scifig_plot_examples_R

Scientific publication figure plotting examples with R.

Usage

Requires R and ggplot2 >= 3.5.0. Install the packages once:

install.packages(c("ggplot2", "patchwork", "scales", "magick", "ggforce", "latex2exp", "svglite"))

Then, from the repository root:

Rscript figure_example.R

This writes figure_example.png, figure_example.svg and figure_example.pdf.

To change font size, colours or model parameters, edit opts in figure_example.R (all settings and their defaults are listed in figure_defaults() in R/figure.R).

Dashboard

app/ is a Shiny app for the figure: change font size, colours, model parameters and which panels to show, and download the result as PNG or SVG. It uses the same plotting code (R/figure.R). To run it locally:

install.packages(c("shiny", "bslib", "ragg"))
shiny::runApp("app")

The app is also online here, built with Shinylive and published by a GitHub Actions workflow on every push to main. It runs R in your browser (WebAssembly), so nothing needs to be installed. The first visit downloads about 120 MB; after that, the browser cache makes it faster.

Layout

Path	Contents
figure_example.R	Script that builds and saves the figure
R/figure.R	Functions for the figure: data loading, one function per panel, saving
app/	Dashboard app (Shiny)
data/	CSV data for panels B–F
images/	Microscopy images for panel A
tests/	Tests (see below)

Tests

The tests check the data loading, that every panel renders without warnings (also with non-default settings), the exported files, the dashboard's server logic, and how each panel looks (visual snapshots with vdiffr). They run on GitHub Actions for every push and pull request. To run them locally:

install.packages(c("testthat", "vdiffr", "withr", "shiny", "bslib", "ragg"))

Rscript -e 'testthat::test_dir("tests/testthat")'

If you change a panel on purpose, the snapshot test for it fails. Review the new version and accept it with:

testthat::snapshot_review("snapshots", path = "tests/testthat")