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https://github.com/theislab/anndata2ri

Convert between AnnData and SingleCellExperiment
https://github.com/theislab/anndata2ri

bioconductor jupyter rpy2 scanpy single-cell

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Convert between AnnData and SingleCellExperiment

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README 

        
|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 ...