Template:Heidelberg/pages/software/plasmid

plasmid.js - Interactive plasmids

It is always cubersome to create vector maps, and then putting the static images on the web. We thought it would be a lot more fun to just autogenerate interactive plasmids dynamically from data. That's why we wrote plasmid.js, a JavaScript library to generate interactive vector maps for web pages.

Why should you use it?

It is dead simple to use!

The includes

<script src="jquery.js" type="text/javascript" charset="utf-8"></script>
<scripr src="raphael.js" type="text/javascript" charset="utf-8"></script>
<script src="plasmid.js" type="text/javascript" charset="utf-8"></script>

Or, if you are working with an iGEM Wiki

{{Heidelberg/plasmid.js}}

The placeholders

<div id="canvas"></div>
<div id="info"></div>

The JavaScript

$(function() {
    // You could also load your data via AJAX
    var inserts = [
    {
        size: 40, // Size in angles! (there are 360 of them available)
        color: "#0F0", // You can use any valid css format
        label: "GFP", // The label to display in the legend
        description: "Green Fluorescent Protein", // The description to put in the infobox
        gap: false, // If not given this defaults to true
        promoter: true // This is a promoter, defaults to false
    },
    {
        size: 10,
        color: "#F00",
        label: "Brow Fox",
        description: "He likes jumping over dogs.",
        gap: true
    },
    {
        size: 46,
        color: "#00F",
        label: "Lazy Dog",
        description: "He likes beeing jumped over."
    },
    {
        size: 19,
        color: "#0FF",
        label: "Short one",
        description: "Wirklich, Wirklich kurz nun auch wieder nicht.",
        promoter: true
    },
    {
        size: 1,
        color: "#FF0",
        label: "Even shorter one",
        description: "Und knackig",
        gap: false,
        promoter: true
    }];

    // Required parameters are: id of the canvas, id of the infobox,
    // the inserts and the diameter of the plasmid. Note, that there
    // is spacing and a legend added (default: width + 575, height + 50)
    // These values can be changed easily, see below.
    var plasmid = new Plasmid('canvas', 'info', inserts, 500);
    plasmid.draw();
});

Plus, it also looks great!

Further options

There are two ways to specify optional settings; you can either pass them via the constructor or set the corresponding attributes after the object is created (it's JavaScript, ...). Below you can see a annotated version of the constructor.

function Plasmid(canvas, infobox, inserts, diameter, legendWidth, insertWidth, defaultText, insertBoxAttr, fontSize, spacing, startAngle) {
    // Are all required parameters given?
    // [...]
    this.canvas = canvas; // The id of the canvas placeholder div
    this.inserts = inserts; // The array whith the given inserts (see above)
    this.diameter = diameter; // The diameter of the plasmid, this is *not* the size of the canvas
    this.infobox = infobox; // The id of the infobox to put the descriptions in

    // Set sane defaults for optional parameters
    this.legendWidth = legendWidth || 500; // The width of the legend
    this.radiusOfInsertBox = insertWidth || diameter / 13; // how "thick" the boxes of the inserts are drawn
    this.defaultText = defaultText || "Hover over an insert to get more information!"; // default text in infobox
    this.fontSize = fontSize || 20; // The font size for legend entries
    this.spacing = spacing || 25; // spacing is the number of pixels put above and below the plasmid and left to the legend
    this.startAngle = startAngle || -40; // The angle at which the first plasmid starts
    this.insertBoxAttr = insertBoxAttr || { // The attributes to set on the boxes representing an insert
        stroke: "#666",
        opacity: 0.7,
        "stroke-width": 1,
        "stroke-linejoin": "round"
    };

    // [...]
}