score:2

Accepted answer

The scale you need is an ordinal scale, like this:

var colourScale = d3.scale.ordinal()
    .domain(["Top Level","Second A", "Second B", "Second C", "Second D"])
    .range(["blue","red", "green", "purple", "gold"]);

Then, you can change this whole thing...

.style("fill", function(d) {
    if (d.name == "Top Level") {
        return d._children ? "blue" : "#fff";
    }
    if (d.name == "Second A") {
        return d._children ? "red" : "#fff";
    }
    if (d.name == "Second B") {
        return d._children ? "green" : "#fff";
    }
    if (d.name == "Second C") {
        return d._children ? "purple" : "#fff";
    }
    if (d.name == "Second D") {
        return d._children ? "gold" : "#fff";
    }
})

...into just:

.style("fill", function(d) {
    return colourScale(d.name)
})

And also get rid of that linkColor function.

Pay attention to the fact that, despite you have linked D3 v5 documentation, you're using D3 v3.

Here is your code with that change:

var treeData = [{
  "name": "Top Level",
  "children": [{
    "name": "Second A",
    "children": [{
      "name": "Third A"
    }, {
      "name": "Third B"
    }]
  }, {
    "name": "Second B",
    "children": [{
      "name": "Third C"
    }, {
      "name": "Third D"
    }]
  }, {
    "name": "Second C",
    "children": [{
      "name": "Third E"
    }, {
      "name": "Third F"
    }]
  }, {
    "name": "Second D",
    "children": [{
      "name": "Third G"
    }, {
      "name": "Third H"
    }, ]
  }, ]
}];

var colourScale = d3.scale.ordinal()
  .domain(["Top Level", "Second A", "Second B", "Second C", "Second D"])
  .range(["blue", "red", "green", "purple", "gold"]);


// ************** 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");


// Collapse after the second level
root.children.forEach(collapse);

update(root);

// Collapse the node and all it's children
function collapse(d) {
  if (d.children) {
    d._children = d.children
    d._children.forEach(collapse)
    d.children = null
  }
}

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 ? "#C0C0C0" : "#fff";
    });

  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.depth === 2 ? colourScale(d.parent.name) : colourScale(d.name);
    })
    .style("stroke", function(d) {
      return d.depth === 2 ? colourScale(d.parent.name) : colourScale(d.name);
    });

  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("stroke-width", function(d) {
      return 1;
    })
    .attr("d", function(d) {
      var o = {
        x: source.x0,
        y: source.y0
      };
      return diagonal({
        source: o,
        target: o
      });
    })
    .style("stroke", function(d) {
      return d.target.depth === 2 ? colourScale(d.target.parent.name) : colourScale(d.target.name);
    });

  // Transition links to their new position.
  link.transition()
    .duration(duration)
    .attr("d", diagonal);

  // 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);
}
.node {
  cursor: pointer;
}

.node circle {
  fill: #fff;
  stroke: #C0C0C0;
  stroke-width: 1.5px;
}

.node text {
  font: 10px sans-serif;
}

.link {
  fill: none;
  stroke: #C0C0C0;
  stroke-width: 1.5px;
}
<script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.17/d3.min.js"></script>


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