Figure cross referencing and knitr::read_chunk

[richardbeare]

Description

Hi,
I'm a fan of having my R code in chunks in a separate file and including what I need in the Rmd file as required. However I'm struggling to get figure labels to work when I do this with quarto. I can't see what I'm missing here - no matter what I try I can't get any version of @fig-label to work. The chunks import just fine - the label/cross reference is the missing part. Any suggestions?

---
title: "Test figure labels from code chunks"
format:
  pdf:
    keep-md: true
    keep-tex: true
---

## Quarto
```{r}
#| echo: FALSE
knitr::read_chunk("qq_code.R")
```

```{r }
#| label: Setup
#| echo: FALSE
#| warning: false
#| message: false
```

```{r}
#| label: APlot
#| echo: FALSE
#| fig.cap: "A caption"
#| fig.link: fig-APlot
```

Figure @APlot

and qq_code.R :

## ---- Setup ----
library(tidyverse)

data(mtcars)

## ---- APlot ----
ggplot(mtcars, aes(x=disp, y=mpg, colour=factor(cyl))) + geom_point()

[mcanouil]

Label needs a prefix such as fig- to be accounted as a cross-reference, see https://quarto.org/docs/authoring/cross-references.html.

Side note: FALSE is R syntax. In yaml, it is false. In Quarto, options use - not . as word separator.
Use execute to set globally option such as echo: false, see https://quarto.org/docs/reference/formats/html.html#execution and https://quarto.org/docs/computations/execution-options.html.
Finally, headers, list, and code cells should be surrounded by empty lines to avoid parsing issues.

In the end your Quarto document should look like the following:

---
title: "Test figure labels from code chunks"
format:
  pdf:
    keep-md: true
    keep-tex: true
execute:
  echo: false
---

## Quarto

```{r}
#| include: false
knitr::read_chunk("qq_code.R")
```

```{r}
#| label: Setup
#| include: false
#| warning: false
#| message: false
```

```{r}
#| label: fig-APlot
#| ref-label: APlot
#| fig-cap: "A caption"
#| fig-link: fig-APlot
```

Figure @fig-APlot

[richardbeare]

Thanks, that seems to work, and means that chunks in the R code producing figures need to have a specific naming structure. i.e. fig-something in the R file. Didn't realise that.

[mcanouil]

I updated to fit your R script, using ref-label knitr option.

[richardbeare]

Hm, I can't get that approach to work. It is OK if I rename the R chunks to include a fig- prefix, but not via ref-label

[mcanouil]

What do you mean?
Which version of knitr and Quarto CLI are you using?

The approach works.

[richardbeare]

Must be a version problem - older on my linux machine where I was doing the work - Quarto 1.3.353, knitr 1.43, rmarkdown 2.23, pandoc 3.1.1. Seems OK on my mac - Quarto 1.3.433, knitr 1.44. Time for upgrades all round.

Thanks