Re: [Rd] Unexpected behaviour for RowSideColors in function heatmap

From: Kevin R. Coombes <kevin.r.coombes_at_gmail.com>
Date: Thu, 08 Mar 2012 11:27:08 -0600

First, I can confirm this problem exists today, and can now vaguely recall seeing it in previous version of R.  > sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)

There is a bigger problem with heatmap.2 in the gplots package. Using "symm=TRUE" with no other arguments causes it to *fail *to print one of the dendrograms:

 > library(gplots)
 > cU <- cor(USJudgeRatings)
 > heatmap.2(cU, symm = TRUE)

Warning message:
In heatmap.2(cU, symm = TRUE) :

   Discrepancy: Colv is FALSE, while dendrogram is `row'. Omitting column dendogram.

In order to get the column dendrogram displayed using heatmap.2, you must use "symm=TRUE, Colv=TRUE". So this *succeeds*:  > heatmap.2(cU, symm = TRUE, Colv=TRUE)

To make things worse, heatmap.2 *sometimes *gets the direction of the column colors wrong. If you omit "Colv=TRUE", it leaves out the column dendrogram and gets one set of colors wrong. That, is, the following command *fails* in two ways:
 > sideCols <- rainbow(ncol(cU))
 > heatmap.2(cU, symm = TRUE, distfun = function(c) as.dist(1 - c),

        ColSideColors=sideCols, RowSideColors=sideCols)

If you include "Colv=TRUE", then it prints the dendrogram and gets both sets of colorbars correct. So the following command *succeeds*:  > heatmap.2(cU, symm = TRUE, Colv=TRUE, distfun = function(c) as.dist(1 - c),
+ ColSideColors=sideCols, RowSideColors=sideCols)

It is a separate esthetic question as to which diagonal axis should be used for symmetry. When it works in heatmap.2, the "origin" is at the bottom left. Since the dendrograms are printed on the top and left, however, the symmetry would be easier to see/confirm if the origin were put at the top left. One might be tempted to fit this by using "revC=TRUE". However, this command *fails* because it gets the colorbar wrong:
 > heatmap.2(cU, symm = TRUE, Colv=TRUE, revC=TRUE,

           distfun = function(c) as.dist(1 - c),
           ColSideColors=sideCols, RowSideColors=sideCols)

I am occasionally of the opinion that both "heatmap" and "heatmap.2" are too complex to be used reliably by mortals....

     Kevin

On 2/28/2012 4:04 AM, Pär Engström wrote:
> Hello,
>
> I have come across some unexpected behaviour of the function heatmap in the stats package. This looks like a bug to me, but I might have misunderstood something.
>
> When calling the function in symmetric mode, the ColSideColors are plotted correctly, but RowSideColors appear in reverse order. This code (modified from the example on the help page) demonstrates the problem:
>
> cU<- cor(USJudgeRatings)
> sideCols<- rainbow(ncol(cU))
> heatmap(cU, symm = TRUE, distfun = function(c) as.dist(1 - c),
> ColSideColors=sideCols, RowSideColors=sideCols)
>
> Reversing the RowSideColors argument does not solve the problem:
>
> heatmap(cU, symm = TRUE, distfun = function(c) as.dist(1 - c),
> ColSideColors=sideCols, RowSideColors=rev(sideCols))
>
> I had a look at the the function code and found that this change fixes the problem:
>
> Replace
>
> image(rbind(1L:nr), col = RowSideColors[rowInd], axes = FALSE)
>
> with
>
> image(rbind(if(revC) nr:1L else 1L:nr), col = RowSideColors[rowInd], axes = FALSE)
>
> I am using the current version of R for Mac OS X:
>
>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
>
> Regards,
>
> Pär Engström
>
> Postdoctoral Fellow
> EMBL European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge, UK
>
>
>
> [[alternative HTML version deleted]]
>
>
>
> ______________________________________________
> R-devel_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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