[R] hclust and heatmap - slightly different dendrograms?

Min-Han Tan minhan.science at gmail.com
Wed Dec 15 21:55:07 CET 2004

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) 
            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

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