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sanshu/d3-heatmap-dendro.js

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d3 heatmap with dendrograms
Raw
d3-heatmap-dendro.js
/*
* Mayya Sedova <msedova.dev@gmail.com>
* See it in action https://sanshu.github.io/d3-heatmap-dendrogram/
*/
(function () {
d3.heatmapDendro = function (data, parent) {
if (!data || !data.matrix)
return;
;
var svg = d3.select(parent)
.append("svg")
.attr("width", "100%")
.attr("height", "150px");
var margin = {top: 10, right: 0, bottom: 10, left: 0},
height = 150 - margin.top - margin.bottom;
var labelsFromTree = function (nodes, cluster) {
var labels = [];
for (var n in nodes) {
if (!nodes[n].children || nodes[n].children.length === 0) {
labels.push(nodes[n].name[0]);
}
}
return labels;
};
var clusterSpace = 150, // size of the cluster tree
cellSize = 12,
colNumber = data.matrix[0].length,
rowNumber = data.matrix.length,
width = cellSize * colNumber + clusterSpace, // - margin.left - margin.right,
height = cellSize * rowNumber + clusterSpace, // - margin.top - margin.bottom,
rowCluster = d3.layout.cluster()
.size([height - clusterSpace, clusterSpace]),
colCluster = d3.layout.cluster()
.size([width - clusterSpace, clusterSpace]),
colors = ["#0084FF", "#188EF7", "#3199EF", "#49A4E8", "#62AFE0", "#7ABAD9", "#93C5D1", "#ABD0C9", "#C4DBC2", "#DCE6BA", "#F5F1B3", "#F5DBA3", "#F6C694", "#F6B085", "#F79B76", "#F78667", "#F87057", "#F85B48", "#F94539", "#F9302A", "#FA1B1B"],
rowNodes = rowCluster.nodes(data.rowJSON),
colNodes = colCluster.nodes(data.colJSON),
rowLabel = labelsFromTree(rowNodes, rowCluster),
colLabel = labelsFromTree(colNodes, colCluster);
var matrix = [], min = 0, max = 0;
for (var r = 0; r < rowNumber; r++) {
for (var c = 0; c < colNumber; c++) {
matrix.push({row: r + 1, col: c + 1, value: data.matrix[r][c]});
min = Math.min(min, data.matrix[r][c]);
max = Math.max(max, data.matrix[r][c]);
}
}
var middle = d3.median(matrix, function (d) {
return d.value;
});
console.log("Current Middle Point: " + middle)
var colorScale = d3.scale.quantile()
.domain([min, middle, max])
.range(colors);
svg.selectAll("*").remove();
svg.attr("width", width + margin.left + margin.right + clusterSpace)
.attr("height", height + margin.top + margin.bottom + clusterSpace);
var rowLabels = svg.append("g")
.selectAll(".rowLabelg")
.data(rowLabel)
.enter()
.append("text")
.text(function (d) {
return d;
})
.attr("x", 0)
.attr("y", function (d, i) {
return (i + 1) * cellSize + clusterSpace;
})
.style("text-anchor", "start")
.attr("transform", "translate(" + (width + cellSize) + "," + cellSize / 1.5 + ")")
.attr("class", function (d, i) {
return "rowLabel mono r" + i;
});
var colLabels = svg.append("g")
.selectAll(".colLabelg")
.data(colLabel)
.enter()
.append("text")
.text(function (d) {
return d;
})
.attr("x", 0)
.attr("y", function (d, i) {
return (i + 1) * cellSize;
})
.style("text-anchor", "end")
.attr("transform", "translate(" + cellSize / 2 + ",-6) rotate (-90) translate( -" + (height + cellSize * 2) + "," + clusterSpace + ")")
.attr("class", function (d, i) {
return "colLabel mono c" + i;
});
var heatMap = svg.append("g").attr("class", "g3")
.selectAll(".cellg")
.data(matrix, function (d) {
return d.row + ":" + d.col;
})
.enter()
.append("rect")
.attr("x", function (d) {
return d.col * cellSize + clusterSpace;
})
.attr("y", function (d) {
return d.row * cellSize + clusterSpace;
})
.attr("class", function (d) {
return "cell cell-border cr" + (d.row - 1) + " cc" + (d.col - 1);
})
.attr("width", cellSize)
.attr("height", cellSize)
.style("fill", function (d) {
return colorScale(d.value);
})
.on("mouseover", function (d) {
d3.select(this).classed("cell-hover", true);
//Update the tooltip position and value
d3.select("#d3tooltip")
.style("left", (d3.event.pageX + 10) + "px")
.style("top", (d3.event.pageY - 10) + "px")
.select("#value")
.html(
"Cell type: " + colLabel[d.col] + "<br>Sample name: " + rowLabel[d.row]
+ "<br>Value: " + d.value
);
//Show the tooltip
d3.select("#d3tooltip").transition()
.duration(200)
.style("opacity", .9);
})
.on("mouseout", function () {
d3.select(this).classed("cell-hover", false);
d3.selectAll(".rowLabel").classed("text-highlight", false);
d3.selectAll(".colLabel").classed("text-highlight", false);
d3.select("#d3tooltip").transition()
.duration(200)
.style("opacity", 0);
})
;
//tree for rows
var rTree = svg.append("g").attr("class", "rtree").attr("transform", "translate (10, " + (clusterSpace + cellSize) + ")");
var rlink = rTree.selectAll(".rlink")
.data(rowCluster.links(rowNodes))
.enter().append("path")
.attr("class", "rlink")
.attr("d", elbow);
var rnode = rTree.selectAll(".rnode")
.data(rowNodes)
.enter().append("g")
.attr("class", "rnode")
.attr("transform", function (d) {
return "translate(" + d.y + "," + d.x + ")";
});
//tree for cols
var cTree = svg.append("g").attr("class", "ctree").attr("transform", "rotate (90), translate (10, -" + (clusterSpace + cellSize) + ") scale(1,-1)");
var clink = cTree.selectAll(".clink")
.data(rowCluster.links(colNodes))
.enter().append("path")
.attr("class", "clink")
.attr("d", elbow);
var cnode = cTree.selectAll(".cnode")
.data(rowNodes)
.enter().append("g")
.attr("class", "cnode")
.attr("transform", function (d) {
return "translate(" + d.y + "," + d.x + ")";
});
function elbow(d, i) {
return "M" + d.source.y + "," + d.source.x
+ "V" + d.target.x + "H" + d.target.y;
}
}
})();
Raw
data.json
{
"matrix": [
[395.68, 417.2, 326.6, 33100, 35052, 20987, 23579, 26239, 128.31, 158.62, 81.803, 326.13, 440.54, 58.217, 1018.6, 104.4, 1316.4],
[26624, 117.3, 243.01, 3392.6, 2245, 842.29, 1265.4, 1225.6, 116.63, 160.4, 107.23, 43.581, 136.18, 85.462, 458.26, 148.22, 589.65],
[21772, 228.12, 378.45, 2782.3, 1358.7, 976.07, 737.17, 1560.2, 145.78, 153.98, 167.6, 156.03, 222.68, 134.86, 476.06, 157.64, 677.66],
[22774, 164.45, 353.57, 1858, 900.13, 604.22, 1247.4, 2371.6, 154.76, 142.59, 135.49, 146.08, 117.63, 82.5, 445.68, 99.639, 669.73],
[17479, 37.977, 40.291, 1374.2, 1319.5, 490.69, 260.48, 239.29, 29.661, 31.289, 33.723, 16.949, 17.981, 21.828, 307.29, 21.088, 506.82],
[13740, 225.52, 170.24, 833.49, 736.14, 618.66, 596.84, 431.99, 153.69, 102.36, 152.68, 951.93, 1748.7, 1715.5, 1771.9, 1287, 1010.8],
[11437, 83.342, 129.57, 1031.8, 738.28, 247.2, 577.24, 779.46, 33.527, 43.392, 50.067, 542.99, 323.12, 194.83, 318.44, 534.58, 585.42],
[14375, 21.426, 32.888, 1187.8, 365.71, 263.56, 626.98, 442.39, 21.037, 35.455, 26.508, 25.957, 9.114, 4.69, 79.328, 7.069, 481.56],
[13019, 30.131, 70.638, 1613, 1120.6, 591.59, 697.15, 670.13, 21.717, 20.484, 21.158, 31.014, 20.293, 8.441, 249.63, 21.981, 316.7],
[44647, 119.1, 225.79, 4950.9, 3547.4, 1665.6, 1460.3, 1353.7, 74.646, 98.779, 83.672, 76.908, 111.4, 144.13, 1240.9, 243.81, 1159.5],
[32592, 38.212, 64.939, 957.48, 592.6, 712.36, 296.25, 472.3, 21.719, 35.352, 25.846, 92.062, 77.439, 42.032, 528.5, 108.54, 476.89],
[37183, 52.139, 67.427, 2046.6, 1716.7, 785.93, 740.4, 838.1, 19.182, 18.784, 32.979, 52.632, 104.09, 123.61, 1072, 205.82, 768.21],
[34431, 58.57, 43.521, 4208.7, 2671.2, 1577.3, 1877, 2561.6, 26.512, 25.412, 29.03, 25.025, 27.54, 12.526, 466.97, 17.373, 443.22],
[34965, 58.244, 53.954, 5042.3, 2888.9, 2118.1, 2838.8, 3291.2, 44.255, 46.657, 47.213, 22.09, 30.102, 23.718, 815.12, 23.298, 968.69],
[162.95, 330.29, 32749, 284.33, 180.1, 91.841, 248.53, 239.36, 1388, 231.55, 466.68, 901.02, 693.72, 130.46, 197.38, 238.39, 420.69],
[494.7, 189.59, 41610, 320.72, 272.32, 165.77, 841.78, 212.16, 161.55, 184.9, 204.06, 260.95, 291.93, 305.18, 263.4, 375.27, 404.54],
[54.863, 76.403, 521.22, 435.28, 230.64, 175.08, 88.643, 54.91, 30.563, 27.257, 31.688, 37240, 11588, 2358.6, 79.084, 8123.5, 2087.8],
[102.34, 3217, 103.22, 79.571, 101.04, 43.168, 62.25, 132.31, 31162, 5132.9, 25407, 3343, 793.16, 36.355, 110.94, 91.258, 314.89],
[180.89, 835.39, 5507.7, 284.26, 339.72, 113.46, 134.87, 123.98, 12909, 267.64, 177.32, 671.24, 314.21, 58.575, 60.392, 78.933, 467.99],
[64, 1936.2, 174.1, 83.267, 94.68, 113.24, 128.71, 106.57, 10839, 1317.1, 8595.5, 600.3, 293.96, 72.915, 107.3, 93.651, 128.66],
[81.386, 3057.7, 329.11, 190.98, 219.39, 144.43, 301.11, 260.52, 13007, 2083.4, 9961.8, 705.38, 383.12, 170.8, 111.78, 150.14, 161.92],
[3178.3, 2697.1, 1902.3, 5716.5, 5135.1, 4152, 2095.9, 2279.2, 21704, 1290.8, 4330.1, 2278, 832.7, 2088.7, 3065.3, 1893.5, 2762.8],
[159.9, 11344, 347.84, 228.91, 150.82, 73.627, 226.83, 219.5, 19857, 896.82, 2299.7, 1117.4, 316.18, 84.429, 95.737, 92.389, 119.11],
[713.21, 1428.6, 348.69, 440.56, 450.22, 469.94, 416.64, 325.97, 23621, 2832.3, 7804.2, 2269, 1457.2, 216.27, 302.08, 495.6, 242.55],
[16.885, 58.443, 165.13, 30.48, 25.495, 42.183, 81.327, 103.35, 16242, 2906, 2883.5, 366.11, 53.143, 26.945, 27.259, 17.197, 26.448],
[16.433, 64.194, 73.793, 59.421, 56.337, 17.899, 52.106, 56.731, 19697, 4511, 4322.9, 698.9, 104.41, 44.304, 23.169, 29.882, 70.789],
[87.434, 27356, 73.882, 53.966, 18.063, 38.137, 56.646, 50.331, 3914.7, 522.63, 131.59, 63.616, 22.828, 26.677, 25.074, 21.049, 24.788],
[25.445, 23846, 2414, 16.161, 26.012, 21.551, 28.498, 43.676, 434.21, 293.33, 79.633, 22.052, 57.425, 22.695, 58.612, 20.681, 75.522],
[111.54, 22595, 323.06, 155.24, 63.8, 81.281, 287.8, 220.03, 2599.8, 660.82, 213.69, 112.61, 77.232, 35.318, 145.24, 90.422, 88.623],
[71.027, 24461, 181.87, 71.147, 96.217, 41.219, 113.71, 115.17, 4287.5, 352.89, 98.613, 83.1, 95.581, 32.963, 108.06, 56.517, 104.82],
[145.62, 34971, 240.88, 320.72, 1588, 284.03, 341.25, 435.91, 1632.4, 2510.5, 204.43, 97.655, 1336.6, 75.292, 440.66, 94.669, 207.34],
[15.912, 33167, 102.86, 33.529, 12.421, 21.868, 49.028, 37.239, 4063.1, 445.88, 20.269, 20.307, 12.939, 3.561, 5.255, 14.219, 32.322],
[91.55, 35585, 1368.5, 109.13, 94.808, 78.084, 156.84, 130.59, 6214.2, 1191.3, 100.46, 86.887, 118.64, 38.146, 72.235, 49.323, 102.29],
[330.25, 406.1, 468.78, 13482, 12327, 7914.7, 12484, 14351, 115.45, 190.71, 130.5, 161.02, 229.51, 55.3, 462.64, 129.79, 756],
[294.53, 525.55, 571.83, 15292, 14082, 8618.6, 14009, 16289, 265.38, 283.11, 198.48, 225.68, 328.16, 92.926, 610.61, 159.55, 909.27],
[329.1, 59.328, 65.166, 21387, 11410, 6419.6, 332.54, 1278.4, 14.306, 23.564, 16.55, 45.323, 42.148, 56.156, 294.22, 50.476, 668.07],
[226.35, 1401.3, 219.41, 23022, 6478.5, 4462, 6503.1, 7265.8, 914.55, 423.65, 239.32, 265.95, 221.32, 126.47, 166.83, 123, 726.74],
[875.88, 69.389, 289.88, 10113, 3156.3, 1094.1, 1986.9, 2423.5, 64.362, 93.924, 74.8, 108.17, 132.07, 114.67, 132.19, 110.29, 416.95],
[293.26, 297.68, 348.28, 11712, 2673.8, 2889.4, 498.98, 831.45, 119.83, 228.53, 185.86, 180.04, 170.35, 83.168, 244.87, 53.831, 413.37],
[275.69, 312.07, 392.58, 13310, 3401.9, 2895.9, 575.35, 902.55, 247, 185.85, 191.15, 286.46, 251.84, 76.966, 399.85, 114.45, 641.02],
[556.32, 1095.6, 897.64, 13389, 4016.6, 2195.3, 3613.9, 4563.9, 669.75, 406.34, 309.15, 476.24, 428.56, 392.15, 453.05, 520.19, 692.64],
[822.34, 301.58, 1098.2, 15403, 7850.1, 4753.7, 3450, 6123.6, 256.69, 334.95, 217.31, 702.73, 706.12, 548.37, 781.16, 583.52, 1149.9],
[17.917, 227.31, 36.823, 9753.7, 6992, 4487.8, 1347.4, 2163, 30.892, 22.836, 28.426, 278.65, 183.3, 118.34, 92.106, 343.14, 533.25],
[312.53, 113.37, 253.83, 8517.3, 10792, 5230.7, 3721.6, 4253.6, 101.59, 103.15, 101.97, 80.829, 114.15, 186.99, 183.21, 166.4, 291.55],
[528.8, 1126.3, 524.55, 13141, 14169, 6339.9, 3436.7, 3985.5, 188.3, 935.66, 142.9, 278.77, 344.03, 59.023, 370.66, 69.794, 338.58],
[1153.1, 109.46, 172.67, 15139, 11615, 7550.3, 4127.6, 4829.9, 44.602, 42.475, 38.954, 188.29, 83.886, 284.77, 815.94, 246.9, 743.39],
[599.46, 280.79, 1264.7, 588.96, 522.78, 231.16, 741.98, 630.24, 167.22, 140.35, 134, 14704, 12273, 1216.9, 2267.2, 2912, 2940.3],
[83.253, 56.232, 78.204, 414.42, 319.18, 33.136, 75.413, 64.085, 32.645, 38.707, 50.011, 10394, 9089.6, 162.36, 282.15, 666.48, 717.93],
[89.718, 55.954, 703.38, 441.76, 79.278, 23.436, 156.29, 157.04, 846.43, 65.088, 46.831, 11626, 7080.3, 42.747, 195.08, 634.97, 1329.3],
[680.29, 408.95, 442.26, 507.74, 597.15, 260.27, 260.49, 282.58, 235.89, 1973.1, 477.37, 3614.4, 9689.2, 1177, 2327.8, 2251.5, 704.07],
[440.33, 521.37, 265.32, 802.1, 999.06, 266.06, 374.46, 472.91, 808.73, 1260, 1982.5, 4649.5, 10693, 928.31, 2785.7, 3143.2, 1839.8],
[356.19, 652.31, 442.03, 1768.9, 1304.9, 762.61, 848.99, 955.81, 617.2, 1482.1, 909.71, 7208.2, 2925.4, 665.37, 1355.1, 1304.4, 2609.8],
[100.14, 74.24, 204.09, 751.36, 240.92, 38.515, 203.31, 195.7, 75.985, 97.755, 100.25, 7620.2, 5981.3, 24.566, 114.8, 131.7, 728.3],
[491.97, 179.31, 541.49, 695.24, 526.92, 334.2, 378.6, 407.28, 130.69, 147.81, 485.75, 6757.7, 6224.2, 415.43, 792.99, 1209.5, 960.31],
[2176.5, 535.76, 849.73, 1694.1, 2391.7, 104.07, 157.76, 419.91, 389.99, 4217.1, 573.04, 2468.3, 25077, 440.99, 9098.1, 1581.8, 768.39],
[1801.9, 272, 388.82, 849.11, 278.5, 127.62, 432.41, 367.02, 142.96, 681.38, 114.99, 7967.4, 15536, 235.33, 2664.6, 3060.1, 2719.8],
[1078.5, 584.64, 1593.1, 1463, 1883.7, 500, 389.29, 544.59, 471.56, 2650.4, 274.6, 4316.6, 19829, 540.35, 5053.9, 3029.7, 878.92],
[2698.5, 541.2, 1137.3, 1880.3, 2386.9, 353.87, 846.09, 942.06, 608.57, 3897.5, 934.09, 2070.9, 15246, 712.66, 9480.5, 1860.7, 1329.8],
[599.11, 2110.6, 1979.3, 1912.9, 2185.9, 1046.7, 922.62, 816.44, 2181.8, 2447.8, 3070.1, 2777.4, 13364, 2493.9, 5750.5, 1562.2, 2470.2],
[30.985, 287.74, 21441, 230.68, 299.56, 120.18, 69.519, 41.807, 196.07, 50.918, 71.192, 35.679, 40.597, 26.748, 96.34, 29.987, 341.03],
[168.83, 4735.8, 19069, 355.24, 189.21, 167.27, 287.16, 314.52, 223.25, 72.248, 44.71, 499.61, 320.66, 12.6, 77.17, 513.82, 269.9],
[68.168, 108.62, 5834.4, 47.653, 44.56, 32.565, 106.81, 102.32, 56.171, 51.768, 66.398, 45.207, 25.599, 32.273, 35.537, 27.734, 52.68],
[9.775, 75.161, 7494, 16.047, 12.525, 12.11, 37.874, 17.543, 40.419, 27.389, 46.084, 23.394, 13.984, 10.705, 17.582, 11.933, 24.745],
[27.242, 47.861, 6702.9, 51.796, 46.036, 23.438, 66.93, 68.085, 38.777, 34.741, 34.59, 150.19, 36.452, 30.118, 34.928, 30.255, 55.571],
[22.424, 29.8, 7096, 29.631, 76.257, 13.312, 70.916, 33.945, 22.463, 24.156, 106.12, 15.617, 12.05, 6.407, 15.818, 7.568, 20.207],
[94.772, 98.004, 7001.1, 101.24, 94.444, 66.289, 143.19, 149.05, 124.52, 127.39, 132, 69.516, 66.842, 72.071, 82.36, 80.849, 122.04],
[53.691, 58.926, 13698, 82.893, 49.74, 28.545, 24.378, 16.613, 94.419, 29.657, 11.755, 27.394, 7.688, 155.29, 26.004, 158.35, 25.175],
[29.283, 100.75, 10132, 176.05, 82.909, 41.943, 74.399, 38.012, 819.72, 109.83, 190.43, 24.289, 44.759, 38.679, 44.825, 45.942, 106.53],
[186.15, 94.765, 10444, 257.38, 151.54, 93.752, 264.46, 229.04, 374.78, 103.53, 1421.8, 315.04, 200.03, 112.99, 282.09, 132.72, 348.74],
[125.79, 33.083, 11321, 49.475, 43.257, 26.589, 45.615, 59.935, 27.844, 39.868, 31.309, 95.751, 43.935, 142.24, 142.03, 83.535, 176.1],
[19.566, 20.749, 12028, 34.921, 15.821, 19.504, 13.723, 15.532, 111.39, 83.791, 453.51, 392.19, 100.84, 4.607, 7.934, 13.365, 48.606],
[45.415, 290.12, 12243, 109.92, 33.965, 25.369, 54.365, 48.216, 406.39, 19.451, 29.735, 97.688, 90.763, 34.934, 28.57, 27.015, 48.013],
[107.37, 6520.7, 144.91, 82.304, 62.179, 22.661, 135.41, 153.81, 85.531, 73.135, 125.32, 52.122, 23.743, 51.693, 49.02, 39.758, 83.836],
[22.751, 7265, 230.31, 251.23, 72.213, 118.18, 67.58, 126.55, 98.807, 43.914, 37.723, 89.089, 27.311, 38.162, 83.076, 38.318, 85.352],
[24.085, 8770.5, 45.827, 31.797, 20.7, 20.595, 48.02, 44.575, 48.317, 803.26, 32.96, 26.193, 269.05, 11.639, 25.351, 15.255, 31.11],
[37.863, 8318.6, 35.132, 28.186, 19.561, 27.081, 64.546, 62.118, 660.08, 180.07, 49.416, 13.75, 34.176, 200.55, 496.06, 87, 30.483],
[8.488, 11449, 19.921, 26.306, 14.216, 20.578, 20.333, 18.133, 536.09, 4927.5, 171.22, 20.287, 104.69, 7.813, 135.48, 7.304, 16.237],
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}
Raw
index.html
<!DOCTYPE html>
<html>
<head>
<title>Heatmap with dendrograms</title>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<style>
#d3tooltip {
position: absolute;
width: 200px;
height: auto;
padding: 10px;
background-color: #fafafa;
-webkit-border-radius: 10px;
-moz-border-radius: 10px;
border-radius: 10px;
-webkit-box-shadow: 4px 4px 10px rgba(0, 0, 0, 0.4);
-moz-box-shadow: 4px 4px 10px rgba(0, 0, 0, 0.4);
box-shadow: 4px 4px 10px rgba(0, 0, 0, 0.4);
pointer-events: none;
opacity:0;
}
#d3tooltip.hidden {
display: none;
}
#d3tooltip p {
margin: 0;
font-family: sans-serif;
font-size: 12px;
line-height: 20px;
}
rect.selection {
stroke : #333;
stroke-dasharray: 4px;
stroke-opacity : 0.5;
fill : transparent;
}
rect.cell-border {
stroke: #eee;
stroke-width:0.3px;
}
rect.cell-selected {
stroke: rgb(51,102,153);
stroke-width:0.5px;
}
rect.cell-hover {
stroke: #F00;
stroke-width:0.3px;
}
text.mono {
font-size: 9pt;
font-family: Consolas, courier;
fill: #aaa;
}
.rlink, .clink {
fill: none;
stroke: #ccc;
stroke-width: 1.5px;
}
</style>
</head>
<body>
<div id="heatmap" width="100%" height="100%" style="overflow:scroll"></div>
<div id="d3tooltip">
<p><span id="value"></p>
</div>
</body>
<script type="text/javascript" src="https://code.jquery.com/jquery-1.12.3.min.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.16/d3.min.js"></script>
<script type="text/javascript" src="d3-heatmap-dendro.js"></script>
<script>
$(document)
.ready(function () {
$.getJSON('data.json',
function (data) {
// params: data set, id of the parent, "middle" point
// middle point is optional, but for this data set
d3.heatmapDendro(data, "#heatmap", 5000);
}
);
});
</script>
</html>
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