On Tue, Dec 23, 2008 at 9:19 AM, Anastasia Gioti <a.gioti@ucl.ac.uk> wrote:

>
> Dear Bioconductors,
> i have a question about parameters of heatmap.2 function in gplots. I am
> plotting log10 pvalues ranging from say -40 to 20 using a redblue and want
> to produce a key which reflects this distribution: Negative pvalues in
> blue, positive in red. as the distribution is not symmetric, there seems
> to be a problem. The symkey parameter, if set in TRUE, makes the color key
>  symmetric about 0). I want to   assign more blue colors of the panel to
> negative pvalues and less colors of the red panel in positive, but I
> realize this is not what symkey does:  the key layout is centred around
> zero, but the color distribution not: white (middle panel) colors are
> around -10, whereas after +10 the key colors are just absent
> Here are my parameters:
> heatmap.2(tabNew, Rowv=as.dendrogram(hrR), Colv=as.dendrogram(hrC),
> col=redblue(100)[100:1], scale="none", key=TRUE, keysize=0.7, symkey=TRUE,
>  trace="none", cexRow=0.8, cexCol=1.1, margins=c(8,32), main=paste(name,
> '_', dim(tabNew)[1], ' categories', sep='') )
> I work with R.2.6 version.
>
> How can I achieve this? I do not want to change my values and make them
> symmetric, as I d like toi reflect the unequal distribution.  Any ideas?
>

You'll want to play with the breaks argument.  See the help for more
details.

Hope that gets you going.

Sean

	[[alternative HTML version deleted]]

