Just had a brief look over this and have to say I am not a fan. The comments are largely redundant, e.g:

    // Get a reference to the canvas
    canvas = document.getElementById("canvas");

    // Set the canvas size
    canvas.width = 512;
    canvas.height = 512;

And then missing when they could be useful (or a more clear data structure should have been used, e.g. an object with colors as keys):

    var colorMap = [
        255,0  ,0  ,    // Initial symbol color
        0  ,0  ,0  ,    // Black
        255,255,255,    // White
        0  ,255,0  ,    // Green
        0  ,0  ,255,    // Blue
        255,255,0  ,
        0  ,255,255,
        255,0  ,255,
    ];