D3 Radial Dendrogram only displaying part

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I have created the code below based on Mike Bostock’s example in Observable (which I know is not the same as raw d3/ javascript) https://observablehq.com/@d3/radial-dendrogram

However, it:

  • only displays if I remove the return svg.attr(“viewBox”, autoBox).node(); at the end of the chart function. I suspect that is causing the issues below
  • is tightly cropped
  • looks like the centre is at coordinate 0,0 in the top left of the screen, so 3 quarters of the viz is off the screen. I have tried adding a transform translate but that doesn’t help

enter image description here

Any ideas warmly welcomed…

index.html

<html lang="en">
<head>
    <meta charset="UTF-8">
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
    <link rel="stylesheet" type="text/css" href="//fonts.googleapis.com/css?family=Open+Sans" />
    <script src="https://d3js.org/d3.v6.js"></script>
    <link rel="shortcut icon" href="#">
    <title>Radial Dendrogram</title>
</head>

<body>
    <div id="vis">  
    </div>
    <script src = 'script.js'></script>
</body>
</html>

script.js

function chart(birdDataSet) {
    const root = tree(d3.hierarchy(birdDataSet)
        .sort((a, b) => d3.ascending(a.data.name, b.data.name)));
  
    svg.append("g")
        .attr("fill", "none")
        .attr("stroke", "#555")
        .attr("stroke-opacity", 0.4)
        .attr("stroke-width", 1.5)
      .selectAll("path")
      .data(root.links())
      .join("path")
        .attr("d", d3.linkRadial()
            .angle(d => d.x)
            .radius(d => d.y));
    
    svg.append("g")
      .selectAll("circle")
      .data(root.descendants())
      .join("circle")
        .attr("transform", d => `
          rotate(${d.x * 180 / Math.PI - 90})
          translate(${d.y},0)
        `)
        .attr("fill", d => d.children ? "#555" : "#999")
        .attr("r", 2.5);
  
    svg.append("g")
        .attr("font-family", "sans-serif")
        .attr("font-size", 10)
        .attr("stroke-linejoin", "round")
        .attr("stroke-width", 3)
      .selectAll("text")
      .data(root.descendants())
      .join("text")
        .attr("transform", d => `
          rotate(${d.x * 180 / Math.PI - 90}) 
          translate(${d.y},0) 
          rotate(${d.x >= Math.PI ? 180 : 0})
        `)
        .attr("dy", "0.31em")
        .attr("x", d => d.x < Math.PI === !d.children ? 6 : -6)
        .attr("text-anchor", d => d.x < Math.PI === !d.children ? "start" : "end")
        .text(d => d.data.name)
      .clone(true).lower()
        .attr("stroke", "white");
  
    //return svg.attr("viewBox", autoBox).node();
  }

function autoBox() {
  document.body.appendChild(this);
  const {x, y, width, height} = this.getBBox();
  document.body.removeChild(this);
  return [x, y, width, height];
}

width = 975
radius = width / 2
tree = d3.cluster().size([2 * Math.PI, radius - 100])

d3.json("data/flare-2.json")
  .then(function(data) {
    console.log(chart(data));
  })
  .catch(function(error) {
    console.warn(error);
  });

flare-2.json

This can be downloaded from https://static.observableusercontent.com/files/e65374209781891f37dea1e7a6e1c5e020a3009b8aedf113b4c80942018887a1176ad4945cf14444603ff91d3da371b3b0d72419fa8d2ee0f6e815732475d5de?response-content-disposition=attachment%3Bfilename*%3DUTF-8%27%27flare-2.json

Answer

Here’s a quick refactor that removes the ObservableHQ craziness and moves it to a simple HTML/JavaScript page. The part you are missing is something like this:

  const svg = d3
    .select('svg')
    .attr('width', width)
    .attr('height', height)
    .append('g')
    .attr('transform', 'translate(' + width / 2 + ',' + height / 2 + ')');

This sizes the SVG and then moves the dendogram to the center of the SVG.

Running code:

<!DOCTYPE html>

<html>
  <head>
    <script src="https://d3js.org/d3.v6.min.js"></script>
  </head>

  <body>
    <svg></svg>
    <script>
      var data = {
        name: 'flare',
        children: [
          {
            name: 'analytics',
            children: [
              {
                name: 'cluster',
                children: [
                  { name: 'AgglomerativeCluster', value: 3938 },
                  { name: 'CommunityStructure', value: 3812 },
                  { name: 'HierarchicalCluster', value: 6714 },
                  { name: 'MergeEdge', value: 743 },
                ],
              },
              {
                name: 'graph',
                children: [
                  { name: 'BetweennessCentrality', value: 3534 },
                  { name: 'LinkDistance', value: 5731 },
                  { name: 'MaxFlowMinCut', value: 7840 },
                  { name: 'ShortestPaths', value: 5914 },
                  { name: 'SpanningTree', value: 3416 },
                ],
              },
              {
                name: 'optimization',
                children: [{ name: 'AspectRatioBanker', value: 7074 }],
              },
            ],
          },
          {
            name: 'animate',
            children: [
              { name: 'Easing', value: 17010 },
              { name: 'FunctionSequence', value: 5842 },
              {
                name: 'interpolate',
                children: [
                  { name: 'ArrayInterpolator', value: 1983 },
                  { name: 'ColorInterpolator', value: 2047 },
                  { name: 'DateInterpolator', value: 1375 },
                  { name: 'Interpolator', value: 8746 },
                  { name: 'MatrixInterpolator', value: 2202 },
                  { name: 'NumberInterpolator', value: 1382 },
                  { name: 'ObjectInterpolator', value: 1629 },
                  { name: 'PointInterpolator', value: 1675 },
                  { name: 'RectangleInterpolator', value: 2042 },
                ],
              },
              { name: 'ISchedulable', value: 1041 },
              { name: 'Parallel', value: 5176 },
              { name: 'Pause', value: 449 },
              { name: 'Scheduler', value: 5593 },
              { name: 'Sequence', value: 5534 },
              { name: 'Transition', value: 9201 },
              { name: 'Transitioner', value: 19975 },
              { name: 'TransitionEvent', value: 1116 },
              { name: 'Tween', value: 6006 },
            ],
          },
          {
            name: 'data',
            children: [
              {
                name: 'converters',
                children: [
                  { name: 'Converters', value: 721 },
                  { name: 'DelimitedTextConverter', value: 4294 },
                  { name: 'GraphMLConverter', value: 9800 },
                  { name: 'IDataConverter', value: 1314 },
                  { name: 'JSONConverter', value: 2220 },
                ],
              },
              { name: 'DataField', value: 1759 },
              { name: 'DataSchema', value: 2165 },
              { name: 'DataSet', value: 586 },
              { name: 'DataSource', value: 3331 },
              { name: 'DataTable', value: 772 },
              { name: 'DataUtil', value: 3322 },
            ],
          },
          {
            name: 'display',
            children: [
              { name: 'DirtySprite', value: 8833 },
              { name: 'LineSprite', value: 1732 },
              { name: 'RectSprite', value: 3623 },
              { name: 'TextSprite', value: 10066 },
            ],
          },
          {
            name: 'flex',
            children: [{ name: 'FlareVis', value: 4116 }],
          },
          {
            name: 'physics',
            children: [
              { name: 'DragForce', value: 1082 },
              { name: 'GravityForce', value: 1336 },
              { name: 'IForce', value: 319 },
              { name: 'NBodyForce', value: 10498 },
              { name: 'Particle', value: 2822 },
              { name: 'Simulation', value: 9983 },
              { name: 'Spring', value: 2213 },
              { name: 'SpringForce', value: 1681 },
            ],
          },
          {
            name: 'query',
            children: [
              { name: 'AggregateExpression', value: 1616 },
              { name: 'And', value: 1027 },
              { name: 'Arithmetic', value: 3891 },
              { name: 'Average', value: 891 },
              { name: 'BinaryExpression', value: 2893 },
              { name: 'Comparison', value: 5103 },
              { name: 'CompositeExpression', value: 3677 },
              { name: 'Count', value: 781 },
              { name: 'DateUtil', value: 4141 },
              { name: 'Distinct', value: 933 },
              { name: 'Expression', value: 5130 },
              { name: 'ExpressionIterator', value: 3617 },
              { name: 'Fn', value: 3240 },
              { name: 'If', value: 2732 },
              { name: 'IsA', value: 2039 },
              { name: 'Literal', value: 1214 },
              { name: 'Match', value: 3748 },
              { name: 'Maximum', value: 843 },
              {
                name: 'methods',
                children: [
                  { name: 'add', value: 593 },
                  { name: 'and', value: 330 },
                  { name: 'average', value: 287 },
                  { name: 'count', value: 277 },
                  { name: 'distinct', value: 292 },
                  { name: 'div', value: 595 },
                  { name: 'eq', value: 594 },
                  { name: 'fn', value: 460 },
                  { name: 'gt', value: 603 },
                  { name: 'gte', value: 625 },
                  { name: 'iff', value: 748 },
                  { name: 'isa', value: 461 },
                  { name: 'lt', value: 597 },
                  { name: 'lte', value: 619 },
                  { name: 'max', value: 283 },
                  { name: 'min', value: 283 },
                  { name: 'mod', value: 591 },
                  { name: 'mul', value: 603 },
                  { name: 'neq', value: 599 },
                  { name: 'not', value: 386 },
                  { name: 'or', value: 323 },
                  { name: 'orderby', value: 307 },
                  { name: 'range', value: 772 },
                  { name: 'select', value: 296 },
                  { name: 'stddev', value: 363 },
                  { name: 'sub', value: 600 },
                  { name: 'sum', value: 280 },
                  { name: 'update', value: 307 },
                  { name: 'variance', value: 335 },
                  { name: 'where', value: 299 },
                  { name: 'xor', value: 354 },
                  { name: '_', value: 264 },
                ],
              },
              { name: 'Minimum', value: 843 },
              { name: 'Not', value: 1554 },
              { name: 'Or', value: 970 },
              { name: 'Query', value: 13896 },
              { name: 'Range', value: 1594 },
              { name: 'StringUtil', value: 4130 },
              { name: 'Sum', value: 791 },
              { name: 'Variable', value: 1124 },
              { name: 'Variance', value: 1876 },
              { name: 'Xor', value: 1101 },
            ],
          },
          {
            name: 'scale',
            children: [
              { name: 'IScaleMap', value: 2105 },
              { name: 'LinearScale', value: 1316 },
              { name: 'LogScale', value: 3151 },
              { name: 'OrdinalScale', value: 3770 },
              { name: 'QuantileScale', value: 2435 },
              { name: 'QuantitativeScale', value: 4839 },
              { name: 'RootScale', value: 1756 },
              { name: 'Scale', value: 4268 },
              { name: 'ScaleType', value: 1821 },
              { name: 'TimeScale', value: 5833 },
            ],
          },
          {
            name: 'util',
            children: [
              { name: 'Arrays', value: 8258 },
              { name: 'Colors', value: 10001 },
              { name: 'Dates', value: 8217 },
              { name: 'Displays', value: 12555 },
              { name: 'Filter', value: 2324 },
              { name: 'Geometry', value: 10993 },
              {
                name: 'heap',
                children: [
                  { name: 'FibonacciHeap', value: 9354 },
                  { name: 'HeapNode', value: 1233 },
                ],
              },
              { name: 'IEvaluable', value: 335 },
              { name: 'IPredicate', value: 383 },
              { name: 'IValueProxy', value: 874 },
              {
                name: 'math',
                children: [
                  { name: 'DenseMatrix', value: 3165 },
                  { name: 'IMatrix', value: 2815 },
                  { name: 'SparseMatrix', value: 3366 },
                ],
              },
              { name: 'Maths', value: 17705 },
              { name: 'Orientation', value: 1486 },
              {
                name: 'palette',
                children: [
                  { name: 'ColorPalette', value: 6367 },
                  { name: 'Palette', value: 1229 },
                  { name: 'ShapePalette', value: 2059 },
                  { name: 'SizePalette', value: 2291 },
                ],
              },
              { name: 'Property', value: 5559 },
              { name: 'Shapes', value: 19118 },
              { name: 'Sort', value: 6887 },
              { name: 'Stats', value: 6557 },
              { name: 'Strings', value: 22026 },
            ],
          },
          {
            name: 'vis',
            children: [
              {
                name: 'axis',
                children: [
                  { name: 'Axes', value: 1302 },
                  { name: 'Axis', value: 24593 },
                  { name: 'AxisGridLine', value: 652 },
                  { name: 'AxisLabel', value: 636 },
                  { name: 'CartesianAxes', value: 6703 },
                ],
              },
              {
                name: 'controls',
                children: [
                  { name: 'AnchorControl', value: 2138 },
                  { name: 'ClickControl', value: 3824 },
                  { name: 'Control', value: 1353 },
                  { name: 'ControlList', value: 4665 },
                  { name: 'DragControl', value: 2649 },
                  { name: 'ExpandControl', value: 2832 },
                  { name: 'HoverControl', value: 4896 },
                  { name: 'IControl', value: 763 },
                  { name: 'PanZoomControl', value: 5222 },
                  { name: 'SelectionControl', value: 7862 },
                  { name: 'TooltipControl', value: 8435 },
                ],
              },
              {
                name: 'data',
                children: [
                  { name: 'Data', value: 20544 },
                  { name: 'DataList', value: 19788 },
                  { name: 'DataSprite', value: 10349 },
                  { name: 'EdgeSprite', value: 3301 },
                  { name: 'NodeSprite', value: 19382 },
                  {
                    name: 'render',
                    children: [
                      { name: 'ArrowType', value: 698 },
                      { name: 'EdgeRenderer', value: 5569 },
                      { name: 'IRenderer', value: 353 },
                      { name: 'ShapeRenderer', value: 2247 },
                    ],
                  },
                  { name: 'ScaleBinding', value: 11275 },
                  { name: 'Tree', value: 7147 },
                  { name: 'TreeBuilder', value: 9930 },
                ],
              },
              {
                name: 'events',
                children: [
                  { name: 'DataEvent', value: 2313 },
                  { name: 'SelectionEvent', value: 1880 },
                  { name: 'TooltipEvent', value: 1701 },
                  { name: 'VisualizationEvent', value: 1117 },
                ],
              },
              {
                name: 'legend',
                children: [
                  { name: 'Legend', value: 20859 },
                  { name: 'LegendItem', value: 4614 },
                  { name: 'LegendRange', value: 10530 },
                ],
              },
              {
                name: 'operator',
                children: [
                  {
                    name: 'distortion',
                    children: [
                      { name: 'BifocalDistortion', value: 4461 },
                      { name: 'Distortion', value: 6314 },
                      { name: 'FisheyeDistortion', value: 3444 },
                    ],
                  },
                  {
                    name: 'encoder',
                    children: [
                      { name: 'ColorEncoder', value: 3179 },
                      { name: 'Encoder', value: 4060 },
                      { name: 'PropertyEncoder', value: 4138 },
                      { name: 'ShapeEncoder', value: 1690 },
                      { name: 'SizeEncoder', value: 1830 },
                    ],
                  },
                  {
                    name: 'filter',
                    children: [
                      { name: 'FisheyeTreeFilter', value: 5219 },
                      { name: 'GraphDistanceFilter', value: 3165 },
                      { name: 'VisibilityFilter', value: 3509 },
                    ],
                  },
                  { name: 'IOperator', value: 1286 },
                  {
                    name: 'label',
                    children: [
                      { name: 'Labeler', value: 9956 },
                      { name: 'RadialLabeler', value: 3899 },
                      { name: 'StackedAreaLabeler', value: 3202 },
                    ],
                  },
                  {
                    name: 'layout',
                    children: [
                      { name: 'AxisLayout', value: 6725 },
                      { name: 'BundledEdgeRouter', value: 3727 },
                      { name: 'CircleLayout', value: 9317 },
                      { name: 'CirclePackingLayout', value: 12003 },
                      { name: 'DendrogramLayout', value: 4853 },
                      { name: 'ForceDirectedLayout', value: 8411 },
                      { name: 'IcicleTreeLayout', value: 4864 },
                      { name: 'IndentedTreeLayout', value: 3174 },
                      { name: 'Layout', value: 7881 },
                      { name: 'NodeLinkTreeLayout', value: 12870 },
                      { name: 'PieLayout', value: 2728 },
                      { name: 'RadialTreeLayout', value: 12348 },
                      { name: 'RandomLayout', value: 870 },
                      { name: 'StackedAreaLayout', value: 9121 },
                      { name: 'TreeMapLayout', value: 9191 },
                    ],
                  },
                  { name: 'Operator', value: 2490 },
                  { name: 'OperatorList', value: 5248 },
                  { name: 'OperatorSequence', value: 4190 },
                  { name: 'OperatorSwitch', value: 2581 },
                  { name: 'SortOperator', value: 2023 },
                ],
              },
              { name: 'Visualization', value: 16540 },
            ],
          },
        ],
      };

      const width = 750,
        height = 750,
        radius = width / 2;
        
      const tree = d3.cluster().size([2 * Math.PI, radius - 100]);

      const root = tree(
        d3
          .hierarchy(data)
          .sort((a, b) => d3.ascending(a.data.name, b.data.name))
      );

      const svg = d3
        .select('svg')
        .attr('width', width)
        .attr('height', height)
        .append('g')
        .attr('transform', 'translate(' + width / 2 + ',' + height / 2 + ')');

      svg
        .append('g')
        .attr('fill', 'none')
        .attr('stroke', '#555')
        .attr('stroke-opacity', 0.4)
        .attr('stroke-width', 1.5)
        .selectAll('path')
        .data(root.links())
        .join('path')
        .attr(
          'd',
          d3
            .linkRadial()
            .angle((d) => d.x)
            .radius((d) => d.y)
        );

      svg
        .append('g')
        .selectAll('circle')
        .data(root.descendants())
        .join('circle')
        .attr(
          'transform',
          (d) => `
        rotate(${(d.x * 180) / Math.PI - 90})
        translate(${d.y},0)
      `
        )
        .attr('fill', (d) => (d.children ? '#555' : '#999'))
        .attr('r', 2.5);

      svg
        .append('g')
        .attr('font-family', 'sans-serif')
        .attr('font-size', 10)
        .attr('stroke-linejoin', 'round')
        .attr('stroke-width', 3)
        .selectAll('text')
        .data(root.descendants())
        .join('text')
        .attr(
          'transform',
          (d) => `
        rotate(${(d.x * 180) / Math.PI - 90}) 
        translate(${d.y},0) 
        rotate(${d.x >= Math.PI ? 180 : 0})
      `
        )
        .attr('dy', '0.31em')
        .attr('x', (d) => (d.x < Math.PI === !d.children ? 6 : -6))
        .attr('text-anchor', (d) =>
          d.x < Math.PI === !d.children ? 'start' : 'end'
        )
        .text((d) => d.data.name)
        .clone(true)
        .lower()
        .attr('stroke', 'white');
    </script>
  </body>
</html>


Source: stackoverflow