CELLxGENE logoApplicationCollectionsDatasetsGene ExpressionCell Guide


How To Write Documentation

Documentation Format

Our documentation is written in MDX, a Markdown-based markup language. It's a simple, declarative, and powerful way to write documentation. MDX is a superset of Markdown, which means you can treat it like Markdown for the most part while also adding additional features.

All our documentation can be found in the doc-site folder in the data-portal repo. Adding directories and files to this folder will automatically update the documentation.


There are a few ways you can edit the documentation, all with various advantages and disadvantages.

  1. GitHub's built-in Markdown editor

    • (+) The Least amount of work needed to edit
    • (+) Built in markdown renderer
    • (-) Site styling isn't available
    • (-) Components will be shown as their raw syntax
    • (-) GitHub is relaxed when it comes to HTML + Markdown syntax, which will error during the building process
  2. VSCode

    • (+) Access to extension library
    • (+) ESLint and Prettier are available
  3. VSCode + Dev Server (recommended)

    • Site styling is available
    • Quick reloading of changes
    • MDX building will render components as intended

Writing Documentation

Creating a new page

The directory and file structure mirrors what will be shown on the website. The directory of this file is doc-site/dev/writing-documentation resulting in the URL cellxgene.cziscience.com/docs/dev/writing-documentation.

Once implemented, the same structure will be shown on the left sidebar. If the file is named index.mdx, it will be shown as the root page for the folder.

Editing page

Edit the file as you would normally for a Markdown file, you also have access to regular HTML tags. You can request for any components to be added to be available for use within the documentation. Feel free to create a ticket and assign @seve or message on Slack. We can also override the default markdown renderer to render our own components (# could render an SDS Header)

Currently available components

  • next/Image

    • <Image src={"/doc-site/poly.jpg"} />
  • EmbeddedGoogleSlides

    • <EmbeddedGoogleSlides src="https://docs.google.com/presentation/d/e/2PACX-1vQzA99mYecRu0Y5v--QsUCAuoTJFxo7VIhApCB-E669-00KCKww8AumBZcX0pwV41qHIuLRTsL7AckB/embed?start=false&loop=true&delayms=3000" />


You can add images to the documentation by adding files to the public directory(single-cell-data-portal/frontend/public/doc-site) and then display it in MDX using the <Image/> component from Next.js (![](/doc-site/image.png)).


Example image

Embedded Google Slides

You can embed a google slide iframe using the <EmbeddedGoogleSlides/> component. Just extract the source url from the published iframe on google slides and pass it in the src prop.

Deleting a page

Deleting a file will delete the corresponding page on the doc site, no other work is necessary.

Linting changes

We use tools to both lint and format the data portal codebase, including these .mdx files. To check if any lint errors were introduced, run npm run lint in the /frontend directory. To format any files, run npm run format to run prettier against all files in the frontend codebase. If you're using VSCode to edit these files, there are extensions to do both of theses actions for you. See the Recommended VSCode Plugins Section

Running the dev server

The first time you run the dev server, you will need to install the necessary tools.

  1. Install nvm
    1. curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.1/install.sh | bash
  2. Install the version of node compatible with our project
    1. Navigate to the frontend directory
    2. Ie. cd single-cell-data-portal/frontend
    3. nvm install node
  3. Install NPM packages
    1. npm install
  4. Set a backend with the configuration
    1. e.g. for staging backend: cp src/configs/staging.js src/configs/configs.js
  5. Run the dev server
    1. npm run dev
  6. View the site on localhost:3000/docs
  7. (temporary) While the navigation sidebar is being worked on, you will have to manually enter the page you want to view.
    1. single-cell-data-portal/frontend/doc-site/dev/writing-documentation ➡️ localhost:3000/docs/dev/writing-documentation/dev/writing-documentation
    2. single-cell-data-portal/frontend/doc-site/desktop/self-hosting/heroku.mdx ➡️ localhost:3000/docs/desktop/self-hosting/heroku

Recommended VSCode plugins