I am making trees using hclust. I have several distances defined on a common set. I want to find, as close to possible, a common order of the set for each distance without any crossing edges in the plot. For example, I would like to have the 1 through 5 leaves on the left side for both trees in this example.
x<-seq(1,10)
y<-c(1.3,2.4,3.6,4.9,5.2,6.9,7.9,8.7,9.6,10.1)
X<-hclust(dist(x))
Y<-hclust(dist(y))
par(mfrow=c(2,1))
plot(X)
plot(Y)
In general, is there an algorithm to find this order, if one exists? Or, at least find one order for each distance that is close to the others? I understand this can be done with dendrograms using order or sort, but I think those trees are less informative.
You could use the sort function from the dendextend library:
library(dendextend)
x<-seq(1,10)
y<-c(1.3,2.4,3.6,4.9,5.2,6.9,7.9,8.7,9.6,10.1)
X<-hclust(dist(x)) %>% as.dendrogram %>% sort %>% as.hclust
Y<-hclust(dist(y)) %>% as.dendrogram %>% sort %>% as.hclust
par(mfrow=c(2,1))
plot( X )
plot( Y )
The function simply tries to sort the plot by the index of each leaf.