Package index • scClustEval

Assessment Functions

Functions for clustering quality assessment

sc_assessment(): Single Cell Clustering Assessment

self_projection(): Self-projection assessment

SCCAF_assessment(): SCCAF Assessment

RunAssessment(): Run clustering assessment on Seurat object

QuickAssess(): Quick assessment from Seurat object

assessment: Assessment Functions for scClustEval

Optimization Functions

Functions for clustering optimization

sc_optimize(): Single round of clustering optimization

sc_optimize_all(): Full iterative optimization pipeline

SCCAF_optimize(): SCCAF Optimize

SCCAF_optimize_all(): SCCAF Optimize All

RunOptimization(): Run clustering optimization on Seurat object

optimization: Optimization Functions for scClustEval

Classifiers

Machine learning classifier interface

create_classifier(): Create a classifier

get_available_classifiers(): Get available classifiers

classifiers: Classifier Functions for scClustEval

print(<scClustEval_classifier>): Print method for classifier

Confusion Matrix

Confusion matrix computation and normalization

calc_confusion_matrix(): Calculate confusion matrix

normalize_confusion_matrix(): Normalize confusion matrix

normalize_confmat_r1(): Normalize confusion matrix (R1 norm)

normalize_confmat_r2(): Normalize confusion matrix (R2 norm)

per_cluster_accuracy(): Compute per-cluster accuracy

per_cell_accuracy(): Compute per-cell accuracy

confusion_matrix: Confusion Matrix Functions for scClustEval

Clustering Utilities

Graph-based clustering and cluster manipulation

cluster_adjacency_matrix(): Cluster adjacency matrix

merge_clusters(): Merge clusters

get_connection_matrix(): Get connection matrix between clusterings

clustering: Clustering Functions for scClustEval

Distance Functions

Distance calculations

get_distance_matrix(): Get distance matrix between clusters

bhattacharyya_distance(): Bhattacharyya distance

bhattacharyya_matrix(): Bhattacharyya distance matrix

Visualization

Plotting functions

plot_roc(): Plot ROC curves

plot_confusion_heatmap(): Plot confusion matrix heatmap

plot_assessment_summary(): Plot assessment summary

plot_optimization_history(): Plot optimization history

plot_cluster_sankey(): Plot Sankey diagram of cluster changes

plot_cluster_links(): Plot cluster connections on embedding

plot_cluster_centers(): Plot cluster centroids on embedding

plot_embedding_with_links(): Plot embedding with cluster links

plot(<scClustEval>): Plot method for scClustEval objects

visualization: Visualization Functions for scClustEval

Seurat Integration

Functions for Seurat object compatibility

AddClusterReliability(): Add cluster reliability scores to Seurat object

GetExpressionMatrix(): Extract feature matrix from Seurat (exported helper)

PlotConfusionLinks(): Plot Seurat embedding with cluster confusion links

seurat_integration: Seurat Integration Functions for scClustEval

Utilities

Helper functions

train_test_split(): Simple train-test split

train_test_split_stratified(): Stratified train-test split

make_unique_names(): Make unique names

get_top_markers(): Get top markers from classifier

utils: Utility Functions for scClustEval

S3 Methods

Print and summary methods

print(<scClustEval>): Print method for scClustEval

print(<scClustEval_optim>): Print method for optimization result

summary(<scClustEval>): Summary method for scClustEval

summary(<scClustEval_optim>): Summary method for optimization result

Package Documentation

Package overview

scClustEval-package scClustEval: scClustEval: Single Cell Clustering Evaluation and Optimization Framework

zzz: Package Startup Functions