Create PyTorch Datasets from AnnData
Installation
Install from PYPI (current version: 0.0.24):
pip install torch-adata
Install the developer version:
git clone https://github.com/mvinyard/torch-adata.git; cd torch-adata;
pip install -e .
The main API
The primary class is the AnnDataset. This is a subclass of the widely-used torch.utils.data.Dataset. The PyTorch Dataset module enables us to take advantage of built-in multiprocessing and other organizational tricks that ultimately standardize workflows and enable reproducibility.
import anndata as a
import torch_adata
adata = a.read_h5ad("/path/to/data.h5ad")
dataset = torch_adata.AnnDataset(adata, use_key="X_pca", groupby="time", obs_keys=["affinity"])
[ torch-adata ]: AnnDataset object with 7131 samples
----------------------------------------------------
Grouped by: 'time' with attributes:
- X (use_key = 'X_pca') torch.Size([3, 7131, 50])
- obs: affinity: torch.Size([3, 7131, 1])
There is an additional approach to this dubbed AnnLoader, highlighted by Sergei Rybakov in Interfacing pytorch models with anndata
For more information, please visit the documentation!
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Metadata
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Release files for torch-adata 0.1.1
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| File | Size | Uploaded | Provenance | |
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| torch_adata-0.1.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 75.5 kB
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