Bookdown文档生成教程

时间:2022-04-26
本文章向大家介绍Bookdown文档生成教程，主要内容包括Get required information、Get a demo example、Build the book、Customize our bookdown、准备YML配置文件、其它定制、预览生成的WEB文件、A template Rmd、References、基本概念、基础应用、原理机制和需要注意的事项等，并结合实例形式分析了其使用技巧，希望通过本文能帮助到大家理解应用这部分内容。

bookdown是一款及其方便的编写技术文档或教材的工具，语法简洁，数据处理灵活。支持Rmarkdown或普通markdown通过pandoc软件转换为HTML或PDF。

Here lists the usage of bookdown for writing documents.

Get required information

Install required software

Rstudio或Pandoc二选一, bookdown必须安装。

  • Install Rstudio (version>1.0.0)
  • Install Pandoc (version>1.17.0.2)或者参照here
  • In R install.packages("bookdown")

Get a demo example

Clone or download en example from https://github.com/rstudio/bookdown-demo.

Build the book

run bash _build.sh in the downloaded demo example, then the books will be in _book dir.

The content of _build.sh is:

#!/bin/sh
Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::gitbook')"
Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::pdf_book')"

Customize our bookdown

准备Rmd文件

基本规则
  • 一个典型的bookdown文档包含多个章节，每个章节在一个R Markdown文件里面 (文件的语法可以是pandoc支持的markdown语法，但后缀必须为Rmd)。
  • 每一个章节都必须以# Chapter title开头。后面可以跟一段概括性语句，概述本章的内容，方便理解，同时也防止二级标题出现在这一页。默认系统会按照文件名的顺序合并Rmd文件。
  • 另外章节的顺序也可在_bookdown.yml文件中通过rmd_files:["file1.Rmd", "file2.Rmd", ..]指定。
  • 如果有index.Rmd，index.Rmd总是出现在第一个位置。通常index.Rmd里面也需要有一章节，如果不需要对这一章节编号的话，可以写作# Preface {-}, 关键是{-}。
  • 在第一个出现的Rmd文件中，可以定义Pandoc相关的YAML metadata, 比如标题、作者、日期等(去掉#及其后的内容)。 ``` title: "My book" author: #可以写多行信息，都会被当做Author处理 - "CT" - "CY" - "chentong_biology@163.com" date: "`r Sys.Date()`" documentclass: article #可以为book或article # 如果需要引用参考文献，则添加下面三行内容 bibliography: [database.bib] #指定存储参考文献的bib文件，endote或zotero都可以导出这种引文格式 biblio-style: apalike #设定参考文献显示类型 link-citations: yes ``` ```{r setup, include=FALSE} knitr::opts_chunk$set(echo = FALSE, fig.align="center", out.width="95%", fig.pos='H') # knitr::opts_chunk$set(cache = FALSE, autodep=TRUE) set.seed(0304) ``` ~~~~~~
插入并引用图片(外部图片)

插入图片最好使用knitr::include_graphics，可以同时适配HTML和PDF输出。另外当目录下同时存在name1.png和name1.pdf文件时，会自动选择在HTML展示name1.png文件，在PDF输出中引入name1.pdf格式的文件。

图的标签为fig-name(不能有下划线)，在引用时需使用如下格式@ref(fig:fig-name)，且fig.cap也要设置内容。

多张图可以同时展示，图的名字以vector形式传给include_graphics，需要设置out.width=1/number-pics 和 fig.show="hold"。

Insert a single pic and refer as Figure @ref(fig:fig-name). `echo=FALSE` will hide the code block and display the output of `r` command only. These options can be set globally as indicated below.

```{r fig-name, fig.cap="Markdown supported string as caption", fig.align="center", echo=FALSE}
knitr::include_graphics("images/1.png")
```

Suppose we have 3 pictures in `images` folder with names as `Fig1_a`, `Fig1_b`,  `Fig1_c`,  we can refer to them using Figure @ref(fig:fig1).

```{r fig1, fig.cap="3 sub-plots.", fig.align="center", out.width=33%, fig.show="hold"}
fig1 = list.files("images", pattern="Fig1_.*", full.names=T)
knitr::include_graphics(fig1)
```

Another way of including two pics.

```{r fig-name2,  out.width="49%", fig.show="hold", fig.cap="Markdown supported string as caption",  fig.align="center", echo=FALSE}
knitr::include_graphics(c("images/1.png", "images/2.png"))
```
~~~~~~~~~~~~~~~~

如果图或表的标题中有Markdown语法，输出为HTML时是可以正确解析的，但是输出为PDF时却不可以。这时可以使用Text Reference。当图或表的标题太长时，也可以使用Text Reference引用一段话作为图和表的标题。

Here is normal text.

(ref:pic-label) This line can be referred in **fig.cap** and markdown syntax is supported for both `HTML` and `PDF` output.

```{r pic-label, fig.cap="(ref:pic-label)"}
knitr::include_graphics("images/1.png")
```
~
插入并引用表格(外部表格)

外部表格的名字中必须包含tab:, 然后是表格的实际名字，格式为(#tab:table-name); 引用时使用Table @ref(tab:table-name)。 表格名字中不能有下划线。

Check Table @ref(tab:seq-sum) for detail.

Table: (#tab:seq-sum) Summary of sequencing reads 测序量总结 (对于双端测序,  *_1* 表示左端reads, *_2* 表示右端reads) 

----------------------------------------------------------------------
Sample     Total reads     Total bases Sequence length (nt)     GC content (%) Encoding               
-------- ------------- --------------- ---------------------- ---------------- -----------------------
T8_1        37,106,941   5,566,036,721 138-150                              47 Sanger / Illumina 1.9  

T8_2        37,106,941   5,566,034,285 138-150                              47 Sanger / Illumina 1.9  
----------------------------------------------------------------------
插入并引用表格(内部表格)

插入表格推荐使用knitr::kable，只要提供数据矩阵，用r读取就可以了。

Check Table @ref(tab:table-id) for detail.

```{r table-id, include=FALSE}
a <- as.data.frame(matrix(rnorm(20), nrow=4))
knitr::kable(a, caption="Test table",  booktabs=TRUE)
```
~
插入脚注

text^[footnote] is used to get the footnote.

where `type` may be `article`,  `book`,  `manual`,  and so on.^[The type name is case-insensitive,  so it does not matter if it is `manual`,  `Manual`,  or `MANUAL`.]
插入引文

假如我们的bib文件中内容如下，如果我们要引用这个文章，只要写 [@chen_m6a_2015]就可以了。

@article{chen_m6a_2015,
    title = {m6A {RNA} {Methylation} {Is} {Regulated} by {MicroRNAs} and {Promotes} {Reprogramming} to {Pluripotency}},
    volume = {16},
    issn = {1934-5909, 1875-9777},
    url = {http://www.cell.com/cell-stem-cell/abstract/S1934-5909(15)00017-X},
    doi = {10.1016/j.stem.2015.01.016},
    language = {English},
    number = {3},
    urldate = {2016-12-08},
    journal = {Cell Stem Cell},
    author = {Chen, Tong and Hao, Ya-Juan and Zhang, Ying and Li, Miao-Miao and Wang, Meng and Han, Weifang and Wu, Yongsheng and Lv, Ying and Hao, Jie and Wang, Libin and Li, Ang and Yang, Ying and Jin, Kang-Xuan and Zhao, Xu and Li, Yuhuan and Ping, Xiao-Li and Lai, Wei-Yi and Wu, Li-Gang and Jiang, Guibin and Wang, Hai-Lin and Sang, Lisi and Wang, Xiu-Jie and Yang, Yun-Gui and Zhou, Qi},
    month = mar,
    year = {2015},
    pmid = {25683224},
    pages = {289--301},
}

准备YML配置文件

_bookdown.yml

配置输入和输出文件参数。

book_filename: "输出文件的名字" 
output_dir: "输出目录的名字，默认_book"
language:
  ui:
      chapter_name: ""
_output.yml

配置产生输出文件的命令行参数。

bookdown::pdf_book:
  template: ehbio.tex #使用自己定制的pandoc latex模板
  includes: # or only customize part latex module
    in_header: preamble.tex
    before_body: latex/before_body.tex
    after_body: latex/after_body.tex
  latex_engine: xelatex
  citation_package: natbib
  keep_tex: yes
  pandoc_args: --chapters
  toc_depth: 3
  toc_unnumbered: no
  toc_appendix: yes
  quote_footer: ["\VA{", "}{}"]
bookdown::epub_book:
  stylesheet: css/style.css
bookdown::gitbook:
  css: style.css
  split_by: section
  config:
    toc:
      collapse: none
      before: | #设置toc开头和结尾的链接
          <li><a href="http://www.ehbio.com"><img src="ehbio_logo.png" width="100%"></a></li>
      after: |
          <li><a href="mailto:ct@ehbio.com" target="blank">ct@ehbio.com</a></li>
    download: [pdf, epub, mobi]
    edit: https://github.com/rstudio/bookdown/edit/master/inst/examples/%s
    sharing:
      twitter: no
      github: no
      facebook: no

其它定制

  • 不同的文件分别用于html和pdf输出 # in _bookdown.yml rmd_files: html: ["index.Rmd", "file2.Rmd"] latex: ["index_pdf.Rmd", "file3.Rmd"] # Different render way #!/bin/sh Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::gitbook')" Rscript -e "bookdown::render_book('index_pdf.Rmd', 'bookdown::pdf_book')"
  • 配置全局变量自适应HTML和PDF输出 ```{r setup, include=FALSE} library(knitr) output <- opts_knit$get("rmarkdown.pandoc.to") html = FALSE latex = FALSE opts_chunk$set(echo = FALSE, fig.align="center", fig.show="hold") if (output=="html") { html = TRUE } if (output=="latex") { opts_chunk$set(out.width="95%", out.height='0.7\textheight', out.extra='keepaspectratio', fig.pos='H') latex = TRUE } #knitr::opts_chunk$set(cache = FALSE, autodep=TRUE) set.seed(0304) ``` Below text will only appear in HTML output. ```{asis, echo=html} # EHBIO Gene Technology {-} ``` Below command will only be executed and displayed in HTML output. ```{r cover, eval=html, out.width="99%"} knitr::include_graphics("ehbio/cover.png") ``` ~~~~~~~~~~~~~~~~~~~~
  • 保留生成的markdown文件 # add below lines to last Rmd file ```{r, include=FALSE} file.rename(from="bookdown_file_name.md", to="bookdown_file_name.saved.md") ``` ~~~~~~~~~~~
  • 包含子文件 (subfile.txt) ```{r child="subfile.txt"} ``` ~~~~~~
  • cahce external file ref ```{r mtime-func} mtime <- function(files){ lapply(Sys.glob(files), function(x) file.info(x)$mtime) } ``` ```{r mtime-usage, cache=T, cache.extra=mtime(c("file1", "file2", file3))} file3 <- paste0(dir, '/', name) data1 <- read.table("file1") data2 <- read.table("file2") ``` ~~~

预览生成的WEB文件

如果没有安装Rstudio，可以在生成的book目录(有index.html的目录)下运行python -m SimpleHTTPServer 11521(11521为端口号，一般选较大值避免冲突), 然后就可以在浏览器输入网址http://server-ip:11521来访问了。

A template Rmd

Use bookdown_init_general.py -o test -t ‘我的文档’ -a “ 作者1 - 北京;2 - 南京;1521082” -b a.bib to generate a minimal template.

References

  • https://bookdown.org/yihui/bookdown/get-started.html
  • https://github.com/rstudio/bookdown/tree/master/inst/examples
  • http://stackoverflow.com/questions/25236850/how-to-set-different-global-options-in-knitr-and-rstudio-for-word-and-html
  • Multiple output with different configs https://github.com/yihui/knitr/issues/1145
  • Multiple output with different configs https://github.com/yihui/knitr/issues/114://github.com/rstudio/rmarkdown/issues/614
  • Citation style http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html
  • Save markdown http://stackoverflow.com/questions/19989325/knit-rmd-file-to-md-and-save-the-md-file-one-level-up-with-a-different-name

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