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.

Examples

Run this code

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