infercnvpy.tl.pca

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infercnvpy.tl.pca#

infercnvpy.tl.pca(adata, svd_solver='arpack', zero_center=False, inplace=True, use_rep='cnv', key_added='cnv_pca', **kwargs)#

Compute the PCA on the result of infercnvpy.tl.infercnv().

Thin wrapper around scanpy.pp.pca().

Parameters:

  • adata (AnnData) – annotated data matrix

  • svd_solver (str (default: 'arpack')) – See scanpy.pp.pca().

  • zero_center (bool (default: False)) – See scanpy.pp.pca().

  • inplace (bool (default: True)) – If True, store the result in adata.obsm. Otherwise return the PCA matrix.

  • use_rep (str (default: 'cnv')) – Key under which the result of infercnv is stored in adata

  • key_added (str (default: 'cnv_pca')) – Key under which the result will be stored in adata.obsm if inplace=True.

  • **kwargs – Additional arguments passed to scanpy.pp.pca().

Return type:

ndarray | None

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