Package: cola 2.13.0

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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NEWS

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

Peer review:

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-2.13.0(bioc 3.21)cola-2.12.0(bioc 3.20)

clusteringgeneexpressionclassificationsoftwareconsensus-clusteringcpp

7.46 score 59 stars 109 scripts 253 downloads 1 mentions 90 exports 57 dependencies

Last updated 2 months agofrom:c1c8dc8a1b. Checks:OK: 7 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-win-x86_64NOTENov 29 2024
R-4.5-linux-x86_64NOTENov 29 2024
R-4.4-win-x86_64OKNov 29 2024
R-4.4-mac-x86_64OKNov 29 2024
R-4.4-mac-aarch64OKNov 29 2024
R-4.3-win-x86_64OKNov 29 2024
R-4.3-mac-x86_64OKNov 29 2024
R-4.3-mac-aarch64OKNov 29 2024

Exports:[.ConsensusPartitionList[.HierarchicalPartition[[.ConsensusPartitionList[[.HierarchicalPartitionadjust_matrixadjust_outlierall_leavesall_nodesall_partition_methodsall_top_value_methodsaPACATCATC_approxcolacola_optcola_reportcollect_classescollect_plotscollect_statscolnamescompare_partitionscompare_signaturesconcordanceconfig_ATCconsensus_heatmapconsensus_partitionconsensus_partition_by_down_samplingConsensusPartitionConsensusPartitionListcorrespond_between_rankingscorrespond_between_two_rankingsdavid_enrichmentdim.ConsensusPartitiondim.ConsensusPartitionListdim.DownSamplingConsensusPartitiondim.HierarchicalPartitiondimension_reductionDownSamplingConsensusPartitionFCCfind_best_kmfunctional_enrichmentget_annoget_anno_colget_children_nodesget_classesget_consensusget_matrixget_membershipget_paramget_signaturesget_statshierarchical_partitionHierarchicalPartitionis_best_kis_leaf_nodeis_stable_kknee_finder2knitr_add_tab_itemknitr_insert_tabsmap_to_entrez_idmax_depthmembership_heatmapmerge_nodemerge_node_paramncolnode_infonode_levelnrowPACplot_ecdfpredict_classesprint.hc_table_suggest_best_krecalc_statsregister_NMFregister_partition_methodsregister_SOMregister_top_value_methodsrelabel_classremove_partition_methodsremove_top_value_methodsrownamesrun_all_consensus_partition_methodsselect_partition_numbersplit_nodesuggest_best_ktest_between_factorstest_to_known_factorstop_elements_overlaptop_rows_heatmaptop_rows_overlap

Dependencies:askpassBiocGenericsbrewcirclizecliclueclustercodetoolscolorspacecommonmarkComplexHeatmapcrayoncurldigestdoParalleldoRNGeulerrevaluateforeachgenericsGenSAGetoptLongGlobalOptionshighrhttrimputeIRangesirlbaiteratorsjsonliteknitrlatticemarkdownMatrixmatrixStatsmclustmicrobenchmarkmimeopensslpngpolyclippolylabelrR6RColorBrewerRcppRcppArmadillorjsonrlangrngtoolsS4Vectorsshapeskmeansslamsysxfunxml2yaml

Use of cola

Zuguang Gu ([email protected])

Rendered fromcola.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2021-07-15
Started: 2018-11-12

Readme and manuals

Help Manual

Help pageTopics
Subset a ConsensusPartitionList objectExtract.ConsensusPartitionList [.ConsensusPartitionList
Subset the HierarchicalPartition objectExtract.HierarchicalPartition [.HierarchicalPartition
Subset a ConsensusPartitionList objectExtractExtract.ConsensusPartitionList [[.ConsensusPartitionList
Subset the HierarchicalPartition objectExtractExtract.HierarchicalPartition [[.HierarchicalPartition
Remove rows with low variance and impute missing valuesadjust_matrix
Adjust outliersadjust_outlier
All leaves in the hierarchyall_leaves all_leaves,HierarchicalPartition-method
All nodes in the hierarchyall_nodes all_nodes,HierarchicalPartition-method
All supported partitioning methodsall_partition_methods
All supported top-value methodsall_top_value_methods
Adapted PAC scoresaPAC
Ability to correlate to other rowsATC
Ability to correlate to other rows - an approximated methodATC_approx
A bottle of colacola
Global parameterscola_opt
Make HTML report from the ConsensusPartition objectcola_report,ConsensusPartition-method
Make HTML report from the ConsensusPartitionList objectcola_report,ConsensusPartitionList-method
Method dispatch page for cola_reportcola_report
Make HTML report from the HierarchicalPartition objectcola_report,HierarchicalPartition-method
Example ConsensusPartitionList objectcola_rl
Collect subgroups from ConsensusPartition objectcollect_classes,ConsensusPartition-method
Collect classes from ConsensusPartitionList objectcollect_classes,ConsensusPartitionList-method
Method dispatch page for collect_classescollect_classes
Collect classes from HierarchicalPartition objectcollect_classes,HierarchicalPartition-method
Collect plots from ConsensusPartition objectcollect_plots,ConsensusPartition-method
Collect plots from ConsensusPartitionList objectcollect_plots,ConsensusPartitionList-method
Method dispatch page for collect_plotscollect_plots
Draw and compare statistics for a single methodcollect_stats,ConsensusPartition-method
Draw and compare statistics for multiple methodscollect_stats,ConsensusPartitionList-method
Method dispatch page for collect_statscollect_stats
Column names of the matrixcolnames,ConsensusPartition-method
Column names of the matrixcolnames,ConsensusPartitionList-method
Method dispatch page for colnamescolnames
Column names of the matrixcolnames,DownSamplingConsensusPartition-method
Column names of the matrixcolnames,HierarchicalPartition-method
Compare two partitioningscompare_partitions compare_partitions,ConsensusPartition-method
Compare Signatures from Different kcompare_signatures,ConsensusPartition-method
Method dispatch page for compare_signaturescompare_signatures
Compare Signatures from Different Nodescompare_signatures,HierarchicalPartition-method
Concordance to the consensus partitionconcordance
Adjust parameters for default ATC methodconfig_ATC
Heatmap of the consensus matrixconsensus_heatmap consensus_heatmap,ConsensusPartition-method
Consensus partitionconsensus_partition
Consensus partitioning only with a subset of columnsconsensus_partition_by_down_sampling
The ConsensusPartition classConsensusPartition ConsensusPartition-class
The ConsensusPartitionList classConsensusPartitionList ConsensusPartitionList-class
Correspond between a list of rankingscorrespond_between_rankings
Correspond two rankingscorrespond_between_two_rankings
Perform DAVID enrichment analysisdavid_enrichment
Dimension of the matrixdim.ConsensusPartition
Dimension of the matrixdim.ConsensusPartitionList
Dimension of the matrixdim.DownSamplingConsensusPartition
Dimension of the matrixdim.HierarchicalPartition
Visualize column after dimension reductiondimension_reduction,ConsensusPartition-method
Method dispatch page for dimension_reductiondimension_reduction
Visualize column after dimension reductiondimension_reduction,DownSamplingConsensusPartition-method
Visualize columns after dimension reductiondimension_reduction,HierarchicalPartition-method
Visualize columns after dimension reductiondimension_reduction,matrix-method
The DownSamplingConsensusPartition classDownSamplingConsensusPartition DownSamplingConsensusPartition-class
Flatness of the CDF curveFCC
Find a best k for the k-means clusteringfind_best_km
Perform functional enrichment on signature genesfunctional_enrichment,ANY-method
Perform functional enrichment on signature genesfunctional_enrichment,ConsensusPartition-method
Perform functional enrichment on signature genesfunctional_enrichment,ConsensusPartitionList-method
Method dispatch page for functional_enrichmentfunctional_enrichment
Perform functional enrichment on signature genesfunctional_enrichment,HierarchicalPartition-method
Get annotation colorsget_anno_col,ConsensusPartition-method
Get annotation colorsget_anno_col,ConsensusPartitionList-method
Method dispatch page for get_anno_colget_anno_col
Get annotation colorsget_anno_col,HierarchicalPartition-method
Get annotationsget_anno,ConsensusPartition-method
Get annotationsget_anno,ConsensusPartitionList-method
Method dispatch page for get_annoget_anno
Get annotationsget_anno,DownSamplingConsensusPartition-method
Get annotationsget_anno,HierarchicalPartition-method
Test whether a node is a leaf nodeget_children_nodes get_children_nodes,HierarchicalPartition-method
Get subgroup labelsget_classes,ConsensusPartition-method
Get subgroup labelsget_classes,ConsensusPartitionList-method
Method dispatch page for get_classesget_classes
Get subgroup labelsget_classes,DownSamplingConsensusPartition-method
Get class IDs from the HierarchicalPartition objectget_classes,HierarchicalPartition-method
Get consensus matrixget_consensus get_consensus,ConsensusPartition-method
Get the original matrixget_matrix,ConsensusPartition-method
Get the original matrixget_matrix,ConsensusPartitionList-method
Method dispatch page for get_matrixget_matrix
Get the original matrixget_matrix,DownSamplingConsensusPartition-method
Get the original matrixget_matrix,HierarchicalPartition-method
Get membership matrixget_membership,ConsensusPartition-method
Get membership matrixget_membership,ConsensusPartitionList-method
Method dispatch page for get_membershipget_membership
Get parametersget_param get_param,ConsensusPartition-method
Get signature rowsget_signatures,ConsensusPartition-method
Method dispatch page for get_signaturesget_signatures
Get signature rowsget_signatures,DownSamplingConsensusPartition-method
Get signatures rowsget_signatures,HierarchicalPartition-method
Get statisticsget_stats,ConsensusPartition-method
Get statisticsget_stats,ConsensusPartitionList-method
Method dispatch page for get_statsget_stats
Example ConsensusPartitionList object from Golub datasetgolub_cola
Example DownSamplingConsensusPartition object from Golub datasetgolub_cola_ds
Example HierarchicalPartition object from Golub datasetgolub_cola_rh
Hierarchical partitionhierarchical_partition
The HierarchicalPartition classHierarchicalPartition HierarchicalPartition-class
Test whether the current k is the best/optional kis_best_k,ConsensusPartition-method
Test whether the current k is the best/optional kis_best_k,ConsensusPartitionList-method
Method dispatch page for is_best_kis_best_k
Test whether a node is a leaf nodeis_leaf_node is_leaf_node,HierarchicalPartition-method
Test whether the current k corresponds to a stable partitionis_stable_k,ConsensusPartition-method
Test whether the current k corresponds to a stable partitionis_stable_k,ConsensusPartitionList-method
Method dispatch page for is_stable_kis_stable_k
Find the knee/elbow of a list of sorted pointsknee_finder2
Add JavaScript tab in the reportknitr_add_tab_item
Generate the HTML fragment for the JavaScript tabsknitr_insert_tabs
Map to Entrez IDsmap_to_entrez_id
Max depth of the hierarchymax_depth max_depth,HierarchicalPartition-method
Heatmap of membership in each partitionmembership_heatmap membership_heatmap,ConsensusPartition-method
Parameters to merge branches in subgroup dendrogram.merge_node_param
Merge nodemerge_node merge_node,HierarchicalPartition-method
Number of columns in the matrixncol,ConsensusPartition-method
Number of columns in the matrixncol,ConsensusPartitionList-method
Method dispatch page for ncolncol
Number of columns in the matrixncol,DownSamplingConsensusPartition-method
Number of columns in the matrixncol,HierarchicalPartition-method
Information on the nodesnode_info node_info,HierarchicalPartition-method
Information on the nodesnode_level node_level,HierarchicalPartition-method
Number of rows in the matrixnrow,ConsensusPartition-method
Number of rows in the matrixnrow,ConsensusPartitionList-method
Method dispatch page for nrownrow
Number of rows in the matrixnrow,HierarchicalPartition-method
The proportion of ambiguous clustering (PAC score)PAC
Plot the empirical cumulative distribution (eCDF) curve of the consensus matrixplot_ecdf plot_ecdf,ConsensusPartition-method
Predict classes for new samples based on cola classificationpredict_classes,ConsensusPartition-method
Method dispatch page for predict_classespredict_classes
Predict classes for new samples based on signature centroid matrixpredict_classes,matrix-method
Print the hc_table_suggest_best_k objectprint.hc_table_suggest_best_k
Recalculate statistics in the ConsensusPartitionList objectrecalc_stats
Register NMF partitioning methodregister_NMF
Register user-defined partitioning methodsregister_partition_methods
Register SOM partitioning methodregister_SOM
Register user-defined top-value methodsregister_top_value_methods
Relabel class labels according to the reference labelsrelabel_class
Remove partitioning methodsremove_partition_methods
Remove top-value methodsremove_top_value_methods
Row names of the matrixrownames,ConsensusPartition-method
Row names of the matrixrownames,ConsensusPartitionList-method
Method dispatch page for rownamesrownames
Row names of the matrixrownames,HierarchicalPartition-method
Consensus partitioning for all combinations of methodsrun_all_consensus_partition_methods
Several plots for determining the optimized number of subgroupsselect_partition_number select_partition_number,ConsensusPartition-method
Print the ConsensusPartition objectshow,ConsensusPartition-method
Print the ConsensusPartitionList objectshow,ConsensusPartitionList-method
Method dispatch page for showshow
Print the DownSamplingConsensusPartition objectshow,DownSamplingConsensusPartition-method
Print the HierarchicalPartition objectshow,HierarchicalPartition-method
Split nodesplit_node split_node,HierarchicalPartition-method
Suggest the best number of subgroupssuggest_best_k,ConsensusPartition-method
Suggest the best number of subgroupssuggest_best_k,ConsensusPartitionList-method
Method dispatch page for suggest_best_ksuggest_best_k
Guess the best number of partitionssuggest_best_k,HierarchicalPartition-method
Test whether a list of factors are correlatedtest_between_factors
Test correspondance between predicted subgroups and known factorstest_to_known_factors,ConsensusPartition-method
Test correspondance between predicted classes and known factorstest_to_known_factors,ConsensusPartitionList-method
Method dispatch page for test_to_known_factorstest_to_known_factors
Test correspondance between predicted subgroups and known factorstest_to_known_factors,DownSamplingConsensusPartition-method
Test correspondance between predicted classes and known factorstest_to_known_factors,HierarchicalPartition-method
Overlap of top elements from different metricstop_elements_overlap
Heatmap of top rowstop_rows_heatmap,ConsensusPartition-method
Heatmap of top rows from different top-value methodstop_rows_heatmap,ConsensusPartitionList-method
Method dispatch page for top_rows_heatmaptop_rows_heatmap
Heatmap of top rows from different top-value methodstop_rows_heatmap,HierarchicalPartition-method
Heatmap of top rows from different top-value methodstop_rows_heatmap,matrix-method
Overlap of top rows from different top-value methodstop_rows_overlap,ConsensusPartitionList-method
Method dispatch page for top_rows_overlaptop_rows_overlap
Overlap of top rows on different nodestop_rows_overlap,HierarchicalPartition-method
Overlap of top rows from different top-value methodstop_rows_overlap,matrix-method