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.
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.
Now-a-days:
Here is some `plot(cars, main = 'A scatterplot.')`{.R} inline R code
Well, I don't know specifically about R and the way you're using it, but for most languages (pandoc uses the skylighting pkg to do this), you can do inline code blocks with the above syntax.
Related
Is it possible to emphasise (e.g., put in bold) some references that contain a particular string (e.g., the name of a particular author) in a papaja .Rmd document (where the refs are taken from a bib file and using the apa7.csl file)?
I can propose this solution based on pandoc lua filter which would work for not just pdf but also html output and doesn't require manual editing of latex or html file.
---
title: "The title"
bibliography: "r-references.bib"
output:
pdf_document:
pandoc_args: [ "--lua-filter", "ref-bold.lua"]
html_document:
pandoc_args: [ "--lua-filter", "ref-bold.lua"]
---
```{r setup, include = FALSE}
library("papaja")
r_refs("r-references.bib")
```
We used `R` [#R-base] and `Tidyverse` [#R-tidyverse] for all our analyses. Especially [#R-tidyverse] made things easy.
\vspace{10mm}
# References
ref-bold.lua
function Cite(el)
if pandoc.utils.stringify(el.content) == "[#R-tidyverse]" then
return (pandoc.Strong(el))
end
end
This demo bolds all of the reference to tidyverse package, if we would wanted to bold the reference to base-R, we would modify the second line in ref-bold.lua as pandoc.utils.stringify(el.content) == "[#R-base]" and all instances of references to base-R would be bold (highlighted).
pdf output
html output
A Lua-Filter would be the most elegant solution. If you use BibLaTeX and biber, you can use the general annotation feature (see this SO answer).
Include the following in your preamble:
\renewcommand*{\mkbibnamegiven}[1]{%
\ifitemannotation{bold}
{\textbf{#1}}
{#1}}
\renewcommand*{\mkbibnamefamily}[1]{%
\ifitemannotation{bold}
{\textbf{#1}}
{#1}}
In your bib-file, use the Author+an field to define which author to highlight:
#Misc{pawel2022power,
title = {Power Priors for Replication Studies},
author = {S Pawel and F Aust and L Held and E J Wagenmakers},
year = {2022},
eprinttype = {arxiv},
eprint = {2207.14720},
url = {https://arxiv.org/abs/2207.14720},
Author+an = {2=bold}
}
Now, render the R Markdown file with XeLaTeX, keep the intermediate files and the TeX file, and render the TeX file again using biber:
rmarkdown::render("paper.Rmd", clean = FALSE)
tinytex::xelatex("academic.tex", bib_engine = "biber")
Posting a solution in case it can be useful to others as well. We can first render the LaTeX file from the RMarkdown document, then find and replace all instances of the name to be emphasised, and finally generate the pdf from the modified LaTeX file.
# knitting the original Rmd file (with "keep_tex: true" in YAML)
rmarkdown::render(input = "some_file.Rmd")
# reading the generated LaTeX file
tex_file <- readLines(con = "some_file.tex")
# putting a particular author in bold in the references list
new_tex_file <- gsub(pattern = "James, W.", replace = "\\textbf{James, W.}", x = tex_file, fixed = TRUE)
# writing the (updated) LaTeX file
writeLines(text = new_tex_file, con = "some_file.tex")
# generating the pdf file (may need to be ran twice)
system(command = "xelatex some_file.tex")
I am using SQL blocks in an RMarkdown document, and I want the echo option to default to FALSE for all of them – but only for sql blocks, not others.
I know I can set knitr::opts_chunk$set(echo = TRUE), but that would set it for all chunks.
As Yihui suggested in a comment, the proper way to do this is to use an option hook. The following sets echo=FALSE for sql chunks and echo=TRUE otherwise:
knitr::opts_hooks$set(echo = function(options) {
options$echo <- options$engine != "sql"
return(options)
})
I'll leave my original answer below … for entertainment. It's a workaround, required in a hypothetical parallel universe without option hooks.
You can query the current engine via opts_current$get("engine"). Based on this, you can use the following function (and extend it however you like) to determine the desired value for echo:
conditionalDefaut_echo <- function() {
return(opts_current$get("engine") != "sql")
}
The challenge is to evaluate this function whenever parsing a new chunk. This can be achieved with quote:
opts_chunk$set(echo = quote(conditionalDefaut_echo()))
To be honest, I am not sure how reliable this is – this kind of metaprogramming depends on the internal workings of knitr and might break in the future. (Maybe Yihui wants to comment on this …)
A full example with engines r and asis, where echo is FALSE for asis chunks and TRUE otherwise:
```{r}
library(knitr)
conditionalDefaut_echo <- function() {
return(opts_current$get("engine") != "asis")
}
opts_chunk$set(echo = quote(conditionalDefaut_echo()))
```
```{asis}
I'm invisible.
```
```{r}
print(1) # code visible
```
Is there a way to automatically make text color of errors red in R Markdown without manually editing the HTML later.
---
title: ""
---
#### Example 1
```{r e1, error = TRUE}
2 + "A"
```
#### Example 2
```{r e2, error = TRUE}
2 + 2
```
In the above code, output of Example 1 would have to be red. Currently, I edit the generated HTML (add style="color:red;" to the appropriate tag) but I am wondering if there is an automatic way. Assume that it is not known before knitting whether the code will generate error.
1. Use a knitr hook
The preferred solution is to use the output hook for errors:
```{r}
knitr::knit_hooks$set(error = function(x, options) {
paste0("<pre style=\"color: red;\"><code>", x, "</code></pre>")
})
```
Output hooks in general allow us to control the output of different parts of our R code (the whole chunk, the source code, errors, warnings, ...). For details check https://yihui.name/knitr/hooks/#output-hooks.
2. Quick and dirty solution using JS/jQuery
And this is my "quick and dirty" solution using jQuery/Javascript. Just add it beneath the YAML header.
Might not be bulletproof, since it checks for error messages using the string "Error" which might occur in other applications as well.
<script type="text/javascript">
$(document).ready(function() {
var $chks = $("pre:not(.r) > code");
$chks.each(function(key, val) {
cntnt = $(this).html();
if (cntnt.indexOf("Error") != -1) {
$(this).css('color', 'red');
}
})
})
</script>
I stumbled here because I had the same question but for PDF output rather than HTML.
It turns out combining #Martin Schmelzer's Solution with some hints from #Yihui Xie found here helps to achieve the same behavior in a PDF output.
Add \usepackage{xcolor} to your YAML header and the following chunk to your .Rmd file.
```{r}
color_block = function(color) {
function(x, options) sprintf('\\color{%s}\\begin{verbatim}%s\\end{verbatim}',
color, x)
}
knitr::knit_hooks$set(error = color_block('red'))
```
The result is red error messages like
How do I create multiple outputs via pander() in a knitted document "asis" ?
When I have multiple calls of pander in a function, only the most recent one is shown in the HTML output. Here's an example:
tmp = function() {
pander('A')
pander('B')
pander('C')
}
tmp()
In the knitted document this gives: C
I could set panderOptions('knitr.auto.asis', FALSE) or I could use cat() so that the pander() output is written to the standard output. But then it's formatted as code, not as part of the document. As I need pander() to format a few tables for me, this does not help.
The tmp function will return only the last object -- that's why only C is printed. If you want to write each object to the stdout right away without the auto-asis convenience option, then you have to both disable the option like you did and use the relate knitr chunk option, eg:
```{r results='asis'}
library(pander)
panderOptions('knitr.auto.asis', FALSE)
tmp = function() {
pander('A')
pander('B')
pander('C')
}
tmp()
```
See more examples in the related "Using pander with knitr" vignette.
I'd like to wrap figures created with knitr and rmarkdown in a "wrapfigure" environment using hooks. However, when running the minimal example below, the figure chunk only gets compiled into a markdown picture:
\begin{wrapfigure}{R}{0.3\textwidth}
\end{wrapfigure}
and not the expected:
\begin{wrapfigure}{R}{0.3\textwidth}
\includegraphics{test_files/figure-latex/unnamed-chunk-2-1.pdf}
\end{wrapfigure}
Minimal example:
---
header-includes:
- \usepackage{wrapfig}
output:
pdf_document:
keep_tex: TRUE
---
```{r}
library(knitr)
knit_hooks$set(wrapf = function(before, options, envir) {
if(before) {
"\\begin{wrapfigure}{R}{0.3\\textwidth}"
} else {
"\\end{wrapfigure}"
}
})
```
```{r, wrapf=TRUE}
library(ggplot2)
qplot(cars$speed, cars$dist)
```
pandoc is responsible for converting the markdown document to a TEX document. As pandoc doesn't touch between \begin{…} and \end{…} the markdown syntax for the image is not being converted to TEX syntax.
You could …
Hide the plot (fig.show = 'hide') and use something along the lines of cat("\includegraphics{figure/unnamed-chunk-2-1.pdf}").
Hide the plot as above and include some magic in the hook that saves the cat.
Write RNW instead of RMD if you want PDF output.
Here's an example for option 2:
knit_hooks$set(wrapf = function(before, options, envir) {
if(before) {
return("\\begin{wrapfigure}{R}{0.3\\textwidth}")
} else {
output <- vector(mode = "character", length = options$fig.num + 1)
for (i in 1:options$fig.num) {
output[i] <- sprintf("\\includegraphics{%s}", fig_path(number = i))
}
output[i+1] <- "\\end{wrapfigure}"
return(paste(output, collapse = ""))
}
})
This hook can be used with wrapf = TRUE and fig.show = "hide". (Moreover, you need to add \usepackage{graphics} to header-includes.)
But note that I would not do it! Too many things can go wrong in more complex settings. Think of cache, captions, labels, cache (again!) …
Therefore, if it is really necessary to control the typesetting of the PDF, I recommend writing RNW (option 3).