How to add Log2FoldChange as an argument for plotMA in DESeq2

Question

[gracechappell]

Hello,

I would like to add an argument to the plotMA function in DESeq2.  Specifically, I would like to highlight points on the MA plot that are not only alpha<0.1, but also log2FoldChange <-1 or >1.  Is there a way to achieve this?  I tried the following "ifelse" statement but it did not work.

plotMA(res,alpha=0.1,col=ifesle(log2FoldChange>0.75 | log2FoldChange<-0.75, "red", "grey"), cex=2, ylim=c(-2,2))

thank you!

Answer 1

[vivekbhr]

You can subset the DESeq result object by abs(logFC) > 1, then plot by plotMA. That's the fastest..

Answer 2

[gracechappell]

Thanks for the reply, Vivek.  I'd like to retain the non-significant points in my plot as grey.  By subsetting I only plot those that meet my criteria. 

 

[vivekbhr]

You can manually make the MA plot with all the genes, then color the genes of interest.