https://github.com/nextstrain/ncov-clades-schema
Renders SVG schema of SARS-CoV-2 clade as defined by Nextstrain
https://github.com/nextstrain/ncov-clades-schema
clades nextstrain phylogenetics sars-cov-2
Last synced: 11 months ago
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Renders SVG schema of SARS-CoV-2 clade as defined by Nextstrain
- Host: GitHub
- URL: https://github.com/nextstrain/ncov-clades-schema
- Owner: nextstrain
- Created: 2021-12-22T00:20:20.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2024-04-22T17:51:50.000Z (over 2 years ago)
- Last Synced: 2024-04-22T19:13:50.747Z (over 2 years ago)
- Topics: clades, nextstrain, phylogenetics, sars-cov-2
- Language: JavaScript
- Homepage: https://ncov-clades-schema.vercel.app/
- Size: 434 KB
- Stars: 9
- Watchers: 10
- Forks: 7
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# 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:
```bash
yarn install
yarn dev
```
Open browser at
```
http://localhost:3000
```
### Develop in docker
Have Docker installed. Run
```bash
./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
