thor.analy.run_commot

thor.analy.run_commot(adata, region=None, gene_symbols_key='feature_name', **kwargs)

Run the cell-cell communication analysis using the modified COMMOT method. This is a wrapper function for the commot.tl.spatial_communication function. The function first prepares the data by filtering and processing the input data, and precompute the cell-cell distances matrix more efficiently, supporting sparse matrix.

Parameters:

• adata (AnnData) – Annotated data matrix.

• region (list, optional) – The region to analyze in the format [left, right, lower, upper]. left < right and lower < upper.

• gene_symbols_key (str, optional) – The key for gene symbols in adata.var. Default is “feature_name”.

• kwargs (dict, optional) – Additional keyword arguments.