score:2

Accepted answer

Simple styling missing from your chart.

Adding the following to your chart:

path.link {
  fill: none;
  stroke: #CCC;
  stroke-width: 2px;
}

Here's a snippet with the above changes:

var treeData = [
  {
    "name": "Top Level",
    "children": [
      {
        "name": "Level 2: A",
        "children": [
          {
            "name": "Son of A",
          },
          {
            "name": "Daughter of A",
          }
        ]
      },
      {
        "name": "Level 2: B",
      }
    ]
  }
];


// ************** Generate the tree diagram  *****************
var margin = { top: 20, right: 120, bottom: 20, left: 120 },
  width = 960 - margin.right - margin.left,
  height = 500 - margin.top - margin.bottom;

var i = 0,
  duration = 750,
  root;

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

var diagonal = d3.svg.diagonal()
  .projection(function (d) { return [d.y, d.x]; });

var svg = d3.select("body").append("svg")
  .attr("width", width + margin.right + margin.left)
  .attr("height", height + margin.top + margin.bottom)
  .append("g")
  .attr("transform", "translate(" + margin.left + "," + margin.top + ")");

root = treeData[0];
root.x0 = height / 2;
root.y0 = 0;

update(root);

d3.select(self.frameElement).style("height", "500px");

function update(source) {

  // Compute the new tree layout.
  var nodes = tree.nodes(root).reverse(),
    links = tree.links(nodes);

  // Normalize for fixed-depth.
  nodes.forEach(function (d) { d.y = d.depth * 180; });

  // Update the nodes…
  var 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.
  var nodeEnter = node.enter().append("g")
    .attr("class", "node")
    .attr("transform", function (d) { return "translate(" + source.y0 + "," + source.x0 + ")"; })
    .on("click", click);

  nodeEnter.append("circle")
    .attr("r", 1e-6)
    .style("fill", function (d) { return d._children ? "#f1a33a" : "#f95c33"; });

  nodeEnter.append("text")
    .attr("x", function (d) { return d.children || d._children ? -13 : 13; })
    .attr("dy", ".35em")
    .attr("text-anchor", function (d) { return d.children || d._children ? "end" : "start"; })
    .text(function (d) { return d.name; })
    .style("fill-opacity", 1e-6);

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

  nodeUpdate.select("circle")
    .attr("r", 10)
    .style("fill", function (d) { return d._children ? "#f1a33a" : "#f95c33"; });

  nodeUpdate.select("text")
    .style("fill-opacity", 1);

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

  nodeExit.select("circle")
    .attr("r", 1e-6);

  nodeExit.select("text")
    .style("fill-opacity", 1e-6);

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

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

  // Transition links to their new position.
  link.transition()
    .duration(duration)
    .attr("d", diagonal)
    .attr("d", function (d) {
      /* calculating the top shift */
      var source = { x: d.source.x, y: d.source.y };
      var target = { x: d.target.x, y: d.target.y };
      return diagonal({ source: source, target: target });
    });

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

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

// 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);
}
path.link {
  fill: none;
  stroke: #CCC;
  stroke-width: 2px;
}
<script src="https://d3js.org/d3.v3.min.js"></script>

score:0

you have to set the fill attribute of the link.path to none and stroke width

link.path{
   fill: none;
   stroke: #000000;
   stroke-width: 1;
}

The easier way is to use a library, here is an example with balkangraph

enter image description here

It is exactly what you want

score:2

var treeData = [
  {
    "name": "Top Level",
    "children": [
      {
        "name": "Level 2: A",
        "children": [
          {
            "name": "Son of A",
          },
          {
            "name": "Daughter of A",
          }
        ]
      },
      {
        "name": "Level 2: B",
      }
    ]
  }
];


// ************** Generate the tree diagram  *****************
var margin = { top: 20, right: 120, bottom: 20, left: 120 },
  width = 960 - margin.right - margin.left,
  height = 500 - margin.top - margin.bottom;

var i = 0,
  duration = 750,
  root;

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

var diagonal = d3.svg.diagonal()
  .projection(function (d) { return [d.y, d.x]; });

var svg = d3.select("body").append("svg")
  .attr("width", width + margin.right + margin.left)
  .attr("height", height + margin.top + margin.bottom)
  .append("g")
  .attr("transform", "translate(" + margin.left + "," + margin.top + ")");

root = treeData[0];
root.x0 = height / 2;
root.y0 = 0;

update(root);

d3.select(self.frameElement).style("height", "500px");

function update(source) {

  // Compute the new tree layout.
  var nodes = tree.nodes(root).reverse(),
    links = tree.links(nodes);

  // Normalize for fixed-depth.
  nodes.forEach(function (d) { d.y = d.depth * 180; });

  // Update the nodes…
  var 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.
  var nodeEnter = node.enter().append("g")
    .attr("class", "node")
    .attr("transform", function (d) { return "translate(" + source.y0 + "," + source.x0 + ")"; })
    .on("click", click);

  nodeEnter.append("circle")
    .attr("r", 1e-6)
    .style("fill", function (d) { return d._children ? "#f1a33a" : "#f95c33"; });

  nodeEnter.append("text")
    .attr("x", function (d) { return d.children || d._children ? -13 : 13; })
    .attr("dy", ".35em")
    .attr("text-anchor", function (d) { return d.children || d._children ? "end" : "start"; })
    .text(function (d) { return d.name; })
    .style("fill-opacity", 1e-6);

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

  nodeUpdate.select("circle")
    .attr("r", 10)
    .style("fill", function (d) { return d._children ? "#f1a33a" : "#f95c33"; });

  nodeUpdate.select("text")
    .style("fill-opacity", 1);

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

  nodeExit.select("circle")
    .attr("r", 1e-6);

  nodeExit.select("text")
    .style("fill-opacity", 1e-6);

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

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

  // Transition links to their new position.
  link.transition()
    .duration(duration)
    .attr("d", diagonal)
    .attr("d", function (d) {
      /* calculating the top shift */
      var source = { x: d.source.x, y: d.source.y };
      var target = { x: d.target.x, y: d.target.y };
      return diagonal({ source: source, target: target });
    });

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

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

// 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);
}
path.link {
  fill: none;
  stroke: #CCC;
  stroke-width: 2px;
}
<script src="https://d3js.org/d3.v3.min.js"></script>


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