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rdendrogramape-phylo

How to draw dendrogram using ape package in R?

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 visibilityenter image description here

Solution

  • 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)