What is a simple way to thumbnail some plots in R Markdown/knitr?

Question

I am using R Markdown with knitr in R Studio to create and update a simple project website to keep my colleagues up to speed with a data analysis model I am building. There are some plots on the page, which (for smaller plots) so far has worked nicely, they can see the code and the results in the same place.

However, some plots have grown very large (and must remain large to allow quick side-by-side comparison of models), and don't fit on the page very well. I've used separately uploaded pdfs (with a link on the page) for some of them. It would be nicer if there was a simple way of generating thumbnails of some of these plots, so that the user can view a small plot image, click on it and then inspect the much larger image in detail. However, if it takes a lot of manual scripting for each plot instance, I'd rather not waste time on it and just upload the couple of pdfs. A similar question here talks about package, knitrbootsrap, but I don't want to thumbnail all my plots, just a select few. The package seems to use Magnific popup, but integrating it myself in a Markdown page seems like a hassle(?). I didn't find anything in the R Markdown reference guide. Of course a one way would be to generate two plots, one tiny, which is shown, and link it to another, larger plot image/pdf that is uploaded separately - but a simpler, more automatic way would be desireable.

Hence the question - is there a simpler way to generate clickable plot thumbnails in R Markdown?

Answer 1

So, this is what I came up with. Add a plot hook, so that you generate a full-resolution pdf image before generating a small image in the chunk:

allow_thumbnails <- function(x, options) {
  if (!is.null(options$thumb)) {
    filename <- sprintf("%s.full.pdf", strsplit(basename(x), "\\.")[[1]][1])
    absolute_path <- file.path(dirname(x), filename)

    # generate the full resolution pdf
    pdf(absolute_path, width = options$thumb$width, height = options$thumb$height)
      eval(parse(text = options$code))
    dev.off()

    # add an html link to the low resolution png
    options$fig.link = absolute_path
  }

  knitr:::hook_plot_md_base(x, options)
}

And then in the Rmd file, I define the size of the full-resolution image using the thumb argument:

```{r init} 
    knit_hooks$set(plot = allow_thumbnails)
```

```{r my_large_plot, fig.width = 15, fig.height = 15, thumb = list(width = 45, height = 45)}
    my_large_plot()
```

This generates an html file with a clickable png that takes you to the pdf.