bioconductor v3.9.0 BiocStyle
Provides standard formatting styles for Bioconductor PDF
Link to this section Summary
Functions
Defunct functions in package BiocStyle
Specify Rmarkdown document metadata
Use Bioconductor style to format R Markdown HTML output
Use Bioconductor style to format LaTeX vignettes
Link to packages on Bioconductor, CRAN and GitHub
Use Bioconductor CSS style to format HTML vignettes
Convert to a BiocStyle markdown document
Output format of an R Markdown document
Use Bioconductor style to format R Markdown PDF output
Link to this section Functions
BiocStyle_defunct()
Defunct functions in package BiocStyle
Description
These functions are defunct and no longer available.
Details
The following functions are no longer available; use the replacement indicated below:
latex_old, latex2:pdf_document_old, pdf_document2:html_document_old, html_document2:
helpers()
Specify Rmarkdown document metadata
Description
Helper functions for including metadata in the document header.
Usage
pkg_ver(pkg)
doc_date()Arguments
| Argument | Description |
|---|---|
pkg | character(1), package name |
Details
Use doc_date to include document compilation date in the document
metadata field 'date', and pkg_ver for package version specification
in the 'package' field.
Value
Markdown-formatted character string.
Author
Andrzej Oleś andrzej.oles@embl.de, 2014-2015
Examples
## current date
doc_date()
## package name with version
pkg_ver("BiocStyle")html_document()
Use Bioconductor style to format R Markdown HTML output
Description
Format for converting from R Markdown to an Bioconductor HTML document.
Usage
html_document(toc = TRUE, number_sections = TRUE, fig_width = NA,
fig_height = NA, self_contained = TRUE, css = NULL,
pandoc_args = NULL, ..., titlecaps = TRUE)Arguments
| Argument | Description |
|---|---|
toc | logical(1), TRUE to include a table of contents in the output |
number_sections | logical(1), TRUE to number section headings |
fig_width | numeric(1), default width (in inches) for figures |
fig_height | numeric(1), default width (in inches) for figures |
self_contained | numeric(1), TRUE to produce a standalone HTML file with no external dependencies, using data: URIs to incorporate the contents of linked scripts, stylesheets, images, and videos. Note that even for self contained documents MathJax is still loaded externally (this is necessary because of it's size). |
css | character, one or more css files to include |
pandoc_args | character, additional command line options to pass to pandoc |
list() | Additional arguments passed to html_document |
titlecaps | logical(1), TRUE to use the emphasize the first sentence in figure and table captions as title |
Details
BiocStyle::html_document format extends the
html_document format. See the
c("online
", "documentation") and the package vignette "Authoring R Markdown Vignettes" for
additional details on using the format,
Value
R Markdown output format to pass to render
Seealso
Author
Andrzej Oleś andrzej.oles@embl.de, 2014-2017
Examples
# simple invocation
render("input.Rmd", BiocStyle::html_document())
# specify options
render("input.Rmd", BiocStyle::html_document(toc = FALSE))latex()
Use Bioconductor style to format LaTeX vignettes
Description
This function inserts code into a document preamble to provide a consistent style to Bioconductor vignettes.
Usage
latex(..., width, titlecaps = TRUE, short.fignames = FALSE, fig.path,
use.unsrturl = TRUE, relative.path = FALSE)Arguments
| Argument | Description |
|---|---|
list() | Additional arguments, passed to options . |
width | integer(1), maximum number of columns on a line used in printing. See options . |
titlecaps | logical(1), emphasize the first sentence of float captions |
short.fignames | logical(1), indicates whether incfig figures should be inserted and referred to using short names equal to corresponding code chunk labels without any additional prefix. |
fig.path | character(1), custom prefix to be used for figure file names when used with knitr ; has no effect when compiled with Sweave . For details see opts_chunk . |
use.unsrturl | logical(1), indicating that the unsrturl style will be used ( ibliographystyle command not required). |
relative.path | logical(1), copy supporting LaTeX files and use relative paths rather than absolute paths to system files. |
Details
Use is described in the Bioconductor LaTeX Style 2.0 vignette.
By default the 'unsrturl' bibliography style is used, which automatically
creates links to URL, DOIs, etc. Use a different bibliographystyle
with use.unsrturl=FALSE and standard LaTeX commands for styling
bibliographies.
Value
The return value is a character string directing LaTex to use the Bioconductor style file.
A side effect is setting any options specified as arguments.
Author
Andrzej Oleś, Martin Morgan, Wolfgang Huber
Examples
## location of the .sty file
BiocStyle:::bioconductor.stymacros()
Link to packages on Bioconductor, CRAN and GitHub
Description
Functions for adding links to Bioconductor, CRAN and GitHub packages into R Markdown documents.
Usage
Biocpkg(pkg, vignette = NULL, label = pkg)
Biocannopkg(pkg)
Biocexptpkg(pkg)
CRANpkg(pkg)
Rpackage(pkg)
Githubpkg(repo, pkg)Arguments
| Argument | Description |
|---|---|
pkg | character(1), package name |
vignette | character(1), basename of vignette link, including html or pdf extension, e.g., "work-0-intro.html". |
label | character(1) label used to identify the package or vignette. |
repo | Repository address in the format username/repo[/subdir] |
Details
Use Biocpkg for Bioconductor software, annotation,
experiment data, and workflow packages. When vignette=NULL ,
the function automatically includes a link to the package landing
page, the version of which depends on the current Bioconductor
version (i.e. if run in a devel environment, it will point towards
the devel landing page; otherwise it will point to the release
landing page).
Use CRANpkg for R packages available on CRAN. The function
automatically includes a link to the master CRAN landing page.
Use Githubpkg for R packages available on GitHub. The repo
should include the repository address in the format username/repo[/subdir].
If package is missing, the package name is assumed to be equal the
repository name and is extracted from repo .
For R packages which are not available on Bioconductor, CRAN or GitHub, use
Rpackage .
Value
Markdown-formatted character vector containing a
hyperlinked package name. If vignette != NULL , the
address of the specified vignette is returned.
Author
Andrzej Oleś andrzej.oles@embl.de, 2014-2015
Examples
## link to a Bioconductor software package
Biocpkg("IRanges")
## link to a Bioconductor annotation package
Biocpkg("org.Mm.eg.db")
## link to a Bioconductor experiment data package
Biocpkg("affydata")
## link to a Bioconductor workflow
Biocpkg("simpleSingleCell")
Biocpkg(
"simpleSingleCell",
vignette = "work-0-intro.html",
label = "Episode 1: analyzing scRNA-seq data with R/Bioconductor"
)
## link to a CRAN package
CRANpkg("data.table")
## link to an R package on GitHub
Githubpkg("rstudio/rmarkdown")markdown()
Use Bioconductor CSS style to format HTML vignettes
Description
This function sets the Bioconductor style sheet to provide a consistent style across Bioconductor HTML vignettes.
Usage
markdown(css.files, self.contained = TRUE, links.target = TRUE)Arguments
| Argument | Description |
|---|---|
css.files | character vector containing the location of additional .css files. |
self.contained | logical(1), should the content of the CSS stylesheet files be included into the html file or should they be saved as separate files. |
links.target | logical(1), should external links open in new browser tab/window. |
Details
Use is described in the Bioconductor CSS Style vignette.
Value
No value is returned. The function is called for its side effect of
setting the markdown and/or knitr specific options controlling
the inclusion of the Bioconductor CSS style file in the HTML output.
Author
Andrzej Oleś andrzej.oles@embl.de, 2014-2015
Examples
## location of the .css file
BiocStyle:::bioconductor.cssmd_document()
Convert to a BiocStyle markdown document
Description
Enable BiocStyle macros and author affiliations in markdown documents.
Usage
md_document(toc = TRUE, ...)Arguments
| Argument | Description |
|---|---|
toc | TRUE to include a table of contents in the output |
... | Additional function arguments to pass to the base R Markdown md_document output formatter |
Details
The BiocStyle::md_document format extends the base
md_document format by means of specifing complex
author affiliations. It also loads the BiocStyle package namespace to enable
the use of helper functions, such as Biocpkg .
Value
R Markdown output format to pass to render
Seealso
Author
Andrzej Oleś andrzej.oles@embl.de, 2015-2016
Examples
rmarkdown::render("input.Rmd", BiocStyle::md_document())output()
Output format of an R Markdown document
Description
Helper function to determine the document's current pandoc output format.
Usage
output()Details
The function is useful for defining different behavior depending on the output format, e.g. figure settings.
Value
A character string specifying the pandoc output format.
Author
Andrzej Oleś andrzej.oles@embl.de, 2016
Examples
## Switch between SVG and PDF figures depending on document output format
knitr::opts_chunk$set(
dev = switch(output(), html = "svg", latex = "pdf")
)pdf_document()
Use Bioconductor style to format R Markdown PDF output
Description
This function sets the Bioconductor style in PDF documents rendered using R Markdown v2.
Usage
pdf_document(toc = TRUE, number_sections = TRUE, fig_width = NA,
fig_height = NA, includes = NULL, ..., titlecaps = TRUE,
toc_newpage = FALSE, use_unsrturl = TRUE, relative_path = FALSE)Arguments
| Argument | Description |
|---|---|
toc | logical(1), TRUE to include a table of contents in the output |
number_sections | logical(1), TRUE to number section headings |
fig_width | numeric(1), default width (in inches) for figures |
fig_height | numeric(1), default width (in inches) for figures |
includes | Named list of additional content to include within the document (typically created using the includes function). |
list() | Additional arguments passed to pdf_document . |
titlecaps | logical(1), TRUE to use the emphasize the first sentence in figure and table captions as title |
toc_newpage | logical(1), TRUE to start the table of contents on a new page. |
use_unsrturl | logical(1), indicating that the unsrturl style will be used ( ibliographystyle command not required). |
relative_path | logical(1), copy supporting LaTeX files and use relative paths rather than absolute paths to system files. |
Value
R Markdown output format to pass to render .
Seealso
Author
Andrzej Oleś andrzej.oles@embl.de, 2014-2017
Examples
# simple invocation
render("input.Rmd", BiocStyle::pdf_document())
# specify an option for latex engine
render("input.Rmd", BiocStyle::pdf_document(toc = FALSE))