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

part I|70 pages

Tree data input, output, and manipulation

chapter 2Chapter 1|30 pages

Importing Tree with Data

chapter Chapter 2|26 pages

Manipulating Tree with Data

chapter Chapter 3|12 pages

Exporting Tree with Data

part II|88 pages

Tree data visualization and annotation

chapter 72Chapter 4|24 pages

Phylogenetic Tree Visualization

chapter Chapter 5|14 pages

Phylogenetic Tree Annotation

chapter Chapter 6|12 pages

Visual Exploration of Phylogenetic Trees

chapter Chapter 7|12 pages

Plotting Tree with Data

chapter Chapter 8|12 pages

Annotating Tree with Silhouette Images and Sub-plots

chapter Chapter 9|12 pages

ggtree for Other Tree-like Objects

part III|22 pages

ggtree extensions

chapter 160Chapter 10|16 pages

ggtreeExtra for Presenting Data on a Circular Layout

chapter Chapter 11|4 pages

Other ggtree Extensions

part IV|28 pages

Miscellaneous topics

chapter 182Chapter 12|14 pages

ggtree Utilities

chapter Chapter 13|12 pages

Gallery of Reproducible Examples