heatmaply: adjust the colour

Question

I am using the package heatmaply to visualise single cell expression data.
I want to use custom colours and to assign "yellow" to expression levels > 2 , "magenta" to expression levels < -2. The range between [-2,2] should be represented by smooth gradient of "magenta"-"black"-"yellow".

Here, my sample file is a matrix 10 rows x 5 columns:

my_palette<-PurpleAndYellow(50) 
heatmaply(test,col = my_palette, dendrogram = "none")

It produces correct "PurpleAndYellow" colour heatmap, however it scaled over whole range [-5, +5]

If I specify scale_fill_gradient_fun, the colour of heatmap becomes "RdBu" spectre (Heatmap2):

heatmaply(ab, col = my_palette, dendroram="none",
          scale_fill_gradient_fun = ggplot2::scale_fill_gradient2(
            low = "magenta", mid="black",high = "yellow", midpoint = 0, 
            limits = c(-2, 2)))

Could you let me know how to change colours and adjust brightness of heatmap using heatmaply ?

Answer 1

I think you were on the right track with the addition of limits, but there is no need to add scale_fill_gradient_fun. This automatically overrides your color palette unless you specify it within this function as well. Regardless, I believe this should work:

library(heatmaply)

my_palette<-PurpleAndYellow(50) 
heatmaply(test,col = my_palette, dendrogram = "none", limits = c(-2, 2))

In terms of brightness, I'm not sure if that can be addressed the way you have in mind. It seems to me that the issue with visibility isn't due to brightness, but the fact that that you are fading in and out of black. I think a good option might be to change your gradient such that the center does not fade to black—maybe a lighter grey or something of that sort.