infercnvpy.tl.tsne

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infercnvpy.tl.tsne#

infercnvpy.tl.tsne(adata, use_rep='cnv_pca', key_added='cnv_tsne', inplace=True, **kwargs)#

Compute the t-SNE on the result of infercnvpy.tl.infercnv().

Thin wrapper around scanpy.tl.tsne()

Parameters:

  • adata (AnnData) – annotated data matrix

  • use_rep (str (default: 'cnv_pca')) – Key under which the result of infercnvpy.tl.pca() is stored in adata

  • key_added (str (default: 'cnv_tsne')) – Key under which the result of t-SNE will be stored in adata.obsm

  • inplace (bool (default: True)) – If True, store the result in adata.obsm, otherwise return the result of t-SNE.

  • **kwargs – Additional arguments passed to scanpy.tl.tsne().

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