Visualize KEGG pathway and fold enrichment

This article is originally published at https://fabiomarroni.wordpress.com

As a useful note to self, I paste here an easy example on the use of the pathview package by Weijun Luo to plot the log fold change of gene expression across a given KEGG pathway. This example is on Vitis vinifera (as the prefix vvi can suggest), but the approach is general.
Basically, you just need to feed pathview the pathway argument and a gene.data argument. In this case, gene.data is a named vector, with names being the (entrez) gene names, and the value is the log Fold Change.
I selected a pathway for which KEGG has a nice representation, you might not be so lucky!

library(pathview)
mypathway<-"vvi03060"
genes<-c("100241050","100243802","100244217","100244265","100247624","100247887","100248517","
100248990","100250268","100250385","100250458","100251379","100252350","100252527","100252725","
100252902","100253826","100254350","100254429","100254996","100255515","100256046","100256113","
100256412","100256941","100257568","100257730","100258179","100258854","100259285","100259443","
100260422","100260431","100261219","100262919","100263033","100264739","100265371","100266802","
100267343","100267692","100852861","100853033","100854110","100854416","100854647","100855182","
104879783","109122671")
logFC<-rnorm(length(genes),-0.5,1)
names(logFC)<-genes
pathview(gene.data=logFC,species="vvi",pathway=mypathway)

The result should be something like this:

Thanks for visiting r-craft.org
This article is originally published at https://fabiomarroni.wordpress.com
Please visit source website for post related comments.