Hi all,

I am using R script  from Getting Genetics Done ( http://www.gettinggeneticsdone.com/2014/05/r-volcano-plots-to-visualize-rnaseq-microarray.html)  to generating Volcano plots but my problem is how to show particular single gene name on volcano plot without any condition (i.e foldchange or pvalue). I just want to highlight my gene name "WNT7A" on volcano plot.


It would be great help if someone help me how to modify following code:

> labs=Gene

I tried `labs <- res$Gene[WNT7A]`

but couldnt work...

This is original code from Getting Genetics Done:

    res <- read.table("results.txt", header=TRUE)
    head(res)
    
    # Make a basic volcano plot 
    with(res, plot(log2FoldChange, -log10(pvalue), pch=20, main="Volcano plot", xlim=c(-2.5,2)))
    
    # Add colored points: red if padj<0.05, orange of log2FC>1, green if both)
    with(subset(res, padj<.05 ), points(log2FoldChange, -log10(pvalue), pch=20, col="red"))
    with(subset(res, abs(log2FoldChange)>1), points(log2FoldChange, -log10(pvalue), pch=20, col="orange"))
    with(subset(res, padj<.05 & abs(log2FoldChange)>1), points(log2FoldChange, -log10(pvalue), pch=20, col="green"))
    
    # Label points with the textxy function from the calibrate plot
    library(calibrate)
    with(subset(res, padj<.05 & abs(log2FoldChange)>1), textxy(log2FoldChange, -log10(pvalue), labs=Gene, cex=.8))
Perhaps I missed something, but it looks quite obvious to me:

    with(subset(res, Gene == "WNT7A"), textxy(log2FoldChange, -log10(pvalue), labs=Gene, cex=.8))


