Include gene ontology codes in the plots generated using the enrochplot package
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Entering edit mode
16 months ago
Gene_MMP8 ▴ 210

I was trying to plot the gene ontology (BP; CC; MF) terms for a set of genes as shown in the figure below. The codes used to generate the plot is
go <- enrichGO(de, OrgDb = "org.Hs.eg.db", ont="all") dotplot(go, split="ONTOLOGY") + facet_grid(ONTOLOGY~., scale="free")

However, instead of the gene ontology names (such as organelle fission), I want to plot the GO codes (GO:0048285) on the y axis. Is there any way to do that? Also, my second question is regarding the x axis. What does "Gene ratio" represent here? Is it the number of genes enriched for that particular term divided by the total number of genes? enter image description here

functional enrichment analysis gsea enrichplot • 2.0k views
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Entering edit mode
16 months ago
ATpoint 60k

Hi,

if I read the source code correctly then the Description column is unfortunately harcoded.

The easiert workaround would simply be to replace this column by the one you want.

library(clusterProfiler)
library(DOSE)

#/ Some example data:
data(geneList)
de <- names(geneList)[1:100]
go <- enrichGO(de, OrgDb = "org.Hs.eg.db", ont = "all")

#/ Make a copy to keep the original and replace description with ID:
go2 <- go
go2@result$Description <- go2@result$ID
dotplot(go2)

enter image description here

You could of course also extract the results and make a custom plot.

For the gene ratio question maybe see ClusterProfiler : What is GeneRatio and BgRatio? but this is most likely explained somewhere in the vignette / manual.

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