Data Integration, Manipulation and Visualization of Phylogenetic Trees  book cover
1st Edition

Data Integration, Manipulation and Visualization of Phylogenetic Trees

ISBN 9781032233574
Published August 26, 2022 by Chapman & Hall
276 Pages 117 B/W Illustrations

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Book Description

Data Integration, Manipulation and Visualization of Phylogenetic Trees introduces and demonstrates data integration, manipulation and visualization of phylogenetic trees using a suite of R packages, tidytree, treeio, ggtree and ggtreeExtra. Using the most comprehensive packages for phylogenetic data integration and visualization, contains numerous examples that can be used for teaching and learning. Ideal for undergraduate readers and researchers with a working knowledge of R and ggplot2.

Key Features:

  • Manipulating phylogenetic tree with associated data using tidy verbs
  • Integrating phylogenetic data from diverse sources
  • Visualizing phylogenetic data using grammar of graphics

Table of Contents

Chapter 1 Importing Tree with Data

Chapter 2 Manipulating Tree with Data

Chapter 3 Exporting tree with data

Chapter 4 Phylogenetic Tree Visualization

Chapter 5 Phylogenetic Tree Annotation

Chapter 6 Visual Exploration of Phylogenetic Tree

Chapter 7 Plotting tree with data

Chapter 8 Annotating Tree with Silhouette Images and Sub-plots

Chapter 9 ggtree for other tree-like objects

Chapter 10 ggtreeExtra for presenting data on a circular layout

Chapter 11 Other ggtree extensions

Chapter 12 ggtree utilities

Frequently asked questions

Related tools

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Guangchuang Yu is a professor of bioinformatics, director of the Department of Bioinformatics, Southern Medical University. He earned his Ph.D. from the School of Public Health, The University of Hong Kong. As an active R user, he has authored several R packages and has supervised post-graduate students to develop a few other packages, including ggmsa, ggtreeExtra, MicrobiomeProfiler and MicrobiotaProcess.