Package: ClustAssess 1.0.0

Andi Munteanu

ClustAssess: Tools for Assessing Clustering

A set of tools for evaluating clustering robustness using proportion of ambiguously clustered pairs (Senbabaoglu et al. (2014) <doi:10.1038/srep06207>), as well as similarity across methods and method stability using element-centric clustering comparison (Gates et al. (2019) <doi:10.1038/s41598-019-44892-y>). Additionally, this package enables stability-based parameter assessment for graph-based clustering pipelines typical in single-cell data analysis.

Authors:Andi Munteanu [aut, cre], Arash Shahsavari [aut], Rafael Kollyfas [ctb], Miguel Larraz Lopez de Novales [aut], Liviu Ciortuz [ctb], Irina Mohorianu [aut]

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ClustAssess.pdf |ClustAssess.html✨
ClustAssess/json (API)

# Install 'ClustAssess' in R:

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

Bug tracker:https://github.com/core-bioinformatics/clustassess/issues

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

software singlecell rnaseq atacseq normalization preprocessing dimensionreduction visualization qualitycontrol clustering classification annotation geneexpression differentialexpression bioinformatics genomics machine-learning parameter-optimization robustness single-cell unsupervised-learning

5.40 score 22 stars 19 scripts 246 downloads 56 exports 149 dependencies

Last updated 7 days agofrom:a5618fd464. Checks:ERROR: 9. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Nov 12 2024
R-4.5-win-x86_64	ERROR	Nov 12 2024
R-4.5-linux-x86_64	ERROR	Nov 12 2024
R-4.4-win-x86_64	ERROR	Nov 12 2024
R-4.4-mac-x86_64	ERROR	Nov 12 2024
R-4.4-mac-aarch64	ERROR	Nov 12 2024
R-4.3-win-x86_64	ERROR	Nov 12 2024
R-4.3-mac-x86_64	ERROR	Nov 12 2024
R-4.3-mac-aarch64	ERROR	Nov 12 2024

Exports:add_metadata assess_clustering_stability assess_feature_stability assess_nn_stability automatic_stability_assessment calculate_markers calculate_markers_shiny choose_stable_clusters consensus_cluster create_monocle_default create_monocle_from_clustassess create_monocle_from_clustassess_app create_seurat_object_default create_seurat_object_from_clustassess_app element_agreement element_consistency element_sim element_sim_elscore element_sim_matrix get_clusters_from_clustassess_object get_highest_prune_param get_highest_prune_param_embedding get_nn_conn_comps getNNmatrix marker_overlap merge_partitions pac_convergence pac_landscape plot_clustering_overall_stability plot_clustering_per_value_stability plot_connected_comps_evolution plot_feature_overall_stability_boxplot plot_feature_overall_stability_incremental plot_feature_per_resolution_stability_boxplot plot_feature_per_resolution_stability_incremental plot_feature_stability_ecs_facet plot_feature_stability_mb_facet plot_k_n_partitions plot_k_resolution_corresp plot_n_neigh_ecs plot_n_neigh_k_correspondence server_comparisons server_dimensionality_reduction server_graph_clustering server_graph_construction server_landing_page server_sandbox ui_comparisons ui_dimensionality_reduction ui_graph_clustering ui_graph_construction ui_landing_page ui_sandbox weighted_element_consistency write_objects write_shiny_app

Dependencies:askpass assertthat base64enc beeswarm BH BiocGenerics bitops bslib cachem Cairo circlize cli clue cluster codetools colorspace commonmark ComplexHeatmap cpp11 crayon crosstalk curl data.table DEoptimR digest doParallel dplyr dqrng DT evaluate fansi farver fastcluster fastmap FNN fontawesome foreach fs generics GetoptLong ggbeeswarm ggnewscale ggplot2 ggrastr ggrepel ggtext GlobalOptions glue Gmedian gprofiler2 gridExtra gridtext gtable highr hms htmltools htmlwidgets httpuv httr igraph IRanges irlba isoband iterators jpeg jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr markdown MASS Matrix matrixStats memoise mgcv mime munsell nlme openssl paletteer pillar pkgconfig plotly plyr png prettyunits prismatic progress promises purrr qualpalr R6 ragg randtoolbox RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppProgress RCurl rematch2 reshape2 rjson rlang rmarkdown rngWELL robustbase RSpectra rstudioapi S4Vectors sass scales shape shiny shinyjs shinyLP shinyWidgets sitmo sm sourcetools stringi stringr sys systemfonts textshaping tibble tidyr tidyselect tinytex utf8 uwot vctrs vioplot vipor viridisLite withr xfun xml2 xtable yaml zoo

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Help page	Topics
Add metadata to ClustAssess ShinyApp	add_metadata
Assessment of Stability for Graph Clustering	assess_clustering_stability
Assess the stability for configurations of feature types and sizes	assess_feature_stability
Assess the stability for Graph Building Parameters	assess_nn_stability
Assessment of Stability for Graph Clustering	automatic_stability_assessment
Calculate markers	calculate_markers
Calculate markers - Shiny	calculate_markers_shiny
Choose stable clusters based on ECC and frequency	choose_stable_clusters
Consensus Clustering and Proportion of Ambiguously Clustered Pairs	consensus_cluster
Create monocle object	create_monocle_default
Create monocle object from a ClustAssess object	create_monocle_from_clustassess
Create monocle object from a ClustAssess shiny app	create_monocle_from_clustassess_app
Create Seurat object	create_seurat_object_default
Create Seurat object from a ClustAssess shiny app	create_seurat_object_from_clustassess_app
Element-Wise Average Agreement Between a Set of Clusterings	element_agreement
Element-Wise Consistency Between a Set of Clusterings	element_consistency
The Element-Centric Clustering Similarity	element_sim
The Element-Centric Clustering Similarity for each Element	element_sim_elscore
Pairwise Comparison of Clusterings	element_sim_matrix
Extract config-specific clusters from a ClustAssess object	get_clusters_from_clustassess_object
Calculate the highest pruning parameter for the SNN graph given NN matrix	get_highest_prune_param
Calculate the highest pruning parameter for the SNN graph given Embedding	get_highest_prune_param_embedding
Relationship Between Nearest Neighbours and Connected Components	get_nn_conn_comps
Computes the NN adjacency matrix given the neighbours	getNNmatrix
Cell-Wise Marker Gene Overlap	marker_overlap
Merge Partitions	merge_partitions
Merge Partitions from different Resolutions	merge_resolutions
PAC Convergence Plot	pac_convergence
PAC Landscape Plot	pac_landscape
Clustering Method Stability Facet Plot	plot_clustering_difference_facet
Clustering Method Overall Stability Boxplot	plot_clustering_overall_stability
Clustering Method per value Stability Boxplot	plot_clustering_per_value_stability
Relationship Between Number of Nearest Neighbours and Graph Connectivity	plot_connected_comps_evolution
Overall Feature Stability Boxplot	plot_feature_overall_stability_boxplot
Overall Feature Stability Incremental Boxplot	plot_feature_overall_stability_incremental
Per resolution Feature Stability Boxplot	plot_feature_per_resolution_stability_boxplot
Per resolution - Feature Stability Incremental Boxplot	plot_feature_per_resolution_stability_incremental
Feature Stability - EC Consistency Facet Plot	plot_feature_stability_ecs_facet
Feature Stability - Cluster Membership Facet Plot	plot_feature_stability_mb_facet
Relationship Between the Number of Clusters and the Number of Unique Partitions	plot_k_n_partitions
Correspondence Between Resolution and the Number of Clusters	plot_k_resolution_corresp
Graph construction parameters - ECC facet	plot_n_neigh_ecs
Relationship Between Number of Nearest Neighbours and Number of Clusters	plot_n_neigh_k_correspondence
Server - Comparison module	server_comparisons
Server - Dimensionality reduction module	server_dimensionality_reduction
Server - Graph clustering module	server_graph_clustering
Server - Graph construction module	server_graph_construction
Server - Landing page module	server_landing_page
Server - Sandbox module	server_sandbox
UI - Comparison module	ui_comparisons
UI - Dimensionality reduction module	ui_dimensionality_reduction
UI - Graph clustering module	ui_graph_clustering
UI - Graph construction module	ui_graph_construction
UI - Landing page module	ui_landing_page
UI - Sandbox module	ui_sandbox
Weighted Element-Centric Consistency	weighted_element_consistency
Write the objects for the ClustAssess ShinyApp	write_objects
Create the ClustAssess ShinyApp	write_shiny_app write_shiny_app.default write_shiny_app.Seurat

Package: ClustAssess 1.0.0

ClustAssess: Tools for Assessing Clustering

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