multivelovae.knn_smooth_chrom

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

Smooth (imputes) the count matrix with k nearest neighbors.

The inputs can be either KNN index (1-based) and distance matrices or a pre-computed connectivities matrix (for example in adata_rna object).

Args:

adata_atac (anndata.AnnData):

ATAC Anndata object.

nn_idx (numpy.ndarray, optional):

KNN index matrix of size (cells, k) (1-based). Defaults to None.

nn_dist (numpy.ndarray, optional):

KNN distance matrix of size (cells, k). Defaults to None.

conn (scipy.sparse.csr_matrix, optional):

Pre-computed connectivities matrix. Defaults to None.

n_neighbors (int, optional):

Top N neighbors to extract for each cell in the connectivities matrix. Defaults to None.