Quarto manuscript cannot properly render tables, supplementary tables, figures, supplementary figures.

[davidzgli]

Description

I ran into troubles when rendering to html or typst format document from a quarto file that has tables, supplementary tables, figures, and supplementary figures. Multiple issues showed up, so I created a github repository to reproduce these issues (https://github.com/davidzgli/manuscript-example).

When rendering the index.qmd file to html, I get the following error:

1. The cross-references for the mtcars-head table are not rendered properly. The cross-references are displayed as raw strings (e.g. @tbl-mtcars-head), not rendered strings (e.g. Table 1).
2. The same issue occurs for the iris-head supplementary table. The cross-references are displayed as raw strings (e.g. @supptbl-iris-head), not rendered strings (e.g. Supplementary Table 1 ).
3. The embdedded code block for creating the mtcars-summary table is not rendered properly. The tables are not displayed in the html file.
4. The same issue occurs for the iris-summary supplementary table. The tables are not displayed in the html file.
   Layout issue. The texts are aligned to the leftmost side of the page. The texts should be aligned with other elements, such as tables and figures.

Some issues were also encountered when rendering the index.qmd file to typst document. The issues are documented at https://github.com/davidzgli/manuscript-example/blob/main/issues.qmd.

I am on macOS Sonoma 14.6.1 with quarto 1.5.56. Thank you for your help!

[mcanouil]

@davidzgli Could you try to make your example smaller by removing all pieces not necessary?
Maybe try outside of a Manuscript project.

[davidzgli]

Thank you for the link. I quoted the qmd file and it looks more readable now.

---
title: "crossref figure panel"
format:
  html: default
  docx: default
  typst: default
---

```{r}
#| label: fig-mtcars-combined

library(tidyverse)
library(patchwork)

# Scatter plot with color
scatter_color <-
ggplot(mtcars) + 
  geom_point(aes(hp, wt, colour = mpg)) + 
  theme(legend.position = 'bottom')

# Bar plot
bar_plot <- 
ggplot(mtcars) + 
  geom_bar(aes(gear)) + 
  facet_wrap(~cyl) + 
  theme(legend.position = 'bottom')

# Combine the plots
scatter_color + bar_plot + plot_layout(ncol = 2) + plot_annotation(title = 'Combined plots', tag_levels = 'A')
```

@fig-mtcars-combined shows the combined plot of a colored scatter and a bar plot for the `mtcars` dataset. [@fig-mtcars-combined]A indicates weight has positive correlation with hp, with higher weights having larger horsepower, accompanied by lower mpg. We can see that four forward gears are most popular for cars with 4 or 6 cylinders, while 3 gears are most popular for cars with 8 cylinders ([@fig-mtcars-combined] B). 

Below is the output of quarto check command.

➜  ~ quarto check
Quarto 1.5.56
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.2.0: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.41.0: OK
      Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.5.56
      Path: /Applications/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: v2022.05
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /Users/liz30/Library/TinyTeX/bin/universal-darwin
      Version: 2022

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

[✓] Checking Python 3 installation....OK
      Version: 3.11.4
      Path: /Users/liz30/homebrew/opt/[email protected]/bin/python3.11
      Jupyter: 5.5.0
      Kernels: python3

(|) Checking Jupyter engine render....Traceback (most recent call last):
  File "/Applications/quarto/share/jupyter/jupyter.py", line 21, in <module>
    from notebook import notebook_execute, RestartKernel
  File "/Applications/quarto/share/jupyter/notebook.py", line 15, in <module>
    from yaml import safe_load as parse_string
ModuleNotFoundError: No module named 'yaml'
[✓] Checking Jupyter engine render....OK

Let me know in case anything else is needed.

[mcanouil]

Sorry, I don't understand.
Are you saying the issue is "only" the space after the reference in Typst?
If so, I assume the following is quite enough:

---
title: "crossref figure panel"
format: typst
---

```{r}
#| label: fig-mtcars-combined
plot(1)
```

[@fig-mtcars-combined]A 

Also, where did you see the square brackets notation for figure/tables cross-reference?

[mcanouil]

There might be a bug here or more likely a Typst limitation, but you could use Quarto feature directly to avoid the issue in the first place and have better cross-reference.
See https://quarto.org/docs/authoring/cross-references.html#figures.

---
title: "crossref figure panel"
format: typst
---

```{r}
#| label: fig-mtcars-combined
#| fig-cap: "Combined figure"
#| fig-subcap: true
#| layout-ncol: 2
plot(1)
plot(2)
```


@fig-mtcars-combined-1 is the first subfigure.

[mcanouil]

If you really want to use patchwork and not get proper/cleaner sub-figures cross-reference, you need to use: [@fig-mtcars-combined]`\`{=typst}A, note the `\`{=typst} to ensure the reference stops there.

[cscheid]

Asking a clarification question upstream: jgm/pandoc#10180

[davidzgli]

Yes, it is much clearer. I guess I have not yet enough linux skills or pandoc knowledge to push the question to this level of clarity. When I tried the command pandoc --version on my mac, it bounced back a "command not found" error.

[davidzgli]

Yes, this example is enough. Sorry for making the example too complicated. I was planning to use one example to demonstrate multiple issues. It turned out to be a bad idea.

…

On Thu, Sep 12, 2024 at 12:30 PM Mickaël Canouil ***@***.***> wrote: Sorry, I don't understand. Are you saying the issue is "only" the space after the reference in Typst? If so, I assume the following is quite enough: ---title: "crossref figure panel"format: typst--- ```{r}#| label: fig-mtcars-combinedplot(1)``` ***@***.***A — Reply to this email directly, view it on GitHub <#10755 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOQTOJRO7H75RXJILZXAJBTZWG6STAVCNFSM6AAAAABN4UF2RKVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANRSHA2DOMQ> . You are receiving this because you were mentioned.Message ID: ***@***.*** com>

[davidzgli]

Thank you. It works. I have many figures in the manuscript I am working on, and every figure has multiple panels. The proper cross-reference to the individual panels is crucial.

…

On Thu, Sep 12, 2024 at 5:23 PM Mickaël Canouil ***@***.***> wrote: If you really want to use patchwork and not get proper/cleaner sub-figures cross-reference, you need to use: ***@***.***`\`{=typst}A, note the `\`{=typst} to ensure the reference stops there. — Reply to this email directly, view it on GitHub <#10755 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOQTOJS2BFFTF2TJYZF53M3ZWIA4DAVCNFSM6AAAAABN4UF2RKVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANRTGA4DQMY> . You are receiving this because you were mentioned.Message ID: ***@***.*** com>

[davidzgli]

The one I selected is sort of hack, but it appears to be compatible with patchwork. Patchwork has more flexibilities to arrange the plots in many ways. I guess I would stick with this "hacky" way for now. I just cannot make sense what the code "\{=typst}" means here.

[mcanouil]

Did you look for the layout option in Quarto?

[davidzgli]

Not fully explore the layout option yet. But I think the Quarto layout option is mainly targeted to the page/article layout. It seems to have limited supports for arrange plots/tables, such as align axis, collect legends, nest plots, etc.

[mcanouil]

I suggest you read the documentation on figures: https://quarto.org/docs/authoring/figures.html

[davidzgli]

It seems to have more supports for arranging figures than I thought. Thank you for the link! I will explore it later.