ETC5513: Collaborative and Reproducible Practices

Tutorial 4: Figures, Tables, and Cross-Referencing

Author

Michael Lydeamore

Published

31 March 2026

🎯 Objectives

Building on our ability to sync repositories and manage branches, today we focus on the technical side of professional reporting:

  • Create a Quarto report with a table, figures, and sections that are labelled and referenced
  • Generate professional figures with captions and sub-figures
  • Use cross-referencing to link text to your figures and tables dynamically
  • (Extension) Implement academic referencing using BibTeX in Quarto

We will be using the repository we made in this week’s workshop. Open this project in your IDE of choice and create a new .qmd file for this tutorial. Make sure to add it to version control.

🖼️ Task 1: Working with Figures

In Quarto, figures are more than just images; they are numbered entities with metadata. To make a figure “referencable,” its label must start with the prefix fig-.

Exercise

  1. Create a new code chunk in your QMD.
  2. Use the following code to generate a plot:
```{r}
#| label: fig-penguins-scatter
#| fig-cap: "Body mass vs. Flipper length for three penguin species."
#| warning: false
library(ggplot2)
library(palmerpenguins)

ggplot(penguins, aes(x = flipper_length_mm, y = body_mass_g, color = species)) +
  geom_point() +
  theme_minimal()
```

Pro-Tip: The #| label: fig-xxx chunk option is vital. Without the fig- prefix, Quarto will not include this in the automatic “List of Figures” or allow for dynamic cross-references.

Commit these changes to your repository with a meaningful commit message, and push to GitHub.

📊 Task 2: Creating Professional Tables

Static Markdown tables are fine for simple notes, but for reproducible research, we generate tables directly from data frames. To cross-reference a table, the label must start with tbl-.

Exercise

Create a summary table of the penguin data using knitr::kable:

```{r}
#| label: tbl-penguin-summary
#| tbl-cap: "Mean body mass of penguins by species and sex."
library(dplyr)

penguins |>
  filter(!is.na(sex)) |>
  group_by(species, sex) |>
  summarise(mean_mass = mean(body_mass_g)) |>
  knitr::kable()
```

Commit these changes to your repository with a meaningful commit message, and push to GitHub.

🔗 Task 3: Dynamic Cross-Referencing

One of the greatest strengths of Quarto is automation. If you add a new figure at the beginning of your document, Quarto renumbers every subsequent figure and update every mention in your text automatically.

Syntax

  • To reference a figure: Use @fig-label
  • To reference a table: Use @tbl-label

Exercise

Write a short paragraph in your document referencing the items you created above:

As shown in ?@fig-penguins-scatter, there is a clear positive correlation between flipper length and body mass. The specific averages for each group are detailed in ?@tbl-penguin-summary.

Commit these changes to your repository with a meaningful commit message, and push to GitHub.

🎓 Extension: Academic Referencing

To use academic citations, you need a bibliography file (usually a .bib file).

1. Create a Bibliography

Create a new text file in your project folder named references.bib and paste this BibTeX entry inside:

@Manual{,
  title = {palmerpenguins: Palmer Archipelago (Antarctica) penguin data},
  author = {Allison Marie Horst and Alison Presmanes Hill and Kristen B Gorman},
  year = {2020},
  note = {R package version 0.1.0},
  doi = {10.5281/zenodo.3960218},
  url = {https://allisonhorst.github.io/palmerpenguins/},
}

2. Update your YAML

Add the bibliography field to the top of your .qmd file:

---
title: "Workshop 4"
bibliography: references.bib
---

3. Cite in Text

Use the key from your .bib file preceded by an @ symbol.

  • Parenthetical: The data was originally collected by Gorman et al. [@penguins_data].
  • Narrative: @penguins_data argues that…

Quarto will automatically generate a References section at the very end of your document.

🧹 Summary Checklist