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.node rect {
  stroke: #3d3d3d;
  stroke-width: 3px;
}

.link {
  fill: none;
  stroke: #3d3d3d;
  stroke-width: 2px;
}

<script src="https://cdnjs.cloudflare.com/ajax/libs/d3/4.5.0/d3.min.js"></script>

const data = {
  "name": "Top Level",
  "children": [
    {
      "name": "Level 2: A",
      "children": [
        {
          "name": "Son of A"
        },
        {
          "name": "Son of A"
        },
        {
          "name": "Daughter of A",
          "children": [
            {
              "name": "Grand Son of A"
            }
          ]
        },
        {
          "name": "Daughter of A"
        }
      ]
    },
    {
      "name": "Level 2: B",
      "children": [
        {
          "name": "Son of B"
        }
      ]
    }
  ]
}



function diagonal(s, d) {
  const path = `M ${d.x},
${d.y} C ${d.x},
${(d.y + s.y) / 2} ${s.x},
${(d.y + s.y) / 2} ${s.x},
${s.y}`
  return path
}

// Toggle children on click.
function click(d) {
  if (d.children) {
    d._children = d.children;
    d.children = null;
  } else {
    d.children = d._children;
    d._children = null;
  }
  update(d);
}

function mousedown () {
  d3.event.stopImmediatePropagation();
}

const margin = {top: 20, right: 120, bottom: 20, left: 120},
    width = 1260 - margin.right - margin.left,
    height = 800 - margin.top - margin.bottom;

const duration = 750,
      rectWidth = 30;

let i = 0,
    root;

const tree = d3.tree().size([height, width]);

const svg = d3.select("body").append("svg")
.attr("width", width + margin.right + margin.left)
.attr("height", height + margin.top + margin.bottom)
.call(d3.zoom().scaleExtent([.4, 2]).on("zoom", function () {
  svg.attr("transform", d3.event.transform)
}))
.append("g")
.attr("transform", "translate(" + margin.left + "," + margin.top + ")");

root = d3.hierarchy(data, function (d) {
      return d.children;
    });
root.x0 = height / 2;
root.y0 = 0;

function collapse(d) {
  if (d.children) {
    d._children = d.children;
    d._children.forEach(collapse);
    d.children = null;
  }
}

root.children.forEach(collapse);
update(root);

function update(source) {

  const treeData = tree(root);

  // Compute the new tree layout.
  let nodes = treeData.descendants(),
      links = treeData.descendants().slice(1);

  // Normalize for fixed-depth.
  nodes.forEach(function(d) { d.y = d.depth * 100; });

  // Update the nodes…
  let node = svg.selectAll("g.node")
  .data(nodes, function(d) { return d.id || (d.id = ++i); });

  // Enter any new nodes at the parent's previous position.
  let nodeEnter = node.enter().append("g")
  .attr("cursor", function(d) {
    return d._children || d.children ? 'pointer' : null;
  })
  .attr("class", "node")
  .attr("transform", function() { return "translate(" + source.x0 + "," + source.y0 + ")"; })
  .on("click", click)
  .on("mousedown", mousedown);

  nodeEnter.append("rect")
    .attr("width", rectWidth)
    .attr("height", rectWidth)
    .attr("x", -rectWidth/2)
    .attr("y", -rectWidth/2)
    .style("fill", function(d) { return d._children ? "lightsteelblue" : "#fff"; });

  let nodeUpdate = nodeEnter.merge(node);

  // Transition nodes to their new position.
  nodeUpdate.transition()
    .duration(duration)
    .attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });

  nodeUpdate.select("rect")
    .attr("width", rectWidth)
    .attr("height", rectWidth)
    .attr("x", -rectWidth/2)
    .attr("y", -rectWidth/2)
    .style("fill", function(d) { return d._children ? "lightsteelblue" : "#fff"; });

  // Transition exiting nodes to the parent's new position.
  let nodeExit = node.exit().transition()
  .duration(duration)
  .attr("transform", function(d) { return "translate(" + source.x + "," + source.y + ")"; })
  .remove();

  nodeExit.select("rect")
    .attr("width", 0)
    .attr("height", 0)
    .attr("x", 0)
    .attr("y", 0);

  // Update the links…
  let link = svg.selectAll("path.link")
  .data(links, function(d) { return d.id; });

  // Enter any new links at the parent's previous position.
  const linkEnter = link.enter().insert("path", "g")
  .attr("class", "link")
  .attr("d", function(d) {
    const o = {x: source.x0, y: source.y0};
    return diagonal(o, o);
  });

  let linkUpdate = linkEnter.merge(link);

  // Transition links to their new position.
  linkUpdate.transition()
    .duration(duration)
    .attr("d", function(d){ return diagonal(d, d.parent)});

  // Transition exiting nodes to the parent's new position.
  link.exit().transition()
    .duration(duration)
    .attr("d", function(d) {
    const o = {x: source.x, y: source.y};
    return diagonal(o, o);
  })
    .remove();

  // Stash the old positions for transition.
  nodes.forEach(function(d) {
    d.x0 = d.x;
    d.y0 = d.y;
  });
}