50000 points

<!DOCTYPE html>
<html>
  <head>
    <meta charset="utf-8">
    <meta name="viewport" content="width=device-width">

<title>Large number of points</title>

font-family: "Open Sans";
        font-size: 14px;
      }
      td {
        text-align: center;
      }
      .entry {
        width: 150px;
        text-align: center;
        padding: 3px 0px 3px 0px;
        font-weight: bold;
      }
    </style>
    <script>
      var points = [];
      var margin = {};
      var xLinear;
      var yLinear;
      var quantLo;
      var quantHi;
      var colorLo;
      var colorCore;
      var colorHi;
      var radiusLo;
      var radiusCore;
      var radiusHi;
      var yLo;
      var yHi;

Math.nrand = function() {
        var x1, x2, rad, y1;
        do {
          x1 = 2 * this.random() - 1;
          x2 = 2 * this.random() - 1;
          rad = x1 * x1 + x2 * x2;
        } while (rad >= 1 || rad == 0);
        var c = this.sqrt(-2 * Math.log(rad) / rad);
        return ( x1 * c ) + 50;
      }

document.addEventListener("DOMContentLoaded", function() {
        // Generate points
        generatePoints();

// Data needs to be sorted before we can calculate quantile values
        points.sort(function(a,b) {
          return parseFloat(a[1]) - parseFloat(b[1]);
        });

// Setup margin values for charts
        margin.width = 960;
        margin.height = 300;
        margin.paddingLeft = 1;
        margin.paddingRight = 1;
        margin.paddingTop = 1;
        margin.paddingBottom = 1;

recalculate();
      });

function recalculate() {
        quantLo = parseFloat(document.getElementById("qLo").textContent) / 100;
        quantHi = parseFloat(document.getElementById("qHi").textContent) / 100;
        colorLo = document.getElementById("cLo").textContent;
        colorCore = document.getElementById("cCore").textContent;
        colorHi = document.getElementById("cHi").textContent;
        radiusLo = parseFloat(document.getElementById("rLo").textContent);
        radiusCore = parseFloat(document.getElementById("rCore").textContent);
        radiusHi = parseFloat(document.getElementById("rHi").textContent);
        yLo = parseFloat(document.getElementById("yLo").textContent);
        yHi = parseFloat(document.getElementById("yHi").textContent);
        createScales();
        render();
      }

function generatePoints() {
        for (var i = 0; i < 50000; i++) {
          points.push([(i % 10000),Math.nrand()]);
        }
      }

function createScales() {
        // Setup scales
        xLinear = d3.scaleLinear()
          .domain([0, 10000])
          .range([ margin.paddingLeft, ( margin.width - margin.paddingRight)])
          .nice();
        yLinear = d3.scaleLinear()
          .domain([yLo,yHi])
          .range([(margin.height - margin.paddingBottom), margin.paddingTop])
          .nice();
      }

function render() {
        var qlo = d3.quantile(points, quantLo, function(d) { return parseFloat(d[1]); });
        var qhi = d3.quantile(points, quantHi, function(d) { return parseFloat(d[1]); });
        
        var scatter = d3.select("svg")
          .selectAll("circle")
          .data(points);

scatter
          .exit()
            .remove();

scatter
          .enter()
          .append("circle")
          .merge(scatter)
          .transition(d3.transition().duration(750))
            .attr("cx", function (d) { return xLinear(d[0]); })
            .attr("cy", function (d) { return yLinear(d[1]); })
            .attr("fill", function (d) { 
              if (qlo >= d[1]) {
                return colorLo;
              } else if (qhi <= d[1]) {
                return colorHi;
              }
              return colorCore;
            })
            .attr("r", function (d) {
              if (qlo >= d[1]) {
                return radiusLo;
              } else if (qhi <= d[1]) {
                return radiusHi;
              }
              return radiusCore;
            });
      }
    </script>
  </head>
  <body>
    <svg width="960" height="300"></svg>
    <div id="controls">
      <table>
        <tr>
          <td></td>
          <td>Low</td>
          <td>Core</td>
          <td>High</td>
          <td></td>
        </tr>
        <tr>
          <td>Quantile</td>
          <td><div class="entry" id="qLo" contenteditable="true">25.0</div></td>
          <td></td>
          <td><div class="entry" id="qHi" contenteditable="true">75.0</div></td>
        </tr>
        <tr>
          <td>Color</td>
          <td><div class="entry" id="cLo" contenteditable="true">rgba( 255, 0, 0, 1.0 )</div></td>
          <td><div class="entry" id="cCore" contenteditable="true">rgba( 0, 0, 255, 0.1 )</div></td>
          <td><div class="entry" id="cHi" contenteditable="true">rgba( 255, 0, 0, 1.0 )</div></td>
        </tr>
        <tr>
          <td>Radius</td>
          <td><div class="entry" id="rLo" contenteditable="true">1</div></td>
          <td><div class="entry" id="rCore" contenteditable="true">1</div></td>
          <td><div class="entry" id="rHi" contenteditable="true">1</div></td>
        </tr>
        <tr>
          <td>Y Range (from-to)</td>
          <td><div class="entry" id="yLo" contenteditable="true">45</div></td>
          <td><div class="entry" id="yHi" contenteditable="true">55</div></td>
          <td></td>
        </tr>
      </table>
      <button onclick="recalculate()">Refresh</button>
    </div>
  </body>
</html>

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