scgen.SCGEN.setup_anndata¶
- classmethod SCGEN.setup_anndata(adata, batch_key=None, labels_key=None, **kwargs)[source]¶
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
|None
Optional
[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
|None
Optional
[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.
- batch_key
Notes
scGen expects the expression data to come from adata.X