How to plot dendrograms with large datasets?

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")

The cut function described in the other answer is a very good solution; if you would like to maintain the whole tree on one page for some interactive investigation you could also plot to a large page on a PDF.

The resulting PDF is vectorized so you can zoom in closely with your favourite PDF viewer without loss of resolution.

Here's an example of how to direct plot output to PDF:

# Open a PDF for plotting; units are inches by default
pdf("/path/to/a/pdf/file.pdf", width=40, height=15)

# Do some plotting
plot(gcPhylo)

# Close the PDF file's associated graphics device (necessary to finalize the output)
dev.off()