infercnvpy.pp.neighbors#
- infercnvpy.pp.neighbors(adata, use_rep='cnv_pca', key_added='cnv_neighbors', inplace=True, **kwargs)#
Compute the neighborhood graph based on the result from
infercnvpy.tl.infercnv()
.- Parameters:
adata (
AnnData
) – AnnData objectuse_rep (
str
(default:'cnv_pca'
)) – Key under which the PCA of the results ofinfercnvpy.tl.infercnv()
are stored in anndata. If not present, attempts to runinfercnvpy.tl.pca()
with default parameters.key_added (
str
(default:'cnv_neighbors'
)) – Distances are stored in .obsp[key_added+’_distances’] and connectivities in .obsp[key_added+’_connectivities’].inplace (
bool
(default:True
)) – IfTrue
, store the neighborhood graph in adata, otherwise return the distance and connectivity matrices.**kwargs – Arguments passed to
scanpy.pp.neighbors()
.
- Returns:
Depending on the value of inplace, updates anndata or returns the distance and connectivity matrices.