t-SNE, a force, and Urquhart graph

This is a t-SNE representation of an array of (random) circles : red, green, blue, opacity and radius are 5 independent dimensions.

The t-SNE is computed by a javascript worker, using science.ai's implementation.

A force is created that tries to:

follow the positions given by t-SNE
collide the centers.

The result is displayed with an Urquhart graph.

Forked from t-SNE, a force, and voronoi.

<!DOCTYPE html>
<head>
  <meta charset="utf-8">
  <script src="https://d3js.org/d3.v4.min.js"></script>
  <style>
    body { margin:0;position:fixed;top:0;right:0;bottom:0;left:0; }
  </style>
</head>

<body>
  <script> 
const maxIter = 500,
    width = 400,
    x = d3.scaleLinear()
    .domain([-200, 200])
    .range([0, width]),
    area = d3.area()
       .x((d,i) => i)
       .y0(width+90)
       .y1((d,i) => width + 90 - parseInt(3 * d||0));

const data = d3.range(300).map(d => [Math.random(), Math.random(), Math.random(), Math.random(), Math.random()]);

let diagram;

const canvas = d3.select("body").append("canvas")
    .attr("width", width)
    .attr("height", width)
.on('mousemove', function() {
  let m = d3.mouse(this);
  let f = diagram.find(m[0], m[1], 30);
  if (f) {
    let d = data[f.index];
    tip
      .html('['+f.index+'] = ' + d.map(d => Math.round(1000*d)/10).join(', '))
    .style('border', 'solid 2px ' + d3.rgb(d[0]*255,d[1]*255,d[2]*255, 0.3 + 0.7 * d[3]).toString())
    .style('left', m[0] + 'px')
    .style('top', m[1] + 'px')
    ;
  }
  else
    tip    .style('top', '-1000px')

});

const tip = d3.select("body").append("div")
        .style('position', 'absolute');

const context = canvas.node().getContext("2d");

const voronoi = d3.voronoi()
        .x(function (d) {
        return d.x;
    })
    .y(function (d) {
        return d.y;
    });
    
d3.queue()
    .defer(d3.text, 'tsne.min.js')
    .defer(d3.text, 'worker.js')
    .await(function (err, t, w) {

const worker = new Worker(window.URL.createObjectURL(new Blob([t + w], {
            type: "text/javascript"
        })));

let pos = data.map(d => [Math.random() - 0.5, Math.random() - 0.5]);
        let costs = [];
  
        let s = 0, c = 1, a = 0;

// debug: show costs graph
          // cost.attr('d', area(costs));
              context.clearRect(0, 0, width, width);

context.beginPath();
    for (var i = 0, n = links.length; i < n; ++i) {
        var link = links[i],
            dx = link.source.x - link.target.x,
            dy = link.source.y - link.target.y;
        context.moveTo(link.source.x, link.source.y);
        context.lineTo(link.target.x, link.target.y);
    }
    context.strokeStyle = "#eee";
    context.lineWidth = 6;
    context.stroke();
    context.beginPath();
    for (var i = 0, n = links.length; i < n; ++i) {
        var link = links[i],
            dx = link.source.x - link.target.x,
            dy = link.source.y - link.target.y;
        context.moveTo(link.source.x, link.source.y);
        context.lineTo(link.target.x, link.target.y);
    }
    context.strokeStyle = "#000";
    context.lineWidth = 0.5;
    context.stroke();

for (var i = 0, n = nodes.length; i < n; ++i) {
        var node = nodes[i]; 
    context.beginPath();
        context.moveTo(node.x, node.y);
        context.arc(node.x, node.y, 2+3*node.r/4, 0, 2*Math.PI);
    context.lineWidth = 1;
    context.fillStyle = node.color;
    context.fill();
    }
        });

worker.onmessage = function (e) {
            if (e.data.pos) pos = e.data.pos;
            if (e.data.iterations) { 
              costs[e.data.iterations] = e.data.cost;
            }
            if (e.data.stop) { 
              console.log("stopped with message", e.data);
              forcetsne.alphaDecay(0.02);
              worker.terminate();
            }
        };
        worker.postMessage({
            nIter: maxIter,
            // dim: 2,
            perplexity: 20.0,
            // earlyExaggeration: 4.0,
            // learningRate: 100.0,
            metric: 'manhattan', //'euclidean',
            data: data
        });

});

function urquhart(diagram) {
    var urquhart = d3.map();
    diagram.links()
        .forEach(function (link) {
            var v = d3.extent([link.source.index, link.target.index]);
            urquhart.set(v, link);
        });
    urquhart._remove = [];
  
    diagram.triangles()
        .forEach(function (t) {

</script>
</body>

https://d3js.org/d3.v4.min.js