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