napari_prism.tl.harmony

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napari_prism.tl.harmony#

napari_prism.tl.harmony(adata, copy=True, **kwargs)#

Performs HarmonyPy batch correction. Wraps sc.external.pp.harmony_integrate or rsc.pp.harmony_integrate.

Parameters:

  • adata (AnnData) – Anndata object.

  • copy (bool (default: True)) – Return a copy instead of writing inplace.

  • kwargs – Additional keyword arguments to pass to pp.harmony_integrate.

Return type:

AnnData

Returns:

Anndata object with Harmony results in .obsm. If copy is False, modifies the AnnData object in place and returns None.

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