Open SillaLIN opened 1 year ago
Hi, you should try using ktplots](https://ktplotspy.readthedocs.io/en/latest/notebooks/tutorial.html) to visualize your results. Also, it look like using an older version of CellPhoneDB, I highly recommend you update to the latest version (pip update -U cellphonedb
) to benefit from newer features.
Thanks for your prompt reply. I'd love to use the latest version of cellphoneDB, but by doing that I will meet #92 error ([WARNING] Database '{value}' is not available. Trying to download it ). So I degrade my cellphoneDB version to v3.0.0 to solve this issue. Can this issue be solved, too?
All in all, thank you again for your reply
Hi SillaLIN,
Apologies for the delay in our response. If this issue is still relevant, could you please let me know if you followed the steps in https://cellphonedb.readthedocs.io/en/latest/RESULTS-DOCUMENTATION.html#installation and then exactly how you tried to run your statistical analysis.
Best,
Robert.
Hi, In previous, I do appreciate your fast response about running statistical analysis. From the successful statistical analysis results, I tried to draw a heatmap plot of cellphoneDB.
However, unexpected error occurs and I am unable to solve this issues. The detail of error is as follow.
(cellphonedb) C:\Users\95369>cellphonedb plot heatmap_plot meta02.txt Warning message: package 'methods' was built in R 3.6.3 During startup - Warning messages: 1: 'datasets'R3.6.3 2: 'utils'R3.6.3 3: 'grDevices'R3.6.3 4: 'graphics'R3.6.3 5: 'stats'R3.6.3 From cffi callback <function _consolewrite_ex at 0x0000021EBF921438>: Traceback (most recent call last): File "C:\Users\95369.conda\envs\cellphonedb\lib\site-packages\rpy2\rinterface_lib\callbacks.py", line 133, in _consolewrite_ex s = conversion._cchar_to_str_with_maxlen(buf, n, _CCHAR_ENCODING) File "C:\Users\95369.conda\envs\cellphonedb\lib\site-packages\rpy2\rinterface_lib\conversion.py", line 138, in _cchar_to_str_with_maxlen s = ffi.string(c, maxlen).decode(encoding) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb2 in position 29: invalid start byte R[write to console]: In addition: R[write to console]: Warning message:
From cffi callback <function _consolewrite_ex at 0x0000021EBF921438>: Traceback (most recent call last): File "C:\Users\95369.conda\envs\cellphonedb\lib\site-packages\rpy2\rinterface_lib\callbacks.py", line 133, in _consolewrite_ex s = conversion._cchar_to_str_with_maxlen(buf, n, _CCHAR_ENCODING) File "C:\Users\95369.conda\envs\cellphonedb\lib\site-packages\rpy2\rinterface_lib\conversion.py", line 138, in _cchar_to_str_with_maxlen s = ffi.string(c, maxlen).decode(encoding) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb3 in position 0: invalid start byte [ ][APP][20/04/23-20:30:54][ERROR] Unexpected error Traceback (most recent call last): File "C:\Users\95369.conda\envs\cellphonedb\lib\site-packages\cellphonedb\src\api_endpoints\terminal_api\plot_terminal_api_endpoints\plot_terminal_commands.py", line 78, in heatmap_plot pvalue=pvalue) File "C:\Users\95369.conda\envs\cellphonedb\lib\site-packages\cellphonedb\src\plotters\r_plotter.py", line 38, in wrapper return f(*args, kwargs, robjects=robjects, r_runtime_error=RRuntimeError) File "C:\Users\95369.conda\envs\cellphonedb\lib\site-packages\cellphonedb\src\plotters\r_plotter.py", line 60, in heatmaps_plot robjects.r.source(os.path.join(this_file_dir, 'R/plot_heatmaps.R')) File "C:\Users\95369.conda\envs\cellphonedb\lib\site-packages\rpy2\robjects\functions.py", line 209, in call .call(*args, *kwargs)) File "C:\Users\95369.conda\envs\cellphonedb\lib\site-packages\rpy2\robjects\functions.py", line 131, in call res = super(Function, self).call(new_args, new_kwargs) File "C:\Users\95369.conda\envs\cellphonedb\lib\site-packages\rpy2\rinterfacelib\conversion.py", line 45, in cdata = function(*args, **kwargs) File "C:\Users\95369.conda\envs\cellphonedb\lib\site-packages\rpy2\rinterface.py", line 817, in call raise embedded.RRuntimeError(_rinterface._geterrmessage()) File "C:\Users\95369.conda\envs\cellphonedb\lib\site-packages\rpy2\rinterface_lib_rinterface_capi.py", line 439, in _geterrmessage res = _string_getitem(res, 0) File "C:\Users\95369.conda\envs\cellphonedb\lib\site-packages\rpy2\rinterface_lib_rinterface_capi.py", line 287, in _string_getitem conversion._R_ENC_PY[openrlib.rlib.Rf_getCharCE(elt)] File "C:\Users\95369.conda\envs\cellphonedb\lib\site-packages\rpy2\rinterface_lib\conversion.py", line 132, in _cchar_to_str s = ffi.string(c).decode(encoding) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb2 in position 29: invalid start byte
It seems that RRuntimeError is the main reason. Can you help me? Looking forward to your early reply, thank you!!