Quarto & Presentation Automation Prompts

This guide gathers prompts and workflows for automatically generating presentations from analysis pipelines and documentation, covering both web-based Reveal.js slide decks and Microsoft PowerPoint (.pptx) presentations.

1. Web-Based Reveal.js Presentations with Quarto

This workflow transforms existing markdown notes into a styled, interactive Reveal.js presentation with a modern aesthetic and custom typography.

Prompt and Response

Prompt:

“Create a quarto slide deck from [slidedeck].md in light mode and place it in folder quarto/ as [slidedeck].qmd. Adjust slide styling to use a more compact layout so that content fits neatly on each slide. Do not use chalkboard features, instead embed all resources. Update .gitignore for quarto documents as needed.”

Key Configurations & Structure:

Quarto Slide Deck ([slidedeck].qmd):
- Converted to the modern web-based Reveal.js format.
- Structured into logical sections using background-colored slide breaks (# Section Title {background-color="..."}).
- Utilizes advanced Quarto features such as column layouts (::: {.columns}), callout boxes, and incremental lists (::: {.incremental}).
- Adjusts all relative file links to match the subdirectory structure.
Custom Presentation Styling (quarto/custom.scss):
- Designed a premium dark-mode aesthetic using Slate and Sky/Rose accents.
- Customized typography using modern sans-serif fonts (Outfit, Inter).
- Added glowing shadows and rounded borders to code blocks, and styled Quarto callouts to pop against dark backgrounds.
Rendered Output:
- Compiled using quarto render quarto/[slidedeck].qmd to ensure syntax validity.

2. Automated PowerPoint Deck Generation from R Pipelines

This workflow automates the assembly of a Microsoft PowerPoint presentation (.pptx) directly from an R data analysis pipeline, embedding generated PNG figures, titles, tables of contents, and biological narrative slides.

Case Study: Glucose Tolerance Test (GTT) Analysis Pipeline

Date: 2026-03-19 (Updated: 2026-03-25)

Execution Prompt Used:

“Run the prompt and do all the steps listed in promptsAlan.md. Make sure all software needed is installed.”

Consolidated Pipeline Instructions

Data Initialization:

Analyze Glucose Tolerance Test (GTT) data from the master spreadsheet 'NDNB-25 B6 and NZO Masterdate sheet v2 R.xlsx'.
Time-Course Line Graphs (Glucose, Insulin, & Log Ratio):
Generate time-course line graphs for GTT data at 0, 15, 30, and 120 minutes vs. time. Create separate plots for:
- Glucose levels
- Insulin levels
- log(Insulin / Glucose) ratio
Output individual figures for both the NZO and B6 strains across each of the three metrics (6 plots total). Map Vehicle-treated to black dots and lines, and Compound-treated to blue dots and lines. Include standard error bars.
Cross-Sectional Scatter Plot:
Create a cross-sectional scatter plot mapping change in fasting glucose (Y-axis) against change in body weight (X-axis) across all mice.
- Color NZO strain blue and B6 strain black.
- Drug-treated mice as circles, vehicle-treated as squares.
- Add linear regression lines for each of the 4 subgroups.
- Calculate and display Pearson correlation coefficients (r) and p-values on the plot.
File Management:

Format spaces to underscores (Hsp90_GTT.R), and explicitly add the .R extension.
Presentation Generation via Quarto:
Use Quarto to automatically generate a PowerPoint deck (.pptx) embedding all of the outputted PNG figures. Ensure the presentation includes:
- A two-column Table of Contents slide with functional intra-document hyperlinks.
- A background section on Gluconeogenesis, split across multiple clean slides with academic references.
Insulin Baseline Normalization:

Remove time 0 insulin baseline measurements and calculate two new subgroup metrics: the Insulin / Insulin_0 ratio and log-regression residuals (log(Insulin) ~ log(Insulin_0)). Plot both over time, splitting NZO and B6 strains side-by-side using facet_wrap. Add these plots to the PowerPoint deck.