Question: highlighting specific genes (from a user-supplied list) in a Volcano plot in R
1
gravatar for Eskimo
2.5 years ago by
Eskimo90
Eskimo90 wrote:

I've generated a volcano plot using DeSeq2 results and would like to specifically highlight a subset of genes by providing a list of gene IDs

Dataset$condition <- relevel(Dataset$condition, "Ctrl")
res <- lfcShrink(DatasetProcessed, contrast=c("condition","Treat","Ctrl")) 
with(res, plot(log2FoldChange, -log10(pvalue), pch=16, cex=0.6, main="Volcano plot", xlim=c(-5,5)))

Given a list of geneIDs (corresponding to IDs in res) that I have converted into a vector, how can I then highlight these in the volcano plot?

gene_list <- scan("genelist.txt", what="", sep="\n") 
gene_list <- as.vector(gene_list)
volcano plot deseq2 R • 1.8k views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Eskimo90

How to add single gene name in volcano plot ?

ADD REPLYlink written 2.5 years ago by genomax91k
6
gravatar for Eskimo
2.5 years ago by
Eskimo90
Eskimo90 wrote:

As always seems to be the case, I figured out the answer five minutes after asking the question...

with(res, plot(log2FoldChange, -log10(pvalue), pch=16, cex=0.6, main="Volcano plot", xlim=c(-5,5))) 
gene_list <- scan("genelist.txt", what="", sep="\n")
gene_list <- as.vector(gene_list) 
with(subset(res, rownames(res) %in% gene_list), points(log2FoldChange, -log10(pvalue), pch=20, col="orange"))

Hopefully this will help someone else down the line

ADD COMMENTlink written 2.5 years ago by Eskimo90
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 958 users visited in the last hour