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Support automatic instantiation of Wrapper objects #331

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Tracked by #1834
keller-mark opened this issue Apr 2, 2024 · 2 comments
Open
Tracked by #1834

Support automatic instantiation of Wrapper objects #331

keller-mark opened this issue Apr 2, 2024 · 2 comments
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feature New feature or request

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@keller-mark
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keller-mark commented Apr 2, 2024

Currently, the user needs to manually configure parameters for wrapper classes like AnnDataWrapper:

AnnDataWrapper(
        adata_path=zarr_filepath,
        obs_embedding_paths=["obsm/X_umap"],
        obs_embedding_names=["UMAP"],
        obs_set_paths=["obs/CellType"],
        obs_set_names=["Cell Type"],
        obs_feature_matrix_path="X",
        feature_filter_path="var/top_highly_variable"
)

but maybe we could support a static method like

AnnDataWrapper.from_object(adata)

or for SpatialData (depends on #286 )

SpatialDataWrapper.from_object(adata)
@keller-mark keller-mark added the feature New feature or request label Apr 2, 2024
@keller-mark
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Or this could just be defined in a separate Wrapper class like

AutoAnnDataWrapper(adata)

@keller-mark
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Or perhaps the AnnDataWrapper class should do this by default, or with an opt-in parameter like

AnnDataWrapper(adata, auto_init=True)

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