Customize range heatmap.2

Question

I am using the heatmap.2 function from the "gplots" package and would like to tweak the vizual output.

I would like to get a symmetric color scheme and I have achieved that using the scale="row" option. However, when doing this, my range gets narrowed down to a small interval c(-1 , 1). The range of my data is c(-1.2 , 2.97), and I would like the color scheme to capture the full resolution of my data. Can I specify the colour range to be e.g. c(-3,3) or is there another way to get a higher resolution of my data

This is my code

>head(hmdat[select,])
          Ind_B    Ind_Z     Ind_P
SVS1 -0.2176648 1.540470 -0.03700749
RHR2  0.3814377 1.425968  0.45827347
ADR1  0.7410964 1.062387  1.37050918
SPI1  0.2722683 1.324529  0.72636276
YAR1  0.7309389 1.278198  0.98776034
DDR2 -0.1727803 2.470086  0.74259052

>hmcol = colorRampPalette(brewer.pal(9, "RdBu"))(100)
>heatmap.2(hmdat[select,],scale="row", col = hmcol, trace="none", margin=c(7, 5),cexCol=0.9,cexRow=0.5,density.info="density")

generating this plot

plot

Another thing that I would like to fix is to remove the title of colour key and being able to specify manually the axis labels of the colour key. Thanks

It doesn't sound like you want to scale by row to me, then. Maybe try `scale = "none"` and setting `breaks` manually with something like `breaks = seq(-3, 3, length.out = 101)` — ping, May 04 '14 at 13:39
OK, I've added it as an answer so this question doesn't stay in the "unanswered" list. — ping, May 05 '14 at 13:13

score 3 · Accepted Answer · edited May 23 '17 at 12:30

Using scale = "row" will scale your data by row and doesn't keep your original, raw values so you should use scale = "none" if you want to preserve those.

You can set breaks manually by using the breaks argument. In this case, I think you could achieve what you're looking for by creating a sequence from -3 to 3, and setting length.out to one more than the number of colours you've defined (there needs to be 1 more breaks than colours):

heatmap.2(hmdat[select,],scale="none", col = hmcol, trace="none", margin=c(7, 5),cexCol=0.9,cexRow=0.5,density.info="density",breaks = seq(-3, 3, length.out = 101))

You might get warnings about there being no data for some values, and you may need to add symbreaks = TRUE to get the symmetrical effect you're looking for.

I don't think there is a simple option to change the labels of the color key, but you can try the solution in this question: How to change the color key value in heatmap.2?

Customize range heatmap.2

1 Answers1