layout inside layout in R

Question

I'm using R to create a heatmap from a matrix using heatmap.2 - and i want to group these images into one big image - What i usually use to achieve this is layout() - but this doesn't work, as heatmap.2 uses layout, and apparently layout does not work recursively.

Does anyone have any suggestions on how to group together 2 images without layout, or how to make layout support recursive calls?

mat = matrix(nrow=3,nrow=3,1:9)
layout(matrix(nrow=2,ncol=1))
heatmap.2(mat) ## overrides the layout and produces only one plot that takes whole screen
heatmap.2(mat) ## still only one image

thanks.

Answer 1

What follows is a hack that is almost certainly not a perfect solution, but it may get you started.

Create your own version of the heatmap.2 function called hm3. In the code for hm3, comment out all the lines between:

 if (missing(lhei) || is.null(lhei))

and the layout call:

layout(lmat, widths = lwid, heights = lhei, respect = FALSE)

it's a big chunk of code, maybe 30 lines. Now the following code produces two heat maps with dendrograms and keys side by side:

x  <- as.matrix(mtcars) 
lhei <- c(1.5, 4,1.5,4)
lwid <- c(1.5, 4,1.5,4)
layout(rbind(c(4,3,8,7),c(2,1,6,5)), 
    widths = lwid, heights = lhei, respect = FALSE)
hm3(x)
hm3(x)

Clearly, this will require considerable tweaks to make it look nice (and a larger plotting area; I've squished everything to be a reasonable size to post here).

This is entirely untested. It is likely that using any of the options in the hm3 function that control the appearance of the plot will cause things to go slightly haywire. But this may be a good starting point for your own experimentation to address those issues.

Answer 2

What are you planning on doing with the results?

If you just want to compare 2 heatmaps side by side on the screen then rather than combine them into one single plot you can open 2 plotting devices and arrange them side by side to compare (much simpler than creating a single graph):

heatmap.2(mat1)
dev.new()
heatmap.2(mat2)

Now drag one to the side of the other using your mouse.

If you want to include the combined graphic in a publication then it may be easiest to create the 2 plots and just set them side by side in whatever program you are using to create the article. If you need them in one file you can still save the 2 heatmaps (or other plots) as 2 files then use tools such as imagemagick, gimp, or inkscape to combine the 2 files into 1 with the graphs side by side.