Nodes

<!DOCTYPE html>
<html>
  <head>
    <title>Force-Directed Layout with Convex Hull</title>
  <script src="https://d3js.org/d3.v4.min.js"></script>
 </head>
  <body>
<style>
  line {
    fill: white;
    stroke: black;
    stroke-width: 1;
  }
  .background {
    fill: none;
    stroke: none;
  }
  .polygons {
    fill: none;
    stroke: #000;
  }
</style>
<script type="text/javascript">
  // parameters
  var w = 960,
      h = 500,
      n = 100,
      nb_groups =9 ,
      nb_simulation = 120,
      fill = d3.scaleOrdinal(d3.schemeCategory20),
      graph = {};
  // we generate n random nodes in nb_groups
  graph.nodes = d3.range(n).map(function(d, i) {
    return {id: i, group: i % nb_groups, r: 10*Math.random()}
  });
  // we don't generate links, yet

//  creation de la liste des liens entre noeuds 
  graph.links = [];
  //  population de liste des liens entre noeuds en utilisant la fct random avec une proba moins de .015 pour générer des liens entre noeuds proche
  graph.nodes.forEach(function(d, i){
    graph.nodes.forEach(function(e, j){
      if(d !== e && Math.random() < .015){
        graph.links.push({source: d, target: e})
      }
    })
  });

/*
  graph.links= [{source : graph.nodes[0],target : graph.nodes[2]},
                {source : graph.nodes[1],target : graph.nodes[2]},
                {source : graph.nodes[2],target : graph.nodes[99]} ]
  */
  /*  LINK NODES TO EACH OTHERS
  graph.nodes.forEach(function(d,i)){
      graph.nodes.forEach(function(e,j))
                     } */ 
  
  
  
  // main svg canvas
  var svg = d3.select("body").append("svg")
    .attr("width", w)
    .attr("height", h);
  // we separate ndoes using 3 arbitrary columns
  var cols = Math.ceil(Math.sqrt(nb_groups));
  //size of matrix
  //var size = Math.sqrt(nb_groups);
  // horizontal scale for the columns
  var x = d3.scaleLinear()
    .domain([0, cols])
    .range([w/4, 3*w/4]);
  var y = d3.scaleLinear()   //  calcule de y  en fonction de cols et h
    .domain([0, cols])
    .range([h/4, 3*h/4]);
  // MAIN LOOP
  // sets positions for each node based on index
  // -we store the pixel values
  // -those are calculated only once
  graph.nodes.forEach(function(d, i) {
    var col = d.group % cols;
    var row = Math.floor(d.group/cols)
    d.x = x(col);
    d.y = y(row);
  });
  // simulation of positions
  
  var simulation = d3.forceSimulation()
      // .force("link", d3.forceLink().id(function(d) { return d.id; }))
      .force("charge", d3.forceManyBody())
      .force("x", d3.forceX(function(d, i) {
        return d.x;
      }))
      .force("y", d3.forceY(function(d, i) {
        return d.y;
      }))
      .force("collide", d3.forceCollide(12).radius(function(d) { return d.r + 0.5; }).iterations(2))
      .force("center", d3.forceCenter(w / 2, h / 2))
      .stop();
  // apply the simulation to nodes
  simulation
      .nodes(graph.nodes);
  // apply the simulation to links
  /*simulation.force("link")
      .links(graph.links); */
  // we run the simulation nb_simulation times
  for (var i = 0; i < nb_simulation; ++i) simulation.tick();
  // we create a Voronoi partition based on nodes positions
  var voronoi = d3.voronoi()
      .extent([[0, 0], [w, h]])
      .x(function(d) { return d.x; })
      .y(function(d) { return d.y; })
  // we draw the voronoi partition using paths
  var polygon = svg.append("g")
      .attr("class", "polygons")
      .selectAll("path")
      .data(voronoi.polygons(graph.nodes))
    .enter()
      .append("path")
      .attr("id", function(d) { return "_" + d.data.id; })
      .style("fill", "white")
      .on("mouseenter", function(d) {
        // highlight nodes in the current partition
        d3.select(this).style("fill", "red").transition().style("fill", "white")
        d3.selectAll("circle#" + d3.select(this).attr("id"))
          .attr("r", 10)
          .transition()
          .attr("r", function(d) { return d.r; });

d3.selectAll(".links").style("opacity", .1).style("stroke-width", 1);

d3.selectAll(".links").filter(function(e) {
          if(d.data === e.source || d.data === e.target){
            return true;
          }
          else {
            return false;
          }
        })
        .style("opacity", 1)
        .style("stroke-width", 3);
      })
      .on("mouseleave", function(d) {
      })
     .call(redrawPolygon);
  // create nodes using the graph.nodes object
  var node = svg.selectAll("circle.node")
      .data(graph.nodes)
    .enter()
      .append("circle")
      .attr("class", "node")
      .attr("r", function(d) { return d.r; })
      .attr("id", function(d) { return "_" + d.id; })
      .style("fill", function(d, i) { return fill(i); })
      .style("stroke", function(d, i) { return d3.rgb(fill(i)).darker(2); })
      .style("stroke-width", 1.5);
  // draw the nodes
  node
      .attr("cx", function(d) { return d.x; })
      .attr("cy", function(d) { return d.y; });

// dessiner pour chaque noeud ses liens avec les autres noeuds de son groupe
      var link = svg.append("g")
      .selectAll("line")
      .data(graph.links)
      .enter()
      .append("line")
      .attr("class", "links");
  // draw links
  link
      .attr("x1", function(d) { return d.source.x; })
      .attr("y1", function(d) { return d.source.y; })
      .attr("x2", function(d) { return d.target.x; })
      .attr("y2", function(d) { return d.target.y; });
  // function to draw the vornoi partition
  function redrawPolygon(polygon) {
    polygon
        .attr("d", function(d) { return d ? "M" + d.join("L") + "Z" : null; });
  }
  
  
    
    </script>
  </body>
</html>

https://d3js.org/d3.v4.min.js