How to change heatmap.2 color range in R?

Question

I\'m using gplot to produce a heatmap showing log2-fold changes of a treatment groups versus paired controls. With the following code:

 heatmap.2(as.matrix(S         


        

Answer 1

You could try to create your own color palette using the RColorBrewer package

my_palette <- colorRampPalette(c("green", "black", "red"))(n = 1000)

and see how this looks like. But I assume in your case only scaling would help if you really want to keep the black in "the middle". You can simply use my_palette instead of the redgreen()

I recommend that you check out the RColorBrewer package, they have pretty nice in-built palettes, and see interactive website for colorbrewer.