thor.analy.run_commot

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

Run the cell-cell communication analysis using the modified COMMOT method. This is a wrapper function the commot.tl.spatial_communication(). 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 for commot.tl.spatial_communication().

Returns:

adata – Annotated data matrix.

Return type:

AnnData