ncov-clade-schema

https://ncov-clades-schema.vercel.app/

Visualizes current tree of SARS-CoV-2 clades. Allows to generate an SVG image of this tree.

Comes originally from these sandboxes:

• https://bl.ocks.org/trvrb/66b2c193117220200eb8e09190a43c85
• https://codesandbox.io/s/nextstrain-clades-schema-43t2m
• https://codesandbox.io/s/nextstrain-clades-schema-forked-cu6fy

Development

Clone the repository and go to its directory.

Develop locally

Have Node.js 12+ (latest LTS is recommended) and yarn 1.x installed. Run:

yarn install
yarn dev

Open browser at

http://localhost:3000

Develop in docker

Have Docker installed. Run

./docker/dev yarn install
./docker/dev yarn dev

Open browser at

http://localhost:3000

Updating with new clades

1. Add new clade to src/clades.json structure, in the right place
2. Run https://github.com/nextstrain/ncov-clades-schema/blob/master/src/replace_colors.py with the right parameters (old number of clades and new number of clades). Currently --prev-row should (probably) be 29 (or higher if more than 1 clade added). If a single clade is added, --future-row should be 32: python src/replace_colors.py --prev-row 31 --future-row 32
3. Set the colors of new clades to the ones suggested by the script (written to stdout)
4. Adjust the width of the svg as necessary in: src/components/NextstrainCladesSchema.tsx
5. Check results using e.g. yarn dev (after dev setup)
6. Commit, push
7. Save produced svg and update clades.svg in this repo (this is where the README and potentially also Nextclade gets the svg from, so this needs to be updated for changes to take effect), see https://github.com/nextstrain/ncov-clades-schema/commit/738d42762aec411c5da6e78d32b1c235601b08a5