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.

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.¹ 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.

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

Document header

author: "Single Author"

author:
- First Author
- Second Author
- Last Author

author:
- name: First Author
  affiliation: 
  - Shared affiliation
  - Additional affiliation
- name: Second Author
  affiliation: Shared affiliation
  email: [email protected]

author:
- name: First Author
  affiliation: 
  - &id Shared affiliation
  - Additional affiliation
- name: Second Author
  affiliation: *id
  email: [email protected]

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

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")`.

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").

Figures

plot(cars)

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 numbered³, 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 @ref(cross-references). The figure label is generated from the code chunk label⁴ 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)⁵, where label is the figure label, e.g., fig:foo. For example, the following code chunk was used to produce Figure @ref(fig:plot).

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

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

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 @ref(fig:wide). Small figures are meant for possibly rectangular plots which are centered with respect to the text column, see Figure @ref(fig:small).

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

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

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

Tables

Like figures, tables with captions will also be numbered and can be referenced. The caption is entered as a paragraph starting with Table:⁶, 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 @ref(tab:table) 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.

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

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

Equations

To number and reference equations, put them in equation environments and append labels to them following the syntax (\#eq:label)⁷, 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.

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

Cross-references

Apart from referencing figures (Section @ref(figures)), tables (Section @ref(tables)), and equations (Section @ref(equations)), 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 @ref(non-existing-label), as well as a warning message in the R console when rendering the document.

Margin notes

Footnotes are displayed as side notes on the right margin⁸, which has the advantage that they appear close to the place where they are defined.

Bibliography

If you wish to include a list of references you can use the special section title # References⁹, 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.

Session info

Here is the output of sessionInfo() on the system on which this document was compiled running pandoc 3.2.1:

## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        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: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocStyle_2.35.0
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.37       R6_2.5.1            fastmap_1.2.0      
##  [4] xfun_0.49           maketools_1.3.1     cachem_1.1.0       
##  [7] knitr_1.49          htmltools_0.5.8.1   rmarkdown_2.29     
## [10] buildtools_1.0.0    lifecycle_1.0.4     cli_3.6.3          
## [13] sass_0.4.9          jquerylib_0.1.4     compiler_4.4.2     
## [16] sys_3.4.3           tools_4.4.2         evaluate_1.0.1     
## [19] bslib_0.8.0         yaml_2.3.10         BiocManager_1.30.25
## [22] jsonlite_1.8.9      rlang_1.1.4