scispy.pp.scvi_annotate

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scispy.pp.scvi_annotate#

scispy.pp.scvi_annotate(ad_spatial, ad_ref, label_ref='celltype', label_key='celltype', layer='counts', batch_size=128, metaref2add=[], filter_under_score=0.5)#

Annotate anndata spatial cells using anndata cells reference using SCVI.

Parameters:

  • ad_spatial (AnnData) – Anndata spatial object.

  • ad_ref (AnnData) – Anndata single-cell reference object.

  • label_ref (str (default: 'celltype')) – .obs key in single-cell reference object.

  • label_key (str (default: 'celltype')) – .obs key in spatial object.

  • layer (str (default: 'counts')) – layer in which we can find the raw count values.

  • metaref2add (tuple (default: [])) – .obs key in single-cell reference object to transfert to spatial.

  • filter_under_score (float (default: 0.5)) – remove cells having a scvi assignment score under this cutoff

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