R: knitr Setup and plotly Service Function

knitrSet {Hmisc}

R Documentation

knitr Setup and plotly Service Function

Description

knitrSet sets up knitr to use better default parameters for base graphics, better code formatting, and to allow several arguments to be passed from code chunk headers, such as bty, mfrow, ps, bot (extra bottom margin for base graphics), top (extra top margin), left (extra left margin), rt (extra right margin), lwd, mgp, las, tcl, axes, xpd, h (usually fig.height in knitr), w (usually fig.width in knitr), cap (character string containing figure caption), scap (character string containing short figure caption for table of figures).

plotlySave saves a plotly graphic with name foo.png where foo is the name of the current chunk. You must have a free plotly account from plot.ly to use this function, and you must have run Sys.setenv(plotly_username="your_plotly_username") and Sys.setenv(plotly_api_key="your_api_key"). The API key can be found in one's profile settings.

Usage

knitrSet(basename=NULL, w=4, h=3,
         fig.path=if(length(basename)) basename else '',
         fig.align='center', fig.show='hold', fig.pos='htbp',
         fig.lp=paste('fig', basename, sep=':'),
         dev=switch(lang, latex='pdf', markdown='png'),
         tidy=FALSE, error=FALSE,
         messages=c('messages.txt', 'console'),
         width=61, decinline=5, size=NULL, cache=FALSE,
         echo=TRUE, results='markup', lang=c('latex','markdown'))

plotlySave(x, ...)

Arguments

`basename`	base name to be added in front of graphics file names. `basename` is followed by a minus sign.
`w,h`	default figure width and height in inches
`fig.path`	path for figures. To put figures in a subdirectory specify e.g. `fig.path='folder/'`.
`fig.align,fig.show,fig.pos,fig.lp,tidy,cache,echo,results,error,size`	see knitr documentation
`dev`	graphics device, with default figured from `lang`
`messages`	By default warning and other messages such as those from loading packages are sent to file `'messages.txt'` in the current working directory. You can specify `messages='console'` to send them directly to the console.
`width`	text output width for R code and output
`decinline`	number of digits to the right of the decimal point to round numeric values appearing inside Sexpr
`lang`	Default is `'latex'` to use LaTeX. Set to `markdown` when using R Markdown.
`x`	a `plotly` graphics object or a named list of such objects. The resulting `png` file will go in the file path given by the `knitr` `fig.path` value, and have a base name equal to the current `knitr` chunk name. If `x` is a list, a minus sign followed by the chunk name are inserted before `.png`.
`...`	additional arguments passed to `plotly::plotly_IMAGE`

Author(s)

Frank Harrell

Examples

## Not run: 
# Typical call (without # comment symbols):
# <<echo=FALSE>>=
# require(Hmisc)
# knitrSet()
# @

knitrSet()    # use all defaults and don't use a graphics file prefix
knitrSet('modeling')   # use modeling- prefix for a major section or chapter
knitrSet(cache=TRUE, echo=FALSE)  # global default to cache and not print code
knitrSet(w=5,h=3.75)   # override default figure width, height

# ```{r chunkname}
# p <- plotly::plot_ly(...)
# plotlySave(p)   # creates fig.path/chunkname.png

## End(Not run)