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mortazavilab / PyWGCNA

PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad415/7218311
MIT License
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TypeError: enrichr() got an unexpected keyword argument 'description' #15

Closed tyaoi closed 1 year ago

tyaoi commented 1 year ago

Hi ! Thank you for developing PyWGCNA ! Running the command pyWGCNA_5xFAD.analyseWGCNA(geneList=geneList) in the Quick start notebook, I get the following error.

TypeError: enrichr() got an unexpected keyword argument 'description'

So, I checked the source code in the file PyWGCNA-main/PyWGCNA/wgcna.py, and I found that the above argument is used at the method gp.enrichr() in line3019.

However, in reading the official GSEApy web documentation, I could not find "description='' as an optional argument to the gp.enrichr() method. In my environment, gseapy==0.14.0 is installed through pypi.

Do I need to install another version of gseapy to solve this problem? Or do I just modify PyWGCNA.py? Which is better? Also, if I modify PyWGCNA.py, how should I install it?

Lastly... it's much easier to use than the R version of WGCNA, and I'm impressed!

Sincerely,

tyaoi commented 1 year ago

After modifying wgcna.py as above, I can install it according to the description "Install with the most recent commits"?

tyaoi commented 1 year ago

This approach wasn't able to dissolve the problem.

nargesr commented 1 year ago

Hi,

I Gald you liked it!

The version of gseapy I have is 0.10.5 but I'm working on a new release! hopefully, it will be out by mid of next week and I will address this problem! Thanks for letting me know

tyaoi commented 1 year ago

Hi ! Thank you for your response.

Looking forward to your new release! There are a lot of Python users in this field, so I know lots of people will like it!