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Last data update: 2014.03.03

R: Use Bioconductor style to format R Markdown HTML output

html_document

R Documentation

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

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.

Value

R Markdown output format to pass to render

Author(s)

Andrzej Ole<c3><85><c2><9b> <andrzej.oles@embl.de>, 2014-2015

Examples

## Not run: 

# simple invocation
render("input.Rmd", BiocStyle::html_document())

# specify options
render("input.Rmd", BiocStyle::html_document(toc = FALSE))

## End(Not run)