I am trying to use d3 as a tool for presenting biological data.
I am trying to open the following example in my Chrome browser so that I can understand how it works. Unfortunately, I get the following error message "Uncaught TypeError: Unable to read the properties of children from undefined."
http://bl.ocks.org/4063550
If you click the link, the source code for the .html and .json file will be displayed below the visualization results. Obviously, visualization works on the above page. I'm not sure what I can do wrong.
I copied the index.html file and the flare.json file to a directory on the web server. If I tried to download it from a local file, I got another error: XMLHttpRequest could not load the file: /// C: / Users / (..omitted ..) /flare.json. Cross-start requests are only supported for HTTP.
The flare.json file can indeed be downloaded from the web server (I can see its text content). It contains tree data that I am trying to execute.
Obviously, the flare.json file starts as follows:
{ "name": "flare", "children": [ ...
Unfortunately, d3.json has problems analyzing this information ...
If this helps, here is the .html file I'm trying to open in Chrome:
<!DOCTYPE html> <html> <head> <title>heirarchical graph</title> <meta charset="utf-8"> <style> .node circle { fill: #fff; stroke: steelblue; stroke-width: 1.5px; } .node { font: 10px sans-serif; } .link { fill: none; stroke: #ccc; stroke-width: 1.5px; } </style> <script type="text/javascript" src="https://raw.github.com/mbostock/d3/master/d3.v2.min.js"> </script> </head> <body> <script> var diameter = 960; var tree = d3.layout.tree() .size([360, diameter / 2 - 120]) .separation(function(a, b) { return (a.parent == b.parent ? 1 : 2) / a.depth; }); var diagonal = d3.svg.diagonal.radial() .projection(function(d) { return [dy, dx / 180 * Math.PI]; }); var svg = d3.select("body").append("svg") .attr("width", diameter) .attr("height", diameter - 150) .append("g") .attr("transform", "translate(" + diameter / 2 + "," + diameter / 2 + ")"); d3.json("flare.json", function(error, root) { var nodes = tree.nodes(root), links = tree.links(nodes); var link = svg.selectAll(".link") .data(links) .enter().append("path") .attr("class", "link") .attr("d", diagonal); var node = svg.selectAll(".node") .data(nodes) .enter().append("g") .attr("class", "node") .attr("transform", function(d) { return "rotate(" + (dx - 90) + ")translate(" + dy + ")"; }) node.append("circle") .attr("r", 4.5); node.append("text") .attr("dy", ".31em") .attr("text-anchor", function(d) { return dx < 180 ? "start" : "end"; }) .attr("transform", function(d) { return dx < 180 ? "translate(8)" : "rotate(180)translate(-8)"; }) .text(function(d) { return d.name; }); }); d3.select(self.frameElement).style("height", diameter - 150 + "px"); </script> </body> </html>
And here is the flare.json file:
{ "name": "flare", "children": [ { "name": "analytics", "children": [ { "name": "cluster", "children": [ {"name": "AgglomerativeCluster", "size": 3938}, {"name": "CommunityStructure", "size": 3812}, {"name": "HierarchicalCluster", "size": 6714}, {"name": "MergeEdge", "size": 743} ] }, { "name": "graph", "children": [ {"name": "BetweennessCentrality", "size": 3534}, {"name": "LinkDistance", "size": 5731}, {"name": "MaxFlowMinCut", "size": 7840}, {"name": "ShortestPaths", "size": 5914}, {"name": "SpanningTree", "size": 3416} ] }, { "name": "optimization", "children": [ {"name": "AspectRatioBanker", "size": 7074} ] } ] }, { "name": "animate", "children": [ {"name": "Easing", "size": 17010}, {"name": "FunctionSequence", "size": 5842}, { "name": "interpolate", "children": [ {"name": "ArrayInterpolator", "size": 1983}, {"name": "ColorInterpolator", "size": 2047}, {"name": "DateInterpolator", "size": 1375}, {"name": "Interpolator", "size": 8746}, {"name": "MatrixInterpolator", "size": 2202}, {"name": "NumberInterpolator", "size": 1382}, {"name": "ObjectInterpolator", "size": 1629}, {"name": "PointInterpolator", "size": 1675}, {"name": "RectangleInterpolator", "size": 2042} ] }, {"name": "ISchedulable", "size": 1041}, {"name": "Parallel", "size": 5176}, {"name": "Pause", "size": 449}, {"name": "Scheduler", "size": 5593}, {"name": "Sequence", "size": 5534}, {"name": "Transition", "size": 9201}, {"name": "Transitioner", "size": 19975}, {"name": "TransitionEvent", "size": 1116}, {"name": "Tween", "size": 6006} ] }, { "name": "data", "children": [ { "name": "converters", "children": [ {"name": "Converters", "size": 721}, {"name": "DelimitedTextConverter", "size": 4294}, {"name": "GraphMLConverter", "size": 9800}, {"name": "IDataConverter", "size": 1314}, {"name": "JSONConverter", "size": 2220} ] }, {"name": "DataField", "size": 1759}, {"name": "DataSchema", "size": 2165}, {"name": "DataSet", "size": 586}, {"name": "DataSource", "size": 3331}, {"name": "DataTable", "size": 772}, {"name": "DataUtil", "size": 3322} ] }, { "name": "display", "children": [ {"name": "DirtySprite", "size": 8833}, {"name": "LineSprite", "size": 1732}, {"name": "RectSprite", "size": 3623}, {"name": "TextSprite", "size": 10066} ] }, { "name": "flex", "children": [ {"name": "FlareVis", "size": 4116} ] }, { "name": "physics", "children": [ {"name": "DragForce", "size": 1082}, {"name": "GravityForce", "size": 1336}, {"name": "IForce", "size": 319}, {"name": "NBodyForce", "size": 10498}, {"name": "Particle", "size": 2822}, {"name": "Simulation", "size": 9983}, {"name": "Spring", "size": 2213}, {"name": "SpringForce", "size": 1681} ] }, { "name": "query", "children": [ {"name": "AggregateExpression", "size": 1616}, {"name": "And", "size": 1027}, {"name": "Arithmetic", "size": 3891}, {"name": "Average", "size": 891}, {"name": "BinaryExpression", "size": 2893}, {"name": "Comparison", "size": 5103}, {"name": "CompositeExpression", "size": 3677}, {"name": "Count", "size": 781}, {"name": "DateUtil", "size": 4141}, {"name": "Distinct", "size": 933}, {"name": "Expression", "size": 5130}, {"name": "ExpressionIterator", "size": 3617}, {"name": "Fn", "size": 3240}, {"name": "If", "size": 2732}, {"name": "IsA", "size": 2039}, {"name": "Literal", "size": 1214}, {"name": "Match", "size": 3748}, {"name": "Maximum", "size": 843}, { "name": "methods", "children": [ {"name": "add", "size": 593}, {"name": "and", "size": 330}, {"name": "average", "size": 287}, {"name": "count", "size": 277}, {"name": "distinct", "size": 292}, {"name": "div", "size": 595}, {"name": "eq", "size": 594}, {"name": "fn", "size": 460}, {"name": "gt", "size": 603}, {"name": "gte", "size": 625}, {"name": "iff", "size": 748}, {"name": "isa", "size": 461}, {"name": "lt", "size": 597}, {"name": "lte", "size": 619}, {"name": "max", "size": 283}, {"name": "min", "size": 283}, {"name": "mod", "size": 591}, {"name": "mul", "size": 603}, {"name": "neq", "size": 599}, {"name": "not", "size": 386}, {"name": "or", "size": 323}, {"name": "orderby", "size": 307}, {"name": "range", "size": 772}, {"name": "select", "size": 296}, {"name": "stddev", "size": 363}, {"name": "sub", "size": 600}, {"name": "sum", "size": 280}, {"name": "update", "size": 307}, {"name": "variance", "size": 335}, {"name": "where", "size": 299}, {"name": "xor", "size": 354}, {"name": "_", "size": 264} ] }, {"name": "Minimum", "size": 843}, {"name": "Not", "size": 1554}, {"name": "Or", "size": 970}, {"name": "Query", "size": 13896}, {"name": "Range", "size": 1594}, {"name": "StringUtil", "size": 4130}, {"name": "Sum", "size": 791}, {"name": "Variable", "size": 1124}, {"name": "Variance", "size": 1876}, {"name": "Xor", "size": 1101} ] }, { "name": "scale", "children": [ {"name": "IScaleMap", "size": 2105}, {"name": "LinearScale", "size": 1316}, {"name": "LogScale", "size": 3151}, {"name": "OrdinalScale", "size": 3770}, {"name": "QuantileScale", "size": 2435}, {"name": "QuantitativeScale", "size": 4839}, {"name": "RootScale", "size": 1756}, {"name": "Scale", "size": 4268}, {"name": "ScaleType", "size": 1821}, {"name": "TimeScale", "size": 5833} ] }, { "name": "util", "children": [ {"name": "Arrays", "size": 8258}, {"name": "Colors", "size": 10001}, {"name": "Dates", "size": 8217}, {"name": "Displays", "size": 12555}, {"name": "Filter", "size": 2324}, {"name": "Geometry", "size": 10993}, { "name": "heap", "children": [ {"name": "FibonacciHeap", "size": 9354}, {"name": "HeapNode", "size": 1233} ] }, {"name": "IEvaluable", "size": 335}, {"name": "IPredicate", "size": 383}, {"name": "IValueProxy", "size": 874}, { "name": "math", "children": [ {"name": "DenseMatrix", "size": 3165}, {"name": "IMatrix", "size": 2815}, {"name": "SparseMatrix", "size": 3366} ] }, {"name": "Maths", "size": 17705}, {"name": "Orientation", "size": 1486}, { "name": "palette", "children": [ {"name": "ColorPalette", "size": 6367}, {"name": "Palette", "size": 1229}, {"name": "ShapePalette", "size": 2059}, {"name": "SizePalette", "size": 2291} ] }, {"name": "Property", "size": 5559}, {"name": "Shapes", "size": 19118}, {"name": "Sort", "size": 6887}, {"name": "Stats", "size": 6557}, {"name": "Strings", "size": 22026} ] }, { "name": "vis", "children": [ { "name": "axis", "children": [ {"name": "Axes", "size": 1302}, {"name": "Axis", "size": 24593}, {"name": "AxisGridLine", "size": 652}, {"name": "AxisLabel", "size": 636}, {"name": "CartesianAxes", "size": 6703} ] }, { "name": "controls", "children": [ {"name": "AnchorControl", "size": 2138}, {"name": "ClickControl", "size": 3824}, {"name": "Control", "size": 1353}, {"name": "ControlList", "size": 4665}, {"name": "DragControl", "size": 2649}, {"name": "ExpandControl", "size": 2832}, {"name": "HoverControl", "size": 4896}, {"name": "IControl", "size": 763}, {"name": "PanZoomControl", "size": 5222}, {"name": "SelectionControl", "size": 7862}, {"name": "TooltipControl", "size": 8435} ] }, { "name": "data", "children": [ {"name": "Data", "size": 20544}, {"name": "DataList", "size": 19788}, {"name": "DataSprite", "size": 10349}, {"name": "EdgeSprite", "size": 3301}, {"name": "NodeSprite", "size": 19382}, { "name": "render", "children": [ {"name": "ArrowType", "size": 698}, {"name": "EdgeRenderer", "size": 5569}, {"name": "IRenderer", "size": 353}, {"name": "ShapeRenderer", "size": 2247} ] }, {"name": "ScaleBinding", "size": 11275}, {"name": "Tree", "size": 7147}, {"name": "TreeBuilder", "size": 9930} ] }, { "name": "events", "children": [ {"name": "DataEvent", "size": 2313}, {"name": "SelectionEvent", "size": 1880}, {"name": "TooltipEvent", "size": 1701}, {"name": "VisualizationEvent", "size": 1117} ] }, { "name": "legend", "children": [ {"name": "Legend", "size": 20859}, {"name": "LegendItem", "size": 4614}, {"name": "LegendRange", "size": 10530} ] }, { "name": "operator", "children": [ { "name": "distortion", "children": [ {"name": "BifocalDistortion", "size": 4461}, {"name": "Distortion", "size": 6314}, {"name": "FisheyeDistortion", "size": 3444} ] }, { "name": "encoder", "children": [ {"name": "ColorEncoder", "size": 3179}, {"name": "Encoder", "size": 4060}, {"name": "PropertyEncoder", "size": 4138}, {"name": "ShapeEncoder", "size": 1690}, {"name": "SizeEncoder", "size": 1830} ] }, { "name": "filter", "children": [ {"name": "FisheyeTreeFilter", "size": 5219}, {"name": "GraphDistanceFilter", "size": 3165}, {"name": "VisibilityFilter", "size": 3509} ] }, {"name": "IOperator", "size": 1286}, { "name": "label", "children": [ {"name": "Labeler", "size": 9956}, {"name": "RadialLabeler", "size": 3899}, {"name": "StackedAreaLabeler", "size": 3202} ] }, { "name": "layout", "children": [ {"name": "AxisLayout", "size": 6725}, {"name": "BundledEdgeRouter", "size": 3727}, {"name": "CircleLayout", "size": 9317}, {"name": "CirclePackingLayout", "size": 12003}, {"name": "DendrogramLayout", "size": 4853}, {"name": "ForceDirectedLayout", "size": 8411}, {"name": "IcicleTreeLayout", "size": 4864}, {"name": "IndentedTreeLayout", "size": 3174}, {"name": "Layout", "size": 7881}, {"name": "NodeLinkTreeLayout", "size": 12870}, {"name": "PieLayout", "size": 2728}, {"name": "RadialTreeLayout", "size": 12348}, {"name": "RandomLayout", "size": 870}, {"name": "StackedAreaLayout", "size": 9121}, {"name": "TreeMapLayout", "size": 9191} ] }, {"name": "Operator", "size": 2490}, {"name": "OperatorList", "size": 5248}, {"name": "OperatorSequence", "size": 4190}, {"name": "OperatorSwitch", "size": 2581}, {"name": "SortOperator", "size": 2023} ] }, {"name": "Visualization", "size": 16540} ] } ] }