scgen.SCGEN.setup_anndata

classmethod SCGEN.setup_anndata(adata, batch_key=None, labels_key=None, **kwargs)

Sets up the AnnData object for this model.

A mapping will be created between data fields used by this model to their respective locations in adata.

None of the data in adata are modified. Only adds fields to adata.

Parameters

batch_key : str | NoneOptional[str] (default: None)

key in adata.obs for batch information. Categories will automatically be converted into integer categories and saved to adata.obs[‘_scvi_batch’]. If None, assigns the same batch to all the data.

labels_key : str | NoneOptional[str] (default: None)

key in adata.obs for label information. Categories will automatically be converted into integer categories and saved to adata.obs[‘_scvi_labels’]. If None, assigns the same label to all the data.

Notes

scGen expects the expression data to come from adata.X