TypeError when following sc-tutorial
mshirazi opened this issue · 4 comments
Hi,
I've been running through the sc-tutorial using the most recent versions of Scanpy and AnnData (anndata 0.7.4 & scanpy 1.6.0 & anndata2ri 1.0.5). I ran into an issue when trying to run the Slingshot code (similar to this issue on the sc-tutorial Github: theislab/single-cell-tutorial#49). It's also similar to issue #50 but the error is different, and I never activate numpy2ri. It's not a problem with the location of the graph data in adata either, since I get the same error with a test script, and even get the same error before I start the subsetting.
When I run
%%R -i adata_ent
print('test')
I get the error
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-45-f526c490bacf> in <module>
----> 1 get_ipython().run_cell_magic('R', '-i adata_ent', "print('test')\n")
~/opt/anaconda3/envs/sc-tutorial/lib/python3.8/site-packages/IPython/core/interactiveshell.py in run_cell_magic(self, magic_name, line, cell)
2379 with self.builtin_trap:
2380 args = (magic_arg_s, cell)
-> 2381 result = fn(*args, **kwargs)
2382 return result
2383
<decorator-gen-121> in R(self, line, cell, local_ns)
~/opt/anaconda3/envs/sc-tutorial/lib/python3.8/site-packages/IPython/core/magic.py in <lambda>(f, *a, **k)
185 # but it's overkill for just that one bit of state.
186 def magic_deco(arg):
--> 187 call = lambda f, *a, **k: f(*a, **k)
188
189 if callable(arg):
~/opt/anaconda3/envs/sc-tutorial/lib/python3.8/site-packages/rpy2/ipython/rmagic.py in R(self, line, cell, local_ns)
735 raise NameError("name '%s' is not defined" % input)
736 with localconverter(converter) as cv:
--> 737 ro.r.assign(input, val)
738
739 if args.display:
~/opt/anaconda3/envs/sc-tutorial/lib/python3.8/site-packages/rpy2/robjects/functions.py in __call__(self, *args, **kwargs)
195 v = kwargs.pop(k)
196 kwargs[r_k] = v
--> 197 return (super(SignatureTranslatedFunction, self)
198 .__call__(*args, **kwargs))
199
~/opt/anaconda3/envs/sc-tutorial/lib/python3.8/site-packages/rpy2/robjects/functions.py in __call__(self, *args, **kwargs)
124 new_kwargs[k] = conversion.py2rpy(v)
125 res = super(Function, self).__call__(*new_args, **new_kwargs)
--> 126 res = conversion.rpy2py(res)
127 return res
128
~/opt/anaconda3/envs/sc-tutorial/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/anaconda3/envs/sc-tutorial/lib/python3.8/site-packages/anndata2ri/r2py.py in rpy2py_s4(obj)
25 return rpy2py_data_frame(obj)
26 elif "SingleCellExperiment" in r_classes:
---> 27 return rpy2py_single_cell_experiment(obj)
28 elif supported_r_matrix_classes() & r_classes:
29 return rmat_to_spmat(obj)
~/opt/anaconda3/envs/sc-tutorial/lib/python3.8/site-packages/anndata2ri/r2py.py in rpy2py_single_cell_experiment(obj)
82
83 # TODO: Once the AnnData bug is fixed, remove the “or None”
---> 84 return AnnData(exprs, obs, var, uns, obsm or None, layers=layers)
~/opt/anaconda3/envs/sc-tutorial/lib/python3.8/site-packages/anndata/_core/anndata.py in __init__(self, X, obs, var, uns, obsm, varm, layers, raw, dtype, shape, filename, filemode, asview, obsp, varp, oidx, vidx)
305 self._init_as_view(X, oidx, vidx)
306 else:
--> 307 self._init_as_actual(
308 X=X,
309 obs=obs,
~/opt/anaconda3/envs/sc-tutorial/lib/python3.8/site-packages/anndata/_core/anndata.py in _init_as_actual(self, X, obs, var, uns, obsm, varm, varp, obsp, raw, layers, dtype, shape, filename, filemode)
514
515 # Backwards compat for connectivities matrices in uns["neighbors"]
--> 516 _move_adj_mtx({"uns": self._uns, "obsp": self._obsp})
517
518 self._check_dimensions()
~/opt/anaconda3/envs/sc-tutorial/lib/python3.8/site-packages/anndata/compat/__init__.py in _move_adj_mtx(d)
153 if (
154 (k in n)
--> 155 and isinstance(n[k], (spmatrix, np.ndarray))
156 and len(n[k].shape) == 2
157 ):
~/opt/anaconda3/envs/sc-tutorial/lib/python3.8/site-packages/rpy2/robjects/vectors.py in __getitem__(self, i)
263
264 def __getitem__(self, i):
--> 265 res = super().__getitem__(i)
266
267 if isinstance(res, Sexp):
~/opt/anaconda3/envs/sc-tutorial/lib/python3.8/site-packages/rpy2/rinterface_lib/sexp.py in __getitem__(self, i)
628 )
629 else:
--> 630 raise TypeError(
631 'Indices must be integers or slices, not %s' % type(i))
632 return res
TypeError: Indices must be integers or slices, not <class 'str'>I tried running the example code
import scanpy.datasets as scd
adata_paul = scd.paul15()
%%R -i adata_paul
print('test')
which worked without any warning messages, so I don't think it's a problem with importing and activating the anndata2ri package.
I tried backtracking to see when the error started appearing, since when I try pulling adata into R right after I create it, it doesn't throw any errors. This exact error message appears after trying to use adata in R in the following part of the tutorial:
sc.pp.highly_variable_genes(adata, flavor='cell_ranger', n_top_genes=4000)
print('\n','Number of highly variable genes: {:d}'.format(np.sum(adata.var['highly_variable'])))
but not right after running combat
# ComBat batch correction
sc.pp.combat(adata, key='sample')
However, I do get the following warning message when testing using R with adata right after the ComBat batch correction:
/Users/Maddie/opt/anaconda3/envs/sc-tutorial/lib/python3.8/site-packages/anndata2ri/py2r.py:38: NotConvertedWarning: Conversion 'py2rpy' not defined for objects of type '<class 'NoneType'>'
warn(str(e), NotConvertedWarning)
It runs error free right before the ComBat batch correction.
Let me know if there's any other information that would help, and thanks in advance!
Hmm, @ivirshup any idea why that might happen?
Looks like self._uns['neighbors'] is a R vector for some reason.
I'm not sure I get what needs to happen for this bug to come up. When did self._uns['neighbors'] become an R vector? Is there a mini-reproducer for this?
I've managed to reproduce the error with the paul dataset: after importing and activating all the packages in python and R, just running
import scanpy.datasets as scd
adata_paul = scd.paul15()%%R -i adata_paul
print('test')sc.pp.highly_variable_genes(adata_paul, flavor='cell_ranger', n_top_genes=4000)
print('\n','Number of highly variable genes: {:d}'.format(np.sum(adata_paul.var['highly_variable'])))# Calculate the visualizations
sc.pp.pca(adata_paul, n_comps=50, use_highly_variable=True, svd_solver='arpack')
sc.pp.neighbors(adata_paul)
sc.tl.tsne(adata_paul, n_jobs=12) #Note n_jobs works for MulticoreTSNE, but not regular implementation)
sc.tl.umap(adata_paul)
sc.tl.diffmap(adata_paul)
sc.tl.draw_graph(adata_paul)%%R -i adata_paul
print('test')First one works, second one throws an error. Also tried running this after:
adata_paul.uns['neighbors']['connectivities'] = adata_paul.obsp['connectivities']
adata_paul.uns['neighbors']['distances'] = adata_paul.obsp['distances']
del adata_paul.obsp%%R -i adata_paul
print('test')And it throws the same error. Not sure if the problem in these mini-examples is all of the steps I cut out, or if that's the proper way to get rid of a field, but it seemed to work when I checked what was in adata_paul.
Hi,
I had the same problem as you reported above. I have no idea how to change my Anndata. I wanna know whether you solve this error and how you pass it?