[R] figuring out the results from hclust

From: Karin Lagesen <karinlag_at_studmed.uio.no>
Date: Sat, 31 May 2008 20:03:53 +0200

I have two examples that I run hclust on:

```a = c(0,1,1.5,1.5)
b = c(1,0,1.5,1.5)
c = c(1.5,1.5,0,0.5)
d = c(1.5,1.5,0.5,0)
```

ll = as.matrix(rbind(a,b,c,d))
test = as.dist(ll)
long = hclust(test)
```a = c(0,0.3,1,1)
b = c(0.3,0,1,1)
c = c(1,1,0,0.5)
d = c(1,1,0.5,0)
ll = as.matrix(rbind(a,b,c,d))
```

test = as.dist(ll)
short = hclust(test)

The main difference between them is whether a and b gets clustered higher up or lower down than the b,c cluster.

I am working on partitioning this kind of data into three clusters. I know I can do that with cutree. The result I get from that is the following:

> cutree(short, k=3)

a b c d
1 1 2 3
> cutree(long, k=3)

a b c d
1 2 3 3
>

And I can also access the height matrix for both:

> short\$height

[1] 0.3 0.5 1.0
> long\$height

[1] 0.5 1.0 1.5
>

So I know at what heights they get merged.

What I seem to be unable to get at is which one of the clusters as shown by cutree correspond to what split. When I examine short in a plot I can easily see that the highest split (i.e corresponding to the last height, 1, in the height matrix) is between the cutree clusters 1 and 2,3. In the long example this split is between 1,2 and 3. I would however like to not examine all of the data I have by hand:)

Could any of you point me to what I need to do to get at this data? I have tried to examine the merge data in both cases, but I am coming up short.

Thanks!

Karin

```--
Karin Lagesen, PhD student
karin.lagesen_at_medisin.uio.no
http://folk.uio.no/karinlag

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