scvi.data.AnnTorchDataset#
- class scvi.data.AnnTorchDataset(adata_manager, getitem_tensors=None)[source]#
Extension of torch dataset to get tensors from AnnData.
- Parameters
adata_manager (
AnnDataManager
) –AnnDataManager
object with a registered AnnData object.getitem_tensors (
Union
[List
[str
],Dict
[str
,type
],None
] (default:None
)) – Dictionary with keys representing keys in data registry (adata_manager.data_registry
) and value equal to desired numpy loading type (later made into torch tensor) or list of such keys. A list can be used to subset to certain keys in the event that more tensors than needed have been registered. IfNone
, defaults to all registered data.
Examples
>>> sd = AnnTorchDataset(adata_manager, ['X', 'batch']) >>> sd[[0, 1, 2]] # Return the X and batch data both as np.float32 >>> sd = AnnTorchDataset(adata_manager, {'X':np.int64, 'batch':np.float32]}) >>> sd[[0, 1, 2]] # Return the X as np.int64 and batch as np.float32
Attributes table#
Returns the keys of the mappings in scvi data registry. |
Methods table#
|
Get the tensor associated with a key. |