How to reference multiple plots from the same code chunk

[lcolladotor]

Hi,

In previous versions I was able to use \@ref(fig:chunkname1) and \@ref(fig:chunkname2) if a single Rmd chunk (here called chunkname) generated two plots. In the current devel version (2.7.8) this doesn't work.

You can see an example at http://research.libd.org/recount-brain/example_SRP027383/example_SRP027383.html that matches this commit LieberInstitute/recount-brain@614316a. I include a screenshot here for simplicity.

I also tried using \@ref(fig:chunkname-1) and it failed. Note that \@ref(fig:chunkname) did work, but it doesn't make sense to me to reference several figures with the same number (even if they come from the same code chunk) as in:

.

I guess that I could use \@ref(fig:chunkname)-1 and \@ref(fig:chunkname)-2 although the links won't point to the correct location.

Is is still possible to reference multiple plots from the same chunk? Maybe there's a new syntax that I'm missing. There are cases where I can't break the code and separate the code so that each code chunk makes a single figure. For example, when a function makes more than 1 plot.

Thanks!
Leo

[aoles]

Hi Leo,
thanks for reporting this. Actually, the problems you are experiencing might indicate an issue with bookdown responsible for managing references, as the following doesn't produce links either.

---
title: "Cross-referencing multiple figures"
output:
  bookdown::html_document2
---

References to Figure \@ref(fig:plot1) and Figure \@ref(fig:plot2).

```{r plot, fig.cap=c("First", "Second"), fig.pos="h"}
plot(cars)
plot(faithful)
```

For some reason the former approach described in rstudio/bookdown#343 doesn't work anymore. Do you happen to know which was the last bookdown version which was fine?

[lcolladotor]

Hi Andrzej,

Thanks for looking into this! From http://bioconductor.org/help/workflows/recountWorkflow/ I believe that it still worked with bookdown version 0.5. My current version is 0.7. It's not the most narrow clue but hopefully it helps.

Best,
Leo