highlighting specific genes (from a user-supplied list) in a Volcano plot in R
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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