How to syntax highlight inline R code in R Markdown?

Question

This question is similar to consistent code html inline and in chunks with knitr. Instead of .Rhtml documents, I want to highlight inline R code in R Markdown documents, e.g., after ``r "plot(cars, main = 'A scatterplot.')"`` is compiled through rmarkdown, the tokens like `plot` should be highlighted. By default, R code chunks are syntax highlighted, but there is no way to highlight inline R code.

Accepted Answer

Here is one solution using the development version of the highr package (`devtools::install_github('yihui/highr')`). Basically you just define your custom LaTeX commands to highlight the tokens. `highr:::cmd_pandoc_latex` is a data frame of LaTeX commands that Pandoc uses to do syntax highlighting.

```
head(highr:::cmd_pandoc_latex)
##                   cmd1 cmd2
## COMMENT  \CommentTok{    }
## FUNCTION  \NormalTok{    }
## IF        \NormalTok{    }
## ELSE      \NormalTok{    }
## WHILE     \NormalTok{    }
## FOR       \NormalTok{    }
```

Then you can redefine the `inline` hook of knitr:

````
---
output:
  pdf_document:
    keep_tex: yes
---

```{r include=FALSE}
local({
  hi_pandoc = function(code) {
    if (knitr:::pandoc_to() != 'latex') return(code)
    if (packageVersion('highr') < '0.6.1') stop('highr >= 0.6.1 is required')
    res = highr::hi_latex(code, markup = highr:::cmd_pandoc_latex)
    sprintf('\texttt{%s}', res)
  }
  hook_inline = knitr::knit_hooks$get('inline')
  knitr::knit_hooks$set(inline = function(x) {
    if (is.character(x) && inherits(x, 'AsIs')) hi_pandoc(x) else hook_inline(x)
  })
})
```

Test inline R code: `r I("plot(cars, main = 'A scatterplot.')")`.
Normal inline code `r pi`.

A code block:

```r
plot(cars, main = 'A scatterplot.')
1 + 2 # a comment
```
````

I used `I()` as a convenient marker to tell the character strings to be syntax highlighted from normal character strings. It is just an arbitrary choice. PDF output:

This is not a perfect solution, though. You will need to tweak it in some cases. For example, most special LaTeX characters are not escaped, such as `~`. You may need to process the LaTeX code returned by `hi_pandoc()` by `gsub()`.

Personally I find multiple colors in inline output distracting, so I would not syntax highlighting it, but this is entirely personal taste.

How to syntax highlight inline R code in R Markdown?

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