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I don't know whether 'rename taxa' is a common task or not. It seems not a good idea to rename taxa in Newick tree text, since it may introduce problems when mapping the original sequence alignment to the tree.
If you just want to show different or additional information when plotting the tree, it is fine and easy to do it using ggtree:
require(treeio)
require(ggtree)
tr <- read.tree(text = "((a,(b,c)),d);")
genus <- c("Gorilla", "Pan", "Homo", "Pongo")
species <- c("gorilla", "spp.", "sapiens", "pygmaeus")
geo <- c("Africa", "Africa", "World", "Asia")
d <- data.frame(label = tr$tip.label, genus = genus,
species = species, geo = geo)
ggtree(tr) %<+% d + xlim(NA, 5) +
geom_tiplab(aes(label=paste0('italic(', genus, ')~bolditalic(', species, ')~', geo)), parse=T)
treedata or phylo) in treeio:
tr2 = rename_taxa(tr, d, label, genus)
write.tree(tr2)
d2 = dplyr::mutate(d, newlab = paste(genus, species, sep='|'))
tr3 = rename_taxa(tr, d2, label, newlab)
write.tree(tr3)
If the input tree object is a treedata instance, you can use write.beast to export the tree with associated data to a BEAST compatible NEXUS file.