scvelo.inference.get_n_neighbors

scvelo.inference.get_n_neighbors(adata, labeling_time_mask, obs_dist_argsort, n_nontrivial_counts, use_rep='X', sparse_op=False, n_jobs=None)

Get number of neighbors required to include n_nontrivial_counts counts per labeling time.

See [Weiler et al., 2023].

adata

AnnData object.

labeling_time_mask

Dictionary with labeling times as keys and masks to subset to relevant observations as values.

obs_dist_argsort

Dictionary with argsorted pairwise distances per labeling_time_point.

n_nontrivial_counts

Number of non-trivial counts to consider for each labeling time point.

use_rep

Representation to use for identifying number of neighbors.

sparse_op

Boolean flag to run operations on sparse or dense matrix.

Return type

Dict[str, DataFrame]

Returns

• Number of neighbors to use for each gene and cell. Returned as a dictionary with variable names as keys

• and Pandas DataFrame of size (n_obs x n_labeling_times) as values.