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@rpgove
Last active Aug 30, 2020
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Automatically Finding Better Force Directed Layout Parameters
license: gpl-3.0
height: 600
scrolling: no
border: yes
(function (global, factory) {
typeof exports === 'object' && typeof module !== 'undefined' ? factory(exports) :
typeof define === 'function' && define.amd ? define(['exports'], factory) :
(factory((global.greadability = global.greadability || {})));
}(this, (function (exports) { 'use strict';
var greadability = function (nodes, links, id) {
var i,
j,
n = nodes.length,
m,
degree = new Array(nodes.length),
cMax,
idealAngle = 70,
dMax;
/*
* Tracks the global graph readability metrics.
*/
var graphStats = {
crossing: 0, // Normalized link crossings
crossingAngle: 0, // Normalized average dev from 70 deg
angularResolutionMin: 0, // Normalized avg dev from ideal min angle
angularResolutionDev: 0, // Normalized avg dev from each link
};
var getSumOfArray = function (numArray) {
var i = 0, n = numArray.length, sum = 0;
for (; i < n; ++i) sum += numArray[i];
return sum;
};
var initialize = function () {
var i, j, link;
var nodeById = {};
// Filter out self loops
links = links.filter(function (l) {
return l.source !== l.target;
});
m = links.length;
if (!id) {
id = function (d) { return d.index; };
}
for (i = 0; i < n; ++i) {
nodes[i].index = i;
degree[i] = [];
nodeById[id(nodes[i], i, nodeById)] = nodes[i];
}
// Make sure source and target are nodes and not indices.
for (i = 0; i < m; ++i) {
link = links[i];
if (typeof link.source !== "object") link.source = nodeById[link.source];
if (typeof link.target !== "object") link.target = nodeById[link.target];
}
// Filter out duplicate links
var filteredLinks = [];
links.forEach(function (l) {
var s = l.source, t = l.target;
if (s.index > t.index) {
filteredLinks.push({source: t, target: s});
} else {
filteredLinks.push({source: s, target: t});
}
});
links = filteredLinks;
links.sort(function (a, b) {
if (a.source.index < b.source.index) return -1;
if (a.source.index > b.source.index) return 1;
if (a.target.index < b.target.index) return -1;
if (a.target.index > b.target.index) return 1;
return 0;
});
i = 1;
while (i < links.length) {
if (links[i-1].source.index === links[i].source.index &&
links[i-1].target.index === links[i].target.index) {
links.splice(i, 1);
}
else ++i;
}
// Update length, if a duplicate was deleted.
m = links.length;
// Calculate degree.
for (i = 0; i < m; ++i) {
link = links[i];
link.index = i;
degree[link.source.index].push(link);
degree[link.target.index].push(link);
};
}
// Assume node.x and node.y are the coordinates
function direction (pi, pj, pk) {
var p1 = [pk[0] - pi[0], pk[1] - pi[1]];
var p2 = [pj[0] - pi[0], pj[1] - pi[1]];
return p1[0] * p2[1] - p2[0] * p1[1];
}
// Is point k on the line segment formed by points i and j?
// Inclusive, so if pk == pi or pk == pj then return true.
function onSegment (pi, pj, pk) {
return Math.min(pi[0], pj[0]) <= pk[0] &&
pk[0] <= Math.max(pi[0], pj[0]) &&
Math.min(pi[1], pj[1]) <= pk[1] &&
pk[1] <= Math.max(pi[1], pj[1]);
}
function linesCross (line1, line2) {
var d1, d2, d3, d4;
// CLRS 2nd ed. pg. 937
d1 = direction(line2[0], line2[1], line1[0]);
d2 = direction(line2[0], line2[1], line1[1]);
d3 = direction(line1[0], line1[1], line2[0]);
d4 = direction(line1[0], line1[1], line2[1]);
if (((d1 > 0 && d2 < 0) || (d1 < 0 && d2 > 0)) &&
((d3 > 0 && d4 < 0) || (d3 < 0 && d4 > 0))) {
return true;
} else if (d1 === 0 && onSegment(line2[0], line2[1], line1[0])) {
return true;
} else if (d2 === 0 && onSegment(line2[0], line2[1], line1[1])) {
return true;
} else if (d3 === 0 && onSegment(line1[0], line1[1], line2[0])) {
return true;
} else if (d4 === 0 && onSegment(line1[0], line1[1], line2[1])) {
return true;
}
return false;
}
function linksCross (link1, link2) {
// Self loops are not intersections
if (link1.index === link2.index ||
link1.source === link1.target ||
link2.source === link2.target) {
return false;
}
// Links cannot intersect if they share a node
if (link1.source === link2.source ||
link1.source === link2.target ||
link1.target === link2.source ||
link1.target === link2.target) {
return false;
}
var line1 = [
[link1.source.x, link1.source.y],
[link1.target.x, link1.target.y]
];
var line2 = [
[link2.source.x, link2.source.y],
[link2.target.x, link2.target.y]
];
return linesCross(line1, line2);
}
function linkCrossings () {
var i, j, c = 0, d = 0, link1, link2, line1, line2;;
// Sum the upper diagonal of the edge crossing matrix.
for (i = 0; i < m; ++i) {
for (j = i + 1; j < m; ++j) {
link1 = links[i], link2 = links[j];
// Check if link i and link j intersect
if (linksCross(link1, link2)) {
line1 = [
[link1.source.x, link1.source.y],
[link1.target.x, link1.target.y]
];
line2 = [
[link2.source.x, link2.source.y],
[link2.target.x, link2.target.y]
];
++c;
d += Math.abs(idealAngle - acuteLinesAngle(line1, line2));
}
}
}
return {c: 2*c, d: 2*d};
}
function linesegmentsAngle (line1, line2) {
// Finds the (counterclockwise) angle from line segement line1 to
// line segment line2. Assumes the lines share one end point.
// If both endpoints are the same, or if both lines have zero
// length, then return 0 angle.
// Param order matters:
// linesegmentsAngle(line1, line2) != linesegmentsAngle(line2, line1)
var temp, len, angle1, angle2, sLine1, sLine2;
// Re-orient so that line1[0] and line2[0] are the same.
if (line1[0][0] === line2[1][0] && line1[0][1] === line2[1][1]) {
temp = line2[1];
line2[1] = line2[0];
line2[0] = temp;
} else if (line1[1][0] === line2[0][0] && line1[1][1] === line2[0][1]) {
temp = line1[1];
line1[1] = line1[0];
line1[0] = temp;
} else if (line1[1][0] === line2[1][0] && line1[1][1] === line2[1][1]) {
temp = line1[1];
line1[1] = line1[0];
line1[0] = temp;
temp = line2[1];
line2[1] = line2[0];
line2[0] = temp;
}
// Shift the line so that the first point is at (0,0).
sLine1 = [
[line1[0][0] - line1[0][0], line1[0][1] - line1[0][1]],
[line1[1][0] - line1[0][0], line1[1][1] - line1[0][1]]
];
// Normalize the line length.
len = Math.hypot(sLine1[1][0], sLine1[1][1]);
if (len === 0) return 0;
sLine1[1][0] /= len;
sLine1[1][1] /= len;
// If y < 0, angle = acos(x), otherwise angle = 360 - acos(x)
angle1 = Math.acos(sLine1[1][0]) * 180 / Math.PI;
if (sLine1[1][1] < 0) angle1 = 360 - angle1;
// Shift the line so that the first point is at (0,0).
sLine2 = [
[line2[0][0] - line2[0][0], line2[0][1] - line2[0][1]],
[line2[1][0] - line2[0][0], line2[1][1] - line2[0][1]]
];
// Normalize the line length.
len = Math.hypot(sLine2[1][0], sLine2[1][1]);
if (len === 0) return 0;
sLine2[1][0] /= len;
sLine2[1][1] /= len;
// If y < 0, angle = acos(x), otherwise angle = 360 - acos(x)
angle2 = Math.acos(sLine2[1][0]) * 180 / Math.PI;
if (sLine2[1][1] < 0) angle2 = 360 - angle2;
return angle1 <= angle2 ? angle2 - angle1 : 360 - (angle1 - angle2);
}
function acuteLinesAngle (line1, line2) {
// Acute angle of intersection, in degrees. Assumes these lines
// intersect.
var slope1 = (line1[1][1] - line1[0][1]) / (line1[1][0] - line1[0][0]);
var slope2 = (line2[1][1] - line2[0][1]) / (line2[1][0] - line2[0][0]);
// If these lines are two links incident on the same node, need
// to check if the angle is 0 or 180.
if (slope1 === slope2) {
// If line2 is not on line1 and line1 is not on line2, then
// the lines share only one point and the angle must be 180.
if (!(onSegment(line1[0], line1[1], line2[0]) && onSegment(line1[0], line1[1], line2[1])) ||
!(onSegment(line2[0], line2[1], line1[0]) && onSegment(line2[0], line2[1], line1[1])))
return 180;
else return 0;
}
var angle = Math.abs(Math.atan(slope1) - Math.atan(slope2));
return (angle > Math.PI / 2 ? Math.PI - angle : angle) * 180 / Math.PI;
}
function angularRes () {
var j,
resMin = 0,
resDev = 0,
nonZeroDeg,
node,
minAngle,
idealMinAngle,
incident,
line0,
line1,
line2,
incidentLinkAngles,
nextLink;
nonZeroDeg = degree.filter(function (d) { return d.length >= 1; }).length;
for (j = 0; j < n; ++j) {
node = nodes[j];
line0 = [[node.x, node.y], [node.x+1, node.y]];
// Links that are incident to this node (already filtered out self loops)
incident = degree[j];
if (incident.length <= 1) continue;
idealMinAngle = 360 / incident.length;
// Sort edges by the angle they make from an imaginary vector
// emerging at angle 0 on the unit circle.
// Necessary for calculating angles of incident edges correctly
incident.sort(function (a, b) {
line1 = [
[a.source.x, a.source.y],
[a.target.x, a.target.y]
];
line2 = [
[b.source.x, b.source.y],
[b.target.x, b.target.y]
];
var angleA = linesegmentsAngle(line0, line1);
var angleB = linesegmentsAngle(line0, line2);
return angleA < angleB ? -1 : angleA > angleB ? 1 : 0;
});
incidentLinkAngles = incident.map(function (l, i) {
nextLink = incident[(i + 1) % incident.length];
line1 = [
[l.source.x, l.source.y],
[l.target.x, l.target.y]
];
line2 = [
[nextLink.source.x, nextLink.source.y],
[nextLink.target.x, nextLink.target.y]
];
return linesegmentsAngle(line1, line2);
});
minAngle = Math.min.apply(null, incidentLinkAngles);
resMin += Math.abs(idealMinAngle - minAngle) / idealMinAngle;
resDev += getSumOfArray(incidentLinkAngles.map(function (angle) {
return Math.abs(idealMinAngle - angle) / idealMinAngle;
})) / (2 * incident.length - 2);
}
// Divide by number of nodes with degree != 0
resMin = resMin / nonZeroDeg;
// Divide by number of nodes with degree != 0
resDev = resDev / nonZeroDeg;
return {resMin: resMin, resDev: resDev};
}
initialize();
cMax = (m * (m - 1) / 2) - getSumOfArray(degree.map(function (d) { return d.length * (d.length - 1); })) / 2;
var crossInfo = linkCrossings();
dMax = crossInfo.c * idealAngle;
graphStats.crossing = 1 - (cMax > 0 ? crossInfo.c / cMax : 0);
graphStats.crossingAngle = 1 - (dMax > 0 ? crossInfo.d / dMax : 0);
var angularResInfo = angularRes();
graphStats.angularResolutionMin = 1 - angularResInfo.resMin;
graphStats.angularResolutionDev = 1 - angularResInfo.resDev;
return graphStats;
};
exports.greadability = greadability;
Object.defineProperty(exports, '__esModule', { value: true });
})));
<!DOCTYPE html>
<meta charset="utf-8">
<style>
html, body {
font: 12px sans-serif;
}
svg {
display: block;
}
.links line {
stroke: #999;
stroke-opacity: 0.6;
stroke-width: 2px;
}
.nodes circle {
fill: #d30000;
stroke: #fff;
stroke-width: 1px;
}
.chart circle {
fill: #aaa;
fill-opacity: 0.1;
stroke: #aaa;
stroke-opacity: 0.4;
cursor: pointer;
}
.chart circle.selected {
fill: #d30000;
fill-opacity: 0.6;
stroke: #d30000;
stroke-opacity: 0.8;
}
.column {
float: left;
margin: 0 10px;
}
</style>
<div class="column">
<svg class="chart"></svg>
<svg class="graph"></svg>
</div>
<div class="column">
<p class="progress">Testing</p>
<p>Best parameters so far:</p>
<ul class="best"></ul>
</div>
<script src="greadability.js"></script>
<script src="https://d3js.org/d3.v4.min.js"></script>
<script>
var width = 600;
var height = 500;
var chartWidth = 600;
var chartHeight = 60;
var margin = {left: 10, right: 10, top: 10, bottom: 40};
var numTicks = 200;
var selectedParams;
var bestParams;
var dispatch = d3.dispatch('layoutend');
var svg = d3.select('svg.graph')
.attr('width', width)
.attr('height', height);
var chartSvg = d3.select('svg.chart')
.attr('width', chartWidth)
.attr('height', chartHeight)
.append('g')
.attr('transform', 'translate(' + margin.left + ',' + margin.top + ')');
chartWidth = chartWidth - margin.left - margin.right;
chartHeight = chartHeight - margin.top - margin.bottom;
var x = d3.scaleLinear()
.domain([0, 1])
.range([0, chartWidth]);
chartSvg.append('g')
.attr('transform', 'translate(0,' + chartHeight + ')')
.call(d3.axisBottom(x).ticks(7))
.append("text")
.attr("fill", "#000")
.attr('transform', 'translate(' + chartWidth/2 + ',' + 0 + ')')
.attr("y", chartHeight + 10)
.attr("dy", "0.71em")
.attr("text-anchor", "middle")
.text("Average readability score");
var readabilityCircles = chartSvg.append('g').selectAll('circle');
d3.json('miserables.json', function (error, graph) {
if (error) throw error;
var link = svg.append('g')
.attr('class', 'links')
.selectAll('line')
.data(graph.links)
.enter().append('line');
var node = svg.append('g')
.attr('class', 'nodes')
.selectAll('circle')
.data(graph.nodes)
.enter().append('circle')
.attr('r', 4);
node.append('title').text(function (d) { return d.name; });
var paramGroups = [
{name: 'chargeStrength', values: [-30, -80]},
{name: 'linkDistance', values: [30, -80]},
{name: 'linkStrength', values: [null, 0.25]},
{name: 'gravity', values: [0, 0.5]},
{name: 'iterations', values: [1, 2]},
{name: 'alphaDecay', values: [0, 0.0228, 0.05]},
{name: 'velocityDecay', values: [0.4, 0.8]}
];
var paramList = generateParams(paramGroups);
var bestSoFar = d3.select('.best').selectAll('li')
.data(paramGroups.map(function (d) { return d.name; }))
.enter().append('li')
.text(function (d) { return d; });
dispatch.on('layoutend', function (params, i) {
if (!bestParams || params.graphReadability > bestParams.graphReadability) {
bestParams = params;
selectedParams = bestParams;
bestSoFar
.data(d3.map(bestParams).keys().filter(function (d) { return d !== 'positions' && d !== 'graphReadability'; }))
.text(function (d) { return d + ' = ' + bestParams[d]; });
}
d3.select('.progress').text('Testing ' + (i + 1) + ' of ' + paramList.length + ' parameter settings');
// Plot the number line.
readabilityCircles = readabilityCircles
.data(readabilityCircles.data().concat(params))
.enter().append('circle')
.attr('cx', function (d) { return x(d.graphReadability); })
.attr('cy', 5)
.attr('r', 4)
.on('click', function (d) {
selectedParams = d;
readabilityCircles.classed('selected', false);
d3.select(this).classed('selected', true).raise();
bestSoFar
.data(d3.map(selectedParams).keys().filter(function (d) { return d !== 'positions' && d !== 'graphReadability'; }))
.text(function (d) { return d + ' = ' + selectedParams[d]; });
drawGraph();
})
.merge(readabilityCircles)
.classed('selected', function (d) { return d === selectedParams; });
readabilityCircles.filter(function (d) { return d === selectedParams; })
.raise();
drawGraph();
});
var i = 0;
var stepper = d3.timer(function () {
var p = paramList[i];
var forceSim = getForceSimFromParams(p);
// Reset node attributes.
graph.nodes.forEach(function (n) {
n.x = n.y = n.vx = n.vy = 0;
});
forceSim.nodes(graph.nodes)
.stop();
forceSim.force('link')
.links(graph.links);
for (var t = 0; t < numTicks; ++t) {
forceSim.tick();
}
p.graphReadability = greadability.greadability(graph.nodes, graph.links);
p.graphReadability = (p.graphReadability.crossing + p.graphReadability.crossingAngle +
p.graphReadability.angularResolutionMin + p.graphReadability.angularResolutionDev) / 4
p.positions = graph.nodes.map(function (n) { return {x: n.x, y: n.y}; });
dispatch.call('layoutend', forceSim, p, i);
++i;
if (i >= paramList.length) {
stepper.stop();
}
});
function drawGraph () {
graph.nodes.forEach(function (n, i) {
n.x = selectedParams.positions[i].x;
n.y = selectedParams.positions[i].y;
});
var xDistance = d3.extent(graph.nodes, function (n) { return n.x; });
var xMin = xDistance[0];
xDistance = xDistance[1] - xDistance[0];
var yDistance = d3.extent(graph.nodes, function (n) { return n.y; });
var yMin = yDistance[0];
yDistance = yDistance[1] - yDistance[0];
graph.nodes.forEach(function (n, i) {
n.x = (height - 10) * (n.x - xMin) / Math.max(xDistance, yDistance);
n.y = (height - 10) * (n.y - yMin) / Math.max(xDistance, yDistance);
});
xDistance = d3.extent(graph.nodes, function (n) { return n.x; });
xMid = (xDistance[1] + xDistance[0]) / 2;
yDistance = d3.extent(graph.nodes, function (n) { return n.y; });
yMid = (yDistance[1] - yDistance[0]) / 2;
graph.nodes.forEach(function (n, i) {
n.x = n.x + width/2 - xMid;
n.y = n.y + height/2 - yMid;
});
link
.attr('x1', function (d) { return d.source.x; })
.attr('x2', function (d) { return d.target.x; })
.attr('y1', function (d) { return d.source.y; })
.attr('y2', function (d) { return d.target.y; });
node
.attr('cx', function (d) { return d.x; })
.attr('cy', function (d) { return d.y; });
}
});
function generateParams (paramGroups, paramList, currParam) {
var p = paramGroups[0];
if (!paramList) paramList = [];
if (!currParam) currParam = {};
p.values.forEach(function (v) {
var setting = {};
setting[p.name] = v;
if (paramGroups.length === 1) {
paramList.push(Object.assign(setting, currParam));
} else {
generateParams(paramGroups.slice(1), paramList, Object.assign(setting, currParam));
}
});
return paramList;
}
function getForceSimFromParams (params) {
var forceSim = d3.forceSimulation()
.force('link', d3.forceLink().iterations(params.iterations))
.force('charge', d3.forceManyBody().strength(params.chargeStrength))
.force('x', d3.forceX(0).strength(params.gravity))
.force('y', d3.forceY(0).strength(params.gravity))
.force('center', d3.forceCenter(0, 0))
.alphaDecay(params.alphaDecay)
.velocityDecay(params.velocityDecay);
if (params.linkStrength !== null) {
forceSim.force('link').strength(params.linkStrength);
}
return forceSim;
}
</script>
{
"nodes":[
{"name":"Myriel","group":1},
{"name":"Napoleon","group":1},
{"name":"Mlle.Baptistine","group":1},
{"name":"Mme.Magloire","group":1},
{"name":"CountessdeLo","group":1},
{"name":"Geborand","group":1},
{"name":"Champtercier","group":1},
{"name":"Cravatte","group":1},
{"name":"Count","group":1},
{"name":"OldMan","group":1},
{"name":"Labarre","group":2},
{"name":"Valjean","group":2},
{"name":"Marguerite","group":3},
{"name":"Mme.deR","group":2},
{"name":"Isabeau","group":2},
{"name":"Gervais","group":2},
{"name":"Tholomyes","group":3},
{"name":"Listolier","group":3},
{"name":"Fameuil","group":3},
{"name":"Blacheville","group":3},
{"name":"Favourite","group":3},
{"name":"Dahlia","group":3},
{"name":"Zephine","group":3},
{"name":"Fantine","group":3},
{"name":"Mme.Thenardier","group":4},
{"name":"Thenardier","group":4},
{"name":"Cosette","group":5},
{"name":"Javert","group":4},
{"name":"Fauchelevent","group":0},
{"name":"Bamatabois","group":2},
{"name":"Perpetue","group":3},
{"name":"Simplice","group":2},
{"name":"Scaufflaire","group":2},
{"name":"Woman1","group":2},
{"name":"Judge","group":2},
{"name":"Champmathieu","group":2},
{"name":"Brevet","group":2},
{"name":"Chenildieu","group":2},
{"name":"Cochepaille","group":2},
{"name":"Pontmercy","group":4},
{"name":"Boulatruelle","group":6},
{"name":"Eponine","group":4},
{"name":"Anzelma","group":4},
{"name":"Woman2","group":5},
{"name":"MotherInnocent","group":0},
{"name":"Gribier","group":0},
{"name":"Jondrette","group":7},
{"name":"Mme.Burgon","group":7},
{"name":"Gavroche","group":8},
{"name":"Gillenormand","group":5},
{"name":"Magnon","group":5},
{"name":"Mlle.Gillenormand","group":5},
{"name":"Mme.Pontmercy","group":5},
{"name":"Mlle.Vaubois","group":5},
{"name":"Lt.Gillenormand","group":5},
{"name":"Marius","group":8},
{"name":"BaronessT","group":5},
{"name":"Mabeuf","group":8},
{"name":"Enjolras","group":8},
{"name":"Combeferre","group":8},
{"name":"Prouvaire","group":8},
{"name":"Feuilly","group":8},
{"name":"Courfeyrac","group":8},
{"name":"Bahorel","group":8},
{"name":"Bossuet","group":8},
{"name":"Joly","group":8},
{"name":"Grantaire","group":8},
{"name":"MotherPlutarch","group":9},
{"name":"Gueulemer","group":4},
{"name":"Babet","group":4},
{"name":"Claquesous","group":4},
{"name":"Montparnasse","group":4},
{"name":"Toussaint","group":5},
{"name":"Child1","group":10},
{"name":"Child2","group":10},
{"name":"Brujon","group":4},
{"name":"Mme.Hucheloup","group":8}
],
"links":[
{"source":1,"target":0,"value":1},
{"source":2,"target":0,"value":8},
{"source":3,"target":0,"value":10},
{"source":3,"target":2,"value":6},
{"source":4,"target":0,"value":1},
{"source":5,"target":0,"value":1},
{"source":6,"target":0,"value":1},
{"source":7,"target":0,"value":1},
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