How to colour the tips of tree by group in ggtree?

Question

How do I simply colour the tips of my tree according to the group the sample belongs to?

nwk <- system.file("extdata", "sample.nwk", package="treeio")
tree <- read.tree(nwk)

group_1 <- rep("1.1.1", 5)
group_2 <- rep("1.1.2", 3)
group_3 <- rep("1.2", 2)
group_4 <- rep("1.2.1", 2)
group_5 <- "1.2"

meta_data <- data.frame(ID = LETTERS[1:13], 
                        group = c(group_1, group_2, group_3, group_4, group_5))

What do I do with the metadata to get the tips to show up as coloured circles or squares (or other shape) and create a legend based on these colours?

I have seen similar trees plotted in the ggtree documentation however their code is hugely complicated (see for example section 4.3.7.3 in https://guangchuangyu.github.io/ggtree-book/chapter-ggtree.html).

Also, I cannot reproduce these examples because they're relying on metadata that they nowhere make clear is available:

treefile <- "RAxML_bestTree.Aln_All_H3.nwk"
tipseqfile <- "Aln_All_H3_filted.fas"

for example.

there must be a simple way of colouring the tips with this metadata.

Answer 1

You can convert the tree to a tibble and then join the meta_data. Then you convert back to a tree and add color to the aestetics of geom_tiplab

x <- full_join(as_tibble(tree), meta_data, by = c("label" = "ID"))

tree2 <- as.treedata(x)

ggtree(tree2) + geom_tiplab(aes(color = group))

EDIT: the legend can be added with theme_tree. I'll leave that up to you