rplotdendrogramhclust

Plotting hclust only to the cut clusters, not every leaf


I have an hclust tree with nearly 2000 samples. I have cut it to an appropriate number of clusters and would like to plot the dendrogram but ending at the height that I cut the clusters rather than all the way to every individual leaf. Every plotting guide is about coloring all the leaves by cluster or drawing a box, but nothing seems to just leave the leaves below the cut line out completely.

My full dendrogram looks like the following:

Full Dendrogram

I would like to plot it as if it stops where I've drawn the abline here (for example):

enter image description here


Solution

  • This should get you started. I suggest reading the help page for "dendrogram"

    Here is the example from the help page:

    hc <- hclust(dist(USArrests))
    dend1 <- as.dendrogram(hc)
    plot(dend1)
    dend2 <- cut(dend1, h = 100)
    plot(dend2$upper)
    plot(dend2$upper, nodePar = list(pch = c(1,7), col = 2:1))
    

    By performing the cut on the dendrogram object (not the hclust object) you can then plot the upper part of the dendrogram. It will take a some work to replace the branch1, 2, 3, and 4 labels depending on your analysis.

    Good luck.