ehrapy.anndata.anndata_to_df

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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, default: None) – The layer to access the values of. If not specified, it uses the X matrix.

  • obs_cols (Iterable[str] | str | None, default: None) – The columns of obs to add to the DataFrame.

  • var_cols (Iterable[str] | str | None, default: None) – The columns of var to fetch values from.

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)
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