This book introduces and demonstrates data integration, manipulation and visualization of phylogenetic trees using a suite of R packages, tidytree, treeio, ggtree and ggtreeExtra.
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
1. Importing Tree with Data,
2. Manipulating Tree with Data,
3. Exporting tree with data,
4. Phylogenetic Tree Visualization,
5. Phylogenetic Tree Annotation,
6. Visual Exploration of Phylogenetic Tree,
7. Plotting tree with data,
8. Annotating Tree with Silhouette Images and Sub-plots,
9. ggtree for other tree-like objects,
10. ggtreeExtra for presenting data on a circular layout,
11. Other ggtree extensions,
12. ggtree utilities, A. Frequently asked questions, B. Related tools, Figures and Tables Publications of the ggtree package suite, References, Index
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.
