kpHeatmap control colors

[diyasen2021]

Hi Bernat,

I was revisiting this figure and in going through it in more detail, I found that the heatmap colors were not consistent with the copy number values and some values were not being printed.

Here is the code.

for (f in 1:2){
  df <-read.table(myFiles[f], header = TRUE)
  CN<-toGRanges(df[,-1])
  print (myFiles[f])
  print (id[f])
  at <- autotrack(current.track = f, total.tracks = 2)
  #kpDataBackground(kp, r0=at$r0, r1=at$r1)
  kpAddLabels(kp, labels = id[f], r0=at$r0, r1=at$r1, cex=0.5, side="right")
  kpHeatmap(kp, data=CN, y=CN$Copy_number, ymin=min(CN$Copy_number), ymax = max(CN$Copy_number), colors = c("red", "white", "blue"),  r0=at$r0, r1=at$r1, cex=0.3)
}

Head of CN dataframe for 3770, where column 4 is copy number
Pag3770_1 1445001 1495000 6.186963177
Pag3770_1 3070001 3125000 2.815778549
Pag3770_1 4385001 4475000 2.578674358
Pag3770_1 6745001 6860000 10.48400049
Pag3770_1 9375001 9560000 6.840217837

Here is the figure.

Chromosome 1 of 3770 is missing the CNV at 3 Mb and 1 CNV on chromsome 7 has been labelled "red", when it should have been "blue".

Is there a way to control the colors so that all copy numbers <2 get labelled red and those >2 labelled blue? I thought this is what was happening, but it seems not.

I am happy to share the copy number file, if it helps.

As always, your help is much appreciated.

Diya