mantispy.tl.grit

mantispy.tl.grit(adata, groupby='Metadata_Perturbation', reference='negcon', metric='pearson', use_rep=None, key_added='grit', copy=False)

Similarity of each replicate to its group, z-scored against its similarity to the controls.

For each profile, the similarities to its replicates are z-scored against its similarities to the control profiles and averaged. A perturbation’s grit is the mean over its replicates.

Parameters:

• adata (AnnData) – Well-level profiles with several replicates per group.

• groupby (str (default: 'Metadata_Perturbation')) – Column whose groups are the replicate sets.

• reference (str (default: 'negcon')) – Which rows are the controls each similarity is z-scored against.

• metric (str (default: 'pearson')) – Similarity between profiles, one of METRICS.

• use_rep (str | None (default: None)) – Score obsm[use_rep] instead of X.

• key_added (str (default: 'grit')) – Name for the outputs.

• copy (bool (default: False)) – Return a modified copy instead of mutating in place.

Return type:

AnnData | None

Returns:

None, or the modified copy. Writes the per-replicate score to obs[key_added] and uns["mantispy"][key_added] with group, key_added (the mean over the group’s replicates) and n_replicates. A replicate is left NaN when it is alone in its group, when fewer than two control profiles are available to it, or when those similarities have no spread, and n_replicates counts only the replicates that were scored.

Raises:

ValueError – reference selects no rows.