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 withpheatmap
package. The package will do the clustering for you.Feel free to ask more questions. Always happy to help.