When I run the functions "np.analysis.cellbrowser.make_kamil_browser" with a var_info parameter that is different than the default "de_res" I get the error below.
This error is cause because in line 278 in the file neals_python_functions/analysis/cellbrowser.py, during the call to the function _make_cell_browser_files, the variable var_info is not being past. Therefore in _make_cell_browser_files function the default parameter is taken. In my case the anndata didn't include a varm object named "de_res" and so I got an error.
I have fixed this by "var_info=var_info" to line 278.
Note that it might be safer to not have default values for parameters in inner functions. Just a suggestion.
The error:
Traceback (most recent call last):
File "", line 1, in
File "", line 28, in CellBrowser_wrapper
File "/home/rnormand/.conda/envs/CellBrowser/lib/python3.7/site-packages/neals_python_functions/analysis/cellbrowser.py", line 230, in make_kamil_browser
pval_precision, round_float)
File "/home/rnormand/.conda/envs/CellBrowser/lib/python3.7/site-packages/neals_python_functions/analysis/cellbrowser.py", line 281, in prepare_cb_files
pval_precision=pval_precision, round_float=round_float)
File "/home/rnormand/.conda/envs/CellBrowser/lib/python3.7/site-packages/neals_python_functions/analysis/cellbrowser.py", line 54, in _make_cell_browser_files
pval_precision, round_float)
File "/home/rnormand/.conda/envs/CellBrowser/lib/python3.7/site-packages/neals_python_functions/analysis/cellbrowser.py", line 183, in _filter_de
df_dict[var] = adata.varm[var_info]["{clust}:{var}".format(var=var, clust=clust)]
File "/home/rnormand/.conda/envs/CellBrowser/lib/python3.7/site-packages/anndata/_core/aligned_mapping.py", line 148, in getitem
return self._data[key]
KeyError: 'de_res'
When I run the functions "np.analysis.cellbrowser.make_kamil_browser" with a var_info parameter that is different than the default "de_res" I get the error below. This error is cause because in line 278 in the file neals_python_functions/analysis/cellbrowser.py, during the call to the function _make_cell_browser_files, the variable var_info is not being past. Therefore in _make_cell_browser_files function the default parameter is taken. In my case the anndata didn't include a varm object named "de_res" and so I got an error. I have fixed this by "var_info=var_info" to line 278.
Note that it might be safer to not have default values for parameters in inner functions. Just a suggestion.
The error:
Traceback (most recent call last): File "", line 1, in
File "", line 28, in CellBrowser_wrapper
File "/home/rnormand/.conda/envs/CellBrowser/lib/python3.7/site-packages/neals_python_functions/analysis/cellbrowser.py", line 230, in make_kamil_browser
pval_precision, round_float)
File "/home/rnormand/.conda/envs/CellBrowser/lib/python3.7/site-packages/neals_python_functions/analysis/cellbrowser.py", line 281, in prepare_cb_files
pval_precision=pval_precision, round_float=round_float)
File "/home/rnormand/.conda/envs/CellBrowser/lib/python3.7/site-packages/neals_python_functions/analysis/cellbrowser.py", line 54, in _make_cell_browser_files
pval_precision, round_float)
File "/home/rnormand/.conda/envs/CellBrowser/lib/python3.7/site-packages/neals_python_functions/analysis/cellbrowser.py", line 183, in _filter_de
df_dict[var] = adata.varm[var_info]["{clust}:{var}".format(var=var, clust=clust)]
File "/home/rnormand/.conda/envs/CellBrowser/lib/python3.7/site-packages/anndata/_core/aligned_mapping.py", line 148, in getitem
return self._data[key]
KeyError: 'de_res'