RPy2 converter from AnnData to SCE and back.
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")')Activate the conversion before you load the extension:
import anndata2ri
anndata2ri.activate()
%load_ext rpy2.ipythonNow 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 ...