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Update to_df to include metadata #1400

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Update to_df to include metadata #1400

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10 changes: 8 additions & 2 deletions anndata/_core/anndata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1284,7 +1284,7 @@

T = property(transpose)

def to_df(self, layer=None) -> pd.DataFrame:
def to_df(self, layer=None, obs: str | list[str] | None = None) -> pd.DataFrame:
"""\
Generate shallow :class:`~pandas.DataFrame`.

Expand All @@ -1299,6 +1299,8 @@
------
layer : str
Key for `.layers`.
obs
Column(s) of `.obs` to include in DataFrame.
"""
if layer is not None:
X = self.layers[layer]
Expand All @@ -1308,7 +1310,11 @@
X = self.X
if issparse(X):
X = X.toarray()
return pd.DataFrame(X, index=self.obs_names, columns=self.var_names)

df = pd.DataFrame(X, index=self.obs_names, columns=self.var_names)
if obs is not None:
df = df.merge(self.obs[obs], left_index=True, right_index=True)

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return df

def _get_X(self, use_raw=False, layer=None):
"""\
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