Country Relationships

README.md

This data visualization is part of my Snapstream Searcher project, which searches through closed-captioning television scripts. Countries are considered related if they frequently co-occur, that is, they are mentioned within 300 characters of each other. Some normalization is done to account for the fact that certain countries more frequently than others, so those countries would appear related to other countries by chance.

To cluster the countries, I used a spring embedding algorithm, which places a spring between each pair of countries. If two countries are strongly related, the spring will be shorter. If the two countries are not related at all, the spring will be very long. The layout is calculated by running a steepest gradient descent algorithm to minimize the potential energy of these springs. It's possible that the algorithm gets stuck in a local min, so you may want to reset or randomize the layout a rerun the spring embedding algorithm by clicking on the buttons.

You can see how these relationships change over time by selecting a time period. Each time corresponds to one month of data. Countries that newly appear in the top 25 will be colored in red. The size of each node corresponds to the absolute number of occurrences of that country.

A more in-depth discussion can be found on my blog, Country Relationships and Spring Embedding.

d3.tip.js

// d3.tip
// Copyright (c) 2013 Justin Palmer
//
// Tooltips for d3.js SVG visualizations

(function (root, factory) {
  if (typeof define === 'function' && define.amd) {
    // AMD. Register as an anonymous module with d3 as a dependency.
    define(['d3'], factory)
  } else if (typeof module === 'object' && module.exports) {
    // CommonJS
    module.exports = function(d3) {
      d3.tip = factory(d3)
      return d3.tip
    }
  } else {
    // Browser global.
    root.d3.tip = factory(root.d3)
  }
}(this, function (d3) {

  // Public - contructs a new tooltip
  //
  // Returns a tip
  return function() {
    var direction = d3_tip_direction,
        offset    = d3_tip_offset,
        html      = d3_tip_html,
        node      = initNode(),
        svg       = null,
        point     = null,
        target    = null

    function tip(vis) {
      svg = getSVGNode(vis)
      point = svg.createSVGPoint()
      document.body.appendChild(node)
    }

    // Public - show the tooltip on the screen
    //
    // Returns a tip
    tip.show = function() {
      var args = Array.prototype.slice.call(arguments)
      if(args[args.length - 1] instanceof SVGElement) target = args.pop()

      var content = html.apply(this, args),
          poffset = offset.apply(this, args),
          dir     = direction.apply(this, args),
          nodel   = getNodeEl(),
          i       = directions.length,
          coords,
          scrollTop  = document.documentElement.scrollTop || document.body.scrollTop,
          scrollLeft = document.documentElement.scrollLeft || document.body.scrollLeft

      nodel.html(content)
        .style({ opacity: 1, 'pointer-events': 'all' })

      while(i--) nodel.classed(directions[i], false)
      coords = direction_callbacks.get(dir).apply(this)
      nodel.classed(dir, true).style({
        top: (coords.top +  poffset[0]) + scrollTop + 'px',
        left: (coords.left + poffset[1]) + scrollLeft + 'px'
      })

      return tip
    }

    // Public - hide the tooltip
    //
    // Returns a tip
    tip.hide = function() {
      var nodel = getNodeEl()
      nodel.style({ opacity: 0, 'pointer-events': 'none' })
      return tip
    }

    // Public: Proxy attr calls to the d3 tip container.  Sets or gets attribute value.
    //
    // n - name of the attribute
    // v - value of the attribute
    //
    // Returns tip or attribute value
    tip.attr = function(n, v) {
      if (arguments.length < 2 && typeof n === 'string') {
        return getNodeEl().attr(n)
      } else {
        var args =  Array.prototype.slice.call(arguments)
        d3.selection.prototype.attr.apply(getNodeEl(), args)
      }

      return tip
    }

    // Public: Proxy style calls to the d3 tip container.  Sets or gets a style value.
    //
    // n - name of the property
    // v - value of the property
    //
    // Returns tip or style property value
    tip.style = function(n, v) {
      if (arguments.length < 2 && typeof n === 'string') {
        return getNodeEl().style(n)
      } else {
        var args =  Array.prototype.slice.call(arguments)
        d3.selection.prototype.style.apply(getNodeEl(), args)
      }

      return tip
    }

    // Public: Set or get the direction of the tooltip
    //
    // v - One of n(north), s(south), e(east), or w(west), nw(northwest),
    //     sw(southwest), ne(northeast) or se(southeast)
    //
    // Returns tip or direction
    tip.direction = function(v) {
      if (!arguments.length) return direction
      direction = v == null ? v : d3.functor(v)

      return tip
    }

    // Public: Sets or gets the offset of the tip
    //
    // v - Array of [x, y] offset
    //
    // Returns offset or
    tip.offset = function(v) {
      if (!arguments.length) return offset
      offset = v == null ? v : d3.functor(v)

      return tip
    }

    // Public: sets or gets the html value of the tooltip
    //
    // v - String value of the tip
    //
    // Returns html value or tip
    tip.html = function(v) {
      if (!arguments.length) return html
      html = v == null ? v : d3.functor(v)

      return tip
    }

    // Public: destroys the tooltip and removes it from the DOM
    //
    // Returns a tip
    tip.destroy = function() {
      if(node) {
        getNodeEl().remove();
        node = null;
      }
      return tip;
    }

    function d3_tip_direction() { return 'n' }
    function d3_tip_offset() { return [0, 0] }
    function d3_tip_html() { return ' ' }

    var direction_callbacks = d3.map({
      n:  direction_n,
      s:  direction_s,
      e:  direction_e,
      w:  direction_w,
      nw: direction_nw,
      ne: direction_ne,
      sw: direction_sw,
      se: direction_se
    }),

    directions = direction_callbacks.keys()

    function direction_n() {
      var bbox = getScreenBBox()
      return {
        top:  bbox.n.y - node.offsetHeight,
        left: bbox.n.x - node.offsetWidth / 2
      }
    }

    function direction_s() {
      var bbox = getScreenBBox()
      return {
        top:  bbox.s.y,
        left: bbox.s.x - node.offsetWidth / 2
      }
    }

    function direction_e() {
      var bbox = getScreenBBox()
      return {
        top:  bbox.e.y - node.offsetHeight / 2,
        left: bbox.e.x
      }
    }

    function direction_w() {
      var bbox = getScreenBBox()
      return {
        top:  bbox.w.y - node.offsetHeight / 2,
        left: bbox.w.x - node.offsetWidth
      }
    }

    function direction_nw() {
      var bbox = getScreenBBox()
      return {
        top:  bbox.nw.y - node.offsetHeight,
        left: bbox.nw.x - node.offsetWidth
      }
    }

    function direction_ne() {
      var bbox = getScreenBBox()
      return {
        top:  bbox.ne.y - node.offsetHeight,
        left: bbox.ne.x
      }
    }

    function direction_sw() {
      var bbox = getScreenBBox()
      return {
        top:  bbox.sw.y,
        left: bbox.sw.x - node.offsetWidth
      }
    }

    function direction_se() {
      var bbox = getScreenBBox()
      return {
        top:  bbox.se.y,
        left: bbox.e.x
      }
    }

    function initNode() {
      var node = d3.select(document.createElement('div'))
      node.style({
        position: 'absolute',
        top: 0,
        opacity: 0,
        'pointer-events': 'none',
        'box-sizing': 'border-box'
      })

      return node.node()
    }

    function getSVGNode(el) {
      el = el.node()
      if(el.tagName.toLowerCase() === 'svg')
        return el

      return el.ownerSVGElement
    }

    function getNodeEl() {
      if(node === null) {
        node = initNode();
        // re-add node to DOM
        document.body.appendChild(node);
      };
      return d3.select(node);
    }

    // Private - gets the screen coordinates of a shape
    //
    // Given a shape on the screen, will return an SVGPoint for the directions
    // n(north), s(south), e(east), w(west), ne(northeast), se(southeast), nw(northwest),
    // sw(southwest).
    //
    //    +-+-+
    //    |   |
    //    +   +
    //    |   |
    //    +-+-+
    //
    // Returns an Object {n, s, e, w, nw, sw, ne, se}
    function getScreenBBox() {
      var targetel   = target || d3.event.target;

      while ('undefined' === typeof targetel.getScreenCTM && 'undefined' === targetel.parentNode) {
          targetel = targetel.parentNode;
      }

      var bbox       = {},
          matrix     = targetel.getScreenCTM(),
          tbbox      = targetel.getBBox(),
          width      = tbbox.width,
          height     = tbbox.height,
          x          = tbbox.x,
          y          = tbbox.y

      point.x = x
      point.y = y
      bbox.nw = point.matrixTransform(matrix)
      point.x += width
      bbox.ne = point.matrixTransform(matrix)
      point.y += height
      bbox.se = point.matrixTransform(matrix)
      point.x -= width
      bbox.sw = point.matrixTransform(matrix)
      point.y -= height / 2
      bbox.w  = point.matrixTransform(matrix)
      point.x += width
      bbox.e = point.matrixTransform(matrix)
      point.x -= width / 2
      point.y -= height / 2
      bbox.n = point.matrixTransform(matrix)
      point.y += height
      bbox.s = point.matrixTransform(matrix)

      return bbox
    }

    return tip
  };

}));

graph.js

/*global graphData */
var width = 500, height = 500;
var minSize = 7;
var maxSize = 28;
var minDistance = 80;
var maxDistance = 700;
// we'll binary search for the correct max distance later
var lowerMaxDistance = 200;
var upperMaxDistance = 1000;
var margin = maxSize;
var rightSidebar = d3.select("#graph")
                   .append("div")
                   .attr("id", "rightSidebar");
var svg = d3.select("#graph")
          .append("svg")
          .attr("width", width)
          .attr("height", height);
var drag = d3.behavior.drag()
           .origin(function(d) { return nodeAttr[d.symbol]; })
           .on("dragstart", dragstarted)
           .on("drag", dragged)
           .on("dragend", dragended);
var layoutSelector = rightSidebar.append("div")
                     .attr("id", "layout-selector");
layoutSelector.append("h2").text("Layouts");
layoutSelector.append("button")
.text("Spring Embed")
.attr('disabled', true)
.attr('class', 'layout spring-embed')
.on("click", function() {
  springEmbedLayout({ offset: true }); draw(1000);
});
layoutSelector.append("br");
layoutSelector.append("button")
.text("Random")
.on("click", function() {
  randomLayout(); draw(1000);
});
layoutSelector.append("br");
layoutSelector.append("button")
.text("Reset")
.on("click", function() {
  circularLayout(); draw(1000);
});
var timeSelector = rightSidebar.append("div")
                   .attr("id","time-selector");
timeSelector.append("h2").text("Time");
var timeSelectorForm = timeSelector.append("form")
                       .on("change", timeChange);
var info = rightSidebar.append("div")
           .attr("id", "info");
info.append("h2").text("Description");
info.append("p")
.text('This visualization shows the relationship between nodes. Nodes are considered to be related if they are frequently mentioned together on television. Mouseover nodes and links to see more information about the nodes and how they are related. Nodes can be dragged. ');
info.append("p")
.html('Using <span style="color:#e41a1c">Spring Embed</span> may help you see the relationship more clearly. The algorithm tries to place nodes that are frequently mentioned together close together. The algorithm works by placing a short spring between closely related nodes and a long spring between unrelated nodes. Then, the total potential energy is minimized by applying a steepest gradient descent method iteratively. One may need to click <span style="color:#e41a1c">Random</span> and <span style="color:#e41a1c">Spring Embed</span> a few times before a desirable layout is found. <span style="color:#e41a1c">Reset</span> puts everything back in a circle.');
info.append("p")
.html('By selecting a different time period, one can see how the relationships between nodes change over time.');

var nodeTip = d3.tip()
              .attr('class', 'tip')
              .direction('e')
              .html(function (d) {
                var formatter = d3.format("0.3f");
                var size = d.size;
                size = formatter(size);
                var tip = d.name + '<br>' + '<strong>Size:</strong> <span style="color:#e41a1c">' + size + '</span>';
                if (d.data) {
                  Object.keys(d.data).forEach(function(key) {
                    tip += '<br><strong>' + key + ':</strong> <span style="color:#e41a1c">' + d.data[key] + '</span>';
                  });
                }
                return tip;
              });
var linkTip = d3.tip()
              .attr('class', 'tip')
              .offset(function() {
                return [this.getBBox().height/2, 120];
              })
              .html(function (d) {
                var formatter = d3.format("0.3f");
                var tip = '<span style="color:#e41a1c">' + nodeAttr[d.source].name + '</span><br>'
                        + '<span style="color:#e41a1c">' + nodeAttr[d.target].name + '</span><br>'
                        + '<strong>Distance:</strong> <span style="color:#e41a1c">' + formatter(d.distance) + '</span>';
                if (d.data) {
                  Object.keys(d.data).forEach(function(key) {
                    tip += '<br><strong>' + key + ':</strong> <span style="color:#e41a1c">' + d.data[key] + '</span>';
                  });
                }
                return tip;                
              });

svg.call(nodeTip);
svg.call(linkTip);

var allGraphData, selectedGraphData;
var nodeAttr = {};
var maxLinkDistance, minLinkDistance;
var link = svg.append('g').selectAll('.link.data');
var node = svg.append('g').selectAll('.node.data');
var nodeLabel = svg.append('g').selectAll('.node-label.data');
var fileName = 'graph.json';
d3.json(fileName, function(err, graph) {
  allGraphData = graph;
  setSpringConstant(allGraphData);
  // add times
  if (Array.isArray(allGraphData.nodes) && Array.isArray(allGraphData.links)) {
    // single time
    selectedGraphData = allGraphData;
    timeSelector.style('display', 'none');
  } else {
    // multiple times
    var times = Object.keys(allGraphData);
    times.sort();
    times.forEach(function(time, idx) {
      var timeSelectorRadio = timeSelectorForm.append("input")
                              .attr("type", "radio")
                              .attr("name", "time")
                              .attr("value", time);
      timeSelectorForm.append("span").attr("class", "time-label").text(time);
      if (idx === 0) {
        timeSelectorRadio.attr("checked", true);
        selectedGraphData = allGraphData[time];
      }
      if (idx !== times.length - 1) timeSelectorForm.append("br");
    });
  }  
  initializeGraph(selectedGraphData, {create: true});
});

// draw graph
function draw(duration) {
  duration = typeof duration !== 'undefined' ? duration : 0;
  link.transition().duration(duration)
  .attr("x1", function(d) { return nodeAttr[d.source].x; })
  .attr("y1", function(d) { return nodeAttr[d.source].y; })
  .attr("x2", function(d) { return nodeAttr[d.target].x; })
  .attr("y2", function(d) { return nodeAttr[d.target].y; })
  .style('opacity', 1);
  node.transition().duration(duration)
  .attr("cx", function(d) { return nodeAttr[d.symbol].x; })
  .attr("cy", function(d) { return nodeAttr[d.symbol].y; })
  .attr("r", function(d) { return nodeAttr[d.symbol].r; })
  .style('opacity', 1);
  nodeLabel.transition().duration(duration)
  .attr("x", function(d) { return nodeAttr[d.symbol].x; })
  .attr("y", function(d) { return nodeAttr[d.symbol].y; })
  .style('opacity', 1);
}


// various layouts
function springEmbedLayout(options) {
  options = options || {};
  var nodes = selectedGraphData.nodes.map(function(d) {
                return {x: nodeAttr[d.symbol].x, y: nodeAttr[d.symbol].y, r: nodeAttr[d.symbol].r};
              });
  var links = selectedGraphData.links;
  var n = nodes.length;
  function distance(a, b) {
    return Math.sqrt((a.x - b.x)*(a.x - b.x) + (a.y - b.y)*(a.y - b.y));
  }
  function energy(nodes) {
    var E = 0;
    for (var i = 0; i < n - 1; ++i) {
      for (var j = i+1; j < n; ++j) {
        var diff = distance(nodes[i], nodes[j]) - links[i][j].l;
        E += 0.5*links[i][j].k*diff*diff;
      }
    }
    return E;
  }
  function dEd(idx, f) {
    var res = 0;
    for (var i = 0; i < n; ++i) {
      if (i === idx) continue;
      res += links[idx][i].k*((f(nodes[idx]) - f(nodes[i])) - links[idx][i].l*(f(nodes[idx]) - f(nodes[i]))/distance(nodes[idx], nodes[i]));            
    }

    return res;
  }
  function dEdx(idx) {
    return dEd(idx, function(d) { return d.x; });
  }
  function dEdy(idx) {
    return dEd(idx, function(d) { return d.y; });
  }  
  function gradient() {
    var grad = [];
    for (var i = 0; i < n; ++i) {
      grad.push({x: dEdx(i), y: dEdy(i)});
    }
    return grad;
  }
  function norm(v) {
    var n = 0;
    v.forEach(function(d) {
      n += d.x*d.x + d.y*d.y;
    });
    return Math.sqrt(n);
  }  
  function addVector(v, w, alpha) {
    var u = [];
    for (var i  = 0; i < n; ++i) {
      u.push({x: v[i].x + w[i].x*alpha, y: v[i].y + w[i].y*alpha});
    }
    return u;
  }
  function divideVector(v, alpha) {
    for (var i  = 0; i < n; ++i) {
      v[i].x /= alpha; v[i].y /= alpha;
    }
    return v;
  }
  function setVector(v, w) {
    for (var i = 0; i < n; ++i) {
      v[i].x = w[i].x; v[i].y = w[i].y;
    }
    return v;
  }
  var TOL = 0.001;
  var E = energy(nodes);
  var grad = gradient();
  var gradNorm = norm(grad);
  var done = gradNorm < TOL;
  var iterations = 0;
  while (!done) {
    divideVector(grad, gradNorm); // make a unit vector
    var alpha1 = 0;
    var alpha3 = 1;
    var E3 = energy(addVector(nodes, grad, -alpha3));
    while (E3 >= E) {
      alpha3 /= 2;
      E3 = energy(addVector(nodes, grad, -alpha3));
    }
    var alpha2 = alpha3/2;
    var E2 = energy(addVector(nodes, grad, -alpha2));
    var h1 = (E2 - E)/alpha2;
    var h2 = (E3 - E2)/(alpha3-alpha2);
    var h3 = (h2-h1)/alpha3;
    var alpha0 = (alpha2 - h1/h3)/2;
    var E0 = energy(addVector(nodes, grad, -alpha0));
    var newE, alpha;
    if (E0 < E3) {
      newE = E0; alpha = alpha0;
    } else {
      newE = E3; alpha = alpha3;
    }        
    // reset state
    if (E - newE < TOL) done = true;
    setVector(nodes, addVector(nodes, grad, -alpha));
    E = newE;
    grad = gradient();
    gradNorm = norm(grad);
    if (gradNorm < TOL) done = true;
    iterations += 1;
  }
  // recenter
  var cX = 0; 
  var cY = 0;
  for (var i = 0; i < n; ++i) {
    cX += nodes[i].x;
    cY += nodes[i].y;
  }
  cX /= n; 
  cY /= n;
  var leftOverflow = 0, topOverflow = 0, rightOverflow = 0, bottomOverflow = 0;
  nodes.forEach(function(d) {
    d.x += width/2 - cX;
    d.y += height/2 - cY;
    if (d.x - d.r < 0 && d.r - d.x > leftOverflow) leftOverflow = d.r - d.x;
    if (d.y - d.r < 0 && d.r - d.y > topOverflow) topOverflow = d.r - d.y;
    if (d.x + d.r > width && d.x + d.r - width > rightOverflow) rightOverflow = d.x + d.r - width;
    if (d.y + d.r > height && d.y + d.r - height > bottomOverflow) bottomOverflow = d.y + d.r - height;
  });
  if (options.offset) {
    var leftOffset = rightOverflow === 0 && leftOverflow;
    var topOffset = bottomOverflow === 0 && topOverflow;
    var rightOffset = leftOverflow === 0 && rightOverflow;
    var bottomOffset = topOverflow === 0 && bottomOverflow;
    nodes.forEach(function(d) {
      d.x += leftOffset - rightOffset;
      d.y += topOffset - bottomOffset;
    });
  }
  
  selectedGraphData.nodes.forEach(function(d, idx) {
    var pos = nodeAttr[d.symbol];
    pos.x = nodes[idx].x;
    pos.y = nodes[idx].y;
  });  
  return E;
}

function randomLayout() {
  node.each(function(d) {
    if (!nodeAttr[d.symbol]) nodeAttr[d.symbol] = {};
    var pos = nodeAttr[d.symbol];
    pos.x = margin + Math.random()*(width - 2*margin);
    pos.y = margin + Math.random()*(height - 2*margin);
  });
}

function circularLayout() {
  node.each(function(d, i) {
    if (!nodeAttr[d.symbol]) nodeAttr[d.symbol] = {};
    var pos = nodeAttr[d.symbol];
    pos.x = margin + (width-2*margin)/2*Math.cos(2*Math.PI*i/node[0].length) + (width-2*margin)/2;
    pos.y = margin + (width-2*margin)/2*Math.sin(2*Math.PI*i/node[0].length) + (width-2*margin)/2;
  });
}


// drag handlers
function dragstarted(d) {
  d3.event.sourceEvent.stopPropagation();
  var target = node.filter(function(dd) { return dd.symbol === d.symbol; });
  nodeTip.hide(d, target.node());
}
function dragged(d) {
  var target = node.filter(function(dd) { return dd.symbol === d.symbol; });
  nodeTip.hide(d, target.node());
  var pos = nodeAttr[d.symbol];
  pos.x = d3.event.x;
  pos.y = d3.event.y;
  draw();
}
function dragended(d) {
  var target = node.filter(function(dd) { return dd.symbol === d.symbol; });
  nodeTip.show(d, target.node());
}

function getTimeKey() {
  return timeSelectorForm.selectAll("input")
         .filter(function() { return this.checked === true; })
         .node().value;
}


function timeChange() {
  selectedGraphData = allGraphData[getTimeKey()];
  initializeGraph(selectedGraphData, {update: true});
  draw(1000);
}

function chooseMaxDistance() {
  // save old layout
  var oldLayout = {};
  node.each(function(d) {
    var pos = nodeAttr[d.symbol];
    oldLayout[d.symbol] = {};
    oldLayout[d.symbol].x = pos.x;
    oldLayout[d.symbol].y = pos.y;
  });  
  var lowerBound = lowerMaxDistance;
  var upperBound = upperMaxDistance;
  var distance = lowerBound + Math.floor((upperBound - lowerBound)/2);
  setIdealDistance(distance);
  // binary search to find the first distance that's invalid  
  while (lowerBound < upperBound) {
    if (!isInside()) {
      upperBound = distance;
    } else {
      lowerBound = distance + 1;
    }
    var oldDistance = distance;
    distance = lowerBound + Math.floor((upperBound - lowerBound)/2);
    setIdealDistance(distance);
  } 
  setIdealDistance(distance - 1);
  maxDistance = distance - 1;
  // restore old layout
  node.each(function(d) {
    var pos = nodeAttr[d.symbol];
    pos.x = oldLayout[d.symbol].x;
    pos.y = oldLayout[d.symbol].y;
  });  
  return distance;
  
  function isInside() {
    circularLayout();
    springEmbedLayout();
    return isInsideArea();
  }  
}

function isInsideArea() {
  return selectedGraphData.nodes.every(function(d) {
           var attr = nodeAttr[d.symbol];
           return attr.x >= attr.r && attr.x <= width - attr.r && attr.y >= attr.r && attr.y <= height - attr.r;
         });
}

function setSpringConstant(data) {
  function setSpringConstantHelper(data) {
    data.links.forEach(function(links, i) {
      links.forEach(function(link, j) {
        link.k = link.distance !== 0 ? 1/link.distance : 100;
      });
    });
  }
  if (Array.isArray(data.nodes) && Array.isArray(data.links)) {
    // single time
    setSpringConstantHelper(data);
  } else {
    // multiple times
    Object.keys(data).forEach(function(key) {
      setSpringConstantHelper(data[key]);
    });
  }
}

function setIdealDistance(maxDistance) {
  selectedGraphData.links.forEach(function(d) {
    d.forEach(function(dd) {
      if (maxLinkDistance !== minLinkDistance) {        
        dd.l = minDistance + (maxDistance - minDistance)*(dd.distance-minLinkDistance)/(maxLinkDistance-minLinkDistance);
      } else {
        dd.l = maxDistance;
      }
    });
  }); 
}


function initializeGraph(graph, options) {    
  options = options || {};
  // build link data
  var links = [];
  minLinkDistance = Infinity;
  maxLinkDistance = -1;
  for (var i = 0; i < graph.nodes.length - 1; ++i) {
    for (var j = i + 1; j < graph.nodes.length; ++j) {
      if (options.create || options.update) {
        links.push({source: graph.nodes[i].symbol, target: graph.nodes[j].symbol, distance: graph.links[i][j].distance, 
                    data: graph.links[i][j].data});
      }
      if (graph.links[i][j].distance > maxLinkDistance) maxLinkDistance = graph.links[i][j].distance;
      if (graph.links[i][j].distance < minLinkDistance) minLinkDistance = graph.links[i][j].distance;
    }
  }  
  var minNodeSize = d3.min(graph.nodes, function(d) { return d.size; })
  var maxNodeSize = d3.max(graph.nodes, function(d) { return d.size; })
  graph.nodes.forEach(function(d) {
    if (!nodeAttr[d.symbol]) nodeAttr[d.symbol] = {};
    nodeAttr[d.symbol].name = d.name;
    if (maxNodeSize !== minNodeSize) {
      nodeAttr[d.symbol].r = minSize + (maxSize-minSize)*Math.sqrt((d.size - minNodeSize)/(maxNodeSize-minNodeSize));
    } else {
      nodeAttr[d.symbol].r = maxSize;
    }
  });

  if (options.create || options.update) {
    // don't bother drawing those with max distance, which is 10?
    links = links.filter(function(d) { return d.distance < maxLinkDistance; })
    link = link.data(links, function(d) { return d.source < d.target ? d.source + '-' + d.target : d.target + '-' + d.source; });
    var newLink = link.enter().append("line")
                  .attr("class", function(d, i) {           
                    return "link data " + d.source + " " + d.target;
                  })
                  .on('mouseover', linkTip.show)
                  .on('mouseout', linkTip.hide);
    node = node.data(selectedGraphData.nodes, function(d) { return d.symbol; });
    if (options.update) node.classed('created', false);
    var newNode = node.enter().append("circle")
                  .attr("class", "node data")
                  .on('mouseover', function(d) { 
                    var target = node.filter(function(dd) { return dd.symbol === d.symbol; });
                    nodeTip.show(d, target.node());
                    this.classList.add('hover');
                  })
                  .on('mouseout',  function(d) { 
                    var target = node.filter(function(dd) { return dd.symbol === d.symbol; });
                    nodeTip.hide(d, target.node());
                    this.classList.remove('hover');
                  });
    newNode.call(drag);
    nodeLabel = nodeLabel.data(selectedGraphData.nodes, function(d) { return d.symbol; });
    var newNodeLabel = nodeLabel.enter().append("text")
                       .attr("class", "node-label data")
                       .attr("text-anchor", "middle")
                       .attr("dy", "5px")
                       .text(function(d) { return d.symbol; })
                       .on('mouseover', function(d) {
                         var target = node.filter(function(dd) { return dd.symbol === d.symbol; });
                         target.node().classList.add('hover');
                         nodeTip.show(d, target.node());
                       })
                       .on("mouseout", function(d) {
                         var target = node.filter(function(dd) { return dd.symbol === d.symbol; });
                         target.node().classList.remove('hover');
                         nodeTip.hide(d, target.node());
                       })
                       .call(drag);
    if (options.update) {
      newNode.classed('created', true);
      newLink.style('opacity', 0);
      newNode.style('opacity', 0);
      newNode.each(function(d) {
        var pos = nodeAttr[d.symbol];
        if (!pos.x) pos.x = margin + Math.random()*(width - 2*margin);
        if (!pos.y) pos.y = margin + Math.random()*(height - 2*margin);
      });
      newNodeLabel.style('opacity', 0);
    }    
    link.exit().transition().duration(1000).style('opacity', 0).remove();
    node.exit().transition().duration(1000).style('opacity', 0).remove();
    nodeLabel.exit().transition().duration(1000).style('opacity', 0).remove();    
  }
  if (options.create) { circularLayout(); draw(); } // initial layout
  // normalize length
  d3.select('button.layout.spring-embed')
  .attr('disabled', true);
  var timeout = options.update ? 1000 : 0;
  setTimeout(function() {
    var distance = chooseMaxDistance();
    d3.select('button.layout.spring-embed')
    .attr('disabled', null);
    if (options.create) {
      springEmbedLayout({ offset: true }); draw(1000);      
    }
  }, timeout);
}

function parseQueryString(qs) {
  var urlQuery = {};
  qs.split('&').forEach(function(keyValues) {
    var kvSplit = keyValues.split('=');  
    var key, value;
    try {      
      key = decodeURIComponent(kvSplit[0]);
      value = decodeURIComponent(kvSplit[1]);
    } catch(err) {
      console.error(err);
    }
    urlQuery[key] = value;    
  });
  return urlQuery;
}

graph.json

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