1 Prerequisites

Bioconductor R Markdown format is build on top of R package bookdown (Xie, Allaire, and Grolemund 2018), which in turn relies on rmarkdown and pandoc to compile the final output document. Therefore, unless you are using RStudio, you will need a recent version of pandoc (>= 1.17.2). See the pandoc installation instructions for details on installing pandoc for your platform.

2 Getting started

To enable the Bioconductor style in your R Markdown vignette you need to:

Edit the DESCRIPTION file by adding

  VignetteBuilder: knitr
  Suggests: BiocStyle, knitr, rmarkdown

Specify BiocStyle::html_document or BiocStyle::pdf_document as output format and add vignette metadata in the document header:

  ---
  title: "Vignette Title"
  author: "Vignette Author"
  package: PackageName
  output: 
    BiocStyle::html_document
  vignette: >
    %\VignetteIndexEntry{Vignette Title}
    %\VignetteEngine{knitr::rmarkdown}
    %\VignetteEncoding{UTF-8}  
  ---

The vignette section is required in order to instruct R how to build the vignette.111 \VignetteIndexEntry should match the title of your vignette The package field which should contain the package name is used to print the package version in the output document header. It is not necessary to specify date as by default the document compilation date will be automatically included. See the following section for details on specifying author affiliations and abstract.

BiocStyle’s html_document and pdf_document format functions extend the corresponding original rmarkdown formats, so they accept the same arguments as html_document and pdf_document, respectively. For example, use toc_float: true to obtain a floating TOC as in this vignette.

2.1 Use with R markdown v1

Apart from the default markdown engine implemented in the rmarkdown package, it is also possible to compile Bioconductor documents with the older markdown v1 engine from the package markdown. There are some differences in setup and the resulting output between these two engines.

To use the markdown vignette builder engine:

Edit the DESCRIPTION file to include

  VignetteBuilder: knitr
  Suggests: BiocStyle, knitr

Specify the vignette engine in the .Rmd files (inside HTML comments)
```
  
```

Add the following code chunk at the beginning of your .Rmd vignettes

  ```{r style, echo = FALSE, results = 'asis'}
  BiocStyle::markdown()
  ```

The way of attaching CSS files when using markdown differs from how this is done with rmarkdown. In the former case additional style sheets can be used by providing them to the BiocStyle::markdown function. To include custom.css file use

```{r style, echo = FALSE, results = 'asis'}
BiocStyle::markdown(css.files = c('custom.css'))
```

3 Document header

3.1 Author affiliations

The author field allows for specifying author names along with affiliation and email information.

In the basic case, when no additional information apart from author names is provided, these can be entered as a single character string

author: "Single Author"

or a list

author:
- First Author
- Second Author
- Last Author

which will print as “First Author, Second Author and Last Author”.

Author affiliations and emails can be entered in named sublists of the author list. Multiple affiliations per author can be specified this way.

author:
- name: First Author
  affiliation: 
  - Shared affiliation
  - Additional affiliation
- name: Second Author
  affiliation: Shared affiliation
  email: corresponding@author.com

A list of unique affiliations will be displayed below the authors, similar as in this document.

For clarity, compactness, and to avoid errors, repeated nodes in YAML header can be initially denoted by an anchor entered with an ampersand &, and later referenced with an asterisk *. For example, the above affiliation metadata is equivalent to the shorthand notation

author:
- name: First Author
  affiliation: 
  - &id Shared affiliation
  - Additional affiliation
- name: Second Author
  affiliation: *id
  email: corresponding@author.com

3.2 Abstract and running headers

Abstract can be entered in the corresponding field of the document front matter, as in the example below.

---
title: "Full title for title page"
shorttitle: "Short title for headers"
author: "Vignette Author"
package: PackageName
abstract: >
  Document summary
output: 
  BiocStyle::pdf_document
---

The shorttitle option specifies the title used in running headers instead of the document title.222 only relevant to PDF output

4 Style macros

BiocStyle introduces the following macros useful when referring to R packages:

Biocpkg("IRanges") for Bioconductor software, annotation and experiment data packages, including a link to the release landing page or if the package is only in devel, to the devel landing page, IRanges.
CRANpkg("data.table") for R packages available on CRAN, including a link to the FHCRC CRAN mirror landing page, data.table.
Githubpkg("rstudio/rmarkdown") for R packages available on GitHub, including a link to the package repository, rmarkdown.
Rpackage("MyPkg") for R packages that are not available on Bioconductor, CRAN or GitHub; MyPkg.

These are meant to be called inline, e.g., `r Biocpkg("IRanges")`.

5 Code chunks

The line length of output code chunks is set to the optimal width of typically 80 characters, so it is not neccessary to adjust it manually through options("width").

6 Figures

6.1 Simple figures

BiocStyle comes with three predefined figure sizes. Regular figures not otherwise specified appear indented with respect to the paragraph text, as in the example below.

plot(cars)

A default sized example figure without a caption.

6.2 Figure captions

Figures which have no captions, like the one above, are just placed wherever they were generated in the R code. If you assign a caption to a figure via the code chunk option fig.cap, the plot will be automatically labeled and numbered333 for PDF output it will be placed in a floating figure environment, and it will be also possible to reference it. These features are provided by bookdown, which defines a format-independent syntax for specifying cross-references, see Section 9. The figure label is generated from the code chunk label444 for cross-references to work the chunk label may only contain alphanumeric characters (a-z, A-Z, 0-9), slashes (/), or dashes (-) by prefixing it with fig:, e.g., the label of a figure originating from the chunk foo will be fig:foo. To reference a figure, use the syntax \@ref(label)555 do not forget the leading backslash!, where label is the figure label, e.g., fig:foo. For example, the following code chunk was used to produce Figure 1.

```{r plot, fig.cap = "Regular figure. The first sentence...", echo = FALSE}
plot(cars)
```

Figure 1: Regular figure
The first sentence of the figure caption is automatically emphasized to serve as figure title.

6.3 Alternative figure sizes

In addition to regular figures, BiocStyle provides small and wide figures which can be specified by fig.small and fig.wide code chunk options. Wide figures are left-aligned with the paragraph and extend on the right margin, as Figure 2. Small figures are meant for possibly rectangular plots which are centered with respect to the text column, see Figure 3.

Figure 2: Wide figure
A plot produced by a code chunk with option fig.wide = TRUE.

Figure 3: Small figure
A plot produced by a code chunk with option fig.small = TRUE.

6.4 Accessibility considerations

Alt (alternative) text is used by screen readers to provide a description of an image to visually impaired readers. If you provide a figure caption with fig.cap the same text will automatically be used as the alt text for the image. However, if you want to include an image without a caption, or you wish to provide different information in the alt text to the caption, this can be done via the fig.alt code chunk option. As an example, the code chunk below was used to include the first image shown in this section, so that its intention could be conveyed to someone using a screen reader.

```{r no-cap, fig.alt="A default sized example figure without a caption."}
plot(cars)
```

You may also want to consider the color palette used in your figures, to ensure they are accessible to color impaired readers. BiocStyle doesn’t provide a specific color palette, but many options are available in packages from CRAN. There have also been significant efforts made to improve the default colors provided by palette() in R-4.0.0. Bioconductor contains some domain specific packages that focus on color blind friendly visualizations e.g. dittoSeq for single-cell and bulk RNA-sequencing data.

7 Tables

Like figures, tables with captions will also be numbered and can be referenced. The caption is entered as a paragraph starting with Table:666 or just :, which may appear either before or after the table. When adding labels, make sure that the label appears at the beginning of the table caption in the form (\#tab:label), and use \@ref(tab:label) to refer to it. For example, Table 1 has been produced with the following code.

Fruit   | Price
------- | -----
bananas | 1.2
apples  | 1.0
oranges | 2.5
  
: (\#tab:table) A simple table. With caption.

Table 1: A simple table
With caption.
Fruit	Price
bananas	1.2
apples	1.0
oranges	2.5

The function knitr::kable() will automatically generate a label for a table environment, which is the chunk label prefixed by tab:, see Table 2.

knitr::kable(
  head(mtcars[, 1:8], 10), caption = 'A table of the first 10 rows of `mtcars`.'
)

Table 2: A table of the first 10 rows of `mtcars`.
	mpg	cyl	disp	hp	drat	wt	qsec	vs
Mazda RX4	21.0	6	160.0	110	3.90	2.620	16.46	0
Mazda RX4 Wag	21.0	6	160.0	110	3.90	2.875	17.02	0
Datsun 710	22.8	4	108.0	93	3.85	2.320	18.61	1
Hornet 4 Drive	21.4	6	258.0	110	3.08	3.215	19.44	1
Hornet Sportabout	18.7	8	360.0	175	3.15	3.440	17.02	0
Valiant	18.1	6	225.0	105	2.76	3.460	20.22	1
Duster 360	14.3	8	360.0	245	3.21	3.570	15.84	0
Merc 240D	24.4	4	146.7	62	3.69	3.190	20.00	1
Merc 230	22.8	4	140.8	95	3.92	3.150	22.90	1
Merc 280	19.2	6	167.6	123	3.92	3.440	18.30	1

8 Equations

To number and reference equations, put them in equation environments and append labels to them following the syntax (\#eq:label)777 due to technical constraints equation labels must start with eq:, e.g.,

\begin{equation}
  f\left(k\right) = \binom{n}{k} p^k\left(1-p\right)^{n-k}
  (\#eq:binom)
\end{equation}

renders the equation below.

\[\begin{equation} f\left(k\right) = \binom{n}{k} p^k\left(1-p\right)^{n-k} \tag{1} \end{equation}\]

You may then refer to Equation (1) by \@ref(eq:binom). Note that in HTML output only labeled equations will appear numbered.

9 Cross-references

Apart from referencing figures (Section 6), tables (Section 7), and equations (Section 8), you can also use the same syntax \@ref(label) to reference sections, where label is the section ID. By default, Pandoc will generate IDs for all section headers, e.g., # Hello World will have an ID hello-world. In order to avoid forgetting to update the reference label after you change the section header, you may also manually assign an ID to a section header by appending {#id} to it.

When a referenced label cannot be found, you will see two question marks like ??, as well as a warning message in the R console when rendering the document.

10 Margin notes

Footnotes are displayed as side notes on the right margin888 this is a side note entered as a footnote, which has the advantage that they appear close to the place where they are defined.

11 Bibliography

If you wish to include a list of references you can use the special section title # References999 it must be exactly this!, and provide a bibtex file in the vignette header. A list of all references used in the text will be automatically inserted after this heading. By default the references section will continue the section level numbering used throughout the document. To suppress the numbering, as seen in this vignette, you can use the Bookdown syntax for unnumbered sections e.g. {-} or {.unnumbered}.

Everything after the list of references will be considered as appendices. See below for an example of the formatting change.
For more details on how to include a bibliography please see the relevant chapter of bookdown.org.

References

Xie, Yihui, J. J. Allaire, and Garrett Grolemund. 2018. R Markdown: The Definitive Guide. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown.

Appendix

A Session info

Here is the output of sessionInfo() on the system on which this document was compiled running pandoc 2.7.3:

## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocStyle_2.30.0
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.33       R6_2.5.1            bookdown_0.36      
##  [4] fastmap_1.1.1       xfun_0.40           magrittr_2.0.3     
##  [7] cachem_1.0.8        knitr_1.44          htmltools_0.5.6.1  
## [10] rmarkdown_2.25      cli_3.6.1           sass_0.4.7         
## [13] jquerylib_0.1.4     compiler_4.3.1      tools_4.3.1        
## [16] evaluate_0.22       bslib_0.5.1         Rcpp_1.0.11        
## [19] magick_2.8.1        yaml_2.3.7          BiocManager_1.30.22
## [22] jsonlite_1.8.7      rlang_1.1.1

Authoring R Markdown vignettes

24 October 2023

Abstract

Package