How to plot dendrograms with large datasets?

Question

I am using ape (Analysis of Phylogenetics and Evolution) package in R that has dendrogram drawing functionality. I use following commands to read the data in Newick format, and draw a dendrogram using the plot function:

library("ape")
gcPhylo <-read.tree(file = "gc.tree")
plot(gcPhylo, show.node.label = TRUE)

As the data set is quite large, it is impossible to see any details in the lower levels of the tree. I can see just black areas but no details. I can only see few levels from the top, and then no detail.

I was wondering if there is any zoom capability of the plot function. I tried to limit the area using xLim and yLim, however, they just limit the area, and do not zoom to make the details visible. Either zooming, or making the details visible without zooming will solve my problem.

I am also appreciated to know any other package, function, or tool that will help me overcoming the problem.

Thanks.

Answer 1

It is possible to cut a dendrogram at a specified height and plot the elements:

First create a clustering using the built-in dataset USArrests. Then convert to a dendrogram:

hc <- hclust(dist(USArrests))
hcd <- as.dendrogram(hc)

Next, use cut.dendrogram to cut at a specified height, in this case h=75. This produces a list of a dendrogram for the upper bit of the cut, and a list of dendograms, one for each branch below the cut:

par(mfrow=c(3,1))

plot(hcd, main="Main")
plot(cut(hcd, h=75)$upper, 
     main="Upper tree of cut at h=75")
plot(cut(hcd, h=75)$lower[[2]], 
     main="Second branch of lower tree with cut at h=75")