BiocStyle (version 2.0.2)

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, toc_depth = 3, number_sections = TRUE, fig_width = 7, fig_height = 5, fig_retina = NULL, fig_caption = FALSE, dev = "png", smart = TRUE, self_contained = TRUE, highlight = "default", mathjax = "default", css = NULL, includes = NULL, keep_md = FALSE, lib_dir = NULL, md_extensions = NULL, pandoc_args = NULL, ...)

Arguments

toc
TRUE to include a table of contents in the output
toc_depth
Depth of headers to include in table of contents
number_sections
TRUE to number section headings
fig_width
Default width (in inches) for figures
fig_height
Default width (in inches) for figures
fig_retina
Scaling to perform for retina displays
fig_caption
TRUE to render figures with captions
dev
Graphics device to use for figure output (defaults to png)
smart
Produce typographically correct output, converting straight quotes to curly quotes, --- to em-dashes, -- to en-dashes, and ... to ellipses.
self_contained
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).
highlight
Syntax highlighting style. Supported styles include "default", "tango", "pygments", "kate", "monochrome", "espresso", "zenburn", "haddock", and "textmate". Pass NULL to prevent syntax highlighting.
mathjax
Include mathjax. The "default" option uses an https URL from the official MathJax CDN. The "local" option uses a local version of MathJax (which is copied into the output directory). You can pass an alternate URL or pass NULL to exclude MathJax entirely.
css
One or more css files to include
includes
Named list of additional content to include within the document (typically created using the includes function).
keep_md
Keep the markdown file generated by knitting.
lib_dir
Directory to copy dependent HTML libraries (e.g. jquery, bootstrap, etc.) into. By default this will be the name of the document with _files appended to it.
md_extensions
Markdown extensions to be added or removed from the default definition or R Markdown. See the rmarkdown_format for additional details.
pandoc_args
Additional command line options to pass to pandoc
...
Additional function arguments to pass to the base R Markdown HTML output formatter

Value

R Markdown output format to pass to render

Details

The BiocStyle::html_document format is based on the html_document format. See the online documentation for additional details on using the html_document format.

R Markdown documents can have optional metadata that is used to generate a document header that includes the title, author, date, package info and abstract. For more details see the documentation on R Markdown metadata.

R Markdown documents also support citations. You can find more information on the markdown syntax for citations in the Bibliographies and Citations article in the online documentation.

See Also

pdf_document, md_document

Examples

## Not run: 
# 
# # simple invocation
# render("input.Rmd", BiocStyle::html_document())
# 
# # specify options
# render("input.Rmd", BiocStyle::html_document(toc = FALSE))
# ## End(Not run)