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smorabit / hdWGCNA

High dimensional weighted gene co-expression network analysis
https://smorabit.github.io/hdWGCNA/
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Further visualization #166

Closed awesomedeer closed 6 months ago

awesomedeer commented 6 months ago

Dear Sam, @smorabit It's great that you developed this useful tool! It works well with my data although I am wondering whether I can plot customized figures without using default commands like HubGeneNetworkPlot and ModuleUMAPPlot or updated commands with more parameters to adjust. In my case, I am interested in 1) a specific module and 2) several genes (some of them are not hub genes) in this module. I want to plot this module and highlight some of the genes. Any suggestion? Or maybe I can extract the information from the network and plot using other softwares?

Best regards Song

awesomedeer commented 6 months ago

Like Figure 5C in the manuscript which looks really good (their color combination seems a bit different with the default one).

smorabit commented 6 months ago

Hi Song,

Glad that you are finding hdWGCNA useful in your work! You can definitely use other plottihng packages for customized plots. There can be a lot of problems when trying to plot networks, like showing too many edges or nodes can make the plot too busy to be easily interpretable. I would recommend trying out igraph or ggraph for plotting within R.