rename phylogeny tip labels in treeio

April 18, 2018
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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)
## Loading required package: treeio
require(ggtree)
## Loading required package: ggtree
## ggtree v1.11.6  For help: https://guangchuangyu.github.io/software/ggtree
## 
## If you use ggtree in published research, please cite:
## Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628
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)
d
##   label   genus  species    geo
## 1     a Gorilla  gorilla Africa
## 2     b     Pan     spp. Africa
## 3     c    Homo  sapiens  World
## 4     d   Pongo pygmaeus   Asia
ggtree(tr) %<+% d + xlim(NA, 5) +
    geom_tiplab(aes(label=paste0('italic(', genus, ')~bolditalic(', species, ')~', geo)), parse=T)
## Warning: package 'bindrcpp' was built under R version 3.4.4

However, it is also possible to rename taxa of the tree object (either treedata or phylo) in treeio:

tr2 = rename_taxa(tr, d, label, genus)
write.tree(tr2)
## [1] "((Gorilla,(Pan,Homo)),Pongo);"
d2 = dplyr::mutate(d, newlab = paste(genus, species, sep='|'))
d2
##   label   genus  species    geo          newlab
## 1     a Gorilla  gorilla Africa Gorilla|gorilla
## 2     b     Pan     spp. Africa        Pan|spp.
## 3     c    Homo  sapiens  World    Homo|sapiens
## 4     d   Pongo pygmaeus   Asia  Pongo|pygmaeus
tr3 = rename_taxa(tr, d2, label, newlab)
write.tree(tr3)
## [1] "((Gorilla|gorilla,(Pan|spp.,Homo|sapiens)),Pongo|pygmaeus);"

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.

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