mantispy.tl.cluster_composition

mantispy.tl.cluster_composition(adata, cluster_key='leiden', by=('Metadata_Plate', 'Metadata_Well'), reference='negcon')

Fraction of each well’s cells in each cluster, as a well-level object.

Parameters:

• adata (AnnData) – Clustered single-cell object.

• cluster_key (str (default: 'leiden')) – obs column holding the cluster label.

• by (Sequence[str] | str (default: ('Metadata_Plate', 'Metadata_Well'))) – Columns defining a row of the result, normally the well.

• reference (str | None (default: 'negcon')) – Controls to test each well’s composition against, or None to skip the test.

Return type:

AnnData

Returns:

A new object with wells as rows and clusters as columns, holding the fraction of each well’s cells in each cluster. It is a well-level mantispy object, so map(), normalize() and the plots accept it. uns["mantispy"]["composition_test"] holds a chi-square test of each well against the pooled control composition.

Notes

A well with few cells has a noisy composition. The chi-square test is computed on counts and accounts for this, but the fractions in X do not. Filter with well_qc() first.