pyXenium.multimodal.build_spatial_niches

build_spatial_niches(adata, *, cell_state_key='joint_cell_state', spatial_obsm='spatial', niche_key='spatial_niche', niche_score_key='spatial_niche_score', niche_margin_key='spatial_niche_margin', n_neighbors=15, min_score=0.25)

Build spatial niches from local composition of joint cell states.

Parameters:

• adata (AnnData)

• cell_state_key (str)

• spatial_obsm (str)

• niche_key (str)

• niche_score_key (str)

• niche_margin_key (str)

• n_neighbors (int)

• min_score (float)

Return type:

dict[str, DataFrame]