How to draw dendrogram using ape package in R?

Question

I have a distance matrix of ~200 x 200 size I an unable to plot a dendrogram using the BioNJ option of ape library in R The size is big to make the plot visible What ways can I improve the visibility

Answer 1

Two options depending on your data

If you need to calculate the distance matrix of your data then use

set.seed(1)                          # makes random sampling with rnorm reproducible
# example matrix
m <- matrix(rnorm(100), nrow = 5)    # any MxN matrix
distm <- dist(m)                     # distance matrix
hm <- hclust(distm)
plot(hm)

If your data is a distance matrix (must be a square matrix!)

set.seed(1)
# example matrix
m <- matrix(rnorm(25), nrow=5)       # must be square matrix!
distm <- as.dist(m)
hm <- hclust(distm)
plot(hm)

A 200 x 200 distance matrix gives me a reasonable plot

set.seed(1)
# example matrix
m <- matrix(rnorm(200*200), nrow=200)       # must be square matrix!
distm <- as.dist(m)
hm <- hclust(distm)
plot(hm)