liana.utils.obsm_to_adata

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liana.utils.obsm_to_adata#

liana.utils.obsm_to_adata(adata, obsm_key, df=None, _uns=None, _obsm=None, _var=None)#

Extracts a dataframe from adata.obsm and returns a new AnnData object with the values stored in X.

Parameters:

  • adata (AnnData) – Annotated data object.

  • obsm_key (str) – .osbm key to extract.

  • df (DataFrame | None (default: None)) – Dataframe with stats per cell/spot. If None, it will be extracted from adata.obsm[obsm_key].

  • _uns (dict[str, DataFrame] | None (default: None)) – Dictionary with uns data. If None, it will be extracted from adata.uns.

  • _obsm (dict[str, DataFrame] | None (default: None)) – Dictionary with obsm data. If None, it will be extracted from adata.obsm.

  • _var (DataFrame | None (default: None)) – Dataframe with var data. If None, it will be extracted from adata.var.

Return type:

AnnData

Returns:

An AnnData object with the values stored in X.

Examples

Turns an .obsm entry into an AnnData of its own, so that its columns can be treated as variables by functions that expect features in .X:

>>> import liana as li
>>> adata = li.testing.generate_toy_adata()
>>> pca = li.ut.obsm_to_adata(adata, 'X_pca')
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