Unable to set colors and generate a legend for a ggtree plot based on Species

[uceleste]

Hi,

I'm using the R package ggtree to plot a phylogenetic tree of 9 plant species and outgroups. I have successfully produced the phylogenetic tree I was interested in, however, I have difficulties adding a "legend". I do not receive an error message concerning the command, but the legend does not appear.

Attached is the tree I am using called "COPIA_FINAL_magg_80aa.algn.txt": COPIA_FINAL_magg_80aa.algn.txt

This is the command I'm running:

# R v4.2.2 | Rstudio 2022.12.0+353 "Elsbeth Geranium" Release (7d165dcfc1b6d300eb247738db2c7076234f6ef0, 2022-12-03) for Ubuntu Bionic

current_dir <- getwd()
setwd(current_dir)

library(ggtree)

# Load the tree
tree=read.tree("COPIA_FINAL_magg_80aa.algn.treefile")

# Set tip labels
seq=tree$tip.label
dd=data.frame(seq)
dd$Species = 0
dd$Species[grep("Balsamifera", dd$seq)]="Balsamifera"
dd$Species[grep("Deltoides", dd$seq)]="Deltoides"
dd$Species[grep("Simonii", dd$seq)]="Simonii"
dd$Species[grep("Tremula", dd$seq)]="Tremula"
dd$Species[grep("Tremuloides", dd$seq)]="Tremuloides"
dd$Species[grep("Trichocarpa", dd$seq)]="Trichocarpa"
dd$Species[grep("Nigra", dd$seq)]="Nigra"
dd$Species[grep("Purpurea", dd$seq)]="Purpurea"
dd$Species[grep("Suchowensis", dd$seq)]="Suchowensis"
dd$Species[grep("Outgroup", dd$seq)]="Outgroup"

# Set tip colors
cls=function(dd){
  ss=sort(unique(dd$Species))
  colors=setNames(palette()[1:length(ss)],ss)
  colors=colors[dd$Species]
  return(colors)
}
colors=cls(dd)

# Plot the tree
ggtree(tree) + 
  geom_tippoint(color=colors, shape=16, size=3, show.legend = TRUE) +
  geom_text2(aes(label=label, subset = !is.na(as.numeric(label)) & as.numeric(label) > 60), hjust=-0.5) +
  theme(legend.position="right")

This is the tree it generates:

The legend should show the names of the species associated with the colour of the tree tips. Here is an example of the tree I'm looking for. The colours don't matter, I can change them later. Do you have any suggestions?

I really appreciate your assistance!