[R] how can I reorder a dendrogram?

[Philippe Grosjean]

Hello,

Perhaps, you should chose another toy example closer to the reality. 
Cases with exactly same distance rarely occur "in the field". You 
should, at least, add some random error:

datamatrix <- matrix(c(2,2,2.5,2,1.5,2,2,1.5,2,2.5,
6,2,6.5,2,5.5,2,6,1.5,6,2.5, 4,4,4.5,4,3.5,4,4,3.5,4,4.5) +
rnorm(30, sd = 0.1), ncol = 2, byrow = TRUE)
distmatrix <- dist(datamatrix, method = "manhattan")
hc <- hclust(distmatrix, method = "single")
dendro <- as.dendrogram(hc)
plot(dendro)

#Now, I want to impose an order:

weights <- c(2.0, 2.0, 2.0, 2.0, 2.0, 6.0, 6.0, 6.0, 6.0, 6.0, 4.0, 4.0,
4.0, 4.0, 4.0)
ddd <- reorder(dendro, weights, agglo.FUN=mean)
plot(ddd)

unlist(ddd)
# [1]  4  2  3  1  5 13 14 15 11 12 10  7  9  6  8


unlist(dendro)
# [1] 10  7  9  6  8 13 14 15 11 12  4  2  3  1  5

Best,

Philippe Grosjean
..............................................<°}))><........
  ) ) ) ) )
( ( ( ( (    Prof. Philippe Grosjean
  ) ) ) ) )
( ( ( ( (    Numerical Ecology of Aquatic Systems
  ) ) ) ) )   Mons-Hainaut University, Belgium
( ( ( ( (
..............................................................

Thomas Walter wrote:
> Hi!
> 
> I am trying to reorder a dendrogram via reorder.dendrogram. However, I 
> observed some problems with this, and I will illustrate them with an 
> example.
> 
> Take the following clustering problem:
> 
> datamatrix <- matrix(c(2,2,2.5,2,1.5,2,2,1.5,2,2.5, 
> 6,2,6.5,2,5.5,2,6,1.5,6,2.5, 4,4,4.5,4,3.5,4,4,3.5,4,4.5), ncol=2, 
> byrow=TRUE)
> distmatrix <- dist(datamatrix, method="manhattan")
> hc <- hclust(distmatrix, method="single")
> dendro <- as.dendrogram(hc)
> 
> The datamatrix contains three equidistant (for manhattan distance) 
> clusters, each of which contains 5 points.
> Now, I want to impose an order:
> 
> weights <- c(2.0, 2.0, 2.0, 2.0, 2.0, 6.0, 6.0, 6.0, 6.0, 6.0, 4.0, 4.0, 
> 4.0, 4.0, 4.0)
> ddd <- reorder(dendro, weights, agglo.FUN=mean)
> 
> but if you compare the order of ddd with dendro, you see no change:
> 
> unlist(ddd)
>  [1] 15 14 13 11 12  5  4  3  1  2 10  9  8  6  7
> 
> unlist(dendro)
>  [1] 15 14 13 11 12  5  4  3  1  2 10  9  8  6  7
> 
> I would have expected something like:
>  5  4  3  1  2 15 14 13 11 12 10  9  8  6  7
> 
> or something of the sort. (I still do not know, if the order should be 
> ascending or descending, but in the obtained result, it is neither nor). 
> I do not see, where my mistake is ...
> 
> Thanks for your advice!
> 
> Thomas.
> 
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