torch-adata
Project description
Create pytorch Datasets from AnnData
Installation
Install from PYPI:
pip install torch-adata
Install the developer version:
git clone https://github.com/mvinyard/torch-adata.git; cd torch-adata;
pip install -e .
Example use of the base class
The base class, AnnDataset
is a subclass of the widely-used torch.utils.data.Dataset
.
import anndata as a
import torch_adata
adata = a.read_h5ad("/path/to/data.h5ad")
dataset = torch_adata.AnnDataset(adata)
Returns sampled data X_batch
as a torch.Tensor
.
# create a dummy index
idx = np.random.choice(range(dataset.__len__()), 5)
X_batch = dataset[idx]
TimeResolvedAnnDataset
Specialized class for time-resolved datasets. A subclass of the class, AnnDataset
.
import anndata as a
import torch_adata as ta
adata = a.read_h5ad("/path/to/data.h5ad")
dataset = torch_adata.TimeResolvedAnnDataset(
adata,
time_key="Time point",
use_key="X_pca",
obs_key="weight_key",
return_t=True,
)
When return_t == True
:
X, y, t = dataset[idx]
When return_t == False
:
X, y = dataset[idx]
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