stereoAlign.alignment.harmony_alignment

stereoAlign.alignment.harmony_alignment(adata: AnnData, batch_key, hvg=None, n_pca=100, **kwargs)[source]

Harmony wrapper function

Based on harmony-pytorch

Parameters:

  • adata – preprocessed anndata object

  • batch_key – batch key in adata.obs

  • hvg – list of highly variables to subset to. If None, the full dataset will be used

  • n_pca – PCA component

Returns:

anndata object containing the corrected feature matrix as well as an embedding representation of the corrected data