'Extract cluster from dendogram
I have a tree and I cut it into several clusters at a certain height.
I generate 5 clusters with cutree(), but they are not sorted according their position on the tree (e.g left to right) I want to know which cluster correspond to which branch of the tree. Can someone help me?
here a simple code:
data = USArrests
out = pheatmap(data)
plot(out$tree_row)
abline(h=80, col="red", lty=2, lwd=2)
clusters = sort(cutree(out$tree_row, h=80))
max(clusters)
clusters.dt = setDT(data.frame(group = as.numeric(clusters) , state = names(clusters), stringsAsFactors=FALSE))
clusters.dt = split(clusters.dt$"state",clusters.dt$"group", )
> clusters.dt
$`1`
[1] "Alabama" "Alaska" "Arizona" "California" "Delaware" "Illinois" "Louisiana" "Maryland" "Michigan" "Mississippi" "Nevada" "New Mexico" "New York" "South Carolina"
$`2`
[1] "Arkansas" "Colorado" "Georgia" "Massachusetts" "Missouri" "New Jersey" "Oklahoma" "Oregon" "Rhode Island" "Tennessee" "Texas" "Virginia" "Washington" "Wyoming"
$`3`
[1] "Connecticut" "Idaho" "Indiana" "Kansas" "Kentucky" "Montana" "Nebraska" "Ohio" "Pennsylvania" "Utah"
$`4`
[1] "Florida" "North Carolina"
$`5`
[1] "Hawaii" "Iowa" "Maine" "Minnesota" "New Hampshire" "North Dakota" "South Dakota" "Vermont" "West Virginia" "Wisconsin"
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