scsilhouette package

Submodules

scsilhouette.cli module

scsilhouette.compute module

scsilhouette.compute.run_silhouette(h5ad_path: str, label_keys: List[str], embedding_key: str, output_dir: str, show_obs: bool = False, save_scores: bool = False, save_cluster_summary: bool = False, save_csv: bool = False, save_plots: bool = False, qc_correlations: bool = False, log_pca_dims: bool = False) → None

scsilhouette.download module

scsilhouette.download.download_h5ad(url: str, output_dir: str) → str

scsilhouette.download.get_filename_from_url(url: str) → str

scsilhouette.viz module

scsilhouette.viz.plot_all(cell_scores: DataFrame, cluster_summary: DataFrame, output_dir: Path, label: str)

scsilhouette.viz.plot_cluster_size_vs_score(cluster_summary: DataFrame, output_dir: Path, label: str)

scsilhouette.viz.plot_cluster_summary(cluster_summary: DataFrame, output_dir: Path, label: str)

scsilhouette.viz.plot_qc_boxplots(cell_scores: DataFrame, obs: DataFrame, output_dir: Path, label: str)

scsilhouette.viz.plot_score_distribution(cell_scores: DataFrame, output_dir: Path, label: str)

Module contents