anndata2ri 1.3

Installation

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.

Usage from Python

Either use the converter manually …

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:

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:

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 ...