Tools for Assessing Clustering
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Documentation for package ‘ClustAssess’ version 1.0.0
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_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 |
| write_shiny_app.default | Create the ClustAssess ShinyApp |
| write_shiny_app.Seurat | Create the ClustAssess ShinyApp |