Encircle Scatterplot with alpha shapes

Using alpha shapes to group or "encircle" sets of points.

It's not fast, but it's fun.

DISCLAIMER: this code is quite hackish, don't copy it blindly.

TODO: buffer the shapes so that they nicely enclose dots as ggplot2's geom_encircle function does.

The scatterplot matrix visualizations pairwise correlations for multi-dimensional data; each cell in the matrix is a scatterplot. This example uses Anderson's data of iris flowers on the Gaspé Peninsula. Scatterplot matrix design invented by J. A. Hartigan; see also R and GGobi. Data on Iris flowers collected by Edgar Anderson and published by Ronald Fisher.

S Forked from mbostock’s Scatterplot Matrix Brushing.

<!DOCTYPE html>
<meta charset="utf-8">
<style>

svg {
  font: 10px sans-serif;
  padding: 10px;
}

.axis,
.frame {
  shape-rendering: crispEdges;
}

.axis line {
  stroke: #ddd;
}

.axis path {
  display: none;
}

.cell text {
  font-weight: bold;
  text-transform: capitalize;
  fill: black;
}

.frame {
  fill: none;
  stroke: #aaa;
}

circle {
  fill-opacity: .7;
}

circle.hidden {
  fill: #ccc !important;
}

.extent {
  fill: #000;
  fill-opacity: .125;
  stroke: #fff;
}

.contour {
    stroke-width: 1.5;
  }
</style>
<body>
<script src="https://d3js.org/d3.v4.min.js"></script>
<script src="https://d3js.org/d3-hexbin.v0.2.min.js"></script>
<script>
  
// Computes boundaries of connected triangles, given an array of triangles.
// Jason Davies - https://bl.ocks.org/jasondavies/1554783
function boundary(mesh) {
  console.log(mesh)
  var counts = {},
      edges = {},
      r,
      result = [];
  // Traverse the edges of all triangles and discard any edges that appear twice.
  mesh.forEach(function(triangle) {
    for (var i = 0; i < 3; i++) {
      var edge = [triangle[i], triangle[(i + 1) % 3]].sort(ascendingCoords).map(String);
      
      (edges[edge[0]] = (edges[edge[0]] || [])).push(edge[1]);
      (edges[edge[1]] = (edges[edge[1]] || [])).push(edge[0]);
      var k = edge.join(":");
      if (counts[k]) delete counts[k];
      else counts[k] = 1;
    }
  });
  while (1) {
    var k = null;
    // Pick an arbitrary starting point on a boundary.
    for (k in counts) break;
    if (k == null) break;
    result.push(r = k.split(":").map(function(d) { return d.split(",").map(Number); }));
    delete counts[k];
    var q = r[1];
    while (q[0] !== r[0][0] || q[1] !== r[0][1]) {
      var p = q,
          qs = edges[p.join(",")],
          n = qs.length;
      for (var i = 0; i < n; i++) {
        q = qs[i].split(",").map(Number);
        var edge = [p, q].sort(ascendingCoords).join(":");
        if (counts[edge]) {
          delete counts[edge];
          r.push(q);
          break;
        }
      }
    }
  }
  return result;
}

function ascendingCoords(a, b) {
  return a[0] === b[0] ? b[1] - a[1] : b[0] - a[0];
}

function encircle_path(points) {
 var a = alphashape(points, 60);
 return a.map(d => d ? "M" + d.join(',') : null)
}
  
  
var width = 960,
    size = 230,
    padding = 20;

var x = d3.scaleLinear()
    .range([padding / 2, size - padding / 2]);

var y = d3.scaleLinear()
    .range([size - padding / 2, padding / 2]);

var xAxis = d3.axisBottom()
    .scale(x)
    .ticks(6);

var yAxis = d3.axisLeft()
    .scale(y)
    .ticks(6);

var color = d3.scaleOrdinal(d3.schemeCategory10);

d3.csv("flowers.csv", function(error, data) {
  if (error) throw error;

var domainByTrait = {},
      traits = d3.keys(data[0]).filter(function(d) { return d !== "species"; }),
      n = traits.length;

traits.forEach(function(trait) {
    domainByTrait[trait] = d3.extent(data, function(d) { return d[trait]; });
  });

xAxis.tickSize(size * n);
  yAxis.tickSize(-size * n);

var brush = d3.brush()
      .on("start", brushstart)
      .on("brush", brushmove)
      .on("end", brushend)
      .extent([[0,0],[size,size]]);

var svg = d3.select("body").append("svg")
      .attr("width", size * n + padding)
      .attr("height", size * n + padding)
    .append("g")
      .attr("transform", "translate(" + padding + "," + padding / 2 + ")");

svg.selectAll(".x.axis")
      .data(traits)
    .enter().append("g")
      .attr("class", "x axis")
      .attr("transform", function(d, i) { return "translate(" + (n - i - 1) * size + ",0)"; })
      .each(function(d) { x.domain(domainByTrait[d]); d3.select(this).call(xAxis); });

svg.selectAll(".y.axis")
      .data(traits)
    .enter().append("g")
      .attr("class", "y axis")
      .attr("transform", function(d, i) { return "translate(0," + i * size + ")"; })
      .each(function(d) { y.domain(domainByTrait[d]); d3.select(this).call(yAxis); });

var cell = svg.selectAll(".cell")
      .data(cross(traits, traits))
    .enter().append("g")
      .attr("class", "cell")
      .attr("transform", function(d) { return "translate(" + (n - d.i - 1) * size + "," + d.j * size + ")"; })
      .each(plot);

// Titles for the diagonal.
  cell.filter(function(d) { return d.i === d.j; }).append("text")
      .attr("x", padding)
      .attr("y", padding)
      .attr("dy", ".71em")
      .text(function(d) { return d.x; });

cell.call(brush);

function plot(p) {
    var cell = d3.select(this);

x.domain(domainByTrait[p.x]);
    y.domain(domainByTrait[p.y]);

cell.append("rect")
        .attr("class", "frame")
        .attr("x", padding / 2)
        .attr("y", padding / 2)
        .attr("width", size - padding)
        .attr("height", size - padding);

cell.selectAll("circle")
        .data(data)
      .enter().append("circle")
        .attr("cx", function(d) { return x(d[p.x]); })
        .attr("cy", function(d) { return y(d[p.y]); })
        .attr("r", 4)
        .style("fill", function(d) { return color(d.species); });

var contours = d3.nest().key(d => d.species).entries(data)
    .map(d => {
      d.path = encircle_path(d.values.map(d => [x(d[p.x]) + Math.random(), y(d[p.y])]));
      return d;
    })
    
    cell.selectAll("path.contour")
    .data(contours, d => d.key)
    .enter()
    .append('path')
    .classed("contour", true)
    .attr('d', d => d.path)
    .attr('stroke', d => color(d.key))
    .attr('fill', d => color(d.key))
    .attr('fill-opacity', 0.3)
  }

var brushCell;

// Clear the previously-active brush, if any.
  function brushstart(p) {
    if (brushCell !== this) {
      d3.select(brushCell).call(brush.move, null);
      brushCell = this;
    x.domain(domainByTrait[p.x]);
    y.domain(domainByTrait[p.y]);
    }
  }

// Highlight the selected circles.
  function brushmove(p) {
    var e = d3.brushSelection(this);
    svg.selectAll("circle").classed("hidden", function(d) {
      return !e
        ? false
        : (
          e[0][0] > x(+d[p.x]) || x(+d[p.x]) > e[1][0]
          || e[0][1] > y(+d[p.y]) || y(+d[p.y]) > e[1][1]
        );
    });

var con = cell.selectAll("path.contour")
    .data((d,i,e) => {
      var c = d3.select(e[i]).selectAll('circle:not(.hidden)');
      var p = d3.select(e[i]).data()[0];
      x.domain(domainByTrait[p.x]);
      y.domain(domainByTrait[p.y]);
      return d3.nest()
        .key(d => d.species)
        .entries(c.data())
        .map(d => {
          d.path = encircle_path(d.values.map(d => [x(d[p.x]) + Math.random(), y(d[p.y])]));
          return d;
        })
    }, d => d.key)
    .attr('d', d => d.path)
      x.domain(domainByTrait[p.x]);
      y.domain(domainByTrait[p.y]);

con.exit().attr('d', null)
  }

// If the brush is empty, select all circles.
  function brushend() {
    var e = d3.brushSelection(this);
    if (e === null) svg.selectAll(".hidden").classed("hidden", false);
  }
});

function cross(a, b) {
  var c = [], n = a.length, m = b.length, i, j;
  for (i = -1; ++i < n;) for (j = -1; ++j < m;) c.push({x: a[i], i: i, y: b[j], j: j});
  return c;
}

</script>

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

https://d3js.org/d3-hexbin.v0.2.min.js