Good day to everyone
My name is Kgopotso Phakwago, and I am a research fellow at the University of Pretoria in South Africa. My research aims at evaluating defense-related genes or pathways associated with a specific fungal plant-pathogen (Fusarium circinatum) responses across different resistance or susceptible pine species. I am currently using WGCNA to generate heat-maps for visualizing the relationship between modules (clusters). I was successful in generating heat-maps within each host but cannot generate heat-maps between samples (host A vs host B). If possible, my question is can WGCNA be used for generating heat-maps between samples (in my case, four different hosts)?
your assistance will be highly appreciated
Kind regards, K. Phakwago
What do you mean exactly by heat-maps between samples? What do you want to show? The module eigengenes? Correlation between module eigengenes and phenotypes?
Well firstly, I forgot to state that I am an amateur when it comes to using Rstudio (WGCNA), but I believe I already have module eigengenes (ME), and I am looking for a correlation between ME of different hosts.
I wanted to do hierarchical clustering on the most connected genes, but between host samples, i.e, I want to look for which genes are co-expressed between my host samples. For example, build a hierarchical clustering between host A and host B, and look at which genes between these two are having similar expression profiles, and which are different
Oh please don't worry about that, there's always a moment in our life when we are a beginner in something.
If I understand correctly, so you want to compare the module eigengene between host A and host B, right? Perhaps you can get the moduleEigengene and then do a simple t-test to compare the module activity between the hosts (or ANOVA if you have >2 groups)?
And for the clustering, you can get the hub genes (i.e. most connected genes) from each module with
chooseTopHubInEachModule, subset your expression matrix with the list of genes, and then create a heatmap withpheatmappackage. The package will do the clustering for you.Feel free to ask more questions. Always happy to help.