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Hi Phil!
I just tried to convert my jupyter anndata2ri usage to a normal python script (i.e. using localconverter rather than ipython cell magics). I am, however, hitting an unexpected error.
So this works fine:
import anndata2ri
anndata2ri.activate()
%load_ext rpy2.ipython%%R -o sce
library(Seurat)
load("tissue.rdata")
new_obj = CreateSeuratObject(counts = tissue@raw.data)
new_obj@meta.data = tissue@meta.data
sce <- as.SingleCellExperiment(new_obj)sce in my python namespace is a now a neat AnnData object, as expected.
However trying to do the same with locaconverter gives me an error:
import anndata2ri
from rpy2.robjects import r
from rpy2.robjects.conversion import localconverter
with localconverter(anndata2ri.converter):
adata = r('''
library(Seurat)
load("tissue.rdata")
new_obj = CreateSeuratObject(counts = tissue@raw.data)
new_obj@meta.data = tissue@meta.data
as.SingleCellExperiment(new_obj)
''')---------------------------------------------------------------------------
NotImplementedError Traceback (most recent call last)
<ipython-input-2-fc7a6d222ec5> in <module>
4
5 with localconverter(anndata2ri.converter):
----> 6 adata = r('''
7 library(Seurat)
8 load("/storage/groups/ml01/datasets/projects/20200101_Various_SfairaDataRepository_leander.dony/raw/d10_1038_s41586_019_1631_3/tissue.rdata")
/opt/python/lib/python3.8/site-packages/rpy2/robjects/__init__.py in __call__(self, string)
436 def __call__(self, string):
437 p = rinterface.parse(string)
--> 438 res = self.eval(p)
439 return conversion.rpy2py(res)
440
/opt/python/lib/python3.8/site-packages/rpy2/robjects/__init__.py in __getattribute__(self, attr)
411
412 try:
--> 413 return self.__getitem__(attr)
414 except LookupError:
415 raise AttributeError(orig_ae)
/opt/python/lib/python3.8/site-packages/rpy2/robjects/__init__.py in __getitem__(self, item)
417 def __getitem__(self, item):
418 res = _globalenv.find(item)
--> 419 res = conversion.rpy2py(res)
420 if hasattr(res, '__rname__'):
421 res.__rname__ = item
/opt/python/lib/python3.8/functools.py in wrapper(*args, **kw)
873 '1 positional argument')
874
--> 875 return dispatch(args[0].__class__)(*args, **kw)
876
877 funcname = getattr(func, '__name__', 'singledispatch function')
/opt/python/lib/python3.8/site-packages/rpy2/robjects/conversion.py in _rpy2py(obj)
198 non-rpy2) objects.
199 """
--> 200 raise NotImplementedError(
201 "Conversion 'rpy2py' not defined for objects of type '%s'" %
202 str(type(obj))
NotImplementedError: Conversion 'rpy2py' not defined for objects of type '<class 'rpy2.rinterface.SexpClosure'>'Metadata
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