Question

This should be relatively simple but for some reason, I’m coming up stumped.

I want to reorder a phylogenetic distance matrix so that the columns are in alphabetical order.

Here is a quick example:

require("ape")
set.seed(5)
dist(cophenetic(rtree(5)))

Any ideas?

Answer 1

if T <- dist(cophenetic(rtree(5)))

T is of class dist so it doesnt have names, just labels.
You can order its labels

ordering <- sort(attr(T, "Labels"))

You can coerce it into a matrix, and then sort it

T.mat <- as.matrix(T)[ordering, ordering]

Then as @Roland suggested, convert it back to dist

T  <- as.dist(T.mat)

If you would like to control the format of the matrix, you can use the following

T.fm <- format(T.mat, digits=3, nsmall=3)
T.fm[row(T.fm) < col(T.fm)] <- ""
print(T.fm, quote=F)

#      t1    t2    t3    t4    t5   
# t1 0.000                        
# t2 3.436 0.000                  
# t3 1.309 3.632 0.000            
# t4 2.145 2.338 2.530 0.000      
# t5 1.756 2.783 2.173 1.136 0.000

T  <- as.dist(T.fm)
T
#       t1    t2    t3    t4
# t2 3.436                  
# t3 1.309 3.632            
# t4 2.145 2.338 2.530      
# t5 1.756 2.783 2.173 1.136