metachat.tl.communication_group_spatial

metachat.tl.communication_group_spatial(adata, database_name=None, group_name=None, summary='sender', sum_metabolites=None, sum_metapathways=None, sum_customerlists=None, sum_ms_pairs=None, n_permutations=100, bins_num=30, use_parallel=True, n_jobs=16, copy=False)[source]

Function for summarizing metabolic MCC communication to group-level communication and computing p-values based on spatial distance distribution.

Parameters

adataanndata.AnnData

The data matrix with shape n_obs × n_var. If compute MCC flow from specific metabolites, metapathways or customerlists, please run mc.tl.summary_communication() first.

database_namestr

Name of the Metabolite-Sensor interaction database.

group_namestr

Key of cell/spot group annotation in adata.obs.

summarystr, optional

‘sender’ or ‘receiver’; defines which communication direction to summarize.

sum_metaboliteslist, optional

List of specific metabolites to summarize communication for. Example: [‘HMDB0000148’,’HMDB0000674’].

sum_metapathwayslist, optional

List of specific metabolic pathways to summarize communication for. Example: [‘Alanine, aspartate and glutamate metabolism’,’Glycerolipid Metabolism’].

sum_customerlistsdict, optional

Custom dictionaries of metabolite–sensor pairs. Example: {‘CustomerA’: [(‘HMDB0000148’, ‘Grm5’), (‘HMDB0000148’, ‘Grm8’)],

‘CustomerB’: [(‘HMDB0000674’, ‘Trpc4’), (‘HMDB0000674’, ‘Trpc5’)]}

sum_ms_pairslist of str, optional

Specific metabolite–sensor pairs, e.g. ['HMDB0000148-Grm5'].

n_permutationsint, optional

Number of label permutations for computing p-values (default: 100).

bins_numint, optional

Number of bins for sampling based on spatial distance distribution (default: 30).

use_parallelbool, optional

Whether to run the computation in parallel using multiprocessing (default: True).

n_jobsint, optional

Number of worker processes for parallelization (default: 16).

copybool, optional

Whether to return a modified copy of the anndata.AnnData object.

Returns

anndata.AnnData or None

Adds group-level communication results to: .uns['MetaChat_group_spatial-{group_name}-{database_name}-{signal_name}'], where each entry is a dictionary containing:

  • 'communication_matrix' : mean MCC intensity between groups

  • 'communication_pvalue' : permutation-based p-value matrix

Returns the AnnData object if copy=True, otherwise modifies in place.