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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
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
Publications of the ggtree package suite
References
Guangchuang Yu is a professor of bioinformatics, and director of the Department of Bioinformatics, Southern Medical University. He earned his PhD 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.
