No color observed in Colour Key of HeatMap.2

Question

[Ming]

Dear All,

I am trying to plot a heatmap with the heatmap.2 function, but I am not getting any color on my Color Key.

The following are my code:

col1 <- colorRampPalette(c("green", "black", "red"))(499)

> col_breaks = c(seq(0, 0.002, length = 50),
>                seq(0.0021, 0.004, length = 50),
>                seq(0.0041, 0.006, length = 50),
>                seq(0.0061, 0.008, length = 50),
>                seq(0.0081, 0.01, length = 50),
>                seq(0.011, 0.04, length = 50),
>                seq(0.041, 0.08, length = 50),
>                seq(0.081, 1.2, length = 50),
>                seq(1.21, 1.4, length = 50),
>                seq(1.41, 1.6, length = 50))

heatmap.2(data.matrix(MTB_genus_RA_T), scale = "none", 
          trace = "none", density.info = "density",
          col = col1, breaks = col_breaks,
          Rowv = as.dendrogram(row.clus), Colv = as.dendrogram(col.clus.MTB),
          margins = c(13, 8),
          main = "Heatmap of MTB at the genus level",
          cexRow = 1.1, cexCol = 1.1,
          keysize = 2,
          # key.par=list(mar=c(bottom, left, top, right))
          key.par=list(mar=c(3,5,4,5)))#, lhei = c(0.1, 0.1), lwei = c(0.1, 0.1))
  

I am not getting any color on my color key. Can anyone please help?

Thank you!

[benformatics]

Perhaps provide an example with a more complete dataset?

Many of your objects (e.g. MTB*) were not included - so we cannot say for sure whether this is a problem that is specifically happening to you or if it is reproducible for others.

[Ming]

Dear @benformatics, what other kind of information will you like?

[AK]

Why not replace col = col1, breaks = col_breaks, with just col = greenred,? Depending on your purpose, but it seems the values are from 0 to ~1.5 instead of something like -3 to 3 (perhaps using a sequential palette here, for example, brewer.pal(9, "YlGnBu"), would be better).

[Ming]

Dear @SMK, how would you change the code?

[AK]

Hi Ming,

Something like:

library(gplots)
library(RColorBrewer)

heatmap.2(
  data.matrix(MTB_genus_RA_T),
  scale = "none",
  trace = "none",
  density.info = "density",
  col = greenred,
  main = "Heatmap of MTB at the genus level"
)

heatmap.2(
  data.matrix(MTB_genus_RA_T),
  scale = "none",
  trace = "none",
  density.info = "density",
  col = brewer.pal(9, "YlGnBu"),
  main = "Heatmap of MTB at the genus level"
)

Answer 1

[morty]

Hi, It is likely because of this line: col1 <- colorRampPalette(c("green", "black", "red"))(499)

Do not specify the 499 at the end. This specification of gradation within the colorRampPalette function will mess up the key.

Try again with: col1 <- colorRampPalette(c("green", "black", "red")