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:
还记得《ggtree hex sticker》一文吧？画了几个六角贴，纯代码生成。时隔半年，原来的ggtree已经分成了treeio和ggtree两个包，而我也做了这两个包的六角贴，终于我花了289美元印了一大波贴纸+磁贴。
I have 8 packages published within the Bioconductor project.
A new package treeio was included in BioC 3.5 release.
I have splitted ggtree to 2 packages, treeio and ggtree. Now ggtree is mainly focus on visualization and annotation, while treeio focus on parsing and exporting tree files. Here is a welcome message from treeio that you can convert ggtree output to tree object which can be exported as newick or nexus file if you want.
Thanks to ggplot2, output of ggtree is actually a ggplot object. The ggtree object can be rendered as graph by print method, but internally it is an object that contains data. treeio defines as.phylo and as.treedata to convert ggtree object to phylo or treedata object.
