mmc.Hierarchy.check_all_markers()

Hierarchy.check_all_markers(adata, data_key=utils.DATA_KEY)

Asserts all markers in hierarchy identified by .get_all_markers() are in adata.X or .obsm[data_key].

Parameters:

• adata (AnnData) – Object containing marker expression in the .X, .obsm[data_key], or .obs for high confidence thresholding.

• data_key (Union[str, list, None] (default: utils.DATA_KEY)) – obsm or .var[utils.MODALITY_COLUMN] location to probe for other modalities beyond the .X