multivelo.knn_smooth_chrom

multivelo.knn_smooth_chrom(adata_atac, nn_idx=None, nn_dist=None, conn=None, n_neighbors=None)

KNN smoothing.

This function smooth (impute) the count matrix with k nearest neighbors. The inputs can be either KNN index and distance matrices or a pre-computed connectivities matrix (for example in adata_rna object).

Parameters:

  • adata_atac (AnnData) – ATAC anndata object.

  • nn_idx (np.darray (default: None)) – KNN index matrix of size (cells, k).

  • nn_dist (np.darray (default: None)) – KNN distance matrix of size (cells, k).

  • conn (csr_matrix (default: None)) – Pre-computed connectivities matrix.

  • n_neighbors (int (default: None)) – Top N neighbors to extract for each cell in the connectivities matrix.

Returns:

.layers[‘Mc’] stores imputed values.