monkeybread.stat.ligand_receptor_score

monkeybread.stat.ligand_receptor_score(adata, contacts, actual_scores, n_perms=100)

Calculates statistical significance of ligand-receptor pairs in contacting cells.

Statistical test is as described in [HBB+22].

Parameters

• adata (AnnData) – Annotated data matrix.

• contacts (Dict[str, Set[str]]) – The cell contacts, as calculated by monkeybread.calc.cell_contact().

• actual_scores (Dict[Tuple[str, str], float]) – The observed scores, as calculated by monkeybread.calc.ligand_receptor_score().

• n_perms (Optional[int] (default: 100)) – The number of permutations to run.

Return type

Dict[Tuple[str, str], Tuple[ndarray, float]]

Returns

A mapping from ligand-receptor tuple pairs to a tuple containing the distribution of scores and p-value.