If you look at the help for heatmap.2 (in the gplots package) you will see
the following explanation for breaks
# mapping data to colors
breaks,
symbreaks=min(x < 0, na.rm=TRUE) || scale!="none",
If you run your code with the second call to the heatmap.2() function with
the argument scale="row" instead of scale="none" the colors are aligned as
in your first call to heatmap.2().
mdd <- t(scale(t(mdd)))
heatmap.2(mdd,col=mypalette, scale="row", breaks=hm$breaks)
Does that help?
Jean
On Tue, Aug 6, 2013 at 6:27 AM, Witold E Wolski <wewol...@gmail.com> wrote:
> I do set the breaks parameter in heatmap.2
> I would expect that the color.key and the histogram (the thing in the
> top left of the plot) are aligned.
> Just that everyone can reproduce the problem:
>
>
> mypalette<-brewer.pal(11,"RdYlBu")
> ddd <- rnorm(400,0,0.1)
> mdd <- matrix(ddd,ncol=50)
> hm <- heatmap.2(mdd,col=mypalette,scale="row") #this is used to
> produce the breaks, (and here it works fine)
>
> mdd <- t(scale(t(mdd)))
> heatmap.2(mdd,col=mypalette,scale="none",breaks=hm$breaks)
>
> # take a look and you will see that the colors are not aligned with the
> breaks
> although the documentation states
> breaks: (optional) Either a numeric vector indicating the splitting
> points for binning x into colors, or a integer number of
> break points to be used, in which case the break points will
> be spaced equally between min(x) and max(x).
>
>
>
> --
> Witold Eryk Wolski
>
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