data-tree_HPV58 {TDbook}

Tree to display with dot and line plots of pairwise nucleotide sequence distances

Description

This tree is to provide accession numbers from its tip labels, which are used to calculates pairwise nucleotide sequence distances. The distance matrix then is visualized as dot and line plots and attached to the tree, demonstrating the abilities of facet_plot() of ggtree that can add multiple layers to a specific panel.
Reproduction fo Fig. 1 of (Chen et al. 2017).
Chap.13.1

Format

S3 class:phylo

References

Chen, Zigui, Wendy C. S. Ho, Siaw Shi Boon, Priscilla T. Y. Law, Martin C. W. Chan, Rob DeSalle, Robert D. Burk, and Paul K. S. Chan. Ancient Evolution and Dispersion of Human Papillomavirus 58 Variants. Journal of Virology, Volume 91, Issue 21, November 2017, e01285–17. doi:10.1128/JVI.01285-17

Examples

data(tree_HPV58)