CodeR-TSV

A group of semi, somewhat, and diehard code-writing scientists who use R (and other languages) to solve a diverse set of problems in our respective fields

1 minute read

Pete (@pete_cowman) gave an intro and demonstrated how to plot phylogenetic trees in R with the package ggtree. After intro he had fun plotting a phylogeny of butterfly fishes. To view Pete’s materials on ggtree see his repository here.

# Lets have fun with a tree
# load libraries
library(tidyverse)
library(ape)
library(ggtree)
library(treeio)
library(tidytree)


# read in a BEAST format tree (the one in exmaple folder)

tr <- read.beast("example_data/Chaetodontidae.tre")
tr@phylo
tr@data %>% glimpse()

# plot with ape to get a few node numbers

plot(tr@phylo, cex = 0.3)
nodelabels()

# plot with ggtree
ggtree(tr, ladderize = T, right = T)
ggtree(tr, layout = "circular")
ggtree(tr, layout = "fan")
ggtree(tr, layout = "slanted")
ggtree(tr, layout = "radial")

# since it is calibrated to time I will reverse the node ages to be time before present
p <- ggtree(tr)
p + theme_tree2()

p1 <- revts(p)
p1 + theme_tree2()
# now lets sort outt he tip labels
p1 + geom_tiplab()

# need to add space for labels
p1 + geom_tiplab(size = 2) + xlim(NA,30)

# we can also change the labels to be displayed to save some space.
tr@phylo$tip.label <- gsub("_", " ", tr@phylo$tip.label)

p1 + geom_tiplab(size = 2, fontface = "italic") + xlim(NA,30)

tibble(label = tr@phylo$tip.label) %>% mutate(newlabel = gsub("Chaetodon ", "C. ", label)) %>% arrange(label) -> d
d %>% data.frame(d)

p1 %<+% d + geom_tiplab(aes(label = newlabel), size = 2, fontface = "italic") + xlim(NA,30) -> p2


# lets label some clades

getMRCA(tr@phylo, tip = grep("Chaetodon", tr@phylo$tip.label, value = T))

p2 + geom_nodelab(aes(label = node), geom = "label")
# 112, 136, 205, 182, 165, 141
p2 + 
  geom_cladelabel(node = 112, label  = "Bannerfishes",offset = 20, offset.text = 1, color='black', barsize = 2) + 
  geom_cladelabel(node = 136, label  = "Prognathodes", offset = 20,offset.text = 1, color='grey', barsize = 2) + 
  geom_cladelabel(node = 205, label  = "Clade 1", offset = 20,offset.text = 1, color='black', barsize = 2) + 
  geom_cladelabel(node = 182, label  = "Clade 2", offset = 20,offset.text = 1, color='grey', barsize = 2) + 
  geom_cladelabel(node = 165, label  = "Clade 3", offset = 20,offset.text = 1, color='black', barsize = 2)

# view a clade
viewClade(p2, node = 112)

You May Also Enjoy