liana.utils.obsm_to_adata

Contents

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

See here [1] or here [2].

Contents