I am working with RStudio/WGCNA to make co-expression networks from RNA-seq data (40 samples and 4000 genes). I succeeded at making the similarity and adjacency matrixes now I did the following to cluster my data (and it worked)
tree <- hclust(as.dist(1 - adj.mat), method="average")
cuttreeDynamicTree: break hc dendrogram in separate modules
modules <- cutreeDynamicTree(dendro=tree, minModuleSize=15, deepSplit=TRUE)
module_colors <- labels2colors(modules)
But I don't know how to visualise this and or export to cytoscape? I checked https://ramellose.github.io/networktutorials/wgcna.html and other posts on this forum but I didn't find anything that's working for me.
Also, does anyone know whether it's meaningful to construct a co-expression network based on rnaseq data under different conditions (e.g. drugA,B,C,D exposure, control)?