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csbl-usp / CEMiTool

Co-Expression Module Identification Tool (CEMiTool) official repository
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Output of hierarchical clustered modules and eigengene plots #87

Closed brettChapman closed 2 years ago

brettChapman commented 3 years ago

Hi

I was wondering if there is a way to get a dendrogram plots of modules and eigengenes, as can be done directly with WGCNA like in this tutorial: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-02-networkConstr-man.pdf

I'm presenting my findings, and I'd like to illustrate exactly how the modules are determined through a few additional plots.

If this isn't already built into or hidden in the code of CemiTool, could you please point me to which R scripts I could modify to add such functionality.

Thanks.

pedrostrusso commented 3 years ago

Hi @brettChapman this isn't implemented in CEMiTool, but you can get there with a bit of work: in the find_modules function you'll find the cutTreeDynamic function implemented similarly to the tutorial you linked to. Also, in the get_merged_mods function, you'll find the similar module merging step if you'd rather make the dendrogram after that step. The three functions can be found here. Hope this helps.