t-SNE with Levenshtein distances, colored by K-means (work in progress)

800 city names, grouped according to their first 4 letters:

Levenshtein-based distance
t-SNE

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

Forked from tsne world

forked from Fil's block: t-SNE with Levenshtein distances

<!DOCTYPE html>

<body>
<script>
    const width = 960,
        height = 500,
        margin = { top: 40, bottom: 40, left: 140, right: 140 },
        scalepop = d3.scaleSqrt().domain([0, 100000]).range([0.2, 28]),
        scalecountry = d3.scaleOrdinal(
          d3.merge([d3.schemeCategory20b, d3.schemeCategory20c])),
        centerx = d3.scaleLinear()
        .range([margin.left, width - margin.right]),
        centery = d3.scaleLinear()
        .range([margin.top, height - margin.bottom]);

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

const data = cities
            .sort((a, b) => d3.descending(+a[2015], +b[2015]))
            .map((d, i) => {
              return {
                lon: +d.Longitude,
                lat: +d.Latitude,
                name: d['Urban Agglomeration'],
                r: scalepop(+d[2015]),
                //color: scalecountry(+d['Country Code'])
              };
            })
            .slice(0, 800);

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

// pos is the array of positions that will be updated by the tsne worker
        // start with the geographic coordinates as is (plate-carrée)
        // random or [0,0] is fine too
        let pos = data.map(d => [d.lon, -d.lat]); 
      
      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) {

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

data.forEach((d, i) => {
                    d.vx += alpha * (centerx(pos[i][0]) - d.x);
                    d.vy += alpha * (centery(pos[i][1]) - d.y);
                    d.color = scalecountry(pos[i][2]);
                });
            })
            .force('collide', d3.forceCollide().radius(d => 1.5 + d.r))
            .on('tick', function () {

// drawcanvas(canvas, data);
              drawsvg(svg, data);

});

function drawcanvas(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();
            }
        }

function drawsvg(svg, nodes) {
          const g = svg.selectAll('g.city')
          .data(nodes);
          
          var enter = g.enter().append('g').classed('city', true);

enter.append('circle')
          .attr('r', d => d.r)
          //.attr('fill', d => d.color)
          .append('title')
          .text(d => d.name); 
          
          enter
          .filter(d => d.r > 6)
          .append('text')
          .attr('fill', 'white')
          .style('font-size', d => d.r > 9 ? '12px' : '9px')
          .attr('text-anchor', 'middle')
          .attr('dominant-baseline', 'middle')
          .attr('pointer-events', 'none')
          .text(d => d.name.substring(0,2));
          
          g
          .attr('fill', d => d.color)
          .attr('transform', d => `translate(${d.x},${d.y})`);

}

d3.queue()
    .defer(d3.text, 'tsne.js')
    .defer(d3.text, 'worker.js')
    .awaitAll(function (err, scripts) {

const worker = new Worker(
      window.URL.createObjectURL(
        new Blob(scripts, {
          type: "text/javascript"
        })
      )
    );
  
  worker.postMessage({
      maxIter: 10,
      dim: 2,
      perplexity: 30.0,
      data: data
  });

worker.onmessage = function (e) {
    if (e.data.log) console.log.apply(this, e.data.log);
    if (e.data.pos) pos = e.data.pos;

if (e.data.done && e.data.done < 10000  && e.data.cost > 1e-2) {
      worker.postMessage({
            maxIter: e.data.done + 10,
      });
    }
  };
});
      
    });
</script>
</body>

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