How to get correct order of tip labels in APE after calling ladderize function

Question

I\'m trying to order the rows of a dataframe based on the tip labels found in a phylogenetic tree. The way I was going to do this was to use the match function

Answer 1

for different package (ggtree), but same issue I quote, "To get tip order of a ggtree plot, do something like this: data(bird.orders) p <- ggtree::ggtree(bird.orders) p[["data"]] # extract 'label' and 'y' columns

coming from this website, and package... though how many R packages does it take to change a light bulb? https://rdrr.io/github/joelnitta/jntools/man/get_tips_in_ape_plot_order.html

Answer 2

It seems the key is to look at the edge property. The tips are always the first nodes to be given an ID, which will simply correspond to the position in the tip.label vector.

library(ape)
tree <- read.tree(text = "(((A,B),(C,D)),E);")
tree2 <- ladderize(tree, right = FALSE)
tree$tip.label
#> [1] "A" "B" "C" "D" "E"
tree2$tip.label
#> [1] "A" "B" "C" "D" "E"
plot(tree2)
nodelabels()
tiplabels()

First step is to filter out internal nodes from the the second column of the edge matrix:

is_tip <- tree2$edge[,2] <= length(tree2$tip.label)
#> [1]  TRUE FALSE FALSE  TRUE  TRUE FALSE  TRUE  TRUE

ordered_tips <- tree2$edge[is_tip, 2]
#> [1] 5 1 2 3 4

Then you can use this vector to extract the tips in the right order:

tree2$tip.label[ordered_tips]
#> [1] "E" "A" "B" "C" "D"