Package: cola 2.19.0

Zuguang Gu

cola: A Framework for Consensus Partitioning

Subgroup classification is a basic task in genomic data analysis, especially for gene expression and DNA methylation data analysis. It can also be used to test the agreement to known clinical annotations, or to test whether there exist significant batch effects. The cola package provides a general framework for subgroup classification by consensus partitioning. It has the following features: 1. It modularizes the consensus partitioning processes that various methods can be easily integrated. 2. It provides rich visualizations for interpreting the results. 3. It allows running multiple methods at the same time and provides functionalities to straightforward compare results. 4. It provides a new method to extract features which are more efficient to separate subgroups. 5. It automatically generates detailed reports for the complete analysis. 6. It allows applying consensus partitioning in a hierarchical manner.

Authors:Zuguang Gu [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cola/json (API)

# Install 'cola' in R:

install.packages('cola', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jokergoo/cola/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

cola_rl - Example ConsensusPartitionList object
golub_cola - Example ConsensusPartitionList object from Golub dataset
golub_cola_ds - Example DownSamplingConsensusPartition object from Golub dataset
golub_cola_rh - Example HierarchicalPartition object from Golub dataset

On BioConductor:cola-2.19.0(bioc 3.24)cola-2.18.0(bioc 3.23)

clustering geneexpression classification software consensus-clustering cpp

7.68 score 64 stars 165 scripts 1 mentions 90 exports 54 dependencies

Last updated from:713af79d9c. Checks:4 ERROR, 2 OK, 8 NOTE. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	352
linux-devel-arm64	ERROR	446
linux-devel-x86_64	ERROR	481
source / vignettes	OK	477
linux-release-arm64	NOTE	421
linux-release-x86_64	NOTE	490
macos-release-arm64	NOTE	275
macos-release-x86_64	NOTE	541
macos-oldrel-arm64	NOTE	216
macos-oldrel-x86_64	NOTE	359
windows-devel	ERROR	364
windows-release	NOTE	419
windows-oldrel	NOTE	376
wasm-release	OK	379

Exports:[.ConsensusPartitionList [.HierarchicalPartition [[.ConsensusPartitionList [[.HierarchicalPartition adjust_matrix adjust_outlier all_leaves all_nodes all_partition_methods all_top_value_methods aPAC ATC ATC_approx cola cola_opt cola_report collect_classes collect_plots collect_stats colnames compare_partitions compare_signatures concordance config_ATC consensus_heatmap consensus_partition consensus_partition_by_down_sampling ConsensusPartition ConsensusPartitionList correspond_between_rankings correspond_between_two_rankings david_enrichment dim.ConsensusPartition dim.ConsensusPartitionList dim.DownSamplingConsensusPartition dim.HierarchicalPartition dimension_reduction DownSamplingConsensusPartition FCC find_best_km functional_enrichment get_anno get_anno_col get_children_nodes get_classes get_consensus get_matrix get_membership get_param get_signatures get_stats hierarchical_partition HierarchicalPartition is_best_k is_leaf_node is_stable_k knee_finder2 knitr_add_tab_item knitr_insert_tabs map_to_entrez_id max_depth membership_heatmap merge_node merge_node_param ncol node_info node_level nrow PAC plot_ecdf predict_classes print.hc_table_suggest_best_k recalc_stats register_NMF register_partition_methods register_SOM register_top_value_methods relabel_class remove_partition_methods remove_top_value_methods rownames run_all_consensus_partition_methods select_partition_number split_node suggest_best_k test_between_factors test_to_known_factors top_elements_overlap top_rows_heatmap top_rows_overlap

Dependencies:askpass BiocGenerics brew circlize cli clue cluster codetools colorspace commonmark ComplexHeatmap crayon curl digest doParallel doRNG eulerr evaluate foreach generics GetoptLong GlobalOptions highr httr impute IRanges irlba iterators jsonlite knitr lattice litedown markdown Matrix matrixStats mclust microbenchmark mime openssl png R6 RColorBrewer Rcpp rjson rlang rngtools S4Vectors shape skmeans slam sys xfun xml2 yaml

The cola package

Rendered fromcola.Rmdusingknitr::rmarkdown

Last update: 2025-02-06
Started: 2018-11-12

Help page	Topics
Subset a ConsensusPartitionList object	Extract.ConsensusPartitionList [.ConsensusPartitionList
Subset the HierarchicalPartition object	Extract.HierarchicalPartition [.HierarchicalPartition
Subset a ConsensusPartitionList object	ExtractExtract.ConsensusPartitionList [[.ConsensusPartitionList
Subset the HierarchicalPartition object	ExtractExtract.HierarchicalPartition [[.HierarchicalPartition
Remove rows with low variance and impute missing values	adjust_matrix
Adjust outliers	adjust_outlier
All leaves in the hierarchy	all_leaves all_leaves,HierarchicalPartition-method
All nodes in the hierarchy	all_nodes all_nodes,HierarchicalPartition-method
All supported partitioning methods	all_partition_methods
All supported top-value methods	all_top_value_methods
Adapted PAC scores	aPAC
Ability to correlate to other rows	ATC
Ability to correlate to other rows - an approximated method	ATC_approx
A bottle of cola	cola
Global parameters	cola_opt
Make HTML report from the ConsensusPartition object	cola_report,ConsensusPartition-method
Make HTML report from the ConsensusPartitionList object	cola_report,ConsensusPartitionList-method
Method dispatch page for cola_report	cola_report
Make HTML report from the HierarchicalPartition object	cola_report,HierarchicalPartition-method
Example ConsensusPartitionList object	cola_rl
Collect subgroups from ConsensusPartition object	collect_classes,ConsensusPartition-method
Collect classes from ConsensusPartitionList object	collect_classes,ConsensusPartitionList-method
Method dispatch page for collect_classes	collect_classes
Collect classes from HierarchicalPartition object	collect_classes,HierarchicalPartition-method
Collect plots from ConsensusPartition object	collect_plots,ConsensusPartition-method
Collect plots from ConsensusPartitionList object	collect_plots,ConsensusPartitionList-method
Method dispatch page for collect_plots	collect_plots
Draw and compare statistics for a single method	collect_stats,ConsensusPartition-method
Draw and compare statistics for multiple methods	collect_stats,ConsensusPartitionList-method
Method dispatch page for collect_stats	collect_stats
Column names of the matrix	colnames,ConsensusPartition-method
Column names of the matrix	colnames,ConsensusPartitionList-method
Method dispatch page for colnames	colnames
Column names of the matrix	colnames,DownSamplingConsensusPartition-method
Column names of the matrix	colnames,HierarchicalPartition-method
Compare two partitionings	compare_partitions compare_partitions,ConsensusPartition-method
Compare Signatures from Different k	compare_signatures,ConsensusPartition-method
Method dispatch page for compare_signatures	compare_signatures
Compare Signatures from Different Nodes	compare_signatures,HierarchicalPartition-method
Concordance to the consensus partition	concordance
Adjust parameters for default ATC method	config_ATC
Heatmap of the consensus matrix	consensus_heatmap consensus_heatmap,ConsensusPartition-method
Consensus partition	consensus_partition
Consensus partitioning only with a subset of columns	consensus_partition_by_down_sampling
The ConsensusPartition class	ConsensusPartition ConsensusPartition-class
The ConsensusPartitionList class	ConsensusPartitionList ConsensusPartitionList-class
Correspond between a list of rankings	correspond_between_rankings
Correspond two rankings	correspond_between_two_rankings
Perform DAVID enrichment analysis	david_enrichment
Dimension of the matrix	dim.ConsensusPartition
Dimension of the matrix	dim.ConsensusPartitionList
Dimension of the matrix	dim.DownSamplingConsensusPartition
Dimension of the matrix	dim.HierarchicalPartition
Visualize column after dimension reduction	dimension_reduction,ConsensusPartition-method
Method dispatch page for dimension_reduction	dimension_reduction
Visualize column after dimension reduction	dimension_reduction,DownSamplingConsensusPartition-method
Visualize columns after dimension reduction	dimension_reduction,HierarchicalPartition-method
Visualize columns after dimension reduction	dimension_reduction,matrix-method
The DownSamplingConsensusPartition class	DownSamplingConsensusPartition DownSamplingConsensusPartition-class
Flatness of the CDF curve	FCC
Find a best k for the k-means clustering	find_best_km
Perform functional enrichment on signature genes	functional_enrichment,ANY-method
Perform functional enrichment on signature genes	functional_enrichment,ConsensusPartition-method
Perform functional enrichment on signature genes	functional_enrichment,ConsensusPartitionList-method
Method dispatch page for functional_enrichment	functional_enrichment
Perform functional enrichment on signature genes	functional_enrichment,HierarchicalPartition-method
Get annotation colors	get_anno_col,ConsensusPartition-method
Get annotation colors	get_anno_col,ConsensusPartitionList-method
Method dispatch page for get_anno_col	get_anno_col
Get annotation colors	get_anno_col,HierarchicalPartition-method
Get annotations	get_anno,ConsensusPartition-method
Get annotations	get_anno,ConsensusPartitionList-method
Method dispatch page for get_anno	get_anno
Get annotations	get_anno,DownSamplingConsensusPartition-method
Get annotations	get_anno,HierarchicalPartition-method
Test whether a node is a leaf node	get_children_nodes get_children_nodes,HierarchicalPartition-method
Get subgroup labels	get_classes,ConsensusPartition-method
Get subgroup labels	get_classes,ConsensusPartitionList-method
Method dispatch page for get_classes	get_classes
Get subgroup labels	get_classes,DownSamplingConsensusPartition-method
Get class IDs from the HierarchicalPartition object	get_classes,HierarchicalPartition-method
Get consensus matrix	get_consensus get_consensus,ConsensusPartition-method
Get the original matrix	get_matrix,ConsensusPartition-method
Get the original matrix	get_matrix,ConsensusPartitionList-method
Method dispatch page for get_matrix	get_matrix
Get the original matrix	get_matrix,DownSamplingConsensusPartition-method
Get the original matrix	get_matrix,HierarchicalPartition-method
Get membership matrix	get_membership,ConsensusPartition-method
Get membership matrix	get_membership,ConsensusPartitionList-method
Method dispatch page for get_membership	get_membership
Get parameters	get_param get_param,ConsensusPartition-method
Get signature rows	get_signatures,ConsensusPartition-method
Method dispatch page for get_signatures	get_signatures
Get signature rows	get_signatures,DownSamplingConsensusPartition-method
Get signatures rows	get_signatures,HierarchicalPartition-method
Get statistics	get_stats,ConsensusPartition-method
Get statistics	get_stats,ConsensusPartitionList-method
Method dispatch page for get_stats	get_stats
Example ConsensusPartitionList object from Golub dataset	golub_cola
Example DownSamplingConsensusPartition object from Golub dataset	golub_cola_ds
Example HierarchicalPartition object from Golub dataset	golub_cola_rh
Hierarchical partition	hierarchical_partition
The HierarchicalPartition class	HierarchicalPartition HierarchicalPartition-class
Test whether the current k is the best/optional k	is_best_k,ConsensusPartition-method
Test whether the current k is the best/optional k	is_best_k,ConsensusPartitionList-method
Method dispatch page for is_best_k	is_best_k
Test whether a node is a leaf node	is_leaf_node is_leaf_node,HierarchicalPartition-method
Test whether the current k corresponds to a stable partition	is_stable_k,ConsensusPartition-method
Test whether the current k corresponds to a stable partition	is_stable_k,ConsensusPartitionList-method
Method dispatch page for is_stable_k	is_stable_k
Find the knee/elbow of a list of sorted points	knee_finder2
Add JavaScript tab in the report	knitr_add_tab_item
Generate the HTML fragment for the JavaScript tabs	knitr_insert_tabs
Map to Entrez IDs	map_to_entrez_id
Max depth of the hierarchy	max_depth max_depth,HierarchicalPartition-method
Heatmap of membership in each partition	membership_heatmap membership_heatmap,ConsensusPartition-method
Parameters to merge branches in subgroup dendrogram.	merge_node_param
Merge node	merge_node merge_node,HierarchicalPartition-method
Number of columns in the matrix	ncol,ConsensusPartition-method
Number of columns in the matrix	ncol,ConsensusPartitionList-method
Method dispatch page for ncol	ncol
Number of columns in the matrix	ncol,DownSamplingConsensusPartition-method
Number of columns in the matrix	ncol,HierarchicalPartition-method
Information on the nodes	node_info node_info,HierarchicalPartition-method
Information on the nodes	node_level node_level,HierarchicalPartition-method
Number of rows in the matrix	nrow,ConsensusPartition-method
Number of rows in the matrix	nrow,ConsensusPartitionList-method
Method dispatch page for nrow	nrow
Number of rows in the matrix	nrow,HierarchicalPartition-method
The proportion of ambiguous clustering (PAC score)	PAC
Plot the empirical cumulative distribution (eCDF) curve of the consensus matrix	plot_ecdf plot_ecdf,ConsensusPartition-method
Predict classes for new samples based on cola classification	predict_classes,ConsensusPartition-method
Method dispatch page for predict_classes	predict_classes
Predict classes for new samples based on signature centroid matrix	predict_classes,matrix-method
Print the hc_table_suggest_best_k object	print.hc_table_suggest_best_k
Recalculate statistics in the ConsensusPartitionList object	recalc_stats
Register NMF partitioning method	register_NMF
Register user-defined partitioning methods	register_partition_methods
Register SOM partitioning method	register_SOM
Register user-defined top-value methods	register_top_value_methods
Relabel class labels according to the reference labels	relabel_class
Remove partitioning methods	remove_partition_methods
Remove top-value methods	remove_top_value_methods
Row names of the matrix	rownames,ConsensusPartition-method
Row names of the matrix	rownames,ConsensusPartitionList-method
Method dispatch page for rownames	rownames
Row names of the matrix	rownames,HierarchicalPartition-method
Consensus partitioning for all combinations of methods	run_all_consensus_partition_methods
Several plots for determining the optimized number of subgroups	select_partition_number select_partition_number,ConsensusPartition-method
Print the ConsensusPartition object	show,ConsensusPartition-method
Print the ConsensusPartitionList object	show,ConsensusPartitionList-method
Method dispatch page for show	show
Print the DownSamplingConsensusPartition object	show,DownSamplingConsensusPartition-method
Print the HierarchicalPartition object	show,HierarchicalPartition-method
Split node	split_node split_node,HierarchicalPartition-method
Suggest the best number of subgroups	suggest_best_k,ConsensusPartition-method
Suggest the best number of subgroups	suggest_best_k,ConsensusPartitionList-method
Method dispatch page for suggest_best_k	suggest_best_k
Guess the best number of partitions	suggest_best_k,HierarchicalPartition-method
Test whether a list of factors are correlated	test_between_factors
Test correspondance between predicted subgroups and known factors	test_to_known_factors,ConsensusPartition-method
Test correspondance between predicted classes and known factors	test_to_known_factors,ConsensusPartitionList-method
Method dispatch page for test_to_known_factors	test_to_known_factors
Test correspondance between predicted subgroups and known factors	test_to_known_factors,DownSamplingConsensusPartition-method
Test correspondance between predicted classes and known factors	test_to_known_factors,HierarchicalPartition-method
Overlap of top elements from different metrics	top_elements_overlap
Heatmap of top rows	top_rows_heatmap,ConsensusPartition-method
Heatmap of top rows from different top-value methods	top_rows_heatmap,ConsensusPartitionList-method
Method dispatch page for top_rows_heatmap	top_rows_heatmap
Heatmap of top rows from different top-value methods	top_rows_heatmap,HierarchicalPartition-method
Heatmap of top rows from different top-value methods	top_rows_heatmap,matrix-method
Overlap of top rows from different top-value methods	top_rows_overlap,ConsensusPartitionList-method
Method dispatch page for top_rows_overlap	top_rows_overlap
Overlap of top rows on different nodes	top_rows_overlap,HierarchicalPartition-method
Overlap of top rows from different top-value methods	top_rows_overlap,matrix-method

Package: cola 2.19.0

cola: A Framework for Consensus Partitioning

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