scmorph.pp.umap

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scmorph.pp.umap#

scmorph.pp.umap(adata, **kwargs)#

Embed the neighborhood graph using UMAP [McInnes et al., 2018].

This function wraps the higher-level function umap() ([Wolf et al., 2018].)

Parameters:

  • adata (AnnData) – AnnData object

  • kwargs – Additional arguments passed to umap().

Return type:

AnnData | None

Returns:

Returns None if copy=False, else returns an AnnData object. Sets the following fields:

adata.obsm['X_umap' | key_added]numpy.ndarray (dtype float)

UMAP coordinates of data.

adata.uns['umap' | key_added]dict

UMAP parameters.

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