zcang
commented
1 year ago Hi, maybe setting up the package following this installation guide could help (see optional dependency): https://commot.readthedocs.io/en/latest/installation.html.
Closed chen-zhan closed 1 year ago
zcang
commented
1 year ago Hi, maybe setting up the package following this installation guide could help (see optional dependency): https://commot.readthedocs.io/en/latest/installation.html.
Hi, Thank you for such a great tool. I meet error when I run
df_deg, df_yhat = ct.tl.communication_deg_detection(adata_dis500, ... database_name = 'cellchat', pathway_name='SPP1', summary = 'receiver')Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/commot/tools/_downstream_analysis.py", line 154, in communication_deg_detection ro.r(string_fitGAM) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/rpy2/robjects/__init__.py", line 438, in __call__ res = self.eval(p) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/rpy2/robjects/functions.py", line 198, in __call__ return (super(SignatureTranslatedFunction, self) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/rpy2/robjects/functions.py", line 126, in __call__ res = conversion.rpy2py(res) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/functools.py", line 874, in wrapper return dispatch(args[0].__class__)(*args, **kw) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/anndata2ri/r2py.py", line 28, in rpy2py_s4 return rpy2py_single_cell_experiment(obj) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/anndata2ri/r2py.py", line 95, in rpy2py_single_cell_experiment obs = rpy2py_data_frame(col_data) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/anndata2ri/r2py.py", line 58, in rpy2py_data_frame columns = {k: rpy2py_vector(v) for k, v in slots["listData"].items()} File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/anndata2ri/r2py.py", line 58, in <dictcomp> columns = {k: rpy2py_vector(v) for k, v in slots["listData"].items()} File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/anndata2ri/r2py.py", line 49, in rpy2py_vector return pandas2ri.rpy2py(v) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/functools.py", line 874, in wrapper return dispatch(args[0].__class__)(*args, **kw) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/rpy2/robjects/conversion.py", line 200, in _rpy2py raise NotImplementedError( NotImplementedError: Conversion 'rpy2py' not defined for objects of type '<class 'rpy2.robjects.methods.RS4'>'Do you have any suggestions?