mypackage.MyPyroModel.setup_anndata
- classmethod MyPyroModel.setup_anndata(adata, batch_key=None, labels_key=None, layer=None, categorical_covariate_keys=None, continuous_covariate_keys=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
- adata :
AnnData
AnnData object containing raw counts. Rows represent cells, columns represent features.
- 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.
- layer :
str
|None
Optional
[str
] (default:None
) if not None, uses this as the key in adata.layers for raw count data.
- categorical_covariate_keys :
List
[str
] |None
Optional
[List
[str
]] (default:None
) keys in adata.obs that correspond to categorical data.
- continuous_covariate_keys :
List
[str
] |None
Optional
[List
[str
]] (default:None
) keys in adata.obs that correspond to continuous data.
- adata :
- Return type
- Returns
If
copy
, will returnAnnData
. Adds the following fields to adata:- .uns[‘_scvi’]
scvi setup dictionary
- .obs[‘_scvi_labels’]
labels encoded as integers
- .obs[‘_scvi_batch’]
batch encoded as integers
- Sets up the