pyXenium.multimodal.annotate_joint_cell_states

annotate_joint_cell_states(adata, *, state_signatures=None, state_hierarchy=None, protein_obsm='protein', state_key='joint_cell_state', class_key='joint_cell_class', hierarchy_key='joint_cell_hierarchy', confidence_key='joint_cell_state_confidence', class_confidence_key='joint_cell_class_confidence', min_score=-0.25, min_margin=0.05)

Annotate joint RNA/protein classes and subtypes using hierarchical rules.

Parameters:

• adata (AnnData)

• state_signatures (Mapping[str, Mapping[str, Sequence[str]]] | None)

• state_hierarchy (Mapping[str, str] | None)

• protein_obsm (str)

• state_key (str)

• class_key (str)

• hierarchy_key (str)

• confidence_key (str)

• class_confidence_key (str)

• min_score (float)

• min_margin (float)

Return type:

dict[str, DataFrame]