# ideogram

[Ideogram.js](https://eweitz.github.io/ideogram/) is a JavaScript library for [chromosome visualization](https://speakerdeck.com/eweitz/designing-genome-visualizations-with-ideogramjs).

Ideogram supports drawing and animating genome-wide datasets for [human](https://eweitz.github.io/ideogram/human), [mouse](https://eweitz.github.io/ideogram/mouse), and [many other eukaryotes](https://eweitz.github.io/ideogram/eukaryotes).  The [Ideogram API](https://github.com/eweitz/ideogram/blob/master/api.md) for annotations supports [histograms](https://eweitz.github.io/ideogram/annotations-histogram), [heatmaps](https://eweitz.github.io/ideogram/annotations-heatmap), [overlays](https://eweitz.github.io/ideogram/annotations-overlaid), and points of arbitrary shape and color layered in [tracks](https://eweitz.github.io/ideogram/annotations-tracks). Ideogram can depict haploid, [diploid](https://eweitz.github.io/ideogram/ploidy-basic) or higher ploidy genomes (e.g. plants), as well as aneuploidy, [genetic recombination](https://eweitz.github.io/ideogram/ploidy-recombination), and [homologous features](https://eweitz.github.io/ideogram/homology-basic) between chromosomes.

Ideogram can be embedded as a [reusable component](https://github.com/eweitz/ideogram#usage) 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](https://github.com/eweitz/ideogram/tree/master/examples/angular), [React](https://github.com/eweitz/ideogram/tree/master/examples/react), and [Vue](https://github.com/eweitz/ideogram/tree/master/examples/vue), as well as data science platforms like [R](https://github.com/eweitz/ideogram/tree/master/examples/r) and [Jupyter Notebook](https://github.com/eweitz/ideogram/tree/master/examples/jupyter).

[![All human genes](https://raw.githubusercontent.com/eweitz/ideogram/master/examples/vanilla/ideogram_histogram_all_human_genes.png)](https://eweitz.github.io/ideogram/annotations_histogram.html)

Check out [live examples](https://eweitz.github.io/ideogram/), get [up and running](#installation) with your own deployment, skim [basic usage](#usage), or dive into the [full API](api.md)!

A [broader overview](https://speakerdeck.com/eweitz/ideogramjs-chromosome-visualization-with-javascript) 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://cdn.jsdelivr.net/npm/ideogram@1.44.0/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/](http://localhost/ideogram/examples/).

Or, if you use npm:
```
npm install ideogram
```

You can then [import](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Statements/import) Ideogram into an application like so:
```
import Ideogram from 'ideogram';
```


# Usage
```html
<head>
  <script src="https://cdn.jsdelivr.net/npm/ideogram@1.44.0/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](https://github.com/eweitz/ideogram/tree/master/examples/angular), [React](https://github.com/eweitz/ideogram/tree/master/examples/react), and [Vue](https://github.com/eweitz/ideogram/tree/master/examples/vue), as well as data science platforms like [R](https://github.com/eweitz/ideogram/tree/master/examples/r) and [Jupyter Notebook](https://github.com/eweitz/ideogram/tree/master/examples/jupyter).


# API

See the [Ideogram API reference](api.md) for detailed documentation on configuration options and methods.
