CODEWITHSUNDEEP
rplothierarchical-clusteringdendrogram
Gilgamesh
Gilgamesh

Reputation: 629

How to line (cut) a dendrogram at the best K

How do I draw a line in a dendrogram that corresponds the best K for a given criteria?

Like this:

enter image description here

Lets suppose that this is my dendrogram, and the best K is 4.

data("mtcars")
myDend <-  as.dendrogram(hclust(dist(mtcars))) 
plot(myDend)

I know that abline function is able to draw lines in graphs similarly to the one showed above. However, I don't know how could I calculate the height, so the function is used as abline(h = myHeight)

Upvotes: 5

Views: 5839

Answers (1)

G5W
G5W

Reputation: 37661

The information that you need to get the heights came with hclust. It has a variable containing the heights. To get the 4 clusters, you want to draw your line between the 3rd biggest and 4th biggest height.

HC = hclust(dist(mtcars))
myDend <-  as.dendrogram(HC) 

par(mar=c(7.5,4,2,2))
plot(myDend)

k = 4
n = nrow(mtcars)
MidPoint = (HC$height[n-k] + HC$height[n-k+1]) / 2
abline(h = MidPoint, lty=2)

Dendrogram

Upvotes: 9

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