[R] hclust and heatmap - slightly different dendrograms?

[Sean Davis]

Hierarchical clustering does NOT give an ordering for the clusters.  It only 
gives the clustering, so order is not invariant.

Sean
----- Original Message ----- 
From: "Min-Han Tan" <minhan.science at gmail.com>
To: <r-help at stat.math.ethz.ch>
Sent: Wednesday, December 15, 2004 3:55 PM
Subject: [R] hclust and heatmap - slightly different dendrograms?


> Good afternoon,
>
> I ran heatmap and hclust on the same matrix x (strictly, I ran
> heatmap(x), and hclust(dist(t(x))), and realized that the two
> dendrograms were slightly different, in that the left-right
> arrangement of one pair of subclusters (columns) was reversed in the
> two functions (but all individual columns were grouped correctly).
>
> Looking through the code for heatmap as a most definite nonexpert, it
> seems to me that hclust is also invoked by heatmap.
>
>> heatmap
> function (x, Rowv = NULL, Colv = if (symm) "Rowv" else NULL,
>    distfun = dist, hclustfun = hclust, add.expr, symm = FALSE,
> ...
>
> hcr <- hclustfun(distfun(x))
>            ddr <- as.dendrogram(hcr)
>
> ....
> hcc <- hclustfun(distfun(if (symm)
>                x
>            else t(x)))
>            ddc <- as.dendrogram(hcc)
>
>
> I understand it is possible to add Rowv=NA and order the samples as
> per hclust, but I'm just wondering if there is a reason for this
> observation. Any pointers would be very much appreciated.
>
> Thanks!
>
> Min-Han Tan
>
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