Function reference • ClustAssess

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

Reference

All functions