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)
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Eskimo •
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
I would rather use padj than pvalue to assess the significance of DEGs. In that case, it comes in handy to also add abline(h=-log(0.05, base = 10), col="red") to see a significance threshold line on the Volcano plot.
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How to add single gene name in volcano plot ?