1
Short introduction to R
2
Short introduction to ggplot2
3
Parsing phylogenetic trees with associated data:
treeio
3.1
Introduction
3.1.1
Newick tree format
3.1.2
NEXUS tree format
3.1.3
New Hampshire eXtended format
3.1.4
Jplace format
3.1.5
Software outputs
3.2
Methods and Materials
3.3
Results
3.3.1
Features of
treeio
3.3.2
Functions demonstrated
3.3.3
Data integration and comparison
3.4
Discussion
4
Visualization and annotation of phylogenetic trees:
ggtree
4.1
Introduction
4.2
Methods and Materials
4.3
Results
4.3.1
Features
4.3.2
Layouts of phylogenetic tree
4.3.3
Annotation layers
4.3.4
Tree manipulation
4.3.5
Tree annotation using data from evolutionary analysis software
4.3.6
Tree annotation based on tree classes defined in other R packages
4.3.7
Advanced annotation on the phylogenetic tree
4.3.8
Performance comparison with other tree-related packages
4.4
Discussion
5
Annotating phylogenetic tree with images
5.1
Annotate tips
5.2
Annotate internal nodes
5.3
Use image as background
References
ggtree: Elegant Graphics for Phylogenetic Tree Visualization and Annotation
ggtree: Elegant Graphics for Phylogenetic Tree Visualization and Annotation
Guangchuang Yu
Chapter 1
Short introduction to R
say hello to R