set fig.cap to options$label - r

How can I programmatically set a figure caption in a knitr hook?
I'd like to set the figure caption, if not explicitly defined, to the chunk label. I've read the knitr docs on options, options, and hooks, and though I think I understand the mechanisms at play, I can't get it to work.
My use-case that perhaps justifies this behavior: my work-flow recently adapted to start my data and visualization exploration in Rmd files. I'll use chunks for cleaning, subsetting, etc, and then a sample chunk for each visualization. This is quick and dirty, meaning minimal markdown. When I look over the report (typically rendered into PDF), I'll look at a figure and want to go straight to the source for it. Though text before/after the figure can provide insight, due to LaTeX figure rules it is not a sure thing. Counting figure numbers is feasible, but not "easy" (and becomes problematic with many figures). Captions are always with the figure, so it'd be great if I can default to filling the caption with the chunk label. (Yes, it's a little lazy of me.)
The MWE is below.
The hook code ran just fine; the returned strings in the hook appeared correctly. However, the figure caption did not change. Exception: when there is a chunk with an undefined fig.cap, all subsequent chunks have their caption set to the first un-captioned chunk name; this doesn't surprise me due to the global nature of opts_chunk, so that's out.
I suspect it might be related to "output hooks" vice "chunk hooks," but this really is a per-chunk thing and I do not want to modify the plot, just set the caption.
MWE:
---
title: "Document Title"
author: "My Name"
output:
pdf_document:
fig_caption: yes
---
# Header
```{r setup}
knit_hooks$set(autocap = function(before, options, envir) {
if (before) {
if (is.null(options$fig.cap)) {
options$fig.cap <- options$label
knitr::opts_current$set(fig.cap = options$label)
knitr::opts_chunk$set(fig.cap = options$label) # wrong!
paste('Set: `', options$label, '`, `',
knitr::opts_current$get('fig.cap'), '`', sep = '')
} else {
paste('Kept: `', options$fig.cap, '`', sep = '')
}
}
})
opts_chunk$set(autocap = TRUE)
```
## No Plot
```{r textOnly}
1+1
```
## Caption Already Set
```{r someplot, fig.cap='someplot caption'}
plot(0)
```
## Caption Not Set
```{r anotherPlot}
plot(1)
```

Is it ok like this ? I simply modify the knitr internal function .img.cap function which can be found here.
```{r}
.img.cap = function(options) {
if(is.null(options$fig.cap)) options$label else options$fig.cap
}
assignInNamespace(".img.cap", .img.cap, ns="knitr")
```

Does it help ?
```{r}
library(knitr)
knit_hooks$set(htmlcap = function(before, options, envir) {
if(!before) {
caption <- ifelse(is.character(options$htmlcap), options$htmlcap, options$label)
paste('<p class="caption">', caption, "</p>", sep="")
}
})
```
```{r Hello, htmlcap=TRUE}
library(ggplot2)
ggplot(diamonds,aes(price,carat)) + geom_point()
```
```{r, htmlcap="Hello again"}
ggplot(diamonds,aes(price,carat)) + geom_point()
```

Related

Insert Pagebreak for Output after Code Chunk

I have a .Rmd file which I am converting to PDF. For layout reasons, I want to display the generated output plot of my code chunk on the next page even though it would just fit in underneath.
Normally with text etc. one would use
\pagebreak
But how can I signalize the code chunk that it should display its output on the next page?
Thanks for helping!
You can write a knitr hook to set up a chunk option to do this.
So here I have modified the source chunk hook and created a chunk option next_page which, if TRUE, the output of that chunk will be on the next page.
---
title: "Chunk Output in Next page"
output: pdf_document
date: "2022-11-25"
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
```{r, include=FALSE}
library(knitr)
default_source_hook <- knit_hooks$get('source')
knit_hooks$set(
source = function(x, options) {
if(isTRUE(options$next_page)) {
paste0(default_source_hook(x, options),
"\n\n\\newpage\n\n")
} else {
default_source_hook(x, options)
}
}
)
```
```{r, next_page=TRUE}
plot(mpg ~ disp, data = mtcars)
```
I would recommend you to save the output in the file (png/jpeg/pdf) and then load it with the markdown or knitr.
Such solution gives you a full control.
Automatic
I found alternative solution in rmarkdown-cookbook.
We generate a plot in this code chunk but do not show it:
```{r cars-plot, dev='png', fig.show='hide'}
plot(cars)
```
\newpage
![A nice plot.](\`r knitr::fig_chunk('cars-plot', 'png')\`)
Manual
```{r}
png("NAME.png")
# your code to generate plot
dev.off()
```
then load image with
![LABEL](PATH/NAME.png) or with
```{r echo=FALSE, out.width='100%', ...}
knitr::include_graphics('PATH/NAME.png')
```

Toggle chunk output using "details" HTML tag

I'm writing some tutorials using blogdown. For a pedagogical reason, I want my students to think before seeing the solution. Here's my current code.
Original
---
title: "Toggle Chuck Output Using details Tag"
output: html_document
---
```{r calc, prompt=TRUE, eval=FALSE}
90 + 30
```
<details>
<summary>Toggle output</summary>
```{r, ref.label='calc', echo=FALSE, prompt=TRUE}
```
</details>
Here's my attempt:
To avoid repeatedly writing the HTML tags, I think I need to define a function similar to ...
togglable <- function(label, summary = "Toggle output"){
cat('<details>')
cat(' <summary>', summary, '</summary>', sep = '')
# Code to print output using 'ref.label' should go here.
# The following doesn't work.
knitr::knit_print(knitr:::knit_code$get(label))
cat('</details>')
}
.... then replace the <detals>...</details> block with a R code chunk similar to the following:
Use case 1 (better)
```{r usecase1, echo=FALSE, results='asis'}
togglable(label = "calc")
```
I tried to make it work, but in vain.
One more thing. If possible, I'd like this togglable() function to override the chunk options so that I don't even need to write echo=FALSE, results='asis', because the following chunk would look nicer.
Use case 2 (best)
```{r usecase2}
togglable(label = "calc")
```
In summary, I would like to ask the following questions.
How can I define this togglable() function so that it behaves in the same way as the original <detals>...</details> block?
Is it possible that this function overrides the options (echo and results in particular) for the chunk where this function is called? If yes, how?
Alternatively, is there any other idea how to produce the result of the original code without repeatedly writing the HTML tags?
Thank you very much!
This can be done by a combination of the chunk option ref.label (to reuse chunks), a chunk hook (to print the <details> tag) and a option hook (to change the chunk options when displaying the results.
---
title: "Toggle Chuck Output Using details Tag"
output: html_document
---
```{r setup, include=FALSE}
library(knitr)
knit_hooks$set(showDetails = function(before, options, envir) {
if (before) {
return("<details>\n")
} else {
return("\n</details>")
}
})
opts_hooks$set(showDetails = function(options) {
if(options$showDetails) {
options$echo = FALSE
options$results = "asis"
}
return(options)
})
```
```{r calc, prompt=TRUE, eval=FALSE}
90 + 30
```
```{r, ref.label="calc", showDetails = TRUE}
```
How it works:
The chunk hook is executed before and after each chunk where the option showDetails is not NULL. It prints (returns) the respective HTML.
The option hook adjusts the other options (echo and results) for each chunk there showDetails is TRUE.
The code could be further improved by globally setting the options of the calc chunk, such that you do not have to repeat them for all other "show code only" chunks: add opts_chunk$set(prompt = TRUE, eval = FALSE) to the setup chunk and options$eval = TRUE to the option hook.
Besides, if you want <detail> tags by default whenever using ref.label, you could use ref.label as option hook:
```{r setup, include=FALSE}
library(knitr)
opts_chunk$set(prompt = TRUE, eval = FALSE)
knit_hooks$set(showDetails = function(before, options, envir) {
if (before) {
return("<details>\n")
} else {
return("\n</details>")
}
})
opts_hooks$set(ref.label = function(options) {
options$echo = FALSE
options$results = "asis"
options$eval = TRUE
options$showDetails = TRUE
return(options)
})
```
```{r calc}
90 + 30
```
```{r, ref.label="calc"}
```

knitr: how to get and override chunk options from inside a chunk

I have 2 questions about knitr chunk options:
1) Is it possible to override knitr chunk options from inside a chunk of code so that the options were applied in the same chunk? e.g. write something like the following lines and get result as-is:
```{r, results= "markup"}
knitr::opts_chunk$set(results= "asis")
for (i in 1:5)
print("# This text should be printed 'as-is'")
```
p.s. I'm familiar with knitr::asis_output.
2) Is it possible to get chunk options from inside a chunk? E.g., to use code like:
```{r}
knitr::opts_chunk$get("results")
```
And get string markup.
```{r, results='asis'}
knitr::opts_chunk$get("results")
```
And get string asis.
Unfortunately, knitr::opts_chunk$get("results") gets global options, and not the ones of a current chunk.
1) Printings can be customized using functions knitr::normal_print and knitr::asis_output (as you mentionned). For instance :
```{r, results='markup'}
knitr::asis_output(replicate(5, "# This text should be printed 'as-is'\n"))
print("# This text should be printed 'normal'")
```
and alternatively
```{r, results='asis'}
for (i in 1:5)
cat("# This text should be printed 'as-is'\n")
knitr::normal_print("# This text should be printed 'normal'\n")
```
2) Current chunk options can be retrieved using knitr::opts_current$get(). Use :
```{r, results='asis'}
knitr::opts_current$get("results")
```
and get string asis

wrapping figure with latex environment in knitr/rmarkdown with hooks

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}
![](test_files/figure-latex/unnamed-chunk-2-1.pdf)
\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).

Chunk reference using knitr, r markdown and pandoc (pander)

I am having trouble trying to reference chunks within a r markdown document which I am trying to convert to .pdf using pandoc.convert.
If I include \label{mylabel} within the text - I can reference this by \ref{mylabel}. However, I thought I might be able to refer to a chunk (or table / figure within a chunk) similarly - but am having no luck.
For instance, for the chunk:
```{r myplot, echo=FALSE, warning=FALSE}
plot(cars)
```
I though I might be able to put \ref{myplot} or \ref{fig:myplot} or even an internal markdown reference [car plot](myplot). The documentation seems to mention that labels are created based on the name of the chunk and these are the formats suggested in relation to similar questions. But none seem to work.
Similarly for tables (which I create using pander) - I have chunks like:
```{r car_sum}
library(pander)
car_summary<-summary(cars)
pander(car_summary, caption = "This is a summary of cars")
```
When converting to .pdf from the .md file using 'pandoc.convert' the tables are given a nice title 'Table 3 This is a summary of cars' and are numbered but I cannot seem to use the label as a reference \ref{car_sum} and it always shows as '??'. Some forums seem to mention that you have to include 'tab:' or 'fig:' before the label name but this still does not work for me.
Can chunk referencing within text be done? If so, what needs to be typed to do this correctly so it works in the final document showing something like 'see Table 2'.
Anything is possible!!
Please see this gist which does what you describe. Just save and knit it to see it in action... For some reason Rpub didn't want to publish it (unknown error).
Testing with converting the knitr generated .html to .pdf via pandoc resulted in working links as well, which is a nice bonus!
The workhorse is::
```{r setup, echo=FALSE, results='hide'}
chunkref <- local({
function(chunklabel) {
sprintf('[%s](#%s)', chunklabel, chunklabel )
}
})
secref <- local({
function(seclabel) {
sprintf('[%s](#%s)', seclabel, seclabel )
}
})
pgref <- local({
function(n)
sprintf('[Page-%i](#Page-%i)', n, n)
})
sec <- local({
function(seclabel) {
sprintf('# <a name="%s"/> %s', seclabel, seclabel )
}
})
pgcount <- local({
pg <- 0
function(inc=T) {
if( inc ) { pg <<- pg + 1 }
return( pg )
}
})
pganchor <- local({
function(doLabel=T) {
if( doLabel) {
sprintf('\n-----\nPage-%i\n<a name="Page-%i"/>\n', pgcount(inc=F), pgcount() )
} else {
sprintf('\n<a name="Page-%i"/>\n', pgcount() )
}
}
})
knit_hooks$set( anchor = function(before, options, envir) {
if ( before ) {
sprintf('<a name="%s"/>\n', options$label )
}
})
knit_hooks$set( echo.label = function(before, options, envir) {
if ( before ) {
sprintf('> %s', options$label )
}
})
knit_hooks$set( pgbreak = function(before, options, envir) {
if ( !before ) {
pganchor();
}
})
````
Which allows for multiple types of references to be created...
Inline: `r sec("Introduction")` then `r secref("Introduction")`
Or
As chunk options:
```{r car-summary, echo=T, warning=FALSE, anchor=T, pgbreak=T, echo.label=F}`
then
`r chunkref("car-summary")`
Even 'top of page' links and 'bottom of page' markers and labels...
Easier solution to referring to figures: put this in the fig.cap field (double \\ to escape the first \):
fig.cap="\\label{mylabel}Caption of my figure."
Then, use \autoref{mylabel} to refer to the figure in the main text.
I am using RStudio with Rmarkdown. Full RMD document:
---
output: pdf_document
---
```{r fig.cap="\\label{mylabel}Caption of my figure."}
plot(1)
```
The generated figure is \autoref{mylabel}.

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