infercnvpy.pp.neighbors

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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 object

  • 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 run infercnvpy.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().

Returns:

Depending on the value of inplace, updates anndata or returns the distance and connectivity matrices.

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