Date: 2021-07-26 10:21:07 CEST, cola version: 1.9.4
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First the variable is renamed to res_rh.
res_rh = rh
The partition hierarchy and all available functions which can be applied to res_rh object.
res_rh
#> A 'HierarchicalPartition' object with 'ATC:skmeans' method.
#> On a matrix with 7179 rows and 337 columns.
#> Performed in total 1200 partitions.
#> There are 5 groups under the following parameters:
#> - min_samples: 6
#> - mean_silhouette_cutoff: 0.9
#> - min_n_signatures: 73 (signatures are selected based on:)
#> - fdr_cutoff: 0.05
#> - group_diff (scaled values): 0.5
#>
#> Hierarchy of the partition:
#> 0, 337 cols
#> |-- 01, 182 cols, 289 signatures
#> | |-- 011, 95 cols (a)
#> | `-- 012, 87 cols (a)
#> `-- 02, 155 cols, 1372 signatures
#> |-- 021, 72 cols (a)
#> |-- 022, 46 cols, 58 signatures (c)
#> `-- 023, 37 cols, 10 signatures (c)
#> Stop reason:
#> a) Mean silhouette score was too small
#> c) There were too few signatures.
#>
#> Following methods can be applied to this 'HierarchicalPartition' object:
#> [1] "all_leaves" "all_nodes" "cola_report" "collect_classes"
#> [5] "colnames" "compare_signatures" "dimension_reduction" "functional_enrichment"
#> [9] "get_anno_col" "get_anno" "get_children_nodes" "get_classes"
#> [13] "get_matrix" "get_signatures" "is_leaf_node" "max_depth"
#> [17] "merge_node" "ncol" "node_info" "node_level"
#> [21] "nrow" "rownames" "show" "split_node"
#> [25] "suggest_best_k" "test_to_known_factors" "top_rows_heatmap" "top_rows_overlap"
#>
#> You can get result for a single node by e.g. object["01"]
The call of hierarchical_partition() was:
#> hierarchical_partition(data = lt$mat, anno = lt$anno, subset = 500, cores = 4)
Dimension of the input matrix:
mat = get_matrix(res_rh)
dim(mat)
#> [1] 7179 337
All the methods that were tried:
res_rh@param$combination_method
#> [[1]]
#> [1] "ATC" "skmeans"
The density distribution for each sample is visualized as one column in the following heatmap. The clustering is based on the distance which is the Kolmogorov-Smirnov statistic between two distributions.
library(ComplexHeatmap)
densityHeatmap(mat, top_annotation = HeatmapAnnotation(df = get_anno(res_rh),
col = get_anno_col(res_rh)), ylab = "value", cluster_columns = TRUE, show_column_names = FALSE,
mc.cores = 1)
Some values about the hierarchy:
all_nodes(res_rh)
#> [1] "0" "01" "011" "012" "02" "021" "022" "023"
all_leaves(res_rh)
#> [1] "011" "012" "021" "022" "023"
node_info(res_rh)
#> id best_method depth best_k n_columns n_signatures p_signatures is_leaf
#> 1 0 ATC:skmeans 1 2 337 1473 0.20518 FALSE
#> 2 01 ATC:skmeans 2 2 182 289 0.04026 FALSE
#> 3 011 ATC:skmeans 3 2 95 NA NA TRUE
#> 4 012 ATC:skmeans 3 2 87 NA NA TRUE
#> 5 02 ATC:skmeans 2 3 155 1372 0.19111 FALSE
#> 6 021 ATC:skmeans 3 2 72 NA NA TRUE
#> 7 022 ATC:skmeans 3 2 46 58 0.00808 TRUE
#> 8 023 ATC:skmeans 3 2 37 10 0.00139 TRUE
In the output from node_info(), there are the following columns:
id: The node id.best_method: The best method selected.depth: Depth of the node in the hierarchy.best_k: Best number of groups of the partition on that node.n_columns: Number of columns in the submatrix.n_signatures: Number of signatures with the best_k.p_signatures: Proportion of hte signatures in total number of rows in the matrix.is_leaf: Whether the node is a leaf.Labels of nodes are encoded in a special way. The number of digits correspond to the depth of the node in the hierarchy and the value of the digits correspond to the index of the subgroup in the current node, E.g. a label of “012” means the node is the second subgroup of the partition which is the first subgroup of the root node.
Following table shows the best k (number of partitions) for each node in the
partition hierarchy. Clicking on the node name in the table goes to the
corresponding section for the partitioning on that node.
The cola vignette explains the definition of the metrics used for determining the best number of partitions.
suggest_best_k(res_rh)
| Node | Best method | Is leaf | Best k | 1-PAC | Mean silhouette | Concordance | #samples | |
|---|---|---|---|---|---|---|---|---|
| Node0 | ATC:skmeans | 2 | 1.00 | 0.98 | 0.99 | 337 | ** | |
| Node01 | ATC:skmeans | 2 | 1.00 | 0.96 | 0.99 | 182 | ** | |
| Node011-leaf | ATC:skmeans | ✓ (a) | 2 | 0.66 | 0.85 | 0.93 | 95 | |
| Node012-leaf | ATC:skmeans | ✓ (a) | 2 | 0.68 | 0.85 | 0.93 | 87 | |
| Node02 | ATC:skmeans | 3 | 1.00 | 0.97 | 0.99 | 155 | ** | |
| Node021-leaf | ATC:skmeans | ✓ (a) | 2 | 0.75 | 0.86 | 0.94 | 72 | |
| Node022-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 0.93 | 0.98 | 46 | ** |
| Node023-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 0.97 | 0.99 | 37 | ** |
Stop reason: a) Mean silhouette score was too small c) There were too few signatures.
**: 1-PAC > 0.95, *: 1-PAC > 0.9
The nodes of the hierarchy can be merged by setting the merge_node parameters. Here we
control the hierarchy with the min_n_signatures parameter. The value of min_n_signatures is
from node_info().
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 289))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1372))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1473))
Following shows the table of the partitions (You need to click the show/hide code output link to see it).
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 289))
#> 1772099-259_E02 1772116-063_D07 1772116-060_E02 1772116-063_E05 1772099-259_C09 1772116-060_A08
#> "012" "021" "023" "021" "022" "021"
#> 1772099-259_F01 1772099-258_H10 1772099-259_A03 1772099-238_A02 1772116-060_C01 1772099-259_C10
#> "012" "021" "012" "022" "012" "012"
#> 1772099-241_A06 1772099-241_D11 1772116-063_B01 1772099-258_H03 1772116-063_H12 1772099-262_G05
#> "021" "022" "022" "021" "021" "023"
#> 1772099-258_E05 1772099-241_G05 1772116-064_C11 1772116-064_E06 1772099-258_H06 1772116-064_A04
#> "021" "012" "021" "021" "012" "012"
#> 1772099-260_D12 1772099-258_B02 1772116-063_E12 1772099-259_F02 1772099-258_G02 1772116-063_E07
#> "012" "022" "021" "021" "023" "022"
#> 1772099-258_G11 1772116-062_A05 1772116-063_G12 1772099-262_H06 1772116-062_D10 1772116-062_H09
#> "021" "012" "021" "012" "012" "023"
#> 1772116-064_H09 1772116-064_G07 1772099-262_B04 1772099-258_C04 1772116-060_C03 1772116-060_G07
#> "021" "012" "021" "023" "021" "012"
#> 1772099-259_A09 1772116-062_A01 1772116-063_B11 1772116-063_A04 1772116-062_H06 1772116-063_E09
#> "011" "021" "022" "023" "022" "012"
#> 1772116-062_A07 1772116-060_D01 1772099-258_F03 1772116-060_D04 1772116-062_E05 1772116-062_D09
#> "023" "021" "022" "022" "021" "011"
#> 1772099-260_F12 1772116-062_A10 1772116-062_B09 1772099-262_D04 1772116-062_G10 1772116-060_C04
#> "012" "021" "023" "023" "021" "023"
#> 1772116-062_A09 1772099-262_H02 1772099-258_D06 1772116-062_G04 1772116-063_B10 1772116-063_B03
#> "022" "023" "022" "022" "012" "021"
#> 1772099-241_B09 1772116-064_E05 1772116-064_C08 1772099-258_G06 1772116-060_G08 1772116-062_G06
#> "012" "011" "021" "022" "021" "023"
#> 1772116-060_F07 1772099-241_A02 1772116-064_F11 1772116-062_H11 1772099-258_G08 1772116-064_E07
#> "022" "012" "023" "021" "022" "022"
#> 1772099-238_D07 1772116-063_D04 1772116-062_E07 1772116-063_F10 1772099-238_C02 1772099-262_E11
#> "021" "021" "022" "011" "022" "022"
#> 1772116-060_D07 1772116-060_G02 1772116-060_A12 1772116-060_D05 1772116-060_C08 1772116-060_E09
#> "021" "022" "022" "021" "021" "023"
#> 1772116-063_B09 1772116-062_F06 1772099-238_A10 1772099-260_H06 1772116-060_C02 1772116-062_E09
#> "011" "022" "021" "023" "023" "012"
#> 1772116-060_F09 1772116-060_D10 1772116-063_F04 1772116-064_C10 1772116-063_A07 1772099-260_E06
#> "022" "011" "021" "011" "023" "021"
#> 1772099-260_F11 1772116-062_C12 1772099-237_G01 1772099-258_H02 1772116-063_D11 1772099-240_G05
#> "023" "012" "011" "023" "022" "021"
#> 1772116-063_C11 1772116-064_A01 1772116-063_E10 1772116-064_D03 1772116-060_C09 1772116-064_B07
#> "022" "021" "022" "021" "022" "022"
#> 1772116-064_H02 1772099-237_G06 1772116-062_A11 1772116-060_B11 1772116-063_C04 1772116-062_F09
#> "022" "023" "021" "022" "023" "021"
#> 1772116-064_D02 1772116-064_B09 1772116-064_C04 1772099-259_D07 1772099-238_C07 1772116-063_A11
#> "023" "023" "023" "012" "023" "012"
#> 1772116-063_E04 1772116-062_F05 1772099-241_A10 1772099-238_F07 1772116-062_H03 1772116-063_B04
#> "021" "011" "012" "012" "011" "012"
#> 1772116-060_A11 1772116-062_B11 1772116-060_B02 1772099-238_A09 1772116-060_B01 1772116-060_E03
#> "012" "022" "012" "023" "021" "021"
#> 1772099-260_F07 1772116-064_H03 1772116-062_E04 1772116-063_C12 1772116-064_G08 1772116-063_H02
#> "012" "011" "022" "011" "011" "022"
#> 1772099-259_F10 1772116-063_F11 1772099-259_G08 1772116-060_F01 1772116-060_B10 1772099-259_C03
#> "011" "021" "012" "021" "021" "011"
#> 1772099-262_B10 1772099-241_F08 1772099-240_A09 1772099-240_D01 1772099-240_D07 1772116-064_B01
#> "011" "011" "011" "012" "012" "011"
#> 1772116-063_A05 1772099-241_F07 1772099-238_A08 1772099-237_B07 1772116-063_C06 1772116-062_H05
#> "011" "012" "012" "011" "012" "012"
#> 1772116-062_B05 1772116-064_B06 1772116-062_B12 1772099-260_D08 1772116-064_F06 1772116-063_F12
#> "011" "011" "011" "012" "012" "011"
#> 1772116-063_G10 1772116-062_C08 1772116-064_D10 1772116-060_H08 1772099-262_C05 1772116-062_D06
#> "011" "012" "012" "021" "011" "011"
#> 1772099-238_H11 1772099-260_A01 1772099-241_H05 1772099-262_F04 1772099-262_D11 1772099-241_C09
#> "012" "011" "021" "011" "011" "011"
#> 1772099-238_G08 1772099-260_H08 1772099-241_C12 1772099-259_C11 1772116-060_B09 1772116-064_D06
#> "011" "011" "011" "011" "012" "011"
#> 1772116-064_B03 1772116-063_E06 1772116-060_A01 1772099-262_B01 1772116-064_A07 1772099-262_C02
#> "011" "012" "011" "011" "011" "011"
#> 1772099-260_G11 1772116-060_C12 1772099-262_G10 1772116-062_B01 1772116-064_B08 1772116-063_B06
#> "012" "011" "011" "011" "011" "021"
#> 1772116-064_C03 1772099-258_F05 1772099-262_F05 1772099-258_A08 1772116-062_F10 1772099-240_G08
#> "011" "012" "011" "011" "011" "012"
#> 1772116-062_D03 1772116-062_F04 1772099-258_E08 1772116-064_D05 1772116-063_H04 1772116-063_C03
#> "012" "012" "012" "011" "012" "012"
#> 1772116-064_E03 1772099-260_C01 1772099-238_C12 1772116-064_D09 1772116-062_E12 1772116-063_G01
#> "011" "011" "011" "011" "011" "011"
#> 1772099-262_H01 1772099-262_F06 1772116-062_D05 1772099-237_E03 1772116-062_B10 1772099-258_G12
#> "012" "011" "012" "011" "011" "012"
#> 1772116-060_C10 1772099-258_D09 1772099-260_H05 1772116-060_A03 1772116-060_E01 1772116-063_A01
#> "011" "021" "011" "012" "011" "011"
#> 1772099-241_E10 1772116-064_F07 1772116-062_C01 1772099-262_G12 1772116-064_F05 1772116-062_G12
#> "011" "012" "011" "012" "011" "012"
#> 1772116-063_D10 1772116-062_C09 1772116-064_E12 1772116-062_H08 1772116-060_G03 1772099-262_C10
#> "011" "012" "011" "012" "012" "011"
#> 1772116-064_D01 1772116-064_D08 1772099-259_D11 1772116-060_E08 1772116-062_F12 1772116-063_H11
#> "011" "011" "012" "011" "011" "022"
#> 1772116-062_C10 1772099-240_H02 1772099-260_A07 1772116-060_D12 1772099-259_C04 1772099-258_B10
#> "021" "022" "023" "011" "022" "012"
#> 1772116-062_F01 1772116-060_E11 1772099-262_B11 1772116-063_D12 1772116-063_H05 1772116-060_A04
#> "021" "023" "021" "011" "021" "012"
#> 1772116-064_B04 1772099-260_B06 1772116-063_F02 1772099-258_B06 1772116-064_F03 1772099-262_C01
#> "023" "023" "012" "021" "012" "011"
#> 1772099-258_F12 1772099-237_H01 1772099-258_D08 1772099-260_H04 1772116-062_E01 1772099-262_A02
#> "011" "012" "011" "012" "011" "021"
#> 1772099-260_A04 1772099-262_G01 1772099-258_B05 1772099-238_F03 1772099-262_F12 1772099-258_D01
#> "011" "011" "011" "021" "011" "012"
#> 1772116-060_F06 1772099-241_H12 1772116-062_G05 1772116-060_G01 1772116-060_B06 1772099-241_H06
#> "012" "012" "021" "021" "021" "023"
#> 1772116-062_B06 1772116-062_D11 1772116-064_E09 1772116-062_E08 1772099-262_H12 1772099-237_D03
#> "022" "021" "023" "021" "011" "011"
#> 1772116-060_H02 1772116-062_C05 1772116-064_C07 1772116-060_A05 1772099-262_D02 1772099-258_C06
#> "022" "012" "022" "021" "023" "022"
#> 1772099-258_F06 1772099-260_A02 1772099-258_C03 1772099-237_F01 1772116-064_F09 1772099-238_H06
#> "021" "022" "021" "021" "011" "011"
#> 1772099-238_H10 1772099-258_G04 1772116-060_F08 1772116-063_A02 1772116-062_D01 1772116-064_C09
#> "021" "023" "012" "012" "012" "012"
#> 1772099-262_D06 1772099-258_G09 1772099-259_G11 1772116-064_B10 1772116-062_F02 1772099-262_F11
#> "012" "023" "012" "011" "022" "021"
#> 1772116-064_C05 1772099-238_B03 1772099-241_F03 1772099-259_A06 1772116-062_A12 1772116-062_E10
#> "012" "012" "012" "012" "011" "021"
#> 1772099-262_B12 1772099-241_E05 1772099-241_G08 1772099-262_E01 1772099-259_C12 1772099-258_C01
#> "011" "011" "011" "011" "011" "021"
#> 1772099-240_D02 1772099-259_G04 1772116-060_H06 1772099-240_C03 1772099-260_C03 1772099-238_E12
#> "021" "012" "012" "012" "021" "012"
#> 1772116-063_A09 1772099-260_C06 1772099-238_C01 1772099-240_F07 1772099-241_G09 1772116-063_G02
#> "022" "022" "021" "022" "023" "023"
#> 1772099-259_H03
#> "012"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1372))
#> 1772099-259_E02 1772116-063_D07 1772116-060_E02 1772116-063_E05 1772099-259_C09 1772116-060_A08
#> "01" "021" "023" "021" "022" "021"
#> 1772099-259_F01 1772099-258_H10 1772099-259_A03 1772099-238_A02 1772116-060_C01 1772099-259_C10
#> "01" "021" "01" "022" "01" "01"
#> 1772099-241_A06 1772099-241_D11 1772116-063_B01 1772099-258_H03 1772116-063_H12 1772099-262_G05
#> "021" "022" "022" "021" "021" "023"
#> 1772099-258_E05 1772099-241_G05 1772116-064_C11 1772116-064_E06 1772099-258_H06 1772116-064_A04
#> "021" "01" "021" "021" "01" "01"
#> 1772099-260_D12 1772099-258_B02 1772116-063_E12 1772099-259_F02 1772099-258_G02 1772116-063_E07
#> "01" "022" "021" "021" "023" "022"
#> 1772099-258_G11 1772116-062_A05 1772116-063_G12 1772099-262_H06 1772116-062_D10 1772116-062_H09
#> "021" "01" "021" "01" "01" "023"
#> 1772116-064_H09 1772116-064_G07 1772099-262_B04 1772099-258_C04 1772116-060_C03 1772116-060_G07
#> "021" "01" "021" "023" "021" "01"
#> 1772099-259_A09 1772116-062_A01 1772116-063_B11 1772116-063_A04 1772116-062_H06 1772116-063_E09
#> "01" "021" "022" "023" "022" "01"
#> 1772116-062_A07 1772116-060_D01 1772099-258_F03 1772116-060_D04 1772116-062_E05 1772116-062_D09
#> "023" "021" "022" "022" "021" "01"
#> 1772099-260_F12 1772116-062_A10 1772116-062_B09 1772099-262_D04 1772116-062_G10 1772116-060_C04
#> "01" "021" "023" "023" "021" "023"
#> 1772116-062_A09 1772099-262_H02 1772099-258_D06 1772116-062_G04 1772116-063_B10 1772116-063_B03
#> "022" "023" "022" "022" "01" "021"
#> 1772099-241_B09 1772116-064_E05 1772116-064_C08 1772099-258_G06 1772116-060_G08 1772116-062_G06
#> "01" "01" "021" "022" "021" "023"
#> 1772116-060_F07 1772099-241_A02 1772116-064_F11 1772116-062_H11 1772099-258_G08 1772116-064_E07
#> "022" "01" "023" "021" "022" "022"
#> 1772099-238_D07 1772116-063_D04 1772116-062_E07 1772116-063_F10 1772099-238_C02 1772099-262_E11
#> "021" "021" "022" "01" "022" "022"
#> 1772116-060_D07 1772116-060_G02 1772116-060_A12 1772116-060_D05 1772116-060_C08 1772116-060_E09
#> "021" "022" "022" "021" "021" "023"
#> 1772116-063_B09 1772116-062_F06 1772099-238_A10 1772099-260_H06 1772116-060_C02 1772116-062_E09
#> "01" "022" "021" "023" "023" "01"
#> 1772116-060_F09 1772116-060_D10 1772116-063_F04 1772116-064_C10 1772116-063_A07 1772099-260_E06
#> "022" "01" "021" "01" "023" "021"
#> 1772099-260_F11 1772116-062_C12 1772099-237_G01 1772099-258_H02 1772116-063_D11 1772099-240_G05
#> "023" "01" "01" "023" "022" "021"
#> 1772116-063_C11 1772116-064_A01 1772116-063_E10 1772116-064_D03 1772116-060_C09 1772116-064_B07
#> "022" "021" "022" "021" "022" "022"
#> 1772116-064_H02 1772099-237_G06 1772116-062_A11 1772116-060_B11 1772116-063_C04 1772116-062_F09
#> "022" "023" "021" "022" "023" "021"
#> 1772116-064_D02 1772116-064_B09 1772116-064_C04 1772099-259_D07 1772099-238_C07 1772116-063_A11
#> "023" "023" "023" "01" "023" "01"
#> 1772116-063_E04 1772116-062_F05 1772099-241_A10 1772099-238_F07 1772116-062_H03 1772116-063_B04
#> "021" "01" "01" "01" "01" "01"
#> 1772116-060_A11 1772116-062_B11 1772116-060_B02 1772099-238_A09 1772116-060_B01 1772116-060_E03
#> "01" "022" "01" "023" "021" "021"
#> 1772099-260_F07 1772116-064_H03 1772116-062_E04 1772116-063_C12 1772116-064_G08 1772116-063_H02
#> "01" "01" "022" "01" "01" "022"
#> 1772099-259_F10 1772116-063_F11 1772099-259_G08 1772116-060_F01 1772116-060_B10 1772099-259_C03
#> "01" "021" "01" "021" "021" "01"
#> 1772099-262_B10 1772099-241_F08 1772099-240_A09 1772099-240_D01 1772099-240_D07 1772116-064_B01
#> "01" "01" "01" "01" "01" "01"
#> 1772116-063_A05 1772099-241_F07 1772099-238_A08 1772099-237_B07 1772116-063_C06 1772116-062_H05
#> "01" "01" "01" "01" "01" "01"
#> 1772116-062_B05 1772116-064_B06 1772116-062_B12 1772099-260_D08 1772116-064_F06 1772116-063_F12
#> "01" "01" "01" "01" "01" "01"
#> 1772116-063_G10 1772116-062_C08 1772116-064_D10 1772116-060_H08 1772099-262_C05 1772116-062_D06
#> "01" "01" "01" "021" "01" "01"
#> 1772099-238_H11 1772099-260_A01 1772099-241_H05 1772099-262_F04 1772099-262_D11 1772099-241_C09
#> "01" "01" "021" "01" "01" "01"
#> 1772099-238_G08 1772099-260_H08 1772099-241_C12 1772099-259_C11 1772116-060_B09 1772116-064_D06
#> "01" "01" "01" "01" "01" "01"
#> 1772116-064_B03 1772116-063_E06 1772116-060_A01 1772099-262_B01 1772116-064_A07 1772099-262_C02
#> "01" "01" "01" "01" "01" "01"
#> 1772099-260_G11 1772116-060_C12 1772099-262_G10 1772116-062_B01 1772116-064_B08 1772116-063_B06
#> "01" "01" "01" "01" "01" "021"
#> 1772116-064_C03 1772099-258_F05 1772099-262_F05 1772099-258_A08 1772116-062_F10 1772099-240_G08
#> "01" "01" "01" "01" "01" "01"
#> 1772116-062_D03 1772116-062_F04 1772099-258_E08 1772116-064_D05 1772116-063_H04 1772116-063_C03
#> "01" "01" "01" "01" "01" "01"
#> 1772116-064_E03 1772099-260_C01 1772099-238_C12 1772116-064_D09 1772116-062_E12 1772116-063_G01
#> "01" "01" "01" "01" "01" "01"
#> 1772099-262_H01 1772099-262_F06 1772116-062_D05 1772099-237_E03 1772116-062_B10 1772099-258_G12
#> "01" "01" "01" "01" "01" "01"
#> 1772116-060_C10 1772099-258_D09 1772099-260_H05 1772116-060_A03 1772116-060_E01 1772116-063_A01
#> "01" "021" "01" "01" "01" "01"
#> 1772099-241_E10 1772116-064_F07 1772116-062_C01 1772099-262_G12 1772116-064_F05 1772116-062_G12
#> "01" "01" "01" "01" "01" "01"
#> 1772116-063_D10 1772116-062_C09 1772116-064_E12 1772116-062_H08 1772116-060_G03 1772099-262_C10
#> "01" "01" "01" "01" "01" "01"
#> 1772116-064_D01 1772116-064_D08 1772099-259_D11 1772116-060_E08 1772116-062_F12 1772116-063_H11
#> "01" "01" "01" "01" "01" "022"
#> 1772116-062_C10 1772099-240_H02 1772099-260_A07 1772116-060_D12 1772099-259_C04 1772099-258_B10
#> "021" "022" "023" "01" "022" "01"
#> 1772116-062_F01 1772116-060_E11 1772099-262_B11 1772116-063_D12 1772116-063_H05 1772116-060_A04
#> "021" "023" "021" "01" "021" "01"
#> 1772116-064_B04 1772099-260_B06 1772116-063_F02 1772099-258_B06 1772116-064_F03 1772099-262_C01
#> "023" "023" "01" "021" "01" "01"
#> 1772099-258_F12 1772099-237_H01 1772099-258_D08 1772099-260_H04 1772116-062_E01 1772099-262_A02
#> "01" "01" "01" "01" "01" "021"
#> 1772099-260_A04 1772099-262_G01 1772099-258_B05 1772099-238_F03 1772099-262_F12 1772099-258_D01
#> "01" "01" "01" "021" "01" "01"
#> 1772116-060_F06 1772099-241_H12 1772116-062_G05 1772116-060_G01 1772116-060_B06 1772099-241_H06
#> "01" "01" "021" "021" "021" "023"
#> 1772116-062_B06 1772116-062_D11 1772116-064_E09 1772116-062_E08 1772099-262_H12 1772099-237_D03
#> "022" "021" "023" "021" "01" "01"
#> 1772116-060_H02 1772116-062_C05 1772116-064_C07 1772116-060_A05 1772099-262_D02 1772099-258_C06
#> "022" "01" "022" "021" "023" "022"
#> 1772099-258_F06 1772099-260_A02 1772099-258_C03 1772099-237_F01 1772116-064_F09 1772099-238_H06
#> "021" "022" "021" "021" "01" "01"
#> 1772099-238_H10 1772099-258_G04 1772116-060_F08 1772116-063_A02 1772116-062_D01 1772116-064_C09
#> "021" "023" "01" "01" "01" "01"
#> 1772099-262_D06 1772099-258_G09 1772099-259_G11 1772116-064_B10 1772116-062_F02 1772099-262_F11
#> "01" "023" "01" "01" "022" "021"
#> 1772116-064_C05 1772099-238_B03 1772099-241_F03 1772099-259_A06 1772116-062_A12 1772116-062_E10
#> "01" "01" "01" "01" "01" "021"
#> 1772099-262_B12 1772099-241_E05 1772099-241_G08 1772099-262_E01 1772099-259_C12 1772099-258_C01
#> "01" "01" "01" "01" "01" "021"
#> 1772099-240_D02 1772099-259_G04 1772116-060_H06 1772099-240_C03 1772099-260_C03 1772099-238_E12
#> "021" "01" "01" "01" "021" "01"
#> 1772116-063_A09 1772099-260_C06 1772099-238_C01 1772099-240_F07 1772099-241_G09 1772116-063_G02
#> "022" "022" "021" "022" "023" "023"
#> 1772099-259_H03
#> "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1473))
#> 1772099-259_E02 1772116-063_D07 1772116-060_E02 1772116-063_E05 1772099-259_C09 1772116-060_A08
#> "01" "02" "02" "02" "02" "02"
#> 1772099-259_F01 1772099-258_H10 1772099-259_A03 1772099-238_A02 1772116-060_C01 1772099-259_C10
#> "01" "02" "01" "02" "01" "01"
#> 1772099-241_A06 1772099-241_D11 1772116-063_B01 1772099-258_H03 1772116-063_H12 1772099-262_G05
#> "02" "02" "02" "02" "02" "02"
#> 1772099-258_E05 1772099-241_G05 1772116-064_C11 1772116-064_E06 1772099-258_H06 1772116-064_A04
#> "02" "01" "02" "02" "01" "01"
#> 1772099-260_D12 1772099-258_B02 1772116-063_E12 1772099-259_F02 1772099-258_G02 1772116-063_E07
#> "01" "02" "02" "02" "02" "02"
#> 1772099-258_G11 1772116-062_A05 1772116-063_G12 1772099-262_H06 1772116-062_D10 1772116-062_H09
#> "02" "01" "02" "01" "01" "02"
#> 1772116-064_H09 1772116-064_G07 1772099-262_B04 1772099-258_C04 1772116-060_C03 1772116-060_G07
#> "02" "01" "02" "02" "02" "01"
#> 1772099-259_A09 1772116-062_A01 1772116-063_B11 1772116-063_A04 1772116-062_H06 1772116-063_E09
#> "01" "02" "02" "02" "02" "01"
#> 1772116-062_A07 1772116-060_D01 1772099-258_F03 1772116-060_D04 1772116-062_E05 1772116-062_D09
#> "02" "02" "02" "02" "02" "01"
#> 1772099-260_F12 1772116-062_A10 1772116-062_B09 1772099-262_D04 1772116-062_G10 1772116-060_C04
#> "01" "02" "02" "02" "02" "02"
#> 1772116-062_A09 1772099-262_H02 1772099-258_D06 1772116-062_G04 1772116-063_B10 1772116-063_B03
#> "02" "02" "02" "02" "01" "02"
#> 1772099-241_B09 1772116-064_E05 1772116-064_C08 1772099-258_G06 1772116-060_G08 1772116-062_G06
#> "01" "01" "02" "02" "02" "02"
#> 1772116-060_F07 1772099-241_A02 1772116-064_F11 1772116-062_H11 1772099-258_G08 1772116-064_E07
#> "02" "01" "02" "02" "02" "02"
#> 1772099-238_D07 1772116-063_D04 1772116-062_E07 1772116-063_F10 1772099-238_C02 1772099-262_E11
#> "02" "02" "02" "01" "02" "02"
#> 1772116-060_D07 1772116-060_G02 1772116-060_A12 1772116-060_D05 1772116-060_C08 1772116-060_E09
#> "02" "02" "02" "02" "02" "02"
#> 1772116-063_B09 1772116-062_F06 1772099-238_A10 1772099-260_H06 1772116-060_C02 1772116-062_E09
#> "01" "02" "02" "02" "02" "01"
#> 1772116-060_F09 1772116-060_D10 1772116-063_F04 1772116-064_C10 1772116-063_A07 1772099-260_E06
#> "02" "01" "02" "01" "02" "02"
#> 1772099-260_F11 1772116-062_C12 1772099-237_G01 1772099-258_H02 1772116-063_D11 1772099-240_G05
#> "02" "01" "01" "02" "02" "02"
#> 1772116-063_C11 1772116-064_A01 1772116-063_E10 1772116-064_D03 1772116-060_C09 1772116-064_B07
#> "02" "02" "02" "02" "02" "02"
#> 1772116-064_H02 1772099-237_G06 1772116-062_A11 1772116-060_B11 1772116-063_C04 1772116-062_F09
#> "02" "02" "02" "02" "02" "02"
#> 1772116-064_D02 1772116-064_B09 1772116-064_C04 1772099-259_D07 1772099-238_C07 1772116-063_A11
#> "02" "02" "02" "01" "02" "01"
#> 1772116-063_E04 1772116-062_F05 1772099-241_A10 1772099-238_F07 1772116-062_H03 1772116-063_B04
#> "02" "01" "01" "01" "01" "01"
#> 1772116-060_A11 1772116-062_B11 1772116-060_B02 1772099-238_A09 1772116-060_B01 1772116-060_E03
#> "01" "02" "01" "02" "02" "02"
#> 1772099-260_F07 1772116-064_H03 1772116-062_E04 1772116-063_C12 1772116-064_G08 1772116-063_H02
#> "01" "01" "02" "01" "01" "02"
#> 1772099-259_F10 1772116-063_F11 1772099-259_G08 1772116-060_F01 1772116-060_B10 1772099-259_C03
#> "01" "02" "01" "02" "02" "01"
#> 1772099-262_B10 1772099-241_F08 1772099-240_A09 1772099-240_D01 1772099-240_D07 1772116-064_B01
#> "01" "01" "01" "01" "01" "01"
#> 1772116-063_A05 1772099-241_F07 1772099-238_A08 1772099-237_B07 1772116-063_C06 1772116-062_H05
#> "01" "01" "01" "01" "01" "01"
#> 1772116-062_B05 1772116-064_B06 1772116-062_B12 1772099-260_D08 1772116-064_F06 1772116-063_F12
#> "01" "01" "01" "01" "01" "01"
#> 1772116-063_G10 1772116-062_C08 1772116-064_D10 1772116-060_H08 1772099-262_C05 1772116-062_D06
#> "01" "01" "01" "02" "01" "01"
#> 1772099-238_H11 1772099-260_A01 1772099-241_H05 1772099-262_F04 1772099-262_D11 1772099-241_C09
#> "01" "01" "02" "01" "01" "01"
#> 1772099-238_G08 1772099-260_H08 1772099-241_C12 1772099-259_C11 1772116-060_B09 1772116-064_D06
#> "01" "01" "01" "01" "01" "01"
#> 1772116-064_B03 1772116-063_E06 1772116-060_A01 1772099-262_B01 1772116-064_A07 1772099-262_C02
#> "01" "01" "01" "01" "01" "01"
#> 1772099-260_G11 1772116-060_C12 1772099-262_G10 1772116-062_B01 1772116-064_B08 1772116-063_B06
#> "01" "01" "01" "01" "01" "02"
#> 1772116-064_C03 1772099-258_F05 1772099-262_F05 1772099-258_A08 1772116-062_F10 1772099-240_G08
#> "01" "01" "01" "01" "01" "01"
#> 1772116-062_D03 1772116-062_F04 1772099-258_E08 1772116-064_D05 1772116-063_H04 1772116-063_C03
#> "01" "01" "01" "01" "01" "01"
#> 1772116-064_E03 1772099-260_C01 1772099-238_C12 1772116-064_D09 1772116-062_E12 1772116-063_G01
#> "01" "01" "01" "01" "01" "01"
#> 1772099-262_H01 1772099-262_F06 1772116-062_D05 1772099-237_E03 1772116-062_B10 1772099-258_G12
#> "01" "01" "01" "01" "01" "01"
#> 1772116-060_C10 1772099-258_D09 1772099-260_H05 1772116-060_A03 1772116-060_E01 1772116-063_A01
#> "01" "02" "01" "01" "01" "01"
#> 1772099-241_E10 1772116-064_F07 1772116-062_C01 1772099-262_G12 1772116-064_F05 1772116-062_G12
#> "01" "01" "01" "01" "01" "01"
#> 1772116-063_D10 1772116-062_C09 1772116-064_E12 1772116-062_H08 1772116-060_G03 1772099-262_C10
#> "01" "01" "01" "01" "01" "01"
#> 1772116-064_D01 1772116-064_D08 1772099-259_D11 1772116-060_E08 1772116-062_F12 1772116-063_H11
#> "01" "01" "01" "01" "01" "02"
#> 1772116-062_C10 1772099-240_H02 1772099-260_A07 1772116-060_D12 1772099-259_C04 1772099-258_B10
#> "02" "02" "02" "01" "02" "01"
#> 1772116-062_F01 1772116-060_E11 1772099-262_B11 1772116-063_D12 1772116-063_H05 1772116-060_A04
#> "02" "02" "02" "01" "02" "01"
#> 1772116-064_B04 1772099-260_B06 1772116-063_F02 1772099-258_B06 1772116-064_F03 1772099-262_C01
#> "02" "02" "01" "02" "01" "01"
#> 1772099-258_F12 1772099-237_H01 1772099-258_D08 1772099-260_H04 1772116-062_E01 1772099-262_A02
#> "01" "01" "01" "01" "01" "02"
#> 1772099-260_A04 1772099-262_G01 1772099-258_B05 1772099-238_F03 1772099-262_F12 1772099-258_D01
#> "01" "01" "01" "02" "01" "01"
#> 1772116-060_F06 1772099-241_H12 1772116-062_G05 1772116-060_G01 1772116-060_B06 1772099-241_H06
#> "01" "01" "02" "02" "02" "02"
#> 1772116-062_B06 1772116-062_D11 1772116-064_E09 1772116-062_E08 1772099-262_H12 1772099-237_D03
#> "02" "02" "02" "02" "01" "01"
#> 1772116-060_H02 1772116-062_C05 1772116-064_C07 1772116-060_A05 1772099-262_D02 1772099-258_C06
#> "02" "01" "02" "02" "02" "02"
#> 1772099-258_F06 1772099-260_A02 1772099-258_C03 1772099-237_F01 1772116-064_F09 1772099-238_H06
#> "02" "02" "02" "02" "01" "01"
#> 1772099-238_H10 1772099-258_G04 1772116-060_F08 1772116-063_A02 1772116-062_D01 1772116-064_C09
#> "02" "02" "01" "01" "01" "01"
#> 1772099-262_D06 1772099-258_G09 1772099-259_G11 1772116-064_B10 1772116-062_F02 1772099-262_F11
#> "01" "02" "01" "01" "02" "02"
#> 1772116-064_C05 1772099-238_B03 1772099-241_F03 1772099-259_A06 1772116-062_A12 1772116-062_E10
#> "01" "01" "01" "01" "01" "02"
#> 1772099-262_B12 1772099-241_E05 1772099-241_G08 1772099-262_E01 1772099-259_C12 1772099-258_C01
#> "01" "01" "01" "01" "01" "02"
#> 1772099-240_D02 1772099-259_G04 1772116-060_H06 1772099-240_C03 1772099-260_C03 1772099-238_E12
#> "02" "01" "01" "01" "02" "01"
#> 1772116-063_A09 1772099-260_C06 1772099-238_C01 1772099-240_F07 1772099-241_G09 1772116-063_G02
#> "02" "02" "02" "02" "02" "02"
#> 1772099-259_H03
#> "01"
Heatmaps of the top rows:
top_rows_heatmap(res_rh)
Top rows on each node:
top_rows_overlap(res_rh, method = "upset")
UMAP plot which shows how samples are separated.
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 289),
method = "UMAP", top_value_method = "SD", top_n = 800, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 289),
method = "UMAP", top_value_method = "ATC", top_n = 800, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1372),
method = "UMAP", top_value_method = "SD", top_n = 800, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1372),
method = "UMAP", top_value_method = "ATC", top_n = 800, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1473),
method = "UMAP", top_value_method = "SD", top_n = 800, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1473),
method = "UMAP", top_value_method = "ATC", top_n = 800, scale_rows = TRUE)
Signatures on the heatmap are the union of all signatures found on every node on the hierarchy. The number of k-means on rows are automatically selected by the function.
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 289))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1372))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1473))
Compare signatures from different nodes:
compare_signatures(res_rh, verbose = FALSE)
If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs. Note it only works on every node and the final signatures
are the union of all signatures of all nodes.
# code only for demonstration
# e.g. to show the top 500 most significant rows on each node.
tb = get_signature(res_rh, top_signatures = 500)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res_rh, merge_node = merge_node_param(min_n_signatures = 289))
#> Cell_type Timepoint
#> class 3.75e-15 0.243
test_to_known_factors(res_rh, merge_node = merge_node_param(min_n_signatures = 1372))
#> Cell_type Timepoint
#> class 4.01e-14 0.163
test_to_known_factors(res_rh, merge_node = merge_node_param(min_n_signatures = 1473))
#> Cell_type Timepoint
#> class 1.18e-18 0.0954
Child nodes: Node01 , Node02 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4.
#> On a matrix with 5724 rows and 337 columns.
#> Top rows (572) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 150 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.977 0.991 0.499 0.502 0.502
#> 3 3 0.880 0.898 0.951 0.235 0.853 0.715
#> 4 4 0.769 0.782 0.896 0.102 0.916 0.783
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is 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 subgroup
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
#> 1772099-259_E02 1 0.000 0.989 1.00 0.00
#> 1772116-063_D07 2 0.000 0.992 0.00 1.00
#> 1772116-060_E02 2 0.000 0.992 0.00 1.00
#> 1772116-063_E05 2 0.000 0.992 0.00 1.00
#> 1772099-259_C09 2 0.000 0.992 0.00 1.00
#> 1772116-060_A08 2 0.000 0.992 0.00 1.00
#> 1772099-259_F01 1 0.000 0.989 1.00 0.00
#> 1772099-258_H10 2 0.000 0.992 0.00 1.00
#> 1772099-259_A03 1 0.000 0.989 1.00 0.00
#> 1772099-238_A02 2 0.000 0.992 0.00 1.00
#> 1772116-060_C01 1 0.000 0.989 1.00 0.00
#> 1772099-259_C10 1 0.000 0.989 1.00 0.00
#> 1772099-241_A06 2 0.000 0.992 0.00 1.00
#> 1772099-241_D11 2 0.000 0.992 0.00 1.00
#> 1772116-063_B01 2 0.000 0.992 0.00 1.00
#> 1772099-258_H03 2 0.402 0.911 0.08 0.92
#> 1772116-063_H12 2 0.000 0.992 0.00 1.00
#> 1772099-262_G05 2 0.000 0.992 0.00 1.00
#> 1772099-258_E05 2 0.529 0.864 0.12 0.88
#> 1772099-241_G05 1 0.000 0.989 1.00 0.00
#> 1772116-064_C11 2 0.000 0.992 0.00 1.00
#> 1772116-064_E06 2 0.402 0.911 0.08 0.92
#> 1772099-258_H06 1 0.000 0.989 1.00 0.00
#> 1772116-064_A04 1 0.327 0.931 0.94 0.06
#> 1772099-260_D12 1 0.000 0.989 1.00 0.00
#> 1772099-258_B02 2 0.000 0.992 0.00 1.00
#> 1772116-063_E12 2 0.000 0.992 0.00 1.00
#> 1772099-259_F02 2 0.000 0.992 0.00 1.00
#> 1772099-258_G02 2 0.000 0.992 0.00 1.00
#> 1772116-063_E07 2 0.000 0.992 0.00 1.00
#> 1772099-258_G11 2 0.000 0.992 0.00 1.00
#> 1772116-062_A05 1 0.000 0.989 1.00 0.00
#> 1772116-063_G12 2 0.000 0.992 0.00 1.00
#> 1772099-262_H06 1 0.000 0.989 1.00 0.00
#> 1772116-062_D10 1 0.000 0.989 1.00 0.00
#> 1772116-062_H09 2 0.000 0.992 0.00 1.00
#> 1772116-064_H09 2 0.000 0.992 0.00 1.00
#> 1772116-064_G07 1 0.000 0.989 1.00 0.00
#> 1772099-262_B04 2 0.000 0.992 0.00 1.00
#> 1772099-258_C04 2 0.000 0.992 0.00 1.00
#> 1772116-060_C03 2 0.000 0.992 0.00 1.00
#> 1772116-060_G07 1 0.000 0.989 1.00 0.00
#> 1772099-259_A09 1 0.000 0.989 1.00 0.00
#> 1772116-062_A01 2 0.000 0.992 0.00 1.00
#> 1772116-063_B11 2 0.000 0.992 0.00 1.00
#> 1772116-063_A04 2 0.000 0.992 0.00 1.00
#> 1772116-062_H06 2 0.000 0.992 0.00 1.00
#> 1772116-063_E09 1 0.327 0.930 0.94 0.06
#> 1772116-062_A07 2 0.000 0.992 0.00 1.00
#> 1772116-060_D01 2 0.000 0.992 0.00 1.00
#> 1772099-258_F03 2 0.000 0.992 0.00 1.00
#> 1772116-060_D04 2 0.000 0.992 0.00 1.00
#> 1772116-062_E05 2 0.000 0.992 0.00 1.00
#> 1772116-062_D09 1 0.000 0.989 1.00 0.00
#> 1772099-260_F12 1 0.000 0.989 1.00 0.00
#> 1772116-062_A10 2 0.000 0.992 0.00 1.00
#> 1772116-062_B09 2 0.000 0.992 0.00 1.00
#> 1772099-262_D04 2 0.000 0.992 0.00 1.00
#> 1772116-062_G10 2 0.000 0.992 0.00 1.00
#> 1772116-060_C04 2 0.327 0.933 0.06 0.94
#> 1772116-062_A09 2 0.000 0.992 0.00 1.00
#> 1772099-262_H02 2 0.000 0.992 0.00 1.00
#> 1772099-258_D06 2 0.000 0.992 0.00 1.00
#> 1772116-062_G04 2 0.000 0.992 0.00 1.00
#> 1772116-063_B10 1 0.402 0.909 0.92 0.08
#> 1772116-063_B03 2 0.000 0.992 0.00 1.00
#> 1772099-241_B09 1 0.000 0.989 1.00 0.00
#> 1772116-064_E05 1 0.000 0.989 1.00 0.00
#> 1772116-064_C08 2 0.584 0.837 0.14 0.86
#> 1772099-258_G06 2 0.000 0.992 0.00 1.00
#> 1772116-060_G08 2 0.000 0.992 0.00 1.00
#> 1772116-062_G06 2 0.000 0.992 0.00 1.00
#> 1772116-060_F07 2 0.000 0.992 0.00 1.00
#> 1772099-241_A02 1 0.000 0.989 1.00 0.00
#> 1772116-064_F11 2 0.000 0.992 0.00 1.00
#> 1772116-062_H11 2 0.000 0.992 0.00 1.00
#> 1772099-258_G08 2 0.000 0.992 0.00 1.00
#> 1772116-064_E07 2 0.000 0.992 0.00 1.00
#> 1772099-238_D07 2 0.000 0.992 0.00 1.00
#> 1772116-063_D04 2 0.000 0.992 0.00 1.00
#> 1772116-062_E07 2 0.000 0.992 0.00 1.00
#> 1772116-063_F10 1 0.000 0.989 1.00 0.00
#> 1772099-238_C02 2 0.000 0.992 0.00 1.00
#> 1772099-262_E11 2 0.000 0.992 0.00 1.00
#> 1772116-060_D07 2 0.000 0.992 0.00 1.00
#> 1772116-060_G02 2 0.000 0.992 0.00 1.00
#> 1772116-060_A12 2 0.000 0.992 0.00 1.00
#> 1772116-060_D05 2 0.000 0.992 0.00 1.00
#> 1772116-060_C08 2 0.000 0.992 0.00 1.00
#> 1772116-060_E09 2 0.000 0.992 0.00 1.00
#> 1772116-063_B09 1 0.000 0.989 1.00 0.00
#> 1772116-062_F06 2 0.000 0.992 0.00 1.00
#> 1772099-238_A10 2 0.000 0.992 0.00 1.00
#> 1772099-260_H06 2 0.000 0.992 0.00 1.00
#> 1772116-060_C02 2 0.000 0.992 0.00 1.00
#> 1772116-062_E09 1 0.000 0.989 1.00 0.00
#> 1772116-060_F09 2 0.000 0.992 0.00 1.00
#> 1772116-060_D10 1 0.000 0.989 1.00 0.00
#> 1772116-063_F04 2 0.000 0.992 0.00 1.00
#> 1772116-064_C10 1 0.000 0.989 1.00 0.00
#> 1772116-063_A07 2 0.000 0.992 0.00 1.00
#> 1772099-260_E06 2 0.402 0.911 0.08 0.92
#> 1772099-260_F11 2 0.000 0.992 0.00 1.00
#> 1772116-062_C12 1 0.000 0.989 1.00 0.00
#> 1772099-237_G01 1 0.000 0.989 1.00 0.00
#> 1772099-258_H02 2 0.000 0.992 0.00 1.00
#> 1772116-063_D11 2 0.000 0.992 0.00 1.00
#> 1772099-240_G05 2 0.000 0.992 0.00 1.00
#> 1772116-063_C11 2 0.000 0.992 0.00 1.00
#> 1772116-064_A01 2 0.000 0.992 0.00 1.00
#> 1772116-063_E10 2 0.000 0.992 0.00 1.00
#> 1772116-064_D03 2 0.000 0.992 0.00 1.00
#> 1772116-060_C09 2 0.000 0.992 0.00 1.00
#> 1772116-064_B07 2 0.000 0.992 0.00 1.00
#> 1772116-064_H02 2 0.000 0.992 0.00 1.00
#> 1772099-237_G06 2 0.000 0.992 0.00 1.00
#> 1772116-062_A11 2 0.000 0.992 0.00 1.00
#> 1772116-060_B11 2 0.000 0.992 0.00 1.00
#> 1772116-063_C04 2 0.000 0.992 0.00 1.00
#> 1772116-062_F09 2 0.000 0.992 0.00 1.00
#> 1772116-064_D02 2 0.000 0.992 0.00 1.00
#> 1772116-064_B09 2 0.990 0.207 0.44 0.56
#> 1772116-064_C04 2 0.000 0.992 0.00 1.00
#> 1772099-259_D07 1 0.000 0.989 1.00 0.00
#> 1772099-238_C07 2 0.000 0.992 0.00 1.00
#> 1772116-063_A11 1 0.000 0.989 1.00 0.00
#> 1772116-063_E04 2 0.000 0.992 0.00 1.00
#> 1772116-062_F05 1 0.000 0.989 1.00 0.00
#> 1772099-241_A10 1 0.000 0.989 1.00 0.00
#> 1772099-238_F07 1 0.000 0.989 1.00 0.00
#> 1772116-062_H03 1 0.000 0.989 1.00 0.00
#> 1772116-063_B04 1 0.795 0.687 0.76 0.24
#> 1772116-060_A11 1 0.000 0.989 1.00 0.00
#> 1772116-062_B11 2 0.000 0.992 0.00 1.00
#> 1772116-060_B02 1 0.141 0.970 0.98 0.02
#> 1772099-238_A09 2 0.000 0.992 0.00 1.00
#> 1772116-060_B01 2 0.000 0.992 0.00 1.00
#> 1772116-060_E03 2 0.000 0.992 0.00 1.00
#> 1772099-260_F07 1 0.000 0.989 1.00 0.00
#> 1772116-064_H03 1 0.000 0.989 1.00 0.00
#> 1772116-062_E04 2 0.000 0.992 0.00 1.00
#> 1772116-063_C12 1 0.000 0.989 1.00 0.00
#> 1772116-064_G08 1 0.000 0.989 1.00 0.00
#> 1772116-063_H02 2 0.000 0.992 0.00 1.00
#> 1772099-259_F10 1 0.000 0.989 1.00 0.00
#> 1772116-063_F11 2 0.000 0.992 0.00 1.00
#> 1772099-259_G08 1 0.000 0.989 1.00 0.00
#> 1772116-060_F01 2 0.000 0.992 0.00 1.00
#> 1772116-060_B10 2 0.000 0.992 0.00 1.00
#> 1772099-259_C03 1 0.000 0.989 1.00 0.00
#> 1772099-262_B10 1 0.000 0.989 1.00 0.00
#> 1772099-241_F08 1 0.000 0.989 1.00 0.00
#> 1772099-240_A09 1 0.000 0.989 1.00 0.00
#> 1772099-240_D01 1 0.141 0.970 0.98 0.02
#> 1772099-240_D07 1 0.000 0.989 1.00 0.00
#> 1772116-064_B01 1 0.000 0.989 1.00 0.00
#> 1772116-063_A05 1 0.000 0.989 1.00 0.00
#> 1772099-241_F07 1 0.000 0.989 1.00 0.00
#> 1772099-238_A08 1 0.000 0.989 1.00 0.00
#> 1772099-237_B07 1 0.000 0.989 1.00 0.00
#> 1772116-063_C06 1 0.000 0.989 1.00 0.00
#> 1772116-062_H05 1 0.000 0.989 1.00 0.00
#> 1772116-062_B05 1 0.000 0.989 1.00 0.00
#> 1772116-064_B06 1 0.000 0.989 1.00 0.00
#> 1772116-062_B12 1 0.000 0.989 1.00 0.00
#> 1772099-260_D08 1 0.000 0.989 1.00 0.00
#> 1772116-064_F06 1 0.000 0.989 1.00 0.00
#> 1772116-063_F12 1 0.000 0.989 1.00 0.00
#> 1772116-063_G10 1 0.000 0.989 1.00 0.00
#> 1772116-062_C08 1 0.000 0.989 1.00 0.00
#> 1772116-064_D10 1 0.000 0.989 1.00 0.00
#> 1772116-060_H08 2 0.000 0.992 0.00 1.00
#> 1772099-262_C05 1 0.000 0.989 1.00 0.00
#> 1772116-062_D06 1 0.000 0.989 1.00 0.00
#> 1772099-238_H11 1 0.000 0.989 1.00 0.00
#> 1772099-260_A01 1 0.000 0.989 1.00 0.00
#> 1772099-241_H05 2 0.000 0.992 0.00 1.00
#> 1772099-262_F04 1 0.000 0.989 1.00 0.00
#> 1772099-262_D11 1 0.000 0.989 1.00 0.00
#> 1772099-241_C09 1 0.000 0.989 1.00 0.00
#> 1772099-238_G08 1 0.000 0.989 1.00 0.00
#> 1772099-260_H08 1 0.000 0.989 1.00 0.00
#> 1772099-241_C12 1 0.000 0.989 1.00 0.00
#> 1772099-259_C11 1 0.000 0.989 1.00 0.00
#> 1772116-060_B09 1 0.000 0.989 1.00 0.00
#> 1772116-064_D06 1 0.000 0.989 1.00 0.00
#> 1772116-064_B03 1 0.000 0.989 1.00 0.00
#> 1772116-063_E06 1 0.000 0.989 1.00 0.00
#> 1772116-060_A01 1 0.000 0.989 1.00 0.00
#> 1772099-262_B01 1 0.000 0.989 1.00 0.00
#> 1772116-064_A07 1 0.000 0.989 1.00 0.00
#> 1772099-262_C02 1 0.000 0.989 1.00 0.00
#> 1772099-260_G11 1 0.000 0.989 1.00 0.00
#> 1772116-060_C12 1 0.000 0.989 1.00 0.00
#> 1772099-262_G10 1 0.000 0.989 1.00 0.00
#> 1772116-062_B01 1 0.000 0.989 1.00 0.00
#> 1772116-064_B08 1 0.000 0.989 1.00 0.00
#> 1772116-063_B06 2 0.000 0.992 0.00 1.00
#> 1772116-064_C03 1 0.000 0.989 1.00 0.00
#> 1772099-258_F05 1 0.000 0.989 1.00 0.00
#> 1772099-262_F05 1 0.000 0.989 1.00 0.00
#> 1772099-258_A08 1 0.000 0.989 1.00 0.00
#> 1772116-062_F10 1 0.000 0.989 1.00 0.00
#> 1772099-240_G08 1 0.000 0.989 1.00 0.00
#> 1772116-062_D03 1 0.000 0.989 1.00 0.00
#> 1772116-062_F04 1 0.000 0.989 1.00 0.00
#> 1772099-258_E08 1 0.000 0.989 1.00 0.00
#> 1772116-064_D05 1 0.000 0.989 1.00 0.00
#> 1772116-063_H04 1 0.855 0.616 0.72 0.28
#> 1772116-063_C03 1 0.000 0.989 1.00 0.00
#> 1772116-064_E03 1 0.000 0.989 1.00 0.00
#> 1772099-260_C01 1 0.000 0.989 1.00 0.00
#> 1772099-238_C12 1 0.000 0.989 1.00 0.00
#> 1772116-064_D09 1 0.000 0.989 1.00 0.00
#> 1772116-062_E12 1 0.000 0.989 1.00 0.00
#> 1772116-063_G01 1 0.000 0.989 1.00 0.00
#> 1772099-262_H01 1 0.000 0.989 1.00 0.00
#> 1772099-262_F06 1 0.000 0.989 1.00 0.00
#> 1772116-062_D05 1 0.000 0.989 1.00 0.00
#> 1772099-237_E03 1 0.000 0.989 1.00 0.00
#> 1772116-062_B10 1 0.000 0.989 1.00 0.00
#> 1772099-258_G12 1 0.000 0.989 1.00 0.00
#> 1772116-060_C10 1 0.000 0.989 1.00 0.00
#> 1772099-258_D09 2 0.000 0.992 0.00 1.00
#> 1772099-260_H05 1 0.000 0.989 1.00 0.00
#> 1772116-060_A03 1 0.000 0.989 1.00 0.00
#> 1772116-060_E01 1 0.000 0.989 1.00 0.00
#> 1772116-063_A01 1 0.000 0.989 1.00 0.00
#> 1772099-241_E10 1 0.000 0.989 1.00 0.00
#> 1772116-064_F07 1 0.000 0.989 1.00 0.00
#> 1772116-062_C01 1 0.000 0.989 1.00 0.00
#> 1772099-262_G12 1 0.000 0.989 1.00 0.00
#> 1772116-064_F05 1 0.000 0.989 1.00 0.00
#> 1772116-062_G12 1 0.000 0.989 1.00 0.00
#> 1772116-063_D10 1 0.000 0.989 1.00 0.00
#> 1772116-062_C09 1 0.000 0.989 1.00 0.00
#> 1772116-064_E12 1 0.000 0.989 1.00 0.00
#> 1772116-062_H08 1 0.000 0.989 1.00 0.00
#> 1772116-060_G03 1 0.000 0.989 1.00 0.00
#> 1772099-262_C10 1 0.000 0.989 1.00 0.00
#> 1772116-064_D01 1 0.000 0.989 1.00 0.00
#> 1772116-064_D08 1 0.000 0.989 1.00 0.00
#> 1772099-259_D11 1 0.000 0.989 1.00 0.00
#> 1772116-060_E08 1 0.000 0.989 1.00 0.00
#> 1772116-062_F12 1 0.000 0.989 1.00 0.00
#> 1772116-063_H11 2 0.000 0.992 0.00 1.00
#> 1772116-062_C10 2 0.000 0.992 0.00 1.00
#> 1772099-240_H02 2 0.000 0.992 0.00 1.00
#> 1772099-260_A07 2 0.000 0.992 0.00 1.00
#> 1772116-060_D12 1 0.000 0.989 1.00 0.00
#> 1772099-259_C04 2 0.000 0.992 0.00 1.00
#> 1772099-258_B10 1 0.000 0.989 1.00 0.00
#> 1772116-062_F01 2 0.000 0.992 0.00 1.00
#> 1772116-060_E11 2 0.000 0.992 0.00 1.00
#> 1772099-262_B11 2 0.000 0.992 0.00 1.00
#> 1772116-063_D12 1 0.000 0.989 1.00 0.00
#> 1772116-063_H05 2 0.000 0.992 0.00 1.00
#> 1772116-060_A04 1 0.000 0.989 1.00 0.00
#> 1772116-064_B04 2 0.000 0.992 0.00 1.00
#> 1772099-260_B06 2 0.000 0.992 0.00 1.00
#> 1772116-063_F02 1 0.995 0.151 0.54 0.46
#> 1772099-258_B06 2 0.000 0.992 0.00 1.00
#> 1772116-064_F03 1 0.000 0.989 1.00 0.00
#> 1772099-262_C01 1 0.000 0.989 1.00 0.00
#> 1772099-258_F12 1 0.000 0.989 1.00 0.00
#> 1772099-237_H01 1 0.000 0.989 1.00 0.00
#> 1772099-258_D08 1 0.000 0.989 1.00 0.00
#> 1772099-260_H04 1 0.000 0.989 1.00 0.00
#> 1772116-062_E01 1 0.000 0.989 1.00 0.00
#> 1772099-262_A02 2 0.680 0.782 0.18 0.82
#> 1772099-260_A04 1 0.000 0.989 1.00 0.00
#> 1772099-262_G01 1 0.000 0.989 1.00 0.00
#> 1772099-258_B05 1 0.000 0.989 1.00 0.00
#> 1772099-238_F03 2 0.000 0.992 0.00 1.00
#> 1772099-262_F12 1 0.000 0.989 1.00 0.00
#> 1772099-258_D01 1 0.000 0.989 1.00 0.00
#> 1772116-060_F06 1 0.000 0.989 1.00 0.00
#> 1772099-241_H12 1 0.634 0.810 0.84 0.16
#> 1772116-062_G05 2 0.000 0.992 0.00 1.00
#> 1772116-060_G01 2 0.000 0.992 0.00 1.00
#> 1772116-060_B06 2 0.000 0.992 0.00 1.00
#> 1772099-241_H06 2 0.000 0.992 0.00 1.00
#> 1772116-062_B06 2 0.000 0.992 0.00 1.00
#> 1772116-062_D11 2 0.000 0.992 0.00 1.00
#> 1772116-064_E09 2 0.000 0.992 0.00 1.00
#> 1772116-062_E08 2 0.000 0.992 0.00 1.00
#> 1772099-262_H12 1 0.000 0.989 1.00 0.00
#> 1772099-237_D03 1 0.000 0.989 1.00 0.00
#> 1772116-060_H02 2 0.000 0.992 0.00 1.00
#> 1772116-062_C05 1 0.760 0.720 0.78 0.22
#> 1772116-064_C07 2 0.000 0.992 0.00 1.00
#> 1772116-060_A05 2 0.000 0.992 0.00 1.00
#> 1772099-262_D02 2 0.000 0.992 0.00 1.00
#> 1772099-258_C06 2 0.000 0.992 0.00 1.00
#> 1772099-258_F06 2 0.000 0.992 0.00 1.00
#> 1772099-260_A02 2 0.000 0.992 0.00 1.00
#> 1772099-258_C03 2 0.000 0.992 0.00 1.00
#> 1772099-237_F01 2 0.141 0.973 0.02 0.98
#> 1772116-064_F09 1 0.000 0.989 1.00 0.00
#> 1772099-238_H06 1 0.000 0.989 1.00 0.00
#> 1772099-238_H10 2 0.000 0.992 0.00 1.00
#> 1772099-258_G04 2 0.000 0.992 0.00 1.00
#> 1772116-060_F08 1 0.000 0.989 1.00 0.00
#> 1772116-063_A02 1 0.000 0.989 1.00 0.00
#> 1772116-062_D01 1 0.000 0.989 1.00 0.00
#> 1772116-064_C09 1 0.000 0.989 1.00 0.00
#> 1772099-262_D06 1 0.000 0.989 1.00 0.00
#> 1772099-258_G09 2 0.000 0.992 0.00 1.00
#> 1772099-259_G11 1 0.000 0.989 1.00 0.00
#> 1772116-064_B10 1 0.000 0.989 1.00 0.00
#> 1772116-062_F02 2 0.000 0.992 0.00 1.00
#> 1772099-262_F11 2 0.000 0.992 0.00 1.00
#> 1772116-064_C05 1 0.000 0.989 1.00 0.00
#> 1772099-238_B03 1 0.943 0.441 0.64 0.36
#> 1772099-241_F03 1 0.000 0.989 1.00 0.00
#> 1772099-259_A06 1 0.000 0.989 1.00 0.00
#> 1772116-062_A12 1 0.000 0.989 1.00 0.00
#> 1772116-062_E10 2 0.000 0.992 0.00 1.00
#> 1772099-262_B12 1 0.000 0.989 1.00 0.00
#> 1772099-241_E05 1 0.000 0.989 1.00 0.00
#> 1772099-241_G08 1 0.000 0.989 1.00 0.00
#> 1772099-262_E01 1 0.000 0.989 1.00 0.00
#> 1772099-259_C12 1 0.000 0.989 1.00 0.00
#> 1772099-258_C01 2 0.000 0.992 0.00 1.00
#> 1772099-240_D02 2 0.000 0.992 0.00 1.00
#> 1772099-259_G04 1 0.000 0.989 1.00 0.00
#> 1772116-060_H06 1 0.000 0.989 1.00 0.00
#> 1772099-240_C03 1 0.242 0.951 0.96 0.04
#> 1772099-260_C03 2 0.000 0.992 0.00 1.00
#> 1772099-238_E12 1 0.000 0.989 1.00 0.00
#> 1772116-063_A09 2 0.000 0.992 0.00 1.00
#> 1772099-260_C06 2 0.000 0.992 0.00 1.00
#> 1772099-238_C01 2 0.000 0.992 0.00 1.00
#> 1772099-240_F07 2 0.000 0.992 0.00 1.00
#> 1772099-241_G09 2 0.000 0.992 0.00 1.00
#> 1772116-063_G02 2 0.000 0.992 0.00 1.00
#> 1772099-259_H03 1 0.000 0.989 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> 1772099-259_E02 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_D07 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-060_E02 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-063_E05 2 0.5016 0.6285 0.00 0.76 0.24
#> 1772099-259_C09 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-060_A08 3 0.6045 0.5226 0.00 0.38 0.62
#> 1772099-259_F01 1 0.1529 0.9503 0.96 0.00 0.04
#> 1772099-258_H10 2 0.4002 0.7697 0.00 0.84 0.16
#> 1772099-259_A03 1 0.6244 0.2552 0.56 0.00 0.44
#> 1772099-238_A02 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-060_C01 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-259_C10 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-241_A06 2 0.0892 0.9424 0.00 0.98 0.02
#> 1772099-241_D11 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-063_B01 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-258_H03 2 0.5643 0.6757 0.02 0.76 0.22
#> 1772116-063_H12 3 0.1529 0.8312 0.00 0.04 0.96
#> 1772099-262_G05 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-258_E05 3 0.0000 0.8246 0.00 0.00 1.00
#> 1772099-241_G05 1 0.4002 0.8261 0.84 0.00 0.16
#> 1772116-064_C11 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-064_E06 3 0.0892 0.8293 0.00 0.02 0.98
#> 1772099-258_H06 1 0.1529 0.9503 0.96 0.00 0.04
#> 1772116-064_A04 1 0.4291 0.7740 0.82 0.00 0.18
#> 1772099-260_D12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-258_B02 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-063_E12 3 0.4291 0.7853 0.00 0.18 0.82
#> 1772099-259_F02 3 0.0000 0.8246 0.00 0.00 1.00
#> 1772099-258_G02 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-063_E07 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-258_G11 2 0.0892 0.9424 0.00 0.98 0.02
#> 1772116-062_A05 3 0.5948 0.3917 0.36 0.00 0.64
#> 1772116-063_G12 3 0.3340 0.8175 0.00 0.12 0.88
#> 1772099-262_H06 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_D10 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_H09 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-064_H09 3 0.0892 0.8287 0.00 0.02 0.98
#> 1772116-064_G07 1 0.2066 0.9347 0.94 0.00 0.06
#> 1772099-262_B04 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-258_C04 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-060_C03 2 0.6280 -0.0477 0.00 0.54 0.46
#> 1772116-060_G07 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-259_A09 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_A01 3 0.3686 0.8079 0.00 0.14 0.86
#> 1772116-063_B11 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-063_A04 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-062_H06 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-063_E09 3 0.6302 0.0664 0.48 0.00 0.52
#> 1772116-062_A07 2 0.0892 0.9421 0.00 0.98 0.02
#> 1772116-060_D01 2 0.4002 0.7654 0.00 0.84 0.16
#> 1772099-258_F03 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-060_D04 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-062_E05 3 0.5216 0.7173 0.00 0.26 0.74
#> 1772116-062_D09 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-260_F12 1 0.0892 0.9658 0.98 0.00 0.02
#> 1772116-062_A10 3 0.2066 0.8306 0.00 0.06 0.94
#> 1772116-062_B09 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-262_D04 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-062_G10 3 0.5706 0.6356 0.00 0.32 0.68
#> 1772116-060_C04 2 0.0892 0.9351 0.02 0.98 0.00
#> 1772116-062_A09 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-262_H02 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-258_D06 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-062_G04 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-063_B10 3 0.5948 0.4353 0.36 0.00 0.64
#> 1772116-063_B03 3 0.1529 0.8312 0.00 0.04 0.96
#> 1772099-241_B09 1 0.1529 0.9503 0.96 0.00 0.04
#> 1772116-064_E05 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-064_C08 3 0.0000 0.8246 0.00 0.00 1.00
#> 1772099-258_G06 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-060_G08 2 0.6244 0.0429 0.00 0.56 0.44
#> 1772116-062_G06 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-060_F07 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-241_A02 1 0.6280 0.2021 0.54 0.00 0.46
#> 1772116-064_F11 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-062_H11 3 0.2959 0.8242 0.00 0.10 0.90
#> 1772099-258_G08 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-064_E07 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-238_D07 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-063_D04 3 0.4796 0.7573 0.00 0.22 0.78
#> 1772116-062_E07 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-063_F10 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-238_C02 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-262_E11 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-060_D07 3 0.5397 0.6954 0.00 0.28 0.72
#> 1772116-060_G02 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-060_A12 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-060_D05 3 0.5560 0.6660 0.00 0.30 0.70
#> 1772116-060_C08 3 0.6280 0.3163 0.00 0.46 0.54
#> 1772116-060_E09 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-063_B09 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_F06 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-238_A10 3 0.0000 0.8246 0.00 0.00 1.00
#> 1772099-260_H06 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-060_C02 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-062_E09 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-060_F09 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-060_D10 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_F04 3 0.3686 0.8000 0.00 0.14 0.86
#> 1772116-064_C10 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_A07 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-260_E06 3 0.0000 0.8246 0.00 0.00 1.00
#> 1772099-260_F11 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-062_C12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-237_G01 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-258_H02 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-063_D11 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-240_G05 3 0.6045 0.5247 0.00 0.38 0.62
#> 1772116-063_C11 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-064_A01 3 0.2537 0.8281 0.00 0.08 0.92
#> 1772116-063_E10 2 0.1529 0.9217 0.00 0.96 0.04
#> 1772116-064_D03 3 0.5835 0.6027 0.00 0.34 0.66
#> 1772116-060_C09 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-064_B07 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-064_H02 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-237_G06 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-062_A11 3 0.5560 0.6680 0.00 0.30 0.70
#> 1772116-060_B11 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-063_C04 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-062_F09 3 0.1529 0.8312 0.00 0.04 0.96
#> 1772116-064_D02 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-064_B09 2 0.4796 0.6106 0.22 0.78 0.00
#> 1772116-064_C04 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-259_D07 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-238_C07 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-063_A11 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_E04 3 0.4555 0.7717 0.00 0.20 0.80
#> 1772116-062_F05 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-241_A10 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-238_F07 1 0.1529 0.9501 0.96 0.00 0.04
#> 1772116-062_H03 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_B04 3 0.0000 0.8246 0.00 0.00 1.00
#> 1772116-060_A11 3 0.5560 0.5352 0.30 0.00 0.70
#> 1772116-062_B11 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-060_B02 3 0.6280 0.0759 0.46 0.00 0.54
#> 1772099-238_A09 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-060_B01 3 0.2959 0.8243 0.00 0.10 0.90
#> 1772116-060_E03 3 0.4555 0.7726 0.00 0.20 0.80
#> 1772099-260_F07 1 0.0892 0.9658 0.98 0.00 0.02
#> 1772116-064_H03 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_E04 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-063_C12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-064_G08 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_H02 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-259_F10 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_F11 3 0.3340 0.8178 0.00 0.12 0.88
#> 1772099-259_G08 1 0.2066 0.9328 0.94 0.00 0.06
#> 1772116-060_F01 3 0.5397 0.6938 0.00 0.28 0.72
#> 1772116-060_B10 3 0.5016 0.7378 0.00 0.24 0.76
#> 1772099-259_C03 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-262_B10 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-241_F08 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-240_A09 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-240_D01 3 0.1529 0.8105 0.04 0.00 0.96
#> 1772099-240_D07 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-064_B01 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_A05 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-241_F07 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-238_A08 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-237_B07 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_C06 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_H05 1 0.1529 0.9501 0.96 0.00 0.04
#> 1772116-062_B05 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-064_B06 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_B12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-260_D08 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-064_F06 3 0.5016 0.6620 0.24 0.00 0.76
#> 1772116-063_F12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_G10 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_C08 1 0.0892 0.9658 0.98 0.00 0.02
#> 1772116-064_D10 1 0.0892 0.9646 0.98 0.00 0.02
#> 1772116-060_H08 3 0.2959 0.8242 0.00 0.10 0.90
#> 1772099-262_C05 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_D06 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-238_H11 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-260_A01 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-241_H05 3 0.2066 0.8314 0.00 0.06 0.94
#> 1772099-262_F04 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-262_D11 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-241_C09 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-238_G08 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-260_H08 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-241_C12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-259_C11 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-060_B09 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-064_D06 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-064_B03 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_E06 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-060_A01 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-262_B01 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-064_A07 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-262_C02 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-260_G11 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-060_C12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-262_G10 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_B01 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-064_B08 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_B06 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-064_C03 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-258_F05 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-262_F05 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-258_A08 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_F10 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-240_G08 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_D03 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_F04 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-258_E08 1 0.0892 0.9658 0.98 0.00 0.02
#> 1772116-064_D05 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_H04 3 0.0000 0.8246 0.00 0.00 1.00
#> 1772116-063_C03 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-064_E03 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-260_C01 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-238_C12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-064_D09 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_E12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_G01 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-262_H01 1 0.2537 0.9142 0.92 0.00 0.08
#> 1772099-262_F06 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_D05 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-237_E03 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_B10 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-258_G12 1 0.0892 0.9658 0.98 0.00 0.02
#> 1772116-060_C10 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-258_D09 3 0.2959 0.8249 0.00 0.10 0.90
#> 1772099-260_H05 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-060_A03 1 0.2537 0.9153 0.92 0.00 0.08
#> 1772116-060_E01 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_A01 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-241_E10 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-064_F07 1 0.4796 0.7172 0.78 0.00 0.22
#> 1772116-062_C01 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-262_G12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-064_F05 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_G12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_D10 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_C09 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-064_E12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_H08 3 0.2066 0.7991 0.06 0.00 0.94
#> 1772116-060_G03 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-262_C10 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-064_D01 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-064_D08 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-259_D11 1 0.4002 0.8247 0.84 0.00 0.16
#> 1772116-060_E08 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_F12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_H11 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-062_C10 3 0.5216 0.7175 0.00 0.26 0.74
#> 1772099-240_H02 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-260_A07 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-060_D12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-259_C04 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-258_B10 1 0.2959 0.8949 0.90 0.00 0.10
#> 1772116-062_F01 3 0.0000 0.8246 0.00 0.00 1.00
#> 1772116-060_E11 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-262_B11 3 0.0000 0.8246 0.00 0.00 1.00
#> 1772116-063_D12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_H05 3 0.5835 0.6018 0.00 0.34 0.66
#> 1772116-060_A04 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-064_B04 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-260_B06 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-063_F02 3 0.0000 0.8246 0.00 0.00 1.00
#> 1772099-258_B06 2 0.1529 0.9218 0.00 0.96 0.04
#> 1772116-064_F03 1 0.6280 0.1938 0.54 0.00 0.46
#> 1772099-262_C01 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-258_F12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-237_H01 1 0.2537 0.9142 0.92 0.00 0.08
#> 1772099-258_D08 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-260_H04 1 0.2959 0.8949 0.90 0.00 0.10
#> 1772116-062_E01 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-262_A02 3 0.0000 0.8246 0.00 0.00 1.00
#> 1772099-260_A04 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-262_G01 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-258_B05 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-238_F03 2 0.6192 0.1297 0.00 0.58 0.42
#> 1772099-262_F12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-258_D01 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-060_F06 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-241_H12 3 0.0000 0.8246 0.00 0.00 1.00
#> 1772116-062_G05 3 0.0892 0.8293 0.00 0.02 0.98
#> 1772116-060_G01 3 0.5016 0.7378 0.00 0.24 0.76
#> 1772116-060_B06 3 0.0892 0.8294 0.00 0.02 0.98
#> 1772099-241_H06 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-062_B06 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-062_D11 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-064_E09 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-062_E08 2 0.5397 0.5673 0.00 0.72 0.28
#> 1772099-262_H12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-237_D03 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-060_H02 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-062_C05 3 0.2537 0.7862 0.08 0.00 0.92
#> 1772116-064_C07 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-060_A05 2 0.4796 0.6667 0.00 0.78 0.22
#> 1772099-262_D02 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-258_C06 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-258_F06 2 0.6045 0.2723 0.00 0.62 0.38
#> 1772099-260_A02 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-258_C03 3 0.1529 0.8318 0.00 0.04 0.96
#> 1772099-237_F01 3 0.0000 0.8246 0.00 0.00 1.00
#> 1772116-064_F09 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-238_H06 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-238_H10 3 0.5397 0.6933 0.00 0.28 0.72
#> 1772099-258_G04 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-060_F08 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_A02 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_D01 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-064_C09 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-262_D06 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-258_G09 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-259_G11 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-064_B10 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_F02 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-262_F11 2 0.0892 0.9422 0.00 0.98 0.02
#> 1772116-064_C05 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-238_B03 3 0.2959 0.7794 0.10 0.00 0.90
#> 1772099-241_F03 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-259_A06 1 0.2537 0.9142 0.92 0.00 0.08
#> 1772116-062_A12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-062_E10 3 0.2537 0.8291 0.00 0.08 0.92
#> 1772099-262_B12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-241_E05 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-241_G08 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-262_E01 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-259_C12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-258_C01 3 0.5560 0.6667 0.00 0.30 0.70
#> 1772099-240_D02 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-259_G04 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-060_H06 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772099-240_C03 1 0.3042 0.9113 0.92 0.04 0.04
#> 1772099-260_C03 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-238_E12 1 0.0000 0.9804 1.00 0.00 0.00
#> 1772116-063_A09 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-260_C06 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-238_C01 3 0.3340 0.8183 0.00 0.12 0.88
#> 1772099-240_F07 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-241_G09 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772116-063_G02 2 0.0000 0.9608 0.00 1.00 0.00
#> 1772099-259_H03 1 0.4002 0.8252 0.84 0.00 0.16
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> 1772099-259_E02 1 0.0707 0.9238 0.98 0.00 0.00 0.02
#> 1772116-063_D07 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-060_E02 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-063_E05 2 0.4855 0.2159 0.00 0.60 0.40 0.00
#> 1772099-259_C09 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-060_A08 3 0.3801 0.7311 0.00 0.22 0.78 0.00
#> 1772099-259_F01 4 0.4907 0.4501 0.42 0.00 0.00 0.58
#> 1772099-258_H10 2 0.4406 0.5001 0.00 0.70 0.30 0.00
#> 1772099-259_A03 4 0.3611 0.5598 0.08 0.00 0.06 0.86
#> 1772099-238_A02 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-060_C01 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-259_C10 1 0.3172 0.7522 0.84 0.00 0.00 0.16
#> 1772099-241_A06 2 0.2345 0.8450 0.00 0.90 0.10 0.00
#> 1772099-241_D11 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-063_B01 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-258_H03 4 0.4949 0.3931 0.00 0.18 0.06 0.76
#> 1772116-063_H12 3 0.2706 0.7477 0.00 0.08 0.90 0.02
#> 1772099-262_G05 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-258_E05 4 0.3975 0.4049 0.00 0.00 0.24 0.76
#> 1772099-241_G05 4 0.2647 0.5900 0.12 0.00 0.00 0.88
#> 1772116-064_C11 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-064_E06 4 0.4977 0.0396 0.00 0.00 0.46 0.54
#> 1772099-258_H06 4 0.4522 0.6040 0.32 0.00 0.00 0.68
#> 1772116-064_A04 3 0.7206 -0.2446 0.40 0.00 0.46 0.14
#> 1772099-260_D12 1 0.3400 0.7159 0.82 0.00 0.00 0.18
#> 1772099-258_B02 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-063_E12 3 0.3172 0.7606 0.00 0.16 0.84 0.00
#> 1772099-259_F02 4 0.5355 0.2373 0.00 0.02 0.36 0.62
#> 1772099-258_G02 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-063_E07 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-258_G11 2 0.1211 0.9133 0.00 0.96 0.04 0.00
#> 1772116-062_A05 4 0.1913 0.5302 0.04 0.00 0.02 0.94
#> 1772116-063_G12 3 0.3037 0.6662 0.00 0.02 0.88 0.10
#> 1772099-262_H06 1 0.2345 0.8372 0.90 0.00 0.00 0.10
#> 1772116-062_D10 1 0.3525 0.7997 0.86 0.00 0.04 0.10
#> 1772116-062_H09 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-064_H09 3 0.3610 0.5508 0.00 0.00 0.80 0.20
#> 1772116-064_G07 4 0.6605 0.3566 0.44 0.00 0.08 0.48
#> 1772099-262_B04 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-258_C04 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-060_C03 3 0.4790 0.5378 0.00 0.38 0.62 0.00
#> 1772116-060_G07 1 0.0707 0.9239 0.98 0.00 0.00 0.02
#> 1772099-259_A09 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_A01 3 0.2921 0.7609 0.00 0.14 0.86 0.00
#> 1772116-063_B11 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-063_A04 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-062_H06 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-063_E09 3 0.7699 -0.3062 0.22 0.00 0.40 0.38
#> 1772116-062_A07 2 0.5489 0.5593 0.00 0.70 0.24 0.06
#> 1772116-060_D01 2 0.4907 0.1122 0.00 0.58 0.42 0.00
#> 1772099-258_F03 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-060_D04 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-062_E05 3 0.3400 0.7562 0.00 0.18 0.82 0.00
#> 1772116-062_D09 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-260_F12 1 0.4948 -0.0308 0.56 0.00 0.00 0.44
#> 1772116-062_A10 3 0.1637 0.7379 0.00 0.06 0.94 0.00
#> 1772116-062_B09 2 0.0707 0.9330 0.00 0.98 0.00 0.02
#> 1772099-262_D04 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-062_G10 3 0.3400 0.7562 0.00 0.18 0.82 0.00
#> 1772116-060_C04 2 0.4905 0.7286 0.02 0.80 0.12 0.06
#> 1772116-062_A09 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-262_H02 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-258_D06 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-062_G04 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-063_B10 3 0.7331 0.0468 0.10 0.02 0.52 0.36
#> 1772116-063_B03 3 0.1637 0.6512 0.00 0.00 0.94 0.06
#> 1772099-241_B09 4 0.4948 0.4053 0.44 0.00 0.00 0.56
#> 1772116-064_E05 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-064_C08 3 0.2647 0.6069 0.00 0.00 0.88 0.12
#> 1772099-258_G06 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-060_G08 3 0.4855 0.4912 0.00 0.40 0.60 0.00
#> 1772116-062_G06 2 0.0707 0.9320 0.00 0.98 0.02 0.00
#> 1772116-060_F07 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-241_A02 4 0.6840 0.5014 0.22 0.00 0.18 0.60
#> 1772116-064_F11 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-062_H11 3 0.2335 0.7381 0.00 0.06 0.92 0.02
#> 1772099-258_G08 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-064_E07 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-238_D07 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-063_D04 3 0.2345 0.7491 0.00 0.10 0.90 0.00
#> 1772116-062_E07 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-063_F10 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-238_C02 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-262_E11 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-060_D07 3 0.3400 0.7562 0.00 0.18 0.82 0.00
#> 1772116-060_G02 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-060_A12 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-060_D05 3 0.6299 0.5564 0.00 0.32 0.60 0.08
#> 1772116-060_C08 3 0.4134 0.6982 0.00 0.26 0.74 0.00
#> 1772116-060_E09 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-063_B09 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_F06 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-238_A10 4 0.4790 0.2193 0.00 0.00 0.38 0.62
#> 1772099-260_H06 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-060_C02 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-062_E09 1 0.5956 0.4549 0.68 0.00 0.10 0.22
#> 1772116-060_F09 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-060_D10 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-063_F04 3 0.6594 0.5803 0.00 0.24 0.62 0.14
#> 1772116-064_C10 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-063_A07 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-260_E06 4 0.4406 0.3374 0.00 0.00 0.30 0.70
#> 1772099-260_F11 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-062_C12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-237_G01 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-258_H02 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-063_D11 2 0.1211 0.9124 0.00 0.96 0.04 0.00
#> 1772099-240_G05 3 0.3801 0.7311 0.00 0.22 0.78 0.00
#> 1772116-063_C11 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-064_A01 3 0.3611 0.7402 0.00 0.08 0.86 0.06
#> 1772116-063_E10 2 0.4134 0.5866 0.00 0.74 0.26 0.00
#> 1772116-064_D03 3 0.3801 0.7311 0.00 0.22 0.78 0.00
#> 1772116-060_C09 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-064_B07 2 0.0707 0.9320 0.00 0.98 0.02 0.00
#> 1772116-064_H02 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-237_G06 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-062_A11 3 0.3400 0.7562 0.00 0.18 0.82 0.00
#> 1772116-060_B11 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-063_C04 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-062_F09 3 0.2706 0.7477 0.00 0.08 0.90 0.02
#> 1772116-064_D02 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-064_B09 2 0.5106 0.5192 0.24 0.72 0.04 0.00
#> 1772116-064_C04 2 0.3853 0.7413 0.00 0.82 0.16 0.02
#> 1772099-259_D07 1 0.1211 0.9053 0.96 0.00 0.00 0.04
#> 1772099-238_C07 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-063_A11 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-063_E04 3 0.2335 0.7381 0.00 0.06 0.92 0.02
#> 1772116-062_F05 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-241_A10 1 0.3821 0.7709 0.84 0.00 0.04 0.12
#> 1772099-238_F07 4 0.4907 0.4504 0.42 0.00 0.00 0.58
#> 1772116-062_H03 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-063_B04 3 0.4134 0.4730 0.00 0.00 0.74 0.26
#> 1772116-060_A11 4 0.7394 0.4298 0.24 0.00 0.24 0.52
#> 1772116-062_B11 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-060_B02 4 0.7768 0.3210 0.24 0.00 0.36 0.40
#> 1772099-238_A09 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-060_B01 3 0.1211 0.7219 0.00 0.04 0.96 0.00
#> 1772116-060_E03 3 0.3400 0.7560 0.00 0.18 0.82 0.00
#> 1772099-260_F07 1 0.4406 0.4666 0.70 0.00 0.00 0.30
#> 1772116-064_H03 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_E04 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-063_C12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-064_G08 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-063_H02 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-259_F10 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-063_F11 3 0.2921 0.7615 0.00 0.14 0.86 0.00
#> 1772099-259_G08 4 0.4624 0.5871 0.34 0.00 0.00 0.66
#> 1772116-060_F01 3 0.3801 0.7311 0.00 0.22 0.78 0.00
#> 1772116-060_B10 3 0.3400 0.7562 0.00 0.18 0.82 0.00
#> 1772099-259_C03 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-262_B10 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-241_F08 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-240_A09 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-240_D01 4 0.5000 -0.0703 0.00 0.00 0.50 0.50
#> 1772099-240_D07 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-064_B01 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-063_A05 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-241_F07 1 0.0707 0.9244 0.98 0.00 0.00 0.02
#> 1772099-238_A08 1 0.2345 0.8444 0.90 0.00 0.00 0.10
#> 1772099-237_B07 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-063_C06 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_H05 1 0.4472 0.6344 0.76 0.00 0.02 0.22
#> 1772116-062_B05 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-064_B06 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_B12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-260_D08 1 0.4713 0.2851 0.64 0.00 0.00 0.36
#> 1772116-064_F06 3 0.5661 0.3639 0.08 0.00 0.70 0.22
#> 1772116-063_F12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-063_G10 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_C08 1 0.6988 -0.1321 0.50 0.00 0.12 0.38
#> 1772116-064_D10 1 0.2411 0.8648 0.92 0.00 0.04 0.04
#> 1772116-060_H08 3 0.4079 0.5802 0.00 0.02 0.80 0.18
#> 1772099-262_C05 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_D06 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-238_H11 1 0.1913 0.8880 0.94 0.00 0.04 0.02
#> 1772099-260_A01 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-241_H05 3 0.3610 0.6108 0.00 0.00 0.80 0.20
#> 1772099-262_F04 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-262_D11 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-241_C09 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-238_G08 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-260_H08 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-241_C12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-259_C11 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-060_B09 1 0.3172 0.7615 0.84 0.00 0.00 0.16
#> 1772116-064_D06 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-064_B03 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-063_E06 1 0.4292 0.7229 0.82 0.00 0.08 0.10
#> 1772116-060_A01 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-262_B01 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-064_A07 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-262_C02 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-260_G11 1 0.0707 0.9241 0.98 0.00 0.00 0.02
#> 1772116-060_C12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-262_G10 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_B01 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-064_B08 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-063_B06 2 0.0707 0.9317 0.00 0.98 0.02 0.00
#> 1772116-064_C03 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-258_F05 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-262_F05 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-258_A08 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_F10 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-240_G08 1 0.0707 0.9240 0.98 0.00 0.00 0.02
#> 1772116-062_D03 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_F04 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-258_E08 4 0.4948 0.4020 0.44 0.00 0.00 0.56
#> 1772116-064_D05 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-063_H04 3 0.4624 0.3609 0.00 0.00 0.66 0.34
#> 1772116-063_C03 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-064_E03 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-260_C01 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-238_C12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-064_D09 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_E12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-063_G01 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-262_H01 4 0.3801 0.6183 0.22 0.00 0.00 0.78
#> 1772099-262_F06 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_D05 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-237_E03 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_B10 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-258_G12 1 0.5000 -0.2579 0.50 0.00 0.00 0.50
#> 1772116-060_C10 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-258_D09 3 0.2345 0.7553 0.00 0.10 0.90 0.00
#> 1772099-260_H05 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-060_A03 4 0.5915 0.4488 0.40 0.00 0.04 0.56
#> 1772116-060_E01 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-063_A01 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-241_E10 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-064_F07 1 0.7805 -0.3213 0.42 0.00 0.28 0.30
#> 1772116-062_C01 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-262_G12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-064_F05 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_G12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-063_D10 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_C09 1 0.2647 0.8238 0.88 0.00 0.00 0.12
#> 1772116-064_E12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_H08 3 0.5271 0.3025 0.02 0.00 0.64 0.34
#> 1772116-060_G03 1 0.0707 0.9240 0.98 0.00 0.00 0.02
#> 1772099-262_C10 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-064_D01 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-064_D08 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-259_D11 4 0.4553 0.6137 0.18 0.00 0.04 0.78
#> 1772116-060_E08 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_F12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-063_H11 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-062_C10 3 0.3400 0.7562 0.00 0.18 0.82 0.00
#> 1772099-240_H02 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-260_A07 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-060_D12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-259_C04 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-258_B10 4 0.3610 0.6198 0.20 0.00 0.00 0.80
#> 1772116-062_F01 3 0.3335 0.6626 0.00 0.02 0.86 0.12
#> 1772116-060_E11 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-262_B11 3 0.3400 0.6161 0.00 0.00 0.82 0.18
#> 1772116-063_D12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-063_H05 3 0.3801 0.7339 0.00 0.22 0.78 0.00
#> 1772116-060_A04 1 0.0707 0.9247 0.98 0.00 0.02 0.00
#> 1772116-064_B04 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-260_B06 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-063_F02 4 0.4994 0.0370 0.00 0.00 0.48 0.52
#> 1772099-258_B06 2 0.1637 0.8930 0.00 0.94 0.06 0.00
#> 1772116-064_F03 4 0.7855 0.3791 0.30 0.00 0.30 0.40
#> 1772099-262_C01 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-258_F12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-237_H01 4 0.3610 0.6196 0.20 0.00 0.00 0.80
#> 1772099-258_D08 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-260_H04 4 0.4406 0.6107 0.30 0.00 0.00 0.70
#> 1772116-062_E01 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-262_A02 4 0.3610 0.4314 0.00 0.00 0.20 0.80
#> 1772099-260_A04 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-262_G01 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-258_B05 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-238_F03 2 0.4948 0.0510 0.00 0.56 0.44 0.00
#> 1772099-262_F12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-258_D01 4 0.4994 0.2987 0.48 0.00 0.00 0.52
#> 1772116-060_F06 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-241_H12 4 0.4994 -0.0113 0.00 0.00 0.48 0.52
#> 1772116-062_G05 3 0.3198 0.7139 0.00 0.04 0.88 0.08
#> 1772116-060_G01 3 0.3172 0.7594 0.00 0.16 0.84 0.00
#> 1772116-060_B06 3 0.3198 0.7092 0.00 0.04 0.88 0.08
#> 1772099-241_H06 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-062_B06 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-062_D11 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-064_E09 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-062_E08 2 0.6074 0.2458 0.00 0.60 0.34 0.06
#> 1772099-262_H12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-237_D03 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-060_H02 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-062_C05 4 0.3610 0.4116 0.00 0.00 0.20 0.80
#> 1772116-064_C07 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-060_A05 3 0.4855 0.4908 0.00 0.40 0.60 0.00
#> 1772099-262_D02 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-258_C06 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-258_F06 2 0.4948 0.0624 0.00 0.56 0.44 0.00
#> 1772099-260_A02 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-258_C03 3 0.3853 0.6547 0.00 0.02 0.82 0.16
#> 1772099-237_F01 4 0.4994 0.0151 0.00 0.00 0.48 0.52
#> 1772116-064_F09 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-238_H06 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-238_H10 3 0.3610 0.7454 0.00 0.20 0.80 0.00
#> 1772099-258_G04 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-060_F08 1 0.2411 0.8645 0.92 0.00 0.04 0.04
#> 1772116-063_A02 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_D01 1 0.3606 0.7618 0.84 0.00 0.02 0.14
#> 1772116-064_C09 1 0.2830 0.8425 0.90 0.00 0.04 0.06
#> 1772099-262_D06 1 0.3525 0.7965 0.86 0.00 0.04 0.10
#> 1772099-258_G09 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-259_G11 1 0.2647 0.8125 0.88 0.00 0.00 0.12
#> 1772116-064_B10 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_F02 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-262_F11 2 0.4134 0.5864 0.00 0.74 0.26 0.00
#> 1772116-064_C05 1 0.5793 0.1885 0.60 0.00 0.04 0.36
#> 1772099-238_B03 4 0.4522 0.2979 0.00 0.00 0.32 0.68
#> 1772099-241_F03 1 0.4907 0.0568 0.58 0.00 0.00 0.42
#> 1772099-259_A06 4 0.3975 0.6204 0.24 0.00 0.00 0.76
#> 1772116-062_A12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-062_E10 3 0.2335 0.7381 0.00 0.06 0.92 0.02
#> 1772099-262_B12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-241_E05 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-241_G08 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-262_E01 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-259_C12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772099-258_C01 3 0.4277 0.6720 0.00 0.28 0.72 0.00
#> 1772099-240_D02 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-259_G04 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-060_H06 1 0.3525 0.7931 0.86 0.00 0.04 0.10
#> 1772099-240_C03 1 0.5487 0.0928 0.58 0.02 0.00 0.40
#> 1772099-260_C03 2 0.0707 0.9316 0.00 0.98 0.02 0.00
#> 1772099-238_E12 1 0.0000 0.9419 1.00 0.00 0.00 0.00
#> 1772116-063_A09 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-260_C06 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-238_C01 3 0.4088 0.7570 0.00 0.14 0.82 0.04
#> 1772099-240_F07 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-241_G09 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772116-063_G02 2 0.0000 0.9496 0.00 1.00 0.00 0.00
#> 1772099-259_H03 4 0.5793 0.5455 0.36 0.00 0.04 0.60
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)
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)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
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)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n_sample Cell_type(p-value) Timepoint(p-value) k
#> ATC:skmeans 334 1.04e-18 1.08e-01 2
#> ATC:skmeans 325 2.50e-14 1.69e-02 3
#> ATC:skmeans 290 1.72e-14 2.11e-05 4
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.
Parent node: Node0. Child nodes: Node011-leaf , Node012-leaf , Node021-leaf , Node022-leaf , Node023-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["01"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4.
#> On a matrix with 6030 rows and 182 columns.
#> Top rows (396) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 150 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.963 0.986 0.502 0.498 0.498
#> 3 3 0.652 0.646 0.843 0.238 0.834 0.678
#> 4 4 0.566 0.596 0.785 0.117 0.889 0.725
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is 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 subgroup
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
#> 1772099-259_E02 2 0.000 0.9879 0.00 1.00
#> 1772099-259_F01 2 0.000 0.9879 0.00 1.00
#> 1772099-259_A03 2 0.000 0.9879 0.00 1.00
#> 1772116-060_C01 2 0.000 0.9879 0.00 1.00
#> 1772099-259_C10 2 0.000 0.9879 0.00 1.00
#> 1772099-241_G05 2 0.000 0.9879 0.00 1.00
#> 1772099-258_H06 2 0.000 0.9879 0.00 1.00
#> 1772116-064_A04 2 0.000 0.9879 0.00 1.00
#> 1772099-260_D12 2 0.000 0.9879 0.00 1.00
#> 1772116-062_A05 2 0.000 0.9879 0.00 1.00
#> 1772099-262_H06 2 0.000 0.9879 0.00 1.00
#> 1772116-062_D10 2 0.000 0.9879 0.00 1.00
#> 1772116-064_G07 2 0.000 0.9879 0.00 1.00
#> 1772116-060_G07 2 0.000 0.9879 0.00 1.00
#> 1772099-259_A09 1 0.000 0.9827 1.00 0.00
#> 1772116-063_E09 2 0.000 0.9879 0.00 1.00
#> 1772116-062_D09 1 0.000 0.9827 1.00 0.00
#> 1772099-260_F12 2 0.000 0.9879 0.00 1.00
#> 1772116-063_B10 2 0.000 0.9879 0.00 1.00
#> 1772099-241_B09 2 0.000 0.9879 0.00 1.00
#> 1772116-064_E05 1 0.327 0.9253 0.94 0.06
#> 1772099-241_A02 2 0.000 0.9879 0.00 1.00
#> 1772116-063_F10 1 0.000 0.9827 1.00 0.00
#> 1772116-063_B09 1 0.000 0.9827 1.00 0.00
#> 1772116-062_E09 2 0.000 0.9879 0.00 1.00
#> 1772116-060_D10 1 0.000 0.9827 1.00 0.00
#> 1772116-064_C10 1 0.000 0.9827 1.00 0.00
#> 1772116-062_C12 2 0.000 0.9879 0.00 1.00
#> 1772099-237_G01 1 0.000 0.9827 1.00 0.00
#> 1772099-259_D07 2 0.000 0.9879 0.00 1.00
#> 1772116-063_A11 2 0.000 0.9879 0.00 1.00
#> 1772116-062_F05 1 0.141 0.9646 0.98 0.02
#> 1772099-241_A10 2 0.000 0.9879 0.00 1.00
#> 1772099-238_F07 2 0.000 0.9879 0.00 1.00
#> 1772116-062_H03 1 0.000 0.9827 1.00 0.00
#> 1772116-063_B04 2 0.000 0.9879 0.00 1.00
#> 1772116-060_A11 2 0.000 0.9879 0.00 1.00
#> 1772116-060_B02 2 0.000 0.9879 0.00 1.00
#> 1772099-260_F07 2 0.000 0.9879 0.00 1.00
#> 1772116-064_H03 1 0.000 0.9827 1.00 0.00
#> 1772116-063_C12 1 0.000 0.9827 1.00 0.00
#> 1772116-064_G08 1 0.000 0.9827 1.00 0.00
#> 1772099-259_F10 1 0.000 0.9827 1.00 0.00
#> 1772099-259_G08 2 0.000 0.9879 0.00 1.00
#> 1772099-259_C03 1 0.000 0.9827 1.00 0.00
#> 1772099-262_B10 1 0.000 0.9827 1.00 0.00
#> 1772099-241_F08 1 0.000 0.9827 1.00 0.00
#> 1772099-240_A09 1 0.000 0.9827 1.00 0.00
#> 1772099-240_D01 2 0.000 0.9879 0.00 1.00
#> 1772099-240_D07 2 0.000 0.9879 0.00 1.00
#> 1772116-064_B01 1 0.000 0.9827 1.00 0.00
#> 1772116-063_A05 1 0.000 0.9827 1.00 0.00
#> 1772099-241_F07 2 0.000 0.9879 0.00 1.00
#> 1772099-238_A08 2 0.000 0.9879 0.00 1.00
#> 1772099-237_B07 1 0.000 0.9827 1.00 0.00
#> 1772116-063_C06 2 0.327 0.9277 0.06 0.94
#> 1772116-062_H05 2 0.000 0.9879 0.00 1.00
#> 1772116-062_B05 1 0.000 0.9827 1.00 0.00
#> 1772116-064_B06 1 0.000 0.9827 1.00 0.00
#> 1772116-062_B12 1 0.000 0.9827 1.00 0.00
#> 1772099-260_D08 2 0.000 0.9879 0.00 1.00
#> 1772116-064_F06 2 0.000 0.9879 0.00 1.00
#> 1772116-063_F12 1 0.000 0.9827 1.00 0.00
#> 1772116-063_G10 1 0.000 0.9827 1.00 0.00
#> 1772116-062_C08 2 0.000 0.9879 0.00 1.00
#> 1772116-064_D10 2 0.000 0.9879 0.00 1.00
#> 1772099-262_C05 1 0.000 0.9827 1.00 0.00
#> 1772116-062_D06 1 0.000 0.9827 1.00 0.00
#> 1772099-238_H11 2 0.000 0.9879 0.00 1.00
#> 1772099-260_A01 1 0.000 0.9827 1.00 0.00
#> 1772099-262_F04 1 0.000 0.9827 1.00 0.00
#> 1772099-262_D11 1 0.000 0.9827 1.00 0.00
#> 1772099-241_C09 1 0.000 0.9827 1.00 0.00
#> 1772099-238_G08 1 0.000 0.9827 1.00 0.00
#> 1772099-260_H08 1 0.000 0.9827 1.00 0.00
#> 1772099-241_C12 1 0.000 0.9827 1.00 0.00
#> 1772099-259_C11 1 0.000 0.9827 1.00 0.00
#> 1772116-060_B09 2 0.000 0.9879 0.00 1.00
#> 1772116-064_D06 1 0.000 0.9827 1.00 0.00
#> 1772116-064_B03 1 0.000 0.9827 1.00 0.00
#> 1772116-063_E06 2 0.000 0.9879 0.00 1.00
#> 1772116-060_A01 1 0.000 0.9827 1.00 0.00
#> 1772099-262_B01 1 0.000 0.9827 1.00 0.00
#> 1772116-064_A07 1 0.000 0.9827 1.00 0.00
#> 1772099-262_C02 1 0.000 0.9827 1.00 0.00
#> 1772099-260_G11 2 0.000 0.9879 0.00 1.00
#> 1772116-060_C12 1 0.000 0.9827 1.00 0.00
#> 1772099-262_G10 1 0.000 0.9827 1.00 0.00
#> 1772116-062_B01 1 0.000 0.9827 1.00 0.00
#> 1772116-064_B08 1 0.000 0.9827 1.00 0.00
#> 1772116-064_C03 1 0.000 0.9827 1.00 0.00
#> 1772099-258_F05 2 0.000 0.9879 0.00 1.00
#> 1772099-262_F05 1 0.000 0.9827 1.00 0.00
#> 1772099-258_A08 1 0.000 0.9827 1.00 0.00
#> 1772116-062_F10 1 0.000 0.9827 1.00 0.00
#> 1772099-240_G08 2 0.000 0.9879 0.00 1.00
#> 1772116-062_D03 2 0.141 0.9687 0.02 0.98
#> 1772116-062_F04 2 0.000 0.9879 0.00 1.00
#> 1772099-258_E08 2 0.000 0.9879 0.00 1.00
#> 1772116-064_D05 1 0.000 0.9827 1.00 0.00
#> 1772116-063_H04 2 0.000 0.9879 0.00 1.00
#> 1772116-063_C03 2 0.000 0.9879 0.00 1.00
#> 1772116-064_E03 1 0.000 0.9827 1.00 0.00
#> 1772099-260_C01 1 0.855 0.6118 0.72 0.28
#> 1772099-238_C12 1 0.000 0.9827 1.00 0.00
#> 1772116-064_D09 1 1.000 0.0056 0.50 0.50
#> 1772116-062_E12 1 0.000 0.9827 1.00 0.00
#> 1772116-063_G01 1 0.000 0.9827 1.00 0.00
#> 1772099-262_H01 2 0.000 0.9879 0.00 1.00
#> 1772099-262_F06 1 0.000 0.9827 1.00 0.00
#> 1772116-062_D05 2 0.000 0.9879 0.00 1.00
#> 1772099-237_E03 1 0.000 0.9827 1.00 0.00
#> 1772116-062_B10 1 0.634 0.8051 0.84 0.16
#> 1772099-258_G12 2 0.000 0.9879 0.00 1.00
#> 1772116-060_C10 1 0.000 0.9827 1.00 0.00
#> 1772099-260_H05 1 0.000 0.9827 1.00 0.00
#> 1772116-060_A03 2 0.000 0.9879 0.00 1.00
#> 1772116-060_E01 1 0.999 0.0758 0.52 0.48
#> 1772116-063_A01 1 0.000 0.9827 1.00 0.00
#> 1772099-241_E10 1 0.000 0.9827 1.00 0.00
#> 1772116-064_F07 2 0.000 0.9879 0.00 1.00
#> 1772116-062_C01 1 0.000 0.9827 1.00 0.00
#> 1772099-262_G12 2 0.680 0.7766 0.18 0.82
#> 1772116-064_F05 1 0.000 0.9827 1.00 0.00
#> 1772116-062_G12 2 0.000 0.9879 0.00 1.00
#> 1772116-063_D10 1 0.000 0.9827 1.00 0.00
#> 1772116-062_C09 2 0.000 0.9879 0.00 1.00
#> 1772116-064_E12 1 0.000 0.9827 1.00 0.00
#> 1772116-062_H08 2 0.000 0.9879 0.00 1.00
#> 1772116-060_G03 2 0.000 0.9879 0.00 1.00
#> 1772099-262_C10 1 0.000 0.9827 1.00 0.00
#> 1772116-064_D01 1 0.000 0.9827 1.00 0.00
#> 1772116-064_D08 1 0.000 0.9827 1.00 0.00
#> 1772099-259_D11 2 0.000 0.9879 0.00 1.00
#> 1772116-060_E08 1 0.000 0.9827 1.00 0.00
#> 1772116-062_F12 1 0.000 0.9827 1.00 0.00
#> 1772116-060_D12 1 0.000 0.9827 1.00 0.00
#> 1772099-258_B10 2 0.000 0.9879 0.00 1.00
#> 1772116-063_D12 1 0.000 0.9827 1.00 0.00
#> 1772116-060_A04 2 0.000 0.9879 0.00 1.00
#> 1772116-063_F02 2 0.000 0.9879 0.00 1.00
#> 1772116-064_F03 2 0.000 0.9879 0.00 1.00
#> 1772099-262_C01 1 0.000 0.9827 1.00 0.00
#> 1772099-258_F12 1 0.000 0.9827 1.00 0.00
#> 1772099-237_H01 2 0.000 0.9879 0.00 1.00
#> 1772099-258_D08 1 0.000 0.9827 1.00 0.00
#> 1772099-260_H04 2 0.000 0.9879 0.00 1.00
#> 1772116-062_E01 1 0.000 0.9827 1.00 0.00
#> 1772099-260_A04 1 0.000 0.9827 1.00 0.00
#> 1772099-262_G01 1 0.000 0.9827 1.00 0.00
#> 1772099-258_B05 1 0.000 0.9827 1.00 0.00
#> 1772099-262_F12 1 0.000 0.9827 1.00 0.00
#> 1772099-258_D01 2 0.000 0.9879 0.00 1.00
#> 1772116-060_F06 2 0.000 0.9879 0.00 1.00
#> 1772099-241_H12 2 0.000 0.9879 0.00 1.00
#> 1772099-262_H12 1 0.000 0.9827 1.00 0.00
#> 1772099-237_D03 1 0.000 0.9827 1.00 0.00
#> 1772116-062_C05 2 0.000 0.9879 0.00 1.00
#> 1772116-064_F09 1 0.000 0.9827 1.00 0.00
#> 1772099-238_H06 1 0.000 0.9827 1.00 0.00
#> 1772116-060_F08 2 0.000 0.9879 0.00 1.00
#> 1772116-063_A02 2 0.971 0.3256 0.40 0.60
#> 1772116-062_D01 2 0.000 0.9879 0.00 1.00
#> 1772116-064_C09 2 0.000 0.9879 0.00 1.00
#> 1772099-262_D06 2 0.000 0.9879 0.00 1.00
#> 1772099-259_G11 2 0.000 0.9879 0.00 1.00
#> 1772116-064_B10 1 0.000 0.9827 1.00 0.00
#> 1772116-064_C05 2 0.000 0.9879 0.00 1.00
#> 1772099-238_B03 2 0.000 0.9879 0.00 1.00
#> 1772099-241_F03 2 0.000 0.9879 0.00 1.00
#> 1772099-259_A06 2 0.000 0.9879 0.00 1.00
#> 1772116-062_A12 1 0.000 0.9827 1.00 0.00
#> 1772099-262_B12 1 0.242 0.9457 0.96 0.04
#> 1772099-241_E05 1 0.000 0.9827 1.00 0.00
#> 1772099-241_G08 1 0.000 0.9827 1.00 0.00
#> 1772099-262_E01 1 0.000 0.9827 1.00 0.00
#> 1772099-259_C12 1 0.327 0.9248 0.94 0.06
#> 1772099-259_G04 2 0.943 0.4351 0.36 0.64
#> 1772116-060_H06 2 0.000 0.9879 0.00 1.00
#> 1772099-240_C03 2 0.000 0.9879 0.00 1.00
#> 1772099-238_E12 2 0.000 0.9879 0.00 1.00
#> 1772099-259_H03 2 0.000 0.9879 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> 1772099-259_E02 2 0.2066 0.6724 0.00 0.94 0.06
#> 1772099-259_F01 2 0.0000 0.6874 0.00 1.00 0.00
#> 1772099-259_A03 2 0.0892 0.6835 0.00 0.98 0.02
#> 1772116-060_C01 2 0.6302 -0.3234 0.00 0.52 0.48
#> 1772099-259_C10 2 0.0000 0.6874 0.00 1.00 0.00
#> 1772099-241_G05 2 0.0892 0.6835 0.00 0.98 0.02
#> 1772099-258_H06 2 0.0000 0.6874 0.00 1.00 0.00
#> 1772116-064_A04 3 0.6280 0.4656 0.00 0.46 0.54
#> 1772099-260_D12 2 0.0000 0.6874 0.00 1.00 0.00
#> 1772116-062_A05 2 0.6045 0.0324 0.00 0.62 0.38
#> 1772099-262_H06 2 0.0000 0.6874 0.00 1.00 0.00
#> 1772116-062_D10 3 0.6309 0.3662 0.00 0.50 0.50
#> 1772116-064_G07 3 0.6302 0.4274 0.00 0.48 0.52
#> 1772116-060_G07 2 0.3686 0.5889 0.00 0.86 0.14
#> 1772099-259_A09 1 0.4002 0.8537 0.84 0.00 0.16
#> 1772116-063_E09 3 0.6302 0.4251 0.00 0.48 0.52
#> 1772116-062_D09 1 0.2959 0.8957 0.90 0.00 0.10
#> 1772099-260_F12 2 0.0892 0.6835 0.00 0.98 0.02
#> 1772116-063_B10 3 0.6244 0.4952 0.00 0.44 0.56
#> 1772099-241_B09 2 0.5560 0.2907 0.00 0.70 0.30
#> 1772116-064_E05 3 0.4555 0.3610 0.20 0.00 0.80
#> 1772099-241_A02 2 0.5016 0.4319 0.00 0.76 0.24
#> 1772116-063_F10 1 0.4555 0.8234 0.80 0.00 0.20
#> 1772116-063_B09 1 0.0892 0.9371 0.98 0.00 0.02
#> 1772116-062_E09 3 0.5397 0.5699 0.00 0.28 0.72
#> 1772116-060_D10 1 0.3686 0.8723 0.86 0.00 0.14
#> 1772116-064_C10 1 0.0892 0.9364 0.98 0.00 0.02
#> 1772116-062_C12 3 0.6280 0.4652 0.00 0.46 0.54
#> 1772099-237_G01 1 0.0892 0.9371 0.98 0.00 0.02
#> 1772099-259_D07 2 0.5216 0.3939 0.00 0.74 0.26
#> 1772116-063_A11 3 0.4291 0.5362 0.00 0.18 0.82
#> 1772116-062_F05 1 0.6280 0.4240 0.54 0.00 0.46
#> 1772099-241_A10 2 0.1529 0.6711 0.00 0.96 0.04
#> 1772099-238_F07 2 0.4291 0.5178 0.00 0.82 0.18
#> 1772116-062_H03 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772116-063_B04 3 0.6280 0.4656 0.00 0.46 0.54
#> 1772116-060_A11 2 0.6280 -0.2783 0.00 0.54 0.46
#> 1772116-060_B02 2 0.6244 -0.2272 0.00 0.56 0.44
#> 1772099-260_F07 2 0.0892 0.6835 0.00 0.98 0.02
#> 1772116-064_H03 1 0.4796 0.8083 0.78 0.00 0.22
#> 1772116-063_C12 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772116-064_G08 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-259_F10 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-259_G08 2 0.0000 0.6874 0.00 1.00 0.00
#> 1772099-259_C03 1 0.2947 0.8923 0.92 0.06 0.02
#> 1772099-262_B10 1 0.0892 0.9371 0.98 0.00 0.02
#> 1772099-241_F08 1 0.0892 0.9371 0.98 0.00 0.02
#> 1772099-240_A09 1 0.0892 0.9371 0.98 0.00 0.02
#> 1772099-240_D01 2 0.6280 -0.2602 0.00 0.54 0.46
#> 1772099-240_D07 3 0.6302 0.4235 0.00 0.48 0.52
#> 1772116-064_B01 1 0.3686 0.8722 0.86 0.00 0.14
#> 1772116-063_A05 1 0.5948 0.6574 0.64 0.00 0.36
#> 1772099-241_F07 2 0.0892 0.6720 0.00 0.98 0.02
#> 1772099-238_A08 2 0.2537 0.6464 0.00 0.92 0.08
#> 1772099-237_B07 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772116-063_C06 3 0.5560 0.4468 0.00 0.30 0.70
#> 1772116-062_H05 3 0.6302 0.4262 0.00 0.48 0.52
#> 1772116-062_B05 1 0.1529 0.9310 0.96 0.00 0.04
#> 1772116-064_B06 1 0.1529 0.9301 0.96 0.00 0.04
#> 1772116-062_B12 1 0.5016 0.7826 0.76 0.00 0.24
#> 1772099-260_D08 2 0.1529 0.6762 0.00 0.96 0.04
#> 1772116-064_F06 3 0.6302 0.4251 0.00 0.48 0.52
#> 1772116-063_F12 1 0.5560 0.7331 0.70 0.00 0.30
#> 1772116-063_G10 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772116-062_C08 2 0.6280 -0.2602 0.00 0.54 0.46
#> 1772116-064_D10 2 0.6309 -0.3799 0.00 0.50 0.50
#> 1772099-262_C05 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772116-062_D06 1 0.3340 0.8860 0.88 0.00 0.12
#> 1772099-238_H11 2 0.6244 -0.2001 0.00 0.56 0.44
#> 1772099-260_A01 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-262_F04 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-262_D11 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-241_C09 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-238_G08 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-260_H08 1 0.0892 0.9371 0.98 0.00 0.02
#> 1772099-241_C12 1 0.2066 0.9240 0.94 0.00 0.06
#> 1772099-259_C11 1 0.0892 0.9371 0.98 0.00 0.02
#> 1772116-060_B09 2 0.6309 -0.3915 0.00 0.50 0.50
#> 1772116-064_D06 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772116-064_B03 1 0.0892 0.9371 0.98 0.00 0.02
#> 1772116-063_E06 3 0.6280 0.4656 0.00 0.46 0.54
#> 1772116-060_A01 1 0.0892 0.9365 0.98 0.00 0.02
#> 1772099-262_B01 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772116-064_A07 1 0.5835 0.6870 0.66 0.00 0.34
#> 1772099-262_C02 1 0.2959 0.9017 0.90 0.00 0.10
#> 1772099-260_G11 2 0.1529 0.6640 0.00 0.96 0.04
#> 1772116-060_C12 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-262_G10 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772116-062_B01 1 0.7208 0.6342 0.62 0.04 0.34
#> 1772116-064_B08 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772116-064_C03 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-258_F05 2 0.3686 0.6079 0.00 0.86 0.14
#> 1772099-262_F05 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-258_A08 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772116-062_F10 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-240_G08 3 0.5835 0.5434 0.00 0.34 0.66
#> 1772116-062_D03 3 0.4555 0.5416 0.00 0.20 0.80
#> 1772116-062_F04 3 0.6126 0.5135 0.00 0.40 0.60
#> 1772099-258_E08 2 0.0000 0.6874 0.00 1.00 0.00
#> 1772116-064_D05 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772116-063_H04 2 0.6244 -0.1924 0.00 0.56 0.44
#> 1772116-063_C03 3 0.3686 0.5309 0.00 0.14 0.86
#> 1772116-064_E03 1 0.1529 0.9301 0.96 0.00 0.04
#> 1772099-260_C01 2 0.9930 0.0018 0.34 0.38 0.28
#> 1772099-238_C12 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772116-064_D09 3 0.1529 0.4428 0.04 0.00 0.96
#> 1772116-062_E12 1 0.0892 0.9365 0.98 0.00 0.02
#> 1772116-063_G01 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-262_H01 2 0.1529 0.6743 0.00 0.96 0.04
#> 1772099-262_F06 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772116-062_D05 3 0.6302 0.2820 0.00 0.48 0.52
#> 1772099-237_E03 1 0.0892 0.9371 0.98 0.00 0.02
#> 1772116-062_B10 3 0.5016 0.3222 0.24 0.00 0.76
#> 1772099-258_G12 2 0.0000 0.6874 0.00 1.00 0.00
#> 1772116-060_C10 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-260_H05 1 0.6126 0.5998 0.60 0.00 0.40
#> 1772116-060_A03 2 0.6126 -0.0455 0.00 0.60 0.40
#> 1772116-060_E01 2 0.9093 0.0600 0.40 0.46 0.14
#> 1772116-063_A01 3 0.3686 0.3774 0.14 0.00 0.86
#> 1772099-241_E10 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772116-064_F07 3 0.6244 0.4952 0.00 0.44 0.56
#> 1772116-062_C01 1 0.1529 0.9300 0.96 0.00 0.04
#> 1772099-262_G12 2 0.4966 0.5410 0.06 0.84 0.10
#> 1772116-064_F05 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772116-062_G12 3 0.4291 0.5503 0.00 0.18 0.82
#> 1772116-063_D10 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772116-062_C09 3 0.5706 0.5696 0.00 0.32 0.68
#> 1772116-064_E12 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772116-062_H08 2 0.6302 -0.3268 0.00 0.52 0.48
#> 1772116-060_G03 3 0.5948 0.5582 0.00 0.36 0.64
#> 1772099-262_C10 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772116-064_D01 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772116-064_D08 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-259_D11 2 0.2537 0.6470 0.00 0.92 0.08
#> 1772116-060_E08 1 0.5397 0.7507 0.72 0.00 0.28
#> 1772116-062_F12 3 0.6244 -0.2747 0.44 0.00 0.56
#> 1772116-060_D12 1 0.2959 0.8983 0.90 0.00 0.10
#> 1772099-258_B10 2 0.0892 0.6835 0.00 0.98 0.02
#> 1772116-063_D12 1 0.2959 0.8961 0.90 0.00 0.10
#> 1772116-060_A04 3 0.6280 0.4407 0.00 0.46 0.54
#> 1772116-063_F02 2 0.4555 0.5053 0.00 0.80 0.20
#> 1772116-064_F03 3 0.6302 0.4213 0.00 0.48 0.52
#> 1772099-262_C01 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-258_F12 1 0.1529 0.9302 0.96 0.00 0.04
#> 1772099-237_H01 2 0.0000 0.6874 0.00 1.00 0.00
#> 1772099-258_D08 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-260_H04 2 0.0000 0.6874 0.00 1.00 0.00
#> 1772116-062_E01 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-260_A04 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-262_G01 1 0.0892 0.9365 0.98 0.00 0.02
#> 1772099-258_B05 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-262_F12 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-258_D01 2 0.0892 0.6720 0.00 0.98 0.02
#> 1772116-060_F06 3 0.2066 0.4926 0.00 0.06 0.94
#> 1772099-241_H12 2 0.5016 0.4333 0.00 0.76 0.24
#> 1772099-262_H12 1 0.1529 0.9199 0.96 0.04 0.00
#> 1772099-237_D03 1 0.0892 0.9340 0.98 0.00 0.02
#> 1772116-062_C05 2 0.5948 0.1182 0.00 0.64 0.36
#> 1772116-064_F09 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-238_H06 1 0.2947 0.9057 0.92 0.02 0.06
#> 1772116-060_F08 3 0.6126 0.5344 0.00 0.40 0.60
#> 1772116-063_A02 3 0.2947 0.4447 0.06 0.02 0.92
#> 1772116-062_D01 3 0.6045 0.5489 0.00 0.38 0.62
#> 1772116-064_C09 3 0.5706 0.5692 0.00 0.32 0.68
#> 1772099-262_D06 2 0.0000 0.6874 0.00 1.00 0.00
#> 1772099-259_G11 2 0.0000 0.6874 0.00 1.00 0.00
#> 1772116-064_B10 1 0.5835 0.6850 0.66 0.00 0.34
#> 1772116-064_C05 2 0.6280 -0.2634 0.00 0.54 0.46
#> 1772099-238_B03 2 0.0000 0.6874 0.00 1.00 0.00
#> 1772099-241_F03 2 0.0000 0.6874 0.00 1.00 0.00
#> 1772099-259_A06 2 0.0000 0.6874 0.00 1.00 0.00
#> 1772116-062_A12 1 0.2959 0.9008 0.90 0.00 0.10
#> 1772099-262_B12 2 0.7555 0.0246 0.44 0.52 0.04
#> 1772099-241_E05 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-241_G08 1 0.0892 0.9362 0.98 0.00 0.02
#> 1772099-262_E01 1 0.0000 0.9417 1.00 0.00 0.00
#> 1772099-259_C12 1 0.6803 0.5769 0.68 0.28 0.04
#> 1772099-259_G04 2 0.6000 0.3709 0.20 0.76 0.04
#> 1772116-060_H06 2 0.5397 0.3468 0.00 0.72 0.28
#> 1772099-240_C03 2 0.0000 0.6874 0.00 1.00 0.00
#> 1772099-238_E12 2 0.0000 0.6874 0.00 1.00 0.00
#> 1772099-259_H03 2 0.0000 0.6874 0.00 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> 1772099-259_E02 2 0.4581 0.6663 0.00 0.80 0.12 0.08
#> 1772099-259_F01 2 0.0707 0.7358 0.00 0.98 0.02 0.00
#> 1772099-259_A03 2 0.2647 0.6753 0.00 0.88 0.12 0.00
#> 1772116-060_C01 3 0.4406 0.7302 0.00 0.30 0.70 0.00
#> 1772099-259_C10 2 0.3198 0.7064 0.00 0.88 0.04 0.08
#> 1772099-241_G05 2 0.1211 0.7295 0.00 0.96 0.04 0.00
#> 1772099-258_H06 2 0.1211 0.7295 0.00 0.96 0.04 0.00
#> 1772116-064_A04 3 0.3801 0.7322 0.00 0.22 0.78 0.00
#> 1772099-260_D12 2 0.3525 0.6924 0.00 0.86 0.04 0.10
#> 1772116-062_A05 3 0.4994 0.4553 0.00 0.48 0.52 0.00
#> 1772099-262_H06 2 0.0000 0.7367 0.00 1.00 0.00 0.00
#> 1772116-062_D10 3 0.4713 0.6647 0.00 0.36 0.64 0.00
#> 1772116-064_G07 3 0.4134 0.7348 0.00 0.26 0.74 0.00
#> 1772116-060_G07 2 0.4277 0.3847 0.00 0.72 0.28 0.00
#> 1772099-259_A09 1 0.5594 0.0487 0.52 0.00 0.02 0.46
#> 1772116-063_E09 3 0.4134 0.7355 0.00 0.26 0.74 0.00
#> 1772116-062_D09 1 0.3801 0.6924 0.78 0.00 0.00 0.22
#> 1772099-260_F12 2 0.0707 0.7358 0.00 0.98 0.02 0.00
#> 1772116-063_B10 3 0.3975 0.7345 0.00 0.24 0.76 0.00
#> 1772099-241_B09 2 0.4790 -0.0052 0.00 0.62 0.38 0.00
#> 1772116-064_E05 4 0.6510 0.5057 0.08 0.00 0.38 0.54
#> 1772099-241_A02 2 0.4994 -0.3677 0.00 0.52 0.48 0.00
#> 1772116-063_F10 1 0.6831 -0.2608 0.48 0.00 0.10 0.42
#> 1772116-063_B09 1 0.3172 0.7401 0.84 0.00 0.00 0.16
#> 1772116-062_E09 3 0.3400 0.7199 0.00 0.18 0.82 0.00
#> 1772116-060_D10 1 0.4522 0.5266 0.68 0.00 0.00 0.32
#> 1772116-064_C10 1 0.2345 0.7789 0.90 0.00 0.00 0.10
#> 1772116-062_C12 3 0.4406 0.7056 0.00 0.30 0.70 0.00
#> 1772099-237_G01 1 0.3172 0.7610 0.84 0.00 0.00 0.16
#> 1772099-259_D07 2 0.4907 -0.1306 0.00 0.58 0.42 0.00
#> 1772116-063_A11 3 0.4491 0.5174 0.00 0.06 0.80 0.14
#> 1772116-062_F05 4 0.8325 0.5959 0.30 0.02 0.26 0.42
#> 1772099-241_A10 2 0.3610 0.5743 0.00 0.80 0.20 0.00
#> 1772099-238_F07 2 0.4406 0.3277 0.00 0.70 0.30 0.00
#> 1772116-062_H03 1 0.0707 0.8095 0.98 0.00 0.00 0.02
#> 1772116-063_B04 3 0.4522 0.7118 0.00 0.32 0.68 0.00
#> 1772116-060_A11 3 0.4907 0.5868 0.00 0.42 0.58 0.00
#> 1772116-060_B02 3 0.4790 0.6620 0.00 0.38 0.62 0.00
#> 1772099-260_F07 2 0.0707 0.7334 0.00 0.98 0.00 0.02
#> 1772116-064_H03 1 0.5570 0.1080 0.54 0.00 0.02 0.44
#> 1772116-063_C12 1 0.0000 0.8115 1.00 0.00 0.00 0.00
#> 1772116-064_G08 1 0.0707 0.8095 0.98 0.00 0.00 0.02
#> 1772099-259_F10 1 0.0707 0.8113 0.98 0.00 0.00 0.02
#> 1772099-259_G08 2 0.0707 0.7353 0.00 0.98 0.02 0.00
#> 1772099-259_C03 1 0.4936 0.5231 0.70 0.00 0.02 0.28
#> 1772099-262_B10 1 0.2345 0.7856 0.90 0.00 0.00 0.10
#> 1772099-241_F08 1 0.2647 0.7754 0.88 0.00 0.00 0.12
#> 1772099-240_A09 1 0.2345 0.7856 0.90 0.00 0.00 0.10
#> 1772099-240_D01 3 0.4624 0.6962 0.00 0.34 0.66 0.00
#> 1772099-240_D07 3 0.3801 0.7143 0.00 0.22 0.78 0.00
#> 1772116-064_B01 1 0.4406 0.5361 0.70 0.00 0.00 0.30
#> 1772116-063_A05 4 0.6005 0.2412 0.46 0.00 0.04 0.50
#> 1772099-241_F07 2 0.3821 0.6899 0.00 0.84 0.12 0.04
#> 1772099-238_A08 2 0.3975 0.4874 0.00 0.76 0.24 0.00
#> 1772099-237_B07 1 0.1211 0.8043 0.96 0.00 0.00 0.04
#> 1772116-063_C06 3 0.7738 0.3435 0.00 0.26 0.44 0.30
#> 1772116-062_H05 3 0.5062 0.7233 0.00 0.30 0.68 0.02
#> 1772116-062_B05 1 0.2345 0.7948 0.90 0.00 0.00 0.10
#> 1772116-064_B06 1 0.3172 0.7447 0.84 0.00 0.00 0.16
#> 1772116-062_B12 1 0.5535 0.1128 0.56 0.00 0.02 0.42
#> 1772099-260_D08 2 0.4581 0.6377 0.00 0.80 0.08 0.12
#> 1772116-064_F06 3 0.4522 0.7118 0.00 0.32 0.68 0.00
#> 1772116-063_F12 1 0.5271 0.4200 0.64 0.00 0.02 0.34
#> 1772116-063_G10 1 0.1211 0.8070 0.96 0.00 0.00 0.04
#> 1772116-062_C08 3 0.4790 0.6543 0.00 0.38 0.62 0.00
#> 1772116-064_D10 3 0.4713 0.6909 0.00 0.36 0.64 0.00
#> 1772099-262_C05 1 0.0000 0.8115 1.00 0.00 0.00 0.00
#> 1772116-062_D06 1 0.5428 0.2891 0.60 0.00 0.02 0.38
#> 1772099-238_H11 3 0.4977 0.5055 0.00 0.46 0.54 0.00
#> 1772099-260_A01 1 0.0000 0.8115 1.00 0.00 0.00 0.00
#> 1772099-262_F04 1 0.0000 0.8115 1.00 0.00 0.00 0.00
#> 1772099-262_D11 1 0.0000 0.8115 1.00 0.00 0.00 0.00
#> 1772099-241_C09 1 0.0000 0.8115 1.00 0.00 0.00 0.00
#> 1772099-238_G08 1 0.1411 0.8130 0.96 0.00 0.02 0.02
#> 1772099-260_H08 1 0.2921 0.7730 0.86 0.00 0.00 0.14
#> 1772099-241_C12 1 0.4936 0.5400 0.70 0.00 0.02 0.28
#> 1772099-259_C11 1 0.2647 0.7932 0.88 0.00 0.00 0.12
#> 1772116-060_B09 3 0.4277 0.7327 0.00 0.28 0.72 0.00
#> 1772116-064_D06 1 0.0000 0.8115 1.00 0.00 0.00 0.00
#> 1772116-064_B03 1 0.2921 0.7478 0.86 0.00 0.00 0.14
#> 1772116-063_E06 3 0.3610 0.7277 0.00 0.20 0.80 0.00
#> 1772116-060_A01 1 0.2011 0.8046 0.92 0.00 0.00 0.08
#> 1772099-262_B01 1 0.0000 0.8115 1.00 0.00 0.00 0.00
#> 1772116-064_A07 4 0.6201 0.5319 0.30 0.00 0.08 0.62
#> 1772099-262_C02 1 0.6336 -0.1536 0.48 0.00 0.06 0.46
#> 1772099-260_G11 2 0.5151 0.6079 0.00 0.76 0.10 0.14
#> 1772116-060_C12 1 0.2345 0.7803 0.90 0.00 0.00 0.10
#> 1772099-262_G10 1 0.0000 0.8115 1.00 0.00 0.00 0.00
#> 1772116-062_B01 4 0.5636 0.6110 0.26 0.00 0.06 0.68
#> 1772116-064_B08 1 0.0707 0.8116 0.98 0.00 0.00 0.02
#> 1772116-064_C03 1 0.2011 0.7982 0.92 0.00 0.00 0.08
#> 1772099-258_F05 2 0.7028 0.4299 0.00 0.56 0.28 0.16
#> 1772099-262_F05 1 0.0000 0.8115 1.00 0.00 0.00 0.00
#> 1772099-258_A08 1 0.0707 0.8114 0.98 0.00 0.00 0.02
#> 1772116-062_F10 1 0.2647 0.7753 0.88 0.00 0.00 0.12
#> 1772099-240_G08 3 0.6104 0.5480 0.00 0.14 0.68 0.18
#> 1772116-062_D03 3 0.7365 0.1633 0.00 0.16 0.44 0.40
#> 1772116-062_F04 3 0.6497 0.5970 0.00 0.20 0.64 0.16
#> 1772099-258_E08 2 0.0707 0.7326 0.00 0.98 0.02 0.00
#> 1772116-064_D05 1 0.0707 0.8116 0.98 0.00 0.00 0.02
#> 1772116-063_H04 3 0.4994 0.4665 0.00 0.48 0.52 0.00
#> 1772116-063_C03 3 0.6110 0.3733 0.00 0.10 0.66 0.24
#> 1772116-064_E03 1 0.4079 0.7113 0.80 0.00 0.02 0.18
#> 1772099-260_C01 4 0.8790 0.4411 0.18 0.22 0.10 0.50
#> 1772099-238_C12 1 0.0000 0.8115 1.00 0.00 0.00 0.00
#> 1772116-064_D09 3 0.5606 -0.3623 0.02 0.00 0.50 0.48
#> 1772116-062_E12 1 0.1637 0.8095 0.94 0.00 0.00 0.06
#> 1772116-063_G01 1 0.0000 0.8115 1.00 0.00 0.00 0.00
#> 1772099-262_H01 2 0.2921 0.6532 0.00 0.86 0.14 0.00
#> 1772099-262_F06 1 0.2011 0.7947 0.92 0.00 0.00 0.08
#> 1772116-062_D05 2 0.7699 0.1546 0.00 0.40 0.38 0.22
#> 1772099-237_E03 1 0.2345 0.7856 0.90 0.00 0.00 0.10
#> 1772116-062_B10 4 0.7810 0.6084 0.16 0.02 0.32 0.50
#> 1772099-258_G12 2 0.1211 0.7296 0.00 0.96 0.04 0.00
#> 1772116-060_C10 1 0.0707 0.8095 0.98 0.00 0.00 0.02
#> 1772099-260_H05 1 0.6605 -0.2083 0.48 0.00 0.08 0.44
#> 1772116-060_A03 3 0.4994 0.4793 0.00 0.48 0.52 0.00
#> 1772116-060_E01 1 0.9818 -0.4257 0.30 0.28 0.16 0.26
#> 1772116-063_A01 4 0.5619 0.5574 0.04 0.00 0.32 0.64
#> 1772099-241_E10 1 0.1637 0.8003 0.94 0.00 0.00 0.06
#> 1772116-064_F07 3 0.4277 0.7302 0.00 0.28 0.72 0.00
#> 1772116-062_C01 1 0.3801 0.6650 0.78 0.00 0.00 0.22
#> 1772099-262_G12 2 0.7446 0.4653 0.04 0.60 0.12 0.24
#> 1772116-064_F05 1 0.0707 0.8095 0.98 0.00 0.00 0.02
#> 1772116-062_G12 3 0.5956 0.5046 0.00 0.10 0.68 0.22
#> 1772116-063_D10 1 0.0707 0.8087 0.98 0.00 0.00 0.02
#> 1772116-062_C09 3 0.4472 0.7317 0.00 0.22 0.76 0.02
#> 1772116-064_E12 1 0.1211 0.8108 0.96 0.00 0.00 0.04
#> 1772116-062_H08 3 0.4713 0.6821 0.00 0.36 0.64 0.00
#> 1772116-060_G03 3 0.4642 0.7312 0.00 0.24 0.74 0.02
#> 1772099-262_C10 1 0.0707 0.8119 0.98 0.00 0.00 0.02
#> 1772116-064_D01 1 0.0707 0.8095 0.98 0.00 0.00 0.02
#> 1772116-064_D08 1 0.0000 0.8115 1.00 0.00 0.00 0.00
#> 1772099-259_D11 2 0.3172 0.6143 0.00 0.84 0.16 0.00
#> 1772116-060_E08 1 0.6150 0.1562 0.58 0.00 0.06 0.36
#> 1772116-062_F12 4 0.7583 0.6270 0.28 0.00 0.24 0.48
#> 1772116-060_D12 1 0.4406 0.5728 0.70 0.00 0.00 0.30
#> 1772099-258_B10 2 0.1211 0.7296 0.00 0.96 0.04 0.00
#> 1772116-063_D12 1 0.4713 0.4432 0.64 0.00 0.00 0.36
#> 1772116-060_A04 3 0.5915 0.4820 0.00 0.40 0.56 0.04
#> 1772116-063_F02 2 0.4948 -0.2223 0.00 0.56 0.44 0.00
#> 1772116-064_F03 3 0.4522 0.7136 0.00 0.32 0.68 0.00
#> 1772099-262_C01 1 0.1211 0.8043 0.96 0.00 0.00 0.04
#> 1772099-258_F12 1 0.3610 0.7133 0.80 0.00 0.00 0.20
#> 1772099-237_H01 2 0.0000 0.7367 0.00 1.00 0.00 0.00
#> 1772099-258_D08 1 0.2011 0.8039 0.92 0.00 0.00 0.08
#> 1772099-260_H04 2 0.0707 0.7327 0.00 0.98 0.00 0.02
#> 1772116-062_E01 1 0.1913 0.8079 0.94 0.00 0.02 0.04
#> 1772099-260_A04 1 0.1211 0.8043 0.96 0.00 0.00 0.04
#> 1772099-262_G01 1 0.2011 0.8082 0.92 0.00 0.00 0.08
#> 1772099-258_B05 1 0.1211 0.8095 0.96 0.00 0.00 0.04
#> 1772099-262_F12 1 0.0000 0.8115 1.00 0.00 0.00 0.00
#> 1772099-258_D01 2 0.1411 0.7237 0.00 0.96 0.02 0.02
#> 1772116-060_F06 3 0.5820 0.3067 0.00 0.08 0.68 0.24
#> 1772099-241_H12 2 0.4790 -0.0421 0.00 0.62 0.38 0.00
#> 1772099-262_H12 1 0.5955 0.5658 0.72 0.02 0.08 0.18
#> 1772099-237_D03 1 0.3400 0.7184 0.82 0.00 0.00 0.18
#> 1772116-062_C05 2 0.4994 -0.3677 0.00 0.52 0.48 0.00
#> 1772116-064_F09 1 0.1637 0.8025 0.94 0.00 0.00 0.06
#> 1772099-238_H06 1 0.5860 0.2637 0.58 0.00 0.04 0.38
#> 1772116-060_F08 3 0.4079 0.6939 0.00 0.18 0.80 0.02
#> 1772116-063_A02 4 0.6831 0.5130 0.10 0.00 0.42 0.48
#> 1772116-062_D01 3 0.3610 0.7305 0.00 0.20 0.80 0.00
#> 1772116-064_C09 3 0.2647 0.6846 0.00 0.12 0.88 0.00
#> 1772099-262_D06 2 0.1211 0.7313 0.00 0.96 0.04 0.00
#> 1772099-259_G11 2 0.1211 0.7312 0.00 0.96 0.04 0.00
#> 1772116-064_B10 4 0.6212 0.4358 0.38 0.00 0.06 0.56
#> 1772116-064_C05 3 0.4907 0.6035 0.00 0.42 0.58 0.00
#> 1772099-238_B03 2 0.0707 0.7353 0.00 0.98 0.02 0.00
#> 1772099-241_F03 2 0.0000 0.7367 0.00 1.00 0.00 0.00
#> 1772099-259_A06 2 0.0000 0.7367 0.00 1.00 0.00 0.00
#> 1772116-062_A12 1 0.3801 0.6988 0.78 0.00 0.00 0.22
#> 1772099-262_B12 2 0.8268 -0.2093 0.28 0.44 0.02 0.26
#> 1772099-241_E05 1 0.2011 0.7896 0.92 0.00 0.00 0.08
#> 1772099-241_G08 1 0.4079 0.6843 0.80 0.00 0.02 0.18
#> 1772099-262_E01 1 0.0707 0.8087 0.98 0.00 0.00 0.02
#> 1772099-259_C12 1 0.8283 -0.1392 0.46 0.12 0.06 0.36
#> 1772099-259_G04 2 0.6600 0.5064 0.04 0.68 0.08 0.20
#> 1772116-060_H06 2 0.4713 0.1315 0.00 0.64 0.36 0.00
#> 1772099-240_C03 2 0.1411 0.7347 0.00 0.96 0.02 0.02
#> 1772099-238_E12 2 0.2411 0.7011 0.00 0.92 0.04 0.04
#> 1772099-259_H03 2 0.0707 0.7353 0.00 0.98 0.02 0.00
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)
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)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
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)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n_sample Cell_type(p-value) Timepoint(p-value) k
#> ATC:skmeans 178 0.003778 7.74e-01 2
#> ATC:skmeans 135 0.000357 2.05e-08 3
#> ATC:skmeans 143 0.000858 9.01e-13 4
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.
Parent node: Node0. Child nodes: Node011-leaf , Node012-leaf , Node021-leaf , Node022-leaf , Node023-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["02"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4.
#> On a matrix with 5759 rows and 155 columns.
#> Top rows (529) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 150 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.970 0.987 0.496 0.506 0.506
#> 3 3 0.999 0.966 0.985 0.295 0.794 0.615
#> 4 4 0.800 0.806 0.911 0.133 0.888 0.698
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 is 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 subgroup
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
#> 1772116-063_D07 1 0.000 0.981 1.00 0.00
#> 1772116-060_E02 1 0.000 0.981 1.00 0.00
#> 1772116-063_E05 1 0.141 0.964 0.98 0.02
#> 1772099-259_C09 2 0.000 0.993 0.00 1.00
#> 1772116-060_A08 1 0.000 0.981 1.00 0.00
#> 1772099-258_H10 1 0.000 0.981 1.00 0.00
#> 1772099-238_A02 2 0.000 0.993 0.00 1.00
#> 1772099-241_A06 1 0.000 0.981 1.00 0.00
#> 1772099-241_D11 2 0.000 0.993 0.00 1.00
#> 1772116-063_B01 2 0.000 0.993 0.00 1.00
#> 1772099-258_H03 1 0.000 0.981 1.00 0.00
#> 1772116-063_H12 1 0.000 0.981 1.00 0.00
#> 1772099-262_G05 1 0.925 0.500 0.66 0.34
#> 1772099-258_E05 1 0.000 0.981 1.00 0.00
#> 1772116-064_C11 1 0.000 0.981 1.00 0.00
#> 1772116-064_E06 1 0.000 0.981 1.00 0.00
#> 1772099-258_B02 2 0.000 0.993 0.00 1.00
#> 1772116-063_E12 1 0.000 0.981 1.00 0.00
#> 1772099-259_F02 1 0.000 0.981 1.00 0.00
#> 1772099-258_G02 2 0.000 0.993 0.00 1.00
#> 1772116-063_E07 2 0.000 0.993 0.00 1.00
#> 1772099-258_G11 1 0.000 0.981 1.00 0.00
#> 1772116-063_G12 1 0.000 0.981 1.00 0.00
#> 1772116-062_H09 2 0.000 0.993 0.00 1.00
#> 1772116-064_H09 1 0.000 0.981 1.00 0.00
#> 1772099-262_B04 1 0.000 0.981 1.00 0.00
#> 1772099-258_C04 2 0.000 0.993 0.00 1.00
#> 1772116-060_C03 1 0.000 0.981 1.00 0.00
#> 1772116-062_A01 1 0.000 0.981 1.00 0.00
#> 1772116-063_B11 2 0.000 0.993 0.00 1.00
#> 1772116-063_A04 1 0.141 0.964 0.98 0.02
#> 1772116-062_H06 2 0.000 0.993 0.00 1.00
#> 1772116-062_A07 1 0.000 0.981 1.00 0.00
#> 1772116-060_D01 1 0.000 0.981 1.00 0.00
#> 1772099-258_F03 2 0.000 0.993 0.00 1.00
#> 1772116-060_D04 2 0.327 0.933 0.06 0.94
#> 1772116-062_E05 1 0.000 0.981 1.00 0.00
#> 1772116-062_A10 1 0.000 0.981 1.00 0.00
#> 1772116-062_B09 1 0.000 0.981 1.00 0.00
#> 1772099-262_D04 1 0.760 0.727 0.78 0.22
#> 1772116-062_G10 1 0.000 0.981 1.00 0.00
#> 1772116-060_C04 1 0.000 0.981 1.00 0.00
#> 1772116-062_A09 2 0.000 0.993 0.00 1.00
#> 1772099-262_H02 2 0.000 0.993 0.00 1.00
#> 1772099-258_D06 2 0.000 0.993 0.00 1.00
#> 1772116-062_G04 2 0.000 0.993 0.00 1.00
#> 1772116-063_B03 1 0.000 0.981 1.00 0.00
#> 1772116-064_C08 1 0.000 0.981 1.00 0.00
#> 1772099-258_G06 2 0.000 0.993 0.00 1.00
#> 1772116-060_G08 1 0.000 0.981 1.00 0.00
#> 1772116-062_G06 1 0.827 0.658 0.74 0.26
#> 1772116-060_F07 2 0.000 0.993 0.00 1.00
#> 1772116-064_F11 1 0.795 0.692 0.76 0.24
#> 1772116-062_H11 1 0.000 0.981 1.00 0.00
#> 1772099-258_G08 2 0.000 0.993 0.00 1.00
#> 1772116-064_E07 2 0.000 0.993 0.00 1.00
#> 1772099-238_D07 1 0.000 0.981 1.00 0.00
#> 1772116-063_D04 1 0.000 0.981 1.00 0.00
#> 1772116-062_E07 2 0.000 0.993 0.00 1.00
#> 1772099-238_C02 2 0.000 0.993 0.00 1.00
#> 1772099-262_E11 2 0.000 0.993 0.00 1.00
#> 1772116-060_D07 1 0.000 0.981 1.00 0.00
#> 1772116-060_G02 2 0.000 0.993 0.00 1.00
#> 1772116-060_A12 2 0.000 0.993 0.00 1.00
#> 1772116-060_D05 1 0.000 0.981 1.00 0.00
#> 1772116-060_C08 1 0.000 0.981 1.00 0.00
#> 1772116-060_E09 2 0.000 0.993 0.00 1.00
#> 1772116-062_F06 2 0.000 0.993 0.00 1.00
#> 1772099-238_A10 1 0.000 0.981 1.00 0.00
#> 1772099-260_H06 2 0.000 0.993 0.00 1.00
#> 1772116-060_C02 2 0.141 0.974 0.02 0.98
#> 1772116-060_F09 2 0.000 0.993 0.00 1.00
#> 1772116-063_F04 1 0.000 0.981 1.00 0.00
#> 1772116-063_A07 2 0.000 0.993 0.00 1.00
#> 1772099-260_E06 1 0.000 0.981 1.00 0.00
#> 1772099-260_F11 1 0.958 0.406 0.62 0.38
#> 1772099-258_H02 2 0.000 0.993 0.00 1.00
#> 1772116-063_D11 2 0.000 0.993 0.00 1.00
#> 1772099-240_G05 1 0.000 0.981 1.00 0.00
#> 1772116-063_C11 2 0.000 0.993 0.00 1.00
#> 1772116-064_A01 1 0.000 0.981 1.00 0.00
#> 1772116-063_E10 2 0.000 0.993 0.00 1.00
#> 1772116-064_D03 1 0.000 0.981 1.00 0.00
#> 1772116-060_C09 2 0.000 0.993 0.00 1.00
#> 1772116-064_B07 2 0.795 0.682 0.24 0.76
#> 1772116-064_H02 2 0.000 0.993 0.00 1.00
#> 1772099-237_G06 2 0.000 0.993 0.00 1.00
#> 1772116-062_A11 1 0.000 0.981 1.00 0.00
#> 1772116-060_B11 2 0.000 0.993 0.00 1.00
#> 1772116-063_C04 2 0.000 0.993 0.00 1.00
#> 1772116-062_F09 1 0.000 0.981 1.00 0.00
#> 1772116-064_D02 1 0.000 0.981 1.00 0.00
#> 1772116-064_B09 1 0.000 0.981 1.00 0.00
#> 1772116-064_C04 1 0.000 0.981 1.00 0.00
#> 1772099-238_C07 2 0.000 0.993 0.00 1.00
#> 1772116-063_E04 1 0.000 0.981 1.00 0.00
#> 1772116-062_B11 2 0.000 0.993 0.00 1.00
#> 1772099-238_A09 2 0.000 0.993 0.00 1.00
#> 1772116-060_B01 1 0.000 0.981 1.00 0.00
#> 1772116-060_E03 1 0.000 0.981 1.00 0.00
#> 1772116-062_E04 2 0.000 0.993 0.00 1.00
#> 1772116-063_H02 2 0.000 0.993 0.00 1.00
#> 1772116-063_F11 1 0.000 0.981 1.00 0.00
#> 1772116-060_F01 1 0.000 0.981 1.00 0.00
#> 1772116-060_B10 1 0.000 0.981 1.00 0.00
#> 1772116-060_H08 1 0.000 0.981 1.00 0.00
#> 1772099-241_H05 1 0.000 0.981 1.00 0.00
#> 1772116-063_B06 1 0.000 0.981 1.00 0.00
#> 1772099-258_D09 1 0.000 0.981 1.00 0.00
#> 1772116-063_H11 2 0.000 0.993 0.00 1.00
#> 1772116-062_C10 1 0.000 0.981 1.00 0.00
#> 1772099-240_H02 2 0.000 0.993 0.00 1.00
#> 1772099-260_A07 2 0.000 0.993 0.00 1.00
#> 1772099-259_C04 2 0.000 0.993 0.00 1.00
#> 1772116-062_F01 1 0.000 0.981 1.00 0.00
#> 1772116-060_E11 2 0.000 0.993 0.00 1.00
#> 1772099-262_B11 1 0.000 0.981 1.00 0.00
#> 1772116-063_H05 1 0.000 0.981 1.00 0.00
#> 1772116-064_B04 1 0.327 0.927 0.94 0.06
#> 1772099-260_B06 1 0.141 0.964 0.98 0.02
#> 1772099-258_B06 1 0.000 0.981 1.00 0.00
#> 1772099-262_A02 1 0.000 0.981 1.00 0.00
#> 1772099-238_F03 1 0.000 0.981 1.00 0.00
#> 1772116-062_G05 1 0.000 0.981 1.00 0.00
#> 1772116-060_G01 1 0.000 0.981 1.00 0.00
#> 1772116-060_B06 1 0.000 0.981 1.00 0.00
#> 1772099-241_H06 2 0.469 0.885 0.10 0.90
#> 1772116-062_B06 2 0.000 0.993 0.00 1.00
#> 1772116-062_D11 1 0.000 0.981 1.00 0.00
#> 1772116-064_E09 2 0.000 0.993 0.00 1.00
#> 1772116-062_E08 1 0.000 0.981 1.00 0.00
#> 1772116-060_H02 2 0.000 0.993 0.00 1.00
#> 1772116-064_C07 2 0.000 0.993 0.00 1.00
#> 1772116-060_A05 1 0.242 0.946 0.96 0.04
#> 1772099-262_D02 1 0.242 0.947 0.96 0.04
#> 1772099-258_C06 2 0.000 0.993 0.00 1.00
#> 1772099-258_F06 1 0.000 0.981 1.00 0.00
#> 1772099-260_A02 2 0.000 0.993 0.00 1.00
#> 1772099-258_C03 1 0.000 0.981 1.00 0.00
#> 1772099-237_F01 1 0.000 0.981 1.00 0.00
#> 1772099-238_H10 1 0.000 0.981 1.00 0.00
#> 1772099-258_G04 2 0.000 0.993 0.00 1.00
#> 1772099-258_G09 2 0.000 0.993 0.00 1.00
#> 1772116-062_F02 2 0.000 0.993 0.00 1.00
#> 1772099-262_F11 1 0.000 0.981 1.00 0.00
#> 1772116-062_E10 1 0.000 0.981 1.00 0.00
#> 1772099-258_C01 1 0.000 0.981 1.00 0.00
#> 1772099-240_D02 1 0.000 0.981 1.00 0.00
#> 1772099-260_C03 1 0.000 0.981 1.00 0.00
#> 1772116-063_A09 2 0.000 0.993 0.00 1.00
#> 1772099-260_C06 2 0.000 0.993 0.00 1.00
#> 1772099-238_C01 1 0.000 0.981 1.00 0.00
#> 1772099-240_F07 2 0.000 0.993 0.00 1.00
#> 1772099-241_G09 2 0.000 0.993 0.00 1.00
#> 1772116-063_G02 2 0.000 0.993 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> 1772116-063_D07 1 0.2066 0.929 0.94 0.00 0.06
#> 1772116-060_E02 3 0.0000 0.964 0.00 0.00 1.00
#> 1772116-063_E05 1 0.2066 0.927 0.94 0.06 0.00
#> 1772099-259_C09 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-060_A08 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-258_H10 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-238_A02 2 0.0000 0.995 0.00 1.00 0.00
#> 1772099-241_A06 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-241_D11 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-063_B01 2 0.2537 0.916 0.00 0.92 0.08
#> 1772099-258_H03 1 0.5216 0.644 0.74 0.00 0.26
#> 1772116-063_H12 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-262_G05 3 0.0000 0.964 0.00 0.00 1.00
#> 1772099-258_E05 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-064_C11 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-064_E06 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-258_B02 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-063_E12 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-259_F02 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-258_G02 3 0.0000 0.964 0.00 0.00 1.00
#> 1772116-063_E07 2 0.0000 0.995 0.00 1.00 0.00
#> 1772099-258_G11 1 0.4555 0.747 0.80 0.00 0.20
#> 1772116-063_G12 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-062_H09 3 0.3340 0.845 0.00 0.12 0.88
#> 1772116-064_H09 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-262_B04 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-258_C04 3 0.0000 0.964 0.00 0.00 1.00
#> 1772116-060_C03 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-062_A01 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-063_B11 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-063_A04 3 0.0000 0.964 0.00 0.00 1.00
#> 1772116-062_H06 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-062_A07 3 0.1529 0.928 0.04 0.00 0.96
#> 1772116-060_D01 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-258_F03 2 0.0892 0.978 0.00 0.98 0.02
#> 1772116-060_D04 2 0.0892 0.973 0.02 0.98 0.00
#> 1772116-062_E05 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-062_A10 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-062_B09 3 0.0000 0.964 0.00 0.00 1.00
#> 1772099-262_D04 3 0.0000 0.964 0.00 0.00 1.00
#> 1772116-062_G10 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-060_C04 3 0.5706 0.543 0.32 0.00 0.68
#> 1772116-062_A09 2 0.0000 0.995 0.00 1.00 0.00
#> 1772099-262_H02 3 0.0000 0.964 0.00 0.00 1.00
#> 1772099-258_D06 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-062_G04 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-063_B03 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-064_C08 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-258_G06 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-060_G08 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-062_G06 3 0.6232 0.702 0.22 0.04 0.74
#> 1772116-060_F07 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-064_F11 3 0.0000 0.964 0.00 0.00 1.00
#> 1772116-062_H11 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-258_G08 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-064_E07 2 0.0000 0.995 0.00 1.00 0.00
#> 1772099-238_D07 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-063_D04 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-062_E07 2 0.0000 0.995 0.00 1.00 0.00
#> 1772099-238_C02 2 0.0000 0.995 0.00 1.00 0.00
#> 1772099-262_E11 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-060_D07 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-060_G02 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-060_A12 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-060_D05 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-060_C08 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-060_E09 3 0.0000 0.964 0.00 0.00 1.00
#> 1772116-062_F06 2 0.0000 0.995 0.00 1.00 0.00
#> 1772099-238_A10 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-260_H06 3 0.0892 0.948 0.00 0.02 0.98
#> 1772116-060_C02 3 0.0000 0.964 0.00 0.00 1.00
#> 1772116-060_F09 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-063_F04 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-063_A07 3 0.0000 0.964 0.00 0.00 1.00
#> 1772099-260_E06 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-260_F11 3 0.0000 0.964 0.00 0.00 1.00
#> 1772099-258_H02 3 0.0000 0.964 0.00 0.00 1.00
#> 1772116-063_D11 2 0.0000 0.995 0.00 1.00 0.00
#> 1772099-240_G05 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-063_C11 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-064_A01 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-063_E10 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-064_D03 1 0.0892 0.968 0.98 0.02 0.00
#> 1772116-060_C09 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-064_B07 2 0.2066 0.926 0.06 0.94 0.00
#> 1772116-064_H02 2 0.0000 0.995 0.00 1.00 0.00
#> 1772099-237_G06 3 0.0000 0.964 0.00 0.00 1.00
#> 1772116-062_A11 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-060_B11 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-063_C04 3 0.0000 0.964 0.00 0.00 1.00
#> 1772116-062_F09 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-064_D02 3 0.0000 0.964 0.00 0.00 1.00
#> 1772116-064_B09 3 0.0000 0.964 0.00 0.00 1.00
#> 1772116-064_C04 3 0.6045 0.402 0.38 0.00 0.62
#> 1772099-238_C07 3 0.0000 0.964 0.00 0.00 1.00
#> 1772116-063_E04 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-062_B11 2 0.0000 0.995 0.00 1.00 0.00
#> 1772099-238_A09 3 0.0000 0.964 0.00 0.00 1.00
#> 1772116-060_B01 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-060_E03 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-062_E04 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-063_H02 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-063_F11 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-060_F01 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-060_B10 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-060_H08 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-241_H05 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-063_B06 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-258_D09 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-063_H11 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-062_C10 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-240_H02 2 0.0892 0.978 0.00 0.98 0.02
#> 1772099-260_A07 3 0.1529 0.930 0.00 0.04 0.96
#> 1772099-259_C04 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-062_F01 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-060_E11 3 0.0000 0.964 0.00 0.00 1.00
#> 1772099-262_B11 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-063_H05 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-064_B04 3 0.0000 0.964 0.00 0.00 1.00
#> 1772099-260_B06 3 0.0000 0.964 0.00 0.00 1.00
#> 1772099-258_B06 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-262_A02 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-238_F03 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-062_G05 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-060_G01 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-060_B06 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-241_H06 3 0.0000 0.964 0.00 0.00 1.00
#> 1772116-062_B06 2 0.0892 0.978 0.00 0.98 0.02
#> 1772116-062_D11 1 0.2959 0.883 0.90 0.00 0.10
#> 1772116-064_E09 3 0.0000 0.964 0.00 0.00 1.00
#> 1772116-062_E08 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-060_H02 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-064_C07 2 0.0000 0.995 0.00 1.00 0.00
#> 1772116-060_A05 1 0.4291 0.782 0.82 0.18 0.00
#> 1772099-262_D02 3 0.0000 0.964 0.00 0.00 1.00
#> 1772099-258_C06 2 0.0000 0.995 0.00 1.00 0.00
#> 1772099-258_F06 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-260_A02 2 0.0000 0.995 0.00 1.00 0.00
#> 1772099-258_C03 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-237_F01 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-238_H10 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-258_G04 3 0.0000 0.964 0.00 0.00 1.00
#> 1772099-258_G09 3 0.0000 0.964 0.00 0.00 1.00
#> 1772116-062_F02 2 0.0000 0.995 0.00 1.00 0.00
#> 1772099-262_F11 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-062_E10 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-258_C01 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-240_D02 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-260_C03 1 0.0000 0.987 1.00 0.00 0.00
#> 1772116-063_A09 2 0.0000 0.995 0.00 1.00 0.00
#> 1772099-260_C06 2 0.0000 0.995 0.00 1.00 0.00
#> 1772099-238_C01 1 0.0000 0.987 1.00 0.00 0.00
#> 1772099-240_F07 2 0.0000 0.995 0.00 1.00 0.00
#> 1772099-241_G09 3 0.0000 0.964 0.00 0.00 1.00
#> 1772116-063_G02 3 0.0000 0.964 0.00 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> 1772116-063_D07 1 0.0707 0.899 0.98 0.00 0.02 0.00
#> 1772116-060_E02 3 0.2011 0.868 0.08 0.00 0.92 0.00
#> 1772116-063_E05 4 0.0000 0.761 0.00 0.00 0.00 1.00
#> 1772099-259_C09 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> 1772116-060_A08 4 0.3975 0.680 0.24 0.00 0.00 0.76
#> 1772099-258_H10 4 0.2921 0.764 0.14 0.00 0.00 0.86
#> 1772099-238_A02 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> 1772099-241_A06 1 0.0707 0.906 0.98 0.00 0.00 0.02
#> 1772099-241_D11 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> 1772116-063_B01 2 0.2921 0.793 0.00 0.86 0.14 0.00
#> 1772099-258_H03 1 0.0707 0.899 0.98 0.00 0.02 0.00
#> 1772116-063_H12 1 0.2011 0.862 0.92 0.00 0.00 0.08
#> 1772099-262_G05 3 0.2011 0.867 0.08 0.00 0.92 0.00
#> 1772099-258_E05 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772116-064_C11 1 0.1211 0.880 0.96 0.00 0.04 0.00
#> 1772116-064_E06 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772099-258_B02 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> 1772116-063_E12 4 0.4948 0.341 0.44 0.00 0.00 0.56
#> 1772099-259_F02 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772099-258_G02 3 0.1637 0.897 0.00 0.06 0.94 0.00
#> 1772116-063_E07 2 0.0707 0.912 0.00 0.98 0.00 0.02
#> 1772099-258_G11 1 0.1637 0.867 0.94 0.00 0.06 0.00
#> 1772116-063_G12 1 0.0707 0.906 0.98 0.00 0.00 0.02
#> 1772116-062_H09 3 0.4277 0.638 0.00 0.28 0.72 0.00
#> 1772116-064_H09 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772099-262_B04 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772099-258_C04 3 0.1211 0.907 0.00 0.04 0.96 0.00
#> 1772116-060_C03 4 0.5000 0.144 0.50 0.00 0.00 0.50
#> 1772116-062_A01 1 0.4713 0.351 0.64 0.00 0.00 0.36
#> 1772116-063_B11 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> 1772116-063_A04 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> 1772116-062_H06 2 0.1211 0.906 0.00 0.96 0.00 0.04
#> 1772116-062_A07 3 0.4907 0.306 0.42 0.00 0.58 0.00
#> 1772116-060_D01 4 0.4977 0.285 0.46 0.00 0.00 0.54
#> 1772099-258_F03 2 0.3198 0.847 0.00 0.88 0.08 0.04
#> 1772116-060_D04 4 0.3610 0.513 0.00 0.20 0.00 0.80
#> 1772116-062_E05 1 0.4855 0.203 0.60 0.00 0.00 0.40
#> 1772116-062_A10 1 0.0707 0.906 0.98 0.00 0.00 0.02
#> 1772116-062_B09 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> 1772099-262_D04 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> 1772116-062_G10 4 0.1211 0.778 0.04 0.00 0.00 0.96
#> 1772116-060_C04 1 0.2921 0.760 0.86 0.00 0.14 0.00
#> 1772116-062_A09 2 0.1211 0.906 0.00 0.96 0.00 0.04
#> 1772099-262_H02 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> 1772099-258_D06 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> 1772116-062_G04 2 0.4522 0.636 0.00 0.68 0.00 0.32
#> 1772116-063_B03 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772116-064_C08 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772099-258_G06 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> 1772116-060_G08 4 0.0000 0.761 0.00 0.00 0.00 1.00
#> 1772116-062_G06 3 0.8106 0.386 0.24 0.08 0.56 0.12
#> 1772116-060_F07 2 0.0707 0.912 0.00 0.98 0.00 0.02
#> 1772116-064_F11 3 0.2345 0.845 0.10 0.00 0.90 0.00
#> 1772116-062_H11 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772099-258_G08 2 0.0707 0.912 0.00 0.98 0.00 0.02
#> 1772116-064_E07 2 0.5956 0.666 0.00 0.68 0.10 0.22
#> 1772099-238_D07 4 0.2647 0.772 0.12 0.00 0.00 0.88
#> 1772116-063_D04 1 0.0707 0.906 0.98 0.00 0.00 0.02
#> 1772116-062_E07 2 0.0707 0.912 0.00 0.98 0.00 0.02
#> 1772099-238_C02 2 0.1211 0.906 0.00 0.96 0.00 0.04
#> 1772099-262_E11 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> 1772116-060_D07 1 0.2011 0.867 0.92 0.00 0.00 0.08
#> 1772116-060_G02 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> 1772116-060_A12 2 0.1211 0.906 0.00 0.96 0.00 0.04
#> 1772116-060_D05 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772116-060_C08 4 0.0707 0.771 0.02 0.00 0.00 0.98
#> 1772116-060_E09 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> 1772116-062_F06 2 0.0707 0.912 0.00 0.98 0.00 0.02
#> 1772099-238_A10 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772099-260_H06 3 0.3610 0.761 0.00 0.20 0.80 0.00
#> 1772116-060_C02 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> 1772116-060_F09 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> 1772116-063_F04 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772116-063_A07 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> 1772099-260_E06 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772099-260_F11 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> 1772099-258_H02 3 0.0707 0.916 0.00 0.02 0.98 0.00
#> 1772116-063_D11 2 0.4977 0.394 0.00 0.54 0.00 0.46
#> 1772099-240_G05 4 0.4907 0.402 0.42 0.00 0.00 0.58
#> 1772116-063_C11 2 0.0707 0.912 0.00 0.98 0.00 0.02
#> 1772116-064_A01 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772116-063_E10 4 0.1211 0.731 0.00 0.04 0.00 0.96
#> 1772116-064_D03 4 0.0000 0.761 0.00 0.00 0.00 1.00
#> 1772116-060_C09 2 0.4624 0.605 0.00 0.66 0.00 0.34
#> 1772116-064_B07 4 0.0707 0.745 0.00 0.02 0.00 0.98
#> 1772116-064_H02 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> 1772099-237_G06 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> 1772116-062_A11 4 0.1637 0.782 0.06 0.00 0.00 0.94
#> 1772116-060_B11 2 0.1211 0.906 0.00 0.96 0.00 0.04
#> 1772116-063_C04 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> 1772116-062_F09 1 0.4907 0.141 0.58 0.00 0.00 0.42
#> 1772116-064_D02 3 0.2345 0.847 0.10 0.00 0.90 0.00
#> 1772116-064_B09 3 0.2921 0.802 0.14 0.00 0.86 0.00
#> 1772116-064_C04 1 0.2647 0.792 0.88 0.00 0.12 0.00
#> 1772099-238_C07 3 0.0707 0.916 0.00 0.02 0.98 0.00
#> 1772116-063_E04 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772116-062_B11 2 0.4994 0.349 0.00 0.52 0.00 0.48
#> 1772099-238_A09 3 0.0707 0.916 0.00 0.02 0.98 0.00
#> 1772116-060_B01 1 0.1211 0.896 0.96 0.00 0.00 0.04
#> 1772116-060_E03 1 0.1211 0.894 0.96 0.00 0.00 0.04
#> 1772116-062_E04 2 0.1637 0.896 0.00 0.94 0.00 0.06
#> 1772116-063_H02 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> 1772116-063_F11 1 0.2921 0.796 0.86 0.00 0.00 0.14
#> 1772116-060_F01 1 0.4790 0.284 0.62 0.00 0.00 0.38
#> 1772116-060_B10 1 0.3610 0.707 0.80 0.00 0.00 0.20
#> 1772116-060_H08 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772099-241_H05 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772116-063_B06 1 0.0707 0.905 0.98 0.00 0.00 0.02
#> 1772099-258_D09 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772116-063_H11 2 0.4948 0.436 0.00 0.56 0.00 0.44
#> 1772116-062_C10 4 0.4948 0.353 0.44 0.00 0.00 0.56
#> 1772099-240_H02 2 0.1211 0.890 0.00 0.96 0.04 0.00
#> 1772099-260_A07 3 0.2921 0.828 0.00 0.14 0.86 0.00
#> 1772099-259_C04 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> 1772116-062_F01 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772116-060_E11 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> 1772099-262_B11 1 0.1211 0.894 0.96 0.00 0.00 0.04
#> 1772116-063_H05 4 0.3400 0.740 0.18 0.00 0.00 0.82
#> 1772116-064_B04 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> 1772099-260_B06 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> 1772099-258_B06 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772099-262_A02 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772099-238_F03 1 0.2345 0.842 0.90 0.00 0.00 0.10
#> 1772116-062_G05 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772116-060_G01 1 0.1211 0.892 0.96 0.00 0.00 0.04
#> 1772116-060_B06 1 0.1211 0.894 0.96 0.00 0.00 0.04
#> 1772099-241_H06 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> 1772116-062_B06 2 0.1211 0.890 0.00 0.96 0.04 0.00
#> 1772116-062_D11 1 0.5147 0.610 0.74 0.00 0.06 0.20
#> 1772116-064_E09 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> 1772116-062_E08 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772116-060_H02 2 0.1211 0.906 0.00 0.96 0.00 0.04
#> 1772116-064_C07 2 0.4994 0.351 0.00 0.52 0.00 0.48
#> 1772116-060_A05 4 0.0000 0.761 0.00 0.00 0.00 1.00
#> 1772099-262_D02 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> 1772099-258_C06 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> 1772099-258_F06 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772099-260_A02 2 0.0707 0.903 0.00 0.98 0.02 0.00
#> 1772099-258_C03 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772099-237_F01 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772099-238_H10 1 0.5000 -0.202 0.50 0.00 0.00 0.50
#> 1772099-258_G04 3 0.0707 0.916 0.00 0.02 0.98 0.00
#> 1772099-258_G09 3 0.1211 0.907 0.00 0.04 0.96 0.00
#> 1772116-062_F02 2 0.1211 0.906 0.00 0.96 0.00 0.04
#> 1772099-262_F11 4 0.2345 0.778 0.10 0.00 0.00 0.90
#> 1772116-062_E10 1 0.0707 0.906 0.98 0.00 0.00 0.02
#> 1772099-258_C01 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772099-240_D02 4 0.6262 0.389 0.40 0.00 0.06 0.54
#> 1772099-260_C03 1 0.0000 0.913 1.00 0.00 0.00 0.00
#> 1772116-063_A09 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> 1772099-260_C06 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> 1772099-238_C01 1 0.3400 0.737 0.82 0.00 0.00 0.18
#> 1772099-240_F07 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> 1772099-241_G09 3 0.2011 0.883 0.00 0.08 0.92 0.00
#> 1772116-063_G02 3 0.2011 0.882 0.00 0.08 0.92 0.00
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)
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)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
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)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n_sample Cell_type(p-value) Timepoint(p-value) k
#> ATC:skmeans 154 0.241 0.344 2
#> ATC:skmeans 154 0.453 0.297 3
#> ATC:skmeans 138 0.362 0.152 4
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 4.1.0 (2021-05-18)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#>
#> Matrix products: default
#> BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
#> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] grid parallel stats4 stats graphics grDevices utils datasets methods
#> [10] base
#>
#> other attached packages:
#> [1] genefilter_1.74.0 ComplexHeatmap_2.8.0 markdown_1.1
#> [4] knitr_1.33 scRNAseq_2.6.1 SingleCellExperiment_1.14.1
#> [7] SummarizedExperiment_1.22.0 Biobase_2.52.0 GenomicRanges_1.44.0
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