Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data

Abstract

While phylogenetic trees and associated data have been getting easier to generate, it has been difficult to reuse, combine, and synthesize the information they provided, because published trees are often only available as image files and associated data are often stored in incompatible formats. To increase the reproducibility and reusability of phylogenetic data, the ggtree object was designed for storing phylogenetic tree and associated data, as well as visualization directives. The ggtree object itself is a graphic object and can be rendered as a static image. More importantly, the input tree and associated data that are used in visualization can be extracted from the graphic object, making it an ideal data structure for publishing tree (image, tree, and data in one single object) and thus enhancing data reuse and analytical reproducibility, as well as facilitating integrative and comparative studies. The ggtree package is freely available at https://www.bioconductor.org/packages/ggtree.

Structural basis of odorant recognition by a human odorant receptor

“…On R studio 202.07.01, alignment reading and matrix of distance between sequences (by sequence identity) calculation were performed with the BiostrinG s 68 and seqinr 69 packages. Neighbor-Joining tree and tree visualization were realized with packages ape 70 and ggtree 71 and the tree is plotted unrooted with the daylight method.…”

MicrobiotaProcess: A comprehensive R package for deep mining microbiome

“…To help users quickly render clear, meaningful, and comprehensive visualizations that give useful microbiome insight, especially through the integration of different data, we developed many visualization methods based on ggplot2 , ggtree , and ggtreeExtra , which are composed of ‘mp_plot_’, and one or two explanatory terms ( Figure 2 C2). These approaches have the advantage of allowing the visualization results to be a proper ggplot or ggtree object 49 ( mp_plot_diff_cladogram and mp_plot_diff_res ), which can be modified, inspected, and reused with the universal and concise ggplot2 or ggtree syntax ( Figures SA.10 , SA.13 and SA.17 ).…”

Karyotype Evolution in Triatominae (Hemiptera, Reduviidae): The Role of Chromosomal Rearrangements in the Diversification of Chagas Disease Vectors

“…The analyses were carried out with a total of 20,000 generations, with burn-in adjusted in 25% of the samples, and convergence (ESS > 200) was evaluated in Tracer 1.8 [ 76 ]. The resulting tree was then plotted in R 4.2 [ 80 ], using the ggtree [ 81 , 82 , 83 , 84 , 85 ] and Revgadgets [ 86 ] packages. Vertical bars and grouping names were inserted using Adobe Illustrator CS6.…”