Guangchuang Yu1. 1. Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China.
Abstract
Ggtree is an R/Bioconductor package for visualizing tree-like structures and associated data. After 5 years of continual development, ggtree has been evolved as a package suite that contains treeio for tree data input and output, tidytree for tree data manipulation, and ggtree for tree data visualization. Ggtree was originally designed to work with phylogenetic trees, and has been expanded to support other tree-like structures, which extends the application of ggtree to present tree data in other disciplines. This article contains five basic protocols describing how to visualize trees using the grammar of graphics syntax, how to visualize hierarchical clustering results with associated data, how to estimate bootstrap values and visualize the values on the tree, how to estimate continuous and discrete ancestral traits and visualize ancestral states on the tree, and how to visualize a multiple sequence alignment with a phylogenetic tree. The ggtree package is freely available at https://www.bioconductor.org/packages/ggtree.
Ggtree is an R/Bioconductor package for visualizing tree-like structures and associated data. After 5 years of continual development, ggtree has been evolved as a package suite that contains treeio for tree data input and output, tidytree for tree data manipulation, and ggtree for tree data visualization. Ggtree was originally designed to work with phylogenetic trees, and has been expanded to support other tree-like structures, which extends the application of ggtree to present tree data in other disciplines. This article contains five basic protocols describing how to visualize trees using the grammar of graphics syntax, how to visualize hierarchical clustering results with associated data, how to estimate bootstrap values and visualize the values on the tree, how to estimate continuous and discrete ancestral traits and visualize ancestral states on the tree, and how to visualize a multiple sequence alignment with a phylogenetic tree. The ggtree package is freely available at https://www.bioconductor.org/packages/ggtree.
Authors: Kara K Tsang; Kartik Sachar; Shehryar Ahmad; Dennis Quentin; Tahmid M Tashin; Nathan P Bullen; Stefan Raunser; Andrew G McArthur; Gerd Prehna; John C Whitney Journal: Elife Date: 2020-12-15 Impact factor: 8.140
Authors: John R Stinchcombe; Stephen I Wright; Julia M Kreiner; George Sandler; Aaron J Stern; Patrick J Tranel; Detlef Weigel Journal: Elife Date: 2022-01-17 Impact factor: 8.140
Authors: Sudaraka Mallawaarachchi; Gerry Tonkin-Hill; Nicholas J Croucher; Paul Turner; Doug Speed; Jukka Corander; David Balding Journal: NAR Genom Bioinform Date: 2022-02-22
Authors: Daniel J Butler; Christopher Mozsary; Cem Meydan; David Danko; Jonathan Foox; Joel Rosiene; Alon Shaiber; Ebrahim Afshinnekoo; Matthew MacKay; Fritz J Sedlazeck; Nikolay A Ivanov; Maria Sierra; Diana Pohle; Michael Zietz; Undina Gisladottir; Vijendra Ramlall; Craig D Westover; Krista Ryon; Benjamin Young; Chandrima Bhattacharya; Phyllis Ruggiero; Bradley W Langhorst; Nathan Tanner; Justyna Gawrys; Dmitry Meleshko; Dong Xu; Peter A D Steel; Amos J Shemesh; Jenny Xiang; Jean Thierry-Mieg; Danielle Thierry-Mieg; Robert E Schwartz; Angelika Iftner; Daniela Bezdan; John Sipley; Lin Cong; Arryn Craney; Priya Velu; Ari M Melnick; Iman Hajirasouliha; Stacy M Horner; Thomas Iftner; Mirella Salvatore; Massimo Loda; Lars F Westblade; Melissa Cushing; Shawn Levy; Shixiu Wu; Nicholas Tatonetti; Marcin Imielinski; Hanna Rennert; Christopher E Mason Journal: bioRxiv Date: 2020-05-01
Authors: Aishwarya Korgaonkar; Clair Han; Andrew L Lemire; Igor Siwanowicz; Djawed Bennouna; Rachel E Kopec; Peter Andolfatto; Shuji Shigenobu; David L Stern Journal: Curr Biol Date: 2021-03-02 Impact factor: 10.834
Authors: Nicola F Müller; Cassia Wagner; Chris D Frazar; Pavitra Roychoudhury; Jover Lee; Louise H Moncla; Benjamin Pelle; Matthew Richardson; Erica Ryke; Hong Xie; Lasata Shrestha; Amin Addetia; Victoria M Rachleff; Nicole A P Lieberman; Meei-Li Huang; Romesh Gautom; Geoff Melly; Brian Hiatt; Philip Dykema; Amanda Adler; Elisabeth Brandstetter; Peter D Han; Kairsten Fay; Misja Ilcisin; Kirsten Lacombe; Thomas R Sibley; Melissa Truong; Caitlin R Wolf; Michael Boeckh; Janet A Englund; Michael Famulare; Barry R Lutz; Mark J Rieder; Matthew Thompson; Jeffrey S Duchin; Lea M Starita; Helen Y Chu; Jay Shendure; Keith R Jerome; Scott Lindquist; Alexander L Greninger; Deborah A Nickerson; Trevor Bedford Journal: Sci Transl Med Date: 2021-05-03 Impact factor: 17.956
Authors: Chase L Ridenour; Jill Cocking; Samuel Poidmore; Daryn Erickson; Breezy Brock; Michael Valentine; Chandler C Roe; Steven J Young; Jennifer A Henke; Kim Y Hung; Jeremy Wittie; Elene Stefanakos; Chris Sumner; Martha Ruedas; Vivek Raman; Nicole Seaton; William Bendik; Heidie M Hornstra O'Neill; Krystal Sheridan; Heather Centner; Darrin Lemmer; Viacheslav Fofanov; Kirk Smith; James Will; John Townsend; Jeffrey T Foster; Paul S Keim; David M Engelthaler; Crystal M Hepp Journal: Front Genet Date: 2021-06-08 Impact factor: 4.772