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Last active April 2, 2024 02:39
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Save rodighiero/c4502b8229e181d365f0f6d6637872e8 to your computer and use it in GitHub Desktop.
Hexagonal force-directed graph

That visualization is a remake of the well-known force-directed graph created by Mike Bostock showing character co-occurrence in Les Misérables. This visualization shows how it is possible to organize a graph into an hexagonal structure. This kind of structure is particularly interesting with high-connected networks that appear as spaghetti nebula. The meaning of the link decreases, while the position is more relevant. Space employed is less applying a gravity force to all nodes through charge, while nodes' distance is preserved by using collision. That allows to avoid any kind of overlapping among nodes and makes the distances among nodes uniform. That uniformity might be successively exploited by situating between nodes, for instance, keywords that help to characterize the space that usually is not employed. This application is used within my PhD thesis Affinity Map.

license: gpl-3.0
height: 500
border: no
<!DOCTYPE html>
<meta charset='utf-8'>
<style>
line { stroke: #999; }
circle { stroke: #fff; stroke-width: 1.5px; }
</style>
<svg width='960' height='500'></svg>
<script src='https://d3js.org/d3.v4.min.js'></script>
<script>
var svg = d3.select('svg'),
width = +svg.attr('width'),
height = +svg.attr('height')
var color = d3.scaleOrdinal(d3.schemeCategory20)
var simulation = d3.forceSimulation()
.force('link', d3.forceLink().id(d => d.id))
.force('charge', d3.forceManyBody().strength(100)) // Gravity force
.force('collide', d3.forceCollide().radius(25).iterations(3)) // Repulsion force
.force('center', d3.forceCenter(width / 2, height / 2)) // Position force
d3.json('miserables.json', function(error, graph) {
if (error) throw error
var link = svg.append('g')
.selectAll('line')
.data(graph.links)
.enter().append('line')
.attr( 'stroke-width', d => d.value * .08 )
var node = svg.append('g')
.selectAll('circle')
.data(graph.nodes)
.enter().append('circle')
.attr('r', 5)
.attr( 'fill', d => color(d.group) )
.call(d3.drag()
.on('start', dragstarted)
.on('drag', dragged)
.on('end', dragended))
simulation
.nodes(graph.nodes)
.on('tick', ticked)
simulation.force('link')
.links(graph.links)
function ticked() {
link
.attr( 'x1', d => d.source.x )
.attr( 'y1', d => d.source.y )
.attr( 'x2', d => d.target.x )
.attr( 'y2', d => d.target.y )
node
.attr( 'cx', d => d.x )
.attr( 'cy', d => d.y )
}
})
function dragstarted(d) {
if (!d3.event.active) simulation.alphaTarget(0.1).restart()
d.fx = d.x
d.fy = d.y
}
function dragged(d) {
d.fx = d3.event.x
d.fy = d3.event.y
}
function dragended(d) {
if (!d3.event.active) simulation.alphaTarget(0)
d.fx = null
d.fy = null
}
</script>
{
"nodes": [
{"id": "Myriel", "group": 1},
{"id": "Napoleon", "group": 1},
{"id": "Mlle.Baptistine", "group": 1},
{"id": "Mme.Magloire", "group": 1},
{"id": "CountessdeLo", "group": 1},
{"id": "Geborand", "group": 1},
{"id": "Champtercier", "group": 1},
{"id": "Cravatte", "group": 1},
{"id": "Count", "group": 1},
{"id": "OldMan", "group": 1},
{"id": "Labarre", "group": 2},
{"id": "Valjean", "group": 2},
{"id": "Marguerite", "group": 3},
{"id": "Mme.deR", "group": 2},
{"id": "Isabeau", "group": 2},
{"id": "Gervais", "group": 2},
{"id": "Tholomyes", "group": 3},
{"id": "Listolier", "group": 3},
{"id": "Fameuil", "group": 3},
{"id": "Blacheville", "group": 3},
{"id": "Favourite", "group": 3},
{"id": "Dahlia", "group": 3},
{"id": "Zephine", "group": 3},
{"id": "Fantine", "group": 3},
{"id": "Mme.Thenardier", "group": 4},
{"id": "Thenardier", "group": 4},
{"id": "Cosette", "group": 5},
{"id": "Javert", "group": 4},
{"id": "Fauchelevent", "group": 0},
{"id": "Bamatabois", "group": 2},
{"id": "Perpetue", "group": 3},
{"id": "Simplice", "group": 2},
{"id": "Scaufflaire", "group": 2},
{"id": "Woman1", "group": 2},
{"id": "Judge", "group": 2},
{"id": "Champmathieu", "group": 2},
{"id": "Brevet", "group": 2},
{"id": "Chenildieu", "group": 2},
{"id": "Cochepaille", "group": 2},
{"id": "Pontmercy", "group": 4},
{"id": "Boulatruelle", "group": 6},
{"id": "Eponine", "group": 4},
{"id": "Anzelma", "group": 4},
{"id": "Woman2", "group": 5},
{"id": "MotherInnocent", "group": 0},
{"id": "Gribier", "group": 0},
{"id": "Jondrette", "group": 7},
{"id": "Mme.Burgon", "group": 7},
{"id": "Gavroche", "group": 8},
{"id": "Gillenormand", "group": 5},
{"id": "Magnon", "group": 5},
{"id": "Mlle.Gillenormand", "group": 5},
{"id": "Mme.Pontmercy", "group": 5},
{"id": "Mlle.Vaubois", "group": 5},
{"id": "Lt.Gillenormand", "group": 5},
{"id": "Marius", "group": 8},
{"id": "BaronessT", "group": 5},
{"id": "Mabeuf", "group": 8},
{"id": "Enjolras", "group": 8},
{"id": "Combeferre", "group": 8},
{"id": "Prouvaire", "group": 8},
{"id": "Feuilly", "group": 8},
{"id": "Courfeyrac", "group": 8},
{"id": "Bahorel", "group": 8},
{"id": "Bossuet", "group": 8},
{"id": "Joly", "group": 8},
{"id": "Grantaire", "group": 8},
{"id": "MotherPlutarch", "group": 9},
{"id": "Gueulemer", "group": 4},
{"id": "Babet", "group": 4},
{"id": "Claquesous", "group": 4},
{"id": "Montparnasse", "group": 4},
{"id": "Toussaint", "group": 5},
{"id": "Child1", "group": 10},
{"id": "Child2", "group": 10},
{"id": "Brujon", "group": 4},
{"id": "Mme.Hucheloup", "group": 8}
],
"links": [
{"source": "Napoleon", "target": "Myriel", "value": 1},
{"source": "Mlle.Baptistine", "target": "Myriel", "value": 8},
{"source": "Mme.Magloire", "target": "Myriel", "value": 10},
{"source": "Mme.Magloire", "target": "Mlle.Baptistine", "value": 6},
{"source": "CountessdeLo", "target": "Myriel", "value": 1},
{"source": "Geborand", "target": "Myriel", "value": 1},
{"source": "Champtercier", "target": "Myriel", "value": 1},
{"source": "Cravatte", "target": "Myriel", "value": 1},
{"source": "Count", "target": "Myriel", "value": 2},
{"source": "OldMan", "target": "Myriel", "value": 1},
{"source": "Valjean", "target": "Labarre", "value": 1},
{"source": "Valjean", "target": "Mme.Magloire", "value": 3},
{"source": "Valjean", "target": "Mlle.Baptistine", "value": 3},
{"source": "Valjean", "target": "Myriel", "value": 5},
{"source": "Marguerite", "target": "Valjean", "value": 1},
{"source": "Mme.deR", "target": "Valjean", "value": 1},
{"source": "Isabeau", "target": "Valjean", "value": 1},
{"source": "Gervais", "target": "Valjean", "value": 1},
{"source": "Listolier", "target": "Tholomyes", "value": 4},
{"source": "Fameuil", "target": "Tholomyes", "value": 4},
{"source": "Fameuil", "target": "Listolier", "value": 4},
{"source": "Blacheville", "target": "Tholomyes", "value": 4},
{"source": "Blacheville", "target": "Listolier", "value": 4},
{"source": "Blacheville", "target": "Fameuil", "value": 4},
{"source": "Favourite", "target": "Tholomyes", "value": 3},
{"source": "Favourite", "target": "Listolier", "value": 3},
{"source": "Favourite", "target": "Fameuil", "value": 3},
{"source": "Favourite", "target": "Blacheville", "value": 4},
{"source": "Dahlia", "target": "Tholomyes", "value": 3},
{"source": "Dahlia", "target": "Listolier", "value": 3},
{"source": "Dahlia", "target": "Fameuil", "value": 3},
{"source": "Dahlia", "target": "Blacheville", "value": 3},
{"source": "Dahlia", "target": "Favourite", "value": 5},
{"source": "Zephine", "target": "Tholomyes", "value": 3},
{"source": "Zephine", "target": "Listolier", "value": 3},
{"source": "Zephine", "target": "Fameuil", "value": 3},
{"source": "Zephine", "target": "Blacheville", "value": 3},
{"source": "Zephine", "target": "Favourite", "value": 4},
{"source": "Zephine", "target": "Dahlia", "value": 4},
{"source": "Fantine", "target": "Tholomyes", "value": 3},
{"source": "Fantine", "target": "Listolier", "value": 3},
{"source": "Fantine", "target": "Fameuil", "value": 3},
{"source": "Fantine", "target": "Blacheville", "value": 3},
{"source": "Fantine", "target": "Favourite", "value": 4},
{"source": "Fantine", "target": "Dahlia", "value": 4},
{"source": "Fantine", "target": "Zephine", "value": 4},
{"source": "Fantine", "target": "Marguerite", "value": 2},
{"source": "Fantine", "target": "Valjean", "value": 9},
{"source": "Mme.Thenardier", "target": "Fantine", "value": 2},
{"source": "Mme.Thenardier", "target": "Valjean", "value": 7},
{"source": "Thenardier", "target": "Mme.Thenardier", "value": 13},
{"source": "Thenardier", "target": "Fantine", "value": 1},
{"source": "Thenardier", "target": "Valjean", "value": 12},
{"source": "Cosette", "target": "Mme.Thenardier", "value": 4},
{"source": "Cosette", "target": "Valjean", "value": 31},
{"source": "Cosette", "target": "Tholomyes", "value": 1},
{"source": "Cosette", "target": "Thenardier", "value": 1},
{"source": "Javert", "target": "Valjean", "value": 17},
{"source": "Javert", "target": "Fantine", "value": 5},
{"source": "Javert", "target": "Thenardier", "value": 5},
{"source": "Javert", "target": "Mme.Thenardier", "value": 1},
{"source": "Javert", "target": "Cosette", "value": 1},
{"source": "Fauchelevent", "target": "Valjean", "value": 8},
{"source": "Fauchelevent", "target": "Javert", "value": 1},
{"source": "Bamatabois", "target": "Fantine", "value": 1},
{"source": "Bamatabois", "target": "Javert", "value": 1},
{"source": "Bamatabois", "target": "Valjean", "value": 2},
{"source": "Perpetue", "target": "Fantine", "value": 1},
{"source": "Simplice", "target": "Perpetue", "value": 2},
{"source": "Simplice", "target": "Valjean", "value": 3},
{"source": "Simplice", "target": "Fantine", "value": 2},
{"source": "Simplice", "target": "Javert", "value": 1},
{"source": "Scaufflaire", "target": "Valjean", "value": 1},
{"source": "Woman1", "target": "Valjean", "value": 2},
{"source": "Woman1", "target": "Javert", "value": 1},
{"source": "Judge", "target": "Valjean", "value": 3},
{"source": "Judge", "target": "Bamatabois", "value": 2},
{"source": "Champmathieu", "target": "Valjean", "value": 3},
{"source": "Champmathieu", "target": "Judge", "value": 3},
{"source": "Champmathieu", "target": "Bamatabois", "value": 2},
{"source": "Brevet", "target": "Judge", "value": 2},
{"source": "Brevet", "target": "Champmathieu", "value": 2},
{"source": "Brevet", "target": "Valjean", "value": 2},
{"source": "Brevet", "target": "Bamatabois", "value": 1},
{"source": "Chenildieu", "target": "Judge", "value": 2},
{"source": "Chenildieu", "target": "Champmathieu", "value": 2},
{"source": "Chenildieu", "target": "Brevet", "value": 2},
{"source": "Chenildieu", "target": "Valjean", "value": 2},
{"source": "Chenildieu", "target": "Bamatabois", "value": 1},
{"source": "Cochepaille", "target": "Judge", "value": 2},
{"source": "Cochepaille", "target": "Champmathieu", "value": 2},
{"source": "Cochepaille", "target": "Brevet", "value": 2},
{"source": "Cochepaille", "target": "Chenildieu", "value": 2},
{"source": "Cochepaille", "target": "Valjean", "value": 2},
{"source": "Cochepaille", "target": "Bamatabois", "value": 1},
{"source": "Pontmercy", "target": "Thenardier", "value": 1},
{"source": "Boulatruelle", "target": "Thenardier", "value": 1},
{"source": "Eponine", "target": "Mme.Thenardier", "value": 2},
{"source": "Eponine", "target": "Thenardier", "value": 3},
{"source": "Anzelma", "target": "Eponine", "value": 2},
{"source": "Anzelma", "target": "Thenardier", "value": 2},
{"source": "Anzelma", "target": "Mme.Thenardier", "value": 1},
{"source": "Woman2", "target": "Valjean", "value": 3},
{"source": "Woman2", "target": "Cosette", "value": 1},
{"source": "Woman2", "target": "Javert", "value": 1},
{"source": "MotherInnocent", "target": "Fauchelevent", "value": 3},
{"source": "MotherInnocent", "target": "Valjean", "value": 1},
{"source": "Gribier", "target": "Fauchelevent", "value": 2},
{"source": "Mme.Burgon", "target": "Jondrette", "value": 1},
{"source": "Gavroche", "target": "Mme.Burgon", "value": 2},
{"source": "Gavroche", "target": "Thenardier", "value": 1},
{"source": "Gavroche", "target": "Javert", "value": 1},
{"source": "Gavroche", "target": "Valjean", "value": 1},
{"source": "Gillenormand", "target": "Cosette", "value": 3},
{"source": "Gillenormand", "target": "Valjean", "value": 2},
{"source": "Magnon", "target": "Gillenormand", "value": 1},
{"source": "Magnon", "target": "Mme.Thenardier", "value": 1},
{"source": "Mlle.Gillenormand", "target": "Gillenormand", "value": 9},
{"source": "Mlle.Gillenormand", "target": "Cosette", "value": 2},
{"source": "Mlle.Gillenormand", "target": "Valjean", "value": 2},
{"source": "Mme.Pontmercy", "target": "Mlle.Gillenormand", "value": 1},
{"source": "Mme.Pontmercy", "target": "Pontmercy", "value": 1},
{"source": "Mlle.Vaubois", "target": "Mlle.Gillenormand", "value": 1},
{"source": "Lt.Gillenormand", "target": "Mlle.Gillenormand", "value": 2},
{"source": "Lt.Gillenormand", "target": "Gillenormand", "value": 1},
{"source": "Lt.Gillenormand", "target": "Cosette", "value": 1},
{"source": "Marius", "target": "Mlle.Gillenormand", "value": 6},
{"source": "Marius", "target": "Gillenormand", "value": 12},
{"source": "Marius", "target": "Pontmercy", "value": 1},
{"source": "Marius", "target": "Lt.Gillenormand", "value": 1},
{"source": "Marius", "target": "Cosette", "value": 21},
{"source": "Marius", "target": "Valjean", "value": 19},
{"source": "Marius", "target": "Tholomyes", "value": 1},
{"source": "Marius", "target": "Thenardier", "value": 2},
{"source": "Marius", "target": "Eponine", "value": 5},
{"source": "Marius", "target": "Gavroche", "value": 4},
{"source": "BaronessT", "target": "Gillenormand", "value": 1},
{"source": "BaronessT", "target": "Marius", "value": 1},
{"source": "Mabeuf", "target": "Marius", "value": 1},
{"source": "Mabeuf", "target": "Eponine", "value": 1},
{"source": "Mabeuf", "target": "Gavroche", "value": 1},
{"source": "Enjolras", "target": "Marius", "value": 7},
{"source": "Enjolras", "target": "Gavroche", "value": 7},
{"source": "Enjolras", "target": "Javert", "value": 6},
{"source": "Enjolras", "target": "Mabeuf", "value": 1},
{"source": "Enjolras", "target": "Valjean", "value": 4},
{"source": "Combeferre", "target": "Enjolras", "value": 15},
{"source": "Combeferre", "target": "Marius", "value": 5},
{"source": "Combeferre", "target": "Gavroche", "value": 6},
{"source": "Combeferre", "target": "Mabeuf", "value": 2},
{"source": "Prouvaire", "target": "Gavroche", "value": 1},
{"source": "Prouvaire", "target": "Enjolras", "value": 4},
{"source": "Prouvaire", "target": "Combeferre", "value": 2},
{"source": "Feuilly", "target": "Gavroche", "value": 2},
{"source": "Feuilly", "target": "Enjolras", "value": 6},
{"source": "Feuilly", "target": "Prouvaire", "value": 2},
{"source": "Feuilly", "target": "Combeferre", "value": 5},
{"source": "Feuilly", "target": "Mabeuf", "value": 1},
{"source": "Feuilly", "target": "Marius", "value": 1},
{"source": "Courfeyrac", "target": "Marius", "value": 9},
{"source": "Courfeyrac", "target": "Enjolras", "value": 17},
{"source": "Courfeyrac", "target": "Combeferre", "value": 13},
{"source": "Courfeyrac", "target": "Gavroche", "value": 7},
{"source": "Courfeyrac", "target": "Mabeuf", "value": 2},
{"source": "Courfeyrac", "target": "Eponine", "value": 1},
{"source": "Courfeyrac", "target": "Feuilly", "value": 6},
{"source": "Courfeyrac", "target": "Prouvaire", "value": 3},
{"source": "Bahorel", "target": "Combeferre", "value": 5},
{"source": "Bahorel", "target": "Gavroche", "value": 5},
{"source": "Bahorel", "target": "Courfeyrac", "value": 6},
{"source": "Bahorel", "target": "Mabeuf", "value": 2},
{"source": "Bahorel", "target": "Enjolras", "value": 4},
{"source": "Bahorel", "target": "Feuilly", "value": 3},
{"source": "Bahorel", "target": "Prouvaire", "value": 2},
{"source": "Bahorel", "target": "Marius", "value": 1},
{"source": "Bossuet", "target": "Marius", "value": 5},
{"source": "Bossuet", "target": "Courfeyrac", "value": 12},
{"source": "Bossuet", "target": "Gavroche", "value": 5},
{"source": "Bossuet", "target": "Bahorel", "value": 4},
{"source": "Bossuet", "target": "Enjolras", "value": 10},
{"source": "Bossuet", "target": "Feuilly", "value": 6},
{"source": "Bossuet", "target": "Prouvaire", "value": 2},
{"source": "Bossuet", "target": "Combeferre", "value": 9},
{"source": "Bossuet", "target": "Mabeuf", "value": 1},
{"source": "Bossuet", "target": "Valjean", "value": 1},
{"source": "Joly", "target": "Bahorel", "value": 5},
{"source": "Joly", "target": "Bossuet", "value": 7},
{"source": "Joly", "target": "Gavroche", "value": 3},
{"source": "Joly", "target": "Courfeyrac", "value": 5},
{"source": "Joly", "target": "Enjolras", "value": 5},
{"source": "Joly", "target": "Feuilly", "value": 5},
{"source": "Joly", "target": "Prouvaire", "value": 2},
{"source": "Joly", "target": "Combeferre", "value": 5},
{"source": "Joly", "target": "Mabeuf", "value": 1},
{"source": "Joly", "target": "Marius", "value": 2},
{"source": "Grantaire", "target": "Bossuet", "value": 3},
{"source": "Grantaire", "target": "Enjolras", "value": 3},
{"source": "Grantaire", "target": "Combeferre", "value": 1},
{"source": "Grantaire", "target": "Courfeyrac", "value": 2},
{"source": "Grantaire", "target": "Joly", "value": 2},
{"source": "Grantaire", "target": "Gavroche", "value": 1},
{"source": "Grantaire", "target": "Bahorel", "value": 1},
{"source": "Grantaire", "target": "Feuilly", "value": 1},
{"source": "Grantaire", "target": "Prouvaire", "value": 1},
{"source": "MotherPlutarch", "target": "Mabeuf", "value": 3},
{"source": "Gueulemer", "target": "Thenardier", "value": 5},
{"source": "Gueulemer", "target": "Valjean", "value": 1},
{"source": "Gueulemer", "target": "Mme.Thenardier", "value": 1},
{"source": "Gueulemer", "target": "Javert", "value": 1},
{"source": "Gueulemer", "target": "Gavroche", "value": 1},
{"source": "Gueulemer", "target": "Eponine", "value": 1},
{"source": "Babet", "target": "Thenardier", "value": 6},
{"source": "Babet", "target": "Gueulemer", "value": 6},
{"source": "Babet", "target": "Valjean", "value": 1},
{"source": "Babet", "target": "Mme.Thenardier", "value": 1},
{"source": "Babet", "target": "Javert", "value": 2},
{"source": "Babet", "target": "Gavroche", "value": 1},
{"source": "Babet", "target": "Eponine", "value": 1},
{"source": "Claquesous", "target": "Thenardier", "value": 4},
{"source": "Claquesous", "target": "Babet", "value": 4},
{"source": "Claquesous", "target": "Gueulemer", "value": 4},
{"source": "Claquesous", "target": "Valjean", "value": 1},
{"source": "Claquesous", "target": "Mme.Thenardier", "value": 1},
{"source": "Claquesous", "target": "Javert", "value": 1},
{"source": "Claquesous", "target": "Eponine", "value": 1},
{"source": "Claquesous", "target": "Enjolras", "value": 1},
{"source": "Montparnasse", "target": "Javert", "value": 1},
{"source": "Montparnasse", "target": "Babet", "value": 2},
{"source": "Montparnasse", "target": "Gueulemer", "value": 2},
{"source": "Montparnasse", "target": "Claquesous", "value": 2},
{"source": "Montparnasse", "target": "Valjean", "value": 1},
{"source": "Montparnasse", "target": "Gavroche", "value": 1},
{"source": "Montparnasse", "target": "Eponine", "value": 1},
{"source": "Montparnasse", "target": "Thenardier", "value": 1},
{"source": "Toussaint", "target": "Cosette", "value": 2},
{"source": "Toussaint", "target": "Javert", "value": 1},
{"source": "Toussaint", "target": "Valjean", "value": 1},
{"source": "Child1", "target": "Gavroche", "value": 2},
{"source": "Child2", "target": "Gavroche", "value": 2},
{"source": "Child2", "target": "Child1", "value": 3},
{"source": "Brujon", "target": "Babet", "value": 3},
{"source": "Brujon", "target": "Gueulemer", "value": 3},
{"source": "Brujon", "target": "Thenardier", "value": 3},
{"source": "Brujon", "target": "Gavroche", "value": 1},
{"source": "Brujon", "target": "Eponine", "value": 1},
{"source": "Brujon", "target": "Claquesous", "value": 1},
{"source": "Brujon", "target": "Montparnasse", "value": 1},
{"source": "Mme.Hucheloup", "target": "Bossuet", "value": 1},
{"source": "Mme.Hucheloup", "target": "Joly", "value": 1},
{"source": "Mme.Hucheloup", "target": "Grantaire", "value": 1},
{"source": "Mme.Hucheloup", "target": "Bahorel", "value": 1},
{"source": "Mme.Hucheloup", "target": "Courfeyrac", "value": 1},
{"source": "Mme.Hucheloup", "target": "Gavroche", "value": 1},
{"source": "Mme.Hucheloup", "target": "Enjolras", "value": 1}
]
}
@rodighiero
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I am not really sure there is a technique to favor the computational charge. I have to admit that in my experience networks are doing great for rather small datasets. This pushed me to explore vector reduction as an alternative to network algorithms. The uselessness of drawing unreadable, overlapping links was also a good point to move in that direction. You can take a look at this ongoing project which is based on UMAP arrangement https://rodighiero.github.io/SPT2021/.

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