Visualize KEGG pathway and fold enrichment

November 14, 2017
By

(This article was first published on R – Fabio Marroni's Blog, and kindly contributed to R-bloggers)

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:

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