plot trait values at the tip of phylogeny

phylo_trait.R

# Script to add a trait matrix over a circular phylogenetic tree

# Packages ---------------------------------------------------------------------

library(ape)
library(ggtree)


# Generate Tree and Traits -----------------------------------------------------

# Number of species
n_species = 200
# Generate tree with 10 species
random_tree = rtree(n_species)

# Generate trait matrix
trait_df = data.frame(
    species = random_tree$tip.label,
    trait1 = rnorm(n_species), # Example of continuous trait
    # Example of categorical traits
    trait2 = sample(c("A", "B", "C"), replace = T, size = n_species))

# Plotting tree ----------------------------------------------------------------
plot_tree = ggtree(random_tree, layout = "fan", right = TRUE, size = 0.1)

# Add trait information into tree
plot_tree %<+% trait_df + geom_tippoint(aes(color = trait1, alpha = 0.5))