I want to find the number of clusters when cutting a tree at given heights.
The tree is of class "dendrogram" in R and so I have been using the package dendextend to explore this.
Example:
# Create a dend:
dend <- 1:5 %>% dist %>% hclust %>% as.dendrogram
# Plot it:
dend %>% plot
I want to find how many clusters there are when I specify, for example, "height = 3" (see y-axis in the generated plot).
At height 3 I should get the answer "2" because at that height a horizontal line should hit two vertical lines, and hence two clusters are generated.
At "height = 1.5" the answer should be "3" because three lines are crossed etc..
I am using object of class dendrogram because my raw data is in Newick format and I have only found the read.dendrogram() function to parse this tree. I have used as.hclust() to convert this to hclust class but I still can't find an answer.
Also, if anyone knows how to plot the clusters generated by specifying height, that would help.
You want to use cutree from dendextend
library(dendextend)
dend <- 1:5 %>% dist %>% hclust %>% as.dendrogram
length(unique(cutree(dend, h = 1.5)))