Treeio

rename phylogeny tip labels in treeio

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.

[Bioc 3.5] NEWS of my BioC packages

I have 8 packages published within the Bioconductor project.

A new package treeio was included in BioC 3.5 release.

convert graphic object to tree object using treeio

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.