[BioC] heatmap 'contrast': suggestions for a zlim adjustment in heatmap.2

[Karl Brand]

Esteemed BioC Users,

In pursuit of a simple method to adjust the "contrast" of a heatmap i 
attempted to use the image() argument "zlim" in heatmap.2, both directly 
and using add.expr. These attempts failed (shown below on my example 
heatmap.2).

heatplot() from library(made4) includes just such a convenient zlim= 
argument, but for now i'd trying to use heatmap.2 for all my heatmap 
needs. For the record, i can achieve what a zlim adjustment using the 
breaks argument to specify the effective range of zlim, but specifying 
breaks interferes with the scale argument in heatmap.2. So no good.

So any suggestions for a zlim adjustment in heatmap.2 are greatly 
appreciated, cheers,

Karl



#example
toy.mat <- matrix(rnorm(1000), nrow=100, ncol=10)
library(gplots)
  windows()
  plot.new()
heatmap.2(toy.mat,
   Rowv=T, Colv=T,
   dendrogram="column",
   scale= "row",
   col=c(greenred(256)),
#  breaks = c(seq(-10, 10, length.out = 257)),#interferes with 'scale'
   trace="none",
   density.info="none",
   zlim=c(-10, 10)                     #no error, but no effect
#  add.expr = (zlim=c(-10, 10))       #no error, but no effect
#  add.expr = "zlim", zlim=c(-10, 10) #no error, but no effect
#  add.expr = zlim, zlim=c(-10, 10)   #produces error
     )
#end

-- 
Karl Brand <k.brand at erasmusmc.nl>
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
P +31 (0)10 704 3409 | F +31 (0)10 704 4743 | M +31 (0)642 777 268