mechanochat.tools.biochemical_lr_communication#

mechanochat.tools.biochemical_lr_communication(adata: AnnData, df_ligrec: DataFrame, spatial_key: str = 'spatial', heteromeric_delimiter: str = '_', lr_delimiter: str = '-', prefix: str = 'LR')[source]#

Biochemical ligand(diffusive)-receptor cell-cell communication inference.

The signal between two cells is weighted by a Gaussian function of their distance.

Parameters:

  • adata (AnnData) – AnnData object providing spatial coordinates in .obsm[spatial_key].

  • df_ligrec (pandas.Dataframe) – Dataframe of ligand-receptor pairs. Required columns: Ligand, Receptor, Pathway.

  • spatial_key (str, default 'spatial') – Key of the spatial coordinates in .obsm.

  • lr_delimiter (str, default '-') – Delimiter used to construct ligand-receptor pair names in output.

  • heteromeric_delimiter (str, default '_') – Delimiter used to separate subunits in heteromeric complexes within df_ligrec.

  • prefix (str, default 'LR') – Prefix of the keys written to .obsp.

Returns:

  • None

  • Sets the following fields in adata –

    • .obsp[‘<key_added>_<ligand>-<receptor>’] : (nc, nc) csr_matrix of cell-cell communication mediated by <ligand>-<receptor> pair.

    • .uns[‘LR_signal_info’] : dict with keys ‘signal’, ‘db’ and ‘params’ (‘dc_m’, ‘gaussian_sigma’)

Notes

Orientation: s[i, j] is the signal from sender j to receiver i (row = receiver, column = sender).