vitessce-python icon indicating copy to clipboard operation
vitessce-python copied to clipboard

Support automatic instantiation of Wrapper objects

Open keller-mark opened this issue 1 year ago • 2 comments

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 avatar Apr 02 '24 20:04 keller-mark

Or this could just be defined in a separate Wrapper class like

AutoAnnDataWrapper(adata)

keller-mark avatar Apr 02 '24 20:04 keller-mark

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

AnnDataWrapper(adata, auto_init=True)

keller-mark avatar Apr 02 '24 20:04 keller-mark