The R function hclust is used to do cluster analysis, but based on R help I see no way to print the actual fusion distances (that is, the vertical distances for each connected branch pairs seen in the cluster dendrogram). Any ideas? I'd like to use them test for significant differences from the mean fusion distance (i.e. The Best Cut Test). To perform a cluster analysis I'm using: x <- dist(mydata, method = "euclidean") # distance matrix y <- hclust(x, method="ward") #clustering (i.e. fusion) method plot(y) # display dendogram Thanks, kbrownk
Is there a way to print branch distances for hclust function?
4 messages · Peter Langfelder, Kerry
On Sun, Dec 11, 2011 at 8:43 PM, kbrownk <kbrownk at gmail.com> wrote:
The R function hclust is used to do cluster analysis, but based on R help I see no way to print the actual fusion distances (that is, the vertical distances for each connected branch pairs seen in the cluster dendrogram). Any ideas? I'd like to use them test for significant differences from the mean fusion distance (i.e. The Best Cut Test). To perform a cluster analysis I'm using: x <- dist(mydata, method = "euclidean") # distance matrix y <- hclust(x, method="ward") #clustering (i.e. fusion) method plot(y) # display dendogram Thanks, kbrownk
You need to dig a bit deeper in the help file :) The return value is a list that contains, among others, components 'merge' and 'height'. The 'merge' component tells you which objects were merged at each particular step, and the 'height' component tells you what the merging height at that step was. The (slightly) tricky part is to relate the merge component to actual objects - AFAIK there is no function for that. The function cutree() using the argument k and varying it between 2 and n should basically do it for you but you need to match it to the entries in 'merge'. Maybe someone else knows a better way to do this. HTH, Peter
Thanks, I had tried using height but I was using it wrong. If I had the distances alone it would be enough, except that the height returns the distance all the way to 0, rather than to the adjacent merge. So, if an initial merge at height 0 has a distance of 10, and that object then merges again at having a distance that reaches height 35, I'd want to see a distance value of 25 not 35. So I will need a way to relate merges with heights somehow so I can subtract lower level distances like this. I have 67 total distances, so if some manual work is involved I can manage. I'm working on the advice you provided, which may provide some answers. Thanks, kbrownk On Dec 12, 1:38?am, Peter Langfelder <peter.langfel... at gmail.com> wrote:
On Sun, Dec 11, 2011 at 8:43 PM,kbrownk<kbro... at gmail.com> wrote:
The R function hclust is used to do cluster analysis, but based on R help I see no way to print the actual fusion distances (that is, the vertical distances for each connected branch pairs seen in the cluster dendrogram).
Any ideas? I'd like to use them test for significant differences from the mean fusion distance (i.e. The Best Cut Test).
To perform a cluster analysis I'm using:
x <- dist(mydata, method = "euclidean") # distance matrix y <- hclust(x, method="ward") #clustering (i.e. fusion) method plot(y) # display dendogram
Thanks, kbrownk
You need to dig a bit deeper in the help file :) The return value is a list that contains, among others, components 'merge' and 'height'. The 'merge' component tells you which objects were merged at each particular step, and the 'height' component tells you what the merging height at that step was. The (slightly) tricky part is to relate the merge component to actual objects - AFAIK there is no function for that. The function cutree() using the argument k and varying it between 2 and n should basically do it for you but you need to match it to the entries in 'merge'. Maybe someone else knows a better way to do this. HTH, Peter
______________________________________________ R-h... at r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Never mind on my reply post (hasn't posted yet, but assuming it does). I found a way to use the merge and height values with Excel to subtract out the lower level distance. Thanks for the help! kbrownk On Dec 12, 1:38?am, Peter Langfelder <peter.langfel... at gmail.com> wrote:
On Sun, Dec 11, 2011 at 8:43 PM,kbrownk<kbro... at gmail.com> wrote:
The R function hclust is used to do cluster analysis, but based on R help I see no way to print the actual fusion distances (that is, the vertical distances for each connected branch pairs seen in the cluster dendrogram).
Any ideas? I'd like to use them test for significant differences from the mean fusion distance (i.e. The Best Cut Test).
To perform a cluster analysis I'm using:
x <- dist(mydata, method = "euclidean") # distance matrix y <- hclust(x, method="ward") #clustering (i.e. fusion) method plot(y) # display dendogram
Thanks, kbrownk
You need to dig a bit deeper in the help file :) The return value is a list that contains, among others, components 'merge' and 'height'. The 'merge' component tells you which objects were merged at each particular step, and the 'height' component tells you what the merging height at that step was. The (slightly) tricky part is to relate the merge component to actual objects - AFAIK there is no function for that. The function cutree() using the argument k and varying it between 2 and n should basically do it for you but you need to match it to the entries in 'merge'. Maybe someone else knows a better way to do this. HTH, Peter
______________________________________________ R-h... at r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.