tsne world

The 800 largest cities in the world. Compute all geodesic distances between them, feed that to t-sne et voilà.

Original work by Philippe Rivière for Visionscarto.net. Comments and variants very welcome!

(Research block at tsne world.)

<!DOCTYPE html>

<body>
<script>
    const width = 960,
        height = 500,
        margin = 40,
        scalepop = d3.scaleSqrt().domain([0, 100000]).range([0.2, 24]),
        scalecountry = d3.scaleOrdinal(d3.schemeCategory20b),
        centerx = d3.scaleLinear()
        .range([width / 2 - height / 2 + margin, width / 2 + height / 2 - margin])
    centery = d3.scaleLinear()
        .range([margin, height - margin]);

d3.csv('cities.csv', function (cities) {

const data = cities
            .sort((a, b) => d3.descending(+a[2015], +b[2015]))
            .map((d, i) => [+d.Longitude, +d.Latitude, d['Urban Agglomeration'], +d[2015], +d['Country Code']])
            .slice(0, 800);

const canvas = d3.select("body").append("canvas")
            .attr("width", width)
            .attr("height", height);

const model = new tsnejs.tSNE({
            dim: 2,
            perplexity: 30,
        });

// initialize data with pairwise distances
        const dists = data.map(d => data.map(e => d3.geoDistance(d, e)));
        model.initDataDist(dists);

const forcetsne = d3.forceSimulation(
          data.map(d => (d.x = width / 2, d.y = height / 2, d))
        )
            .alphaDecay(0.005)
            .alpha(0.1)
            .force('tsne', function (alpha) {
                // every time you call this, solution gets better
                model.step();

// Y is an array of 2-D points that you can plot
                let pos = model.getSolution();

centerx.domain(d3.extent(pos.map(d => d[0])));
                centery.domain(d3.extent(pos.map(d => d[1])));

data.forEach((d, i) => {
                    d.x += alpha * (centerx(pos[i][0]) - d.x);
                    d.y += alpha * (centery(pos[i][1]) - d.y);
                });
            })
            .force('collide', d3.forceCollide().radius(d => 1.5 + scalepop(d[3])))
            .on('tick', function () {

let nodes = data.map((d, i) => {
                    return {
                        x: d.x,
                        y: d.y,
                        r: scalepop(d[3]),
                        color: scalecountry(d[4]),
                    };
                });

draw(canvas, nodes);

});

function draw(canvas, nodes) {
            let context = canvas.node().getContext("2d");
            context.clearRect(0, 0, width, width);

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, node.r, 0, 2 * Math.PI);
                context.lineWidth = 0.5;
                context.fillStyle = node.color;
                context.fill();
            }
        }

});
</script>
</body>

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

https://raw.githack.com/karpathy/tsnejs/master/tsne.js