[R] hclust and heatmap - slightly different dendrograms?
sdavis2 at mail.nih.gov
Wed Dec 15 22:46:58 CET 2004
Hierarchical clustering does NOT give an ordering for the clusters. It only
gives the clustering, so order is not invariant.
----- 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.
> 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)
> 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.
> Min-Han Tan
> R-help at stat.math.ethz.ch mailing list
> PLEASE do read the posting guide!
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