CODEWITHSUNDEEP
rcolorsheatmap
Lippy
Lippy

Reputation: 383

How to change heatmap.2 color range in R?

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(SeqCountTable), col=redgreen(75), 
           density.info="none", trace="none", dendrogram=c("row"), 
            symm=F,symkey=T,symbreaks=T, scale="none")

I output a heat map with real fold change values (i.e., non Row-Z score) which is what I'm after, in the Red-Black-Green color scheme that is every biologist's favorite!

https://i.sstatic.net/uhFbP.jpg

The actual range of log2-fold change is -3/+7, with many values in the -2/-1 and +1/+2 range, which appear as dark red/green (respectively). This makes the whole heatmap quite dark and so difficult to interpret.

Upvotes: 19

Views: 134114

Answers (4)

bruce.moran
bruce.moran

Reputation: 347

Here's another option for those not using heatmap.2 (aheatmap is good!)

Make a sequential vector of 100 values from min to max of your input matrix, find value closest to 0 in that, make two vector of colours to and from desired midpoint, combine and use them:

breaks <- seq(from=min(range(inputMatrix)), to=max(range(inputMatrix)), length.out=100)
midpoint <- which.min(abs(breaks - 0))
rampCol1 <- colorRampPalette(c("forestgreen", "darkgreen", "black"))(midpoint)
rampCol2 <- colorRampPalette(c("black", "darkred", "red"))(100-(midpoint+1))
rampCols <- c(rampCol1,rampCol2)

Upvotes: 2

Whsky Steve
Whsky Steve

Reputation: 119

I think you need to set symbreaks = FALSE That should allow for asymmetrical color scales.

Upvotes: 2

user2489252
user2489252

Reputation:

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.

Upvotes: 15

Lippy
Lippy

Reputation: 383

I got the color range to be asymmetric simply by changing the symkey argument to FALSE

symm=F,symkey=F,symbreaks=T, scale="none"

Solved the color issue with colorRampPalette with the breaks argument to specify the range of each color, e.g.

colors = c(seq(-3,-2,length=100),seq(-2,0.5,length=100),seq(0.5,6,length=100))

my_palette <- colorRampPalette(c("red", "black", "green"))(n = 299)

Altogether

heatmap.2(as.matrix(SeqCountTable), col=my_palette, 
    breaks=colors, density.info="none", trace="none", 
        dendrogram=c("row"), symm=F,symkey=F,symbreaks=T, scale="none")

Upvotes: 18

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