metachat.tl.summary_pathway
- metachat.tl.summary_pathway(adata, database_name=None, group_name=None, summary='sender', sender_group=None, receiver_group=None, permutation_spatial=False)[source]
Summarize MCC (Metabolite–Sensor Communication) patterns between specific sender and receiver groups, and rank metabolic and sensor pathways.
Parameters
- adataanndata.AnnData
The data matrix of shape
n_obs×n_var.- database_namestr
Name of the Metabolite-Sensor interaction database.
- group_namestr
Group name of the cell annotation previously saved in
adata.obs.- summarystr, default=’sender’
The communication summary type (‘sender’ or ‘receiver’).
- sender_groupstr
Name of the sender group
- receiver_groupstr
Name of the receiver group
- permutation_spatialbool, default=False
Whether to use results from
mc.tl.communication_group_spatial.
Returns
- metapathway_rankpd.DataFrame
Ranking of metabolic pathways by communication score and p-value.
- senspathway_rankpd.DataFrame
Ranked sensor pathways by HITS authority score.
- ms_resultpd.DataFrame
Matrix of summed communication intensity between metabolic and sensor pathways.
- metapathway_pair_contributionsdict[str, pd.DataFrame]
For each metabolic pathway, detailed metabolite–sensor pair contributions.