703 0.736 0.000 0.000 0.000 0.000 0.264
#> SRR2001112 5 0.2597 0.998 0.000 0.000 0.176 0.000 0.824 0.000
#> SRR2001113 5 0.2597 0.998 0.000 0.000 0.176 0.000 0.824 0.000
#> SRR2001114 5 0.2597 0.998 0.000 0.000 0.176 0.000 0.824 0.000
#> SRR2001115 5 0.2597 0.998 0.000 0.000 0.176 0.000 0.824 0.000
#> SRR2001108 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001109 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001110 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001111 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001104 4 0.5134 0.661 0.000 0.228 0.000 0.620 0.152 0.000
#> SRR2001105 4 0.5134 0.661 0.000 0.228 0.000 0.620 0.152 0.000
#> SRR2001106 4 0.5134 0.661 0.000 0.228 0.000 0.620 0.152 0.000
#> SRR2001107 4 0.5134 0.661 0.000 0.228 0.000 0.620 0.152 0.000
#> SRR2001100 4 0.4079 0.682 0.000 0.288 0.000 0.680 0.032 0.000
#> SRR2001101 4 0.4079 0.682 0.000 0.288 0.000 0.680 0.032 0.000
#> SRR2001102 4 0.4079 0.682 0.000 0.288 0.000 0.680 0.032 0.000
#> SRR2001103 4 0.4079 0.682 0.000 0.288 0.000 0.680 0.032 0.000
#> SRR2001096 2 0.0000 1.000 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001097 2 0.0000 1.000 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001098 2 0.0000 1.000 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001099 2 0.0000 1.000 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001092 4 0.3852 0.789 0.000 0.064 0.000 0.760 0.176 0.000
#> SRR2001093 4 0.3852 0.789 0.000 0.064 0.000 0.760 0.176 0.000
#> SRR2001094 4 0.3852 0.789 0.000 0.064 0.000 0.760 0.176 0.000
#> SRR2001095 4 0.3852 0.789 0.000 0.064 0.000 0.760 0.176 0.000
#> SRR2001088 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001089 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001090 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001091 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001084 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001085 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001086 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001087 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001080 4 0.3168 0.815 0.000 0.024 0.000 0.804 0.172 0.000
#> SRR2001081 4 0.3168 0.815 0.000 0.024 0.000 0.804 0.172 0.000
#> SRR2001082 4 0.3168 0.815 0.000 0.024 0.000 0.804 0.172 0.000
#> SRR2001083 4 0.3168 0.815 0.000 0.024 0.000 0.804 0.172 0.000
#> SRR2001076 4 0.5117 0.676 0.000 0.200 0.000 0.628 0.172 0.000
#> SRR2001077 4 0.5117 0.676 0.000 0.200 0.000 0.628 0.172 0.000
#> SRR2001078 4 0.5117 0.676 0.000 0.200 0.000 0.628 0.172 0.000
#> SRR2001079 4 0.5117 0.676 0.000 0.200 0.000 0.628 0.172 0.000
#> SRR2001072 4 0.0146 0.876 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR2001073 4 0.0146 0.876 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR2001074 4 0.0146 0.876 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR2001075 4 0.0146 0.876 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR2001068 4 0.3636 0.669 0.000 0.320 0.000 0.676 0.004 0.000
#> SRR2001069 4 0.3636 0.669 0.000 0.320 0.000 0.676 0.004 0.000
#> SRR2001070 4 0.3636 0.669 0.000 0.320 0.000 0.676 0.004 0.000
#> SRR2001071 4 0.3636 0.669 0.000 0.320 0.000 0.676 0.004 0.000
#> SRR2001064 2 0.0000 1.000 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001065 2 0.0000 1.000 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001066 2 0.0000 1.000 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001067 2 0.0000 1.000 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001060 4 0.0146 0.876 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR2001061 4 0.0146 0.876 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR2001062 4 0.0146 0.876 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR2001063 4 0.0146 0.876 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR2001056 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001057 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001058 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001059 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001052 4 0.4117 0.783 0.000 0.140 0.000 0.748 0.112 0.000
#> SRR2001053 4 0.4117 0.783 0.000 0.140 0.000 0.748 0.112 0.000
#> SRR2001054 4 0.4117 0.783 0.000 0.140 0.000 0.748 0.112 0.000
#> SRR2001055 4 0.4117 0.783 0.000 0.140 0.000 0.748 0.112 0.000
#> SRR2001048 4 0.3802 0.672 0.000 0.312 0.000 0.676 0.012 0.000
#> SRR2001049 4 0.3802 0.672 0.000 0.312 0.000 0.676 0.012 0.000
#> SRR2001050 4 0.3802 0.672 0.000 0.312 0.000 0.676 0.012 0.000
#> SRR2001051 4 0.3802 0.672 0.000 0.312 0.000 0.676 0.012 0.000
#> SRR2001044 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001045 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001046 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001047 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001040 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001041 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001042 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001043 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001036 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001037 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001038 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001039 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001028 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001029 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001030 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001031 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001024 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001025 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001026 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001027 4 0.0000 0.876 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001020 4 0.2302 0.842 0.000 0.008 0.000 0.872 0.120 0.000
#> SRR2001021 4 0.2302 0.842 0.000 0.008 0.000 0.872 0.120 0.000
#> SRR2001022 4 0.2302 0.842 0.000 0.008 0.000 0.872 0.120 0.000
#> SRR2001023 4 0.2302 0.842 0.000 0.008 0.000 0.872 0.120 0.000
#> SRR2001016 4 0.0865 0.869 0.000 0.036 0.000 0.964 0.000 0.000
#> SRR2001017 4 0.0865 0.869 0.000 0.036 0.000 0.964 0.000 0.000
#> SRR2001018 4 0.0865 0.869 0.000 0.036 0.000 0.964 0.000 0.000
#> SRR2001019 4 0.0865 0.869 0.000 0.036 0.000 0.964 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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.5031 0.497 0.497
#> 3 3 0.762 0.450 0.590 0.2362 0.897 0.792
#> 4 4 0.654 0.911 0.811 0.1185 0.757 0.458
#> 5 5 0.593 0.855 0.787 0.0647 1.000 1.000
#> 6 6 0.803 0.816 0.739 0.0629 0.946 0.792
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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001033 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001034 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001035 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001204 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001205 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001206 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001207 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001200 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001201 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001202 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001203 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001196 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001197 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001198 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001199 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001192 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001193 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001194 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001195 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001188 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001189 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001190 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001191 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001184 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001185 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001186 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001187 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001180 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001181 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001182 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001183 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001176 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001177 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001178 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001179 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001172 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001173 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001174 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001175 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001168 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001169 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001170 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001171 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001164 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001165 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001166 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001167 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001160 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001161 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001162 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001163 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001156 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001157 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001158 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001159 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001152 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001153 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001154 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001155 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001148 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001149 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001150 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001151 3 0.0000 0.463 0.000 0.000 1.000
#> SRR2001144 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001145 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001146 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001147 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001140 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001142 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001143 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001136 3 0.1031 0.454 0.024 0.000 0.976
#> SRR2001137 3 0.1031 0.454 0.024 0.000 0.976
#> SRR2001138 3 0.1031 0.454 0.024 0.000 0.976
#> SRR2001139 3 0.1031 0.454 0.024 0.000 0.976
#> SRR2001132 3 0.0747 0.458 0.016 0.000 0.984
#> SRR2001133 3 0.0747 0.458 0.016 0.000 0.984
#> SRR2001134 3 0.0747 0.458 0.016 0.000 0.984
#> SRR2001135 3 0.0747 0.458 0.016 0.000 0.984
#> SRR2001128 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001129 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001130 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001131 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001124 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001125 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001126 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001127 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001120 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001121 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001122 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001123 3 0.6305 -0.900 0.484 0.000 0.516
#> SRR2001116 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001117 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001118 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001119 1 0.6308 1.000 0.508 0.000 0.492
#> SRR2001112 3 0.1031 0.454 0.024 0.000 0.976
#> SRR2001113 3 0.1031 0.454 0.024 0.000 0.976
#> SRR2001114 3 0.1031 0.454 0.024 0.000 0.976
#> SRR2001115 3 0.1031 0.454 0.024 0.000 0.976
#> SRR2001108 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001109 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001110 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001111 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001104 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001105 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001106 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001107 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001100 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001101 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001102 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001103 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001096 2 0.6308 0.777 0.492 0.508 0.000
#> SRR2001097 2 0.6308 0.777 0.492 0.508 0.000
#> SRR2001098 2 0.6308 0.777 0.492 0.508 0.000
#> SRR2001099 2 0.6308 0.777 0.492 0.508 0.000
#> SRR2001092 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001093 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001094 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001095 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001088 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001089 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001090 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001091 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001084 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001085 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001086 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001087 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001080 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001081 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001082 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001083 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001076 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001077 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001078 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001079 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001072 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001073 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001074 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001075 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001068 2 0.6308 0.777 0.492 0.508 0.000
#> SRR2001069 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001070 2 0.6308 0.777 0.492 0.508 0.000
#> SRR2001071 2 0.6308 0.777 0.492 0.508 0.000
#> SRR2001064 2 0.6308 0.777 0.492 0.508 0.000
#> SRR2001065 2 0.6308 0.777 0.492 0.508 0.000
#> SRR2001066 2 0.6308 0.777 0.492 0.508 0.000
#> SRR2001067 2 0.6308 0.777 0.492 0.508 0.000
#> SRR2001060 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001061 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001062 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001063 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001056 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001057 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001058 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001059 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001052 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001053 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001054 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001055 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001048 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001049 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001050 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001051 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001044 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001045 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001046 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001047 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001040 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001041 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001042 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001043 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001036 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001037 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001038 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001039 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001028 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001029 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001030 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001031 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001024 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001025 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001026 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001027 2 0.0000 0.778 0.000 1.000 0.000
#> SRR2001020 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001021 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001022 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001023 2 0.6307 0.778 0.488 0.512 0.000
#> SRR2001016 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001017 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001018 2 0.0237 0.777 0.004 0.996 0.000
#> SRR2001019 2 0.0237 0.777 0.004 0.996 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.1474 0.922 0.000 0.948 0.052 0.000
#> SRR2001033 2 0.1474 0.922 0.000 0.948 0.052 0.000
#> SRR2001034 2 0.1474 0.922 0.000 0.948 0.052 0.000
#> SRR2001035 2 0.1474 0.922 0.000 0.948 0.052 0.000
#> SRR2001204 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001205 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001206 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001207 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001200 1 0.3718 0.837 0.820 0.000 0.012 0.168
#> SRR2001201 1 0.3718 0.837 0.820 0.000 0.012 0.168
#> SRR2001202 1 0.3718 0.837 0.820 0.000 0.012 0.168
#> SRR2001203 1 0.3718 0.837 0.820 0.000 0.012 0.168
#> SRR2001196 1 0.3672 0.840 0.824 0.000 0.012 0.164
#> SRR2001197 1 0.3672 0.840 0.824 0.000 0.012 0.164
#> SRR2001198 1 0.3672 0.840 0.824 0.000 0.012 0.164
#> SRR2001199 1 0.3672 0.840 0.824 0.000 0.012 0.164
#> SRR2001192 3 0.4781 0.983 0.336 0.000 0.660 0.004
#> SRR2001193 3 0.4781 0.983 0.336 0.000 0.660 0.004
#> SRR2001194 3 0.4781 0.983 0.336 0.000 0.660 0.004
#> SRR2001195 3 0.4781 0.983 0.336 0.000 0.660 0.004
#> SRR2001188 1 0.1867 0.852 0.928 0.000 0.000 0.072
#> SRR2001189 1 0.1716 0.853 0.936 0.000 0.000 0.064
#> SRR2001190 1 0.1716 0.853 0.936 0.000 0.000 0.064
#> SRR2001191 1 0.1792 0.853 0.932 0.000 0.000 0.068
#> SRR2001184 3 0.4605 0.985 0.336 0.000 0.664 0.000
#> SRR2001185 3 0.4605 0.985 0.336 0.000 0.664 0.000
#> SRR2001186 3 0.4605 0.985 0.336 0.000 0.664 0.000
#> SRR2001187 3 0.4605 0.985 0.336 0.000 0.664 0.000
#> SRR2001180 1 0.0188 0.852 0.996 0.000 0.000 0.004
#> SRR2001181 1 0.0000 0.852 1.000 0.000 0.000 0.000
#> SRR2001182 1 0.0000 0.852 1.000 0.000 0.000 0.000
#> SRR2001183 1 0.0592 0.850 0.984 0.000 0.000 0.016
#> SRR2001176 3 0.4761 0.984 0.332 0.000 0.664 0.004
#> SRR2001177 3 0.4761 0.984 0.332 0.000 0.664 0.004
#> SRR2001178 3 0.4761 0.984 0.332 0.000 0.664 0.004
#> SRR2001179 3 0.4761 0.984 0.332 0.000 0.664 0.004
#> SRR2001172 3 0.4605 0.985 0.336 0.000 0.664 0.000
#> SRR2001173 3 0.4605 0.985 0.336 0.000 0.664 0.000
#> SRR2001174 3 0.4605 0.985 0.336 0.000 0.664 0.000
#> SRR2001175 3 0.4605 0.985 0.336 0.000 0.664 0.000
#> SRR2001168 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001169 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001170 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001171 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001164 1 0.3672 0.840 0.824 0.000 0.012 0.164
#> SRR2001165 1 0.3672 0.840 0.824 0.000 0.012 0.164
#> SRR2001166 1 0.3672 0.840 0.824 0.000 0.012 0.164
#> SRR2001167 1 0.3672 0.840 0.824 0.000 0.012 0.164
#> SRR2001160 1 0.3577 0.842 0.832 0.000 0.012 0.156
#> SRR2001161 1 0.3577 0.842 0.832 0.000 0.012 0.156
#> SRR2001162 1 0.3577 0.842 0.832 0.000 0.012 0.156
#> SRR2001163 1 0.3577 0.842 0.832 0.000 0.012 0.156
#> SRR2001156 1 0.3672 0.840 0.824 0.000 0.012 0.164
#> SRR2001157 1 0.3672 0.840 0.824 0.000 0.012 0.164
#> SRR2001158 1 0.3672 0.840 0.824 0.000 0.012 0.164
#> SRR2001159 1 0.3672 0.840 0.824 0.000 0.012 0.164
#> SRR2001152 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001153 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001154 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001155 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001148 3 0.4605 0.985 0.336 0.000 0.664 0.000
#> SRR2001149 3 0.4605 0.985 0.336 0.000 0.664 0.000
#> SRR2001150 3 0.4605 0.985 0.336 0.000 0.664 0.000
#> SRR2001151 3 0.4605 0.985 0.336 0.000 0.664 0.000
#> SRR2001144 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001145 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001146 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001147 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001140 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001142 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001143 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001136 3 0.5110 0.976 0.328 0.000 0.656 0.016
#> SRR2001137 3 0.5110 0.976 0.328 0.000 0.656 0.016
#> SRR2001138 3 0.5110 0.976 0.328 0.000 0.656 0.016
#> SRR2001139 3 0.5110 0.976 0.328 0.000 0.656 0.016
#> SRR2001132 3 0.4999 0.977 0.328 0.000 0.660 0.012
#> SRR2001133 3 0.4999 0.977 0.328 0.000 0.660 0.012
#> SRR2001134 3 0.4999 0.977 0.328 0.000 0.660 0.012
#> SRR2001135 3 0.4999 0.977 0.328 0.000 0.660 0.012
#> SRR2001128 1 0.1109 0.847 0.968 0.000 0.004 0.028
#> SRR2001129 1 0.1209 0.847 0.964 0.000 0.004 0.032
#> SRR2001130 1 0.1109 0.847 0.968 0.000 0.004 0.028
#> SRR2001131 1 0.1109 0.847 0.968 0.000 0.004 0.028
#> SRR2001124 1 0.3672 0.840 0.824 0.000 0.012 0.164
#> SRR2001125 1 0.3672 0.840 0.824 0.000 0.012 0.164
#> SRR2001126 1 0.3672 0.840 0.824 0.000 0.012 0.164
#> SRR2001127 1 0.3672 0.840 0.824 0.000 0.012 0.164
#> SRR2001120 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001121 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001122 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001123 1 0.1978 0.838 0.928 0.000 0.004 0.068
#> SRR2001116 1 0.3577 0.842 0.832 0.000 0.012 0.156
#> SRR2001117 1 0.3577 0.842 0.832 0.000 0.012 0.156
#> SRR2001118 1 0.3577 0.842 0.832 0.000 0.012 0.156
#> SRR2001119 1 0.3577 0.842 0.832 0.000 0.012 0.156
#> SRR2001112 3 0.5110 0.976 0.328 0.000 0.656 0.016
#> SRR2001113 3 0.5110 0.976 0.328 0.000 0.656 0.016
#> SRR2001114 3 0.5110 0.976 0.328 0.000 0.656 0.016
#> SRR2001115 3 0.5110 0.976 0.328 0.000 0.656 0.016
#> SRR2001108 4 0.4391 0.956 0.000 0.252 0.008 0.740
#> SRR2001109 4 0.4391 0.956 0.000 0.252 0.008 0.740
#> SRR2001110 4 0.4391 0.956 0.000 0.252 0.008 0.740
#> SRR2001111 4 0.4391 0.956 0.000 0.252 0.008 0.740
#> SRR2001104 2 0.0707 0.935 0.000 0.980 0.020 0.000
#> SRR2001105 2 0.0707 0.935 0.000 0.980 0.020 0.000
#> SRR2001106 2 0.0707 0.935 0.000 0.980 0.020 0.000
#> SRR2001107 2 0.0707 0.935 0.000 0.980 0.020 0.000
#> SRR2001100 2 0.1716 0.931 0.000 0.936 0.064 0.000
#> SRR2001101 2 0.1716 0.931 0.000 0.936 0.064 0.000
#> SRR2001102 2 0.1716 0.931 0.000 0.936 0.064 0.000
#> SRR2001103 2 0.1716 0.931 0.000 0.936 0.064 0.000
#> SRR2001096 2 0.3024 0.914 0.000 0.852 0.148 0.000
#> SRR2001097 2 0.3024 0.914 0.000 0.852 0.148 0.000
#> SRR2001098 2 0.3024 0.914 0.000 0.852 0.148 0.000
#> SRR2001099 2 0.3024 0.914 0.000 0.852 0.148 0.000
#> SRR2001092 2 0.2011 0.926 0.000 0.920 0.080 0.000
#> SRR2001093 2 0.2081 0.924 0.000 0.916 0.084 0.000
#> SRR2001094 2 0.2011 0.926 0.000 0.920 0.080 0.000
#> SRR2001095 2 0.2011 0.926 0.000 0.920 0.080 0.000
#> SRR2001088 4 0.5907 0.945 0.000 0.252 0.080 0.668
#> SRR2001089 4 0.5907 0.945 0.000 0.252 0.080 0.668
#> SRR2001090 4 0.5907 0.945 0.000 0.252 0.080 0.668
#> SRR2001091 4 0.5907 0.945 0.000 0.252 0.080 0.668
#> SRR2001084 4 0.5508 0.949 0.000 0.252 0.056 0.692
#> SRR2001085 4 0.5508 0.949 0.000 0.252 0.056 0.692
#> SRR2001086 4 0.5508 0.949 0.000 0.252 0.056 0.692
#> SRR2001087 4 0.5508 0.949 0.000 0.252 0.056 0.692
#> SRR2001080 2 0.1118 0.926 0.000 0.964 0.036 0.000
#> SRR2001081 2 0.1118 0.926 0.000 0.964 0.036 0.000
#> SRR2001082 2 0.1118 0.926 0.000 0.964 0.036 0.000
#> SRR2001083 2 0.1118 0.926 0.000 0.964 0.036 0.000
#> SRR2001076 2 0.1118 0.928 0.000 0.964 0.036 0.000
#> SRR2001077 2 0.1118 0.928 0.000 0.964 0.036 0.000
#> SRR2001078 2 0.1118 0.928 0.000 0.964 0.036 0.000
#> SRR2001079 2 0.1118 0.928 0.000 0.964 0.036 0.000
#> SRR2001072 4 0.6195 0.936 0.000 0.252 0.100 0.648
#> SRR2001073 4 0.6195 0.936 0.000 0.252 0.100 0.648
#> SRR2001074 4 0.6195 0.936 0.000 0.252 0.100 0.648
#> SRR2001075 4 0.6195 0.936 0.000 0.252 0.100 0.648
#> SRR2001068 2 0.2408 0.925 0.000 0.896 0.104 0.000
#> SRR2001069 2 0.2345 0.926 0.000 0.900 0.100 0.000
#> SRR2001070 2 0.2408 0.925 0.000 0.896 0.104 0.000
#> SRR2001071 2 0.2408 0.925 0.000 0.896 0.104 0.000
#> SRR2001064 2 0.3024 0.914 0.000 0.852 0.148 0.000
#> SRR2001065 2 0.3024 0.914 0.000 0.852 0.148 0.000
#> SRR2001066 2 0.3024 0.914 0.000 0.852 0.148 0.000
#> SRR2001067 2 0.3024 0.914 0.000 0.852 0.148 0.000
#> SRR2001060 4 0.5907 0.945 0.000 0.252 0.080 0.668
#> SRR2001061 4 0.5907 0.945 0.000 0.252 0.080 0.668
#> SRR2001062 4 0.5907 0.945 0.000 0.252 0.080 0.668
#> SRR2001063 4 0.5907 0.945 0.000 0.252 0.080 0.668
#> SRR2001056 4 0.4391 0.956 0.000 0.252 0.008 0.740
#> SRR2001057 4 0.4391 0.956 0.000 0.252 0.008 0.740
#> SRR2001058 4 0.4391 0.956 0.000 0.252 0.008 0.740
#> SRR2001059 4 0.4391 0.956 0.000 0.252 0.008 0.740
#> SRR2001052 2 0.2589 0.926 0.000 0.884 0.116 0.000
#> SRR2001053 2 0.2530 0.927 0.000 0.888 0.112 0.000
#> SRR2001054 2 0.2589 0.926 0.000 0.884 0.116 0.000
#> SRR2001055 2 0.2589 0.926 0.000 0.884 0.116 0.000
#> SRR2001048 2 0.2149 0.927 0.000 0.912 0.088 0.000
#> SRR2001049 2 0.2149 0.927 0.000 0.912 0.088 0.000
#> SRR2001050 2 0.2149 0.927 0.000 0.912 0.088 0.000
#> SRR2001051 2 0.2149 0.927 0.000 0.912 0.088 0.000
#> SRR2001044 4 0.4737 0.951 0.000 0.252 0.020 0.728
#> SRR2001045 4 0.4737 0.951 0.000 0.252 0.020 0.728
#> SRR2001046 4 0.4737 0.951 0.000 0.252 0.020 0.728
#> SRR2001047 4 0.4737 0.951 0.000 0.252 0.020 0.728
#> SRR2001040 4 0.4630 0.957 0.000 0.252 0.016 0.732
#> SRR2001041 4 0.4630 0.957 0.000 0.252 0.016 0.732
#> SRR2001042 4 0.4630 0.957 0.000 0.252 0.016 0.732
#> SRR2001043 4 0.4630 0.957 0.000 0.252 0.016 0.732
#> SRR2001036 4 0.4516 0.957 0.000 0.252 0.012 0.736
#> SRR2001037 4 0.4516 0.957 0.000 0.252 0.012 0.736
#> SRR2001038 4 0.4516 0.957 0.000 0.252 0.012 0.736
#> SRR2001039 4 0.4516 0.957 0.000 0.252 0.012 0.736
#> SRR2001028 4 0.4737 0.951 0.000 0.252 0.020 0.728
#> SRR2001029 4 0.4737 0.951 0.000 0.252 0.020 0.728
#> SRR2001030 4 0.4737 0.951 0.000 0.252 0.020 0.728
#> SRR2001031 4 0.4737 0.951 0.000 0.252 0.020 0.728
#> SRR2001024 4 0.4934 0.955 0.000 0.252 0.028 0.720
#> SRR2001025 4 0.4934 0.955 0.000 0.252 0.028 0.720
#> SRR2001026 4 0.4934 0.955 0.000 0.252 0.028 0.720
#> SRR2001027 4 0.4934 0.955 0.000 0.252 0.028 0.720
#> SRR2001020 2 0.2737 0.906 0.000 0.888 0.104 0.008
#> SRR2001021 2 0.2737 0.906 0.000 0.888 0.104 0.008
#> SRR2001022 2 0.2737 0.906 0.000 0.888 0.104 0.008
#> SRR2001023 2 0.2737 0.906 0.000 0.888 0.104 0.008
#> SRR2001016 4 0.6723 0.878 0.000 0.260 0.140 0.600
#> SRR2001017 4 0.6723 0.878 0.000 0.260 0.140 0.600
#> SRR2001018 4 0.6723 0.878 0.000 0.260 0.140 0.600
#> SRR2001019 4 0.6723 0.878 0.000 0.260 0.140 0.600
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.5091 0.869 0.000 0.720 0.016 0.180 0.084
#> SRR2001033 2 0.5091 0.869 0.000 0.720 0.016 0.180 0.084
#> SRR2001034 2 0.5091 0.869 0.000 0.720 0.016 0.180 0.084
#> SRR2001035 2 0.5091 0.869 0.000 0.720 0.016 0.180 0.084
#> SRR2001204 1 0.4804 0.774 0.624 0.024 0.004 0.000 0.348
#> SRR2001205 1 0.4804 0.774 0.624 0.024 0.004 0.000 0.348
#> SRR2001206 1 0.4804 0.774 0.624 0.024 0.004 0.000 0.348
#> SRR2001207 1 0.4804 0.774 0.624 0.024 0.004 0.000 0.348
#> SRR2001200 1 0.1386 0.779 0.952 0.032 0.000 0.000 0.016
#> SRR2001201 1 0.1386 0.779 0.952 0.032 0.000 0.000 0.016
#> SRR2001202 1 0.1386 0.779 0.952 0.032 0.000 0.000 0.016
#> SRR2001203 1 0.1386 0.779 0.952 0.032 0.000 0.000 0.016
#> SRR2001196 1 0.0955 0.787 0.968 0.028 0.000 0.000 0.004
#> SRR2001197 1 0.0955 0.787 0.968 0.028 0.000 0.000 0.004
#> SRR2001198 1 0.0955 0.787 0.968 0.028 0.000 0.000 0.004
#> SRR2001199 1 0.0955 0.787 0.968 0.028 0.000 0.000 0.004
#> SRR2001192 3 0.3648 0.948 0.188 0.004 0.792 0.000 0.016
#> SRR2001193 3 0.3648 0.948 0.188 0.004 0.792 0.000 0.016
#> SRR2001194 3 0.3648 0.948 0.188 0.004 0.792 0.000 0.016
#> SRR2001195 3 0.3648 0.948 0.188 0.004 0.792 0.000 0.016
#> SRR2001188 1 0.2681 0.802 0.876 0.012 0.004 0.000 0.108
#> SRR2001189 1 0.2783 0.802 0.868 0.012 0.004 0.000 0.116
#> SRR2001190 1 0.2783 0.802 0.868 0.012 0.004 0.000 0.116
#> SRR2001191 1 0.2783 0.802 0.868 0.012 0.004 0.000 0.116
#> SRR2001184 3 0.3282 0.949 0.188 0.008 0.804 0.000 0.000
#> SRR2001185 3 0.3282 0.949 0.188 0.008 0.804 0.000 0.000
#> SRR2001186 3 0.3282 0.949 0.188 0.008 0.804 0.000 0.000
#> SRR2001187 3 0.3282 0.949 0.188 0.008 0.804 0.000 0.000
#> SRR2001180 1 0.3883 0.800 0.764 0.016 0.004 0.000 0.216
#> SRR2001181 1 0.3851 0.800 0.768 0.016 0.004 0.000 0.212
#> SRR2001182 1 0.3914 0.799 0.760 0.016 0.004 0.000 0.220
#> SRR2001183 1 0.4169 0.795 0.724 0.016 0.004 0.000 0.256
#> SRR2001176 3 0.3997 0.948 0.188 0.004 0.776 0.000 0.032
#> SRR2001177 3 0.3997 0.948 0.188 0.004 0.776 0.000 0.032
#> SRR2001178 3 0.3997 0.948 0.188 0.004 0.776 0.000 0.032
#> SRR2001179 3 0.3997 0.948 0.188 0.004 0.776 0.000 0.032
#> SRR2001172 3 0.3282 0.949 0.188 0.008 0.804 0.000 0.000
#> SRR2001173 3 0.3282 0.949 0.188 0.008 0.804 0.000 0.000
#> SRR2001174 3 0.3282 0.949 0.188 0.008 0.804 0.000 0.000
#> SRR2001175 3 0.3282 0.949 0.188 0.008 0.804 0.000 0.000
#> SRR2001168 1 0.4688 0.771 0.616 0.016 0.004 0.000 0.364
#> SRR2001169 1 0.4688 0.771 0.616 0.016 0.004 0.000 0.364
#> SRR2001170 1 0.4688 0.771 0.616 0.016 0.004 0.000 0.364
#> SRR2001171 1 0.4688 0.771 0.616 0.016 0.004 0.000 0.364
#> SRR2001164 1 0.0865 0.788 0.972 0.024 0.000 0.000 0.004
#> SRR2001165 1 0.0865 0.788 0.972 0.024 0.000 0.000 0.004
#> SRR2001166 1 0.0865 0.788 0.972 0.024 0.000 0.000 0.004
#> SRR2001167 1 0.0865 0.788 0.972 0.024 0.000 0.000 0.004
#> SRR2001160 1 0.0404 0.792 0.988 0.012 0.000 0.000 0.000
#> SRR2001161 1 0.0404 0.792 0.988 0.012 0.000 0.000 0.000
#> SRR2001162 1 0.0404 0.792 0.988 0.012 0.000 0.000 0.000
#> SRR2001163 1 0.0404 0.792 0.988 0.012 0.000 0.000 0.000
#> SRR2001156 1 0.0865 0.788 0.972 0.024 0.000 0.000 0.004
#> SRR2001157 1 0.0865 0.788 0.972 0.024 0.000 0.000 0.004
#> SRR2001158 1 0.0865 0.788 0.972 0.024 0.000 0.000 0.004
#> SRR2001159 1 0.0865 0.788 0.972 0.024 0.000 0.000 0.004
#> SRR2001152 1 0.4434 0.776 0.640 0.008 0.004 0.000 0.348
#> SRR2001153 1 0.4434 0.776 0.640 0.008 0.004 0.000 0.348
#> SRR2001154 1 0.4434 0.776 0.640 0.008 0.004 0.000 0.348
#> SRR2001155 1 0.4434 0.776 0.640 0.008 0.004 0.000 0.348
#> SRR2001148 3 0.3282 0.949 0.188 0.008 0.804 0.000 0.000
#> SRR2001149 3 0.3282 0.949 0.188 0.008 0.804 0.000 0.000
#> SRR2001150 3 0.3282 0.949 0.188 0.008 0.804 0.000 0.000
#> SRR2001151 3 0.3282 0.949 0.188 0.008 0.804 0.000 0.000
#> SRR2001144 1 0.4276 0.773 0.616 0.000 0.004 0.000 0.380
#> SRR2001145 1 0.4276 0.773 0.616 0.000 0.004 0.000 0.380
#> SRR2001146 1 0.4276 0.773 0.616 0.000 0.004 0.000 0.380
#> SRR2001147 1 0.4276 0.773 0.616 0.000 0.004 0.000 0.380
#> SRR2001140 1 0.4491 0.774 0.624 0.008 0.004 0.000 0.364
#> SRR2001142 1 0.4491 0.774 0.624 0.008 0.004 0.000 0.364
#> SRR2001143 1 0.4491 0.774 0.624 0.008 0.004 0.000 0.364
#> SRR2001136 3 0.6109 0.913 0.192 0.088 0.656 0.000 0.064
#> SRR2001137 3 0.6109 0.913 0.192 0.088 0.656 0.000 0.064
#> SRR2001138 3 0.6109 0.913 0.192 0.088 0.656 0.000 0.064
#> SRR2001139 3 0.6109 0.913 0.192 0.088 0.656 0.000 0.064
#> SRR2001132 3 0.5407 0.932 0.192 0.044 0.704 0.000 0.060
#> SRR2001133 3 0.5407 0.932 0.192 0.044 0.704 0.000 0.060
#> SRR2001134 3 0.5407 0.932 0.192 0.044 0.704 0.000 0.060
#> SRR2001135 3 0.5407 0.932 0.192 0.044 0.704 0.000 0.060
#> SRR2001128 1 0.4178 0.791 0.696 0.008 0.004 0.000 0.292
#> SRR2001129 1 0.4220 0.789 0.688 0.008 0.004 0.000 0.300
#> SRR2001130 1 0.4178 0.791 0.696 0.008 0.004 0.000 0.292
#> SRR2001131 1 0.4178 0.791 0.696 0.008 0.004 0.000 0.292
#> SRR2001124 1 0.0865 0.789 0.972 0.024 0.000 0.000 0.004
#> SRR2001125 1 0.0865 0.789 0.972 0.024 0.000 0.000 0.004
#> SRR2001126 1 0.0865 0.789 0.972 0.024 0.000 0.000 0.004
#> SRR2001127 1 0.0865 0.789 0.972 0.024 0.000 0.000 0.004
#> SRR2001120 1 0.4517 0.772 0.616 0.008 0.004 0.000 0.372
#> SRR2001121 1 0.4517 0.772 0.616 0.008 0.004 0.000 0.372
#> SRR2001122 1 0.4517 0.772 0.616 0.008 0.004 0.000 0.372
#> SRR2001123 1 0.4517 0.772 0.616 0.008 0.004 0.000 0.372
#> SRR2001116 1 0.0290 0.792 0.992 0.008 0.000 0.000 0.000
#> SRR2001117 1 0.0290 0.792 0.992 0.008 0.000 0.000 0.000
#> SRR2001118 1 0.0290 0.792 0.992 0.008 0.000 0.000 0.000
#> SRR2001119 1 0.0290 0.792 0.992 0.008 0.000 0.000 0.000
#> SRR2001112 3 0.6263 0.907 0.192 0.096 0.644 0.000 0.068
#> SRR2001113 3 0.6263 0.907 0.192 0.096 0.644 0.000 0.068
#> SRR2001114 3 0.6263 0.907 0.192 0.096 0.644 0.000 0.068
#> SRR2001115 3 0.6263 0.907 0.192 0.096 0.644 0.000 0.068
#> SRR2001108 4 0.1357 0.903 0.000 0.000 0.004 0.948 0.048
#> SRR2001109 4 0.1357 0.903 0.000 0.000 0.004 0.948 0.048
#> SRR2001110 4 0.1357 0.903 0.000 0.000 0.004 0.948 0.048
#> SRR2001111 4 0.1357 0.903 0.000 0.000 0.004 0.948 0.048
#> SRR2001104 2 0.3881 0.886 0.000 0.788 0.008 0.180 0.024
#> SRR2001105 2 0.3881 0.886 0.000 0.788 0.008 0.180 0.024
#> SRR2001106 2 0.3881 0.886 0.000 0.788 0.008 0.180 0.024
#> SRR2001107 2 0.3881 0.886 0.000 0.788 0.008 0.180 0.024
#> SRR2001100 2 0.5373 0.878 0.000 0.704 0.024 0.180 0.092
#> SRR2001101 2 0.5373 0.878 0.000 0.704 0.024 0.180 0.092
#> SRR2001102 2 0.5373 0.878 0.000 0.704 0.024 0.180 0.092
#> SRR2001103 2 0.5373 0.878 0.000 0.704 0.024 0.180 0.092
#> SRR2001096 2 0.7504 0.806 0.000 0.528 0.144 0.180 0.148
#> SRR2001097 2 0.7504 0.806 0.000 0.528 0.144 0.180 0.148
#> SRR2001098 2 0.7504 0.806 0.000 0.528 0.144 0.180 0.148
#> SRR2001099 2 0.7504 0.806 0.000 0.528 0.144 0.180 0.148
#> SRR2001092 2 0.5624 0.873 0.000 0.696 0.056 0.180 0.068
#> SRR2001093 2 0.5681 0.872 0.000 0.692 0.056 0.180 0.072
#> SRR2001094 2 0.5681 0.872 0.000 0.692 0.056 0.180 0.072
#> SRR2001095 2 0.5681 0.872 0.000 0.692 0.056 0.180 0.072
#> SRR2001088 4 0.2852 0.880 0.000 0.000 0.000 0.828 0.172
#> SRR2001089 4 0.2852 0.880 0.000 0.000 0.000 0.828 0.172
#> SRR2001090 4 0.2852 0.880 0.000 0.000 0.000 0.828 0.172
#> SRR2001091 4 0.2852 0.880 0.000 0.000 0.000 0.828 0.172
#> SRR2001084 4 0.2930 0.885 0.000 0.000 0.004 0.832 0.164
#> SRR2001085 4 0.2930 0.885 0.000 0.000 0.004 0.832 0.164
#> SRR2001086 4 0.2930 0.885 0.000 0.000 0.004 0.832 0.164
#> SRR2001087 4 0.2930 0.885 0.000 0.000 0.004 0.832 0.164
#> SRR2001080 2 0.4899 0.871 0.000 0.736 0.020 0.180 0.064
#> SRR2001081 2 0.4899 0.871 0.000 0.736 0.020 0.180 0.064
#> SRR2001082 2 0.4899 0.871 0.000 0.736 0.020 0.180 0.064
#> SRR2001083 2 0.4899 0.871 0.000 0.736 0.020 0.180 0.064
#> SRR2001076 2 0.4183 0.879 0.000 0.776 0.020 0.180 0.024
#> SRR2001077 2 0.4183 0.879 0.000 0.776 0.020 0.180 0.024
#> SRR2001078 2 0.4183 0.879 0.000 0.776 0.020 0.180 0.024
#> SRR2001079 2 0.4183 0.879 0.000 0.776 0.020 0.180 0.024
#> SRR2001072 4 0.3039 0.871 0.000 0.000 0.000 0.808 0.192
#> SRR2001073 4 0.3039 0.871 0.000 0.000 0.000 0.808 0.192
#> SRR2001074 4 0.3039 0.871 0.000 0.000 0.000 0.808 0.192
#> SRR2001075 4 0.3039 0.871 0.000 0.000 0.000 0.808 0.192
#> SRR2001068 2 0.6071 0.869 0.000 0.656 0.044 0.180 0.120
#> SRR2001069 2 0.5889 0.871 0.000 0.668 0.036 0.180 0.116
#> SRR2001070 2 0.6113 0.868 0.000 0.652 0.044 0.180 0.124
#> SRR2001071 2 0.6113 0.868 0.000 0.652 0.044 0.180 0.124
#> SRR2001064 2 0.7502 0.806 0.000 0.528 0.140 0.180 0.152
#> SRR2001065 2 0.7502 0.806 0.000 0.528 0.140 0.180 0.152
#> SRR2001066 2 0.7502 0.806 0.000 0.528 0.140 0.180 0.152
#> SRR2001067 2 0.7502 0.806 0.000 0.528 0.140 0.180 0.152
#> SRR2001060 4 0.2891 0.878 0.000 0.000 0.000 0.824 0.176
#> SRR2001061 4 0.2891 0.878 0.000 0.000 0.000 0.824 0.176
#> SRR2001062 4 0.2891 0.878 0.000 0.000 0.000 0.824 0.176
#> SRR2001063 4 0.2891 0.878 0.000 0.000 0.000 0.824 0.176
#> SRR2001056 4 0.1430 0.902 0.000 0.000 0.004 0.944 0.052
#> SRR2001057 4 0.1430 0.902 0.000 0.000 0.004 0.944 0.052
#> SRR2001058 4 0.1430 0.902 0.000 0.000 0.004 0.944 0.052
#> SRR2001059 4 0.1430 0.902 0.000 0.000 0.004 0.944 0.052
#> SRR2001052 2 0.6295 0.867 0.000 0.644 0.064 0.180 0.112
#> SRR2001053 2 0.6193 0.869 0.000 0.652 0.060 0.180 0.108
#> SRR2001054 2 0.6295 0.867 0.000 0.644 0.064 0.180 0.112
#> SRR2001055 2 0.6295 0.867 0.000 0.644 0.064 0.180 0.112
#> SRR2001048 2 0.5780 0.873 0.000 0.672 0.028 0.180 0.120
#> SRR2001049 2 0.5780 0.873 0.000 0.672 0.028 0.180 0.120
#> SRR2001050 2 0.5780 0.873 0.000 0.672 0.028 0.180 0.120
#> SRR2001051 2 0.5780 0.873 0.000 0.672 0.028 0.180 0.120
#> SRR2001044 4 0.1197 0.898 0.000 0.000 0.000 0.952 0.048
#> SRR2001045 4 0.1197 0.898 0.000 0.000 0.000 0.952 0.048
#> SRR2001046 4 0.1197 0.898 0.000 0.000 0.000 0.952 0.048
#> SRR2001047 4 0.1197 0.898 0.000 0.000 0.000 0.952 0.048
#> SRR2001040 4 0.0404 0.908 0.000 0.000 0.000 0.988 0.012
#> SRR2001041 4 0.0404 0.908 0.000 0.000 0.000 0.988 0.012
#> SRR2001042 4 0.0404 0.908 0.000 0.000 0.000 0.988 0.012
#> SRR2001043 4 0.0404 0.908 0.000 0.000 0.000 0.988 0.012
#> SRR2001036 4 0.0000 0.908 0.000 0.000 0.000 1.000 0.000
#> SRR2001037 4 0.0000 0.908 0.000 0.000 0.000 1.000 0.000
#> SRR2001038 4 0.0000 0.908 0.000 0.000 0.000 1.000 0.000
#> SRR2001039 4 0.0000 0.908 0.000 0.000 0.000 1.000 0.000
#> SRR2001028 4 0.1341 0.896 0.000 0.000 0.000 0.944 0.056
#> SRR2001029 4 0.1341 0.896 0.000 0.000 0.000 0.944 0.056
#> SRR2001030 4 0.1341 0.896 0.000 0.000 0.000 0.944 0.056
#> SRR2001031 4 0.1341 0.896 0.000 0.000 0.000 0.944 0.056
#> SRR2001024 4 0.1043 0.905 0.000 0.000 0.000 0.960 0.040
#> SRR2001025 4 0.1043 0.905 0.000 0.000 0.000 0.960 0.040
#> SRR2001026 4 0.1043 0.905 0.000 0.000 0.000 0.960 0.040
#> SRR2001027 4 0.1043 0.905 0.000 0.000 0.000 0.960 0.040
#> SRR2001020 2 0.6308 0.851 0.000 0.632 0.044 0.180 0.144
#> SRR2001021 2 0.6308 0.851 0.000 0.632 0.044 0.180 0.144
#> SRR2001022 2 0.6308 0.851 0.000 0.632 0.044 0.180 0.144
#> SRR2001023 2 0.6308 0.851 0.000 0.632 0.044 0.180 0.144
#> SRR2001016 4 0.4153 0.819 0.000 0.004 0.020 0.736 0.240
#> SRR2001017 4 0.4153 0.819 0.000 0.004 0.020 0.736 0.240
#> SRR2001018 4 0.4153 0.819 0.000 0.004 0.020 0.736 0.240
#> SRR2001019 4 0.4153 0.819 0.000 0.004 0.020 0.736 0.240
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 2 0.2103 0.8100 0.020 0.912 0.012 0.000 NA 0.000
#> SRR2001033 2 0.2103 0.8100 0.020 0.912 0.012 0.000 NA 0.000
#> SRR2001034 2 0.2103 0.8100 0.020 0.912 0.012 0.000 NA 0.000
#> SRR2001035 2 0.2103 0.8100 0.020 0.912 0.012 0.000 NA 0.000
#> SRR2001204 6 0.1682 0.7883 0.000 0.000 0.000 0.020 NA 0.928
#> SRR2001205 6 0.1682 0.7883 0.000 0.000 0.000 0.020 NA 0.928
#> SRR2001206 6 0.1682 0.7883 0.000 0.000 0.000 0.020 NA 0.928
#> SRR2001207 6 0.1682 0.7883 0.000 0.000 0.000 0.020 NA 0.928
#> SRR2001200 1 0.4929 0.9057 0.544 0.000 0.000 0.016 NA 0.404
#> SRR2001201 1 0.4929 0.9057 0.544 0.000 0.000 0.016 NA 0.404
#> SRR2001202 1 0.4929 0.9057 0.544 0.000 0.000 0.016 NA 0.404
#> SRR2001203 1 0.4929 0.9057 0.544 0.000 0.000 0.016 NA 0.404
#> SRR2001196 1 0.4344 0.9367 0.568 0.000 0.000 0.008 NA 0.412
#> SRR2001197 1 0.4344 0.9367 0.568 0.000 0.000 0.008 NA 0.412
#> SRR2001198 1 0.4344 0.9367 0.568 0.000 0.000 0.008 NA 0.412
#> SRR2001199 1 0.4344 0.9367 0.568 0.000 0.000 0.008 NA 0.412
#> SRR2001192 3 0.2417 0.9284 0.008 0.000 0.888 0.012 NA 0.088
#> SRR2001193 3 0.2417 0.9284 0.008 0.000 0.888 0.012 NA 0.088
#> SRR2001194 3 0.2417 0.9284 0.008 0.000 0.888 0.012 NA 0.088
#> SRR2001195 3 0.2417 0.9284 0.008 0.000 0.888 0.012 NA 0.088
#> SRR2001188 6 0.4760 -0.2014 0.332 0.000 0.000 0.032 NA 0.616
#> SRR2001189 6 0.4686 -0.0724 0.312 0.000 0.000 0.032 NA 0.636
#> SRR2001190 6 0.4686 -0.0724 0.312 0.000 0.000 0.032 NA 0.636
#> SRR2001191 6 0.4702 -0.0987 0.316 0.000 0.000 0.032 NA 0.632
#> SRR2001184 3 0.1663 0.9308 0.000 0.000 0.912 0.000 NA 0.088
#> SRR2001185 3 0.1663 0.9308 0.000 0.000 0.912 0.000 NA 0.088
#> SRR2001186 3 0.1663 0.9308 0.000 0.000 0.912 0.000 NA 0.088
#> SRR2001187 3 0.1663 0.9308 0.000 0.000 0.912 0.000 NA 0.088
#> SRR2001180 6 0.4096 0.4645 0.204 0.000 0.000 0.028 NA 0.744
#> SRR2001181 6 0.4037 0.4908 0.196 0.000 0.000 0.028 NA 0.752
#> SRR2001182 6 0.4037 0.4908 0.196 0.000 0.000 0.028 NA 0.752
#> SRR2001183 6 0.3670 0.6056 0.152 0.000 0.000 0.028 NA 0.796
#> SRR2001176 3 0.3116 0.9283 0.008 0.000 0.856 0.012 NA 0.088
#> SRR2001177 3 0.3116 0.9283 0.008 0.000 0.856 0.012 NA 0.088
#> SRR2001178 3 0.3116 0.9283 0.008 0.000 0.856 0.012 NA 0.088
#> SRR2001179 3 0.3116 0.9283 0.008 0.000 0.856 0.012 NA 0.088
#> SRR2001172 3 0.1663 0.9308 0.000 0.000 0.912 0.000 NA 0.088
#> SRR2001173 3 0.1663 0.9308 0.000 0.000 0.912 0.000 NA 0.088
#> SRR2001174 3 0.1663 0.9308 0.000 0.000 0.912 0.000 NA 0.088
#> SRR2001175 3 0.1663 0.9308 0.000 0.000 0.912 0.000 NA 0.088
#> SRR2001168 6 0.1434 0.7922 0.000 0.000 0.000 0.012 NA 0.940
#> SRR2001169 6 0.1434 0.7922 0.000 0.000 0.000 0.012 NA 0.940
#> SRR2001170 6 0.1434 0.7922 0.000 0.000 0.000 0.012 NA 0.940
#> SRR2001171 6 0.1434 0.7922 0.000 0.000 0.000 0.012 NA 0.940
#> SRR2001164 1 0.3923 0.9435 0.580 0.000 0.000 0.000 NA 0.416
#> SRR2001165 1 0.3923 0.9435 0.580 0.000 0.000 0.000 NA 0.416
#> SRR2001166 1 0.3923 0.9435 0.580 0.000 0.000 0.000 NA 0.416
#> SRR2001167 1 0.3923 0.9435 0.580 0.000 0.000 0.000 NA 0.416
#> SRR2001160 1 0.4648 0.8948 0.520 0.000 0.000 0.004 NA 0.444
#> SRR2001161 1 0.4648 0.8948 0.520 0.000 0.000 0.004 NA 0.444
#> SRR2001162 1 0.4648 0.8948 0.520 0.000 0.000 0.004 NA 0.444
#> SRR2001163 1 0.4648 0.8948 0.520 0.000 0.000 0.004 NA 0.444
#> SRR2001156 1 0.4158 0.9421 0.572 0.000 0.000 0.004 NA 0.416
#> SRR2001157 1 0.4158 0.9421 0.572 0.000 0.000 0.004 NA 0.416
#> SRR2001158 1 0.4158 0.9421 0.572 0.000 0.000 0.004 NA 0.416
#> SRR2001159 1 0.4158 0.9421 0.572 0.000 0.000 0.004 NA 0.416
#> SRR2001152 6 0.1675 0.7870 0.008 0.000 0.000 0.032 NA 0.936
#> SRR2001153 6 0.1675 0.7870 0.008 0.000 0.000 0.032 NA 0.936
#> SRR2001154 6 0.1562 0.7889 0.004 0.000 0.000 0.032 NA 0.940
#> SRR2001155 6 0.1562 0.7889 0.004 0.000 0.000 0.032 NA 0.940
#> SRR2001148 3 0.1663 0.9308 0.000 0.000 0.912 0.000 NA 0.088
#> SRR2001149 3 0.1663 0.9308 0.000 0.000 0.912 0.000 NA 0.088
#> SRR2001150 3 0.1663 0.9308 0.000 0.000 0.912 0.000 NA 0.088
#> SRR2001151 3 0.1663 0.9308 0.000 0.000 0.912 0.000 NA 0.088
#> SRR2001144 6 0.0603 0.8050 0.000 0.000 0.000 0.004 NA 0.980
#> SRR2001145 6 0.0603 0.8050 0.000 0.000 0.000 0.004 NA 0.980
#> SRR2001146 6 0.0603 0.8050 0.000 0.000 0.000 0.004 NA 0.980
#> SRR2001147 6 0.0603 0.8050 0.000 0.000 0.000 0.004 NA 0.980
#> SRR2001140 6 0.0806 0.8040 0.000 0.000 0.000 0.008 NA 0.972
#> SRR2001142 6 0.0806 0.8040 0.000 0.000 0.000 0.008 NA 0.972
#> SRR2001143 6 0.0806 0.8040 0.000 0.000 0.000 0.008 NA 0.972
#> SRR2001136 3 0.4960 0.8777 0.024 0.000 0.680 0.000 NA 0.084
#> SRR2001137 3 0.4960 0.8777 0.024 0.000 0.680 0.000 NA 0.084
#> SRR2001138 3 0.4960 0.8777 0.024 0.000 0.680 0.000 NA 0.084
#> SRR2001139 3 0.4960 0.8777 0.024 0.000 0.680 0.000 NA 0.084
#> SRR2001132 3 0.4388 0.9018 0.020 0.000 0.748 0.000 NA 0.084
#> SRR2001133 3 0.4388 0.9018 0.020 0.000 0.748 0.000 NA 0.084
#> SRR2001134 3 0.4388 0.9018 0.020 0.000 0.748 0.000 NA 0.084
#> SRR2001135 3 0.4388 0.9018 0.020 0.000 0.748 0.000 NA 0.084
#> SRR2001128 6 0.3269 0.6717 0.120 0.000 0.000 0.028 NA 0.832
#> SRR2001129 6 0.3269 0.6717 0.120 0.000 0.000 0.028 NA 0.832
#> SRR2001130 6 0.3269 0.6717 0.120 0.000 0.000 0.028 NA 0.832
#> SRR2001131 6 0.3269 0.6717 0.120 0.000 0.000 0.028 NA 0.832
#> SRR2001124 1 0.3923 0.9423 0.580 0.000 0.000 0.000 NA 0.416
#> SRR2001125 1 0.3923 0.9423 0.580 0.000 0.000 0.000 NA 0.416
#> SRR2001126 1 0.3923 0.9423 0.580 0.000 0.000 0.000 NA 0.416
#> SRR2001127 1 0.3923 0.9423 0.580 0.000 0.000 0.000 NA 0.416
#> SRR2001120 6 0.0692 0.8043 0.000 0.000 0.000 0.004 NA 0.976
#> SRR2001121 6 0.0603 0.8050 0.000 0.000 0.000 0.004 NA 0.980
#> SRR2001122 6 0.0692 0.8043 0.000 0.000 0.000 0.004 NA 0.976
#> SRR2001123 6 0.0603 0.8050 0.000 0.000 0.000 0.004 NA 0.980
#> SRR2001116 1 0.4584 0.8976 0.524 0.000 0.000 0.004 NA 0.444
#> SRR2001117 1 0.4584 0.8976 0.524 0.000 0.000 0.004 NA 0.444
#> SRR2001118 1 0.4584 0.8976 0.524 0.000 0.000 0.004 NA 0.444
#> SRR2001119 1 0.4584 0.8976 0.524 0.000 0.000 0.004 NA 0.444
#> SRR2001112 3 0.5108 0.8699 0.028 0.000 0.664 0.000 NA 0.084
#> SRR2001113 3 0.5108 0.8699 0.028 0.000 0.664 0.000 NA 0.084
#> SRR2001114 3 0.5108 0.8699 0.028 0.000 0.664 0.000 NA 0.084
#> SRR2001115 3 0.5108 0.8699 0.028 0.000 0.664 0.000 NA 0.084
#> SRR2001108 4 0.3502 0.8568 0.004 0.084 0.032 0.836 NA 0.000
#> SRR2001109 4 0.3502 0.8568 0.004 0.084 0.032 0.836 NA 0.000
#> SRR2001110 4 0.3502 0.8568 0.004 0.084 0.032 0.836 NA 0.000
#> SRR2001111 4 0.3502 0.8568 0.004 0.084 0.032 0.836 NA 0.000
#> SRR2001104 2 0.1820 0.8352 0.056 0.924 0.008 0.000 NA 0.000
#> SRR2001105 2 0.1820 0.8352 0.056 0.924 0.008 0.000 NA 0.000
#> SRR2001106 2 0.1820 0.8352 0.056 0.924 0.008 0.000 NA 0.000
#> SRR2001107 2 0.1820 0.8352 0.056 0.924 0.008 0.000 NA 0.000
#> SRR2001100 2 0.3731 0.8275 0.124 0.796 0.008 0.000 NA 0.000
#> SRR2001101 2 0.3731 0.8275 0.124 0.796 0.008 0.000 NA 0.000
#> SRR2001102 2 0.3731 0.8275 0.124 0.796 0.008 0.000 NA 0.000
#> SRR2001103 2 0.3731 0.8275 0.124 0.796 0.008 0.000 NA 0.000
#> SRR2001096 2 0.5578 0.7490 0.316 0.536 0.004 0.000 NA 0.000
#> SRR2001097 2 0.5578 0.7490 0.316 0.536 0.004 0.000 NA 0.000
#> SRR2001098 2 0.5578 0.7490 0.316 0.536 0.004 0.000 NA 0.000
#> SRR2001099 2 0.5578 0.7490 0.316 0.536 0.004 0.000 NA 0.000
#> SRR2001092 2 0.3264 0.8143 0.072 0.840 0.012 0.000 NA 0.000
#> SRR2001093 2 0.3264 0.8143 0.072 0.840 0.012 0.000 NA 0.000
#> SRR2001094 2 0.3264 0.8143 0.072 0.840 0.012 0.000 NA 0.000
#> SRR2001095 2 0.3264 0.8143 0.072 0.840 0.012 0.000 NA 0.000
#> SRR2001088 4 0.5033 0.8162 0.000 0.084 0.012 0.636 NA 0.000
#> SRR2001089 4 0.5033 0.8162 0.000 0.084 0.012 0.636 NA 0.000
#> SRR2001090 4 0.5033 0.8162 0.000 0.084 0.012 0.636 NA 0.000
#> SRR2001091 4 0.5071 0.8131 0.000 0.084 0.012 0.628 NA 0.000
#> SRR2001084 4 0.5637 0.8129 0.008 0.084 0.036 0.620 NA 0.000
#> SRR2001085 4 0.5617 0.8146 0.008 0.084 0.036 0.624 NA 0.000
#> SRR2001086 4 0.5637 0.8129 0.008 0.084 0.036 0.620 NA 0.000
#> SRR2001087 4 0.5637 0.8129 0.008 0.084 0.036 0.620 NA 0.000
#> SRR2001080 2 0.1398 0.8144 0.008 0.940 0.000 0.000 NA 0.000
#> SRR2001081 2 0.1398 0.8144 0.008 0.940 0.000 0.000 NA 0.000
#> SRR2001082 2 0.1398 0.8144 0.008 0.940 0.000 0.000 NA 0.000
#> SRR2001083 2 0.1398 0.8144 0.008 0.940 0.000 0.000 NA 0.000
#> SRR2001076 2 0.0865 0.8210 0.000 0.964 0.000 0.000 NA 0.000
#> SRR2001077 2 0.0865 0.8210 0.000 0.964 0.000 0.000 NA 0.000
#> SRR2001078 2 0.0865 0.8210 0.000 0.964 0.000 0.000 NA 0.000
#> SRR2001079 2 0.0865 0.8210 0.000 0.964 0.000 0.000 NA 0.000
#> SRR2001072 4 0.5181 0.7902 0.008 0.084 0.000 0.580 NA 0.000
#> SRR2001073 4 0.5181 0.7902 0.008 0.084 0.000 0.580 NA 0.000
#> SRR2001074 4 0.5181 0.7902 0.008 0.084 0.000 0.580 NA 0.000
#> SRR2001075 4 0.5181 0.7902 0.008 0.084 0.000 0.580 NA 0.000
#> SRR2001068 2 0.4723 0.8133 0.176 0.704 0.012 0.000 NA 0.000
#> SRR2001069 2 0.4508 0.8153 0.160 0.728 0.012 0.000 NA 0.000
#> SRR2001070 2 0.4723 0.8133 0.176 0.704 0.012 0.000 NA 0.000
#> SRR2001071 2 0.4723 0.8133 0.176 0.704 0.012 0.000 NA 0.000
#> SRR2001064 2 0.5578 0.7490 0.316 0.536 0.004 0.000 NA 0.000
#> SRR2001065 2 0.5578 0.7490 0.316 0.536 0.004 0.000 NA 0.000
#> SRR2001066 2 0.5578 0.7490 0.316 0.536 0.004 0.000 NA 0.000
#> SRR2001067 2 0.5578 0.7490 0.316 0.536 0.004 0.000 NA 0.000
#> SRR2001060 4 0.4977 0.8061 0.004 0.084 0.000 0.612 NA 0.000
#> SRR2001061 4 0.4977 0.8061 0.004 0.084 0.000 0.612 NA 0.000
#> SRR2001062 4 0.4993 0.8043 0.004 0.084 0.000 0.608 NA 0.000
#> SRR2001063 4 0.4993 0.8043 0.004 0.084 0.000 0.608 NA 0.000
#> SRR2001056 4 0.3807 0.8494 0.012 0.084 0.024 0.820 NA 0.000
#> SRR2001057 4 0.3807 0.8494 0.012 0.084 0.024 0.820 NA 0.000
#> SRR2001058 4 0.3865 0.8483 0.012 0.084 0.024 0.816 NA 0.000
#> SRR2001059 4 0.3865 0.8483 0.012 0.084 0.024 0.816 NA 0.000
#> SRR2001052 2 0.4951 0.8126 0.196 0.676 0.012 0.000 NA 0.000
#> SRR2001053 2 0.4854 0.8157 0.188 0.688 0.012 0.000 NA 0.000
#> SRR2001054 2 0.4951 0.8126 0.196 0.676 0.012 0.000 NA 0.000
#> SRR2001055 2 0.4951 0.8126 0.196 0.676 0.012 0.000 NA 0.000
#> SRR2001048 2 0.4358 0.8182 0.148 0.744 0.012 0.000 NA 0.000
#> SRR2001049 2 0.4312 0.8187 0.148 0.748 0.012 0.000 NA 0.000
#> SRR2001050 2 0.4358 0.8182 0.148 0.744 0.012 0.000 NA 0.000
#> SRR2001051 2 0.4358 0.8182 0.148 0.744 0.012 0.000 NA 0.000
#> SRR2001044 4 0.2677 0.8542 0.016 0.084 0.000 0.876 NA 0.000
#> SRR2001045 4 0.2677 0.8542 0.016 0.084 0.000 0.876 NA 0.000
#> SRR2001046 4 0.2677 0.8542 0.016 0.084 0.000 0.876 NA 0.000
#> SRR2001047 4 0.2677 0.8542 0.016 0.084 0.000 0.876 NA 0.000
#> SRR2001040 4 0.1897 0.8624 0.000 0.084 0.004 0.908 NA 0.000
#> SRR2001041 4 0.1897 0.8624 0.000 0.084 0.004 0.908 NA 0.000
#> SRR2001042 4 0.1753 0.8622 0.000 0.084 0.000 0.912 NA 0.000
#> SRR2001043 4 0.1897 0.8624 0.000 0.084 0.004 0.908 NA 0.000
#> SRR2001036 4 0.1753 0.8620 0.000 0.084 0.004 0.912 NA 0.000
#> SRR2001037 4 0.1753 0.8620 0.000 0.084 0.004 0.912 NA 0.000
#> SRR2001038 4 0.1753 0.8620 0.000 0.084 0.004 0.912 NA 0.000
#> SRR2001039 4 0.1753 0.8620 0.000 0.084 0.004 0.912 NA 0.000
#> SRR2001028 4 0.2677 0.8542 0.016 0.084 0.000 0.876 NA 0.000
#> SRR2001029 4 0.2677 0.8542 0.016 0.084 0.000 0.876 NA 0.000
#> SRR2001030 4 0.2677 0.8542 0.016 0.084 0.000 0.876 NA 0.000
#> SRR2001031 4 0.2677 0.8542 0.016 0.084 0.000 0.876 NA 0.000
#> SRR2001024 4 0.3158 0.8574 0.000 0.084 0.008 0.844 NA 0.000
#> SRR2001025 4 0.3158 0.8574 0.000 0.084 0.008 0.844 NA 0.000
#> SRR2001026 4 0.3158 0.8574 0.000 0.084 0.008 0.844 NA 0.000
#> SRR2001027 4 0.3214 0.8565 0.000 0.084 0.008 0.840 NA 0.000
#> SRR2001020 2 0.4563 0.7581 0.068 0.724 0.024 0.000 NA 0.000
#> SRR2001021 2 0.4563 0.7581 0.068 0.724 0.024 0.000 NA 0.000
#> SRR2001022 2 0.4563 0.7581 0.068 0.724 0.024 0.000 NA 0.000
#> SRR2001023 2 0.4563 0.7581 0.068 0.724 0.024 0.000 NA 0.000
#> SRR2001016 4 0.6558 0.7112 0.056 0.084 0.024 0.492 NA 0.000
#> SRR2001017 4 0.6558 0.7112 0.056 0.084 0.024 0.492 NA 0.000
#> SRR2001018 4 0.6558 0.7112 0.056 0.084 0.024 0.492 NA 0.000
#> SRR2001019 4 0.6558 0.7112 0.056 0.084 0.024 0.492 NA 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 6.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.5031 0.497 0.497
#> 3 3 1.000 0.996 0.993 0.2211 0.889 0.777
#> 4 4 1.000 0.995 0.985 0.2015 0.873 0.671
#> 5 5 0.955 0.939 0.937 0.0712 0.945 0.789
#> 6 6 0.928 0.902 0.914 0.0281 0.987 0.935
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3 4 5
There is also optional best \(k\) = 2 3 4 5 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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001033 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001034 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001035 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001204 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001205 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001206 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001207 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001200 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001201 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001202 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001203 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001196 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001197 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001198 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001199 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001192 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001193 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001194 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001195 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001188 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001189 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001190 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001191 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001184 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001185 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001186 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001187 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001180 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001181 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001182 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001183 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001176 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001177 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001178 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001179 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001172 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001173 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001174 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001175 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001168 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001169 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001170 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001171 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001164 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001165 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001166 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001167 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001160 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001161 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001162 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001163 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001156 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001157 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001158 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001159 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001152 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001153 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001154 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001155 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001148 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001149 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001150 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001151 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001144 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001145 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001146 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001147 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001140 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001142 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001143 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001136 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001137 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001138 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001139 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001132 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001133 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001134 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001135 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001128 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001129 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001130 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001131 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001124 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001125 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001126 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001127 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001120 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001121 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001122 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001123 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001116 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001117 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001118 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001119 1 0.0000 1.000 1.000 0.000 0.000
#> SRR2001112 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001113 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001114 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001115 3 0.0747 1.000 0.016 0.000 0.984
#> SRR2001108 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001109 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001110 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001111 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001104 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001105 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001106 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001107 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001100 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001101 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001102 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001103 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001096 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001097 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001098 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001099 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001092 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001093 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001094 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001095 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001088 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001089 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001090 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001091 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001084 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001085 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001086 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001087 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001080 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001081 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001082 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001083 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001076 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001077 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001078 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001079 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001072 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001073 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001074 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001075 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001068 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001069 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001070 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001071 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001064 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001065 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001066 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001067 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001060 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001061 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001062 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001063 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001056 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001057 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001058 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001059 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001052 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001053 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001054 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001055 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001048 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001049 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001050 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001051 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001044 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001045 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001046 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001047 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001040 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001041 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001042 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001043 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001036 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001037 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001038 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001039 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001028 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001029 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001030 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001031 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001024 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001025 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001026 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001027 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001020 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001021 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001022 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001023 2 0.0000 0.993 0.000 1.000 0.000
#> SRR2001016 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001017 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001018 2 0.0747 0.993 0.000 0.984 0.016
#> SRR2001019 2 0.0747 0.993 0.000 0.984 0.016
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001033 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001034 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001035 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001204 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001205 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001206 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001207 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001200 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001201 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001202 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001203 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001196 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001197 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001198 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001199 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001192 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001193 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001194 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001195 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001188 1 0.0000 0.987 1.000 0.000 0.000 0.000
#> SRR2001189 1 0.0000 0.987 1.000 0.000 0.000 0.000
#> SRR2001190 1 0.0000 0.987 1.000 0.000 0.000 0.000
#> SRR2001191 1 0.0000 0.987 1.000 0.000 0.000 0.000
#> SRR2001184 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001185 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001186 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001187 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001180 1 0.0000 0.987 1.000 0.000 0.000 0.000
#> SRR2001181 1 0.0000 0.987 1.000 0.000 0.000 0.000
#> SRR2001182 1 0.0000 0.987 1.000 0.000 0.000 0.000
#> SRR2001183 1 0.0000 0.987 1.000 0.000 0.000 0.000
#> SRR2001176 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001177 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001178 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001179 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001172 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001173 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001174 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001175 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001168 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001169 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001170 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001171 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001164 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001165 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001166 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001167 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001160 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001161 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001162 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001163 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001156 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001157 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001158 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001159 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001152 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001153 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001154 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001155 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001148 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001149 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001150 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001151 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001144 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001145 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001146 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001147 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001140 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001142 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001143 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001136 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001137 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001138 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001139 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001132 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001133 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001134 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001135 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001128 1 0.0469 0.986 0.988 0.012 0.000 0.000
#> SRR2001129 1 0.0469 0.986 0.988 0.012 0.000 0.000
#> SRR2001130 1 0.0469 0.986 0.988 0.012 0.000 0.000
#> SRR2001131 1 0.0469 0.986 0.988 0.012 0.000 0.000
#> SRR2001124 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001125 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001126 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001127 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001120 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001121 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001122 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001123 1 0.0707 0.985 0.980 0.020 0.000 0.000
#> SRR2001116 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001117 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001118 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001119 1 0.0592 0.987 0.984 0.016 0.000 0.000
#> SRR2001112 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001113 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001114 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001115 3 0.0188 1.000 0.004 0.000 0.996 0.000
#> SRR2001108 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001109 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001110 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001111 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001104 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001105 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001106 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001107 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001100 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001101 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001102 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001103 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001096 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001097 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001098 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001099 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001092 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001093 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001094 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001095 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001088 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001089 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001090 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001091 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001084 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001085 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001086 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001087 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001080 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001081 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001082 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001083 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001076 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001077 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001078 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001079 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001072 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001073 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001074 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001075 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001068 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001069 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001070 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001071 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001064 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001065 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001066 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001067 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001060 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001061 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001062 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001063 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001056 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001057 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001058 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001059 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001052 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001053 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001054 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001055 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001048 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001049 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001050 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001051 2 0.1118 0.999 0.000 0.964 0.000 0.036
#> SRR2001044 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001045 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001046 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001047 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001040 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001041 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001042 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001043 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001036 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001037 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001038 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001039 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001028 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001029 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001030 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001031 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001024 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001025 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001026 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001027 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001020 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001021 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001022 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001023 2 0.1305 0.998 0.000 0.960 0.004 0.036
#> SRR2001016 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001017 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001018 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR2001019 4 0.0000 1.000 0.000 0.000 0.000 1.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.0794 0.98577 0.000 0.972 0.000 0.000 0.028
#> SRR2001033 2 0.0794 0.98577 0.000 0.972 0.000 0.000 0.028
#> SRR2001034 2 0.0794 0.98577 0.000 0.972 0.000 0.000 0.028
#> SRR2001035 2 0.0794 0.98577 0.000 0.972 0.000 0.000 0.028
#> SRR2001204 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001205 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001206 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001207 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001200 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001201 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001202 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001203 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001196 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001197 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001198 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001199 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001192 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001193 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001194 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001195 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001188 1 0.4249 -0.00757 0.568 0.000 0.000 0.000 0.432
#> SRR2001189 1 0.4268 -0.05873 0.556 0.000 0.000 0.000 0.444
#> SRR2001190 1 0.4268 -0.05873 0.556 0.000 0.000 0.000 0.444
#> SRR2001191 1 0.4256 -0.02448 0.564 0.000 0.000 0.000 0.436
#> SRR2001184 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001185 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001186 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001187 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001180 5 0.4297 0.33591 0.472 0.000 0.000 0.000 0.528
#> SRR2001181 5 0.4273 0.41015 0.448 0.000 0.000 0.000 0.552
#> SRR2001182 5 0.4256 0.44352 0.436 0.000 0.000 0.000 0.564
#> SRR2001183 5 0.3586 0.78991 0.264 0.000 0.000 0.000 0.736
#> SRR2001176 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001177 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001178 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001179 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001172 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001173 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001174 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001175 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001168 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001169 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001170 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001171 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001164 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001165 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001166 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001167 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001160 1 0.0162 0.92383 0.996 0.000 0.000 0.000 0.004
#> SRR2001161 1 0.0290 0.92065 0.992 0.000 0.000 0.000 0.008
#> SRR2001162 1 0.0290 0.92065 0.992 0.000 0.000 0.000 0.008
#> SRR2001163 1 0.0290 0.92065 0.992 0.000 0.000 0.000 0.008
#> SRR2001156 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001157 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001158 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001159 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001152 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001153 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001154 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001155 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001148 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001149 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001150 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001151 3 0.0000 0.98186 0.000 0.000 1.000 0.000 0.000
#> SRR2001144 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001145 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001146 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001147 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001140 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001142 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001143 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001136 3 0.1544 0.96771 0.000 0.000 0.932 0.000 0.068
#> SRR2001137 3 0.1544 0.96771 0.000 0.000 0.932 0.000 0.068
#> SRR2001138 3 0.1544 0.96771 0.000 0.000 0.932 0.000 0.068
#> SRR2001139 3 0.1544 0.96771 0.000 0.000 0.932 0.000 0.068
#> SRR2001132 3 0.1410 0.96997 0.000 0.000 0.940 0.000 0.060
#> SRR2001133 3 0.1410 0.96997 0.000 0.000 0.940 0.000 0.060
#> SRR2001134 3 0.1410 0.96997 0.000 0.000 0.940 0.000 0.060
#> SRR2001135 3 0.1410 0.96997 0.000 0.000 0.940 0.000 0.060
#> SRR2001128 5 0.3003 0.88672 0.188 0.000 0.000 0.000 0.812
#> SRR2001129 5 0.3003 0.88672 0.188 0.000 0.000 0.000 0.812
#> SRR2001130 5 0.3003 0.88672 0.188 0.000 0.000 0.000 0.812
#> SRR2001131 5 0.3003 0.88672 0.188 0.000 0.000 0.000 0.812
#> SRR2001124 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001125 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001126 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001127 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001120 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001121 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001122 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001123 5 0.2280 0.94016 0.120 0.000 0.000 0.000 0.880
#> SRR2001116 1 0.0162 0.92383 0.996 0.000 0.000 0.000 0.004
#> SRR2001117 1 0.0162 0.92383 0.996 0.000 0.000 0.000 0.004
#> SRR2001118 1 0.0000 0.92594 1.000 0.000 0.000 0.000 0.000
#> SRR2001119 1 0.0162 0.92383 0.996 0.000 0.000 0.000 0.004
#> SRR2001112 3 0.1544 0.96771 0.000 0.000 0.932 0.000 0.068
#> SRR2001113 3 0.1544 0.96771 0.000 0.000 0.932 0.000 0.068
#> SRR2001114 3 0.1544 0.96771 0.000 0.000 0.932 0.000 0.068
#> SRR2001115 3 0.1544 0.96771 0.000 0.000 0.932 0.000 0.068
#> SRR2001108 4 0.0162 0.99565 0.000 0.000 0.000 0.996 0.004
#> SRR2001109 4 0.0162 0.99565 0.000 0.000 0.000 0.996 0.004
#> SRR2001110 4 0.0162 0.99565 0.000 0.000 0.000 0.996 0.004
#> SRR2001111 4 0.0162 0.99565 0.000 0.000 0.000 0.996 0.004
#> SRR2001104 2 0.0290 0.98851 0.000 0.992 0.000 0.000 0.008
#> SRR2001105 2 0.0290 0.98851 0.000 0.992 0.000 0.000 0.008
#> SRR2001106 2 0.0290 0.98851 0.000 0.992 0.000 0.000 0.008
#> SRR2001107 2 0.0290 0.98851 0.000 0.992 0.000 0.000 0.008
#> SRR2001100 2 0.0162 0.98802 0.000 0.996 0.000 0.000 0.004
#> SRR2001101 2 0.0162 0.98802 0.000 0.996 0.000 0.000 0.004
#> SRR2001102 2 0.0162 0.98802 0.000 0.996 0.000 0.000 0.004
#> SRR2001103 2 0.0162 0.98802 0.000 0.996 0.000 0.000 0.004
#> SRR2001096 2 0.0404 0.98706 0.000 0.988 0.000 0.000 0.012
#> SRR2001097 2 0.0404 0.98706 0.000 0.988 0.000 0.000 0.012
#> SRR2001098 2 0.0404 0.98706 0.000 0.988 0.000 0.000 0.012
#> SRR2001099 2 0.0404 0.98706 0.000 0.988 0.000 0.000 0.012
#> SRR2001092 2 0.0880 0.98633 0.000 0.968 0.000 0.000 0.032
#> SRR2001093 2 0.0963 0.98511 0.000 0.964 0.000 0.000 0.036
#> SRR2001094 2 0.0880 0.98633 0.000 0.968 0.000 0.000 0.032
#> SRR2001095 2 0.0880 0.98633 0.000 0.968 0.000 0.000 0.032
#> SRR2001088 4 0.0290 0.99506 0.000 0.000 0.000 0.992 0.008
#> SRR2001089 4 0.0290 0.99506 0.000 0.000 0.000 0.992 0.008
#> SRR2001090 4 0.0290 0.99506 0.000 0.000 0.000 0.992 0.008
#> SRR2001091 4 0.0290 0.99506 0.000 0.000 0.000 0.992 0.008
#> SRR2001084 4 0.0404 0.99485 0.000 0.000 0.000 0.988 0.012
#> SRR2001085 4 0.0404 0.99485 0.000 0.000 0.000 0.988 0.012
#> SRR2001086 4 0.0404 0.99485 0.000 0.000 0.000 0.988 0.012
#> SRR2001087 4 0.0404 0.99485 0.000 0.000 0.000 0.988 0.012
#> SRR2001080 2 0.0794 0.98577 0.000 0.972 0.000 0.000 0.028
#> SRR2001081 2 0.0794 0.98577 0.000 0.972 0.000 0.000 0.028
#> SRR2001082 2 0.0794 0.98577 0.000 0.972 0.000 0.000 0.028
#> SRR2001083 2 0.0794 0.98577 0.000 0.972 0.000 0.000 0.028
#> SRR2001076 2 0.0703 0.98671 0.000 0.976 0.000 0.000 0.024
#> SRR2001077 2 0.0703 0.98671 0.000 0.976 0.000 0.000 0.024
#> SRR2001078 2 0.0703 0.98671 0.000 0.976 0.000 0.000 0.024
#> SRR2001079 2 0.0703 0.98671 0.000 0.976 0.000 0.000 0.024
#> SRR2001072 4 0.0404 0.99485 0.000 0.000 0.000 0.988 0.012
#> SRR2001073 4 0.0404 0.99485 0.000 0.000 0.000 0.988 0.012
#> SRR2001074 4 0.0404 0.99485 0.000 0.000 0.000 0.988 0.012
#> SRR2001075 4 0.0404 0.99485 0.000 0.000 0.000 0.988 0.012
#> SRR2001068 2 0.0162 0.98802 0.000 0.996 0.000 0.000 0.004
#> SRR2001069 2 0.0162 0.98802 0.000 0.996 0.000 0.000 0.004
#> SRR2001070 2 0.0162 0.98802 0.000 0.996 0.000 0.000 0.004
#> SRR2001071 2 0.0162 0.98802 0.000 0.996 0.000 0.000 0.004
#> SRR2001064 2 0.0404 0.98706 0.000 0.988 0.000 0.000 0.012
#> SRR2001065 2 0.0404 0.98706 0.000 0.988 0.000 0.000 0.012
#> SRR2001066 2 0.0404 0.98706 0.000 0.988 0.000 0.000 0.012
#> SRR2001067 2 0.0404 0.98706 0.000 0.988 0.000 0.000 0.012
#> SRR2001060 4 0.0404 0.99485 0.000 0.000 0.000 0.988 0.012
#> SRR2001061 4 0.0404 0.99485 0.000 0.000 0.000 0.988 0.012
#> SRR2001062 4 0.0404 0.99485 0.000 0.000 0.000 0.988 0.012
#> SRR2001063 4 0.0404 0.99485 0.000 0.000 0.000 0.988 0.012
#> SRR2001056 4 0.0162 0.99565 0.000 0.000 0.000 0.996 0.004
#> SRR2001057 4 0.0162 0.99565 0.000 0.000 0.000 0.996 0.004
#> SRR2001058 4 0.0162 0.99565 0.000 0.000 0.000 0.996 0.004
#> SRR2001059 4 0.0162 0.99565 0.000 0.000 0.000 0.996 0.004
#> SRR2001052 2 0.0510 0.98766 0.000 0.984 0.000 0.000 0.016
#> SRR2001053 2 0.0510 0.98816 0.000 0.984 0.000 0.000 0.016
#> SRR2001054 2 0.0510 0.98766 0.000 0.984 0.000 0.000 0.016
#> SRR2001055 2 0.0510 0.98766 0.000 0.984 0.000 0.000 0.016
#> SRR2001048 2 0.0162 0.98802 0.000 0.996 0.000 0.000 0.004
#> SRR2001049 2 0.0162 0.98802 0.000 0.996 0.000 0.000 0.004
#> SRR2001050 2 0.0162 0.98802 0.000 0.996 0.000 0.000 0.004
#> SRR2001051 2 0.0162 0.98802 0.000 0.996 0.000 0.000 0.004
#> SRR2001044 4 0.0162 0.99417 0.000 0.000 0.000 0.996 0.004
#> SRR2001045 4 0.0162 0.99417 0.000 0.000 0.000 0.996 0.004
#> SRR2001046 4 0.0162 0.99417 0.000 0.000 0.000 0.996 0.004
#> SRR2001047 4 0.0162 0.99417 0.000 0.000 0.000 0.996 0.004
#> SRR2001040 4 0.0000 0.99547 0.000 0.000 0.000 1.000 0.000
#> SRR2001041 4 0.0000 0.99547 0.000 0.000 0.000 1.000 0.000
#> SRR2001042 4 0.0000 0.99547 0.000 0.000 0.000 1.000 0.000
#> SRR2001043 4 0.0000 0.99547 0.000 0.000 0.000 1.000 0.000
#> SRR2001036 4 0.0000 0.99547 0.000 0.000 0.000 1.000 0.000
#> SRR2001037 4 0.0000 0.99547 0.000 0.000 0.000 1.000 0.000
#> SRR2001038 4 0.0000 0.99547 0.000 0.000 0.000 1.000 0.000
#> SRR2001039 4 0.0000 0.99547 0.000 0.000 0.000 1.000 0.000
#> SRR2001028 4 0.0162 0.99417 0.000 0.000 0.000 0.996 0.004
#> SRR2001029 4 0.0162 0.99417 0.000 0.000 0.000 0.996 0.004
#> SRR2001030 4 0.0162 0.99417 0.000 0.000 0.000 0.996 0.004
#> SRR2001031 4 0.0162 0.99417 0.000 0.000 0.000 0.996 0.004
#> SRR2001024 4 0.0000 0.99547 0.000 0.000 0.000 1.000 0.000
#> SRR2001025 4 0.0000 0.99547 0.000 0.000 0.000 1.000 0.000
#> SRR2001026 4 0.0000 0.99547 0.000 0.000 0.000 1.000 0.000
#> SRR2001027 4 0.0000 0.99547 0.000 0.000 0.000 1.000 0.000
#> SRR2001020 2 0.0880 0.98569 0.000 0.968 0.000 0.000 0.032
#> SRR2001021 2 0.0880 0.98569 0.000 0.968 0.000 0.000 0.032
#> SRR2001022 2 0.0880 0.98569 0.000 0.968 0.000 0.000 0.032
#> SRR2001023 2 0.0880 0.98569 0.000 0.968 0.000 0.000 0.032
#> SRR2001016 4 0.0404 0.99485 0.000 0.000 0.000 0.988 0.012
#> SRR2001017 4 0.0404 0.99485 0.000 0.000 0.000 0.988 0.012
#> SRR2001018 4 0.0404 0.99485 0.000 0.000 0.000 0.988 0.012
#> SRR2001019 4 0.0404 0.99485 0.000 0.000 0.000 0.988 0.012
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 2 0.2378 0.9048 0.000 0.848 0.000 0.000 0.152 0.000
#> SRR2001033 2 0.2378 0.9048 0.000 0.848 0.000 0.000 0.152 0.000
#> SRR2001034 2 0.2378 0.9048 0.000 0.848 0.000 0.000 0.152 0.000
#> SRR2001035 2 0.2378 0.9048 0.000 0.848 0.000 0.000 0.152 0.000
#> SRR2001204 6 0.0260 0.9137 0.008 0.000 0.000 0.000 0.000 0.992
#> SRR2001205 6 0.0260 0.9137 0.008 0.000 0.000 0.000 0.000 0.992
#> SRR2001206 6 0.0260 0.9137 0.008 0.000 0.000 0.000 0.000 0.992
#> SRR2001207 6 0.0260 0.9137 0.008 0.000 0.000 0.000 0.000 0.992
#> SRR2001200 1 0.0146 0.9258 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001201 1 0.0146 0.9258 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001202 1 0.0146 0.9258 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001203 1 0.0146 0.9258 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001196 1 0.0146 0.9258 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001197 1 0.0146 0.9258 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001198 1 0.0146 0.9258 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001199 1 0.0146 0.9258 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001192 3 0.0000 0.9985 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001193 3 0.0000 0.9985 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001194 3 0.0000 0.9985 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001195 3 0.0000 0.9985 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001188 1 0.3975 0.0789 0.544 0.000 0.000 0.000 0.004 0.452
#> SRR2001189 1 0.3989 0.0199 0.528 0.000 0.000 0.000 0.004 0.468
#> SRR2001190 1 0.3989 0.0199 0.528 0.000 0.000 0.000 0.004 0.468
#> SRR2001191 1 0.3986 0.0354 0.532 0.000 0.000 0.000 0.004 0.464
#> SRR2001184 3 0.0000 0.9985 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001185 3 0.0000 0.9985 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001186 3 0.0000 0.9985 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001187 3 0.0000 0.9985 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001180 6 0.3982 0.1892 0.460 0.000 0.000 0.000 0.004 0.536
#> SRR2001181 6 0.3966 0.2422 0.444 0.000 0.000 0.000 0.004 0.552
#> SRR2001182 6 0.3961 0.2544 0.440 0.000 0.000 0.000 0.004 0.556
#> SRR2001183 6 0.3265 0.6779 0.248 0.000 0.000 0.000 0.004 0.748
#> SRR2001176 3 0.0146 0.9940 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001177 3 0.0146 0.9940 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001178 3 0.0146 0.9940 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001179 3 0.0146 0.9940 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR2001172 3 0.0000 0.9985 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001173 3 0.0000 0.9985 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001174 3 0.0000 0.9985 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001175 3 0.0000 0.9985 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001168 6 0.0405 0.9133 0.008 0.000 0.000 0.000 0.004 0.988
#> SRR2001169 6 0.0405 0.9133 0.008 0.000 0.000 0.000 0.004 0.988
#> SRR2001170 6 0.0405 0.9133 0.008 0.000 0.000 0.000 0.004 0.988
#> SRR2001171 6 0.0405 0.9133 0.008 0.000 0.000 0.000 0.004 0.988
#> SRR2001164 1 0.0000 0.9261 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001165 1 0.0000 0.9261 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001166 1 0.0000 0.9261 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001167 1 0.0000 0.9261 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001160 1 0.0146 0.9251 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR2001161 1 0.0146 0.9251 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR2001162 1 0.0146 0.9251 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR2001163 1 0.0146 0.9251 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR2001156 1 0.0146 0.9258 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001157 1 0.0146 0.9258 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001158 1 0.0146 0.9258 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001159 1 0.0146 0.9258 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR2001152 6 0.0405 0.9129 0.008 0.000 0.000 0.000 0.004 0.988
#> SRR2001153 6 0.0405 0.9129 0.008 0.000 0.000 0.000 0.004 0.988
#> SRR2001154 6 0.0405 0.9129 0.008 0.000 0.000 0.000 0.004 0.988
#> SRR2001155 6 0.0405 0.9129 0.008 0.000 0.000 0.000 0.004 0.988
#> SRR2001148 3 0.0000 0.9985 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001149 3 0.0000 0.9985 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001150 3 0.0000 0.9985 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001151 3 0.0000 0.9985 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001144 6 0.0520 0.9130 0.008 0.000 0.000 0.000 0.008 0.984
#> SRR2001145 6 0.0520 0.9130 0.008 0.000 0.000 0.000 0.008 0.984
#> SRR2001146 6 0.0405 0.9133 0.008 0.000 0.000 0.000 0.004 0.988
#> SRR2001147 6 0.0405 0.9133 0.008 0.000 0.000 0.000 0.004 0.988
#> SRR2001140 6 0.0260 0.9137 0.008 0.000 0.000 0.000 0.000 0.992
#> SRR2001142 6 0.0260 0.9137 0.008 0.000 0.000 0.000 0.000 0.992
#> SRR2001143 6 0.0260 0.9137 0.008 0.000 0.000 0.000 0.000 0.992
#> SRR2001136 5 0.3737 0.9430 0.000 0.000 0.392 0.000 0.608 0.000
#> SRR2001137 5 0.3737 0.9430 0.000 0.000 0.392 0.000 0.608 0.000
#> SRR2001138 5 0.3737 0.9430 0.000 0.000 0.392 0.000 0.608 0.000
#> SRR2001139 5 0.3737 0.9430 0.000 0.000 0.392 0.000 0.608 0.000
#> SRR2001132 5 0.3864 0.8744 0.000 0.000 0.480 0.000 0.520 0.000
#> SRR2001133 5 0.3864 0.8744 0.000 0.000 0.480 0.000 0.520 0.000
#> SRR2001134 5 0.3864 0.8744 0.000 0.000 0.480 0.000 0.520 0.000
#> SRR2001135 5 0.3864 0.8744 0.000 0.000 0.480 0.000 0.520 0.000
#> SRR2001128 6 0.2520 0.8061 0.152 0.000 0.000 0.000 0.004 0.844
#> SRR2001129 6 0.2482 0.8099 0.148 0.000 0.000 0.000 0.004 0.848
#> SRR2001130 6 0.2520 0.8061 0.152 0.000 0.000 0.000 0.004 0.844
#> SRR2001131 6 0.2558 0.8018 0.156 0.000 0.000 0.000 0.004 0.840
#> SRR2001124 1 0.0000 0.9261 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001125 1 0.0000 0.9261 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001126 1 0.0000 0.9261 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001127 1 0.0000 0.9261 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001120 6 0.0405 0.9133 0.008 0.000 0.000 0.000 0.004 0.988
#> SRR2001121 6 0.0405 0.9133 0.008 0.000 0.000 0.000 0.004 0.988
#> SRR2001122 6 0.0405 0.9133 0.008 0.000 0.000 0.000 0.004 0.988
#> SRR2001123 6 0.0405 0.9133 0.008 0.000 0.000 0.000 0.004 0.988
#> SRR2001116 1 0.0146 0.9251 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR2001117 1 0.0146 0.9251 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR2001118 1 0.0146 0.9251 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR2001119 1 0.0146 0.9251 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR2001112 5 0.3727 0.9414 0.000 0.000 0.388 0.000 0.612 0.000
#> SRR2001113 5 0.3727 0.9414 0.000 0.000 0.388 0.000 0.612 0.000
#> SRR2001114 5 0.3727 0.9414 0.000 0.000 0.388 0.000 0.612 0.000
#> SRR2001115 5 0.3727 0.9414 0.000 0.000 0.388 0.000 0.612 0.000
#> SRR2001108 4 0.0291 0.9677 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR2001109 4 0.0291 0.9677 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR2001110 4 0.0291 0.9677 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR2001111 4 0.0291 0.9677 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR2001104 2 0.1007 0.9221 0.000 0.956 0.000 0.000 0.044 0.000
#> SRR2001105 2 0.1007 0.9221 0.000 0.956 0.000 0.000 0.044 0.000
#> SRR2001106 2 0.1007 0.9221 0.000 0.956 0.000 0.000 0.044 0.000
#> SRR2001107 2 0.1007 0.9221 0.000 0.956 0.000 0.000 0.044 0.000
#> SRR2001100 2 0.0508 0.9176 0.000 0.984 0.000 0.000 0.012 0.004
#> SRR2001101 2 0.0508 0.9176 0.000 0.984 0.000 0.000 0.012 0.004
#> SRR2001102 2 0.0508 0.9176 0.000 0.984 0.000 0.000 0.012 0.004
#> SRR2001103 2 0.0508 0.9176 0.000 0.984 0.000 0.000 0.012 0.004
#> SRR2001096 2 0.2402 0.8683 0.000 0.856 0.000 0.000 0.140 0.004
#> SRR2001097 2 0.2402 0.8683 0.000 0.856 0.000 0.000 0.140 0.004
#> SRR2001098 2 0.2402 0.8683 0.000 0.856 0.000 0.000 0.140 0.004
#> SRR2001099 2 0.2402 0.8683 0.000 0.856 0.000 0.000 0.140 0.004
#> SRR2001092 2 0.2668 0.9102 0.000 0.828 0.000 0.000 0.168 0.004
#> SRR2001093 2 0.2668 0.9102 0.000 0.828 0.000 0.000 0.168 0.004
#> SRR2001094 2 0.2668 0.9102 0.000 0.828 0.000 0.000 0.168 0.004
#> SRR2001095 2 0.2668 0.9102 0.000 0.828 0.000 0.000 0.168 0.004
#> SRR2001088 4 0.1501 0.9601 0.000 0.000 0.000 0.924 0.076 0.000
#> SRR2001089 4 0.1501 0.9601 0.000 0.000 0.000 0.924 0.076 0.000
#> SRR2001090 4 0.1501 0.9601 0.000 0.000 0.000 0.924 0.076 0.000
#> SRR2001091 4 0.1501 0.9601 0.000 0.000 0.000 0.924 0.076 0.000
#> SRR2001084 4 0.1411 0.9606 0.000 0.000 0.000 0.936 0.060 0.004
#> SRR2001085 4 0.1411 0.9606 0.000 0.000 0.000 0.936 0.060 0.004
#> SRR2001086 4 0.1411 0.9606 0.000 0.000 0.000 0.936 0.060 0.004
#> SRR2001087 4 0.1411 0.9606 0.000 0.000 0.000 0.936 0.060 0.004
#> SRR2001080 2 0.2300 0.9077 0.000 0.856 0.000 0.000 0.144 0.000
#> SRR2001081 2 0.2300 0.9077 0.000 0.856 0.000 0.000 0.144 0.000
#> SRR2001082 2 0.2300 0.9077 0.000 0.856 0.000 0.000 0.144 0.000
#> SRR2001083 2 0.2300 0.9077 0.000 0.856 0.000 0.000 0.144 0.000
#> SRR2001076 2 0.2092 0.9124 0.000 0.876 0.000 0.000 0.124 0.000
#> SRR2001077 2 0.2092 0.9124 0.000 0.876 0.000 0.000 0.124 0.000
#> SRR2001078 2 0.2092 0.9124 0.000 0.876 0.000 0.000 0.124 0.000
#> SRR2001079 2 0.2048 0.9131 0.000 0.880 0.000 0.000 0.120 0.000
#> SRR2001072 4 0.1501 0.9601 0.000 0.000 0.000 0.924 0.076 0.000
#> SRR2001073 4 0.1501 0.9601 0.000 0.000 0.000 0.924 0.076 0.000
#> SRR2001074 4 0.1501 0.9601 0.000 0.000 0.000 0.924 0.076 0.000
#> SRR2001075 4 0.1501 0.9601 0.000 0.000 0.000 0.924 0.076 0.000
#> SRR2001068 2 0.0603 0.9161 0.000 0.980 0.000 0.000 0.016 0.004
#> SRR2001069 2 0.0603 0.9161 0.000 0.980 0.000 0.000 0.016 0.004
#> SRR2001070 2 0.0508 0.9163 0.000 0.984 0.000 0.000 0.012 0.004
#> SRR2001071 2 0.0508 0.9163 0.000 0.984 0.000 0.000 0.012 0.004
#> SRR2001064 2 0.2402 0.8683 0.000 0.856 0.000 0.000 0.140 0.004
#> SRR2001065 2 0.2402 0.8683 0.000 0.856 0.000 0.000 0.140 0.004
#> SRR2001066 2 0.2402 0.8683 0.000 0.856 0.000 0.000 0.140 0.004
#> SRR2001067 2 0.2402 0.8683 0.000 0.856 0.000 0.000 0.140 0.004
#> SRR2001060 4 0.1501 0.9601 0.000 0.000 0.000 0.924 0.076 0.000
#> SRR2001061 4 0.1501 0.9601 0.000 0.000 0.000 0.924 0.076 0.000
#> SRR2001062 4 0.1501 0.9601 0.000 0.000 0.000 0.924 0.076 0.000
#> SRR2001063 4 0.1501 0.9601 0.000 0.000 0.000 0.924 0.076 0.000
#> SRR2001056 4 0.0291 0.9677 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR2001057 4 0.0291 0.9677 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR2001058 4 0.0291 0.9677 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR2001059 4 0.0291 0.9677 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR2001052 2 0.1644 0.9126 0.000 0.920 0.000 0.000 0.076 0.004
#> SRR2001053 2 0.1753 0.9142 0.000 0.912 0.000 0.000 0.084 0.004
#> SRR2001054 2 0.1644 0.9126 0.000 0.920 0.000 0.000 0.076 0.004
#> SRR2001055 2 0.1588 0.9118 0.000 0.924 0.000 0.000 0.072 0.004
#> SRR2001048 2 0.0603 0.9169 0.000 0.980 0.000 0.000 0.016 0.004
#> SRR2001049 2 0.0603 0.9169 0.000 0.980 0.000 0.000 0.016 0.004
#> SRR2001050 2 0.0603 0.9169 0.000 0.980 0.000 0.000 0.016 0.004
#> SRR2001051 2 0.0603 0.9169 0.000 0.980 0.000 0.000 0.016 0.004
#> SRR2001044 4 0.0458 0.9642 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR2001045 4 0.0458 0.9642 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR2001046 4 0.0458 0.9642 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR2001047 4 0.0458 0.9642 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR2001040 4 0.0363 0.9686 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR2001041 4 0.0363 0.9686 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR2001042 4 0.0363 0.9686 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR2001043 4 0.0363 0.9686 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR2001036 4 0.0260 0.9686 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR2001037 4 0.0260 0.9686 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR2001038 4 0.0260 0.9686 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR2001039 4 0.0260 0.9686 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR2001028 4 0.0547 0.9624 0.000 0.000 0.000 0.980 0.020 0.000
#> SRR2001029 4 0.0547 0.9624 0.000 0.000 0.000 0.980 0.020 0.000
#> SRR2001030 4 0.0547 0.9624 0.000 0.000 0.000 0.980 0.020 0.000
#> SRR2001031 4 0.0547 0.9624 0.000 0.000 0.000 0.980 0.020 0.000
#> SRR2001024 4 0.0547 0.9678 0.000 0.000 0.000 0.980 0.020 0.000
#> SRR2001025 4 0.0547 0.9678 0.000 0.000 0.000 0.980 0.020 0.000
#> SRR2001026 4 0.0547 0.9678 0.000 0.000 0.000 0.980 0.020 0.000
#> SRR2001027 4 0.0547 0.9678 0.000 0.000 0.000 0.980 0.020 0.000
#> SRR2001020 2 0.2772 0.9051 0.000 0.816 0.000 0.000 0.180 0.004
#> SRR2001021 2 0.2772 0.9051 0.000 0.816 0.000 0.000 0.180 0.004
#> SRR2001022 2 0.2772 0.9051 0.000 0.816 0.000 0.000 0.180 0.004
#> SRR2001023 2 0.2772 0.9051 0.000 0.816 0.000 0.000 0.180 0.004
#> SRR2001016 4 0.1946 0.9491 0.000 0.012 0.000 0.912 0.072 0.004
#> SRR2001017 4 0.1946 0.9491 0.000 0.012 0.000 0.912 0.072 0.004
#> SRR2001018 4 0.1946 0.9491 0.000 0.012 0.000 0.912 0.072 0.004
#> SRR2001019 4 0.1946 0.9491 0.000 0.012 0.000 0.912 0.072 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", "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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 6.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.5031 0.497 0.497
#> 3 3 1.000 1.000 1.000 0.2206 0.889 0.777
#> 4 4 1.000 0.991 0.995 0.2061 0.873 0.671
#> 5 5 0.995 0.969 0.985 0.0721 0.946 0.792
#> 6 6 0.924 0.925 0.930 0.0236 0.989 0.948
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3 4 5
There is also optional best \(k\) = 2 3 4 5 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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0 1 0 1 0
#> SRR2001033 2 0 1 0 1 0
#> SRR2001034 2 0 1 0 1 0
#> SRR2001035 2 0 1 0 1 0
#> SRR2001204 1 0 1 1 0 0
#> SRR2001205 1 0 1 1 0 0
#> SRR2001206 1 0 1 1 0 0
#> SRR2001207 1 0 1 1 0 0
#> SRR2001200 1 0 1 1 0 0
#> SRR2001201 1 0 1 1 0 0
#> SRR2001202 1 0 1 1 0 0
#> SRR2001203 1 0 1 1 0 0
#> SRR2001196 1 0 1 1 0 0
#> SRR2001197 1 0 1 1 0 0
#> SRR2001198 1 0 1 1 0 0
#> SRR2001199 1 0 1 1 0 0
#> SRR2001192 3 0 1 0 0 1
#> SRR2001193 3 0 1 0 0 1
#> SRR2001194 3 0 1 0 0 1
#> SRR2001195 3 0 1 0 0 1
#> SRR2001188 1 0 1 1 0 0
#> SRR2001189 1 0 1 1 0 0
#> SRR2001190 1 0 1 1 0 0
#> SRR2001191 1 0 1 1 0 0
#> SRR2001184 3 0 1 0 0 1
#> SRR2001185 3 0 1 0 0 1
#> SRR2001186 3 0 1 0 0 1
#> SRR2001187 3 0 1 0 0 1
#> SRR2001180 1 0 1 1 0 0
#> SRR2001181 1 0 1 1 0 0
#> SRR2001182 1 0 1 1 0 0
#> SRR2001183 1 0 1 1 0 0
#> SRR2001176 3 0 1 0 0 1
#> SRR2001177 3 0 1 0 0 1
#> SRR2001178 3 0 1 0 0 1
#> SRR2001179 3 0 1 0 0 1
#> SRR2001172 3 0 1 0 0 1
#> SRR2001173 3 0 1 0 0 1
#> SRR2001174 3 0 1 0 0 1
#> SRR2001175 3 0 1 0 0 1
#> SRR2001168 1 0 1 1 0 0
#> SRR2001169 1 0 1 1 0 0
#> SRR2001170 1 0 1 1 0 0
#> SRR2001171 1 0 1 1 0 0
#> SRR2001164 1 0 1 1 0 0
#> SRR2001165 1 0 1 1 0 0
#> SRR2001166 1 0 1 1 0 0
#> SRR2001167 1 0 1 1 0 0
#> SRR2001160 1 0 1 1 0 0
#> SRR2001161 1 0 1 1 0 0
#> SRR2001162 1 0 1 1 0 0
#> SRR2001163 1 0 1 1 0 0
#> SRR2001156 1 0 1 1 0 0
#> SRR2001157 1 0 1 1 0 0
#> SRR2001158 1 0 1 1 0 0
#> SRR2001159 1 0 1 1 0 0
#> SRR2001152 1 0 1 1 0 0
#> SRR2001153 1 0 1 1 0 0
#> SRR2001154 1 0 1 1 0 0
#> SRR2001155 1 0 1 1 0 0
#> SRR2001148 3 0 1 0 0 1
#> SRR2001149 3 0 1 0 0 1
#> SRR2001150 3 0 1 0 0 1
#> SRR2001151 3 0 1 0 0 1
#> SRR2001144 1 0 1 1 0 0
#> SRR2001145 1 0 1 1 0 0
#> SRR2001146 1 0 1 1 0 0
#> SRR2001147 1 0 1 1 0 0
#> SRR2001140 1 0 1 1 0 0
#> SRR2001142 1 0 1 1 0 0
#> SRR2001143 1 0 1 1 0 0
#> SRR2001136 3 0 1 0 0 1
#> SRR2001137 3 0 1 0 0 1
#> SRR2001138 3 0 1 0 0 1
#> SRR2001139 3 0 1 0 0 1
#> SRR2001132 3 0 1 0 0 1
#> SRR2001133 3 0 1 0 0 1
#> SRR2001134 3 0 1 0 0 1
#> SRR2001135 3 0 1 0 0 1
#> SRR2001128 1 0 1 1 0 0
#> SRR2001129 1 0 1 1 0 0
#> SRR2001130 1 0 1 1 0 0
#> SRR2001131 1 0 1 1 0 0
#> SRR2001124 1 0 1 1 0 0
#> SRR2001125 1 0 1 1 0 0
#> SRR2001126 1 0 1 1 0 0
#> SRR2001127 1 0 1 1 0 0
#> SRR2001120 1 0 1 1 0 0
#> SRR2001121 1 0 1 1 0 0
#> SRR2001122 1 0 1 1 0 0
#> SRR2001123 1 0 1 1 0 0
#> SRR2001116 1 0 1 1 0 0
#> SRR2001117 1 0 1 1 0 0
#> SRR2001118 1 0 1 1 0 0
#> SRR2001119 1 0 1 1 0 0
#> SRR2001112 3 0 1 0 0 1
#> SRR2001113 3 0 1 0 0 1
#> SRR2001114 3 0 1 0 0 1
#> SRR2001115 3 0 1 0 0 1
#> SRR2001108 2 0 1 0 1 0
#> SRR2001109 2 0 1 0 1 0
#> SRR2001110 2 0 1 0 1 0
#> SRR2001111 2 0 1 0 1 0
#> SRR2001104 2 0 1 0 1 0
#> SRR2001105 2 0 1 0 1 0
#> SRR2001106 2 0 1 0 1 0
#> SRR2001107 2 0 1 0 1 0
#> SRR2001100 2 0 1 0 1 0
#> SRR2001101 2 0 1 0 1 0
#> SRR2001102 2 0 1 0 1 0
#> SRR2001103 2 0 1 0 1 0
#> SRR2001096 2 0 1 0 1 0
#> SRR2001097 2 0 1 0 1 0
#> SRR2001098 2 0 1 0 1 0
#> SRR2001099 2 0 1 0 1 0
#> SRR2001092 2 0 1 0 1 0
#> SRR2001093 2 0 1 0 1 0
#> SRR2001094 2 0 1 0 1 0
#> SRR2001095 2 0 1 0 1 0
#> SRR2001088 2 0 1 0 1 0
#> SRR2001089 2 0 1 0 1 0
#> SRR2001090 2 0 1 0 1 0
#> SRR2001091 2 0 1 0 1 0
#> SRR2001084 2 0 1 0 1 0
#> SRR2001085 2 0 1 0 1 0
#> SRR2001086 2 0 1 0 1 0
#> SRR2001087 2 0 1 0 1 0
#> SRR2001080 2 0 1 0 1 0
#> SRR2001081 2 0 1 0 1 0
#> SRR2001082 2 0 1 0 1 0
#> SRR2001083 2 0 1 0 1 0
#> SRR2001076 2 0 1 0 1 0
#> SRR2001077 2 0 1 0 1 0
#> SRR2001078 2 0 1 0 1 0
#> SRR2001079 2 0 1 0 1 0
#> SRR2001072 2 0 1 0 1 0
#> SRR2001073 2 0 1 0 1 0
#> SRR2001074 2 0 1 0 1 0
#> SRR2001075 2 0 1 0 1 0
#> SRR2001068 2 0 1 0 1 0
#> SRR2001069 2 0 1 0 1 0
#> SRR2001070 2 0 1 0 1 0
#> SRR2001071 2 0 1 0 1 0
#> SRR2001064 2 0 1 0 1 0
#> SRR2001065 2 0 1 0 1 0
#> SRR2001066 2 0 1 0 1 0
#> SRR2001067 2 0 1 0 1 0
#> SRR2001060 2 0 1 0 1 0
#> SRR2001061 2 0 1 0 1 0
#> SRR2001062 2 0 1 0 1 0
#> SRR2001063 2 0 1 0 1 0
#> SRR2001056 2 0 1 0 1 0
#> SRR2001057 2 0 1 0 1 0
#> SRR2001058 2 0 1 0 1 0
#> SRR2001059 2 0 1 0 1 0
#> SRR2001052 2 0 1 0 1 0
#> SRR2001053 2 0 1 0 1 0
#> SRR2001054 2 0 1 0 1 0
#> SRR2001055 2 0 1 0 1 0
#> SRR2001048 2 0 1 0 1 0
#> SRR2001049 2 0 1 0 1 0
#> SRR2001050 2 0 1 0 1 0
#> SRR2001051 2 0 1 0 1 0
#> SRR2001044 2 0 1 0 1 0
#> SRR2001045 2 0 1 0 1 0
#> SRR2001046 2 0 1 0 1 0
#> SRR2001047 2 0 1 0 1 0
#> SRR2001040 2 0 1 0 1 0
#> SRR2001041 2 0 1 0 1 0
#> SRR2001042 2 0 1 0 1 0
#> SRR2001043 2 0 1 0 1 0
#> SRR2001036 2 0 1 0 1 0
#> SRR2001037 2 0 1 0 1 0
#> SRR2001038 2 0 1 0 1 0
#> SRR2001039 2 0 1 0 1 0
#> SRR2001028 2 0 1 0 1 0
#> SRR2001029 2 0 1 0 1 0
#> SRR2001030 2 0 1 0 1 0
#> SRR2001031 2 0 1 0 1 0
#> SRR2001024 2 0 1 0 1 0
#> SRR2001025 2 0 1 0 1 0
#> SRR2001026 2 0 1 0 1 0
#> SRR2001027 2 0 1 0 1 0
#> SRR2001020 2 0 1 0 1 0
#> SRR2001021 2 0 1 0 1 0
#> SRR2001022 2 0 1 0 1 0
#> SRR2001023 2 0 1 0 1 0
#> SRR2001016 2 0 1 0 1 0
#> SRR2001017 2 0 1 0 1 0
#> SRR2001018 2 0 1 0 1 0
#> SRR2001019 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.1211 0.970 0 0.960 0 0.040
#> SRR2001033 2 0.1211 0.970 0 0.960 0 0.040
#> SRR2001034 2 0.1211 0.970 0 0.960 0 0.040
#> SRR2001035 2 0.1211 0.970 0 0.960 0 0.040
#> SRR2001204 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001205 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001206 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001207 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001200 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001201 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001202 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001203 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001196 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001197 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001198 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001199 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001192 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001193 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001194 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001195 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001188 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001189 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001190 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001191 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001184 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001185 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001186 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001187 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001180 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001181 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001182 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001183 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001176 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001177 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001178 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001179 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001172 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001173 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001174 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001175 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001168 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001169 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001170 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001171 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001164 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001165 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001166 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001167 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001160 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001161 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001162 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001163 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001156 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001157 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001158 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001159 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001152 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001153 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001154 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001155 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001148 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001149 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001150 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001151 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001144 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001145 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001146 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001147 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001140 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001142 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001143 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001136 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001137 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001138 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001139 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001132 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001133 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001134 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001135 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001128 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001129 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001130 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001131 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001124 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001125 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001126 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001127 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001120 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001121 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001122 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001123 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001116 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001117 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001118 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001119 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001112 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001113 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001114 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001115 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001108 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001109 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001110 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001111 4 0.1211 0.953 0 0.040 0 0.960
#> SRR2001104 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001105 2 0.0469 0.988 0 0.988 0 0.012
#> SRR2001106 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001107 2 0.0469 0.988 0 0.988 0 0.012
#> SRR2001100 2 0.0592 0.986 0 0.984 0 0.016
#> SRR2001101 2 0.0592 0.986 0 0.984 0 0.016
#> SRR2001102 2 0.0592 0.986 0 0.984 0 0.016
#> SRR2001103 2 0.0592 0.986 0 0.984 0 0.016
#> SRR2001096 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001097 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001098 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001099 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001092 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001093 2 0.0707 0.981 0 0.980 0 0.020
#> SRR2001094 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001095 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001088 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001089 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001090 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001091 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001084 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001085 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001086 4 0.0188 0.986 0 0.004 0 0.996
#> SRR2001087 4 0.0188 0.986 0 0.004 0 0.996
#> SRR2001080 2 0.0592 0.986 0 0.984 0 0.016
#> SRR2001081 2 0.0469 0.988 0 0.988 0 0.012
#> SRR2001082 2 0.0592 0.986 0 0.984 0 0.016
#> SRR2001083 2 0.0469 0.988 0 0.988 0 0.012
#> SRR2001076 2 0.0188 0.990 0 0.996 0 0.004
#> SRR2001077 2 0.0469 0.988 0 0.988 0 0.012
#> SRR2001078 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001079 2 0.0188 0.990 0 0.996 0 0.004
#> SRR2001072 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001073 4 0.0469 0.980 0 0.012 0 0.988
#> SRR2001074 4 0.0188 0.986 0 0.004 0 0.996
#> SRR2001075 4 0.0921 0.967 0 0.028 0 0.972
#> SRR2001068 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001069 2 0.0188 0.990 0 0.996 0 0.004
#> SRR2001070 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001071 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001064 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001065 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001066 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001067 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001060 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001061 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001062 4 0.0188 0.986 0 0.004 0 0.996
#> SRR2001063 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001056 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001057 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001058 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001059 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001052 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001053 2 0.0336 0.988 0 0.992 0 0.008
#> SRR2001054 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001055 2 0.0000 0.990 0 1.000 0 0.000
#> SRR2001048 2 0.0188 0.990 0 0.996 0 0.004
#> SRR2001049 2 0.0188 0.990 0 0.996 0 0.004
#> SRR2001050 2 0.0188 0.990 0 0.996 0 0.004
#> SRR2001051 2 0.0188 0.990 0 0.996 0 0.004
#> SRR2001044 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001045 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001046 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001047 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001040 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001041 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001042 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001043 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001036 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001037 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001038 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001039 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001028 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001029 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001030 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001031 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001024 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001025 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001026 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001027 4 0.0000 0.988 0 0.000 0 1.000
#> SRR2001020 2 0.0707 0.981 0 0.980 0 0.020
#> SRR2001021 2 0.1118 0.972 0 0.964 0 0.036
#> SRR2001022 2 0.0707 0.981 0 0.980 0 0.020
#> SRR2001023 2 0.0707 0.981 0 0.980 0 0.020
#> SRR2001016 4 0.2408 0.894 0 0.104 0 0.896
#> SRR2001017 4 0.2589 0.881 0 0.116 0 0.884
#> SRR2001018 4 0.2408 0.894 0 0.104 0 0.896
#> SRR2001019 4 0.2345 0.898 0 0.100 0 0.900
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.1043 0.968 0.000 0.960 0.000 0.040 0.000
#> SRR2001033 2 0.1043 0.968 0.000 0.960 0.000 0.040 0.000
#> SRR2001034 2 0.1043 0.968 0.000 0.960 0.000 0.040 0.000
#> SRR2001035 2 0.1043 0.968 0.000 0.960 0.000 0.040 0.000
#> SRR2001204 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001205 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001206 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001207 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001200 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001201 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001202 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001203 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001196 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001197 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001198 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001199 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001192 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001193 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001194 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001195 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001188 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001189 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001190 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001191 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001184 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001185 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001186 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001187 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001180 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001181 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001182 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001183 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001176 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001177 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001178 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001179 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001172 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001173 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001174 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001175 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001168 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001169 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001170 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001171 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001164 5 0.0290 0.945 0.008 0.000 0.000 0.000 0.992
#> SRR2001165 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001166 5 0.0510 0.939 0.016 0.000 0.000 0.000 0.984
#> SRR2001167 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001160 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001161 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001162 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001163 5 0.0162 0.948 0.004 0.000 0.000 0.000 0.996
#> SRR2001156 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001157 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001158 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001159 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001152 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001153 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001154 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001155 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001148 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001149 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001150 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001151 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001144 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001145 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001146 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001147 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001140 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001142 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001143 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001136 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001137 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001138 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001139 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001132 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001133 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001134 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001135 3 0.0000 0.981 0.000 0.000 1.000 0.000 0.000
#> SRR2001128 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001129 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001130 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001131 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001124 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001125 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001126 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001127 5 0.0000 0.950 0.000 0.000 0.000 0.000 1.000
#> SRR2001120 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001121 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001122 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001123 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001116 5 0.3932 0.551 0.328 0.000 0.000 0.000 0.672
#> SRR2001117 5 0.3452 0.698 0.244 0.000 0.000 0.000 0.756
#> SRR2001118 5 0.3816 0.602 0.304 0.000 0.000 0.000 0.696
#> SRR2001119 5 0.4101 0.463 0.372 0.000 0.000 0.000 0.628
#> SRR2001112 3 0.1792 0.907 0.000 0.000 0.916 0.000 0.084
#> SRR2001113 3 0.3424 0.701 0.000 0.000 0.760 0.000 0.240
#> SRR2001114 3 0.2377 0.859 0.000 0.000 0.872 0.000 0.128
#> SRR2001115 3 0.2561 0.841 0.000 0.000 0.856 0.000 0.144
#> SRR2001108 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001109 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001110 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001111 4 0.1043 0.951 0.000 0.040 0.000 0.960 0.000
#> SRR2001104 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001105 2 0.0404 0.987 0.000 0.988 0.000 0.012 0.000
#> SRR2001106 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001107 2 0.0404 0.987 0.000 0.988 0.000 0.012 0.000
#> SRR2001100 2 0.0510 0.985 0.000 0.984 0.000 0.016 0.000
#> SRR2001101 2 0.0510 0.985 0.000 0.984 0.000 0.016 0.000
#> SRR2001102 2 0.0510 0.985 0.000 0.984 0.000 0.016 0.000
#> SRR2001103 2 0.0510 0.985 0.000 0.984 0.000 0.016 0.000
#> SRR2001096 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001097 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001098 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001099 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001092 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001093 2 0.0609 0.981 0.000 0.980 0.000 0.020 0.000
#> SRR2001094 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001095 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001088 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001089 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001090 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001091 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001084 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001085 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001086 4 0.0162 0.985 0.000 0.004 0.000 0.996 0.000
#> SRR2001087 4 0.0162 0.985 0.000 0.004 0.000 0.996 0.000
#> SRR2001080 2 0.0510 0.985 0.000 0.984 0.000 0.016 0.000
#> SRR2001081 2 0.0404 0.987 0.000 0.988 0.000 0.012 0.000
#> SRR2001082 2 0.0510 0.985 0.000 0.984 0.000 0.016 0.000
#> SRR2001083 2 0.0404 0.987 0.000 0.988 0.000 0.012 0.000
#> SRR2001076 2 0.0162 0.989 0.000 0.996 0.000 0.004 0.000
#> SRR2001077 2 0.0404 0.987 0.000 0.988 0.000 0.012 0.000
#> SRR2001078 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001079 2 0.0162 0.989 0.000 0.996 0.000 0.004 0.000
#> SRR2001072 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001073 4 0.0404 0.979 0.000 0.012 0.000 0.988 0.000
#> SRR2001074 4 0.0162 0.985 0.000 0.004 0.000 0.996 0.000
#> SRR2001075 4 0.0794 0.965 0.000 0.028 0.000 0.972 0.000
#> SRR2001068 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001069 2 0.0162 0.989 0.000 0.996 0.000 0.004 0.000
#> SRR2001070 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001071 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001064 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001065 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001066 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001067 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001060 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001061 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001062 4 0.0162 0.985 0.000 0.004 0.000 0.996 0.000
#> SRR2001063 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001056 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001057 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001058 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001059 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001052 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001053 2 0.0290 0.988 0.000 0.992 0.000 0.008 0.000
#> SRR2001054 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001055 2 0.0000 0.989 0.000 1.000 0.000 0.000 0.000
#> SRR2001048 2 0.0162 0.989 0.000 0.996 0.000 0.004 0.000
#> SRR2001049 2 0.0162 0.989 0.000 0.996 0.000 0.004 0.000
#> SRR2001050 2 0.0162 0.989 0.000 0.996 0.000 0.004 0.000
#> SRR2001051 2 0.0162 0.989 0.000 0.996 0.000 0.004 0.000
#> SRR2001044 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001045 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001046 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001047 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001040 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001041 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001042 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001043 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001036 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001037 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001038 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001039 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001028 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001029 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001030 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001031 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001024 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001025 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001026 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001027 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000
#> SRR2001020 2 0.0609 0.981 0.000 0.980 0.000 0.020 0.000
#> SRR2001021 2 0.0963 0.971 0.000 0.964 0.000 0.036 0.000
#> SRR2001022 2 0.0609 0.981 0.000 0.980 0.000 0.020 0.000
#> SRR2001023 2 0.0609 0.981 0.000 0.980 0.000 0.020 0.000
#> SRR2001016 4 0.2074 0.888 0.000 0.104 0.000 0.896 0.000
#> SRR2001017 4 0.2230 0.874 0.000 0.116 0.000 0.884 0.000
#> SRR2001018 4 0.2074 0.888 0.000 0.104 0.000 0.896 0.000
#> SRR2001019 4 0.2020 0.893 0.000 0.100 0.000 0.900 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 2 0.4709 0.803 0.000 0.680 0.000 0.132 0.188 0.000
#> SRR2001033 2 0.4680 0.804 0.000 0.684 0.000 0.132 0.184 0.000
#> SRR2001034 2 0.4709 0.803 0.000 0.680 0.000 0.132 0.188 0.000
#> SRR2001035 2 0.4709 0.803 0.000 0.680 0.000 0.132 0.188 0.000
#> SRR2001204 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001205 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001206 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001207 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001200 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001201 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001202 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001203 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001196 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001197 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001198 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001199 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001192 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001193 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001194 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001195 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001188 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001189 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001190 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001191 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001184 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001185 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001186 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001187 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001180 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001181 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001182 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001183 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001176 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001177 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001178 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001179 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001172 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001173 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001174 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001175 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001168 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001169 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001170 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001171 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001164 1 0.0260 0.930 0.992 0.000 0.000 0.000 0.000 0.008
#> SRR2001165 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001166 1 0.0458 0.922 0.984 0.000 0.000 0.000 0.000 0.016
#> SRR2001167 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001160 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001161 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001162 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001163 1 0.0146 0.933 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR2001156 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001157 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001158 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001159 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001152 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001153 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001154 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001155 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001148 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001149 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001150 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001151 3 0.0000 0.996 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR2001144 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001145 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001146 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001147 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001140 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001142 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001143 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001136 5 0.3531 0.931 0.000 0.000 0.328 0.000 0.672 0.000
#> SRR2001137 5 0.3531 0.931 0.000 0.000 0.328 0.000 0.672 0.000
#> SRR2001138 5 0.3531 0.931 0.000 0.000 0.328 0.000 0.672 0.000
#> SRR2001139 5 0.3531 0.931 0.000 0.000 0.328 0.000 0.672 0.000
#> SRR2001132 3 0.0363 0.983 0.000 0.000 0.988 0.000 0.012 0.000
#> SRR2001133 3 0.0790 0.956 0.000 0.000 0.968 0.000 0.032 0.000
#> SRR2001134 3 0.0458 0.978 0.000 0.000 0.984 0.000 0.016 0.000
#> SRR2001135 3 0.0363 0.983 0.000 0.000 0.988 0.000 0.012 0.000
#> SRR2001128 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001129 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001130 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001131 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001124 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001125 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001126 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001127 1 0.0000 0.937 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR2001120 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001121 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001122 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001123 6 0.0000 1.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR2001116 1 0.3531 0.527 0.672 0.000 0.000 0.000 0.000 0.328
#> SRR2001117 1 0.3101 0.651 0.756 0.000 0.000 0.000 0.000 0.244
#> SRR2001118 1 0.3428 0.571 0.696 0.000 0.000 0.000 0.000 0.304
#> SRR2001119 1 0.3684 0.462 0.628 0.000 0.000 0.000 0.000 0.372
#> SRR2001112 5 0.4065 0.932 0.028 0.000 0.300 0.000 0.672 0.000
#> SRR2001113 5 0.4721 0.829 0.116 0.000 0.212 0.000 0.672 0.000
#> SRR2001114 5 0.4332 0.917 0.052 0.000 0.276 0.000 0.672 0.000
#> SRR2001115 5 0.4294 0.921 0.048 0.000 0.280 0.000 0.672 0.000
#> SRR2001108 4 0.1007 0.938 0.000 0.000 0.000 0.956 0.044 0.000
#> SRR2001109 4 0.0260 0.945 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR2001110 4 0.1075 0.937 0.000 0.000 0.000 0.952 0.048 0.000
#> SRR2001111 4 0.2129 0.915 0.000 0.040 0.000 0.904 0.056 0.000
#> SRR2001104 2 0.1556 0.890 0.000 0.920 0.000 0.000 0.080 0.000
#> SRR2001105 2 0.1082 0.889 0.000 0.956 0.000 0.004 0.040 0.000
#> SRR2001106 2 0.0713 0.887 0.000 0.972 0.000 0.000 0.028 0.000
#> SRR2001107 2 0.0858 0.888 0.000 0.968 0.000 0.004 0.028 0.000
#> SRR2001100 2 0.1082 0.870 0.000 0.956 0.000 0.040 0.004 0.000
#> SRR2001101 2 0.1082 0.870 0.000 0.956 0.000 0.040 0.004 0.000
#> SRR2001102 2 0.1082 0.870 0.000 0.956 0.000 0.040 0.004 0.000
#> SRR2001103 2 0.1082 0.870 0.000 0.956 0.000 0.040 0.004 0.000
#> SRR2001096 2 0.0146 0.882 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR2001097 2 0.0000 0.881 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001098 2 0.0458 0.885 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR2001099 2 0.0458 0.885 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR2001092 2 0.2697 0.882 0.000 0.812 0.000 0.000 0.188 0.000
#> SRR2001093 2 0.2697 0.882 0.000 0.812 0.000 0.000 0.188 0.000
#> SRR2001094 2 0.2697 0.882 0.000 0.812 0.000 0.000 0.188 0.000
#> SRR2001095 2 0.2697 0.882 0.000 0.812 0.000 0.000 0.188 0.000
#> SRR2001088 4 0.0458 0.944 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR2001089 4 0.0458 0.944 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR2001090 4 0.0458 0.944 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR2001091 4 0.0458 0.944 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR2001084 4 0.2219 0.899 0.000 0.000 0.000 0.864 0.136 0.000
#> SRR2001085 4 0.2178 0.901 0.000 0.000 0.000 0.868 0.132 0.000
#> SRR2001086 4 0.2219 0.899 0.000 0.000 0.000 0.864 0.136 0.000
#> SRR2001087 4 0.2219 0.899 0.000 0.000 0.000 0.864 0.136 0.000
#> SRR2001080 2 0.2948 0.881 0.000 0.804 0.000 0.008 0.188 0.000
#> SRR2001081 2 0.2805 0.883 0.000 0.812 0.000 0.004 0.184 0.000
#> SRR2001082 2 0.3046 0.880 0.000 0.800 0.000 0.012 0.188 0.000
#> SRR2001083 2 0.2838 0.882 0.000 0.808 0.000 0.004 0.188 0.000
#> SRR2001076 2 0.2838 0.882 0.000 0.808 0.000 0.004 0.188 0.000
#> SRR2001077 2 0.2838 0.882 0.000 0.808 0.000 0.004 0.188 0.000
#> SRR2001078 2 0.2697 0.882 0.000 0.812 0.000 0.000 0.188 0.000
#> SRR2001079 2 0.2838 0.882 0.000 0.808 0.000 0.004 0.188 0.000
#> SRR2001072 4 0.2178 0.901 0.000 0.000 0.000 0.868 0.132 0.000
#> SRR2001073 4 0.2346 0.902 0.000 0.008 0.000 0.868 0.124 0.000
#> SRR2001074 4 0.2219 0.899 0.000 0.000 0.000 0.864 0.136 0.000
#> SRR2001075 4 0.2790 0.888 0.000 0.024 0.000 0.844 0.132 0.000
#> SRR2001068 2 0.0937 0.868 0.000 0.960 0.000 0.000 0.040 0.000
#> SRR2001069 2 0.0937 0.868 0.000 0.960 0.000 0.000 0.040 0.000
#> SRR2001070 2 0.0937 0.868 0.000 0.960 0.000 0.000 0.040 0.000
#> SRR2001071 2 0.0937 0.868 0.000 0.960 0.000 0.000 0.040 0.000
#> SRR2001064 2 0.0146 0.880 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR2001065 2 0.0363 0.884 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR2001066 2 0.0000 0.881 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR2001067 2 0.0260 0.881 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR2001060 4 0.0790 0.942 0.000 0.000 0.000 0.968 0.032 0.000
#> SRR2001061 4 0.0937 0.940 0.000 0.000 0.000 0.960 0.040 0.000
#> SRR2001062 4 0.1204 0.934 0.000 0.000 0.000 0.944 0.056 0.000
#> SRR2001063 4 0.1204 0.934 0.000 0.000 0.000 0.944 0.056 0.000
#> SRR2001056 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001057 4 0.0937 0.938 0.000 0.000 0.000 0.960 0.040 0.000
#> SRR2001058 4 0.1714 0.921 0.000 0.000 0.000 0.908 0.092 0.000
#> SRR2001059 4 0.2178 0.901 0.000 0.000 0.000 0.868 0.132 0.000
#> SRR2001052 2 0.2697 0.882 0.000 0.812 0.000 0.000 0.188 0.000
#> SRR2001053 2 0.2854 0.876 0.000 0.792 0.000 0.000 0.208 0.000
#> SRR2001054 2 0.2793 0.879 0.000 0.800 0.000 0.000 0.200 0.000
#> SRR2001055 2 0.2941 0.871 0.000 0.780 0.000 0.000 0.220 0.000
#> SRR2001048 2 0.1092 0.871 0.000 0.960 0.000 0.020 0.020 0.000
#> SRR2001049 2 0.1088 0.871 0.000 0.960 0.000 0.016 0.024 0.000
#> SRR2001050 2 0.1049 0.871 0.000 0.960 0.000 0.032 0.008 0.000
#> SRR2001051 2 0.1092 0.871 0.000 0.960 0.000 0.020 0.020 0.000
#> SRR2001044 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001045 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001046 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001047 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001040 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001041 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001042 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001043 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001036 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001037 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001038 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001039 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001028 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001029 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001030 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001031 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001024 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001025 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001026 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001027 4 0.0000 0.945 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR2001020 2 0.3244 0.844 0.000 0.732 0.000 0.000 0.268 0.000
#> SRR2001021 2 0.3674 0.839 0.000 0.716 0.000 0.016 0.268 0.000
#> SRR2001022 2 0.3244 0.844 0.000 0.732 0.000 0.000 0.268 0.000
#> SRR2001023 2 0.3244 0.844 0.000 0.732 0.000 0.000 0.268 0.000
#> SRR2001016 4 0.4279 0.776 0.000 0.128 0.000 0.732 0.140 0.000
#> SRR2001017 4 0.4393 0.760 0.000 0.140 0.000 0.720 0.140 0.000
#> SRR2001018 4 0.4279 0.776 0.000 0.128 0.000 0.732 0.140 0.000
#> SRR2001019 4 0.4279 0.776 0.000 0.128 0.000 0.732 0.140 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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.5031 0.497 0.497
#> 3 3 0.718 0.860 0.887 0.2303 0.880 0.758
#> 4 4 0.961 0.955 0.978 0.1843 0.884 0.694
#> 5 5 0.885 0.893 0.927 0.0623 0.949 0.810
#> 6 6 0.772 0.668 0.811 0.0388 0.925 0.687
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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001033 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001034 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001035 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001204 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001205 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001206 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001207 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001200 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001201 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001202 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001203 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001196 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001197 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001198 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001199 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001192 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001193 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001194 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001195 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001188 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001189 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001190 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001191 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001184 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001185 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001186 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001187 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001180 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001181 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001182 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001183 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001176 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001177 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001178 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001179 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001172 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001173 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001174 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001175 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001168 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001169 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001170 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001171 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001164 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001165 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001166 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001167 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001160 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001161 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001162 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001163 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001156 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001157 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001158 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001159 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001152 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001153 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001154 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001155 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001148 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001149 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001150 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001151 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001144 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001145 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001146 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001147 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001140 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001142 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001143 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001136 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001137 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001138 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001139 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001132 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001133 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001134 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001135 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001128 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001129 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001130 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001131 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001124 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001125 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001126 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001127 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001120 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001121 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001122 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001123 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001116 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001117 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001118 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001119 1 0.0000 0.9495 1.000 0.000 0.000
#> SRR2001112 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001113 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001114 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001115 1 0.4178 0.8966 0.828 0.000 0.172
#> SRR2001108 2 0.2165 0.8087 0.000 0.936 0.064
#> SRR2001109 2 0.2959 0.8053 0.000 0.900 0.100
#> SRR2001110 2 0.2959 0.8083 0.000 0.900 0.100
#> SRR2001111 2 0.3340 0.8063 0.000 0.880 0.120
#> SRR2001104 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001105 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001106 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001107 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001100 2 0.5465 0.6363 0.000 0.712 0.288
#> SRR2001101 2 0.5733 0.5663 0.000 0.676 0.324
#> SRR2001102 2 0.5988 0.4604 0.000 0.632 0.368
#> SRR2001103 2 0.6045 0.4260 0.000 0.620 0.380
#> SRR2001096 3 0.4178 0.9656 0.000 0.172 0.828
#> SRR2001097 3 0.4178 0.9656 0.000 0.172 0.828
#> SRR2001098 3 0.4178 0.9656 0.000 0.172 0.828
#> SRR2001099 3 0.4178 0.9656 0.000 0.172 0.828
#> SRR2001092 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001093 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001094 3 0.4178 0.9656 0.000 0.172 0.828
#> SRR2001095 3 0.4235 0.9636 0.000 0.176 0.824
#> SRR2001088 2 0.4235 0.7921 0.000 0.824 0.176
#> SRR2001089 2 0.4235 0.7921 0.000 0.824 0.176
#> SRR2001090 2 0.4235 0.7921 0.000 0.824 0.176
#> SRR2001091 2 0.4235 0.7921 0.000 0.824 0.176
#> SRR2001084 2 0.3879 0.7995 0.000 0.848 0.152
#> SRR2001085 2 0.3340 0.8063 0.000 0.880 0.120
#> SRR2001086 2 0.4235 0.7921 0.000 0.824 0.176
#> SRR2001087 2 0.4235 0.7921 0.000 0.824 0.176
#> SRR2001080 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001081 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001082 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001083 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001076 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001077 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001078 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001079 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001072 2 0.4291 0.7913 0.000 0.820 0.180
#> SRR2001073 2 0.4291 0.7913 0.000 0.820 0.180
#> SRR2001074 2 0.4291 0.7913 0.000 0.820 0.180
#> SRR2001075 2 0.4291 0.7913 0.000 0.820 0.180
#> SRR2001068 2 0.6274 0.1760 0.000 0.544 0.456
#> SRR2001069 2 0.6274 0.1760 0.000 0.544 0.456
#> SRR2001070 2 0.6274 0.1760 0.000 0.544 0.456
#> SRR2001071 2 0.6267 0.1925 0.000 0.548 0.452
#> SRR2001064 3 0.4178 0.9656 0.000 0.172 0.828
#> SRR2001065 3 0.4178 0.9656 0.000 0.172 0.828
#> SRR2001066 3 0.4178 0.9656 0.000 0.172 0.828
#> SRR2001067 3 0.4178 0.9656 0.000 0.172 0.828
#> SRR2001060 2 0.4235 0.7921 0.000 0.824 0.176
#> SRR2001061 2 0.4235 0.7921 0.000 0.824 0.176
#> SRR2001062 2 0.4235 0.7921 0.000 0.824 0.176
#> SRR2001063 2 0.4235 0.7921 0.000 0.824 0.176
#> SRR2001056 2 0.0237 0.8047 0.000 0.996 0.004
#> SRR2001057 2 0.0000 0.8034 0.000 1.000 0.000
#> SRR2001058 2 0.0000 0.8034 0.000 1.000 0.000
#> SRR2001059 2 0.1289 0.8076 0.000 0.968 0.032
#> SRR2001052 2 0.6299 0.0882 0.000 0.524 0.476
#> SRR2001053 3 0.6274 0.2177 0.000 0.456 0.544
#> SRR2001054 2 0.6295 0.1071 0.000 0.528 0.472
#> SRR2001055 2 0.6307 0.0274 0.000 0.512 0.488
#> SRR2001048 3 0.5397 0.8050 0.000 0.280 0.720
#> SRR2001049 3 0.4399 0.9540 0.000 0.188 0.812
#> SRR2001050 3 0.5363 0.8119 0.000 0.276 0.724
#> SRR2001051 3 0.5760 0.6980 0.000 0.328 0.672
#> SRR2001044 2 0.0000 0.8034 0.000 1.000 0.000
#> SRR2001045 2 0.0000 0.8034 0.000 1.000 0.000
#> SRR2001046 2 0.0000 0.8034 0.000 1.000 0.000
#> SRR2001047 2 0.0000 0.8034 0.000 1.000 0.000
#> SRR2001040 2 0.0000 0.8034 0.000 1.000 0.000
#> SRR2001041 2 0.0000 0.8034 0.000 1.000 0.000
#> SRR2001042 2 0.0000 0.8034 0.000 1.000 0.000
#> SRR2001043 2 0.0000 0.8034 0.000 1.000 0.000
#> SRR2001036 2 0.0000 0.8034 0.000 1.000 0.000
#> SRR2001037 2 0.0000 0.8034 0.000 1.000 0.000
#> SRR2001038 2 0.0000 0.8034 0.000 1.000 0.000
#> SRR2001039 2 0.0000 0.8034 0.000 1.000 0.000
#> SRR2001028 2 0.0237 0.8046 0.000 0.996 0.004
#> SRR2001029 2 0.0237 0.8046 0.000 0.996 0.004
#> SRR2001030 2 0.0424 0.8053 0.000 0.992 0.008
#> SRR2001031 2 0.0237 0.8046 0.000 0.996 0.004
#> SRR2001024 2 0.0000 0.8034 0.000 1.000 0.000
#> SRR2001025 2 0.0000 0.8034 0.000 1.000 0.000
#> SRR2001026 2 0.0000 0.8034 0.000 1.000 0.000
#> SRR2001027 2 0.0237 0.8047 0.000 0.996 0.004
#> SRR2001020 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001021 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001022 3 0.4235 0.9680 0.000 0.176 0.824
#> SRR2001023 3 0.4399 0.9545 0.000 0.188 0.812
#> SRR2001016 2 0.4346 0.7883 0.000 0.816 0.184
#> SRR2001017 2 0.4399 0.7845 0.000 0.812 0.188
#> SRR2001018 2 0.4346 0.7883 0.000 0.816 0.184
#> SRR2001019 2 0.4346 0.7883 0.000 0.816 0.184
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.0188 0.955 0 0.996 0 0.004
#> SRR2001033 2 0.0188 0.955 0 0.996 0 0.004
#> SRR2001034 2 0.0188 0.955 0 0.996 0 0.004
#> SRR2001035 2 0.0188 0.955 0 0.996 0 0.004
#> SRR2001204 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001205 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001206 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001207 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001200 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001201 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001202 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001203 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001196 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001197 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001198 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001199 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001192 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001193 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001194 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001195 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001188 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001189 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001190 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001191 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001184 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001185 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001186 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001187 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001180 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001181 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001182 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001183 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001176 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001177 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001178 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001179 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001172 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001173 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001174 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001175 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001168 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001169 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001170 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001171 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001164 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001165 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001166 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001167 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001160 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001161 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001162 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001163 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001156 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001157 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001158 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001159 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001152 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001153 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001154 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001155 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001148 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001149 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001150 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001151 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001144 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001145 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001146 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001147 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001140 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001142 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001143 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001136 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001137 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001138 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001139 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001132 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001133 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001134 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001135 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001128 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001129 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001130 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001131 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001124 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001125 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001126 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001127 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001120 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001121 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001122 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001123 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001116 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001117 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001118 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001119 1 0.0000 1.000 1 0.000 0 0.000
#> SRR2001112 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001113 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001114 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001115 3 0.0000 1.000 0 0.000 1 0.000
#> SRR2001108 4 0.0188 0.950 0 0.004 0 0.996
#> SRR2001109 4 0.0188 0.950 0 0.004 0 0.996
#> SRR2001110 4 0.0469 0.949 0 0.012 0 0.988
#> SRR2001111 4 0.0336 0.950 0 0.008 0 0.992
#> SRR2001104 2 0.0000 0.956 0 1.000 0 0.000
#> SRR2001105 2 0.0000 0.956 0 1.000 0 0.000
#> SRR2001106 2 0.0000 0.956 0 1.000 0 0.000
#> SRR2001107 2 0.0000 0.956 0 1.000 0 0.000
#> SRR2001100 4 0.2530 0.877 0 0.112 0 0.888
#> SRR2001101 4 0.2530 0.877 0 0.112 0 0.888
#> SRR2001102 4 0.3266 0.822 0 0.168 0 0.832
#> SRR2001103 4 0.3266 0.820 0 0.168 0 0.832
#> SRR2001096 2 0.0000 0.956 0 1.000 0 0.000
#> SRR2001097 2 0.0000 0.956 0 1.000 0 0.000
#> SRR2001098 2 0.0000 0.956 0 1.000 0 0.000
#> SRR2001099 2 0.0000 0.956 0 1.000 0 0.000
#> SRR2001092 2 0.0000 0.956 0 1.000 0 0.000
#> SRR2001093 2 0.0000 0.956 0 1.000 0 0.000
#> SRR2001094 2 0.0188 0.956 0 0.996 0 0.004
#> SRR2001095 2 0.0188 0.955 0 0.996 0 0.004
#> SRR2001088 4 0.0592 0.949 0 0.016 0 0.984
#> SRR2001089 4 0.0469 0.949 0 0.012 0 0.988
#> SRR2001090 4 0.0592 0.949 0 0.016 0 0.984
#> SRR2001091 4 0.0469 0.949 0 0.012 0 0.988
#> SRR2001084 4 0.0336 0.950 0 0.008 0 0.992
#> SRR2001085 4 0.0188 0.950 0 0.004 0 0.996
#> SRR2001086 4 0.0336 0.950 0 0.008 0 0.992
#> SRR2001087 4 0.0336 0.950 0 0.008 0 0.992
#> SRR2001080 2 0.0336 0.954 0 0.992 0 0.008
#> SRR2001081 2 0.0336 0.954 0 0.992 0 0.008
#> SRR2001082 2 0.0336 0.954 0 0.992 0 0.008
#> SRR2001083 2 0.0188 0.955 0 0.996 0 0.004
#> SRR2001076 2 0.0000 0.956 0 1.000 0 0.000
#> SRR2001077 2 0.0000 0.956 0 1.000 0 0.000
#> SRR2001078 2 0.0000 0.956 0 1.000 0 0.000
#> SRR2001079 2 0.0000 0.956 0 1.000 0 0.000
#> SRR2001072 4 0.0921 0.942 0 0.028 0 0.972
#> SRR2001073 4 0.0592 0.949 0 0.016 0 0.984
#> SRR2001074 4 0.1022 0.940 0 0.032 0 0.968
#> SRR2001075 4 0.1211 0.934 0 0.040 0 0.960
#> SRR2001068 4 0.3486 0.798 0 0.188 0 0.812
#> SRR2001069 4 0.3486 0.798 0 0.188 0 0.812
#> SRR2001070 4 0.3486 0.798 0 0.188 0 0.812
#> SRR2001071 4 0.3486 0.798 0 0.188 0 0.812
#> SRR2001064 2 0.0188 0.956 0 0.996 0 0.004
#> SRR2001065 2 0.0000 0.956 0 1.000 0 0.000
#> SRR2001066 2 0.0000 0.956 0 1.000 0 0.000
#> SRR2001067 2 0.0000 0.956 0 1.000 0 0.000
#> SRR2001060 4 0.0592 0.949 0 0.016 0 0.984
#> SRR2001061 4 0.0592 0.949 0 0.016 0 0.984
#> SRR2001062 4 0.0592 0.949 0 0.016 0 0.984
#> SRR2001063 4 0.0592 0.949 0 0.016 0 0.984
#> SRR2001056 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001057 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001058 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001059 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001052 4 0.3942 0.734 0 0.236 0 0.764
#> SRR2001053 4 0.4925 0.320 0 0.428 0 0.572
#> SRR2001054 4 0.3688 0.773 0 0.208 0 0.792
#> SRR2001055 4 0.4164 0.690 0 0.264 0 0.736
#> SRR2001048 2 0.4406 0.557 0 0.700 0 0.300
#> SRR2001049 2 0.0817 0.943 0 0.976 0 0.024
#> SRR2001050 2 0.4543 0.506 0 0.676 0 0.324
#> SRR2001051 2 0.4916 0.223 0 0.576 0 0.424
#> SRR2001044 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001045 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001046 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001047 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001040 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001041 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001042 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001043 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001036 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001037 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001038 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001039 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001028 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001029 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001030 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001031 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001024 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001025 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001026 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001027 4 0.0000 0.950 0 0.000 0 1.000
#> SRR2001020 2 0.0817 0.943 0 0.976 0 0.024
#> SRR2001021 2 0.1118 0.933 0 0.964 0 0.036
#> SRR2001022 2 0.1302 0.926 0 0.956 0 0.044
#> SRR2001023 2 0.2081 0.887 0 0.916 0 0.084
#> SRR2001016 4 0.0817 0.944 0 0.024 0 0.976
#> SRR2001017 4 0.0921 0.941 0 0.028 0 0.972
#> SRR2001018 4 0.0921 0.941 0 0.028 0 0.972
#> SRR2001019 4 0.0469 0.949 0 0.012 0 0.988
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.0510 0.949 0.000 0.984 0 0.000 0.016
#> SRR2001033 2 0.0510 0.949 0.000 0.984 0 0.000 0.016
#> SRR2001034 2 0.0510 0.949 0.000 0.984 0 0.000 0.016
#> SRR2001035 2 0.0510 0.949 0.000 0.984 0 0.000 0.016
#> SRR2001204 5 0.0794 0.929 0.028 0.000 0 0.000 0.972
#> SRR2001205 5 0.0794 0.929 0.028 0.000 0 0.000 0.972
#> SRR2001206 5 0.0794 0.929 0.028 0.000 0 0.000 0.972
#> SRR2001207 5 0.0794 0.929 0.028 0.000 0 0.000 0.972
#> SRR2001200 1 0.0162 0.820 0.996 0.000 0 0.000 0.004
#> SRR2001201 1 0.0162 0.820 0.996 0.000 0 0.000 0.004
#> SRR2001202 1 0.0162 0.820 0.996 0.000 0 0.000 0.004
#> SRR2001203 1 0.0162 0.820 0.996 0.000 0 0.000 0.004
#> SRR2001196 1 0.0000 0.819 1.000 0.000 0 0.000 0.000
#> SRR2001197 1 0.0000 0.819 1.000 0.000 0 0.000 0.000
#> SRR2001198 1 0.0000 0.819 1.000 0.000 0 0.000 0.000
#> SRR2001199 1 0.0000 0.819 1.000 0.000 0 0.000 0.000
#> SRR2001192 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001193 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001194 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001195 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001188 1 0.2648 0.821 0.848 0.000 0 0.000 0.152
#> SRR2001189 1 0.3074 0.813 0.804 0.000 0 0.000 0.196
#> SRR2001190 1 0.2329 0.830 0.876 0.000 0 0.000 0.124
#> SRR2001191 1 0.2280 0.831 0.880 0.000 0 0.000 0.120
#> SRR2001184 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001185 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001186 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001187 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001180 1 0.3452 0.803 0.756 0.000 0 0.000 0.244
#> SRR2001181 1 0.3305 0.816 0.776 0.000 0 0.000 0.224
#> SRR2001182 1 0.3274 0.818 0.780 0.000 0 0.000 0.220
#> SRR2001183 1 0.3274 0.818 0.780 0.000 0 0.000 0.220
#> SRR2001176 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001177 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001178 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001179 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001172 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001173 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001174 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001175 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001168 5 0.0794 0.929 0.028 0.000 0 0.000 0.972
#> SRR2001169 5 0.0794 0.929 0.028 0.000 0 0.000 0.972
#> SRR2001170 5 0.0794 0.929 0.028 0.000 0 0.000 0.972
#> SRR2001171 5 0.0794 0.929 0.028 0.000 0 0.000 0.972
#> SRR2001164 1 0.3143 0.823 0.796 0.000 0 0.000 0.204
#> SRR2001165 1 0.3274 0.818 0.780 0.000 0 0.000 0.220
#> SRR2001166 1 0.3210 0.820 0.788 0.000 0 0.000 0.212
#> SRR2001167 1 0.3534 0.793 0.744 0.000 0 0.000 0.256
#> SRR2001160 1 0.3752 0.752 0.708 0.000 0 0.000 0.292
#> SRR2001161 1 0.3143 0.823 0.796 0.000 0 0.000 0.204
#> SRR2001162 1 0.3586 0.785 0.736 0.000 0 0.000 0.264
#> SRR2001163 1 0.4268 0.444 0.556 0.000 0 0.000 0.444
#> SRR2001156 1 0.0000 0.819 1.000 0.000 0 0.000 0.000
#> SRR2001157 1 0.0000 0.819 1.000 0.000 0 0.000 0.000
#> SRR2001158 1 0.0000 0.819 1.000 0.000 0 0.000 0.000
#> SRR2001159 1 0.0000 0.819 1.000 0.000 0 0.000 0.000
#> SRR2001152 1 0.3336 0.813 0.772 0.000 0 0.000 0.228
#> SRR2001153 1 0.3274 0.818 0.780 0.000 0 0.000 0.220
#> SRR2001154 1 0.3876 0.717 0.684 0.000 0 0.000 0.316
#> SRR2001155 1 0.3305 0.816 0.776 0.000 0 0.000 0.224
#> SRR2001148 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001149 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001150 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001151 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001144 5 0.0794 0.929 0.028 0.000 0 0.000 0.972
#> SRR2001145 5 0.0794 0.929 0.028 0.000 0 0.000 0.972
#> SRR2001146 5 0.0794 0.929 0.028 0.000 0 0.000 0.972
#> SRR2001147 5 0.0794 0.929 0.028 0.000 0 0.000 0.972
#> SRR2001140 5 0.0794 0.929 0.028 0.000 0 0.000 0.972
#> SRR2001142 5 0.0794 0.929 0.028 0.000 0 0.000 0.972
#> SRR2001143 5 0.0794 0.929 0.028 0.000 0 0.000 0.972
#> SRR2001136 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001137 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001138 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001139 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001132 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001133 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001134 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001135 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001128 5 0.4060 0.350 0.360 0.000 0 0.000 0.640
#> SRR2001129 5 0.3730 0.535 0.288 0.000 0 0.000 0.712
#> SRR2001130 5 0.3796 0.520 0.300 0.000 0 0.000 0.700
#> SRR2001131 5 0.3837 0.495 0.308 0.000 0 0.000 0.692
#> SRR2001124 1 0.0000 0.819 1.000 0.000 0 0.000 0.000
#> SRR2001125 1 0.0000 0.819 1.000 0.000 0 0.000 0.000
#> SRR2001126 1 0.0000 0.819 1.000 0.000 0 0.000 0.000
#> SRR2001127 1 0.0000 0.819 1.000 0.000 0 0.000 0.000
#> SRR2001120 5 0.0794 0.929 0.028 0.000 0 0.000 0.972
#> SRR2001121 5 0.0794 0.929 0.028 0.000 0 0.000 0.972
#> SRR2001122 5 0.0794 0.929 0.028 0.000 0 0.000 0.972
#> SRR2001123 5 0.0794 0.929 0.028 0.000 0 0.000 0.972
#> SRR2001116 1 0.4278 0.421 0.548 0.000 0 0.000 0.452
#> SRR2001117 1 0.3966 0.684 0.664 0.000 0 0.000 0.336
#> SRR2001118 1 0.3586 0.784 0.736 0.000 0 0.000 0.264
#> SRR2001119 1 0.3684 0.767 0.720 0.000 0 0.000 0.280
#> SRR2001112 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001113 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001114 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001115 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR2001108 4 0.2248 0.934 0.000 0.088 0 0.900 0.012
#> SRR2001109 4 0.2305 0.934 0.000 0.092 0 0.896 0.012
#> SRR2001110 4 0.2305 0.934 0.000 0.092 0 0.896 0.012
#> SRR2001111 4 0.2361 0.932 0.000 0.096 0 0.892 0.012
#> SRR2001104 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001105 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001106 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001107 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001100 4 0.2574 0.924 0.000 0.112 0 0.876 0.012
#> SRR2001101 4 0.3011 0.903 0.000 0.140 0 0.844 0.016
#> SRR2001102 4 0.3171 0.874 0.000 0.176 0 0.816 0.008
#> SRR2001103 4 0.2583 0.913 0.000 0.132 0 0.864 0.004
#> SRR2001096 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001097 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001098 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001099 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001092 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001093 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001094 2 0.0162 0.956 0.000 0.996 0 0.004 0.000
#> SRR2001095 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001088 4 0.2110 0.934 0.000 0.072 0 0.912 0.016
#> SRR2001089 4 0.1952 0.934 0.000 0.084 0 0.912 0.004
#> SRR2001090 4 0.2300 0.935 0.000 0.072 0 0.904 0.024
#> SRR2001091 4 0.2130 0.935 0.000 0.080 0 0.908 0.012
#> SRR2001084 4 0.2361 0.933 0.000 0.096 0 0.892 0.012
#> SRR2001085 4 0.2305 0.934 0.000 0.092 0 0.896 0.012
#> SRR2001086 4 0.2361 0.933 0.000 0.096 0 0.892 0.012
#> SRR2001087 4 0.2361 0.933 0.000 0.096 0 0.892 0.012
#> SRR2001080 2 0.0162 0.957 0.000 0.996 0 0.000 0.004
#> SRR2001081 2 0.0404 0.952 0.000 0.988 0 0.000 0.012
#> SRR2001082 2 0.0162 0.957 0.000 0.996 0 0.000 0.004
#> SRR2001083 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001076 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001077 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001078 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001079 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001072 4 0.1965 0.933 0.000 0.096 0 0.904 0.000
#> SRR2001073 4 0.1965 0.933 0.000 0.096 0 0.904 0.000
#> SRR2001074 4 0.1908 0.934 0.000 0.092 0 0.908 0.000
#> SRR2001075 4 0.1908 0.934 0.000 0.092 0 0.908 0.000
#> SRR2001068 4 0.2773 0.887 0.000 0.164 0 0.836 0.000
#> SRR2001069 4 0.2813 0.884 0.000 0.168 0 0.832 0.000
#> SRR2001070 4 0.2813 0.884 0.000 0.168 0 0.832 0.000
#> SRR2001071 4 0.2732 0.891 0.000 0.160 0 0.840 0.000
#> SRR2001064 2 0.0162 0.957 0.000 0.996 0 0.004 0.000
#> SRR2001065 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001066 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001067 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001060 4 0.2110 0.934 0.000 0.072 0 0.912 0.016
#> SRR2001061 4 0.2110 0.934 0.000 0.072 0 0.912 0.016
#> SRR2001062 4 0.2110 0.934 0.000 0.072 0 0.912 0.016
#> SRR2001063 4 0.2110 0.934 0.000 0.072 0 0.912 0.016
#> SRR2001056 4 0.0807 0.925 0.000 0.012 0 0.976 0.012
#> SRR2001057 4 0.0693 0.923 0.000 0.008 0 0.980 0.012
#> SRR2001058 4 0.0807 0.925 0.000 0.012 0 0.976 0.012
#> SRR2001059 4 0.1281 0.930 0.000 0.032 0 0.956 0.012
#> SRR2001052 4 0.3274 0.826 0.000 0.220 0 0.780 0.000
#> SRR2001053 4 0.4171 0.499 0.000 0.396 0 0.604 0.000
#> SRR2001054 4 0.3039 0.859 0.000 0.192 0 0.808 0.000
#> SRR2001055 4 0.3366 0.810 0.000 0.232 0 0.768 0.000
#> SRR2001048 2 0.4366 0.471 0.000 0.664 0 0.320 0.016
#> SRR2001049 2 0.1386 0.926 0.000 0.952 0 0.032 0.016
#> SRR2001050 2 0.4366 0.470 0.000 0.664 0 0.320 0.016
#> SRR2001051 2 0.4225 0.350 0.000 0.632 0 0.364 0.004
#> SRR2001044 4 0.0000 0.920 0.000 0.000 0 1.000 0.000
#> SRR2001045 4 0.0000 0.920 0.000 0.000 0 1.000 0.000
#> SRR2001046 4 0.0000 0.920 0.000 0.000 0 1.000 0.000
#> SRR2001047 4 0.0000 0.920 0.000 0.000 0 1.000 0.000
#> SRR2001040 4 0.0000 0.920 0.000 0.000 0 1.000 0.000
#> SRR2001041 4 0.0000 0.920 0.000 0.000 0 1.000 0.000
#> SRR2001042 4 0.0000 0.920 0.000 0.000 0 1.000 0.000
#> SRR2001043 4 0.0000 0.920 0.000 0.000 0 1.000 0.000
#> SRR2001036 4 0.0000 0.920 0.000 0.000 0 1.000 0.000
#> SRR2001037 4 0.0162 0.922 0.000 0.004 0 0.996 0.000
#> SRR2001038 4 0.0000 0.920 0.000 0.000 0 1.000 0.000
#> SRR2001039 4 0.0000 0.920 0.000 0.000 0 1.000 0.000
#> SRR2001028 4 0.0693 0.923 0.000 0.008 0 0.980 0.012
#> SRR2001029 4 0.0912 0.926 0.000 0.016 0 0.972 0.012
#> SRR2001030 4 0.0566 0.925 0.000 0.012 0 0.984 0.004
#> SRR2001031 4 0.0693 0.923 0.000 0.008 0 0.980 0.012
#> SRR2001024 4 0.0162 0.922 0.000 0.004 0 0.996 0.000
#> SRR2001025 4 0.0162 0.922 0.000 0.004 0 0.996 0.000
#> SRR2001026 4 0.0290 0.924 0.000 0.008 0 0.992 0.000
#> SRR2001027 4 0.0404 0.925 0.000 0.012 0 0.988 0.000
#> SRR2001020 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001021 2 0.0000 0.959 0.000 1.000 0 0.000 0.000
#> SRR2001022 2 0.0290 0.953 0.000 0.992 0 0.008 0.000
#> SRR2001023 2 0.0162 0.957 0.000 0.996 0 0.004 0.000
#> SRR2001016 4 0.2361 0.933 0.000 0.096 0 0.892 0.012
#> SRR2001017 4 0.2361 0.933 0.000 0.096 0 0.892 0.012
#> SRR2001018 4 0.2361 0.933 0.000 0.096 0 0.892 0.012
#> SRR2001019 4 0.2361 0.933 0.000 0.096 0 0.892 0.012
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 5 0.3737 0.4039 0.000 0.392 0 0.000 0.608 0.000
#> SRR2001033 5 0.3847 0.2745 0.000 0.456 0 0.000 0.544 0.000
#> SRR2001034 5 0.3706 0.4202 0.000 0.380 0 0.000 0.620 0.000
#> SRR2001035 5 0.3765 0.3996 0.000 0.404 0 0.000 0.596 0.000
#> SRR2001204 6 0.0363 0.9040 0.000 0.000 0 0.000 0.012 0.988
#> SRR2001205 6 0.0363 0.9040 0.000 0.000 0 0.000 0.012 0.988
#> SRR2001206 6 0.0363 0.9040 0.000 0.000 0 0.000 0.012 0.988
#> SRR2001207 6 0.0363 0.9040 0.000 0.000 0 0.000 0.012 0.988
#> SRR2001200 1 0.0458 0.8026 0.984 0.000 0 0.000 0.000 0.016
#> SRR2001201 1 0.0458 0.8026 0.984 0.000 0 0.000 0.000 0.016
#> SRR2001202 1 0.0458 0.8026 0.984 0.000 0 0.000 0.000 0.016
#> SRR2001203 1 0.0458 0.8026 0.984 0.000 0 0.000 0.000 0.016
#> SRR2001196 1 0.0000 0.7984 1.000 0.000 0 0.000 0.000 0.000
#> SRR2001197 1 0.0000 0.7984 1.000 0.000 0 0.000 0.000 0.000
#> SRR2001198 1 0.0000 0.7984 1.000 0.000 0 0.000 0.000 0.000
#> SRR2001199 1 0.0000 0.7984 1.000 0.000 0 0.000 0.000 0.000
#> SRR2001192 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001193 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001194 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001195 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001188 1 0.3368 0.7704 0.756 0.000 0 0.000 0.012 0.232
#> SRR2001189 1 0.3541 0.7470 0.728 0.000 0 0.000 0.012 0.260
#> SRR2001190 1 0.3078 0.7923 0.796 0.000 0 0.000 0.012 0.192
#> SRR2001191 1 0.2948 0.7981 0.804 0.000 0 0.000 0.008 0.188
#> SRR2001184 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001185 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001186 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001187 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001180 1 0.3175 0.7928 0.744 0.000 0 0.000 0.000 0.256
#> SRR2001181 1 0.3101 0.7989 0.756 0.000 0 0.000 0.000 0.244
#> SRR2001182 1 0.3101 0.7989 0.756 0.000 0 0.000 0.000 0.244
#> SRR2001183 1 0.3101 0.7989 0.756 0.000 0 0.000 0.000 0.244
#> SRR2001176 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001177 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001178 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001179 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001172 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001173 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001174 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001175 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001168 6 0.0713 0.9013 0.000 0.000 0 0.000 0.028 0.972
#> SRR2001169 6 0.0713 0.9013 0.000 0.000 0 0.000 0.028 0.972
#> SRR2001170 6 0.0713 0.9013 0.000 0.000 0 0.000 0.028 0.972
#> SRR2001171 6 0.0713 0.9013 0.000 0.000 0 0.000 0.028 0.972
#> SRR2001164 1 0.3126 0.7970 0.752 0.000 0 0.000 0.000 0.248
#> SRR2001165 1 0.3175 0.7922 0.744 0.000 0 0.000 0.000 0.256
#> SRR2001166 1 0.3175 0.7922 0.744 0.000 0 0.000 0.000 0.256
#> SRR2001167 1 0.3464 0.7382 0.688 0.000 0 0.000 0.000 0.312
#> SRR2001160 1 0.3578 0.7029 0.660 0.000 0 0.000 0.000 0.340
#> SRR2001161 1 0.3189 0.8008 0.760 0.000 0 0.000 0.004 0.236
#> SRR2001162 1 0.3508 0.7615 0.704 0.000 0 0.000 0.004 0.292
#> SRR2001163 6 0.3868 -0.3526 0.496 0.000 0 0.000 0.000 0.504
#> SRR2001156 1 0.0000 0.7984 1.000 0.000 0 0.000 0.000 0.000
#> SRR2001157 1 0.0000 0.7984 1.000 0.000 0 0.000 0.000 0.000
#> SRR2001158 1 0.0000 0.7984 1.000 0.000 0 0.000 0.000 0.000
#> SRR2001159 1 0.0000 0.7984 1.000 0.000 0 0.000 0.000 0.000
#> SRR2001152 1 0.3101 0.7989 0.756 0.000 0 0.000 0.000 0.244
#> SRR2001153 1 0.3101 0.7989 0.756 0.000 0 0.000 0.000 0.244
#> SRR2001154 1 0.3446 0.7435 0.692 0.000 0 0.000 0.000 0.308
#> SRR2001155 1 0.3101 0.7989 0.756 0.000 0 0.000 0.000 0.244
#> SRR2001148 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001149 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001150 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001151 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001144 6 0.0000 0.9049 0.000 0.000 0 0.000 0.000 1.000
#> SRR2001145 6 0.0000 0.9049 0.000 0.000 0 0.000 0.000 1.000
#> SRR2001146 6 0.0000 0.9049 0.000 0.000 0 0.000 0.000 1.000
#> SRR2001147 6 0.0000 0.9049 0.000 0.000 0 0.000 0.000 1.000
#> SRR2001140 6 0.0363 0.9040 0.000 0.000 0 0.000 0.012 0.988
#> SRR2001142 6 0.0458 0.9033 0.000 0.000 0 0.000 0.016 0.984
#> SRR2001143 6 0.0458 0.9033 0.000 0.000 0 0.000 0.016 0.984
#> SRR2001136 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001137 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001138 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001139 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001132 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001133 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001134 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001135 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001128 6 0.3729 0.4643 0.296 0.000 0 0.000 0.012 0.692
#> SRR2001129 6 0.3141 0.6627 0.200 0.000 0 0.000 0.012 0.788
#> SRR2001130 6 0.3287 0.6391 0.220 0.000 0 0.000 0.012 0.768
#> SRR2001131 6 0.3342 0.6166 0.228 0.000 0 0.000 0.012 0.760
#> SRR2001124 1 0.0000 0.7984 1.000 0.000 0 0.000 0.000 0.000
#> SRR2001125 1 0.0000 0.7984 1.000 0.000 0 0.000 0.000 0.000
#> SRR2001126 1 0.0000 0.7984 1.000 0.000 0 0.000 0.000 0.000
#> SRR2001127 1 0.0000 0.7984 1.000 0.000 0 0.000 0.000 0.000
#> SRR2001120 6 0.0632 0.9021 0.000 0.000 0 0.000 0.024 0.976
#> SRR2001121 6 0.0632 0.9021 0.000 0.000 0 0.000 0.024 0.976
#> SRR2001122 6 0.0632 0.9021 0.000 0.000 0 0.000 0.024 0.976
#> SRR2001123 6 0.0632 0.9021 0.000 0.000 0 0.000 0.024 0.976
#> SRR2001116 1 0.3867 0.3514 0.512 0.000 0 0.000 0.000 0.488
#> SRR2001117 1 0.3706 0.6274 0.620 0.000 0 0.000 0.000 0.380
#> SRR2001118 1 0.3330 0.7699 0.716 0.000 0 0.000 0.000 0.284
#> SRR2001119 1 0.3634 0.6720 0.644 0.000 0 0.000 0.000 0.356
#> SRR2001112 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001113 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001114 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001115 3 0.0000 1.0000 0.000 0.000 1 0.000 0.000 0.000
#> SRR2001108 4 0.4425 0.6675 0.000 0.176 0 0.712 0.112 0.000
#> SRR2001109 4 0.4587 0.6462 0.000 0.204 0 0.688 0.108 0.000
#> SRR2001110 4 0.4344 0.6618 0.000 0.188 0 0.716 0.096 0.000
#> SRR2001111 4 0.4206 0.6735 0.000 0.176 0 0.732 0.092 0.000
#> SRR2001104 2 0.2003 0.5659 0.000 0.884 0 0.000 0.116 0.000
#> SRR2001105 2 0.1814 0.5671 0.000 0.900 0 0.000 0.100 0.000
#> SRR2001106 2 0.1863 0.5674 0.000 0.896 0 0.000 0.104 0.000
#> SRR2001107 2 0.1910 0.5672 0.000 0.892 0 0.000 0.108 0.000
#> SRR2001100 4 0.5715 0.4243 0.000 0.224 0 0.520 0.256 0.000
#> SRR2001101 4 0.5736 0.3473 0.000 0.180 0 0.480 0.340 0.000
#> SRR2001102 2 0.6058 0.0614 0.000 0.384 0 0.356 0.260 0.000
#> SRR2001103 4 0.5882 0.3173 0.000 0.280 0 0.476 0.244 0.000
#> SRR2001096 2 0.1501 0.5318 0.000 0.924 0 0.000 0.076 0.000
#> SRR2001097 2 0.1501 0.5318 0.000 0.924 0 0.000 0.076 0.000
#> SRR2001098 2 0.1501 0.5318 0.000 0.924 0 0.000 0.076 0.000
#> SRR2001099 2 0.1501 0.5318 0.000 0.924 0 0.000 0.076 0.000
#> SRR2001092 2 0.0713 0.5639 0.000 0.972 0 0.000 0.028 0.000
#> SRR2001093 2 0.1663 0.5684 0.000 0.912 0 0.000 0.088 0.000
#> SRR2001094 2 0.0547 0.5551 0.000 0.980 0 0.000 0.020 0.000
#> SRR2001095 2 0.0363 0.5579 0.000 0.988 0 0.000 0.012 0.000
#> SRR2001088 4 0.4835 0.3394 0.000 0.072 0 0.592 0.336 0.000
#> SRR2001089 4 0.4371 0.6243 0.000 0.180 0 0.716 0.104 0.000
#> SRR2001090 4 0.4783 0.5017 0.000 0.088 0 0.636 0.276 0.000
#> SRR2001091 4 0.4893 0.5761 0.000 0.168 0 0.660 0.172 0.000
#> SRR2001084 4 0.4513 0.6717 0.000 0.172 0 0.704 0.124 0.000
#> SRR2001085 4 0.4482 0.6757 0.000 0.168 0 0.708 0.124 0.000
#> SRR2001086 4 0.4863 0.6361 0.000 0.200 0 0.660 0.140 0.000
#> SRR2001087 4 0.4890 0.6255 0.000 0.204 0 0.656 0.140 0.000
#> SRR2001080 2 0.3595 0.4294 0.000 0.704 0 0.008 0.288 0.000
#> SRR2001081 2 0.3975 0.2315 0.000 0.600 0 0.008 0.392 0.000
#> SRR2001082 2 0.3349 0.4947 0.000 0.748 0 0.008 0.244 0.000
#> SRR2001083 2 0.3043 0.5258 0.000 0.792 0 0.008 0.200 0.000
#> SRR2001076 2 0.1814 0.5671 0.000 0.900 0 0.000 0.100 0.000
#> SRR2001077 2 0.1863 0.5671 0.000 0.896 0 0.000 0.104 0.000
#> SRR2001078 2 0.1814 0.5671 0.000 0.900 0 0.000 0.100 0.000
#> SRR2001079 2 0.2135 0.5623 0.000 0.872 0 0.000 0.128 0.000
#> SRR2001072 2 0.5784 0.0792 0.000 0.460 0 0.356 0.184 0.000
#> SRR2001073 2 0.5722 0.0288 0.000 0.432 0 0.404 0.164 0.000
#> SRR2001074 2 0.5769 0.0773 0.000 0.460 0 0.360 0.180 0.000
#> SRR2001075 2 0.5769 0.0773 0.000 0.460 0 0.360 0.180 0.000
#> SRR2001068 2 0.5191 -0.1695 0.000 0.456 0 0.456 0.088 0.000
#> SRR2001069 2 0.5190 -0.1589 0.000 0.460 0 0.452 0.088 0.000
#> SRR2001070 2 0.5227 -0.1644 0.000 0.456 0 0.452 0.092 0.000
#> SRR2001071 4 0.5227 0.1399 0.000 0.452 0 0.456 0.092 0.000
#> SRR2001064 2 0.1204 0.5415 0.000 0.944 0 0.000 0.056 0.000
#> SRR2001065 2 0.1387 0.5353 0.000 0.932 0 0.000 0.068 0.000
#> SRR2001066 2 0.1267 0.5393 0.000 0.940 0 0.000 0.060 0.000
#> SRR2001067 2 0.1327 0.5408 0.000 0.936 0 0.000 0.064 0.000
#> SRR2001060 5 0.4809 0.4617 0.000 0.072 0 0.328 0.600 0.000
#> SRR2001061 5 0.4964 0.3327 0.000 0.072 0 0.388 0.540 0.000
#> SRR2001062 5 0.4871 0.4296 0.000 0.072 0 0.348 0.580 0.000
#> SRR2001063 5 0.4809 0.4617 0.000 0.072 0 0.328 0.600 0.000
#> SRR2001056 4 0.2118 0.7239 0.000 0.008 0 0.888 0.104 0.000
#> SRR2001057 4 0.1858 0.7228 0.000 0.004 0 0.904 0.092 0.000
#> SRR2001058 4 0.2740 0.7081 0.000 0.028 0 0.852 0.120 0.000
#> SRR2001059 4 0.3168 0.7180 0.000 0.056 0 0.828 0.116 0.000
#> SRR2001052 2 0.5171 -0.0423 0.000 0.496 0 0.416 0.088 0.000
#> SRR2001053 2 0.5077 0.1430 0.000 0.552 0 0.360 0.088 0.000
#> SRR2001054 2 0.5178 -0.0705 0.000 0.488 0 0.424 0.088 0.000
#> SRR2001055 2 0.5201 -0.0149 0.000 0.500 0 0.408 0.092 0.000
#> SRR2001048 5 0.5878 0.1266 0.000 0.356 0 0.204 0.440 0.000
#> SRR2001049 2 0.4526 -0.0272 0.000 0.512 0 0.032 0.456 0.000
#> SRR2001050 2 0.5811 0.0527 0.000 0.468 0 0.196 0.336 0.000
#> SRR2001051 2 0.6014 0.0801 0.000 0.432 0 0.288 0.280 0.000
#> SRR2001044 4 0.0937 0.7357 0.000 0.000 0 0.960 0.040 0.000
#> SRR2001045 4 0.0937 0.7368 0.000 0.000 0 0.960 0.040 0.000
#> SRR2001046 4 0.0937 0.7357 0.000 0.000 0 0.960 0.040 0.000
#> SRR2001047 4 0.0632 0.7346 0.000 0.000 0 0.976 0.024 0.000
#> SRR2001040 4 0.0790 0.7298 0.000 0.000 0 0.968 0.032 0.000
#> SRR2001041 4 0.0713 0.7304 0.000 0.000 0 0.972 0.028 0.000
#> SRR2001042 4 0.0790 0.7298 0.000 0.000 0 0.968 0.032 0.000
#> SRR2001043 4 0.0790 0.7298 0.000 0.000 0 0.968 0.032 0.000
#> SRR2001036 4 0.0632 0.7299 0.000 0.000 0 0.976 0.024 0.000
#> SRR2001037 4 0.0632 0.7299 0.000 0.000 0 0.976 0.024 0.000
#> SRR2001038 4 0.1010 0.7324 0.000 0.004 0 0.960 0.036 0.000
#> SRR2001039 4 0.0790 0.7286 0.000 0.000 0 0.968 0.032 0.000
#> SRR2001028 4 0.2309 0.7208 0.000 0.028 0 0.888 0.084 0.000
#> SRR2001029 4 0.2230 0.7232 0.000 0.024 0 0.892 0.084 0.000
#> SRR2001030 4 0.2308 0.7245 0.000 0.040 0 0.892 0.068 0.000
#> SRR2001031 4 0.2658 0.7135 0.000 0.036 0 0.864 0.100 0.000
#> SRR2001024 4 0.0865 0.7275 0.000 0.000 0 0.964 0.036 0.000
#> SRR2001025 4 0.1007 0.7262 0.000 0.000 0 0.956 0.044 0.000
#> SRR2001026 4 0.1007 0.7227 0.000 0.000 0 0.956 0.044 0.000
#> SRR2001027 4 0.1411 0.7243 0.000 0.004 0 0.936 0.060 0.000
#> SRR2001020 2 0.2772 0.5389 0.000 0.816 0 0.004 0.180 0.000
#> SRR2001021 2 0.2805 0.5361 0.000 0.812 0 0.004 0.184 0.000
#> SRR2001022 2 0.2805 0.5361 0.000 0.812 0 0.004 0.184 0.000
#> SRR2001023 2 0.2805 0.5361 0.000 0.812 0 0.004 0.184 0.000
#> SRR2001016 4 0.5119 0.5879 0.000 0.220 0 0.624 0.156 0.000
#> SRR2001017 4 0.5214 0.5772 0.000 0.216 0 0.612 0.172 0.000
#> SRR2001018 4 0.5319 0.5612 0.000 0.220 0 0.596 0.184 0.000
#> SRR2001019 4 0.5180 0.5876 0.000 0.220 0 0.616 0.164 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", "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 14431 rows and 191 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.5031 0.497 0.497
#> 3 3 0.889 0.938 0.934 0.0806 1.000 1.000
#> 4 4 0.747 0.822 0.811 0.1383 0.879 0.756
#> 5 5 0.702 0.891 0.811 0.0951 0.835 0.587
#> 6 6 0.616 0.858 0.819 0.0537 1.000 1.000
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 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
#> SRR2001032 2 0 1 0 1
#> SRR2001033 2 0 1 0 1
#> SRR2001034 2 0 1 0 1
#> SRR2001035 2 0 1 0 1
#> SRR2001204 1 0 1 1 0
#> SRR2001205 1 0 1 1 0
#> SRR2001206 1 0 1 1 0
#> SRR2001207 1 0 1 1 0
#> SRR2001200 1 0 1 1 0
#> SRR2001201 1 0 1 1 0
#> SRR2001202 1 0 1 1 0
#> SRR2001203 1 0 1 1 0
#> SRR2001196 1 0 1 1 0
#> SRR2001197 1 0 1 1 0
#> SRR2001198 1 0 1 1 0
#> SRR2001199 1 0 1 1 0
#> SRR2001192 1 0 1 1 0
#> SRR2001193 1 0 1 1 0
#> SRR2001194 1 0 1 1 0
#> SRR2001195 1 0 1 1 0
#> SRR2001188 1 0 1 1 0
#> SRR2001189 1 0 1 1 0
#> SRR2001190 1 0 1 1 0
#> SRR2001191 1 0 1 1 0
#> SRR2001184 1 0 1 1 0
#> SRR2001185 1 0 1 1 0
#> SRR2001186 1 0 1 1 0
#> SRR2001187 1 0 1 1 0
#> SRR2001180 1 0 1 1 0
#> SRR2001181 1 0 1 1 0
#> SRR2001182 1 0 1 1 0
#> SRR2001183 1 0 1 1 0
#> SRR2001176 1 0 1 1 0
#> SRR2001177 1 0 1 1 0
#> SRR2001178 1 0 1 1 0
#> SRR2001179 1 0 1 1 0
#> SRR2001172 1 0 1 1 0
#> SRR2001173 1 0 1 1 0
#> SRR2001174 1 0 1 1 0
#> SRR2001175 1 0 1 1 0
#> SRR2001168 1 0 1 1 0
#> SRR2001169 1 0 1 1 0
#> SRR2001170 1 0 1 1 0
#> SRR2001171 1 0 1 1 0
#> SRR2001164 1 0 1 1 0
#> SRR2001165 1 0 1 1 0
#> SRR2001166 1 0 1 1 0
#> SRR2001167 1 0 1 1 0
#> SRR2001160 1 0 1 1 0
#> SRR2001161 1 0 1 1 0
#> SRR2001162 1 0 1 1 0
#> SRR2001163 1 0 1 1 0
#> SRR2001156 1 0 1 1 0
#> SRR2001157 1 0 1 1 0
#> SRR2001158 1 0 1 1 0
#> SRR2001159 1 0 1 1 0
#> SRR2001152 1 0 1 1 0
#> SRR2001153 1 0 1 1 0
#> SRR2001154 1 0 1 1 0
#> SRR2001155 1 0 1 1 0
#> SRR2001148 1 0 1 1 0
#> SRR2001149 1 0 1 1 0
#> SRR2001150 1 0 1 1 0
#> SRR2001151 1 0 1 1 0
#> SRR2001144 1 0 1 1 0
#> SRR2001145 1 0 1 1 0
#> SRR2001146 1 0 1 1 0
#> SRR2001147 1 0 1 1 0
#> SRR2001140 1 0 1 1 0
#> SRR2001142 1 0 1 1 0
#> SRR2001143 1 0 1 1 0
#> SRR2001136 1 0 1 1 0
#> SRR2001137 1 0 1 1 0
#> SRR2001138 1 0 1 1 0
#> SRR2001139 1 0 1 1 0
#> SRR2001132 1 0 1 1 0
#> SRR2001133 1 0 1 1 0
#> SRR2001134 1 0 1 1 0
#> SRR2001135 1 0 1 1 0
#> SRR2001128 1 0 1 1 0
#> SRR2001129 1 0 1 1 0
#> SRR2001130 1 0 1 1 0
#> SRR2001131 1 0 1 1 0
#> SRR2001124 1 0 1 1 0
#> SRR2001125 1 0 1 1 0
#> SRR2001126 1 0 1 1 0
#> SRR2001127 1 0 1 1 0
#> SRR2001120 1 0 1 1 0
#> SRR2001121 1 0 1 1 0
#> SRR2001122 1 0 1 1 0
#> SRR2001123 1 0 1 1 0
#> SRR2001116 1 0 1 1 0
#> SRR2001117 1 0 1 1 0
#> SRR2001118 1 0 1 1 0
#> SRR2001119 1 0 1 1 0
#> SRR2001112 1 0 1 1 0
#> SRR2001113 1 0 1 1 0
#> SRR2001114 1 0 1 1 0
#> SRR2001115 1 0 1 1 0
#> SRR2001108 2 0 1 0 1
#> SRR2001109 2 0 1 0 1
#> SRR2001110 2 0 1 0 1
#> SRR2001111 2 0 1 0 1
#> SRR2001104 2 0 1 0 1
#> SRR2001105 2 0 1 0 1
#> SRR2001106 2 0 1 0 1
#> SRR2001107 2 0 1 0 1
#> SRR2001100 2 0 1 0 1
#> SRR2001101 2 0 1 0 1
#> SRR2001102 2 0 1 0 1
#> SRR2001103 2 0 1 0 1
#> SRR2001096 2 0 1 0 1
#> SRR2001097 2 0 1 0 1
#> SRR2001098 2 0 1 0 1
#> SRR2001099 2 0 1 0 1
#> SRR2001092 2 0 1 0 1
#> SRR2001093 2 0 1 0 1
#> SRR2001094 2 0 1 0 1
#> SRR2001095 2 0 1 0 1
#> SRR2001088 2 0 1 0 1
#> SRR2001089 2 0 1 0 1
#> SRR2001090 2 0 1 0 1
#> SRR2001091 2 0 1 0 1
#> SRR2001084 2 0 1 0 1
#> SRR2001085 2 0 1 0 1
#> SRR2001086 2 0 1 0 1
#> SRR2001087 2 0 1 0 1
#> SRR2001080 2 0 1 0 1
#> SRR2001081 2 0 1 0 1
#> SRR2001082 2 0 1 0 1
#> SRR2001083 2 0 1 0 1
#> SRR2001076 2 0 1 0 1
#> SRR2001077 2 0 1 0 1
#> SRR2001078 2 0 1 0 1
#> SRR2001079 2 0 1 0 1
#> SRR2001072 2 0 1 0 1
#> SRR2001073 2 0 1 0 1
#> SRR2001074 2 0 1 0 1
#> SRR2001075 2 0 1 0 1
#> SRR2001068 2 0 1 0 1
#> SRR2001069 2 0 1 0 1
#> SRR2001070 2 0 1 0 1
#> SRR2001071 2 0 1 0 1
#> SRR2001064 2 0 1 0 1
#> SRR2001065 2 0 1 0 1
#> SRR2001066 2 0 1 0 1
#> SRR2001067 2 0 1 0 1
#> SRR2001060 2 0 1 0 1
#> SRR2001061 2 0 1 0 1
#> SRR2001062 2 0 1 0 1
#> SRR2001063 2 0 1 0 1
#> SRR2001056 2 0 1 0 1
#> SRR2001057 2 0 1 0 1
#> SRR2001058 2 0 1 0 1
#> SRR2001059 2 0 1 0 1
#> SRR2001052 2 0 1 0 1
#> SRR2001053 2 0 1 0 1
#> SRR2001054 2 0 1 0 1
#> SRR2001055 2 0 1 0 1
#> SRR2001048 2 0 1 0 1
#> SRR2001049 2 0 1 0 1
#> SRR2001050 2 0 1 0 1
#> SRR2001051 2 0 1 0 1
#> SRR2001044 2 0 1 0 1
#> SRR2001045 2 0 1 0 1
#> SRR2001046 2 0 1 0 1
#> SRR2001047 2 0 1 0 1
#> SRR2001040 2 0 1 0 1
#> SRR2001041 2 0 1 0 1
#> SRR2001042 2 0 1 0 1
#> SRR2001043 2 0 1 0 1
#> SRR2001036 2 0 1 0 1
#> SRR2001037 2 0 1 0 1
#> SRR2001038 2 0 1 0 1
#> SRR2001039 2 0 1 0 1
#> SRR2001028 2 0 1 0 1
#> SRR2001029 2 0 1 0 1
#> SRR2001030 2 0 1 0 1
#> SRR2001031 2 0 1 0 1
#> SRR2001024 2 0 1 0 1
#> SRR2001025 2 0 1 0 1
#> SRR2001026 2 0 1 0 1
#> SRR2001027 2 0 1 0 1
#> SRR2001020 2 0 1 0 1
#> SRR2001021 2 0 1 0 1
#> SRR2001022 2 0 1 0 1
#> SRR2001023 2 0 1 0 1
#> SRR2001016 2 0 1 0 1
#> SRR2001017 2 0 1 0 1
#> SRR2001018 2 0 1 0 1
#> SRR2001019 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR2001032 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001033 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001034 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001035 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001204 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001205 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001206 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001207 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001200 1 0.1753 0.914 0.952 0.00 NA
#> SRR2001201 1 0.1753 0.914 0.952 0.00 NA
#> SRR2001202 1 0.1411 0.917 0.964 0.00 NA
#> SRR2001203 1 0.1529 0.916 0.960 0.00 NA
#> SRR2001196 1 0.0747 0.921 0.984 0.00 NA
#> SRR2001197 1 0.0592 0.922 0.988 0.00 NA
#> SRR2001198 1 0.0592 0.922 0.988 0.00 NA
#> SRR2001199 1 0.0747 0.921 0.984 0.00 NA
#> SRR2001192 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001193 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001194 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001195 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001188 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001189 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001190 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001191 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001184 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001185 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001186 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001187 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001180 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001181 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001182 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001183 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001176 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001177 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001178 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001179 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001172 1 0.5497 0.849 0.708 0.00 NA
#> SRR2001173 1 0.5497 0.849 0.708 0.00 NA
#> SRR2001174 1 0.5497 0.849 0.708 0.00 NA
#> SRR2001175 1 0.5497 0.849 0.708 0.00 NA
#> SRR2001168 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001169 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001170 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001171 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001164 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001165 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001166 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001167 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001160 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001161 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001162 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001163 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001156 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001157 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001158 1 0.0237 0.923 0.996 0.00 NA
#> SRR2001159 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001152 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001153 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001154 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001155 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001148 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001149 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001150 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001151 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001144 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001145 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001146 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001147 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001140 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001142 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001143 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001136 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001137 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001138 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001139 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001132 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001133 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001134 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001135 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001128 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001129 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001130 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001131 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001124 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001125 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001126 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001127 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001120 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001121 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001122 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001123 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001116 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001117 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001118 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001119 1 0.0000 0.924 1.000 0.00 NA
#> SRR2001112 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001113 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001114 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001115 1 0.5529 0.848 0.704 0.00 NA
#> SRR2001108 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001109 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001110 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001111 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001104 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001105 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001106 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001107 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001100 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001101 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001102 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001103 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001096 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001097 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001098 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001099 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001092 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001093 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001094 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001095 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001088 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001089 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001090 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001091 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001084 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001085 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001086 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001087 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001080 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001081 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001082 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001083 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001076 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001077 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001078 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001079 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001072 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001073 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001074 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001075 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001068 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001069 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001070 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001071 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001064 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001065 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001066 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001067 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001060 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001061 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001062 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001063 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001056 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001057 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001058 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001059 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001052 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001053 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001054 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001055 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001048 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001049 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001050 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001051 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001044 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001045 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001046 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001047 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001040 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001041 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001042 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001043 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001036 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001037 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001038 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001039 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001028 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001029 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001030 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001031 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001024 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001025 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001026 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001027 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001020 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001021 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001022 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001023 2 0.0000 0.977 0.000 1.00 NA
#> SRR2001016 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001017 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001018 2 0.2066 0.977 0.000 0.94 NA
#> SRR2001019 2 0.2066 0.977 0.000 0.94 NA
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR2001032 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001033 2 0.4454 0.854 0.000 0.692 0.000 NA
#> SRR2001034 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001035 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001204 1 0.5055 0.945 0.624 0.000 0.368 NA
#> SRR2001205 1 0.5040 0.947 0.628 0.000 0.364 NA
#> SRR2001206 1 0.5040 0.947 0.628 0.000 0.364 NA
#> SRR2001207 1 0.5040 0.947 0.628 0.000 0.364 NA
#> SRR2001200 3 0.5189 -0.154 0.372 0.000 0.616 NA
#> SRR2001201 3 0.5204 -0.173 0.376 0.000 0.612 NA
#> SRR2001202 3 0.5204 -0.173 0.376 0.000 0.612 NA
#> SRR2001203 3 0.5217 -0.193 0.380 0.000 0.608 NA
#> SRR2001196 3 0.5337 -0.397 0.424 0.000 0.564 NA
#> SRR2001197 3 0.5329 -0.379 0.420 0.000 0.568 NA
#> SRR2001198 3 0.5345 -0.415 0.428 0.000 0.560 NA
#> SRR2001199 3 0.5310 -0.345 0.412 0.000 0.576 NA
#> SRR2001192 3 0.0592 0.839 0.016 0.000 0.984 NA
#> SRR2001193 3 0.0592 0.839 0.016 0.000 0.984 NA
#> SRR2001194 3 0.0592 0.839 0.016 0.000 0.984 NA
#> SRR2001195 3 0.0707 0.838 0.020 0.000 0.980 NA
#> SRR2001188 1 0.4837 0.945 0.648 0.000 0.348 NA
#> SRR2001189 1 0.4661 0.946 0.652 0.000 0.348 NA
#> SRR2001190 1 0.4661 0.946 0.652 0.000 0.348 NA
#> SRR2001191 1 0.4837 0.945 0.648 0.000 0.348 NA
#> SRR2001184 3 0.0921 0.836 0.028 0.000 0.972 NA
#> SRR2001185 3 0.0921 0.836 0.028 0.000 0.972 NA
#> SRR2001186 3 0.0921 0.836 0.028 0.000 0.972 NA
#> SRR2001187 3 0.0921 0.836 0.028 0.000 0.972 NA
#> SRR2001180 1 0.4661 0.946 0.652 0.000 0.348 NA
#> SRR2001181 1 0.4661 0.946 0.652 0.000 0.348 NA
#> SRR2001182 1 0.4661 0.946 0.652 0.000 0.348 NA
#> SRR2001183 1 0.4973 0.947 0.644 0.000 0.348 NA
#> SRR2001176 3 0.0592 0.839 0.016 0.000 0.984 NA
#> SRR2001177 3 0.0592 0.839 0.016 0.000 0.984 NA
#> SRR2001178 3 0.0592 0.839 0.016 0.000 0.984 NA
#> SRR2001179 3 0.0592 0.839 0.016 0.000 0.984 NA
#> SRR2001172 3 0.1389 0.821 0.048 0.000 0.952 NA
#> SRR2001173 3 0.1474 0.817 0.052 0.000 0.948 NA
#> SRR2001174 3 0.1716 0.802 0.064 0.000 0.936 NA
#> SRR2001175 3 0.1474 0.817 0.052 0.000 0.948 NA
#> SRR2001168 1 0.5070 0.936 0.620 0.000 0.372 NA
#> SRR2001169 1 0.5070 0.936 0.620 0.000 0.372 NA
#> SRR2001170 1 0.5055 0.940 0.624 0.000 0.368 NA
#> SRR2001171 1 0.5055 0.940 0.624 0.000 0.368 NA
#> SRR2001164 1 0.5217 0.910 0.608 0.000 0.380 NA
#> SRR2001165 1 0.5189 0.920 0.616 0.000 0.372 NA
#> SRR2001166 1 0.5040 0.932 0.628 0.000 0.364 NA
#> SRR2001167 1 0.5040 0.932 0.628 0.000 0.364 NA
#> SRR2001160 1 0.4837 0.945 0.648 0.000 0.348 NA
#> SRR2001161 1 0.4837 0.945 0.648 0.000 0.348 NA
#> SRR2001162 1 0.4837 0.945 0.648 0.000 0.348 NA
#> SRR2001163 1 0.4837 0.945 0.648 0.000 0.348 NA
#> SRR2001156 1 0.5406 0.692 0.508 0.000 0.480 NA
#> SRR2001157 1 0.5402 0.715 0.516 0.000 0.472 NA
#> SRR2001158 1 0.5404 0.704 0.512 0.000 0.476 NA
#> SRR2001159 1 0.5402 0.715 0.516 0.000 0.472 NA
#> SRR2001152 1 0.5024 0.948 0.632 0.000 0.360 NA
#> SRR2001153 1 0.5024 0.948 0.632 0.000 0.360 NA
#> SRR2001154 1 0.5024 0.948 0.632 0.000 0.360 NA
#> SRR2001155 1 0.5040 0.947 0.628 0.000 0.364 NA
#> SRR2001148 3 0.0921 0.836 0.028 0.000 0.972 NA
#> SRR2001149 3 0.0921 0.836 0.028 0.000 0.972 NA
#> SRR2001150 3 0.0921 0.836 0.028 0.000 0.972 NA
#> SRR2001151 3 0.0921 0.836 0.028 0.000 0.972 NA
#> SRR2001144 1 0.5070 0.941 0.620 0.000 0.372 NA
#> SRR2001145 1 0.5055 0.944 0.624 0.000 0.368 NA
#> SRR2001146 1 0.5070 0.941 0.620 0.000 0.372 NA
#> SRR2001147 1 0.5070 0.941 0.620 0.000 0.372 NA
#> SRR2001140 1 0.5040 0.947 0.628 0.000 0.364 NA
#> SRR2001142 1 0.5040 0.947 0.628 0.000 0.364 NA
#> SRR2001143 1 0.5040 0.947 0.628 0.000 0.364 NA
#> SRR2001136 3 0.0672 0.821 0.008 0.000 0.984 NA
#> SRR2001137 3 0.0469 0.829 0.012 0.000 0.988 NA
#> SRR2001138 3 0.0188 0.831 0.004 0.000 0.996 NA
#> SRR2001139 3 0.0188 0.831 0.004 0.000 0.996 NA
#> SRR2001132 3 0.0188 0.828 0.004 0.000 0.996 NA
#> SRR2001133 3 0.0000 0.831 0.000 0.000 1.000 NA
#> SRR2001134 3 0.0000 0.831 0.000 0.000 1.000 NA
#> SRR2001135 3 0.0000 0.831 0.000 0.000 1.000 NA
#> SRR2001128 1 0.4990 0.948 0.640 0.000 0.352 NA
#> SRR2001129 1 0.4990 0.948 0.640 0.000 0.352 NA
#> SRR2001130 1 0.4990 0.948 0.640 0.000 0.352 NA
#> SRR2001131 1 0.4990 0.948 0.640 0.000 0.352 NA
#> SRR2001124 1 0.5279 0.878 0.588 0.000 0.400 NA
#> SRR2001125 1 0.5279 0.878 0.588 0.000 0.400 NA
#> SRR2001126 1 0.5204 0.915 0.612 0.000 0.376 NA
#> SRR2001127 1 0.5085 0.919 0.616 0.000 0.376 NA
#> SRR2001120 1 0.5055 0.940 0.624 0.000 0.368 NA
#> SRR2001121 1 0.5055 0.940 0.624 0.000 0.368 NA
#> SRR2001122 1 0.5055 0.940 0.624 0.000 0.368 NA
#> SRR2001123 1 0.5055 0.940 0.624 0.000 0.368 NA
#> SRR2001116 1 0.5007 0.939 0.636 0.000 0.356 NA
#> SRR2001117 1 0.4990 0.941 0.640 0.000 0.352 NA
#> SRR2001118 1 0.4990 0.941 0.640 0.000 0.352 NA
#> SRR2001119 1 0.4990 0.941 0.640 0.000 0.352 NA
#> SRR2001112 3 0.1733 0.806 0.024 0.000 0.948 NA
#> SRR2001113 3 0.1733 0.806 0.024 0.000 0.948 NA
#> SRR2001114 3 0.1629 0.808 0.024 0.000 0.952 NA
#> SRR2001115 3 0.1733 0.806 0.024 0.000 0.948 NA
#> SRR2001108 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001109 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001110 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001111 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001104 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001105 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001106 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001107 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001100 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001101 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001102 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001103 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001096 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001097 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001098 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001099 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001092 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001093 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001094 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001095 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001088 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001089 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001090 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001091 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001084 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001085 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001086 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001087 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001080 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001081 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001082 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001083 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001076 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001077 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001078 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001079 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001072 2 0.0336 0.854 0.000 0.992 0.000 NA
#> SRR2001073 2 0.0336 0.854 0.000 0.992 0.000 NA
#> SRR2001074 2 0.0336 0.854 0.000 0.992 0.000 NA
#> SRR2001075 2 0.0336 0.854 0.000 0.992 0.000 NA
#> SRR2001068 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001069 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001070 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001071 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001064 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001065 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001066 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001067 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001060 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001061 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001062 2 0.0188 0.854 0.000 0.996 0.000 NA
#> SRR2001063 2 0.0188 0.854 0.000 0.996 0.000 NA
#> SRR2001056 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001057 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001058 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001059 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001052 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001053 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001054 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001055 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001048 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001049 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001050 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001051 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001044 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001045 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001046 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001047 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001040 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001041 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001042 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001043 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001036 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001037 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001038 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001039 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001028 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001029 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001030 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001031 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001024 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001025 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001026 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001027 2 0.0000 0.853 0.000 1.000 0.000 NA
#> SRR2001020 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001021 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001022 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001023 2 0.4500 0.854 0.000 0.684 0.000 NA
#> SRR2001016 2 0.0188 0.854 0.000 0.996 0.000 NA
#> SRR2001017 2 0.0336 0.854 0.000 0.992 0.000 NA
#> SRR2001018 2 0.0336 0.854 0.000 0.992 0.000 NA
#> SRR2001019 2 0.0336 0.854 0.000 0.992 0.000 NA
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR2001032 2 0.1026 0.968 0.000 0.968 0.004 0.024 NA
#> SRR2001033 2 0.1662 0.916 0.000 0.936 0.004 0.056 NA
#> SRR2001034 2 0.1116 0.963 0.000 0.964 0.004 0.028 NA
#> SRR2001035 2 0.1026 0.969 0.000 0.968 0.004 0.024 NA
#> SRR2001204 1 0.1211 0.836 0.960 0.000 0.024 0.000 NA
#> SRR2001205 1 0.1195 0.837 0.960 0.000 0.028 0.000 NA
#> SRR2001206 1 0.1300 0.834 0.956 0.000 0.028 0.000 NA
#> SRR2001207 1 0.1195 0.837 0.960 0.000 0.028 0.000 NA
#> SRR2001200 1 0.5480 0.366 0.616 0.000 0.288 0.000 NA
#> SRR2001201 1 0.5441 0.396 0.624 0.000 0.280 0.000 NA
#> SRR2001202 1 0.5480 0.366 0.616 0.000 0.288 0.000 NA
#> SRR2001203 1 0.5400 0.406 0.632 0.000 0.272 0.000 NA
#> SRR2001196 1 0.5024 0.567 0.692 0.000 0.212 0.000 NA
#> SRR2001197 1 0.5082 0.549 0.684 0.000 0.220 0.000 NA
#> SRR2001198 1 0.5024 0.563 0.692 0.000 0.212 0.000 NA
#> SRR2001199 1 0.5082 0.549 0.684 0.000 0.220 0.000 NA
#> SRR2001192 3 0.3910 0.929 0.272 0.000 0.720 0.000 NA
#> SRR2001193 3 0.3885 0.929 0.268 0.000 0.724 0.000 NA
#> SRR2001194 3 0.3766 0.929 0.268 0.000 0.728 0.000 NA
#> SRR2001195 3 0.3766 0.929 0.268 0.000 0.728 0.000 NA
#> SRR2001188 1 0.0912 0.839 0.972 0.000 0.012 0.000 NA
#> SRR2001189 1 0.0671 0.840 0.980 0.000 0.016 0.000 NA
#> SRR2001190 1 0.0510 0.841 0.984 0.000 0.016 0.000 NA
#> SRR2001191 1 0.0912 0.839 0.972 0.000 0.016 0.000 NA
#> SRR2001184 3 0.4374 0.923 0.272 0.000 0.700 0.000 NA
#> SRR2001185 3 0.4594 0.912 0.284 0.000 0.680 0.000 NA
#> SRR2001186 3 0.4520 0.914 0.284 0.000 0.684 0.000 NA
#> SRR2001187 3 0.4594 0.912 0.284 0.000 0.680 0.000 NA
#> SRR2001180 1 0.0162 0.840 0.996 0.000 0.004 0.000 NA
#> SRR2001181 1 0.0162 0.838 0.996 0.000 0.004 0.000 NA
#> SRR2001182 1 0.0162 0.838 0.996 0.000 0.004 0.000 NA
#> SRR2001183 1 0.0510 0.838 0.984 0.000 0.016 0.000 NA
#> SRR2001176 3 0.3741 0.929 0.264 0.000 0.732 0.000 NA
#> SRR2001177 3 0.3741 0.929 0.264 0.000 0.732 0.000 NA
#> SRR2001178 3 0.3741 0.929 0.264 0.000 0.732 0.000 NA
#> SRR2001179 3 0.3741 0.929 0.264 0.000 0.732 0.000 NA
#> SRR2001172 3 0.4990 0.854 0.324 0.000 0.628 0.000 NA
#> SRR2001173 3 0.5080 0.824 0.348 0.000 0.604 0.000 NA
#> SRR2001174 3 0.5094 0.816 0.352 0.000 0.600 0.000 NA
#> SRR2001175 3 0.5052 0.833 0.340 0.000 0.612 0.000 NA
#> SRR2001168 1 0.2914 0.778 0.872 0.000 0.076 0.000 NA
#> SRR2001169 1 0.2790 0.785 0.880 0.000 0.068 0.000 NA
#> SRR2001170 1 0.2790 0.787 0.880 0.000 0.068 0.000 NA
#> SRR2001171 1 0.2853 0.783 0.876 0.000 0.072 0.000 NA
#> SRR2001164 1 0.3479 0.771 0.836 0.000 0.080 0.000 NA
#> SRR2001165 1 0.3303 0.781 0.848 0.000 0.076 0.000 NA
#> SRR2001166 1 0.3180 0.791 0.856 0.000 0.068 0.000 NA
#> SRR2001167 1 0.3242 0.788 0.852 0.000 0.072 0.000 NA
#> SRR2001160 1 0.1568 0.832 0.944 0.000 0.036 0.000 NA
#> SRR2001161 1 0.1386 0.833 0.952 0.000 0.032 0.000 NA
#> SRR2001162 1 0.1485 0.832 0.948 0.000 0.032 0.000 NA
#> SRR2001163 1 0.1211 0.835 0.960 0.000 0.024 0.000 NA
#> SRR2001156 1 0.4803 0.621 0.720 0.000 0.184 0.000 NA
#> SRR2001157 1 0.4803 0.621 0.720 0.000 0.184 0.000 NA
#> SRR2001158 1 0.4768 0.625 0.724 0.000 0.180 0.000 NA
#> SRR2001159 1 0.4768 0.625 0.724 0.000 0.180 0.000 NA
#> SRR2001152 1 0.1195 0.838 0.960 0.000 0.028 0.000 NA
#> SRR2001153 1 0.1106 0.837 0.964 0.000 0.024 0.000 NA
#> SRR2001154 1 0.1195 0.837 0.960 0.000 0.028 0.000 NA
#> SRR2001155 1 0.1364 0.836 0.952 0.000 0.036 0.000 NA
#> SRR2001148 3 0.4229 0.923 0.276 0.000 0.704 0.000 NA
#> SRR2001149 3 0.4090 0.927 0.268 0.000 0.716 0.000 NA
#> SRR2001150 3 0.4275 0.919 0.284 0.000 0.696 0.000 NA
#> SRR2001151 3 0.4442 0.916 0.284 0.000 0.688 0.000 NA
#> SRR2001144 1 0.1992 0.821 0.924 0.000 0.044 0.000 NA
#> SRR2001145 1 0.1818 0.825 0.932 0.000 0.044 0.000 NA
#> SRR2001146 1 0.1992 0.821 0.924 0.000 0.044 0.000 NA
#> SRR2001147 1 0.2074 0.818 0.920 0.000 0.044 0.000 NA
#> SRR2001140 1 0.1211 0.836 0.960 0.000 0.024 0.000 NA
#> SRR2001142 1 0.1399 0.835 0.952 0.000 0.028 0.000 NA
#> SRR2001143 1 0.1300 0.835 0.956 0.000 0.028 0.000 NA
#> SRR2001136 3 0.4527 0.901 0.260 0.000 0.700 0.000 NA
#> SRR2001137 3 0.4576 0.899 0.268 0.000 0.692 0.000 NA
#> SRR2001138 3 0.4503 0.906 0.268 0.000 0.696 0.000 NA
#> SRR2001139 3 0.4428 0.909 0.268 0.000 0.700 0.000 NA
#> SRR2001132 3 0.3835 0.924 0.260 0.000 0.732 0.000 NA
#> SRR2001133 3 0.3942 0.923 0.260 0.000 0.728 0.000 NA
#> SRR2001134 3 0.3809 0.921 0.256 0.000 0.736 0.000 NA
#> SRR2001135 3 0.3942 0.923 0.260 0.000 0.728 0.000 NA
#> SRR2001128 1 0.0693 0.839 0.980 0.000 0.012 0.000 NA
#> SRR2001129 1 0.1018 0.838 0.968 0.000 0.016 0.000 NA
#> SRR2001130 1 0.0798 0.838 0.976 0.000 0.016 0.000 NA
#> SRR2001131 1 0.0798 0.838 0.976 0.000 0.016 0.000 NA
#> SRR2001124 1 0.4002 0.732 0.796 0.000 0.120 0.000 NA
#> SRR2001125 1 0.3857 0.746 0.808 0.000 0.108 0.000 NA
#> SRR2001126 1 0.3362 0.778 0.844 0.000 0.076 0.000 NA
#> SRR2001127 1 0.3242 0.784 0.852 0.000 0.076 0.000 NA
#> SRR2001120 1 0.2446 0.802 0.900 0.000 0.056 0.000 NA
#> SRR2001121 1 0.2376 0.806 0.904 0.000 0.052 0.000 NA
#> SRR2001122 1 0.2446 0.802 0.900 0.000 0.056 0.000 NA
#> SRR2001123 1 0.2376 0.806 0.904 0.000 0.052 0.000 NA
#> SRR2001116 1 0.2797 0.805 0.880 0.000 0.060 0.000 NA
#> SRR2001117 1 0.2729 0.807 0.884 0.000 0.056 0.000 NA
#> SRR2001118 1 0.2514 0.812 0.896 0.000 0.044 0.000 NA
#> SRR2001119 1 0.2514 0.812 0.896 0.000 0.044 0.000 NA
#> SRR2001112 3 0.5570 0.818 0.288 0.000 0.608 0.000 NA
#> SRR2001113 3 0.5551 0.819 0.284 0.000 0.612 0.000 NA
#> SRR2001114 3 0.5551 0.819 0.284 0.000 0.612 0.000 NA
#> SRR2001115 3 0.5570 0.818 0.288 0.000 0.608 0.000 NA
#> SRR2001108 4 0.4060 0.978 0.000 0.360 0.000 0.640 NA
#> SRR2001109 4 0.4060 0.978 0.000 0.360 0.000 0.640 NA
#> SRR2001110 4 0.4074 0.980 0.000 0.364 0.000 0.636 NA
#> SRR2001111 4 0.4074 0.980 0.000 0.364 0.000 0.636 NA
#> SRR2001104 2 0.0162 0.984 0.000 0.996 0.000 0.000 NA
#> SRR2001105 2 0.0162 0.984 0.000 0.996 0.000 0.000 NA
#> SRR2001106 2 0.0000 0.984 0.000 1.000 0.000 0.000 NA
#> SRR2001107 2 0.0000 0.984 0.000 1.000 0.000 0.000 NA
#> SRR2001100 2 0.0671 0.978 0.000 0.980 0.000 0.016 NA
#> SRR2001101 2 0.0579 0.984 0.000 0.984 0.000 0.008 NA
#> SRR2001102 2 0.0451 0.984 0.000 0.988 0.000 0.008 NA
#> SRR2001103 2 0.0451 0.984 0.000 0.988 0.000 0.008 NA
#> SRR2001096 2 0.0162 0.984 0.000 0.996 0.000 0.000 NA
#> SRR2001097 2 0.0162 0.984 0.000 0.996 0.000 0.000 NA
#> SRR2001098 2 0.0162 0.984 0.000 0.996 0.000 0.000 NA
#> SRR2001099 2 0.0162 0.984 0.000 0.996 0.000 0.000 NA
#> SRR2001092 2 0.0162 0.985 0.000 0.996 0.004 0.000 NA
#> SRR2001093 2 0.0324 0.984 0.000 0.992 0.004 0.000 NA
#> SRR2001094 2 0.0162 0.985 0.000 0.996 0.004 0.000 NA
#> SRR2001095 2 0.0162 0.985 0.000 0.996 0.004 0.000 NA
#> SRR2001088 4 0.4074 0.980 0.000 0.364 0.000 0.636 NA
#> SRR2001089 4 0.4074 0.980 0.000 0.364 0.000 0.636 NA
#> SRR2001090 4 0.4074 0.980 0.000 0.364 0.000 0.636 NA
#> SRR2001091 4 0.4074 0.980 0.000 0.364 0.000 0.636 NA
#> SRR2001084 4 0.4074 0.980 0.000 0.364 0.000 0.636 NA
#> SRR2001085 4 0.4074 0.980 0.000 0.364 0.000 0.636 NA
#> SRR2001086 4 0.4225 0.979 0.000 0.364 0.000 0.632 NA
#> SRR2001087 4 0.4225 0.979 0.000 0.364 0.000 0.632 NA
#> SRR2001080 2 0.0727 0.980 0.000 0.980 0.004 0.012 NA
#> SRR2001081 2 0.0727 0.980 0.000 0.980 0.004 0.012 NA
#> SRR2001082 2 0.0727 0.980 0.000 0.980 0.004 0.012 NA
#> SRR2001083 2 0.0613 0.983 0.000 0.984 0.004 0.008 NA
#> SRR2001076 2 0.0324 0.984 0.000 0.992 0.004 0.000 NA
#> SRR2001077 2 0.0324 0.984 0.000 0.992 0.004 0.000 NA
#> SRR2001078 2 0.0324 0.984 0.000 0.992 0.004 0.000 NA
#> SRR2001079 2 0.0324 0.984 0.000 0.992 0.004 0.000 NA
#> SRR2001072 4 0.4490 0.939 0.000 0.404 0.004 0.588 NA
#> SRR2001073 4 0.4460 0.954 0.000 0.392 0.004 0.600 NA
#> SRR2001074 4 0.4480 0.944 0.000 0.400 0.004 0.592 NA
#> SRR2001075 4 0.4524 0.913 0.000 0.420 0.004 0.572 NA
#> SRR2001068 2 0.0324 0.985 0.000 0.992 0.000 0.004 NA
#> SRR2001069 2 0.0451 0.984 0.000 0.988 0.000 0.008 NA
#> SRR2001070 2 0.0324 0.985 0.000 0.992 0.000 0.004 NA
#> SRR2001071 2 0.0451 0.984 0.000 0.988 0.000 0.008 NA
#> SRR2001064 2 0.0162 0.984 0.000 0.996 0.000 0.000 NA
#> SRR2001065 2 0.0162 0.984 0.000 0.996 0.000 0.000 NA
#> SRR2001066 2 0.0162 0.984 0.000 0.996 0.000 0.000 NA
#> SRR2001067 2 0.0162 0.984 0.000 0.996 0.000 0.000 NA
#> SRR2001060 4 0.4264 0.972 0.000 0.376 0.000 0.620 NA
#> SRR2001061 4 0.4264 0.972 0.000 0.376 0.000 0.620 NA
#> SRR2001062 4 0.4449 0.959 0.000 0.388 0.004 0.604 NA
#> SRR2001063 4 0.4288 0.965 0.000 0.384 0.000 0.612 NA
#> SRR2001056 4 0.4060 0.978 0.000 0.360 0.000 0.640 NA
#> SRR2001057 4 0.4060 0.978 0.000 0.360 0.000 0.640 NA
#> SRR2001058 4 0.4074 0.980 0.000 0.364 0.000 0.636 NA
#> SRR2001059 4 0.4074 0.980 0.000 0.364 0.000 0.636 NA
#> SRR2001052 2 0.0000 0.984 0.000 1.000 0.000 0.000 NA
#> SRR2001053 2 0.0162 0.985 0.000 0.996 0.004 0.000 NA
#> SRR2001054 2 0.0000 0.984 0.000 1.000 0.000 0.000 NA
#> SRR2001055 2 0.0000 0.984 0.000 1.000 0.000 0.000 NA
#> SRR2001048 2 0.0451 0.984 0.000 0.988 0.000 0.008 NA
#> SRR2001049 2 0.0579 0.984 0.000 0.984 0.000 0.008 NA
#> SRR2001050 2 0.0451 0.984 0.000 0.988 0.000 0.008 NA
#> SRR2001051 2 0.0451 0.984 0.000 0.988 0.000 0.008 NA
#> SRR2001044 4 0.4251 0.973 0.000 0.372 0.000 0.624 NA
#> SRR2001045 4 0.4251 0.973 0.000 0.372 0.000 0.624 NA
#> SRR2001046 4 0.4251 0.973 0.000 0.372 0.000 0.624 NA
#> SRR2001047 4 0.4251 0.973 0.000 0.372 0.000 0.624 NA
#> SRR2001040 4 0.4045 0.975 0.000 0.356 0.000 0.644 NA
#> SRR2001041 4 0.4045 0.975 0.000 0.356 0.000 0.644 NA
#> SRR2001042 4 0.4045 0.975 0.000 0.356 0.000 0.644 NA
#> SRR2001043 4 0.4060 0.978 0.000 0.360 0.000 0.640 NA
#> SRR2001036 4 0.4060 0.978 0.000 0.360 0.000 0.640 NA
#> SRR2001037 4 0.4045 0.975 0.000 0.356 0.000 0.644 NA
#> SRR2001038 4 0.4060 0.978 0.000 0.360 0.000 0.640 NA
#> SRR2001039 4 0.4060 0.978 0.000 0.360 0.000 0.640 NA
#> SRR2001028 4 0.4251 0.974 0.000 0.372 0.004 0.624 NA
#> SRR2001029 4 0.4402 0.971 0.000 0.372 0.004 0.620 NA
#> SRR2001030 4 0.4264 0.973 0.000 0.376 0.004 0.620 NA
#> SRR2001031 4 0.4251 0.976 0.000 0.372 0.004 0.624 NA
#> SRR2001024 4 0.4074 0.980 0.000 0.364 0.000 0.636 NA
#> SRR2001025 4 0.4074 0.980 0.000 0.364 0.000 0.636 NA
#> SRR2001026 4 0.4074 0.980 0.000 0.364 0.000 0.636 NA
#> SRR2001027 4 0.4074 0.980 0.000 0.364 0.000 0.636 NA
#> SRR2001020 2 0.0932 0.973 0.000 0.972 0.004 0.020 NA
#> SRR2001021 2 0.0932 0.973 0.000 0.972 0.004 0.020 NA
#> SRR2001022 2 0.0771 0.974 0.000 0.976 0.004 0.020 NA
#> SRR2001023 2 0.0771 0.974 0.000 0.976 0.004 0.020 NA
#> SRR2001016 4 0.4470 0.950 0.000 0.396 0.004 0.596 NA
#> SRR2001017 4 0.4480 0.945 0.000 0.400 0.004 0.592 NA
#> SRR2001018 4 0.4470 0.950 0.000 0.396 0.004 0.596 NA
#> SRR2001019 4 0.4480 0.945 0.000 0.400 0.004 0.592 NA
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR2001032 2 0.2629 0.892 0.000 0.868 0.000 0.040 NA NA
#> SRR2001033 2 0.3063 0.862 0.000 0.840 0.000 0.068 NA NA
#> SRR2001034 2 0.2629 0.892 0.000 0.868 0.000 0.040 NA NA
#> SRR2001035 2 0.2487 0.898 0.000 0.876 0.000 0.032 NA NA
#> SRR2001204 1 0.2030 0.812 0.908 0.000 0.064 0.000 NA NA
#> SRR2001205 1 0.2046 0.809 0.908 0.000 0.060 0.000 NA NA
#> SRR2001206 1 0.2046 0.810 0.908 0.000 0.060 0.000 NA NA
#> SRR2001207 1 0.2088 0.809 0.904 0.000 0.068 0.000 NA NA
#> SRR2001200 1 0.5336 0.498 0.584 0.000 0.256 0.000 NA NA
#> SRR2001201 1 0.5279 0.522 0.596 0.000 0.244 0.000 NA NA
#> SRR2001202 1 0.5336 0.498 0.584 0.000 0.256 0.000 NA NA
#> SRR2001203 1 0.5259 0.532 0.600 0.000 0.240 0.000 NA NA
#> SRR2001196 1 0.4815 0.639 0.668 0.000 0.188 0.000 NA NA
#> SRR2001197 1 0.4910 0.625 0.656 0.000 0.192 0.000 NA NA
#> SRR2001198 1 0.4854 0.640 0.664 0.000 0.184 0.000 NA NA
#> SRR2001199 1 0.4931 0.620 0.652 0.000 0.200 0.000 NA NA
#> SRR2001192 3 0.2491 0.910 0.164 0.000 0.836 0.000 NA NA
#> SRR2001193 3 0.2632 0.909 0.164 0.000 0.832 0.000 NA NA
#> SRR2001194 3 0.2668 0.908 0.168 0.000 0.828 0.000 NA NA
#> SRR2001195 3 0.2814 0.908 0.172 0.000 0.820 0.000 NA NA
#> SRR2001188 1 0.2070 0.822 0.908 0.000 0.048 0.000 NA NA
#> SRR2001189 1 0.1644 0.821 0.932 0.000 0.040 0.000 NA NA
#> SRR2001190 1 0.2088 0.821 0.904 0.000 0.068 0.000 NA NA
#> SRR2001191 1 0.2433 0.821 0.884 0.000 0.072 0.000 NA NA
#> SRR2001184 3 0.3388 0.902 0.172 0.000 0.792 0.000 NA NA
#> SRR2001185 3 0.3585 0.897 0.172 0.000 0.780 0.000 NA NA
#> SRR2001186 3 0.3585 0.897 0.172 0.000 0.780 0.000 NA NA
#> SRR2001187 3 0.3585 0.897 0.172 0.000 0.780 0.000 NA NA
#> SRR2001180 1 0.1341 0.819 0.948 0.000 0.024 0.000 NA NA
#> SRR2001181 1 0.1261 0.819 0.952 0.000 0.024 0.000 NA NA
#> SRR2001182 1 0.1257 0.818 0.952 0.000 0.020 0.000 NA NA
#> SRR2001183 1 0.1498 0.818 0.940 0.000 0.028 0.000 NA NA
#> SRR2001176 3 0.2706 0.907 0.160 0.000 0.832 0.000 NA NA
#> SRR2001177 3 0.2706 0.907 0.160 0.000 0.832 0.000 NA NA
#> SRR2001178 3 0.2700 0.908 0.156 0.000 0.836 0.000 NA NA
#> SRR2001179 3 0.2706 0.907 0.160 0.000 0.832 0.000 NA NA
#> SRR2001172 3 0.3948 0.875 0.188 0.000 0.748 0.000 NA NA
#> SRR2001173 3 0.3948 0.875 0.188 0.000 0.748 0.000 NA NA
#> SRR2001174 3 0.4062 0.864 0.196 0.000 0.736 0.000 NA NA
#> SRR2001175 3 0.4002 0.873 0.188 0.000 0.744 0.000 NA NA
#> SRR2001168 1 0.3570 0.723 0.792 0.000 0.144 0.000 NA NA
#> SRR2001169 1 0.3532 0.724 0.796 0.000 0.140 0.000 NA NA
#> SRR2001170 1 0.3626 0.718 0.788 0.000 0.144 0.000 NA NA
#> SRR2001171 1 0.3548 0.729 0.796 0.000 0.136 0.000 NA NA
#> SRR2001164 1 0.3370 0.775 0.812 0.000 0.064 0.000 NA NA
#> SRR2001165 1 0.2930 0.788 0.840 0.000 0.036 0.000 NA NA
#> SRR2001166 1 0.2887 0.791 0.844 0.000 0.036 0.000 NA NA
#> SRR2001167 1 0.2999 0.786 0.836 0.000 0.040 0.000 NA NA
#> SRR2001160 1 0.2165 0.799 0.884 0.000 0.008 0.000 NA NA
#> SRR2001161 1 0.1970 0.802 0.900 0.000 0.008 0.000 NA NA
#> SRR2001162 1 0.2118 0.800 0.888 0.000 0.008 0.000 NA NA
#> SRR2001163 1 0.1866 0.804 0.908 0.000 0.008 0.000 NA NA
#> SRR2001156 1 0.4570 0.681 0.700 0.000 0.148 0.000 NA NA
#> SRR2001157 1 0.4570 0.681 0.700 0.000 0.152 0.000 NA NA
#> SRR2001158 1 0.4704 0.666 0.684 0.000 0.160 0.000 NA NA
#> SRR2001159 1 0.4535 0.687 0.704 0.000 0.144 0.000 NA NA
#> SRR2001152 1 0.1921 0.811 0.916 0.000 0.052 0.000 NA NA
#> SRR2001153 1 0.1856 0.814 0.920 0.000 0.048 0.000 NA NA
#> SRR2001154 1 0.1789 0.811 0.924 0.000 0.044 0.000 NA NA
#> SRR2001155 1 0.2129 0.804 0.904 0.000 0.056 0.000 NA NA
#> SRR2001148 3 0.3168 0.905 0.172 0.000 0.804 0.000 NA NA
#> SRR2001149 3 0.3088 0.906 0.172 0.000 0.808 0.000 NA NA
#> SRR2001150 3 0.3318 0.903 0.172 0.000 0.796 0.000 NA NA
#> SRR2001151 3 0.3456 0.900 0.172 0.000 0.788 0.000 NA NA
#> SRR2001144 1 0.3332 0.753 0.808 0.000 0.144 0.000 NA NA
#> SRR2001145 1 0.2934 0.772 0.844 0.000 0.112 0.000 NA NA
#> SRR2001146 1 0.3044 0.768 0.836 0.000 0.116 0.000 NA NA
#> SRR2001147 1 0.3235 0.752 0.820 0.000 0.128 0.000 NA NA
#> SRR2001140 1 0.1720 0.811 0.928 0.000 0.040 0.000 NA NA
#> SRR2001142 1 0.1644 0.812 0.932 0.000 0.028 0.000 NA NA
#> SRR2001143 1 0.1865 0.809 0.920 0.000 0.040 0.000 NA NA
#> SRR2001136 3 0.3695 0.874 0.164 0.000 0.776 0.000 NA NA
#> SRR2001137 3 0.4012 0.858 0.164 0.000 0.752 0.000 NA NA
#> SRR2001138 3 0.3860 0.865 0.164 0.000 0.764 0.000 NA NA
#> SRR2001139 3 0.3637 0.876 0.164 0.000 0.780 0.000 NA NA
#> SRR2001132 3 0.3025 0.899 0.156 0.000 0.820 0.000 NA NA
#> SRR2001133 3 0.3065 0.896 0.152 0.000 0.820 0.000 NA NA
#> SRR2001134 3 0.3065 0.896 0.152 0.000 0.820 0.000 NA NA
#> SRR2001135 3 0.3065 0.896 0.152 0.000 0.820 0.000 NA NA
#> SRR2001128 1 0.1492 0.819 0.940 0.000 0.036 0.000 NA NA
#> SRR2001129 1 0.1492 0.817 0.940 0.000 0.036 0.000 NA NA
#> SRR2001130 1 0.1391 0.818 0.944 0.000 0.040 0.000 NA NA
#> SRR2001131 1 0.1176 0.817 0.956 0.000 0.024 0.000 NA NA
#> SRR2001124 1 0.4045 0.740 0.756 0.000 0.124 0.000 NA NA
#> SRR2001125 1 0.3962 0.745 0.764 0.000 0.116 0.000 NA NA
#> SRR2001126 1 0.3655 0.767 0.792 0.000 0.096 0.000 NA NA
#> SRR2001127 1 0.3370 0.778 0.812 0.000 0.064 0.000 NA NA
#> SRR2001120 1 0.3435 0.732 0.804 0.000 0.136 0.000 NA NA
#> SRR2001121 1 0.3395 0.737 0.808 0.000 0.132 0.000 NA NA
#> SRR2001122 1 0.3435 0.733 0.804 0.000 0.136 0.000 NA NA
#> SRR2001123 1 0.3395 0.738 0.808 0.000 0.132 0.000 NA NA
#> SRR2001116 1 0.2712 0.801 0.864 0.000 0.048 0.000 NA NA
#> SRR2001117 1 0.2579 0.801 0.872 0.000 0.040 0.000 NA NA
#> SRR2001118 1 0.2527 0.802 0.876 0.000 0.040 0.000 NA NA
#> SRR2001119 1 0.2509 0.802 0.876 0.000 0.036 0.000 NA NA
#> SRR2001112 3 0.4931 0.746 0.216 0.000 0.648 0.000 NA NA
#> SRR2001113 3 0.4965 0.741 0.216 0.000 0.644 0.000 NA NA
#> SRR2001114 3 0.4974 0.742 0.212 0.000 0.644 0.000 NA NA
#> SRR2001115 3 0.4989 0.734 0.220 0.000 0.640 0.000 NA NA
#> SRR2001108 4 0.3265 0.946 0.000 0.248 0.000 0.748 NA NA
#> SRR2001109 4 0.3240 0.944 0.000 0.244 0.000 0.752 NA NA
#> SRR2001110 4 0.3290 0.945 0.000 0.252 0.000 0.744 NA NA
#> SRR2001111 4 0.3126 0.946 0.000 0.248 0.000 0.752 NA NA
#> SRR2001104 2 0.1007 0.929 0.000 0.956 0.000 0.000 NA NA
#> SRR2001105 2 0.1285 0.930 0.000 0.944 0.000 0.004 NA NA
#> SRR2001106 2 0.0865 0.930 0.000 0.964 0.000 0.000 NA NA
#> SRR2001107 2 0.0865 0.931 0.000 0.964 0.000 0.000 NA NA
#> SRR2001100 2 0.2030 0.907 0.000 0.908 0.000 0.064 NA NA
#> SRR2001101 2 0.2030 0.911 0.000 0.908 0.000 0.064 NA NA
#> SRR2001102 2 0.1334 0.931 0.000 0.948 0.000 0.032 NA NA
#> SRR2001103 2 0.1575 0.927 0.000 0.936 0.000 0.032 NA NA
#> SRR2001096 2 0.1461 0.926 0.000 0.940 0.000 0.016 NA NA
#> SRR2001097 2 0.1528 0.925 0.000 0.936 0.000 0.016 NA NA
#> SRR2001098 2 0.1461 0.926 0.000 0.940 0.000 0.016 NA NA
#> SRR2001099 2 0.1461 0.926 0.000 0.940 0.000 0.016 NA NA
#> SRR2001092 2 0.1349 0.926 0.000 0.940 0.000 0.004 NA NA
#> SRR2001093 2 0.1524 0.924 0.000 0.932 0.000 0.008 NA NA
#> SRR2001094 2 0.0937 0.932 0.000 0.960 0.000 0.000 NA NA
#> SRR2001095 2 0.1204 0.927 0.000 0.944 0.000 0.000 NA NA
#> SRR2001088 4 0.3421 0.946 0.000 0.256 0.000 0.736 NA NA
#> SRR2001089 4 0.3398 0.946 0.000 0.252 0.000 0.740 NA NA
#> SRR2001090 4 0.3421 0.946 0.000 0.256 0.000 0.736 NA NA
#> SRR2001091 4 0.3541 0.943 0.000 0.260 0.000 0.728 NA NA
#> SRR2001084 4 0.3290 0.946 0.000 0.252 0.000 0.744 NA NA
#> SRR2001085 4 0.3290 0.946 0.000 0.252 0.000 0.744 NA NA
#> SRR2001086 4 0.3398 0.945 0.000 0.252 0.000 0.740 NA NA
#> SRR2001087 4 0.3421 0.944 0.000 0.256 0.000 0.736 NA NA
#> SRR2001080 2 0.1967 0.914 0.000 0.904 0.000 0.012 NA NA
#> SRR2001081 2 0.2230 0.912 0.000 0.892 0.000 0.024 NA NA
#> SRR2001082 2 0.1866 0.916 0.000 0.908 0.000 0.008 NA NA
#> SRR2001083 2 0.1753 0.917 0.000 0.912 0.000 0.004 NA NA
#> SRR2001076 2 0.1285 0.929 0.000 0.944 0.000 0.004 NA NA
#> SRR2001077 2 0.1644 0.921 0.000 0.920 0.000 0.004 NA NA
#> SRR2001078 2 0.1285 0.928 0.000 0.944 0.000 0.004 NA NA
#> SRR2001079 2 0.0865 0.932 0.000 0.964 0.000 0.000 NA NA
#> SRR2001072 4 0.4361 0.892 0.000 0.308 0.000 0.648 NA NA
#> SRR2001073 4 0.4247 0.906 0.000 0.296 0.000 0.664 NA NA
#> SRR2001074 4 0.4344 0.895 0.000 0.304 0.000 0.652 NA NA
#> SRR2001075 4 0.4480 0.851 0.000 0.340 0.000 0.616 NA NA
#> SRR2001068 2 0.1245 0.929 0.000 0.952 0.000 0.016 NA NA
#> SRR2001069 2 0.1334 0.930 0.000 0.948 0.000 0.032 NA NA
#> SRR2001070 2 0.1408 0.927 0.000 0.944 0.000 0.020 NA NA
#> SRR2001071 2 0.1492 0.926 0.000 0.940 0.000 0.024 NA NA
#> SRR2001064 2 0.1391 0.927 0.000 0.944 0.000 0.016 NA NA
#> SRR2001065 2 0.1461 0.926 0.000 0.940 0.000 0.016 NA NA
#> SRR2001066 2 0.1461 0.926 0.000 0.940 0.000 0.016 NA NA
#> SRR2001067 2 0.1461 0.926 0.000 0.940 0.000 0.016 NA NA
#> SRR2001060 4 0.3778 0.933 0.000 0.272 0.000 0.708 NA NA
#> SRR2001061 4 0.3586 0.939 0.000 0.268 0.000 0.720 NA NA
#> SRR2001062 4 0.4047 0.915 0.000 0.296 0.000 0.676 NA NA
#> SRR2001063 4 0.3876 0.928 0.000 0.276 0.000 0.700 NA NA
#> SRR2001056 4 0.3076 0.944 0.000 0.240 0.000 0.760 NA NA
#> SRR2001057 4 0.3101 0.945 0.000 0.244 0.000 0.756 NA NA
#> SRR2001058 4 0.3101 0.945 0.000 0.244 0.000 0.756 NA NA
#> SRR2001059 4 0.3151 0.946 0.000 0.252 0.000 0.748 NA NA
#> SRR2001052 2 0.0725 0.933 0.000 0.976 0.000 0.012 NA NA
#> SRR2001053 2 0.0777 0.935 0.000 0.972 0.000 0.004 NA NA
#> SRR2001054 2 0.0622 0.933 0.000 0.980 0.000 0.008 NA NA
#> SRR2001055 2 0.0909 0.932 0.000 0.968 0.000 0.012 NA NA
#> SRR2001048 2 0.1644 0.927 0.000 0.932 0.000 0.040 NA NA
#> SRR2001049 2 0.1644 0.934 0.000 0.932 0.000 0.028 NA NA
#> SRR2001050 2 0.1245 0.931 0.000 0.952 0.000 0.032 NA NA
#> SRR2001051 2 0.1003 0.932 0.000 0.964 0.000 0.020 NA NA
#> SRR2001044 4 0.4476 0.901 0.000 0.272 0.000 0.664 NA NA
#> SRR2001045 4 0.4654 0.883 0.000 0.268 0.000 0.652 NA NA
#> SRR2001046 4 0.4368 0.903 0.000 0.272 0.000 0.672 NA NA
#> SRR2001047 4 0.4371 0.906 0.000 0.284 0.000 0.664 NA NA
#> SRR2001040 4 0.3023 0.940 0.000 0.232 0.000 0.768 NA NA
#> SRR2001041 4 0.3163 0.940 0.000 0.232 0.000 0.764 NA NA
#> SRR2001042 4 0.3163 0.940 0.000 0.232 0.000 0.764 NA NA
#> SRR2001043 4 0.3023 0.940 0.000 0.232 0.000 0.768 NA NA
#> SRR2001036 4 0.3023 0.940 0.000 0.232 0.000 0.768 NA NA
#> SRR2001037 4 0.3023 0.940 0.000 0.232 0.000 0.768 NA NA
#> SRR2001038 4 0.3023 0.940 0.000 0.232 0.000 0.768 NA NA
#> SRR2001039 4 0.3189 0.939 0.000 0.236 0.000 0.760 NA NA
#> SRR2001028 4 0.4476 0.895 0.000 0.272 0.000 0.664 NA NA
#> SRR2001029 4 0.4775 0.861 0.000 0.284 0.000 0.632 NA NA
#> SRR2001030 4 0.4427 0.900 0.000 0.284 0.000 0.660 NA NA
#> SRR2001031 4 0.4445 0.897 0.000 0.288 0.000 0.656 NA NA
#> SRR2001024 4 0.3126 0.945 0.000 0.248 0.000 0.752 NA NA
#> SRR2001025 4 0.3265 0.945 0.000 0.248 0.000 0.748 NA NA
#> SRR2001026 4 0.3126 0.945 0.000 0.248 0.000 0.752 NA NA
#> SRR2001027 4 0.3101 0.945 0.000 0.244 0.000 0.756 NA NA
#> SRR2001020 2 0.2948 0.859 0.000 0.848 0.000 0.092 NA NA
#> SRR2001021 2 0.2852 0.874 0.000 0.856 0.000 0.080 NA NA
#> SRR2001022 2 0.2376 0.898 0.000 0.888 0.000 0.068 NA NA
#> SRR2001023 2 0.2488 0.889 0.000 0.880 0.000 0.076 NA NA
#> SRR2001016 4 0.4330 0.865 0.000 0.332 0.000 0.632 NA NA
#> SRR2001017 4 0.4219 0.885 0.000 0.320 0.000 0.648 NA NA
#> SRR2001018 4 0.4420 0.849 0.000 0.340 0.000 0.620 NA NA
#> SRR2001019 4 0.4406 0.857 0.000 0.336 0.000 0.624 NA NA
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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