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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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Image too large. How suppress drawing when using pyWGCNA_obj.preprocess() ? #84

Closed yizhang-zoey closed 5 months ago

yizhang-zoey commented 5 months ago

I am using pyWGCNA on a large data pyWGCNA_obj .

 AnnData object with n_obs × n_vars = 11963 × 28991

There is an Error when I use pyWGCNA_obj.preprocess() .

Image size of 85900x1000 pixels is too large. It must be less than 2^16 in each direction.
<Figure size 85900x1000 with 0 Axes>

How can I suppress drawing the hierarchical clustering plot when using pyWGCNA_obj.preprocess() to resolve the issue?

nargesr commented 5 months ago

Hi,

right now, I don't have any parameters to suppress drawing. you can put save to False to avoid saving but it will draw it anyway so I assume it's not gonna solve your problem. I'll add another parameter for this in the next few days but just make sure you don't have any outliers.

nargesr commented 5 months ago

Hi @yizhang-zoey

I added an option (show) to suppress the drawing in v2.0.1. Hopefully, that will fix your problem more info in API doc.

yizhang-zoey commented 5 months ago

Hi @yizhang-zoey

I added an option (show) to suppress the drawing in v2.0.1. Hopefully, that will fix your problem more info in API doc.

Thanks, it has been fixed!