R help - Apr 2006 - questioin about cluster in R

Hi,All.Sorry for the group mail.
I recently met a question and I have struggled on that for a while but 
failed to found the solution.
I have a distance matrix as below.

---
0    35    33    9    36
35    0    10    32    51
33    10    0    30    49
9    32    30    0    35
36    51    49    35    0
-------------------
I want to do cluster with average method.
----
rown<-c("A", "B", "C", "D",
"E")
mydistMatrix <- read.table("D:\\5.distance",row.names = rown)

mydistObj<-as.dist(mydistMatrix, diag = FALSE, upper = FALSE)

mycluster <- hclust(mydistObj,method="average")

bmp(filename = " D:\\5_ave.bmp")
plot(mycluster,hang=-1)

dev.off()
---
The result is something like

        |
    20|
        |       _______________
    15|       |                             |
        |       |                             |
    10|       |                 -------------------
        |       |                 |  (intersection)      |
    5  |       |           -------                        |
        |       |          |          |                  ----------
    0  |       |          |          |                 |              |

                E        A       D                B            C

Then I want to set a threshold to cluster them. Say 5.
But I don't know when A-D  distance is larger than 5 or not.
I can draw a line to see whether A-D distance is larger than 5 or but. When 
when the dataset is large, it is difficult to tell.

So I wonder whether there is a way in R to display the distance value at the 
intersection so that we can see the exact value of it.
or there is way to show or save the distance matrix after the average 
algorithm.
Thanks a  lots!
Focus

_________________________________________________________________
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Hello,

> -----Urspr?ngliche Nachricht-----
> Von: r-help-bounces at stat.math.ethz.ch [mailto:r-help-
> bounces at stat.math.ethz.ch] Im Auftrag von Jane Ren
> Gesendet: Dienstag, 18. April 2006 21:33
> An: R-help at stat.math.ethz.ch
> Betreff: [R] questioin about cluster in R
> 
> Hi,All.Sorry for the group mail.
> I recently met a question and I have struggled on that for a while but
> failed to found the solution.
> I have a distance matrix as below.
> 
> ---
> 0    35    33    9    36
> 35    0    10    32    51
> 33    10    0    30    49
> 9    32    30    0    35
> 36    51    49    35    0
> -------------------
> I want to do cluster with average method.
> ----
> rown<-c("A", "B", "C", "D",
"E")
> mydistMatrix <- read.table("D:\\5.distance",row.names = rown)
> 
> mydistObj<-as.dist(mydistMatrix, diag = FALSE, upper = FALSE)
> 
> mycluster <- hclust(mydistObj,method="average")
> 
> bmp(filename = " D:\\5_ave.bmp")
> plot(mycluster,hang=-1)
> 
> dev.off()
> ---
> The result is something like
> 
>         |
>     20|
>         |       _______________
>     15|       |                             |
>         |       |                             |
>     10|       |                 -------------------
>         |       |                 |  (intersection)      |
>     5  |       |           -------                        |
>         |       |          |          |                  ----------
>     0  |       |          |          |                 |              |
> 
>                 E        A       D                B            C
> 
> Then I want to set a threshold to cluster them. Say 5.
## Make an executable example (!)...
## threshold 1
set.seed(123)
a <- dist(rnorm(100))
ah <- hclust(a)
cutree(ah, h=1)
> But I don't know when A-D  distance is larger than 5 or not.
## for 70-44 distance:
d <- ah$height[which(abs(ah$merge) == c(70,44))[1]]
d > 1   ## FALSE
## for 91-95:
d <- ah$height[which(ah$merge == c(91,95))[1]]
d > 1   ## TRUE

I don't know if this is exactly what you want, but probably this helps a
little bit.

Best,
Matthias

> I can draw a line to see whether A-D distance is larger than 5 or but.
> When
> when the dataset is large, it is difficult to tell.
> 
> So I wonder whether there is a way in R to display the distance value at
> the
> intersection so that we can see the exact value of it.
> or there is way to show or save the distance matrix after the average
> algorithm.
> Thanks a  lots!
> Focus
> 
> _________________________________________________________________
> Don't just search. Find. Check out the new MSN Search!

Jane,

I know that you can tweak dendrogram objects to display such info
(as.dendrogram() converts your tree), but I have no example code at hand.

Good luck


Jens Oehlschl?gel

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