ValueError: Unknown dtype dtype('uint16') cannot be converted to ?gRMatrix. #111
Description
I'm encountering error below while saving the AnnData object in the R environment in this step of the tutorial.
> ro.globalenv["adata"] = adata
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[58], line 1
----> 1 ro.globalenv["adata"] = adata
File ~/opt/anaconda3/envs/velocyto/lib/python3.10/site-packages/rpy2/robjects/environments.py:35, in Environment.__setitem__(self, item, value)
34 def __setitem__(self, item: str, value: typing.Any) -> None:
---> 35 robj = conversion.get_conversion().py2rpy(value)
36 super(Environment, self).__setitem__(item, robj)
File ~/opt/anaconda3/envs/velocyto/lib/python3.10/functools.py:889, in singledispatch.<locals>.wrapper(*args, **kw)
885 if not args:
886 raise TypeError(f'{funcname} requires at least '
887 '1 positional argument')
--> 889 return dispatch(args[0].__class__)(*args, **kw)
File ~/opt/anaconda3/envs/velocyto/lib/python3.10/site-packages/anndata2ri/py2r.py:56, in py2rpy_anndata(obj)
54 # TODO: sparse
55 x = {} if obj.X is None else dict(X=mat_converter.py2rpy(obj.X.T))
---> 56 layers = {k: mat_converter.py2rpy(v.T) for k, v in obj.layers.items()}
57 assays = ListVector({**x, **layers})
59 row_args = {k: pandas2ri.py2rpy(v) for k, v in obj.var.items()}
File ~/opt/anaconda3/envs/velocyto/lib/python3.10/site-packages/anndata2ri/py2r.py:56, in <dictcomp>(.0)
54 # TODO: sparse
55 x = {} if obj.X is None else dict(X=mat_converter.py2rpy(obj.X.T))
---> 56 layers = {k: mat_converter.py2rpy(v.T) for k, v in obj.layers.items()}
57 assays = ListVector({**x, **layers})
59 row_args = {k: pandas2ri.py2rpy(v) for k, v in obj.var.items()}
File ~/opt/anaconda3/envs/velocyto/lib/python3.10/functools.py:889, in singledispatch.<locals>.wrapper(*args, **kw)
885 if not args:
886 raise TypeError(f'{funcname} requires at least '
887 '1 positional argument')
--> 889 return dispatch(args[0].__class__)(*args, **kw)
File ~/opt/anaconda3/envs/velocyto/lib/python3.10/site-packages/anndata2ri/scipy2ri/py2r.py:88, in py2r_context.<locals>.wrapper(obj)
36 importr('Matrix') # make class available
37 matrix = SignatureTranslatedAnonymousPackage(
38 """
39 sparse_matrix <- function(x, conv_data, dims, ...) {
(...)
85 'matrix',
86 )
---> 88 return f(obj)
File ~/opt/anaconda3/envs/velocyto/lib/python3.10/site-packages/anndata2ri/scipy2ri/py2r.py:97, in csc_to_rmat(csc)
93 @converter.py2rpy.register(sparse.csc_matrix)
94 @py2r_context
95 def csc_to_rmat(csc: sparse.csc_matrix):
96 csc.sort_indices()
---> 97 conv_data = get_type_conv(csc.dtype)
98 with localconverter(default_converter + numpy2ri.converter):
99 return matrix.from_csc(i=csc.indices, p=csc.indptr, x=csc.data, dims=list(csc.shape), conv_data=conv_data)
File ~/opt/anaconda3/envs/velocyto/lib/python3.10/site-packages/anndata2ri/scipy2ri/py2r.py:28, in get_type_conv(dtype)
26 return base.as_logical
27 else:
---> 28 raise ValueError(f'Unknown dtype {dtype!r} cannot be converted to ?gRMatrix.')
ValueError: Unknown dtype dtype('uint16') cannot be converted to ?gRMatrix.