Is there a way to get the citation generated in Quarto (like the Quarto Subcaption) and pass it to a ggplot2 plot, without manually creating the reference string?

[lphmn]

Description

Hello,

I posted this also on Posit Community and once I get responses, I will update both places Quarto Cross Reference references.bib in ggplot2

I know how to reference figures in Quarto thanks to Quarto Subcaptions. For example, I can create subcaptions like figSubcap <- "Data Source: @x" and the cross reference works great when using the div syntax. However, when I pass figSubcap into a ggplot2 plot, it just passes the literal string Data Source: @x instead of Data Source: Reference (2020)... .

Question: Is there a way to get the citation generated in Quarto (like the Quarto Subcaption) and pass it to a ggplot2 plot, without manually creating the reference string?

Here's an example (not fully representative as it lacks a references.bib file). I pass the reference into the x-axis because when converting a ggplot2 plot to plotly via plotly::ggplotly, the ggplot2 caption is not carried forward. However, by putting the reference on the x-axis, we avoid adding an extra argument to plotly::ggplotly.

It really doesn't matter where I pass the reference; I just want to know if there's a syntax that allows the citation to be referenced in a ggplot2 plot.

library(ggplot2)

# Define the custom ggplot function
create_scatter_plot <- function(x_axis_label) {
  ggplot(mtcars, aes(x = wt, y = mpg)) +
    geom_point() +
    labs(x = x_axis_label, y = "Miles per Gallon (mpg)") +
    theme_minimal()
}

"@x" <- "Reference (2020)..."

quartoReference <- "@x"

# Example usage
plot <- create_scatter_plot(quartoReference)
print(plot)

[mcanouil]

That's not possible.

Code is evaluated first and is not aware of anything from the document.

Input

Output

--- title: "Quarto Playground" format: html references: - id: canouil_jointly_2018 author: - family: Canouil given: Mickaël - family: Balkau given: Beverley - family: Roussel given: Ronan - family: Froguel given: Philippe - family: Rocheleau given: Ghislain container-title: Frontiers in Genetics doi: 10.3389/fgene.2018.00210 issued: 2018 title: "Jointly Modelling Single Nucleotide Polymorphisms With Longitudinal and Time-to-Event Trait: An Application to Type 2 Diabetes and Fasting Plasma Glucose" type: article-journal journal-title: '*Frontiers in Genetics*' my-reference: "@canouil_jointly_2018" --- ::: {#fig-ref} ```{r} library(ggplot2) ggplot(mtcars, aes(x = wt, y = mpg)) + geom_point() + labs(title = "{{< meta my-reference >}}") ``` A caption with a {{< meta my-reference >}} reference. :::

Even if the code was aware, you would not end up with the formatted citation but with "@canouil_jointly_2018" in this case.

[lphmn]

Thank you for the quick response.

Would it be possible to address this with a future enhancement request, or is it inherently unfeasible due to the code execution occurring before the document is built?

Use Case: When creating plots, I aim to ensure proper credit is given by including the data source on all my graphs. If someone uses one of my designs (e.g., screenshot or PNG download via Plotly), I want the source to be clearly visible. However, I prefer not to manage references in multiple places if Quarto can handle this for me. If this isn't possible in Quarto (currently or in the future), I can manage my references in two places: a .bib file and multiple literal strings. However, I would prefer to find a process that avoids repetition.

Edit: I borrowed your example. It does work when you have a .bib file but the below syntax does not display the same output as what I see in my quarto book. Having a string in an r code chunk can be passed as a reference. This is what I was hoping to doin my ggplot but like you mentioned I just get the @canouil_jointly_2018. I'm not used to the {{< meta my-reference >}} syntax you used (also neat to learn a new syntax).

---
title: "Quarto Playground"
format: html
references:
  - id: canouil_jointly_2018
    author:
      - family: Canouil
        given: Mickaël
      - family: Balkau
        given: Beverley
      - family: Roussel
        given: Ronan
      - family: Froguel
        given: Philippe
      - family: Rocheleau
        given: Ghislain
    container-title: Frontiers in Genetics
    doi: 10.3389/fgene.2018.00210
    issued: 2018
    title: "Jointly Modelling Single Nucleotide Polymorphisms With
      Longitudinal and Time-to-Event Trait: An Application to Type 2
      Diabetes and Fasting Plasma Glucose"
    type: article-journal
    journal-title: '*Frontiers in Genetics*'
my-reference: "@canouil_jointly_2018"
---

::: {#fig-ref}

```{r} 
library(ggplot2)
ggplot(mtcars, aes(x = wt, y = mpg)) +
  geom_point() +
  labs(title = "@canouil_jointly_2018")


caption <- "A caption with a @canouil_jointly_2018 reference."
```

`{r} caption`
:::

[mcanouil]

There are tools in R to handle references, I would suggest you use them.

It's very unlikely Quarto can do something about it as it would mean to compile references several times.

[lphmn]

Sounds good thank you.

As a side note, if you pass a reference from a code block to the document, underscores in the reference name can break the reference. You might already know this, but underscores _ prevent the reference from being passed from a code block. However, if there are no underscores _, cross-referencing currently works in Quarto from a code block. Please see images below (they are from my other Quarto document not the example that @mcanouil provided).

Image one with underscore

Image two with no underscore

Edit 1 based on @mcanouil next response: Thank you for the advice. I will do better in the future. While it won't look as nice as my screenshots above, the overall syntax below is based on @mcanouil example, with the only change of removing the underscores _. While I agree that passing references from a code block to a Quarto document is different from my original question (passing references from a code block to a ggplot) and may need a new discussion, it still aligns with the example provided in this thread based on the example @mcanouil provided.

My reasoning for not creating a new discussion, but please move this to a new discussion if it should be its own discussion. As someone who has to search multiple places to figure out solutions (due to my beginner experience level), I find it extremely tiring when a solution is not provided in a thread. While the solution to my ggplot2 question is not answered yet, the use case shown in @mcanouil example uses underscores was brought up here which created a different syntax issue/question. By including the solution in this thread, people can follow the thread and don't have to go searching for the solution in another place, if it is provided here. My plan is when I figure out a working solution for my references to ggplot2 question, I will provide a response with a solution, so others don't have to spend hours figuring out a solution. Thank you

---
title: "Quarto Playground"
format: html
references:
  - id: canouil_jointly_2018
    author:
      - family: Canouil
        given: Mickaël
      - family: Balkau
        given: Beverley
      - family: Roussel
        given: Ronan
      - family: Froguel
        given: Philippe
      - family: Rocheleau
        given: Ghislain
    container-title: Frontiers in Genetics
    doi: 10.3389/fgene.2018.00210
    issued: 2018
    title: "Jointly Modelling Single Nucleotide Polymorphisms With
      Longitudinal and Time-to-Event Trait: An Application to Type 2
      Diabetes and Fasting Plasma Glucose"
    type: article-journal
    journal-title: '*Frontiers in Genetics*'
my-reference: "@canouilJointly2018"
---

::: {#fig-ref}

```{r} 
library(ggplot2)
ggplot(mtcars, aes(x = wt, y = mpg)) +
  geom_point() +
  labs(title = "@canouilJointly2018")


caption <- "A caption with a @canouilJointly2018 reference"
```

`{r} caption`

:::

Edit 2 For anyone reading this in the future, click here for a solution to my initial question that, while not perfect, meets my current needs; I was assisted by MS Copilot.

[mcanouil]

@lphmn Please don't share only screenshots, share actual code. Possibly open a new discussion with this use case.

---

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 blocks (i.e., using three backticks ```txt), see https://quarto.org/bug-reports.html#check.