anndata2ri 1.0

Installation

Install it directly from GitHub via pip (version 19.0 or higher).

pip install git+https://github.com/flying-sheep/anndata2ri.git

You can install a locally checked out version with pip or flit:

cd anndata2ri
pip install .
# or
flit install

Usage from Python

Either use the converter manually …

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

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

… or activate it globally:

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

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

Usage from IPython

Activate the conversion before you load the extension:

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

Now you can move objects from Python to R …

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

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

… and back:

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

print(adata_allen)  # AnnData object with ...