Metadata-Version: 2.1
Name: anndata2ri
Version: 1.0.3
Summary: Converter between Python’s AnnData and R’s SingleCellExperiment.
Home-page: https://github.com/flying-sheep/anndata2ri
License: UNKNOWN
Author: Philipp A.
Author-email: flying-sheep@web.de
Requires-Python: >= 3.6
Description-Content-Type: text/x-rst
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: R
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: get_version
Requires-Dist: rpy2 >= 3.0.1
Requires-Dist: tzlocal
Requires-Dist: anndata
Requires-Dist: pytest ; extra == "test"
Requires-Dist: pytest-faulthandler ; extra == "test"
Requires-Dist: pygments ; extra == "test"
Requires-Dist: scanpy ; extra == "test"
Provides-Extra: test

|pypi| |conda| |travis| |doi|

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

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

.. |travis| image:: https://travis-ci.org/theislab/anndata2ri.svg?branch=master
   :target: https://travis-ci.org/theislab/anndata2ri

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

AnnData ↭ SingleCellExperiment
==============================

RPy2 converter from AnnData_ to SingleCellExperiment_ and back.

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
.. _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 ...

