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 (str) – The layer to access the values of. Defaults to None (X).
obs_cols (Iterable[str] | str | None) – obs columns to add to the DataFrame. Defaults to None.
var_cols (Iterable[str] | str | None) – var columns to fetch values of. Defaults to None.

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)