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ideogram

Chromosome visualization with D3.js

1.12.0  •  Updated 6 months ago  •  by Eric Weitz  •  Creative Commons Zero v1.0 Universal

Build Status Coverage Status

Ideogram.js is a JavaScript library for chromosome visualization.

Ideogram supports drawing and animating genome-wide datasets for human, mouse, and many other eukaryotes. The Ideogram API for annotations supports histograms, heatmaps, overlays, and points of arbitrary shape and color layered in tracks. Ideogram can depict haploid, diploid or higher ploidy genomes (e.g. plants), as well as aneuploidy, genetic recombination, and homologous features between chromosomes.

Ideogram can be embedded as a reusable component in any web page or application, and leverages D3.js and SVG to achieve fast, crisp client-side rendering. You can also integrate Ideogram with JavaScript frameworks like Angular, React, and Vue, as well as data science platforms like R and Jupyter Notebook.

All human genes

Check out live examples, get up and running with your own deployment, skim basic usage, or dive into the full API!

A broader overview is also available. It discusses Ideogram’s chromosome biology, technical architecture, and more.

Installation

To link directly to the latest release, copy this snippet:

<script src="https://unpkg.com/ideogram@1.12.0/dist/js/ideogram.min.js"></script>

You can also easily use the library locally:

$ cd <your local web server document root>
$ git clone https://github.com/eweitz/ideogram.git

Then go to http://localhost/ideogram/examples/.

Or, if you use npm:

npm install ideogram

You can then import Ideogram into an application like so:

import Ideogram from 'ideogram';

Usage

<head>
  <script src="https://unpkg.com/ideogram@1.12.0/dist/js/ideogram.min.js"></script>
</head>
<body>
<script>
  var ideogram = new Ideogram({
    organism: 'human',
    annotations: [{
      name: 'BRCA1',
      chr: '17',
      start: 43044294,
      stop: 43125482
    }]
  });
</script>
</body>

Many more usage examples are available at https://eweitz.github.io/ideogram/.

You can also find examples of integrating Ideogram with JavaScript frameworks like Angular, React, and Vue, as well as data science platforms like R and Jupyter Notebook.

API

See the Ideogram API reference for detailed documentation on configuration options and methods.

Popularity

Weekly Downloads
431
Stars
153

Maintenance

Development

Last ver 6 months ago
Created 4 years ago
Last commit 2 months ago
18 hours between commits

Technology

Node version: 10.16.0
19553.6K unpacked

Compliance

Creative Commons Zero v1.0 Universal
Not OSI Approved
0 vulnerabilities

Contributors

4 contributors
Eric Weitz
Maintainer, 1009 commits, 114 merges, 103 PRs
Works at Broad Institute
Manfred Cheung
8 commits, 6 PRs
Matthew Chan
2 commits, 2 PRs
Jim Lund
1 commits, 1 PRs
Lighthouse Bot
Maintainer
Works at GoogleChrome
ProjectProgramAMark
1 PRs

Tags

chromosome
ideogram
cytogenetics
genomics
visualization
d3
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