HiC contact matrix visualization

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Prototype juicebox.js site

The examples/website folder in the juicebox.js GitHub repository contains a prototype website hosting a juicebox instance. To use this code to jumpstart your own page copy the folder, edit the file data/mapMenuData.txt to customize the load menu, and optionally supply a bitly and/or Google apiKey to support sharable URLs (see below). For an example of a production instance using this pattern see http://aidenlab.org/juicebox.

The config object used for initialization in the example:

    var config = {
        mapMenu: {
            id: 'dataset_selector',
            items: 'res/mapMenuData.txt'
        trackMenu: {
            id: 'annotation-selector',
            items: 'https://hicfiles.s3.amazonaws.com/internal/tracksMenu_$GENOME_ID.txt'
        trackMenu2D: {
            id: 'annotation-2D-selector',
            items: 'https://hicfiles.s3.amazonaws.com/internal/tracksMenu_2D.$GENOME_ID.txt'

        // URL shortener(s).  Optional.   If developing on localhost use Google,  otherwise Bitly.  Bitly will not shorten localhost
        // If more than 1 shortener is defined the first is used to shorten URLs
        urlShortener: [
                provider: "bitly",
                apiKey: "ABCD",        // TODO -- replace with your Bitly access token, or function to fetch token
                hostname: 'bit.ly'
                provider: "google",
                apiKey: "ABCD",        // TODO -- replace with your Google API Key, or function to fetch key
                hostname: "goo.gl"

        apiKey: "ABCD",   // Optional.  TODO -- replace with your Google API Key if supporting Google Drive

        embedTarget: "https://igv.org/web/jb/release/1.0.0/site/embed.html"   // "Embed" sharable links will use this url

The mapMenuData.txt file is a tab-delimited list of .hic file - menu label tuples.

A Google API key or Bitly oauth token is required to use the Share button. A Google API key is also required to support GoogleDrive urls. See the Google documentation for instructions on obtaining an API key.

Bootstrap is used for the user controls for loading files and tracks in this prototype site, but Bootstrap is not required for the juicebox.js component. You are free to use any framework or none at all. For more details on juicebox.js dependencies see the page on embedding.

Shareable URLs

The prototype site includes the ability to create shareable URLs. These URLs encapsulate the current state of the juicebox instance. Thes URLs do not expire, and remain valid as long as the underlying website and data are available.

Resources referenced in the URLs can be public or private, and can be protected with oAuth credentials. In the case of private data the receiver of the shareable URL must have access to the resources referenced. If the resources are protected the user must be prompted on the hosting website to sign in with the approriate oAuth provider before the encapsualeted data can be loaded and viewed. Details will vary by provider and website, but see the file oauth.html in our prototype website for an example of sharing URLs using private data on Google Drive.