https://github.com/cdcgov/tidytree
Uncompromisingly Flexible Phylogenetic Trees in Javascript
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
-
○Academic publication links
-
✓Committers with academic emails
1 of 5 committers (20.0%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (12.7%) to scientific vocabulary
Keywords from Contributors
Repository
Uncompromisingly Flexible Phylogenetic Trees in Javascript
Basic Info
- Host: GitHub
- Owner: CDCgov
- License: apache-2.0
- Language: JavaScript
- Default Branch: master
- Homepage: https://cdcgov.github.io/TidyTree/
- Size: 7.27 MB
Statistics
- Stars: 20
- Watchers: 8
- Forks: 12
- Open Issues: 16
- Releases: 4
Metadata Files
README.md
TidyTree
Uncompromisingly Flexible Phylogenetic Trees in Javascript, powered by d3
This repository was created for use by CDC programs to collaborate on public health surveillance related projects in support of the CDC Surveillance Strategy. Github is not hosted by the CDC, but is used by CDC and its partners to share information and collaborate on software.
TidyTree is both a full-featured web application for users, along with the underlying library for developers.
Launch the Application
It's designed to replicate much of the functionality of FigTree, though it's by no means a perfect replacement. It does, however, run entirely in-browser.
Developer Quick Start
First import the library:
HTML
<script src="https://d3js.org/d3.v5.min.js"></script>
<script src="https://unpkg.com/tidytree@0.5.0/dist/tidytree.min.js"></script>
(It requires d3!)
Then stick this in an HTML script tag:
javascript
let newick = "(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);";
let tree = new TidyTree(newick, { parent: "body" });
And Voila! Your body will be populated by a phylogenetic tree.
Developer Documentation
Shoutouts
tidytree is based on this gist (See in action), which "mostly just duplicates the cannonical[sic] d3.tree and d3.cluster bl.ocks by Mike Bostock."
Why?
MicrobeTrace needed a Phylogenetic Tree renderer that enabled rerooting and distance scaling. Additionally, there were a bunch of nice-to-haves, like Unrooted and Circular views, Zooming, Colorable and Selectable nodes... You get the idea.
As for the viewer, well, we needed a platform to rapidly prototype features for the library. The product of that is a single-page web application that leverages literally all of the features of the library. If you're a dork like me, you can see this in the coding of the index.html file. Notice how all of the select widgets are programmatically populated--that's so we could implement new features (e.g. layouts) without having to update the Demo HTML. After that, all we had to do was keep the UI clean.
Public Domain
This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.
License
The repository utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later.
This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.
This source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details.
You should have received a copy of the Apache Software License along with this program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html
The source code forked from other open source projects will inherit its license.
Privacy
This repository contains only non-sensitive, publicly available data and information. All material and community participation is covered by the Surveillance Platform Disclaimer and Code of Conduct. For more information about CDC's privacy policy, please visit http://www.cdc.gov/privacy.html.
Contributing
Anyone is encouraged to contribute to the repository by forking and submitting a pull request. (If you are new to GitHub, you might start with a basic tutorial.) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the Apache Software License v2 or later.
All comments, messages, pull requests, and other submissions received through CDC including this GitHub page are subject to the Presidential Records Act and may be archived. Learn more at http://www.cdc.gov/other/privacy.html.
In order to test your changes locally before submitting a pull request, make your changes to src/main.js and app/index.html. Then,
use rollup -c from the root of the project directory. You can then open app/index.html in your browser to test your changes.
Records
This repository is not a source of government records, but is a copy to increase collaboration and collaborative potential. All government records will be published through the CDC web site.
Notices
Please refer to CDC's Template Repository for more information about contributing to this repository, public domain notices and disclaimers, and code of conduct.
Owner
- Name: Centers for Disease Control and Prevention
- Login: CDCgov
- Kind: organization
- Email: data@cdc.gov
- Location: Atlanta, GA
- Website: http://open.cdc.gov/
- Twitter: CDCgov
- Repositories: 114
- Profile: https://github.com/CDCgov
CDC's collaborative software projects to protect America from health, safety, and security threats, both foreign and in the U.S.
GitHub Events
Total
- Issues event: 2
- Watch event: 1
- Delete event: 1
- Issue comment event: 9
- Push event: 1
- Pull request review event: 1
- Pull request event: 7
- Fork event: 4
- Create event: 1
Last Year
- Issues event: 2
- Watch event: 1
- Delete event: 1
- Issue comment event: 9
- Push event: 1
- Pull request review event: 1
- Pull request event: 7
- Fork event: 4
- Create event: 1
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Tony Boyles | A****y@B****c | 141 |
| Danielle Callan | d****n@u****u | 47 |
| Reagan Kelly | r****k@g****m | 7 |
| dependabot[bot] | 4****] | 2 |
| czk2 | c****2@c****v | 2 |
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 45
- Total pull requests: 38
- Average time to close issues: about 1 month
- Average time to close pull requests: 8 months
- Total issue authors: 7
- Total pull request authors: 6
- Average comments per issue: 0.82
- Average comments per pull request: 1.24
- Merged pull requests: 14
- Bot issues: 0
- Bot pull requests: 14
Past Year
- Issues: 2
- Pull requests: 7
- Average time to close issues: 5 months
- Average time to close pull requests: 2 months
- Issue authors: 1
- Pull request authors: 3
- Average comments per issue: 1.5
- Average comments per pull request: 1.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 4
Top Authors
Issue Authors
- AABoyles (24)
- danielhjacobs (2)
- sneurlax (1)
- LB26121 (1)
- MrTomRod (1)
- jaywokim (1)
- ikb6 (1)
Pull Request Authors
- dependabot[bot] (9)
- AABoyles (5)
- d-callan (5)
- snyk-bot (4)
- ms609 (2)
- danielhjacobs (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- npm 82 last-month
- Total dependent packages: 0
- Total dependent repositories: 11
- Total versions: 34
- Total maintainers: 6
npmjs.org: tidytree
Uncompromisingly Flexible Phylogenetic Trees, Powered by D3.js
- Homepage: https://github.com/cdcgov/TidyTree#readme
- License: Apache-2.0
-
Latest release: 0.7.0
published over 2 years ago
Rankings
Dependencies
- @rollup/plugin-node-resolve 9.0.0 development
- @rollup/pluginutils 3.1.0 development
- @types/estree 0.0.39 development
- @types/node 14.14.34 development
- @types/resolve 1.17.1 development
- acorn 7.4.1 development
- builtin-modules 3.2.0 development
- deepmerge 4.2.2 development
- estree-walker 1.0.1 development
- function-bind 1.1.1 development
- has 1.0.3 development
- is-core-module 2.2.0 development
- is-module 1.0.0 development
- path-parse 1.0.6 development
- picomatch 2.2.2 development
- resolve 1.20.0 development
- rollup 1.32.1 development
- commander 2.20.3
- d3 5.16.0
- d3-array 1.2.4
- d3-axis 1.0.12
- d3-brush 1.1.6
- d3-chord 1.0.6
- d3-collection 1.0.7
- d3-color 1.4.1
- d3-contour 1.3.2
- d3-dispatch 1.0.6
- d3-drag 1.2.5
- d3-dsv 1.2.0
- d3-ease 1.0.7
- d3-fetch 1.2.0
- d3-force 1.2.1
- d3-format 1.4.5
- d3-geo 1.12.1
- d3-hierarchy 1.1.9
- d3-interpolate 1.4.0
- d3-path 1.0.9
- d3-polygon 1.0.6
- d3-quadtree 1.0.7
- d3-random 1.1.2
- d3-scale 2.2.2
- d3-scale-chromatic 1.5.0
- d3-selection 1.4.2
- d3-shape 1.3.7
- d3-time 1.1.0
- d3-time-format 2.3.0
- d3-timer 1.0.10
- d3-transition 1.3.2
- d3-voronoi 1.1.4
- d3-zoom 1.8.3
- iconv-lite 0.4.24
- patristic 0.5.7
- rw 1.3.3
- safer-buffer 2.1.2
- @rollup/plugin-node-resolve ^9.0.0 development
- rollup ^1.32.1 development
- d3 ^5.16.0
- patristic ^0.5.7
- actions/checkout v3 composite
- actions/setup-node v3 composite