GUIDE
- Left-click and drag the background to move the graph
- Left-click and drag the nodes to reorganize
- Left-click a node to view first level connections
- Double left-click a node to navigate to its page
- Double left-click the background to zoom in
- Right-click the background to zoom out
sigma.utils.pkg('sigma.canvas.nodes');
sigma.canvas.nodes.image = (function() {
var _cache = {},
_loading = {},
_callbacks = {};
// Return the renderer itself:
var renderer = function(node, context, settings) {
var args = arguments,
prefix = settings('prefix') || '',
size = node[prefix + 'size'],
color = node.color || settings('defaultNodeColor'),
url = node.url;
if (_cache[url]) {
context.save();
// Draw the clipping disc:
context.beginPath();
context.arc(
node[prefix + 'x'],
node[prefix + 'y'],
node[prefix + 'size'],
0,
Math.PI * 2,
true
);
context.closePath();
context.clip();
// Draw the image
context.drawImage(
_cache[url],
node[prefix + 'x'] - size,
node[prefix + 'y'] - size,
2 * size,
2 * size
);
// Quit the "clipping mode":
context.restore();
// Draw the border:
context.beginPath();
context.arc(
node[prefix + 'x'],
node[prefix + 'y'],
node[prefix + 'size'],
0,
Math.PI * 2,
true
);
context.lineWidth = 1;
context.strokeStyle = node.color || settings('defaultNodeColor');
context.stroke();
} else {
sigma.canvas.nodes.image.cache(url);
sigma.canvas.nodes.def.apply(
sigma.canvas.nodes,
args
);
}
};
// Let's add a public method to cache images, to make it possible to
// preload images before the initial rendering:
renderer.cache = function(url, callback) {
if (callback)
_callbacks[url] = callback;
if (_loading[url])
return;
var img = new Image();
img.onload = function() {
_loading[url] = false;
_cache[url] = img;
if (_callbacks[url]) {
_callbacks[url].call(this, img);
delete _callbacks[url];
}
};
_loading[url] = true;
img.src = url;
};
return renderer;
})();
var i,
s,
o,
offset_left = 0.5,
N = 1,
E = 40,
C = 5,
d = 0.5,
cs = [],
g = {
nodes: [],
edges: []
};
if (!sigma.classes.graph.hasMethod('neighbors')){
sigma.classes.graph.addMethod('neighbors', function(nodeId) {
var k,
neighbors = {},
index = this.allNeighborsIndex[nodeId] || {};
for (k in index)
neighbors[k] = this.nodesIndex[k];
return neighbors;
});
}
//adding the central node
g.nodes.push({
id: 4607,
label: 'Alexandra Tachtsidi',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2019/08/research_pasteur-capture-decran-2019-08-01-a-13.26.07-150x150.png',
x: 0,
y: 0,
size: 30,
color: '#DDDDDD'
});
var biggest_node_size = 0;
N=3
// adding node
var x_node = Math.cos(2 * 0 * Math.PI / N) * 10;
var y_node = Math.sin(2 * 0 * Math.PI / N) * 10;
g.nodes.push({
id: 116628,
label: 'EVENT: Thesis Defense: « Nuclear organization and regulation of gene expression in Mouse Embryonic Stem Cells by long non-coding RNAs.» ALEXANDRA TACHTSIDI – December 11th @ 9:30 am',
x: x_node,
y: y_node,
type: 'image',
url: '',
page_url: 'https://research.pasteur.fr/en/event/thesis-defense-nuclear-organization-and-regulation-of-gene-expression-in-mouse-embryonic-stem-cells-by-long-non-coding-rnas-alexandra-tachtsidi-december-11th-930-am/',
size: 35,
color: '#DDDDDD'
});
//link content to central post
g.edges.push({
id: 4607116628,
size: 0.5,
source: 4607,
target: 116628,
});
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 4606,
label: 'Pablo Navarro Gil',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2019/10/research_pasteur-institut-pasteur_portraits-studio_gcc_162-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/member/pablo-navarro-gil/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 1166284606,
size: 0.5,
source: 116628,
target: 4606 });
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 4607) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 1166284607,
size: 0.5,
source: 116628,
target: 4607 });
// adding node
var x_node = Math.cos(2 * 1 * Math.PI / N) * 10;
var y_node = Math.sin(2 * 1 * Math.PI / N) * 10;
g.nodes.push({
id: 16079,
label: 'PROJECT: The contribution of long non-coding RNAs to the network’s activity',
x: x_node,
y: y_node,
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2019/10/research_pasteur-next-150x150.png',
page_url: 'https://research.pasteur.fr/en/project/the-contribution-of-long-non-coding-rnas-to-the-networks-activity/',
size: 35,
color: '#DDDDDD'
});
//link content to central post
g.edges.push({
id: 460716079,
size: 0.5,
source: 4607,
target: 16079,
});
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 4606) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 160794606,
size: 0.5,
source: 16079,
target: 4606 });
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 4607) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 160794607,
size: 0.5,
source: 16079,
target: 4607 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 4608,
label: 'Victor Heurtier',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2019/08/research_pasteur-capture-decran-2019-08-01-a-13.25.43-150x150.png',
page_url: 'https://research.pasteur.fr/en/member/victor-heurtier/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 160794608,
size: 0.5,
source: 16079,
target: 4608 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 130120,
label: 'Laure Bernard',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2019/08/research_pasteur-photo-laure-150x150.png',
page_url: 'https://research.pasteur.fr/en/member/laure-bernard/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 16079130120,
size: 0.5,
source: 16079,
target: 130120 });
// adding node
var x_node = Math.cos(2 * 2 * Math.PI / N) * 10;
var y_node = Math.sin(2 * 2 * Math.PI / N) * 10;
g.nodes.push({
id: 6110,
label: 'TEAM: Epigenomics, Proliferation and the Identity of Cells – EPIC',
x: x_node,
y: y_node,
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2019/10/research_pasteur-unite-navarro-gil_bandeau-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/team/epigenomics-proliferation-and-the-identity-of-cells/',
size: 35,
color: '#DDDDDD'
});
//link content to central post
g.edges.push({
id: 46076110,
size: 0.5,
source: 4607,
target: 6110,
});
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 4605,
label: 'Nicola Festuccia',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2019/08/research_pasteur-capture-decran-2019-08-01-a-13.26.30-150x150.png',
page_url: 'https://research.pasteur.fr/en/member/nicola-festuccia/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 61104605,
size: 0.5,
source: 6110,
target: 4605 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 4609,
label: 'Agnès Dubois',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2019/09/research_pasteur-agnes-150x150.jpeg',
page_url: 'https://research.pasteur.fr/en/member/agnes-dubois/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 61104609,
size: 0.5,
source: 6110,
target: 4609 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 130102,
label: 'Inmaculada Gonzalez Garcia',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2019/07/research_pasteur-photo-inma-150x150.jpeg',
page_url: 'https://research.pasteur.fr/en/member/inmaculada-gonzalez-garcia/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 6110130102,
size: 0.5,
source: 6110,
target: 130102 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 102938,
label: 'Rémi-Xavier Coux',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2018/02/research_pasteur-coux-7c-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/member/remi-xavier-coux/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 6110102938,
size: 0.5,
source: 6110,
target: 102938 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 4649,
label: 'Sandrine Vandormael-Pournin',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2017/01/research.pasteur.fr_mdiwmjm3-2.jpg',
page_url: 'https://research.pasteur.fr/en/member/sandrine-vandormael-pournin/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 61104649,
size: 0.5,
source: 6110,
target: 4649 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 4637,
label: 'Michel Cohen-Tannoudji',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2015/12/research.pasteur.fr_dsc8515-150x150.jpeg',
page_url: 'https://research.pasteur.fr/en/member/michel-cohen-tannoudji/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 61104637,
size: 0.5,
source: 6110,
target: 4637 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 139712,
label: 'Almira Chervova',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2020/02/research_pasteur-capture-decran-2020-02-21-a-16.49.52-150x150.png',
page_url: 'https://research.pasteur.fr/en/member/fr-almira-chervova/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 6110139712,
size: 0.5,
source: 6110,
target: 139712 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 161963,
label: 'Ashish Kumar Singh',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2021/06/research_pasteur-ashish-k-singh-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/member/ashish-kumar-singh/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 6110161963,
size: 0.5,
source: 6110,
target: 161963 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 174012,
label: 'Adèle Micouin',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2022/01/research_pasteur-adele-micouin-20220114-101055-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/member/adele-micouin/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 6110174012,
size: 0.5,
source: 6110,
target: 174012 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 163287,
label: 'Tara Moheb',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2021/07/research_pasteur-tara-moheb-tara-moheb-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/member/tara-moheb/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 6110163287,
size: 0.5,
source: 6110,
target: 163287 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 200535,
label: 'Luis Fernando Altamirano Pacheco',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2023/04/research_pasteur-picture-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/member/luis-fernando-altamirano-pacheco/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 6110200535,
size: 0.5,
source: 6110,
target: 200535 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 189234,
label: 'Guillaume burnet',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2022/10/research_pasteur-guillaume-burnet-picturegb-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/member/guillaume-burnet/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 6110189234,
size: 0.5,
source: 6110,
target: 189234 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 200549,
label: 'Guillaume Giraud',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2023/04/research_pasteur-guillaume-giraud-giraud-collet-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/member/guillaume-giraud/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 6110200549,
size: 0.5,
source: 6110,
target: 200549 });
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 4606) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 61104606,
size: 0.5,
source: 6110,
target: 4606 });
var s = new sigma({
//container: document.getElementById('graph-main'),
graph: g,
renderer: {
// IMPORTANT:
// This works only with the canvas renderer, so the
// renderer type set as "canvas" is necessary here.
container: document.getElementById('graph-main'),
type: 'canvas'
},
settings: {
minNodeSize: 6,
maxNodeSize: 35,
mouseWheelEnabled: false,
font: 'Montserrat',
labelThreshold:25,
borderSize:1,
defaultNodeBorderColor: '#999',
sideMargin:25,
}
});
// We first need to save the original colors of our
// nodes and edges, like this:
s.graph.nodes().forEach(function(n) {
n.originalColor = n.color;
});
s.graph.edges().forEach(function(e) {
e.originalColor = e.color;
});
// When a node is clicked, we check for each node
// if it is a neighbor of the clicked one. If not,
// we set its color as grey, and else, it takes its
// original color.
// We do the same for the edges, and we only keep
// edges that have both extremities colored.
s.bind('clickNode', function(e) {
var nodeId = e.data.node.id,
toKeep = s.graph.neighbors(nodeId);
toKeep[nodeId] = e.data.node;
s.graph.nodes().forEach(function(n) {
if (toKeep[n.id])
n.color = '#35a9f5';
else
n.color = '#dddddd';
});
s.graph.edges().forEach(function(e) {
if (toKeep[e.source] && toKeep[e.target])
e.color = '#35a9f5';
else
e.color = '#dddddd';
});
// Since the data has been modified, we need to
// call the refresh method to make the colors
// update effective.
s.refresh();
});
// When the stage is clicked, we just color each
// node and edge with its original color.
s.bind('clickStage', function(e) {
s.graph.nodes().forEach(function(n) {
n.color = n.originalColor;
});
s.graph.edges().forEach(function(e) {
e.color = e.originalColor;
});
// Same as in the previous event:
s.refresh();
});
s.bind("doubleClickNode", function (e) {
$("#canvas-wrap, .sigma-scene, .sigma-mouse").val();
ajax_load_page( e.data.node.page_url );
});
var c = s.camera;
s.bind("rightClickStage", function (e) {
sigma.misc.animation.camera(c, {
ratio: c.ratio * c.settings('zoomingRatio')
}, {
duration: 200
});
});
// Configure the noverlap layout:
var noverlapListener = s.configNoverlap({
nodeMargin: 10,
scaleNodes: 0.3,
gridSize: 1,
easing: 'quadraticInOut', // animation transition function
duration: 4000 // animation duration. Long here for the purposes of this example only
});
// Bind the events:
noverlapListener.bind('start stop interpolate', function(e) {
//console.log(e.type);
if(e.type === 'start') {
//console.time('noverlap');
}
if(e.type === 'interpolate') {
//console.timeEnd('noverlap');
}
});
// Start the layout:
s.startNoverlap();
//s.refresh();
// Initialize the dragNodes plugin:
var dragListener = sigma.plugins.dragNodes(s, s.renderers[0]);
dragListener.bind('startdrag', function(event) {
});
dragListener.bind('drag', function(event) {
});
dragListener.bind('drop', function(event) {
});
dragListener.bind('dragend', function(event) {
});