ehrapy.anndata.anndata_to_df#

ehrapy.anndata.anndata_to_df(adata, layer=None, obs_cols=None, var_cols=None)[source]#

Transform an AnnData object to a pandas dataframe.

Parameters:

  • adata (AnnData) – The AnnData object to be transformed into a pandas Dataframe

  • layer (Optional[str]) – The layer to use for X.

  • obs_cols (Union[list[str], str, None]) – List of obs columns to add to X.

  • var_cols (Union[list[str], str, None]) – List of var columns to add to X.

Return type:

DataFrame

Returns:

The AnnData object as a pandas Dataframe

Examples

>>> import ehrapy as ep
>>> adata = ep.dt.mimic_2(encoded=True)
>>> df = ep.ad.anndata_to_df(adata)