LogosJ: Embeddable SVG Sequence Logos
LogosJ is a Javascipt package for creating SVG sequence logos. LogosJ supports a wide range of biological use cases. This README provides a quick overview of LogosJ installation and usage. For detailed examples with code samples are available at our companion site and documentation at GitHub Pages.
LogosJ can be used with and without ReactJS. A companion web app makes it easy to share SVG logos and generate them in batches from the output of common tools such as the MEME Suite.
Using in your web application
You can add LogosJ to your project using NPM or Yarn:
yarn add logosj-reactor
npm install logosj-reactIf you want to use LogosJ in a static web page, you can simply include the package with a
static script tag, which will add LogosJ to the global namespace as logosj:
<script src="https://bundle.logosj.wenglab.org/bundle.js" type="text/javascript">
</script>Quick example: a DNA logo
The transcription factor CTCF binds a well-known consensus DNA sequence, rendered below with LogosJ:
If you use ReactJS, the following code creates the CTCF consensus binding logo:
import { DNALogo } from 'logosj-react';
const CTCF_PPM = [
[0.09, 0.31, 0.08, 0.50], [0.18, 0.15, 0.45, 0.20], [0.30, 0.05, 0.49, 0.14],
[0.06, 0.87, 0.02, 0.03], [0.00, 0.98, 0.00, 0.02], [0.81, 0.01, 0.07, 0.09],
[0.04, 0.57, 0.36, 0.01], [0.11, 0.47, 0.05, 0.35], [0.93, 0.01, 0.03, 0.01],
[0.00, 0.00, 0.99, 0.01], [0.36, 0.00, 0.64, 0.00], [0.05, 0.01, 0.55, 0.37],
[0.03, 0.00, 0.97, 0.00], [0.06, 0.00, 0.85, 0.07], [0.11, 0.80, 0.00, 0.07],
[0.40, 0.01, 0.55, 0.01], [0.09, 0.53, 0.33, 0.04], [0.12, 0.35, 0.08, 0.43],
[0.44, 0.19, 0.29, 0.06]
];
export const CTCFLogo = props => (
<DNALogo ppm={CTCF_PPM} />
);If you don't use React, the following code embeds the DNA logo in a div element:
<!doctype html>
<html>
<body>
<script src="https://bundle.logosj.wenglab.org/bundle.js" type="text/javascript"></script>
<div id="logo" style="width:500px"></div>
<script type="text/javascript">
const CTCF_PPM = [
[0.09, 0.31, 0.08, 0.50], [0.18, 0.15, 0.45, 0.20], [0.30, 0.05, 0.49, 0.14],
[0.06, 0.87, 0.02, 0.03], [0.00, 0.98, 0.00, 0.02], [0.81, 0.01, 0.07, 0.09],
[0.04, 0.57, 0.36, 0.01], [0.11, 0.47, 0.05, 0.35], [0.93, 0.01, 0.03, 0.01],
[0.00, 0.00, 0.99, 0.01], [0.36, 0.00, 0.64, 0.00], [0.05, 0.01, 0.55, 0.37],
[0.03, 0.00, 0.97, 0.00], [0.06, 0.00, 0.85, 0.07], [0.11, 0.80, 0.00, 0.07],
[0.40, 0.01, 0.55, 0.01], [0.09, 0.53, 0.33, 0.04], [0.12, 0.35, 0.08, 0.43],
[0.44, 0.19, 0.29, 0.06]
];
logosj.embedDNALogo(document.getElementById("logo"), { ppm: CTCF_PPM });
</script>
</body>
</html>