stereoAlign.alignment.spatialign_alignment

stereoAlign.alignment.spatialign_alignment(adata: AnnData, batch_key='batch', latent_dims=100, n_neigh=15, is_verbose=False, tau1=0.2, tau2=1.0, tau3=0.5, save_path='./spatialign_output')[source]

spatiAlign wrapper function

Parameters:

  • adata – preprocessed anndata object

  • batch_key – batch key in adata.obs

  • latent_dims – The number of embedding dimensions, default, 100.

  • n_neigh – The number of neighbors selected when constructing a spatial neighbor graph. default, 15.

  • is_verbose – Whether the detail information is print, default, True.

  • tau1 – Instance level and pseudo prototypical cluster level contrastive learning parameters, default, 0.2

  • tau2 – Pseudo prototypical cluster entropy parameter, default, 1.

  • tau3 – Cross-batch instance self-supervised learning parameter, default, 0.5

  • save_path – The path of alignment dataset and saved spatialign.

Returns:

anndata object containing the corrected feature matrix