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
- use_rep :
str(default:'cnv_pca') Key under which the PCA of the results of
infercnvpy.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) If
True, store the neighborhood graph in adata, otherwise return the distance and connectivity matrices.- **kwargs
Arguments passed to
scanpy.pp.neighbors().
- use_rep :
- Returns
Depending on the value of inplace, updates anndata or returns the distance and connectivity matrices.