I have done a functional analysis with DAVID about the genes corresponding each module of my WGCNA.
My objective now is to plot the biologicals process of each module using a barplot, but I want all biologicals process of each module in an unique graph using diferent colors to distinguish each module with their biologicals process. I want something like in the image:
If someone can say or show me any tutorial, I will appreciate it
This is a barplot and can be made easily in R using ggplot. First remove all the unnecessary columns in the DAVID output file. Just keep the GO terms and their associated pvalue. Assuming you can get the data in a three column format where first column is GO term, second is module name and third is pvalues, you can try this:
head(data)
term module pvalue
1 defense response to fungus blue 0.000207773
2 MAPK cascade blue 0.000545800
3 chondrocyte differentiation blue 0.001003693
4 antibacterial humoral response blue 0.001419371
5 killing of cells of other organism blue 0.002021502
6 defense response to Gram-negative bacterium blue 0.002072591
library(ggplot2)
ggplot(data, aes(x = term,
y = -log10(pvalue),
fill = module)) + geom_bar(stat = "identity", position = "dodge") + coord_flip()
If you want to make your plot exactly like the one you showed you will have to add theme() in the ggplot command and specify parameters inside it. See this for an intro on making custom theme.
I got it!
Thank you very much for your help!