pass on DT::datatable(caption =) argument, label datatables as tables

[maxheld83]

I'm relying a lot on DT::datatable() tables, rather than knitr::kable() static ones.

Because DT::datatable() is an htmlwidget, I seem to be able to set a reference-able, numbered caption only by relying on the knitr chunk option fig.cap =. (I hope I got this right). This makes sense for most of the htmlwidgets, many of which are plots, but, I'd say, not for DT::datatable(), which is actually a table.

Referencing/captioning it as a figure might be confusing for users.

I've tried several approaches to get a DT::datatable() to be properly labeled as a table in bookdown::gitbook(), but without success.

library(DT)
DT::datatable(head(iris), caption = "Table: This is the caption from inside DT")

DT::datatable(head(iris), caption = "(\\#tab:dt-repro) Table: This is the caption from inside DT")

knitr::kable(head(iris), caption = "This is the caption from inside kable")

yield, respectively,

I think it would be nice if I the caption set inside DT::datatable() could be passed on to bookdown() in the appropriate way.

Alternatively, and to remain open to more custom tables, I was wondering whether a chunk option tab.cap= inside knitr might make sense, to be treated analogously to fig.cap = .

Ps.: This might seem like a somewhat trivial issue (whether an actual table is called a figure), but this gets thornier in use cases where people use DT::datatable() for HTML-type outputs, and knitr::kable() for others. In that (my) scenario, the whole numbering and referencing diverges between the different outputs.

[yihui]

I see your point, but I'm afraid I'm not going to deal with this special case. Calling a table a figure is probably not the end of the world (nobody has complained so far that Figure 2.5 is not a figure at https://bookdown.org/yihui/bookdown/html-widgets.html). On the other hand, in non-HTML output, the DT widget will be a screenshot, which is probably qualified as a "figure".

In short, I tend not to make exceptions for DT widgets, but if this issue makes you sleepless at night, I'll be happy to reconsider it when I have time. Thanks!

[lmcgrath82]

I agree that having a separate table numbering system for DT tables would be very helpful. In fact, in most of the articles/reports I write, we use separate numbering for Figures and Tables, and therefore using the Figure labelling for tables is not really an option. If you have any other advice, or work-arounds it would be really helpful.

[yihui]

I'll reconsider this issue, but probably not very soon. Thanks!

[millerjef]

Thanks for reopening this issue. I think it is an important feature for a robust bookdown. I'm generating a government report using the DT package for dynamic tables. While I understand the argument for calling it a figure in the context of a screen capture for LaTeX, this mis-labeling creates confusion for readers especially if DT and kable tables are intermixed (since the numbering is incremented as if it is a figure). Also, a DT table, labeled as a figure, is likely to raise the ire of communications folks in government that review such things but don't understand the reason behind it being labeled as a figure.

[millerjef]

I propose a more general approach. Why not label and increment counters based on the html <div class = "table"> and/or <p class="caption"> (\#tab:myDT)My labeled DT</p>? This could set up a new counter for any arbitrary class.

I'm more of a scientist than a coder but I'm hoping my explorations helps someone come up with a nifty, efficient solution.

I explored a bunch of things to try to find a work around to get a DT into a table environment/counter. I used the bookdown-demo and edited the 01-intro.Rmd file as my MRE.

By setting keep_md: yes in the _output.yml file and inspecting the compiled .md, I note that:

```{r myDT-fig, fig.cap = "my super duper caption", echo = FALSE, message=FALSE, warning=FALSE}
library(DT)
datatable(head(iris))
```

Produces a <div class="figure"> chunk with the DT widget followed by:

<p class="caption">(\#fig:myDT-fig)my super duper caption</p>
</div>

I pursued this, including:

1. Setting chunk hooks to prepend the table reference anchor; and
2. Using htmltools::div and htmltools::p and htmltools::HTML to mimic the .md output generated above.

Using the above techniques (especially htmltools), I can get output that looks very close to the way fig.cap and DT get handled:

```{r myDThtmltools}
library(DT)
library(htmltools)
div(
    class = "table", 
    p(class = "caption", "(\\#tab:myDThtmltools)my caption created using htmltools"), 
    datatable(head(iris))
)
```

The output (snipped) starts as follows:

<div class="table">
<p class="caption">(\#tab:myDTdiv)my caption created using htmltools</p>

<div id="htmlwidget-365bb828ea197c7c2c1f" 
style="width:960px;height:500px;" 
class="datatables html-widget">
</div>

The DT widget renders with this at the top: (\#tab:myDThtmltools)my caption created using htmltools

I'm not sure why this gets parsed differently than a chunk processed with fig.cap. Maybe an easy solution?

[UrszulaCzerwinska]

I have found the following workaround for html from https://github.com/rstudio/bookdown/issues/372 After the table produced with DT

library(DT)
datatable(head(iris))

I insert html tag

cat("<table>",paste0("<caption>", "(#tab:mytab)", "caption", " some texte", "</caption>"),"</table>", sep ="\n")

Tab. \@ref(tab:mytab) which gives a desired output

For latex output, I use knitr tables

[ldecicco-USGS]

I see 4 people posted 👍 ...so the directions are pretty clear...but I'm still a bit confused. If the R markdown looks like this:

---
title: "Untitled"
site: bookdown::bookdown_site
output: bookdown::gitbook
documentclass: book
---

```{r myDThtmltools}
library(DT)
library(htmltools)
div(
    class = "table", 
    p(class = "caption", "(\\#tab:myDThtmltools)my caption created using htmltools"), 
    datatable(head(iris))
)
```
Tab. \@ref(tab:myDThtmltools)

and then I run:

render_book(input = "test.Rmd")

What would I change to "insert html tag" as described above?

[ldecicco-USGS]

Nevermind - I figured it out 1 minute after posting, I think the solution is this:

---
title: "Untitled"
site: bookdown::bookdown_site
output: bookdown::gitbook
documentclass: book
---

```{r myDThtmltools, results="asis", echo=FALSE}
library(DT)

datatable(head(iris))
    
cat("<table>",paste0("<caption>", "(#tab:myDThtmltools)", "caption", "Here's my caption", "</caption>"),"</table>", sep ="\n")
```


Tab. \@ref(tab:myDThtmltools)

[markbneal]

A small note: If your code chunk name has an underscore, the caption label fails. I have no idea why, but I guess that must mean something else in html.

[cderv]

A small note: If your code chunk name has an underscore, the caption label fails. I have no idea why, but I guess that must mean something else in html.

About this, you can't use _ in chunk name when using referencing mechanism in bookdown. As documented in https://bookdown.org/yihui/rmarkdown/r-code.html we advice to not use underscore

I strongly recommend that you only use alphanumeric characters (a-z, A-Z and 0-9) and dashes (-) in labels, because they are not special characters and will surely work for all output formats. Other characters, spaces and underscores in particular, may cause trouble in certain packages, such as bookdown.

[IdoBar]

I have found the following workaround for html from #372 After the table produced with DT

library(DT)
datatable(head(iris))

I insert html tag

cat("<table>",paste0("<caption>", "(#tab:mytab)", "caption", " some texte", "</caption>"),"</table>", sep ="\n")

Tab. \@ref(tab:mytab) which gives a desired output

For latex output, I use knitr tables

Thanks for the solution! I'm trying this approach, but my caption is being wrapped as if it's being resized to fit a narrow column (I guess it's because it's in a <table> environment.

Any idea how I can make it fill the entire width of the table that follows?

Thanks, Ido

[IdoBar]

I managed to fix this by adding a width argument to the table tag <table width=100%>