Using scsilhouette from the Command Line

This page provides example commands for using scsilhouette’s CLI.

Compute Silhouette Scores

scsilhouette compute-silhouette \
--h5ad-path sample.h5ad \
--label-keys cell_type \
--embedding-key X_umap \
--use-binary-genes \
--gene-list-path \
--metric euclidean \
--save-scores \
--save-cluster-summary \
--save-annotation

Visualize Summary Statistics

scsilhouette viz-summary \
  --silhouette-score-path cell_type_silhouette_scores.csv \
  --label cell_type \
  --score-col silhouette_score \
  --fscore-path nsforest_scores.csv \
  --mapping-path cell_type_cluster_map.csv \
  --sort-by median

Visualize Correlation

scsilhouette viz-correlation \
  --cluster-summary-path cell_type_cluster_summary.csv
  --x-metric silhouette_score \
  --y-metrics median \
  --label cell_type \
  --fscore-path nsforest_scores.csv \
  --mapping-path cell_type_cluster_map.csv

Visualize Dotplot

scsilhouette viz-dotplot \
--h5ad-path sample.h5ad \
--label-keys cell_type \
--embedding-key X_umap

Visualize Distribution

scsilhouette viz-distribution \
--cluster-summary-path cluster_summary.csv \
--label-keys cell_type