sciduck.entropy_qc module
- sciduck.entropy_qc.cell_entropy_qc_metric(adata: AnnData, annotation_columns: list, nearest_neighbors: int = 15, dim: str = 'X_scVI') AnnData
Compute entropy (mixing) of annotations within a cells local neighborhood.
- Parameters:
adata – AnnData object with annotations
annotations – Cell level annotations.
nearest_neighbors – Number of nearest neighbors.
dim – Dimensionality reduction
- Returns:
Returns the updated AnnData object.
- sciduck.entropy_qc.cluster_entropy_qc_metric(adata: AnnData, cluster_column: str, annotation_column: str) list
Compute entropy (mixing) of an annotation within a pre-defined cluster.
- Parameters:
adata – Anndata object.
cluster_column – Column name in obs containing cluster labels.
annotation_columns – Column name in obs containing annotations.
- Returns:
A list of cluster entropy quality control metrics.
- sciduck.entropy_qc.filter_on_cluster_entropy(adata: AnnData, cluster_column: str, annotation_columns: list, annotation_thresholds: dict) AnnData | None
Filter samples based on cluster entropy.
- Parameters:
adata – Anndata object.
cluster_column – Column name in adata.obs containing cluster labels.
entropy_columns – Column name in adata.obs to compute entropy on.
entropy_thresholds – Minimum entropy values for each annotation being considered.
- Returns:
Returns either AnnData | None