Storing and calling images generated by R in a quarto book project

[giabaio]

Description

So: I have a quarto book project. I have a simple index.qmd, say

--- 
title: "title here"
---
some text.

and then my first real chapter, say a file chapter1.qmd

# Chapter 1

Here I have a "normal" R compile figure
```r
#| label: figure1
#| fig-cap: "some caption here"
plot(rnorm(1000))
```
But I also have lots of images compiled by R with `dev: tikz`, because I am a freak and really like my variables/Maths to be processed nicely, like

```{r}
#| label: figure2
#| dev: "tikz"
#| fig-cap: "some other caption"
plot(rnorm(1000),xlab="$x$",ylab="$\\Pr(X)$")
```

When I compile to pdf (from Rstudio or terminal), the "normal" image gets stored into chapter1_files/figure-pdf/figure1.pdf, but the images generated by tikz get stored in the root of my project (eg under /figure2.pdf). The resulting tex file points to the correct path for the two images, which get rendered OK, but I don't looove this because it clutters the root and makes it a bit more complicated to manage the project...

Also, I would want to output to both pdf and html, so I have a slight issue when compiling to html because all the files processed by tikz are natively pdf, which wouldn't work. I have in the past used a hook in a setup.R file (which I would load in the .Rprofile) to do something like

# Defines basic knitr options (global)
opts_chunk$set(
  fig.pos = 'h',
  out.width = "75%",
  warning = FALSE,
  message = FALSE
)
# Trick to automatically convert pdf graphs generated with dev='tikz' into png so they work in html format
# see: https://github.com/rstudio/bookdown/issues/275
knitr::opts_hooks$set(dev = function(options) {
  if (identical(options$dev, 'tikz') && !knitr:::is_latex_output()) {
    options$fig.process = function(x) {
      if (!grepl('[.]pdf$', x)) return(x)
      x2 = sub('pdf$', 'png', x)
      magick::image_write(magick::image_read(x,density=300), x2, format='png',quality=100)
      x2
    }
  }
  options
})

(or versions thereof... I tried to force the png files and pdf files to be stored under _files/figure-pdf/... but to no avail...

Ultimately, nothing is really broken, but I can't seem to force quarto to behave how I want (which I appreciate may be unreasonable...). Do I need to live with the fact that some images are stored away and others must remain in the main root of the project?

Many thanks and apologies if I'm missing something obvious!
Gianluca

[mcanouil]

This seems to be a knitr issue which you could likely replicate outside of a book, using a single HTML file and rmarkdown.

Note that in your first example, the first code block is not executable as it's missing brackets.

I believe you get the exact same behaviour with rmarkdown and the following rmd file.

---
output:
  html_document: default
  pdf_document: default
---

# Chapter 1

Here I have a "normal" R compile figure

```{r}
#| label: fig-figure1
#| fig-cap: "some caption here"
plot(rnorm(1000))
```

But I also have lots of images compiled by R with `dev: tikz`, because I am a freak and really like my variables/Maths to be processed nicely, like

```{r}
#| label: fig-figure2
#| dev: "tikz"
#| fig-cap: "some other caption"
plot(rnorm(1000),xlab="$x$",ylab="$\\Pr(X)$")
```

In the end, if the tikz graphics device (thus the R package providing this device) does not respect fig.path option from knitr, that's nothing to be done at the Quarto level. You can still try to set it at the code cell level.

[giabaio]

Thank you, @mcanouil. I think this should fix it:

# Global chunk options
knitr::opts_chunk$set(
  fig.pos = 'h',
  out.width = "75%",
  warning = FALSE,
  message = FALSE
)

# Trick to automatically convert pdf graphs generated with dev='tikz' into png so they work in html format
# see: https://github.com/rstudio/bookdown/issues/275
# Hook to post-process 'tikz' figures
knitr::opts_hooks$set(dev = function(options) {
  if (identical(options$dev, 'tikz')) {
    options$fig.process <- function(x) {
      if (!grepl("\\.pdf$", x)) return(x)
      
      input_file <- knitr::current_input()
      base_input <- tools::file_path_sans_ext(basename(input_file))
      fig_dir <- file.path(paste0(base_input, "_files"), "figure-pdf")
      dir.create(fig_dir, recursive = TRUE, showWarnings = FALSE)
      
      new_path_pdf <- file.path(fig_dir, basename(x))
      file.rename(x, new_path_pdf)
      
      if (!knitr:::is_latex_output()) {
        # HTML output → convert to PNG
        new_path_png <- sub("\\.pdf$", ".png", new_path_pdf)
        img <- magick::image_read(new_path_pdf, density = 300)
        magick::image_write(img, new_path_png, format = "png", quality = 100)
        file.remove(new_path_pdf)
        return(new_path_png)
      }
      
      # PDF output → keep PDF
      return(new_path_pdf)
    }
  }
  return(options)
})

adding this to the setup.R seem to be able to trick the whole thing to store the files (and point to them) correctly... I'll do more testing, but this look promising on the back of the couple chapters I've just compiled...

[mcanouil]

@giabaio What are the fig-label and fig-caption options you've set in your original example? I'm guessing you are using some kind of AI as those options are not valid (in Quarto and knitr/rmarkdown).

[giabaio]

My apologies for the confusion. I have fixed the original post and replying to this instead of the new thread below, which maybe could get removed? Hope this is OK!

[mcanouil]

We don't remove content (unless it really violates the code of conduct in a pretty strong or harmful way).
I'm hiding the other sub-threads.
Thanks!