# Tools for Assessing Clustering

## Documentation for package ‘ClustAssess’ version 1.1.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

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
choose_stable_clusters | Choose stable clusters based on ECC and frequency
consensus_cluster | Consensus Clustering and Proportion of Ambiguously Clustered Pairs
create_monocle_default | Create monocle object
create_monocle_from_clustassess | Create monocle object from a ClustAssess object
create_monocle_from_clustassess_app | Create monocle object from a ClustAssess shiny app
create_seurat_object_default | Create Seurat object
create_seurat_object_from_clustassess_app | Create Seurat object from a ClustAssess shiny app
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_clusters_from_clustassess_object | Extract config-specific clusters from a ClustAssess object
get_colour_vector_from_palette | Get the vector of colours from a palette
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_clust_hierarchical | Hierarchical relationship between partitions with different number of clusters
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
write_shiny_app.default | Create the ClustAssess ShinyApp
write_shiny_app.Seurat | Create the ClustAssess ShinyApp