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: 4095,
label: 'Juan Jose Quereda Torres',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2015/09/research.pasteur.fr_juan-150x150.jpg',
x: 0,
y: 0,
size: 30,
color: '#DDDDDD'
});
var biggest_node_size = 0;
N=4
// 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: 67584,
label: 'PROJECT: Host microbiota modification by epidemic Listeria monocytogenes',
x: x_node,
y: y_node,
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2016/05/research.pasteur.fr_listeriolysin-s-1-150x150.png',
page_url: 'https://research.pasteur.fr/fr/project/host-microbiota-modification-by-the-pathogen-listeria-monocytogenes/',
size: 35,
color: '#DDDDDD'
});
//link content to central post
g.edges.push({
id: 409567584,
size: 0.5,
source: 4095,
target: 67584,
});
//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: 906,
label: 'Marie-Agnès Dillies',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2018/09/research_pasteur-photomadillies2-150x150.jpg',
page_url: 'https://research.pasteur.fr/fr/member/marie-agnes-dillies/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 67584906,
size: 0.5,
source: 67584,
target: 906 });
//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: 7762,
label: 'Stevenn Volant',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2015/07/research.pasteur.fr_stevennvolant-150x150.png',
page_url: 'https://research.pasteur.fr/fr/member/stevenn-volant/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 675847762,
size: 0.5,
source: 67584,
target: 7762 });
//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: 37658,
label: 'Amine Ghozlane',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2020/06/research_pasteur-20200223_122542-1-150x150.jpg',
page_url: 'https://research.pasteur.fr/fr/member/amine-ghozlane/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 6758437658,
size: 0.5,
source: 67584,
target: 37658 });
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 4095) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 675844095,
size: 0.5,
source: 67584,
target: 4095 });
//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: 4094,
label: 'Javier Pizarro-Cerda',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2015/05/research_pasteur-javier-pizarro-cerda-javier-pizarro-1300-1-150x150.jpg',
page_url: 'https://research.pasteur.fr/fr/member/javier-pizarro-cerda/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 675844094,
size: 0.5,
source: 67584,
target: 4094 });
// 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: 68928,
label: 'NEWS: A bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection (PNAS May 2nd, 2016)',
x: x_node,
y: y_node,
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2016/05/research.pasteur.fr_lm-ptk2-2-150x150.png',
page_url: 'https://research.pasteur.fr/fr/news/a-bacteriocin-from-epidemic-listeria-strains-alters-the-host-intestinal-microbiota-to-favor-infection/',
size: 35,
color: '#DDDDDD'
});
//link content to central post
g.edges.push({
id: 409568928,
size: 0.5,
source: 4095,
target: 68928,
});
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 4094) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 689284094,
size: 0.5,
source: 68928,
target: 4094 });
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 4095) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 689284095,
size: 0.5,
source: 68928,
target: 4095 });
//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: 3783,
label: 'Pascale Cossart',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2015/05/research.pasteur.fr_pascale-cossart-150x150.jpg',
page_url: 'https://research.pasteur.fr/fr/member/pascale-cossart/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 689283783,
size: 0.5,
source: 68928,
target: 3783 });
//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: 4081,
label: 'Olivier Dussurget',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2015/07/research.pasteur.fr_dussurget-150x150.jpg',
page_url: 'https://research.pasteur.fr/fr/member/olivier-dussurget/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 689284081,
size: 0.5,
source: 68928,
target: 4081 });
//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: 4101,
label: 'Marie-Anne Nahori',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2015/07/research.pasteur.fr_nahori-150x150.jpg',
page_url: 'https://research.pasteur.fr/fr/member/marie-anne-nahori/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 689284101,
size: 0.5,
source: 68928,
target: 4101 });
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 37658) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 6892837658,
size: 0.5,
source: 68928,
target: 37658 });
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 7762) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 689287762,
size: 0.5,
source: 68928,
target: 7762 });
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 906) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 68928906,
size: 0.5,
source: 68928,
target: 906 });
//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: 996,
label: 'Béatrice Regnault',
type: 'image',
url: '',
page_url: 'https://research.pasteur.fr/fr/?post_type=member&p=996',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 68928996,
size: 0.5,
source: 68928,
target: 996 });
//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: 2669,
label: 'Sean Kennedy',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2015/03/Kennedy-150x150.jpg',
page_url: 'https://research.pasteur.fr/fr/member/sean-kennedy/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 689282669,
size: 0.5,
source: 68928,
target: 2669 });
// 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: 67742,
label: 'TOOL: Dual microscopy assay to discriminate Listeria cellular entry & vacuolar escape',
x: x_node,
y: y_node,
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2016/04/research.pasteur.fr_150716-4colors-b2-3colors-150x150.png',
page_url: 'https://research.pasteur.fr/fr/tool/dual-microscopy-assay-to-discriminate-listeria-cellular-entry-vacuolar-escape/',
size: 35,
color: '#DDDDDD'
});
//link content to central post
g.edges.push({
id: 409567742,
size: 0.5,
source: 4095,
target: 67742,
});
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 3783) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 677423783,
size: 0.5,
source: 67742,
target: 3783 });
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 4095) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 677424095,
size: 0.5,
source: 67742,
target: 4095 });
//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: 4237,
label: 'Jost Enninga',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2016/06/research.pasteur.fr_jost2015-3-150x150.jpg',
page_url: 'https://research.pasteur.fr/fr/member/jost-enninga/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 677424237,
size: 0.5,
source: 67742,
target: 4237 });
//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: 2232,
label: 'Nathalie Aulner',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2015/07/research.pasteur.fr_dsc03316-150x150.jpeg',
page_url: 'https://research.pasteur.fr/fr/member/nathalie-aulner/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 677422232,
size: 0.5,
source: 67742,
target: 2232 });
//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: 1585,
label: 'Anne Danckaert',
type: 'image',
url: '',
page_url: 'https://research.pasteur.fr/fr/member/anne-danckaert/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 677421585,
size: 0.5,
source: 67742,
target: 1585 });
//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: 1589,
label: 'Archivé: Spencer Shorte',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2015/02/spencer-150x150.jpg',
page_url: 'https://research.pasteur.fr/fr/?post_type=member&p=1589',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 677421589,
size: 0.5,
source: 67742,
target: 1589 });
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 4094) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 677424094,
size: 0.5,
source: 67742,
target: 4094 });
// adding node
var x_node = Math.cos(2 * 3 * Math.PI / N) * 10;
var y_node = Math.sin(2 * 3 * Math.PI / N) * 10;
g.nodes.push({
id: 345,
label: 'TEAM: Interactions bactéries-cellules',
x: x_node,
y: y_node,
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2014/11/research.pasteur.fr_bacteria-cell-interactions-150x150.jpg',
page_url: 'https://research.pasteur.fr/fr/team/bacteria-cell-interactions/',
size: 35,
color: '#DDDDDD'
});
//link content to central post
g.edges.push({
id: 4095345,
size: 0.5,
source: 4095,
target: 345,
});
//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: 8652,
label: 'Marie-Thérèse Vicente',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2015/07/research.pasteur.fr_marie-therese-150x150.jpeg',
page_url: 'https://research.pasteur.fr/fr/member/marie-therese-vicente/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 3458652,
size: 0.5,
source: 345,
target: 8652 });
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 3783) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 3453783,
size: 0.5,
source: 345,
target: 3783 });
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) {
});