senid.spatial

Functions

infer_spatial_communication(adata[, ...])

subset_for_spatial_sasp_communication(adata[, layer, ...])

Subset the AnnData object for spatial SASP communication analysis.

Package Contents

senid.spatial.infer_spatial_communication(adata, ligand_receptor_db=None, db_name=None, model='human', signaling_type='Secreted Signaling', filter_spots=None, min_spots=1, min_spot_pct=0.05, distance_thr=20.0, **kwargs)
Parameters:

  • adata (anndata.AnnData)

  • ligand_receptor_db (pandas.DataFrame)

  • db_name (str)

  • model (Literal['human', 'mouse'])

  • signaling_type (Literal['Secreted Signaling', 'Cell-Cell Contact', 'ECM-Receptor'])

  • filter_spots (bool)

  • min_spots (int)

  • min_spot_pct (float)

  • distance_thr (float)

Return type:

None

senid.spatial.subset_for_spatial_sasp_communication(adata, layer='counts', db_name=None, model='human')

Subset the AnnData object for spatial SASP communication analysis.

Parameters:
Return type:

anndata.AnnData