scvi.data.AnnTorchDataset

class scvi.data.AnnTorchDataset(adata_manager, getitem_tensors=None, load_sparse_tensor=False)

Extension of Dataset for AnnData objects.

Parameters:

• adata_manager (AnnDataManager) – AnnDataManager object with a registered AnnData object.

• getitem_tensors (list | dict[str, type] | None (default: None)) –

  Specifies the keys in the data registry (adata_manager.data_registry) to return in __getitem__. One of the following:

  • dict: Keys correspond to keys in the data registry and values correspond to the

  desired dtype of the returned data. * list: Elements correspond to keys in the data registry. Continuous data will be returned as float32 and discrete data will be returned as int64. * None: All registered data will be returned. Continuous data will be returned as float32 and discrete data will be returned as int64.

• load_sparse_tensor (bool (default: False)) – EXPERIMENTAL If True, loads data with sparse CSR or CSC layout as a Tensor with the same layout. Can lead to speedups in data transfers to GPUs, depending on the sparsity of the data.

Attributes table

data	Dictionary of data tensors.
keys_and_dtypes	Keys and corresponding dtype of data to fetch in __getitem__.
registered_keys	Keys in the data registry.

Methods table

Attributes

AnnTorchDataset.data

Dictionary of data tensors.

First time this is accessed, data is fetched from the underlying AnnData object. Subsequent accesses will return the cached dictionary.

AnnTorchDataset.keys_and_dtypes

Keys and corresponding dtype of data to fetch in __getitem__.

AnnTorchDataset.registered_keys

Keys in the data registry.

Methods