How to make figures with panels render properly in PDF?

[jgostick]

Description

Quarto Version: 1.6.39
MacOS: 15.2

I want to render my document to both the web and to PDF (it's a "book" type project with chapters). The web version looks great, but the PDF version is wonky. Specifically, figures with panels (i.e layout-ncols="2") are behaving badly.

Here is the web version:

And here is the PDF version:

Two things seems to going wrong in the PDF version:

1. In the web version I need to add the panel label to my subtitles, like "(a)" followed by the text, while in the PDF version it adds an "(a)", so it ends up with two "(a)"s.
2. The web version does a great job of vertically aligning the figures on each row and adding the necessary space to accommodate the subtitles of varying length, but the PDF version shifts the figures vertically upward to each row is no longer aligned.

I suspect the first problem can be fixed by passing the necessary arguments to the latex engine, but I don't know which ones. I am guessing it's possible to tell latex to stop adding subfigure numbering to prevent the extra "(a)"s.

Regarding the second problem (misalignment), perhaps it's possible to tell latex to vertically align figures on the same row. But it's more likely related to the following warning which I get during the PDF rendering:

WARNING (/Applications/quarto/share/filters/main.lua:10951) FloatRefTarget elements should not be the only content in a div with column classes. This will not render as expected. Consider moving the floatref targets to their own divs and using the `offset` attribute.

[mcanouil]

Could you share a small self-contained "working" (reproducible) example to work with, i.e., a complete Quarto document or a Git repository? The goal is to make it as easy as possible for us to recreate your problem so that we can fix it: please help us help you! Thanks.

---

You can share a self-contained "working" (reproducible) Quarto document using the following syntax, i.e., using more backticks than you have in your document (usually four ````).
See https://quarto.org/bug-reports.html#small-is-beautiful-aim-for-a-single-document-with-10-lines.

If you have multiple files (and if it is absolutely required to have multiple files), please share as a Git repository.

R	Python
````qmd --- title: "Reproducible Quarto Document" format: html engine: knitr --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{r} x <- c(1, 2, 3, 4, 5) y <- c(1, 4, 9, 16, 25) plot(x, y) ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````	````qmd --- title: "Reproducible Quarto Document" format: html engine: jupyter --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{python} import matplotlib.pyplot as plt x = [1, 2, 3, 4, 5] y = [1, 4, 9, 16, 25] plt.plot(x, y) plt.show() ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````

Additionally and if not already given, please share the output of quarto check within a code block (i.e., using three backticks ```txt), see https://quarto.org/bug-reports.html#check.

[jgostick]

Here is the output of quarto check...all seems well:

Quarto 1.6.39
[✓] Checking environment information...
      Quarto cache location: /Users/jeffgostick/Library/Caches/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.4.0: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.46.3: OK
      Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.6.39
      Path: /Applications/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: v2025.02
      Chromium: 869685

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /Users/jeffgostick/Library/TinyTeX/bin/universal-darwin
      Version: 2024

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
      Version: 3.12.7
      Path: /Users/jeffgostick/Code/ibsi/.venv/bin/python3
      Jupyter: 5.7.2
      Kernels: python3

[✓] Checking Jupyter engine render....OK

[✓] Checking R installation...........OK
      Version: 4.4.2
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
      knitr: (None)
      rmarkdown: (None)

      The knitr package is not available in this R installation.
      Install with install.packages("knitr")
      The rmarkdown package is not available in this R installation.
      Install with install.packages("rmarkdown")

[jgostick]

And here is a minimum working example. If you 'preview' this in the browser it all looks OK, but if you do quarto render index_demo.qmd --to pdf the resultant PDF has the issues I mentioned.

---
title: "Quarto Document"
author: "Norah Jones"
toc: true
number-sections: true
highlight-style: pygments
---


::: {#fig-wMRnV5ktRN layout-ncol="2"}

![(a) A short caption](https://imgs.xkcd.com/comics/rotary_tool.png)

![(b) A much longer caption which spans multiple lines so causes the row below to get bumped down. In HTML the following rows are all bumped down together, but in PDF only the figures in this column are bumped down.](https://imgs.xkcd.com/comics/rotary_tool.png)

![(c) The "(c)" has been typed by hand which is necessary for the HTML output](https://imgs.xkcd.com/comics/rotary_tool.png)

![(d) When rendering in PDF, the latex engine adds another subfigure label (i.e. "(d)") so you end up with "(d) (d)"](https://imgs.xkcd.com/comics/rotary_tool.png)

The same comics 4 times means that each figure is exactly the same size.  The top row illustrates the problem where long subfigure captions cause subsequent rows to be offset in the PDF version.  The bottom row illustrates the problem where extra subfigure captions are added by the PDF renderer. 
:::

[jgostick]

Note that I am running the above 'render' in the same folder as my larger project since that is where my uv venv is. I am pretty sure though, that my quarto settings are standard basic default stuff.

[mcanouil]

You need to add IDs (fig-) to your sub-figures.

[jgostick]

That solves problem 2 (thank you very much!!), but the figures are still mis-aligned in the PDF due to the differing caption length.

index_demo.txt

[mcanouil]

Use keep-tex: true and investigate the LaTeX code.

[jgostick]

I am not a latex pro so looking through that will be gibberish to me. I can ask a colleague maybe. I have attached the tex file here, on the off chance that you can spot something quickly, but I don't expect you to dig into this. You've already helped so much! And so fast (it's like a live chat app!)

index_demo.txt

[jgostick]

Actually, asking a colleague for latex help might not work, because the latex is generated by quarto, so I think I need to know how to tell quarto to tell latex that the subfigures should be vertically aligned regardless of how much text there is in each subfigure caption.

And BTW, this very old stackexchange item explores exactly this problem.