index.Rmd

---
title: 'Data Integration, Manipulation and Visualization of Phylogenetic Trees'
author: "Guangchuang Yu"
knit: "bookdown::render_book"
site: bookdown::bookdown_site
output:
  bookdown::gitbook:
  bookdown::pdf_book:
    dev: "cairo_pdf"
    latex_engine: xelatex
bibliography: references.bib
biblio-style: apalike
always_allow_html: yes
toc_appendix: yes
fontsize: "12pt"
mainfont: Times New Roman
sansfont: Arial
monofontoptions: "Scale=0.7"
linestretch: 1.5
toc-depth: 2
link-citations: yes
documentclass: book
papersize: A4
classoption: twoside
highlight_bw: yes
geometry: "left=35mm,right=35mm,top=25mm,bottom=25mm"
---


```{r include=FALSE}
library(ape)
library(Biostrings)
library(cowplot)
library(ggplot2)
library(dplyr)
library(kableExtra)
library(tidytree)
library(treeio)
library(ggtree)

options(width=60)

theme_set(theme_grey())

CRANpkg <- function (pkg) {
    cran <- "https://CRAN.R-project.org/package"
    fmt <- "[%s](%s=%s)"
    sprintf(fmt, pkg, cran, pkg)
}

Biocpkg <- function (pkg) {
    sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg)
}

library(knitr)
opts_chunk$set(message=FALSE, warning=FALSE, eval=TRUE, echo=TRUE, cache=TRUE)
```




# Preface {-}

> You can't even begin to understand biology, you can't understand life, unless
> you understand what it's all there for, how it arose - and that means
> evolution.
>
> --- Richard Dawkins


The book is meant as a guide for data integration, manipulation and visualization of phylogenetic trees using a suite of R packages, `r CRANpkg("tidytree")`, `r Biocpkg("treeio")` and `r Biocpkg("ggtree")`.

If you use the software suite in published research, please cite the most appropriate paper(s) from this list:

1. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.
doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
2. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for
visualization and annotation of phylogenetic trees with their covariates and
other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.
doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).

<center>
<img src="book-cover.png" style="width:500px;border:2px solid black;"/>
</center>

The book’s source code is hosted on GitHub, at <https://github.com/YuLab-SMU/treedata-book>. If you notice typos or other issues, feel free to open an issue on GitHub or send me a pull request. If you do the latter, in your commit message, please add the sentence "I assign the copyright of this contribution to Guangchuang Yu," so that I can maintain the option of publishing this book in other forms.

This work is licensed under the [Attribution-NonCommercial-NoDerivatives 4.0 International](https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode) License.