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Include metadata when converting to Pandas DataFrame #1399

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WeilerP opened this issue Mar 6, 2024 · 4 comments · May be fixed by #1400
Open

Include metadata when converting to Pandas DataFrame #1399

WeilerP opened this issue Mar 6, 2024 · 4 comments · May be fixed by #1400
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@WeilerP
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WeilerP commented Mar 6, 2024

Please describe your wishes and possible alternatives to achieve the desired result.

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AnnData.to_df only converts data from .X or a layer to a DataFrame. It'd be great to also add metadata column from AnnData.obs. This feature would make it easier to work with Pandas groupby on the generated DataFrame, for example.
@ivirshup
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ivirshup commented Mar 6, 2024

To me, this kind of use case is covered by sc.get.obs_df. Is there some reason that doesn't do what you need?

@WeilerP WeilerP linked a pull request Mar 6, 2024 that will close this issue
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@ivirshup
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ivirshup commented Mar 6, 2024

Alternatively, adata.to_df().join(adata.obs)

@WeilerP
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WeilerP commented Mar 6, 2024

To me, this kind of use case is covered by sc.get.obs_df. Is there some reason that doesn't do what you need?

It requires Scanpy instead of using AnnData directly. And yes, you can always merge the relevant columns; it'd just be easier via an argument.

@ivirshup
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ivirshup commented Mar 6, 2024

It requires Scanpy instead of using AnnData directly.

Just to establish an alternative: if sc.get.obs_df instead lived in anndata, that would be sufficient?

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Update to_df to include metadata WeilerP/anndata
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@flying-sheep @ivirshup @WeilerP