liana.pp.obsm_to_adata

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liana.pp.obsm_to_adata#

liana.pp.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.ds.generate_toy_adata()
>>> pca = li.pp.obsm_to_adata(adata, "X_pca")
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