how to give limitation in heatmap3

Question

[miniymay101]

Hi,

now I am drawing a heatmap using heatmap3 package in R.

I have a question in drawing heatmap.

My read count datas are ranged from about [-8,8], but I want to make the colors presented in [-1,1].

For example, if my read count data is bigger than 1 (e.g. 4), than it should be represented in the color of 1.

I thought I can do this by using "range" options in heamap3, but it doesn't really work...

Is there anyone who can help me to figure out this...?

I would be very grateful.. Thank you!

My code is :

ColSideAnn <- wholeSampleName_with_false

RowSideColors<-colorRampPalette(c("green", "black", "red"))(34)

result<-heatmap3(logCPM_with_immune,ColSideCut=1.2,ColSideAnn=ColSideAnn,ColSideFun=function(x) showAnn(x),RowSideColors=RowSideColors,
                                  col=colorRampPalette(c("green","black", "red"))(1024),RowAxisColors=1,verbose=TRUE,labCol = "", balanceColor = T)

I thought this might work, but it doesn't help :

col <- colByValue(logCPM_with_immune, range = c(-1, 1), col = colorRampPalette(c("green","black", "red"))(1024))

result<-heatmap3(logCPM_with_immune,ColSideCut=1.2,ColSideAnn=ColSideAnn,ColSideFun=function(x) showAnn(x),RowSideColors=RowSideColors,
                 RowAxisColors=1,verbose=TRUE,labCol = "", col=col)

Answer 1

[tiago211287]

First, nice R package. Second, it should be easier to help you with a sample of your dataset ~10 lines.

I never used heatmap3 but, if you do not need to represent datapoints bigger than 1 or smaller than -1, why not just simply change your values in your dataset to 1 or -1? something like: make backup data

backup.dataset <- dataset

assign 1 to values bigger than 1 or smaller than -1

for ( i in seq(1,ncol)){
      for ( f in seq(1,nrow)){
        if (dataset[f,i] > 1){
          dataset[f,i] <- 1} else{}
        if (dataset[f,i] < -1){
          dataset[f,i] <- -1} else{}

      }
    }

Answer 2

[zhaoshilin]

Hello,

Here is my example code to answer your question. Let me know if you have further question on it.

testData<-matrix(1:12,ncol=3)
heatmap3(testData,scale="none",Rowv=NA,Colv=NA,col=colorRampPalette(c('chartreuse4','white','firebrick'))(1024))

If we only want to show color in 1 to 5 range, for values>5, using 5 color

col<-colByValue(testData,col=colorRampPalette(c('chartreuse4','white','firebrick'))(1024),range=c(1,5))
heatmap3(testData,scale="none",Rowv=NA,Colv=NA,col=col)

Or

heatmap3(testData,scale="none",Rowv=NA,Colv=NA,col=as.vector(col)[order(as.vector(testData))])