commot.tl.group_cell_communication
- commot.tl.group_cell_communication(adata, keys=None, bin_method='gaussian_mixture', bin_append_zeros='full', bin_random_state=1, bin_cutoff=0, knn=2, dissimilarity_method='graphwave', kw_graphwave={}, leiden_k=5, leiden_resolution=1.0, leiden_random_seed=1, leiden_n_iterations=- 1)
Idenfitify groups of cell-cell communication with similar pattern.
- Parameters
adata (
AnnData
) – The data matrix with the cell-cell communication info stored inadata.obsp
.keys – A list of keys for the analyzed communication connections as tuples (database_name, ligand, receptor).
bin_method (
str
) – Method for binarize communication connections. Choices: ‘gaussian_mixture’, ‘kmeans’.bin_append_zeros (
str
) – Number of zeros to append to the non-zero entries when running the binarization. ‘full’ use the full flattened cell-by-cell communication matrix. ‘match’ append the same number of zeros to the vector of non-zero entries.bin_random_state (
int
) – The random seed for binarization methods.bin_cutoff (
float
) – Force all connections with a weight smaller than or equal to bin_cutoff to be zero , regardless of binarization result.knn (
int
) – Number of neighbors for building the spatial knn graph.dissimilarity_method (
str
) – The method for quantifying dissimilarity. ‘graphwave’, node structural embedding by GraphWave [Donnat2018] implemented in Karate Club.kw_graphwave (
dict
) –Keywords for GraphWave. Defaults: {‘sample_number’:200, ‘step_size’:0.1, ‘heat_coefficient’: 1.0 ‘approximation’:100, ‘mechanism’:’approximation’, ‘switch’:1000, ‘seed’:42} See details at Karate Club.
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).
communication_clusterid (np.ndarray) – The group id of the cell-cell communications.
D (np.ndarray) – The dissimilarity matrix for the cell-cell communications.
References
- Donnat2018
Donnat, C., Zitnik, M., Hallac, D., & Leskovec, J. (2018, July). Learning structural node embeddings via diffusion wavelets. In Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining (pp. 1320-1329).