workshop-data-visualization-r

This repo contains the course material for NBIS workshop Advanced Data Visualization. The rendered view of this repo is available here.

Contributing

To add or update contents of this repo (for collaborators), first clone the repo.

git clone --depth 1 --single-branch --branch main https://github.com/nbisweden/workshop-data-visualization-r.git

Then navigate to the repo directory and create new branch.

cd workshop-data-visualization-r
git checkout -b my-branch

Make changes/updates as needed. Add the changed files. Commit it. Then push the repo back.

git add .
git commit -m "I did this and that"
git push origin my-branch

Then create a pull request to the main branch of this repo. You can do this from the GitHub website.

If you are not a collaborator, you can still contribute by creating a pull request. You can do this by forking the repo to your account, making changes, and then creating a pull request from your forked repo to this repo.

❗ When updating repo for a new course, change output-dir: XXXX in _quarto.yml as the first thing, so that old rendered files are not overwritten.

❗ Do not push any rendered .html files or intermediates.

Docker

Local build/preview using Docker

You can preview changes and build the whole website locally without a local installation of R or dependency packages by using the pre-built Docker image.

Clone the repo if not already done. Make sure you are standing in the repo directory.

To build the complete site,

docker run --platform linux/amd64 --rm -u 1000:1000 -v ${PWD}:/qmd ghcr.io/nbisweden/workshop-adv-data-viz:latest

To build a single file (for example index.qmd),

docker run --platform linux/amd64 --rm -u 1000:1000 -v ${PWD}:/qmd ghcr.io/nbisweden/workshop-adv-data-viz:latest quarto render index.qmd

❗ Output files are for local preview only. Do not push any rendered .html files or intermediates.

Convert HTML slides to PDF

docker run --platform=linux/amd64 -v $PWD:/work astefanutti/decktape https://nbisweden.github.io/workshop-data-visualization-r/2505/topics/ggplot/slide_gg1.html /work/slide_ggplot_intro.pdf

Serving and automatic rendering

You can use quarto preview to serve the site, and handle automatic rebuilding of pages when any .qmd file is changed.

# serve the site
docker run --rm -it --platform linux/amd64 -u $(id -u):$(id -g) -v ${PWD}:/qmd -p 8800:8800  ghcr.io/nbisweden/workshop-adv-data-viz:latest quarto preview --port 8800 --host 0.0.0.0

Go to http://localhost:8800/ or http://0.0.0.0:8800 in your browser.

Building your own docker container

# build container
docker build --platform linux/amd64 -t ghcr.io/nbisweden/workshop-adv-data-viz:latest .

# push to ghcr
# docker login ghcr.io
docker push ghcr.io/nbisweden/workshop-adv-data-viz:latest

# run container in the root of the repo
docker run --rm --platform linux/amd64 -u $(id -u):$(id -g) -v ${PWD}:/qmd ghcr.io/nbisweden/workshop-adv-data-viz:latest
docker run --rm --platform linux/amd64 -u $(id -u):$(id -g) -v ${PWD}:/qmd ghcr.io/nbisweden/workshop-adv-data-viz:latest quarto render index.qmd

Repo organisation

The source material is located on the main branch (default). The rendered material is located on the gh-pages branch. One only needs to update source materials in main. Changes pushed to the main branch is automatically rendered to the gh-pages branch using github actions.

❗ Every push rebuilds the whole website using a pre-built docker image.

This repo is loosely based on the quarto template specky.

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2025 • NBIS • SciLifeLab