Entering edit mode
I was analyzing three data sets using wgcna independently. Each data set gave me several modules and I want to see their overlapping. With the help of the tutorial "Consensus-RelateToFemMods", I could modify some code to generate a overlapping heatmap containing the overlapped counts and p values. But when it comes assigning highly overlapped modules in different data sets with the same color, I'm a bit confused.
I'm wondering if there is a function for this reassigning module colors according to overlapping status. If there is not, what kind of rules do I have to follow to write my own code?
You want to compare how much several networks overlap their modules?
You can only compare between two networks to see the overlapping status. So you would need to compare A with B, B with C and A with C, and then extract your conclusions from there. I recommend a venn diagram of the overlapping modules.
Another option would be to plot them with color bars and see the resulting image how many sections/genes are predominantly of the same color