index.Rmd

---
title: 'Data Integration, Manipulation and Visualization of Phylogenetic Trees'
author: Guangchuang Yu
date: "`r Sys.Date()`"
knit: "bookdown::render_book"
site: bookdown::bookdown_site
output:
  bookdown::bs4_book:
  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
github-repo: YuLab-SMU/treedata-book
twiter-handle: guangchuangyu
description: "Master ggtree package suit to handle tree with data."
documentclass: book
papersize: A4
classoption: twoside
highlight_bw: yes
geometry: "left=35mm,right=35mm,top=25mm,bottom=25mm"
---


```{r include=FALSE}
library(conflicted)
library(ape)
library(Biostrings)
## library(OutbreakTools)
library(igraph)
library(phylobase)

library(emojifont)
library(cowplot)
library(ggplot2)
library(dplyr)
library(kableExtra)
library(tidytree)
library(treeio)
library(ggtree)

conflict_prefer("expand", "ggtree")
conflict_prefer("mask", "treeio")
conflict_prefer("parent", "treeio")
conflict_prefer("ancestor", "treeio")
conflict_prefer("get.data", "treeio")
conflict_prefer("drop.tip", "treeio")
conflict_prefer("paste", "base")

conflict_prefer("MRCA", "tidytree")

conflict_prefer("filter", "dplyr")
conflict_prefer("rename", "dplyr")
conflict_prefer("collapse", "dplyr")
conflict_prefer("intersect", "dplyr")
conflict_prefer("union", "dplyr")

conflict_prefer("strsplit", "base")

conflict_prefer("geom_errorbarh", "ggplot2")

conflict_prefer("as.data.frame", "BiocGenerics")


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)
}

Githubpkg <- function (user, pkg) {
    gh <- "https://github.com"
    fmt <- "[%s](%s/%s/%s)"
    sprintf(fmt, pkg, gh, user, pkg)
}

badge_version <- function(pkg, color="green") {
    v <- packageVersion(pkg)
    url <- paste0("https://github.com/YuLab-SMU/", pkg)
    badger::badge_custom(pkg, v, color, url)
}


## based on https://bookdown.org/yihui/rmarkdown-cookbook/fig-process.html

svg2png <- function(path, options) {
    if (!grepl('[.]svg$', path)) return(path)

    output <- sub(".svg$", ".png", path)
    system2("convert", paste("-density 150", path, output))
    file.remove(path)
    return(output)
}

## manual setting. the ropenscilabs/icon package will set up everything for you.
## fontawesome supports
## htmltools::tagList(rmarkdown::html_dependency_font_awesome())

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


# Welcome {-}

<img class="cover" src="book-cover.png" width="210" height="297" /> This is the online work-in-progress book of "Data Integration, Manipulation and Visualization of Phylogenetic Trees". This book gives your all the details of using the ggtree package suit to handle tree with data. The book is written by Guangchuang Yu.


`r if (knitr::is_latex_output()) '-->'`




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