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), `wo` (`out.width` in knitr), `ho` (`out.height` 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=if(! bd) 4, h=if(! bd) 3, wo=NULL, ho=NULL,
             fig.path=if(length(basename)) basename else '',
             fig.align=if(! bd) 'center', fig.show='hold',
             fig.pos=if(! bd) 'htbp',
             fig.lp=if(! bd) paste('fig', basename, sep=':'),
             dev=switch(lang, latex='pdf', markdown='png', blogdown=NULL),
             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','blogdown'))

    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
`wo,ho` | default figure rendering width and height, in integer pixels or percent as a character string, e.g. `'40%'`
`fig.path` | path for figures. To put figures in a subdirectory specify e.g. `fig.path='folder/'`. Ignored for blogdown.
`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 or `'blogdown'`. For `'blogdown'` `par` and `knitr` graphics-related hooks are not called as this would prevent `blogdown` from putting graphics files in the correct directory for the blog system.
`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

### See Also

`knit`

### 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)

[Package Hmisc version 4.3-0 Index]