|pypi| |conda| |rtd| |tests| |doi|

.. |pypi| image:: https://img.shields.io/pypi/v/anndata2ri :target: https://pypi.org/project/anndata2ri/ :alt: PyPI Version

.. |conda| image:: https://img.shields.io/conda/vn/bioconda/anndata2ri :target: https://anaconda.org/bioconda/anndata2ri :alt: Bioconda Version

.. |rtd| image:: https://readthedocs.com/projects/icb-anndata2ri/badge/?version=latest&token=ee358f7efe36cbbd7d04db1b708fa81cefc44634ae7f3f8e0afcd03a1f0b1158 :target: docs_ :alt: Documentation Status

.. |tests| image:: https://github.com/theislab/anndata2ri/actions/workflows/run_tests.yml/badge.svg :target: https://github.com/theislab/anndata2ri/actions/workflows/run_tests.yml :alt: Unit Tests

.. |doi| image:: https://zenodo.org/badge/171714778.svg :target: https://zenodo.org/badge/latestdoi/171714778 :alt: Publication DOI

AnnData ↭ SingleCellExperiment

RPy2 converter from AnnData_ to SingleCellExperiment_ and back. (For details about conversion see the docs_)

You can for example use it to process your data using both Scanpy_ and Seurat_, as described in this example notebook_

.. _AnnData: https://anndata.readthedocs.io/en/latest/ .. _SingleCellExperiment: http://bioconductor.org/packages/release/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html .. _docs: https://icb-anndata2ri.readthedocs-hosted.com/en/latest/ .. _Scanpy: https://scanpy.readthedocs.io/en/stable/ .. _Seurat: https://satijalab.org/seurat/ .. _example notebook: https://github.com/LuckyMD/Code_snippets/blob/master/Seurat_to_anndata.ipynb

Installation

.. code-block:: bash

pip install anndata2ri

or

conda install -c bioconda anndata2ri

Troubleshooting

If you have problems installing or importing anndata2ri, please make sure you first:

1. Check the stack trace: If the error happens while installing or importing a dependency such as rpy2_, report your problem in that project’s bug tracker.
2. Search the issues_. At the time of writing 17 of the 29 bugs (60%) are invalid or rpy2 bugs / install problems.
3. Make sure you have a compatible R version: rpy2 requires R ≥ 3.6.

.. _rpy2: https://github.com/rpy2/rpy2#readme .. _issues: https://github.com/theislab/anndata2ri/issues

Usage from Python

Either use the converter manually …

.. code-block:: python

import anndata2ri from rpy2.robjects import r from rpy2.robjects.conversion import localconverter

with localconverter(anndata2ri.converter): adata = r('as(some_data, "SingleCellExperiment")')

… or activate it globally:

.. code-block:: python

import anndata2ri from rpy2.robjects import r anndata2ri.activate()

adata = r('as(some_data, "SingleCellExperiment")')

Usage from Jupyter

Activate the conversion before you load the extension:

.. code-block:: python

import anndata2ri anndata2ri.activate() %load_ext rpy2.ipython

Now you can move objects from Python to R …

.. code-block:: python

import scanpy.datasets as scd adata_paul = scd.paul15()

.. code-block:: r

%%R -i adata_paul adata_paul # class: SingleCellExperiment ...

… and back:

.. code-block:: r

%%R -o adata_allen data(allen, package = 'scRNAseq') adata_allen <- as(allen, 'SingleCellExperiment')

.. code-block:: python

print(adata_allen) # AnnData object with ...