commot.tl.group_communication_direction

commot.tl.group_communication_direction(adata, keys=None, summary='sender', knn_smoothing=- 1, normalize_vf='quantile', normalize_quantile=0.99, dissimilarity_method='dot_product', leiden_k=5, leiden_resolution=1.0, leiden_random_seed=1, leiden_n_iterations=- 1)

Idenfitify groups of communication directions with similar pattern.

Parameters
  • adata (AnnData) – The data matrix with the communication direction info stored in adata.obsm, e.g. adata.obsm[‘commot_sender_vf-pathway-lig-rec’].

  • keys (Optional[list]) – A list of keys for the analyzed communication connections as tuples (database_name, ligand, receptor).

  • summary (str) – If ‘sender’, use the vector field describing to which direction the signals are sent. If ‘receiver’, use the vector field describing from which direction the signals are from.

  • knn_smoothing (int) – The number of neighbors to smooth the communication direction. If -1, no smoothing is performed.

  • normalize_vf (str) – If ‘quantile’, divide all values by the length given by the normalize_quantile parameter. If ‘unit_norm’, normalize each individual vector into unit norm. If None, original unit is used.

  • normalize_quantile (float) – The quantile parameter to use if normalize_vf is set to ‘quantile’.

  • dissimilarity_method (str) – Currently, only dot_product is implemented.

  • leiden_k (int) – Number of neighbors for the knn-graph to be fed to leiden clustering algorithm.

  • leiden_resolution (float) – The resolution parameter for the leiden clustering algorithm.

  • leiden_random_seed (int) – The random seed for the leiden clustering algorithm.

  • leiden_n_iterations (int) – The maximum number of iterations for the leiden algorithm. The algorithm will run until convergence if set to -1.

Returns

  • keys (list) – The list of keys for the analyzed communication connections as tuples (pathway_name, ligand, receptor).

  • direction_clusterid (np.ndarray) – The group id of the communication directions.

  • D (np.ndarray) – The dissimilarity matrix for the communication directions.