Cytoscape.js
WebGL Demo
Network
Background Color:
WebGL Settings
Texture Size:
ℹ️
Texture Size
This size of each dimension of each texture atlas. Affects buffering time and texture quality.
Texture Rows (Labels):
ℹ️
Texture Rows
Number of rows to divide the texture atlas into. Affects number of textures used and texture quality.
Texture Rows (Node Body):
ℹ️
Texture Rows
Number of rows to divide the texture atlas into. Affects number of textures used and texture quality.
Max Textures Per Batch:
ℹ️
Textures Per Batch
Number of texture units to use per batch.
Max Elements Per Batch:
ℹ️
Elements Per Batch
Number of nodes or edges to draw in a batch. Affects the size of data buffers.
Open the debug console for more info.
(Option + Command + J)
================================================
FILE: debug/webgl/init.js
================================================
/* eslint-disable no-console, no-unused-vars */
/* global $, cytoscape, options, cy, networks */
var cy;
const paramDefs = {
networkID: {
default: 'style_test',
control: '#network-select'
},
bgcolor: {
default: 'white',
control: '#bg-color-select'
},
webgl: {
default: 'true',
control: '#webgl-check'
},
hover: {
default: 'false',
control: '#hover-check'
},
animate: {
default: 'false',
control: '#animate-check'
},
// webglDebugShowAtlases: {
// default: false,
// control: '#atlas-checkbox'
// },
webglTexSize: {
default: 2048,
control: '#texture-size-select'
},
webglTexRows: {
default: 36,
control: '#texture-rows-select'
},
webglTexRowsNodes: {
default: 18,
control: '#texture-rows-nodes-select'
},
webglBatchSize: {
default: 2048,
control: '#batch-size-select'
},
webglTexPerBatch: {
default: 14,
control: '#texture-units-select'
},
};
(function(){
const params = {};
// Load URL params
const urlParams = new URLSearchParams(window.location.search);
for(const p of Object.keys(paramDefs)) {
const def = paramDefs[p];
params[p] = urlParams.get(p) || def.default;
}
console.log('params', params);
$('#cytoscape').style.backgroundColor = params.bgcolor;
// Load network and style
function loadNetwork(elements, style) {
const options = {
container: $('#cytoscape'),
renderer: {
name: 'canvas',
showFps: true,
webgl: params.webgl === 'true',
webglDebug: true,
webglDebugShowAtlases: params.webglDebugShowAtlases === 'true',
webglTexSize: params.webglTexSize,
webglTexRows: params.webglTexRows,
webglTexRowsNodes: params.webglTexRowsNodes,
webglBatchSize: params.webglBatchSize,
webglTexPerBatch: params.webglTexPerBatch,
},
style: style,
elements: elements,
layout: network.layout
};
options.layout.animate = false;
cy = cytoscape(options);
if(params.animate === 'true' && params.networkID === 'style_test') {
cy.ready(() => {
var node = cy.getElementById('n8');
var expand = true;
var duration = 1000;
var timeout = duration + 100;
const originalWidth = node.width();
function testAnimate() {
if(expand) {
node.animate({
style: {
width: originalWidth + 50
},
duration: duration,
queue: false,
});
expand = false;
} else {
node.animate({
style: {
width: originalWidth
},
duration: duration,
queue: false,
});
expand = true;
}
setTimeout(testAnimate, timeout);
}
setTimeout(testAnimate, timeout);
});
}
cy.on('pan zoom', (e) => {
const { x, y } = cy.pan();
const zoom = cy.zoom();
const panDiv = document.getElementById('pan');
panDiv.innerHTML = `Pan: x: ${x.toFixed(2)}, y: ${y.toFixed(2)}`;
const zoomDiv = document.getElementById('zoom');
zoomDiv.innerHTML = `Zoom: ${zoom.toFixed(4)}`;
});
if(params.hover === 'true') { // add hover effect
cy.ready(() => {
const hoverMapping = {
selector: `.hover`,
style: {
'underlay-color': 'lightblue',
'underlay-padding': 12,
'underlay-opacity': 0.7,
'underlay-shape': 'roundrectangle',
},
};
cy.style().fromJson(cy.style().json().concat(hoverMapping)).update();
let lastHoveredElementID;
cy.on('mouseover', 'node, edge', e => {
const ele = e.target;
ele.addClass('hover');
lastHoveredElementID = ele.data('id');
});
cy.on('mouseout', 'node, edge', e => {
const lastEle = cy.getElementById(lastHoveredElementID);
if(lastEle !== undefined) {
lastEle.removeClass('hover');
}
lastHoveredElementID = undefined;
});
});
}
}
const network = networks[params.networkID];
const style = network.style;
if(style && style.file) {
// style is in a separate file
console.log('loading style from file: ', style.file);
Promise.all([
fetch(network.url).then(res => res.json()),
fetch(style.file).then(res => res.json())
]).then(([networkJson, styleJson]) => {
loadNetwork(networkJson.elements, styleJson.style);
});
} else {
// style is in the same file as the network
fetch(network.url)
.then(res => res.json())
.then(networkJson => {
loadNetwork(networkJson.elements, networkJson.style);
});
}
// Initialize controls
for(const [networkID, network] of Object.entries(networks)) {
const option = document.createElement('option');
option.value = networkID;
option.innerHTML = `${network.desc} (${network.nodes} nodes, ${network.edges} edges)`;
$("#network-select").appendChild(option);
}
for(const p of Object.keys(paramDefs)) {
const control = $(paramDefs[p].control);
if(control.type == 'checkbox') {
control.checked = params[p] === 'true';
control.addEventListener('click', () => reloadPage());
} else {
control.value = params[p];
control.addEventListener('change', () => reloadPage());
}
}
// Add listeners to controls
function reloadPage(reset = false) {
const { origin, pathname } = window.location;
if(reset) {
window.location.href = origin + pathname;
return;
}
const urlParams = new URLSearchParams();
for(const p of Object.keys(paramDefs)) {
console.log(p);
const control = $(paramDefs[p].control);
const value = control.type == 'checkbox' ? control.checked : control.value;
console.log(paramDefs[p], value, paramDefs[p].default);
if(String(value) !== String(paramDefs[p].default)) {
urlParams.set(p, value);
}
}
window.location.href = origin + pathname + '?' + urlParams.toString();
}
$('#hide-commands').addEventListener('click', () => {
document.body.classList.remove('commands-shown');
document.body.classList.add('commands-hidden');
if(cy) {
cy.resize();
}
});
$('#show-commands').addEventListener('click', () => {
document.body.classList.add('commands-shown');
document.body.classList.remove('commands-hidden');
if(cy) {
cy.resize();
}
});
$("#fit-button").addEventListener('click', () => cy.fit());
$("#reset-button").addEventListener('click', () => reloadPage(true));
// $("#delete-button").addEventListener('click', () => {
// cy.remove(':selected');
// });
// $("#animate-button").addEventListener('click', () => {
// const nodes = cy.nodes(':selected');
// nodes.forEach(n => {
// const w = n.width();
// n.animate({
// style: { 'width': w + 100 }
// }, {
// duration: 1000
// })
// .delay(1000)
// .animate({
// style: { 'width': w }
// }, {
// duration: 1000
// });
// });
// });
// $("#select-button").addEventListener('click', () => {
// cy.nodes().select();
// });
// $("#gc-button").addEventListener('click', () => {
// cy.gc();
// });
})();
================================================
FILE: debug/webgl/network-compound-nodes.json
================================================
{
"style": [
{
"selector": "node",
"css": {
"shape": "rectangle",
"content": "data(id)",
"text-valign": "center",
"text-halign": "center"
}
},
{
"selector": ":parent",
"css": {
"text-valign": "top",
"text-halign": "center",
"shape": "round-rectangle",
"corner-radius": "10",
"padding": 10,
"background-opacity": 0.0
}
},
{
"selector": "node#e",
"css": {
"corner-radius": "10",
"padding": 0
}
},
{
"selector": "node#d",
"css": {
"padding": 10
}
},
{
"selector": "edge",
"css": {
"curve-style": "bezier",
"target-arrow-shape": "triangle"
}
}
],
"elements": {
"nodes": [
{ "data": { "id": "a", "parent": "b" }, "position": { "x": 215, "y": 85 } },
{ "data": { "id": "b" } },
{ "data": { "id": "c", "parent": "b" }, "position": { "x": 300, "y": 85 } },
{ "data": { "id": "d" }, "position": { "x": 215, "y": 175 } },
{ "data": { "id": "e" } },
{ "data": { "id": "f", "parent": "e" }, "position": { "x": 300, "y": 175 } }
],
"edges": [
{ "data": { "id": "ad", "source": "a", "target": "d" } },
{ "data": { "id": "eb", "source": "e", "target": "b" } }
]
}
}
================================================
FILE: debug/webgl/network-curve.json
================================================
{
"elements": {
"nodes": [
{ "data": { "id": "n1", "weight": 1 }, "position": { "x": 0, "y": 0 } },
{ "data": { "id": "n2", "weight": 2 }, "position": { "x": 0, "y": 150 } },
{ "data": { "id": "n3", "weight": 3 }, "position": { "x": 150, "y": -25 } }
],
"edges": [
{ "data": { "id":"n1-n2-0", "source": "n1", "target": "n2", "directed": "false" } },
{ "data": { "id":"n1-n2-1", "source": "n1", "target": "n2", "directed": "false" } },
{ "data": { "id":"n1-n2-2", "source": "n1", "target": "n2", "directed": "false" } },
{ "data": { "id":"n1-n2-3", "source": "n1", "target": "n2", "directed": "false" } },
{ "data": { "id":"self-0", "source": "n1", "target": "n1", "directed": "false" } },
{ "data": { "id":"self-1", "source": "n1", "target": "n1", "directed": "false" } },
{ "data": { "id":"n1-n3", "source": "n1", "target": "n3", "directed": "false" } }
]
},
"style": [
{
"selector": "node",
"style": {
"label": "data(id)",
"text-valign": "center",
"color": "#000000",
"background-color": "#3a7ecf",
"font-family": "Helvetica"
}
},
{
"selector": "node:selected",
"style": {
"border-color": "yellow",
"border-opacity": 1,
"border-width": 2
}
},
{
"selector": "edge",
"style": {
"width": 4,
"line-color": "#3a7ecf",
"opacity": 0.5,
"curve-style": "bezier"
}
}, {
"selector": "#n1-n3",
"style": {
"curve-style": "unbundled-bezier",
"control-point-distances": [40, -40],
"control-point-weights": [0.250, 0.75],
"source-arrow-shape": "triangle",
"source-arrow-color": "green",
"target-arrow-shape": "triangle",
"target-arrow-color": "green",
"width": 3
}
}
]
}
================================================
FILE: debug/webgl/network-em-desktop-style.json
================================================
{
"format_version" : "1.0",
"generated_by" : "cytoscape-3.10.3",
"target_cytoscapejs_version" : "~2.1",
"title" : "Enrichment Map TEP-Style",
"style" : [ {
"selector" : "node",
"css" : {
"shape" : "ellipse",
"width" : 20.0,
"background-color" : "rgb(240,240,240)",
"color" : "rgb(0,0,0)",
"border-width" : 1.0,
"background-opacity" : 0.8627450980392157,
"border-color" : "rgb(51,51,51)",
"height" : 20.0,
"font-size" : 12,
"border-opacity" : 0.8627450980392157,
"text-valign" : "center",
"text-halign" : "center",
"text-opacity" : 0.8627450980392157,
"content" : "data(EM1_GS_DESCR)"
}
}, {
"selector" : "node[EM1_GS_Type = 'SIG']",
"css" : {
"border-color" : "rgb(239,138,98)"
}
}, {
"selector" : "node",
"css" : {
"width" : "mapData(EM1_gs_size, 0, 1300, 20, 60)",
"height" : "mapData(EM1_gs_size, 0, 1300, 20, 60)"
}
}, {
"selector" : "node[EM1_GS_Type = 'ENR']",
"css" : {
"border-color" : "rgb(51,51,51)"
}
}, {
"selector" : "node[EM1_GS_Type = 'SIG']",
"css" : {
"shape" : "diamond"
}
}, {
"selector" : "node[EM1_GS_Type = 'ENR']",
"css" : {
"shape" : "ellipse"
}
}, {
"selector" : "node[EM1_Colouring_Data_Set_1_ > 1]",
"css" : {
"background-color" : "rgb(178,24,43)"
}
}, {
"selector" : "node[EM1_Colouring_Data_Set_1_ = 1]",
"css" : {
"background-color" : "rgb(178,24,43)"
}
}, {
"selector" : "node[EM1_Colouring_Data_Set_1_ > 0.995][EM1_Colouring_Data_Set_1_ < 1]",
"css" : {
"background-color" : "mapData(EM1_Colouring_Data_Set_1_,0.995,1,rgb(178,24,43),rgb(178,24,43))"
}
}, {
"selector" : "node[EM1_Colouring_Data_Set_1_ > 0.95][EM1_Colouring_Data_Set_1_ < 0.995]",
"css" : {
"background-color" : "mapData(EM1_Colouring_Data_Set_1_,0.95,0.995,rgb(214,96,77),rgb(214,96,77))"
}
}, {
"selector" : "node[EM1_Colouring_Data_Set_1_ > 0.9][EM1_Colouring_Data_Set_1_ < 0.95]",
"css" : {
"background-color" : "mapData(EM1_Colouring_Data_Set_1_,0.9,0.95,rgb(244,165,130),rgb(244,165,130))"
}
}, {
"selector" : "node[EM1_Colouring_Data_Set_1_ > 0][EM1_Colouring_Data_Set_1_ < 0.9]",
"css" : {
"background-color" : "mapData(EM1_Colouring_Data_Set_1_,0,0.9,rgb(247,247,247),rgb(247,247,247))"
}
}, {
"selector" : "node[EM1_Colouring_Data_Set_1_ > -0.9][EM1_Colouring_Data_Set_1_ < 0]",
"css" : {
"background-color" : "mapData(EM1_Colouring_Data_Set_1_,-0.9,0,rgb(247,247,247),rgb(247,247,247))"
}
}, {
"selector" : "node[EM1_Colouring_Data_Set_1_ > -0.95][EM1_Colouring_Data_Set_1_ < -0.9]",
"css" : {
"background-color" : "mapData(EM1_Colouring_Data_Set_1_,-0.95,-0.9,rgb(67,147,195),rgb(146,197,222))"
}
}, {
"selector" : "node[EM1_Colouring_Data_Set_1_ > -0.995][EM1_Colouring_Data_Set_1_ < -0.95]",
"css" : {
"background-color" : "mapData(EM1_Colouring_Data_Set_1_,-0.995,-0.95,rgb(33,102,172),rgb(146,197,222))"
}
}, {
"selector" : "node[EM1_Colouring_Data_Set_1_ > -1][EM1_Colouring_Data_Set_1_ < -0.995]",
"css" : {
"background-color" : "mapData(EM1_Colouring_Data_Set_1_,-1,-0.995,rgb(33,102,172),rgb(67,147,195))"
}
}, {
"selector" : "node[EM1_Colouring_Data_Set_1_ = -1]",
"css" : {
"background-color" : "rgb(33,102,172)"
}
}, {
"selector" : "node[EM1_Colouring_Data_Set_1_ < -1]",
"css" : {
"background-color" : "rgb(33,102,172)"
}
}, {
"selector" : "node:selected",
"css" : {
"background-color" : "rgb(255,255,0)"
}
}, {
"selector" : "edge",
"css" : {
"text-opacity" : 0.7843137254901961,
"opacity" : 0.7843137254901961,
"target-arrow-shape" : "none",
"source-arrow-color" : "rgb(0,0,0)",
"content" : "",
"target-arrow-color" : "rgb(0,0,0)",
"width" : 1.0,
"color" : "rgb(0,0,0)",
"line-color" : "rgb(64,64,64)",
"line-style" : "solid",
"font-size" : 10,
"source-arrow-shape" : "none"
}
}, {
"selector" : "edge[interaction = 'sig']",
"css" : {
"line-color" : "rgb(252,141,98)",
"target-arrow-color" : "rgb(252,141,98)",
"source-arrow-color" : "rgb(252,141,98)"
}
}, {
"selector" : "edge[interaction = 'Geneset_Overlap']",
"css" : {
"line-color" : "rgb(166,206,227)",
"target-arrow-color" : "rgb(166,206,227)",
"source-arrow-color" : "rgb(166,206,227)"
}
}, {
"selector" : "edge[interaction = 'Data Set 1']",
"css" : {
"line-color" : "rgb(166,206,227)",
"target-arrow-color" : "rgb(166,206,227)",
"source-arrow-color" : "rgb(166,206,227)"
}
}, {
"selector" : "edge[interaction = 'sig']",
"css" : {
"line-style" : "dashed"
}
}, {
"selector" : "edge[interaction = 'compound']",
"css" : {
"line-style" : "solid"
}
}, {
"selector" : "edge[EM1_similarity_coefficient > 1]",
"css" : {
"width" : 6.0
}
}, {
"selector" : "edge[EM1_similarity_coefficient = 1]",
"css" : {
"width" : 5.0
}
}, {
"selector" : "edge[EM1_similarity_coefficient > 0.375][EM1_similarity_coefficient < 1]",
"css" : {
"width" : "mapData(EM1_similarity_coefficient,0.375,1,1.0,5.0)"
}
}, {
"selector" : "edge[EM1_similarity_coefficient = 0.375]",
"css" : {
"width" : 1.0
}
}, {
"selector" : "edge[EM1_similarity_coefficient < 0.375]",
"css" : {
"width" : 0.5
}
}, {
"selector" : "edge[interaction = 'sig']",
"css" : {
"line-color" : "rgb(252,141,98)"
}
}, {
"selector" : "edge[interaction = 'Geneset_Overlap']",
"css" : {
"line-color" : "rgb(166,206,227)"
}
}, {
"selector" : "edge[interaction = 'Data Set 1']",
"css" : {
"line-color" : "rgb(166,206,227)"
}
}, {
"selector" : "edge:selected",
"css" : {
"line-color" : "rgb(255,0,0)"
}
} ]
}
================================================
FILE: debug/webgl/network-em-desktop.json
================================================
[File too large to display: 23.4 MB]
================================================
FILE: debug/webgl/network-em-web.json
================================================
{
"style": [
{
"selector": "node",
"style": {
"border-width": "12px",
"border-opacity": "0",
"width": "40px",
"height": "40px",
"font-size": "8px",
"text-valign": "center",
"text-wrap": "wrap",
"text-max-width": "80px",
"z-index": "1",
"label": "data(description)",
"text-outline-width": 2,
"color": "#fff",
"background-color": "mapData(NES, -3.14, 3.14, #0571b0, #ca0020)",
"text-outline-color": "mapData(NES, -3.14, 3.14, #0571b0, #ca0020)"
}
},
{
"selector": "node:selected",
"style": {
"border-width": 8,
"border-color": "#333333",
"border-opacity": 1.0,
"text-outline-color": "#333333",
"z-index": 99999999
}
},
{
"selector": "edge",
"style": {
"label": "data(overlap_size)",
"edge-text-rotation": "autorotate",
"line-color": "#888",
"line-opacity": 0.3,
"curve-style": "haystack",
"haystack-radius": 0,
"width": "mapData(similarity_coefficient, 0, 1.0, 0, 15.0)"
}
}
],
"elements": {
"nodes": [
{
"data": {
"id": "24d0e101-0864-4553-a93d-335729308753",
"name": [
"PKR-MEDIATED SIGNALING%REACTOME DATABASE ID RELEASE 81%9833482"
],
"description": [
"PKR-mediated signaling"
],
"pvalue": 0.0002,
"gs_type": null,
"gs_size": 56,
"padj": 0.0033,
"mcode_cluster_id": null,
"NES": -1.8618,
"genes": [
"ADAR",
"ARIH1",
"CDK1",
"CENPS",
"CENPX",
"CHUK",
"DHX9",
"DNAJC3",
"DUS2",
"EIF2AK2",
"EIF2S1",
"EIF2S2",
"EIF2S3",
"FAAP100",
"FAAP20",
"FAAP24",
"FANCA",
"FANCB",
"FANCC",
"FANCE",
"FANCF",
"FANCG",
"FANCL",
"FANCM",
"HERC5",
"HSPA1A",
"HSPA1B",
"HSPA1L",
"HSPA2",
"HSPA8",
"IKBKB",
"IKBKG",
"ILF2",
"ILF3",
"ISG15",
"MAP2K6",
"MAVS",
"NCK1",
"NPM1",
"PPP2CA",
"PPP2CB",
"PPP2R1A",
"PPP2R1B",
"PPP2R5A",
"PRKRA",
"PTPN2",
"SNCA",
"SPHK1",
"STAT1",
"STAT3",
"SUMO1",
"TARBP2",
"TP53",
"TRIM25",
"UBE2I",
"UBE2L6"
]
},
"position": {
"x": 15,
"y": 1331.019477691585,
"id": "24d0e101-0864-4553-a93d-335729308753"
},
"group": "nodes",
"removed": false,
"selected": false,
"selectable": true,
"locked": false,
"grabbable": true,
"pannable": false,
"classes": ""
},
{
"data": {
"id": "d603bd43-39df-46a4-a6d6-57b7c7d7f39d",
"name": [
"PROTEASOME DEGRADATION%WIKIPATHWAYS_20240410%WP183%HOMO SAPIENS"
],
"description": [
"Proteasome degradation"
],
"pvalue": 0.0001,
"gs_type": null,
"gs_size": 47,
"padj": 0.0014,
"mcode_cluster_id": null,
"NES": -1.9808,
"genes": [
"H2AX",
"H2AZ1",
"HEL-117",
"HEL-S-276",
"HEL-S-283",
"HEL-S-91n",
"HIST1H2AB",
"HLA-A",
"HLA-B",
"HLA-C",
"HLA-E",
"HLA-F",
"HLA-G",
"IF2F",
"NEDD4",
"PSM8",
"PSMA2",
"PSMA4",
"PSMB10",
"PSMB2",
"PSMB3",
"PSMB6",
"PSMC1",
"PSMC4",
"PSMC6",
"PSMD1",
"PSMD10",
"PSMD11",
"PSMD12",
"PSMD13",
"PSMD2",
"PSMD3",
"PSMD4",
"PSMD5",
"PSMD6",
"PSMD7",
"PSMD9",
"PSME2",
"RPN1",
"RPN2",
"UBA7",
"UBB",
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"MEFV",
"MFHAS1",
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"MMP25",
"MYLK3",
"NAIP",
"NCR3",
"NFAM1",
"NFATC3",
"NFATC4",
"NFKB1",
"NFKB2",
"NFX1",
"NINJ1",
"NLRC4",
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"NLRP3",
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"NOD1",
"NOS2",
"NOX1",
"NOX4",
"NRROS",
"ODAM",
"ORM1",
"PARP4",
"PF4",
"PF4V1",
"PIK3CD",
"PIK3CG",
"PJA2",
"PLA2G2D",
"PLA2G4B",
"PLA2G4C",
"PLSCR1",
"PNMA1",
"PPBP",
"PRDX5",
"PROK2",
"PSEN1",
"PTGDR",
"PTGER1",
"PTGER2",
"PTGER3",
"PTGER4",
"PTGFR",
"PTGIR",
"PTN",
"PTX3",
"PXK",
"PYCARD",
"RAC1",
"REL",
"RELA",
"RELB",
"RIPK2",
"S100A8",
"S100A9",
"SCG2",
"SCUBE1",
"SELE",
"SERPINA3",
"SIGIRR",
"SIGLEC1",
"SLAMF8",
"SLC11A1",
"SNAP23",
"SNCA",
"STAT3",
"SYK",
"TAB2",
"TAC1",
"TAC4",
"TACR1",
"TBK1",
"TBXA2R",
"TGFB1",
"THBS1",
"TLR1",
"TLR10",
"TLR2",
"TLR3",
"TLR4",
"TLR5",
"TLR6",
"TMIGD3",
"TNF",
"TNFAIP6",
"TNFRSF1A",
"TNFRSF4",
"TNFSF4",
"TRAF3IP2",
"TREM2",
"TRIM14",
"TUSC2",
"TXNIP",
"TYROBP",
"VCAM1",
"VNN1",
"WNT5A",
"XCL1",
"XCL2",
"XCR1"
]
},
"position": {
"x": 2732.5,
"y": 2195.9446642487483,
"id": "13b8588c-61ed-4f34-99fa-8913a2d70119"
},
"group": "nodes",
"removed": false,
"selected": false,
"selectable": true,
"locked": false,
"grabbable": true,
"pannable": false,
"classes": ""
},
{
"data": {
"id": "38fcc406-d8ea-4899-8aba-08c8cb9d70f8",
"name": [
"IMMUNE RESPONSE%GOBP%GO:0006955"
],
"description": [
"immune response"
],
"pvalue": 5.5974e-22,
"gs_type": null,
"gs_size": 1094,
"padj": 6.512e-19,
"mcode_cluster_id": null,
"NES": -2.2362,
"genes": [
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"ACKR3",
"ACKR4",
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"ADAM15",
"ADAM17",
"ADAMDEC1",
"ADAR",
"ADGRE5",
"AIF1",
"AIM2",
"AIRE",
"AKAP1",
"ALOX5",
"ALPK1",
"ANG",
"ANKHD1",
"ANKRD17",
"ANXA3",
"APCS",
"APLN",
"APOA4",
"APOBEC3A",
"APOBEC3F",
"APOBEC3G",
"APOL1",
"APP",
"AQP4",
"ARL8B",
"ATAD3A",
"ATP6V0A2",
"ATP7A",
"AZGP1",
"AZI2",
"AZU1",
"BACH2",
"BATF",
"BCL10",
"BCL2",
"BCL6",
"BLK",
"BLNK",
"BMP6",
"BMPR1A",
"BMX",
"BPI",
"BPIFA1",
"BPIFB1",
"BPIFB3",
"BST1",
"BST2",
"BTK",
"BTN3A2",
"BTN3A3",
"C17orf99",
"C1QA",
"C1QB",
"C1QBP",
"C1QC",
"C1R",
"C2",
"C3",
"C4A",
"C4BPA",
"C4B_2",
"C5AR1",
"C6",
"C7",
"C8A",
"C8B",
"C9",
"CADM1",
"CALCOCO2",
"CALM1",
"CAMK2A",
"CAMP",
"CARD8",
"CARD9",
"CASP1",
"CCL1",
"CCL11",
"CCL13",
"CCL14",
"CCL15",
"CCL16",
"CCL17",
"CCL18",
"CCL19",
"CCL2",
"CCL20",
"CCL21",
"CCL22",
"CCL23",
"CCL24",
"CCL25",
"CCL26",
"CCL3",
"CCL3L3",
"CCL4",
"CCL4L2",
"CCL5",
"CCL7",
"CCL8",
"CCR1",
"CCR10",
"CCR2",
"CCR3",
"CCR4",
"CCR5",
"CCR6",
"CCR7",
"CCR8",
"CCR9",
"CCRL2",
"CD164",
"CD180",
"CD19",
"CD1A",
"CD1B",
"CD1C",
"CD1D",
"CD1E",
"CD2",
"CD209",
"CD244",
"CD247",
"CD27",
"CD274",
"CD28",
"CD3D",
"CD3E",
"CD3G",
"CD4",
"CD40LG",
"CD46",
"CD47",
"CD58",
"CD6",
"CD68",
"CD7",
"CD70",
"CD74",
"CD79B",
"CD80",
"CD81",
"CD83",
"CD86",
"CD8A",
"CD8B",
"CD96",
"CEACAM8",
"CEBPB",
"CEBPG",
"CERT1",
"CFB",
"CFD",
"CFH",
"CFHR1",
"CFHR2",
"CFHR3",
"CFHR4",
"CFHR5",
"CFP",
"CGAS",
"CH25H",
"CHGA",
"CHIT1",
"CHST4",
"CHUK",
"CIITA",
"CITED1",
"CLEC2A",
"CLEC4A",
"CLEC4C",
"CLEC4D",
"CLEC4E",
"CLEC4G",
"CLEC4M",
"CLEC5A",
"CLEC6A",
"CLEC7A",
"CLPB",
"CLU",
"CMKLR1",
"CNIH1",
"CNR2",
"COLEC10",
"COLEC11",
"COLEC12",
"CORO1A",
"CR1",
"CR1L",
"CR2",
"CRHR1",
"CRIP1",
"CRIPTO",
"CRISP3",
"CRP",
"CRTAM",
"CSF2RB",
"CST9",
"CST9L",
"CST9LP1",
"CTLA4",
"CTSC",
"CTSG",
"CTSH",
"CTSK",
"CTSL",
"CTSS",
"CTSV",
"CTSW",
"CX3CL1",
"CX3CR1",
"CXCL1",
"CXCL10",
"CXCL11",
"CXCL13",
"CXCL14",
"CXCL16",
"CXCL2",
"CXCL3",
"CXCL5",
"CXCL6",
"CXCL8",
"CXCL9",
"CXCR1",
"CXCR2",
"CXCR3",
"CXCR4",
"CXCR5",
"CXCR6",
"CYBA",
"CYBB",
"CYBC1",
"CYLD",
"CYP11B1",
"CYP27B1",
"CYSLTR2",
"DAPK1",
"DAPK3",
"DDX3X",
"DEFA1B",
"DEFA3",
"DEFA4",
"DEFA5",
"DEFA6",
"DEFB1",
"DEFB104B",
"DEFB106B",
"DEFB114",
"DEFB118",
"DEFB119",
"DEFB126",
"DEFB127",
"DEFB136",
"DEFB4B",
"DHX15",
"DHX16",
"DHX58",
"DLL1",
"DMBT1",
"DNASE1",
"DNASE1L3",
"DOCK10",
"DOCK11",
"DOCK2",
"DPP8",
"DUS2",
"DYSF",
"EBI3",
"ECSIT",
"EIF2AK2",
"EIF2AK4",
"ELANE",
"EMP2",
"ENPP3",
"EOMES",
"EPRS1",
"ETS1",
"EXOSC3",
"EXOSC6",
"EXOSC9",
"F12",
"F2",
"F2RL1",
"FAM3A",
"FAU",
"FCAR",
"FCER1A",
"FCER1G",
"FCER2",
"FCGR1A",
"FCGR1BP",
"FCGR2A",
"FCGR2B",
"FCGR2C",
"FCGR3A",
"FCGR3B",
"FCGRT",
"FCMR",
"FCN1",
"FCN2",
"FCN3",
"FCRL2",
"FCRL3",
"FCRL4",
"FCRL5",
"FCRL6",
"FCRLA",
"FCRLB",
"FFAR2",
"FFAR3",
"FGA",
"FGB",
"FGR",
"FOXJ1",
"FOXP1",
"FRK",
"FTH1",
"FYB1",
"FYN",
"GALP",
"GAPDH",
"GAPT",
"GARIN5A",
"GATA3",
"GBF1",
"GBP1",
"GBP2",
"GBP3",
"GBP4",
"GBP5",
"GBP6",
"GBP7",
"GCH1",
"GEM",
"GNL1",
"GNLY",
"GP2",
"GPI",
"GPR15LG",
"GPR183",
"GPR65",
"GRB2",
"GRN",
"GRP",
"GTPBP1",
"GZMA",
"GZMB",
"H2BC11",
"H2BC12",
"H2BC12L",
"H2BC21",
"H2BC8",
"HAMP",
"HCK",
"HCST",
"HDAC4",
"HERC5",
"HLA-A",
"HLA-B",
"HLA-C",
"HLA-DPA1",
"HLA-DQA1",
"HLA-DQA2",
"HLA-DQB1",
"HLA-DQB2",
"HLA-DRA",
"HLA-DRB1",
"HLA-E",
"HLA-F",
"HLA-G",
"HLA-H",
"HMGB1",
"HMGB2",
"HMGN2",
"HRG",
"HRH2",
"HSPD1",
"ICAM1",
"ICOS",
"IFI27",
"IFI35",
"IFI44",
"IFI44L",
"IFI6",
"IFIH1",
"IFIT1",
"IFIT2",
"IFIT3",
"IFITM1",
"IFITM2",
"IFITM3",
"IFNA10",
"IFNA13",
"IFNA14",
"IFNA16",
"IFNA17",
"IFNA2",
"IFNA21",
"IFNA4",
"IFNA5",
"IFNA6",
"IFNA7",
"IFNA8",
"IFNAR1",
"IFNAR2",
"IFNB1",
"IFNE",
"IFNG",
"IFNGR1",
"IFNGR2",
"IFNK",
"IFNL1",
"IFNL2",
"IFNL3",
"IFNL4",
"IFNLR1",
"IFNW1",
"IGF1R",
"IGHA1",
"IGHA2",
"IGHD",
"IGHE",
"IGHG1",
"IGHG2",
"IGHG3",
"IGHG4",
"IGHM",
"IGHV1-18",
"IGHV1-2",
"IGHV1-24",
"IGHV1-3",
"IGHV1-38-4",
"IGHV1-45",
"IGHV1-46",
"IGHV1-58",
"IGHV1-69",
"IGHV1-69-2",
"IGHV1-69D",
"IGHV1-8",
"IGHV1OR15-1",
"IGHV1OR15-9",
"IGHV1OR21-1",
"IGHV2-26",
"IGHV2-5",
"IGHV2-70",
"IGHV2-70D",
"IGHV2OR16-5",
"IGHV3-11",
"IGHV3-13",
"IGHV3-15",
"IGHV3-16",
"IGHV3-20",
"IGHV3-21",
"IGHV3-23",
"IGHV3-30",
"IGHV3-30-3",
"IGHV3-30-5",
"IGHV3-33",
"IGHV3-35",
"IGHV3-38",
"IGHV3-38-3",
"IGHV3-43",
"IGHV3-43D",
"IGHV3-48",
"IGHV3-49",
"IGHV3-53",
"IGHV3-64",
"IGHV3-64D",
"IGHV3-66",
"IGHV3-7",
"IGHV3-72",
"IGHV3-73",
"IGHV3-74",
"IGHV3-9",
"IGHV3OR15-7",
"IGHV3OR16-10",
"IGHV3OR16-12",
"IGHV3OR16-13",
"IGHV3OR16-17",
"IGHV3OR16-8",
"IGHV4-28",
"IGHV4-30-2",
"IGHV4-30-4",
"IGHV4-31",
"IGHV4-34",
"IGHV4-38-2",
"IGHV4-39",
"IGHV4-4",
"IGHV4-59",
"IGHV4-61",
"IGHV4OR15-8",
"IGHV5-10-1",
"IGHV5-51",
"IGHV6-1",
"IGHV7-4-1",
"IGHV7-81",
"IGHV8-51-1",
"IGKC",
"IGKV1-12",
"IGKV1-13",
"IGKV1-16",
"IGKV1-17",
"IGKV1-27",
"IGKV1-33",
"IGKV1-37",
"IGKV1-39",
"IGKV1-5",
"IGKV1-6",
"IGKV1-8",
"IGKV1-9",
"IGKV1D-12",
"IGKV1D-13",
"IGKV1D-16",
"IGKV1D-17",
"IGKV1D-33",
"IGKV1D-37",
"IGKV1D-39",
"IGKV1D-42",
"IGKV1D-43",
"IGKV1D-8",
"IGKV1OR2-108",
"IGKV2-24",
"IGKV2-28",
"IGKV2-29",
"IGKV2-30",
"IGKV2-40",
"IGKV2D-24",
"IGKV2D-26",
"IGKV2D-28",
"IGKV2D-29",
"IGKV2D-30",
"IGKV2D-40",
"IGKV3-11",
"IGKV3-15",
"IGKV3-20",
"IGKV3-7",
"IGKV3D-11",
"IGKV3D-15",
"IGKV3D-20",
"IGKV3D-7",
"IGKV3OR2-268",
"IGKV4-1",
"IGKV5-2",
"IGKV6-21",
"IGKV6D-21",
"IGKV6D-41",
"IGLC1",
"IGLC2",
"IGLC3",
"IGLC6",
"IGLC7",
"IGLL1",
"IGLL5",
"IGLV1-36",
"IGLV1-40",
"IGLV1-44",
"IGLV1-47",
"IGLV1-50",
"IGLV1-51",
"IGLV10-54",
"IGLV11-55",
"IGLV2-11",
"IGLV2-14",
"IGLV2-18",
"IGLV2-23",
"IGLV2-33",
"IGLV2-8",
"IGLV3-1",
"IGLV3-10",
"IGLV3-12",
"IGLV3-16",
"IGLV3-19",
"IGLV3-21",
"IGLV3-22",
"IGLV3-25",
"IGLV3-27",
"IGLV3-32",
"IGLV3-9",
"IGLV4-3",
"IGLV4-60",
"IGLV4-69",
"IGLV5-37",
"IGLV5-39",
"IGLV5-45",
"IGLV5-48",
"IGLV5-52",
"IGLV6-57",
"IGLV7-43",
"IGLV7-46",
"IGLV8-61",
"IGLV9-49",
"IGSF6",
"IKBKB",
"IKBKE",
"IKBKG",
"IL10",
"IL10RB",
"IL12A",
"IL12B",
"IL12RB1",
"IL16",
"IL17A",
"IL17B",
"IL18",
"IL18BP",
"IL18R1",
"IL18RAP",
"IL19",
"IL1F10",
"IL1R1",
"IL1R2",
"IL1RAP",
"IL1RL1",
"IL1RN",
"IL2",
"IL21",
"IL21R",
"IL23R",
"IL27RA",
"IL2RA",
"IL2RB",
"IL2RG",
"IL36A",
"IL36B",
"IL36G",
"IL36RN",
"IL37",
"IL4",
"IL4R",
"IL6",
"IL6R",
"IL7",
"IL7R",
"IL9R",
"INAVA",
"IRAK1",
"IRAK4",
"IRF1",
"IRF3",
"IRF4",
"IRF5",
"IRF7",
"IRF8",
"IRGM",
"ISG15",
"ITGA4",
"ITGAD",
"ITGAL",
"ITGB7",
"ITK",
"JAG1",
"JAK1",
"JAK2",
"JCHAIN",
"KAAG1",
"KARS1",
"KIF5B",
"KIR2DL1",
"KIR2DL3",
"KIR2DS1",
"KIR2DS2",
"KIR2DS5",
"KIR3DL1",
"KIR3DS1",
"KIT",
"KLRC2",
"KLRD1",
"KLRF2",
"KLRK1",
"KMT2A",
"KRT1",
"KRT16",
"KRT6A",
"KYNU",
"LAT",
"LAX1",
"LBP",
"LCK",
"LCN2",
"LCP1",
"LCP2",
"LEAP2",
"LEF1",
"LFNG",
"LGALS9",
"LIG4",
"LILRA2",
"LILRB1",
"LILRB2",
"LRP1",
"LST1",
"LTB4R",
"LTF",
"LY75",
"LY86",
"LY9",
"LY96",
"LYN",
"LYST",
"LYZ",
"MAD2L2",
"MADCAM1",
"MALT1",
"MAP3K14",
"MAP3K7",
"MAP4K2",
"MARCHF1",
"MARCHF2",
"MARCHF8",
"MASP1",
"MASP2",
"MAVS",
"MBL2",
"MBP",
"MDK",
"MEF2C",
"MEFV",
"MEN1",
"MFHAS1",
"MFNG",
"MICA",
"MICB",
"MID2",
"MILR1",
"MORC3",
"MPEG1",
"MPL",
"MR1",
"MRGPRX2",
"MS4A1",
"MS4A2",
"MSH2",
"MSH6",
"MSRB1",
"MUC7",
"MX1",
"MYB",
"MYD88",
"MYO1G",
"N4BP3",
"NCF1",
"NCF2",
"NCK1",
"NCR3",
"NCR3LG1",
"NECTIN1",
"NEDD4",
"NFKB1",
"NFKB2",
"NKG7",
"NLRC5",
"NLRP1",
"NLRP6",
"NLRP9",
"NMB",
"NMBR",
"NMI",
"NOD2",
"NOS2",
"NOTCH1",
"NOTCH2",
"NR4A3",
"NRROS",
"NUB1",
"OAS1",
"OAS2",
"OPRD1",
"OPRK1",
"OTUD7B",
"OTULIN",
"PDCD1",
"PDCD1LG2",
"PDE12",
"PDP2",
"PECAM1",
"PF4",
"PF4V1",
"PGLYRP1",
"PGLYRP2",
"PGLYRP3",
"PGLYRP4",
"PHB1",
"PHB2",
"PHF14",
"PI3",
"PIGR",
"PIK3CD",
"PIK3CG",
"PIK3R1",
"PIK3R2",
"PIK3R3",
"PIK3R5",
"PIK3R6",
"PIM1",
"PJA2",
"PKHD1L1",
"PLA2G1B",
"PLA2G6",
"PLCG2",
"PLEKHM2",
"PML",
"PNMA1",
"PNP",
"POLR3A",
"POU2AF1",
"POU2F2",
"PPARG",
"PPBP",
"PPP1R14B",
"PRF1",
"PRKRA",
"PRSS2",
"PRSS3",
"PRTN3",
"PSEN1",
"PSG9",
"PSMB10",
"PTAFR",
"PTGDR2",
"PTGER4",
"PTK2B",
"PTK6",
"PTX3",
"PXDN",
"PYCARD",
"PYDC1",
"RAB17",
"RAB2B",
"RAET1E",
"RAET1G",
"RAET1L",
"RAF1",
"RAG1",
"RAP1GAP",
"RAP1GAP2",
"RAPGEF3",
"RAPGEF4",
"RARRES2",
"RASGRP4",
"REG1A",
"REG1B",
"REG3A",
"REG3G",
"REL",
"RELA",
"RELB",
"RFPL1",
"RFPL2",
"RFPL3",
"RFPL4A",
"RFPL4AL1",
"RFTN1",
"RFX1",
"RGCC",
"RGS1",
"RIGI",
"RIPK2",
"RNASE2",
"RNASE3",
"RNASE4",
"RNASE6",
"RNASE7",
"RNASE8",
"RNF135",
"RNF168",
"RNF8",
"ROMO1",
"RORC",
"RPL13A",
"RPL30",
"RPL39",
"RPS19",
"RPSA",
"S100A12",
"S100A13",
"S100A7",
"S100A9",
"S1PR4",
"SAMHD1",
"SANBR",
"SBNO2",
"SCART1",
"SEMA3C",
"SEMA4D",
"SEMA7A",
"SEMG1",
"SEMG2",
"SENP7",
"SERINC3",
"SERINC5",
"SERPINB9",
"SETD2",
"SFTPD",
"SH2D1B",
"SHFL",
"SHLD1",
"SHLD2",
"SHLD3",
"SHMT2",
"SIPA1",
"SIRPA",
"SKP2",
"SLA2",
"SLAMF1",
"SLAMF6",
"SLAMF7",
"SLC11A1",
"SLC15A2",
"SLC22A5",
"SLC26A6",
"SLPI",
"SMAD3",
"SMAD6",
"SMARCA5",
"SMPD1",
"SNAP23",
"SNCA",
"SOCS3",
"SP100",
"SP2",
"SPAG11A",
"SPAG11B",
"SPN",
"SPRR2A",
"SRC",
"SRMS",
"SRPK1",
"SRPK2",
"ST6GAL1",
"STAT1",
"STAT2",
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FILE: debug/webgl/network-images.json
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================================================
FILE: debug/webgl/network-ndex-large-style.json
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"selector" : "node[MCL = 20]",
"style" : {
"background-color" : "rgb(160,14,217)"
}
}, {
"selector" : "node[MCL = 21]",
"style" : {
"background-color" : "rgb(35,191,93)"
}
}, {
"selector" : "node[MCL = 22]",
"style" : {
"background-color" : "rgb(63,236,129)"
}
}, {
"selector" : "node[MCL = 23]",
"style" : {
"background-color" : "rgb(123,59,244)"
}
}, {
"selector" : "node[MCL = 24]",
"style" : {
"background-color" : "rgb(4,22,64)"
}
}, {
"selector" : "node[MCL = 25]",
"style" : {
"background-color" : "rgb(8,212,129)"
}
}, {
"selector" : "node[MCL = 26]",
"style" : {
"background-color" : "rgb(173,59,163)"
}
}, {
"selector" : "node[MCL = 27]",
"style" : {
"background-color" : "rgb(206,207,54)"
}
}, {
"selector" : "node[MCL = 28]",
"style" : {
"background-color" : "rgb(243,182,239)"
}
}, {
"selector" : "node[MCL = 29]",
"style" : {
"background-color" : "rgb(33,150,126)"
}
}, {
"selector" : "node[MCL = 30]",
"style" : {
"background-color" : "rgb(76,119,10)"
}
}, {
"selector" : "node:selected",
"style" : {
"background-color" : "rgb(255,255,0)"
}
}, {
"selector" : "edge",
"style" : {
"line-style" : "solid",
"opacity" : 1.0,
"target-arrow-shape" : "none",
"target-arrow-color" : "rgb(0,0,0)",
"width" : 12.0,
"font-family" : "Dialog",
"font-weight" : "normal",
"text-opacity" : 1.0,
"source-arrow-color" : "rgb(0,0,0)",
"font-size" : 10,
"color" : "rgb(0,0,0)",
"line-color" : "rgb(204,204,204)",
"source-arrow-shape" : "none",
"content" : "data(interaction)"
}
}, {
"selector" : "edge:selected",
"style" : {
"line-color" : "rgb(255,0,0)"
}
} ]
}
================================================
FILE: debug/webgl/network-ndex-large.json
================================================
[File too large to display: 31.6 MB]
================================================
FILE: debug/webgl/network-ndex-x-large-style.json
================================================
{
"format_version" : "1.0",
"generated_by" : "cytoscape-3.10.3",
"target_cytoscapejs_version" : "~2.1",
"title" : "Regulon LIHC - Liver Hepatocellular Carcinoma-Style",
"style" : [ {
"selector" : "node",
"css" : {
"height" : 40.0,
"border-width" : 2.0,
"font-family" : "Dialog",
"font-weight" : "normal",
"background-opacity" : 1.0,
"background-color" : "rgb(102,204,255)",
"color" : "rgb(0,0,0)",
"font-size" : 14,
"border-opacity" : 1.0,
"text-opacity" : 1.0,
"border-color" : "rgb(0,102,255)",
"shape" : "vee",
"width" : 75.0,
"text-valign" : "bottom",
"text-halign" : "center",
"content" : "data(name)"
}
}, {
"selector" : "node[Node_Type = 'TF']",
"css" : {
"height" : 55.0
}
}, {
"selector" : "node[Node_Type = 'TF']",
"css" : {
"background-color" : "rgb(51,102,255)"
}
}, {
"selector" : "node[Node_Type = 'TF']",
"css" : {
"width" : 95.0
}
}, {
"selector" : "node[Node_Type = 'TF']",
"css" : {
"color" : "rgb(255,255,255)"
}
}, {
"selector" : "node[Node_Type = 'TF']",
"css" : {
"text-valign" : "center"
}
}, {
"selector" : "node[Node_Type = 'TF']",
"css" : {
"shape" : "diamond"
}
}, {
"selector" : "node[Node_Type = 'TF']",
"css" : {
"border-color" : "rgb(0,0,153)"
}
}, {
"selector" : "node:selected",
"css" : {
"background-color" : "rgb(255,153,51)"
}
}, {
"selector" : "edge",
"css" : {
"text-opacity" : 1.0,
"line-color" : "rgb(132,132,132)",
"source-arrow-color" : "rgb(0,0,0)",
"font-family" : "Dialog",
"font-weight" : "normal",
"target-arrow-color" : "rgb(0,0,0)",
"content" : "",
"opacity" : 1.0,
"width" : 1.0,
"line-style" : "solid",
"font-size" : 10,
"source-arrow-shape" : "none",
"color" : "rgb(0,0,0)",
"target-arrow-shape" : "none"
}
}, {
"selector" : "edge[Mechanism_of_Action > 1]",
"css" : {
"line-color" : "rgb(0,153,102)"
}
}, {
"selector" : "edge[Mechanism_of_Action = 1]",
"css" : {
"line-color" : "rgb(0,153,102)"
}
}, {
"selector" : "edge[Mechanism_of_Action > 0][Mechanism_of_Action < 1]",
"css" : {
"line-color" : "mapData(Mechanism_of_Action,0,1,rgb(247,247,247),rgb(0,153,102))"
}
}, {
"selector" : "edge[Mechanism_of_Action > -1][Mechanism_of_Action < 0]",
"css" : {
"line-color" : "mapData(Mechanism_of_Action,-1,0,rgb(204,0,51),rgb(247,247,247))"
}
}, {
"selector" : "edge[Mechanism_of_Action = -1]",
"css" : {
"line-color" : "rgb(204,0,51)"
}
}, {
"selector" : "edge[Mechanism_of_Action < -1]",
"css" : {
"line-color" : "rgb(204,0,51)"
}
}, {
"selector" : "edge[Likelihood > 1]",
"css" : {
"width" : 1.0
}
}, {
"selector" : "edge[Likelihood = 1]",
"css" : {
"width" : 10.0
}
}, {
"selector" : "edge[Likelihood > 0][Likelihood < 1]",
"css" : {
"width" : "mapData(Likelihood,0,1,1.0,10.0)"
}
}, {
"selector" : "edge[Likelihood = 0]",
"css" : {
"width" : 1.0
}
}, {
"selector" : "edge[Likelihood < 0]",
"css" : {
"width" : 1.0
}
}, {
"selector" : "edge:selected",
"css" : {
"line-color" : "rgb(255,0,0)"
}
} ]
}
================================================
FILE: debug/webgl/network-styles.json
================================================
{
"elements": {
"nodes": [
{ "data": { "id": "n1", "weight": 1 }, "position": { "x": -29, "y": 26 } },
{ "data": { "id": "n2", "weight": 2 }, "position": { "x": 77, "y": -15 } },
{ "data": { "id": "n3", "weight": 3 }, "position": { "x": 178, "y": 36 } },
{ "data": { "id": "n4", "weight": 4 }, "position": { "x": -17, "y": 146 } },
{ "data": { "id": "n5", "weight": 5 }, "position": { "x": 134, "y": 160 } },
{ "data": { "id": "n6", "weight": 5 }, "position": { "x": 134, "y": 195 } },
{ "data": { "id": "n7", "weight": 5 }, "position": { "x": 134, "y": 225 } },
{ "data": { "id": "n7i", "weight": 5 }, "position": { "x": 20, "y": 225 } },
{ "data": { "id": "n7o", "weight": 5 }, "position": { "x": 250, "y": 225 } },
{ "data": { "id": "n8", "weight": 5 }, "position": { "x": 134, "y": 275 } },
{ "data": { "id": "n9", "weight": 5 }, "position": { "x": 134, "y": 315 } }
],
"edges": [
{ "data": { "id":"n1-n2", "source": "n1", "target": "n2", "directed": "false" } },
{ "data": { "id":"n1-n3", "source": "n1", "target": "n3", "directed": "false" } },
{ "data": { "id":"n1-n4", "source": "n1", "target": "n4", "directed": "false" } },
{ "data": { "id":"n1-n5", "source": "n1", "target": "n5", "directed": "false" } },
{ "data": { "id":"n2-n3", "source": "n2", "target": "n3", "directed": "false" } },
{ "data": { "id":"n2-n4", "source": "n2", "target": "n4", "directed": "false" } },
{ "data": { "id":"n2-n5", "source": "n2", "target": "n5", "directed": "false" } },
{ "data": { "id":"n3-n4", "source": "n3", "target": "n4", "directed": "false" } },
{ "data": { "id":"n3-n5", "source": "n3", "target": "n5", "directed": "false" } },
{ "data": { "id":"n4-n5", "source": "n4", "target": "n5", "directed": "false" } },
{ "data": { "id":"n1-n2-2", "source": "n1", "target": "n2", "directed": "false" } },
{ "data": { "id":"n1-n2-3", "source": "n1", "target": "n2", "directed": "false" } },
{ "data": { "id":"n1-n2-4", "source": "n1", "target": "n2", "directed": "false" } }
]
},
"style": [
{
"selector": "node",
"style": {
"label": "data(id)",
"text-valign": "center",
"color": "#000000",
"background-color": "#3a7ecf",
"font-family": "Helvetica"
}
},
{
"selector": "#n1",
"style": {
"background-fill": "linear-gradient",
"background-gradient-stop-colors": "cyan magenta yellow",
"underlay-color": "red",
"underlay-shape": "round-rectangle",
"underlay-opacity": 0.5
}
},
{
"selector": "#n2",
"style": {
"border-color": "black",
"border-width": 2,
"background-image": "https://picsum.photos/600",
"background-fit": "cover",
"text-valign": "top",
"label": "n2 (random image)",
"font-size": "8px"
}
},
{
"selector": "#n3",
"style": {
"background-fill": "radial-gradient",
"background-gradient-stop-colors": "cyan magenta yellow",
"text-valign": "top",
"text-rotation": 0.7853981633974483,
"label": "n3 - Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod",
"text-events": "yes"
}
},
{
"selector": "#n4",
"style": {
"border-color": "black",
"border-style": "dashed",
"border-width": 2,
"background-opacity": 0.0
}
},
{
"selector": "#n5",
"style": {
"width": 100,
"border-color": "red",
"border-style": "dotted",
"border-width": 4,
"background-opacity": 0.5,
"label": "n5\nsecond line\nthird line\nfourth line",
"font-size": 10,
"text-valign": "top",
"text-wrap": "wrap",
"text-rotation": 0.0
}
},
{
"selector": "#n6",
"style": {
"shape": "rectangle",
"border-width": 0,
"width": 100,
"background-opacity": 0.5,
"background-color": "green",
"padding": 0
}
},
{
"selector": "#n7",
"style": {
"shape": "ellipse",
"border-width": 5,
"border-opacity": 0.5,
"width": 100,
"background-opacity": 0.5,
"background-color": "orange"
}
},
{
"selector": "#n7i",
"style": {
"shape": "ellipse",
"border-width": 5,
"border-opacity": 0.5,
"width": 100,
"background-opacity": 0.5,
"background-color": "orange",
"border-position": "inside"
}
},
{
"selector": "#n7o",
"style": {
"shape": "ellipse",
"border-width": 5,
"border-opacity": 0.5,
"width": 100,
"background-opacity": 0.5,
"background-color": "orange",
"border-position": "outside"
}
},
{
"selector": "#n8",
"style": {
"shape": "roundrectangle",
"corner-radius": 10,
"border-width": 0,
"width": 100,
"height": 30,
"background-opacity": 0.5,
"background-color": "purple"
}
},
{
"selector": "#n9",
"style": {
"shape": "bottom-round-rectangle",
"corner-radius": 20,
"border-width": 0,
"width": 100,
"height": 30,
"background-opacity": 0.5,
"background-color": "mediumpurple"
}
},
{
"selector": "node:selected",
"style": {
"border-color": "yellow",
"border-opacity": 1,
"border-width": 2
}
},
{
"selector": "edge",
"style": {
"width": 2,
"line-color": "#3a7ecf",
"opacity": 0.5,
"curve-style": "bezier"
}
},
{
"selector": "#n1-n2",
"style": {
"line-style": "solid"
}
},
{
"selector": "#n1-n3",
"style": {
"line-style": "dotted"
}
},
{
"selector": "#n1-n4",
"style": {
"line-style": "dashed"
}
},
{
"selector": "#n1-n5",
"style": {
"line-style": "dashed",
"line-dash-pattern": [1, 1, 4, 1]
}
},
{
"selector": "#n2-n3",
"style": {
"line-fill": "linear-gradient",
"line-gradient-stop-colors": "lawngreen red"
}
},
{
"selector": "#n2-n4",
"style": {
"label": "normal label",
"font-size": "6px",
"edge-text-rotation": "autorotate"
}
},
{
"selector": "#n2-n5",
"style": {
"label": "bold label",
"font-size": "6px",
"edge-text-rotation": "autorotate",
"font-weight": "bold"
}
},
{
"selector": "#n3-n4",
"style": {
"source-arrow-shape": "triangle",
"source-arrow-color": "red",
"target-arrow-shape": "triangle",
"target-arrow-color": "green",
"curve-style": "straight",
"label": "mid",
"source-label": "source",
"target-label": "target",
"edge-text-rotation": "autorotate",
"font-size": "10px",
"source-text-offset": "20px",
"target-text-offset": "20px"
}
}
]
}
================================================
FILE: debug/webgl/network-white-matter-style.json
================================================
{
"format_version" : "1.0",
"generated_by" : "cytoscape-3.11.0-SNAPSHOT",
"target_cytoscapejs_version" : "~2.1",
"title" : "Copy of Genetic white matter disorders expanded network-Style",
"style" : [ {
"selector" : "node",
"css" : {
"text-valign" : "bottom",
"text-halign" : "right",
"color" : "rgb(0,0,0)",
"border-width" : 0.0,
"text-opacity" : 1.0,
"width" : 15.0,
"font-size" : 8,
"background-color" : "rgb(255,255,255)",
"shape" : "ellipse",
"height" : 15.0,
"border-opacity" : 1.0,
"font-family" : "Dialog",
"font-weight" : "normal",
"border-color" : "rgb(0,153,0)",
"background-opacity" : 1.0,
"content" : "data(alias)"
}
}, {
"selector" : "node[Classification = 'candidate']",
"css" : {
"background-color" : "rgb(0,153,255)"
}
}, {
"selector" : "node[Classification = 'WM']",
"css" : {
"background-color" : "rgb(255,255,51)"
}
}, {
"selector" : "node[Classification = 'WMexpanded']",
"css" : {
"background-color" : "rgb(0,204,153)"
}
}, {
"selector" : "node:selected",
"css" : {
"background-color" : "rgb(255,255,0)"
}
}, {
"selector" : "edge",
"css" : {
"content" : "",
"target-arrow-color" : "rgb(0,0,0)",
"font-size" : 10,
"line-color" : "rgb(0,153,0)",
"opacity" : 0.19607843137254902,
"font-family" : "Dialog",
"font-weight" : "normal",
"source-arrow-color" : "rgb(0,0,0)",
"line-style" : "solid",
"width" : 2.0,
"text-opacity" : 1.0,
"source-arrow-shape" : "none",
"target-arrow-shape" : "none",
"color" : "rgb(0,0,0)"
}
}, {
"selector" : "edge:selected",
"css" : {
"line-color" : "rgb(255,0,0)"
}
} ]
}
================================================
FILE: debug/webgl/network-white-matter.json
================================================
{
"format_version" : "1.0",
"generated_by" : "cytoscape-3.11.0-SNAPSHOT",
"target_cytoscapejs_version" : "~2.1",
"data" : {
"rightsHolder" : "Agatha Schlüter",
"disease" : "Genetic white matter disorders",
"organism" : "Homo Sapiens",
"Blue" : "GWMD Candidate",
"author" : "Agatha Schlüter",
"__Annotations" : [ ],
"shared_name" : "Copy of Genetic white matter disorders expanded network",
"reference" : "Agatha Schlüter, Agustí Rodríguez-Palmero, Edgard Verdura, Valentina Vélez-Santamaría, Montserrat Ruiz, Stéphane Fourcade, Laura Planas-Serra, Juan José Martínez, Cristina Guilera, Marisa Girós, Rafael Artuch, María Eugenia Yoldi, Mar O'Callaghan, Angels García-Cazorla, Judith Armstrong, Itxaso Marti, Elisabet Mondragón Rezola, Claire Redin, Jean Louis Mandel, David Conejo, Concepción Sierra-Córcoles, Sergi Beltran, Marta Gut, Elida Vázquez, Mireia del Toro, Mónica Troncoso, Luis A. Pérez-Jurado, Luis G. Gutiérrez-Solana, Adolfo López de Munain, Carlos Casasnovas, Sergio Aguilera-Albesa, Alfons Macaya, Aurora Pujol
[](https://github.com/cytoscape/cytoscape.js)
[](https://www.phind.com/search?q=I%27m%20using%20the%20Cytoscape.js%20graph%20theory%20JS%20library.%20How%20do%20I%20create%20a%20graph%20in%20my%20HTML%20page)
[](https://blog.js.cytoscape.org)
[](https://raw.githubusercontent.com/cytoscape/cytoscape.js/master/LICENSE)
[](https://www.npmjs.com/package/cytoscape)
[](https://zenodo.org/badge/latestdoi/2255947)
[](https://www.npmjs.com/package/cytoscape)
[](https://github.com/cytoscape/cytoscape.js/actions/workflows/tests.yml)
[](https://js.cytoscape.org/#extensions)
[](https://cloudflare.com)
Created at the [University of Toronto](https://utoronto.ca) and published in [Oxford Bioinformatics](https://js.cytoscape.org/#introduction/citation) ([2016](https://academic.oup.com/bioinformatics/article/32/2/309/1744007), [2023](https://academic.oup.com/bioinformatics/article/39/1/btad031/6988031)). 
A [live demo](https://js.cytoscape.org/demos/tokyo-railways/) and [source code](https://github.com/cytoscape/cytoscape.js/tree/master/documentation/demos/tokyo-railways) are available for the Tokyo railway stations graph. More demos are available in the [documentation](https://js.cytoscape.org/#demos).
## Documentation
You can find the documentation and downloads on the [project website](https://js.cytoscape.org).
## Roadmap
Future versions of Cytoscape.js are planned in the [milestones of the Github issue tracker](https://github.com/cytoscape/cytoscape.js/milestones). You can use the milestones to see what's currently planned for future releases.
## Contributing to Cytoscape.js
Would you like to become a Cytoscape.js contributor? You can contribute in technical roles (e.g. features, testing) or non-technical roles (e.g. documentation, outreach), depending on your interests. [Get in touch with us by posting a GitHub discussion](https://github.com/cytoscape/cytoscape.js/discussions).
For the mechanics of contributing a pull request, refer to [CONTRIBUTING.md](CONTRIBUTING.md).
Feature releases are made monthly, while patch releases are made weekly. This allows for rapid releases of first- and third-party contributions.
## Citation
To cite Cytoscape.js in a paper, please cite the Oxford Bioinformatics issue:
*Cytoscape.js: a graph theory library for visualisation and analysis*
Franz M, Lopes CT, Huck G, Dong Y, Sumer O, Bader GD
[Bioinformatics (2016) 32 (2): 309-311 first published online September 28, 2015 doi:10.1093/bioinformatics/btv557](https://bioinformatics.oxfordjournals.org/content/32/2/309) [(PDF)](http://bioinformatics.oxfordjournals.org/content/32/2/309.full.pdf)
- [PubMed abstract for the original 2016 article](http://www.ncbi.nlm.nih.gov/pubmed/26415722)
- [PubMed abstract for the 2023 update article](https://pubmed.ncbi.nlm.nih.gov/36645249)
## Build dependencies
Install `node` and `npm`. Run `npm install` before using `npm run`.
## Build instructions
Run `npm run 
### Feature version
1. Go to [Actions > Feature release](https://github.com/cytoscape/cytoscape.js/actions/workflows/feature-release.yml)
1. Go to the 'Run workflow' dropdown
1. [Optional] The 'unstable' branch should be preselected for you
1. Press the green 'Run workflow' button
1. Close the milestone for the release
1. Make the release announcement [on the blog](https://github.com/cytoscape/cytoscape.js-blog)
### Notes on GitHub Actions UI
- 'Use workflow from' in the GitHub UI selects the branch from which the workflow YML file is selected. Since the workflow files should usually be the same on the master and unstable branches, it shouldn't matter what's selected.
- 'Branch to run the action on' in the GitHub UI is preselected for you. You don't need to change it.
## Tests
Mocha tests are found in the [test directory](https://github.com/cytoscape/cytoscape.js/tree/master/test). The tests can be run in the browser or they can be run via Node.js (`npm run test:js`).
================================================
FILE: benchmark/a-star.js
================================================
var eles, root, goal;
var Suite = require('./suite');
var suite = new Suite('eles.aStar()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal') });
eles = cy.elements();
root = cy.$('#367');
goal = cy.$('#381');
return cy;
}
});
suite
.add( function( cy ) {
eles.aStar({
root: root,
goal: goal
});
})
;
module.exports = suite;
================================================
FILE: benchmark/add-remove-class.js
================================================
var Suite = require('./suite');
var a;
var suite = new Suite('eles.addClass(); ... eles.removeClass();', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal'), styleEnabled: false });
a = cy.nodes();
return cy;
}
});
suite
.add( function( cy ) {
a.addClass('foo bar');
a.removeClass('foo bar');
})
;
module.exports = suite;
================================================
FILE: benchmark/add-remove.js
================================================
var Suite = require('./suite');
var suite = new Suite('cy.add(); ... cy.remove();');
suite
.add( function( cy ){
var N = 1000;
var eles = [];
for( var i = 0; i < N; i++ ){
eles.push({
group: 'nodes',
data: { id: 'node-'+i }
});
if( i >= 1 ){
eles.push({
group: 'edges',
data: { source: 'node-'+(i-1), target: 'node-'+(i) }
});
}
}
cy.add( eles );
cy.elements().remove();
} )
;
module.exports = suite;
================================================
FILE: benchmark/add.js
================================================
var Suite = require('./suite');
var suite = new Suite('cy.add()');
var eles = [];
var N = 100;
for( var i = 0; i < N; i++ ){
eles.push({
group: 'nodes',
data: { id: 'node-'+i }
});
if( i >= 1 ){
eles.push({
group: 'edges',
data: { source: 'node-'+(i-1), target: 'node-'+(i) }
});
}
}
global.elesJson = JSON.stringify( eles );
suite
.add( function( cy ){
cy.add( eles );
}, {
setup: function( cytoscape ){
global.eles = JSON.parse( global.elesJson );
return cytoscape();
}
} )
;
module.exports = suite;
================================================
FILE: benchmark/all/index.js
================================================
var fs = require('fs');
var path = require('path');
var isJs = function( name ){ return name.match(/\.js$/) != null; };
var suiteFiles = fs.readdirSync( path.join(__dirname, '..') ).filter( isJs );
suiteFiles.forEach(function( fileName ){
var suite = require('../' + fileName);
suite.run();
});
================================================
FILE: benchmark/all-are-neighbors.js
================================================
var Suite = require('./suite');
var a, b;
var suite = new Suite('eles.allAreNeighbors()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal') });
a = cy.nodes();
b = cy.nodes();
return cy;
}
});
suite
.add( function( cy ) {
a.allAreNeighbors( b );
})
;
module.exports = suite;
================================================
FILE: benchmark/all-are.js
================================================
var Suite = require('./suite');
var a;
var suite = new Suite('eles.allAre()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal') });
a = cy.nodes();
return cy;
}
});
suite
.add( function( cy ) {
a.allAre('node');
})
;
module.exports = suite;
================================================
FILE: benchmark/any-same.js
================================================
var Suite = require('./suite');
var a, b;
var suite = new Suite('eles.anySame()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal') });
a = cy.nodes();
b = cy.nodes();
return cy;
}
});
suite
.add( function( cy ) {
a.anySame(b);
})
;
module.exports = suite;
================================================
FILE: benchmark/bellman-ford.js
================================================
var root, eles;
var Suite = require('./suite');
var suite = new Suite('eles.bellmanFord()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal') });
eles = cy.elements();
root = cy.$('#367');
return cy;
}
});
suite
.add( function( cy ) {
eles.bellmanFord({
root: root
});
})
;
module.exports = suite;
================================================
FILE: benchmark/betweenness-centrality.js
================================================
var eles, root;
var Suite = require('./suite');
var suite = new Suite('eles.betweennessCentrality()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal') });
eles = cy.elements();
root = cy.$('#269');
return cy;
}
});
suite
.add( function( cy ) {
eles.betweennessCentrality({
root: root
});
})
;
module.exports = suite;
================================================
FILE: benchmark/bfs.js
================================================
var eles, root;
var Suite = require('./suite');
var suite = new Suite('eles.bfs()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal') });
eles = cy.elements();
root = cy.$('#367');
return cy;
}
});
suite
.add( function( cy ) {
eles.bfs({
root: root
});
})
;
module.exports = suite;
================================================
FILE: benchmark/classes.js
================================================
var Suite = require('./suite');
var a;
var suite = new Suite('eles.classes()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal'), styleEnabled: false });
a = cy.nodes();
return cy;
}
});
suite
.add( function( cy ) {
a.classes('foo bar');
})
;
module.exports = suite;
================================================
FILE: benchmark/closeness-centrality.js
================================================
var eles, root;
var Suite = require('./suite');
var suite = new Suite('eles.closenessCentrality()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal') });
eles = cy.elements();
root = cy.$('#367');
return cy;
}
});
suite
.add( function( cy ) {
eles.closenessCentrality({
root: root
});
})
;
module.exports = suite;
================================================
FILE: benchmark/collection-creation.js
================================================
var Suite = require('./suite');
var suite = new Suite('new Collection()', {
setup: function( cytoscape ){
return cytoscape({ elements: require('./graphs/gal') });
}
});
suite
.add( function( cy ) {
var eles = cy.elements().spawn();
// make sure the collection is used so it's not optimised out
var n = 0;
for( var i = 0; i < eles.length; i++ ){
n++;
}
return n;
})
;
module.exports = suite;
================================================
FILE: benchmark/contains.js
================================================
var Suite = require('./suite');
var a, b;
var suite = new Suite('eles.contains()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal') });
a = cy.nodes();
b = cy.nodes();
return cy;
}
});
suite
.add( function( cy ) {
a.contains( b );
})
;
module.exports = suite;
================================================
FILE: benchmark/degree-centrality.js
================================================
var eles, root;
var Suite = require('./suite');
var suite = new Suite('eles.degreeCentrality()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal') });
eles = cy.elements();
root = cy.$('#367');
return cy;
}
});
suite
.add( function( cy ) {
eles.degreeCentrality({
root: root
});
})
;
module.exports = suite;
================================================
FILE: benchmark/dfs.js
================================================
var eles, root;
var Suite = require('./suite');
var eles, root;
var suite = new Suite('eles.dfs()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal') });
eles = cy.elements();
root = cy.$('#367');
return cy;
}
});
suite
.add( function( cy ) {
eles.dfs({
root: root
});
})
;
module.exports = suite;
================================================
FILE: benchmark/dijkstra.js
================================================
var eles, root;
var Suite = require('./suite');
var suite = new Suite('eles.dijkstra()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal') });
eles = cy.elements();
root = cy.$('#367');
return cy;
}
});
suite
.add( function( cy ) {
eles.dijkstra({
root: root
});
})
;
module.exports = suite;
================================================
FILE: benchmark/floyd-warshall.js
================================================
var eles;
var Suite = require('./suite');
var suite = new Suite('eles.floydWarshall()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal') });
eles = cy.elements();
return cy;
}
});
suite
.add( function( cy ) {
eles.floydWarshall();
})
;
module.exports = suite;
================================================
FILE: benchmark/graphs/abcde.json
================================================
{
"nodes": [
{ "data": { "id": "a" } },
{ "data": { "id": "b" } },
{ "data": { "id": "c" } },
{ "data": { "id": "d" } },
{ "data": { "id": "e" } }
],
"edges": [
{ "data": { "id": "ae", "weight": 1, "source": "a", "target": "e" } },
{ "data": { "id": "ab", "weight": 3, "source": "a", "target": "b" } },
{ "data": { "id": "be", "weight": 4, "source": "b", "target": "e" } },
{ "data": { "id": "bc", "weight": 5, "source": "b", "target": "c" } },
{ "data": { "id": "ce", "weight": 6, "source": "c", "target": "e" } },
{ "data": { "id": "cd", "weight": 2, "source": "c", "target": "d" } },
{ "data": { "id": "de", "weight": 7, "source": "d", "target": "e" } }
]
}
================================================
FILE: benchmark/graphs/gal.json
================================================
{
"nodes" : [ {
"data" : {
"id" : "392",
"degree_layout" : 1,
"gal80Rexp" : 0.292,
"gal1RGsig" : 9.1177E-4,
"Eccentricity" : 26,
"gal4RGsig" : 3.5692E-6,
"shared_name" : "YKR026C",
"TopologicalCoefficient" : 0.0,
"SUID" : 392,
"SelfLoops" : 0,
"NumberOfDirectedEdges" : 1,
"AverageShortestPathLength" : 15.37096774,
"selected" : false,
"gal80Rsig" : 0.011229,
"ClosenessCentrality" : 0.06505771,
"Degree" : 1,
"PartnerOfMultiEdgedNodePairs" : 0,
"ClusteringCoefficient" : 0.0,
"Radiality" : 0.46774194,
"Stress" : 0,
"BetweennessCentrality" : 0.0,
"NumberOfUndirectedEdges" : 0,
"gal1RGexp" : -0.154,
"name" : "YKR026C",
"COMMON" : "GCN3",
"gal4RGexp" : -0.501,
"IsSingleNode" : false,
"NeighborhoodConnectivity" : 3.0
}
}, {
"data" : {
"id" : "391",
"degree_layout" : 3,
"gal80Rexp" : 0.187,
"gal1RGsig" : 8.7295E-4,
"Eccentricity" : 25,
"gal4RGsig" : 0.61707,
"shared_name" : "YGL122C",
"TopologicalCoefficient" : 0.33333333,
"SUID" : 391,
"SelfLoops" : 0,
"NumberOfDirectedEdges" : 3,
"AverageShortestPathLength" : 14.375,
"selected" : false,
"gal80Rsig" : 0.0059966,
"ClosenessCentrality" : 0.06956522,
"Degree" : 3,
"PartnerOfMultiEdgedNodePairs" : 0,
"ClusteringCoefficient" : 0.0,
"Radiality" : 0.50462963,
"Stress" : 5902,
"BetweennessCentrality" : 0.02406295,
"NumberOfUndirectedEdges" : 0,
"gal1RGexp" : 0.174,
"name" : "YGL122C",
"COMMON" : "NAB2",
"gal4RGexp" : 0.02,
"IsSingleNode" : false,
"NeighborhoodConnectivity" : 1.66666667
}
}, {
"data" : {
"id" : "390",
"degree_layout" : 1,
"gal80Rexp" : -0.018,
"gal1RGsig" : 0.61381,
"Eccentricity" : 2,
"gal4RGsig" : 0.9794,
"shared_name" : "YGR218W",
"TopologicalCoefficient" : 0.0,
"SUID" : 390,
"SelfLoops" : 0,
"NumberOfDirectedEdges" : 1,
"AverageShortestPathLength" : 1.66666667,
"selected" : false,
"gal80Rsig" : 0.80969,
"ClosenessCentrality" : 0.6,
"Degree" : 1,
"PartnerOfMultiEdgedNodePairs" : 0,
"ClusteringCoefficient" : 0.0,
"Radiality" : 0.66666667,
"Stress" : 0,
"BetweennessCentrality" : 0.0,
"NumberOfUndirectedEdges" : 0,
"gal1RGexp" : -0.018,
"name" : "YGR218W",
"COMMON" : "CRM1",
"gal4RGexp" : -0.001,
"IsSingleNode" : false,
"NeighborhoodConnectivity" : 3.0
}
}, {
"data" : {
"id" : "389",
"degree_layout" : 3,
"gal80Rexp" : 0.008,
"gal1RGsig" : 0.0021913,
"Eccentricity" : 1,
"gal4RGsig" : 0.0022461,
"shared_name" : "YGL097W",
"TopologicalCoefficient" : 0.0,
"SUID" : 389,
"SelfLoops" : 0,
"NumberOfDirectedEdges" : 3,
"AverageShortestPathLength" : 1.0,
"selected" : false,
"gal80Rsig" : 0.93826,
"ClosenessCentrality" : 1.0,
"Degree" : 3,
"PartnerOfMultiEdgedNodePairs" : 0,
"ClusteringCoefficient" : 0.0,
"Radiality" : 1.0,
"Stress" : 6,
"BetweennessCentrality" : 1.0,
"NumberOfUndirectedEdges" : 0,
"gal1RGexp" : 0.16,
"name" : "YGL097W",
"COMMON" : "SRM1",
"gal4RGexp" : -0.23,
"IsSingleNode" : false,
"NeighborhoodConnectivity" : 1.0
}
}, {
"data" : {
"id" : "388",
"degree_layout" : 1,
"gal80Rexp" : -0.91,
"gal1RGsig" : 0.39944,
"Eccentricity" : 2,
"gal4RGsig" : 0.31268,
"shared_name" : "YOR204W",
"TopologicalCoefficient" : 0.0,
"SUID" : 388,
"SelfLoops" : 0,
"NumberOfDirectedEdges" : 1,
"AverageShortestPathLength" : 1.66666667,
"selected" : false,
"gal80Rsig" : 8.349E-16,
"ClosenessCentrality" : 0.6,
"Degree" : 1,
"PartnerOfMultiEdgedNodePairs" : 0,
"ClusteringCoefficient" : 0.0,
"Radiality" : 0.66666667,
"Stress" : 0,
"BetweennessCentrality" : 0.0,
"NumberOfUndirectedEdges" : 0,
"gal1RGexp" : -0.033,
"name" : "YOR204W",
"COMMON" : "DED1",
"gal4RGexp" : -0.056,
"IsSingleNode" : false,
"NeighborhoodConnectivity" : 3.0
}
}, {
"data" : {
"id" : "387",
"degree_layout" : 2,
"gal80Rexp" : -0.769,
"gal1RGsig" : 2.713E-8,
"Eccentricity" : 2,
"gal4RGsig" : 0.04747,
"shared_name" : "YLR249W",
"TopologicalCoefficient" : 1.0,
"SUID" : 387,
"SelfLoops" : 0,
"NumberOfDirectedEdges" : 2,
"AverageShortestPathLength" : 1.33333333,
"selected" : false,
"gal80Rsig" : 0.035939,
"ClosenessCentrality" : 0.75,
"Degree" : 2,
"PartnerOfMultiEdgedNodePairs" : 0,
"ClusteringCoefficient" : 0.0,
"Radiality" : 0.83333333,
"Stress" : 2,
"BetweennessCentrality" : 0.16666667,
"NumberOfUndirectedEdges" : 0,
"gal1RGexp" : -0.39,
"name" : "YLR249W",
"COMMON" : "YEF3",
"gal4RGexp" : -0.394,
"IsSingleNode" : false,
"NeighborhoodConnectivity" : 2.0
}
}, {
"data" : {
"id" : "386",
"degree_layout" : 2,
"gal80Rexp" : -0.278,
"gal1RGsig" : 9.8725E-4,
"Eccentricity" : 2,
"gal4RGsig" : 0.89728,
"shared_name" : "YPR080W",
"TopologicalCoefficient" : 1.0,
"SUID" : 386,
"SelfLoops" : 0,
"NumberOfDirectedEdges" : 2,
"AverageShortestPathLength" : 1.33333333,
"selected" : false,
"gal80Rsig" : 6.7798E-4,
"ClosenessCentrality" : 0.75,
"Degree" : 2,
"PartnerOfMultiEdgedNodePairs" : 0,
"ClusteringCoefficient" : 0.0,
"Radiality" : 0.83333333,
"Stress" : 2,
"BetweennessCentrality" : 0.16666667,
"NumberOfUndirectedEdges" : 0,
"gal1RGexp" : -0.138,
"name" : "YPR080W",
"COMMON" : "TEF1",
"gal4RGexp" : 0.009,
"IsSingleNode" : false,
"NeighborhoodConnectivity" : 2.0
}
}, {
"data" : {
"id" : "385",
"degree_layout" : 2,
"gal80Rexp" : 0.044,
"gal1RGsig" : 0.053125,
"Eccentricity" : 2,
"gal4RGsig" : 0.15497,
"shared_name" : "YBR118W",
"TopologicalCoefficient" : 1.0,
"SUID" : 385,
"SelfLoops" : 0,
"NumberOfDirectedEdges" : 2,
"AverageShortestPathLength" : 1.33333333,
"selected" : false,
"gal80Rsig" : 0.54556,
"ClosenessCentrality" : 0.75,
"Degree" : 2,
"PartnerOfMultiEdgedNodePairs" : 0,
"ClusteringCoefficient" : 0.0,
"Radiality" : 0.83333333,
"Stress" : 2,
"BetweennessCentrality" : 0.16666667,
"NumberOfUndirectedEdges" : 0,
"gal1RGexp" : -0.074,
"name" : "YBR118W",
"COMMON" : "TEF2",
"gal4RGexp" : -0.063,
"IsSingleNode" : false,
"NeighborhoodConnectivity" : 2.0
}
}, {
"data" : {
"id" : "384",
"degree_layout" : 1,
"gal80Rexp" : -0.128,
"gal1RGsig" : 1.7601E-5,
"Eccentricity" : 2,
"gal4RGsig" : 6.7968E-4,
"shared_name" : "YLR293C",
"TopologicalCoefficient" : 0.0,
"SUID" : 384,
"SelfLoops" : 0,
"NumberOfDirectedEdges" : 1,
"AverageShortestPathLength" : 1.66666667,
"selected" : false,
"gal80Rsig" : 0.012703,
"ClosenessCentrality" : 0.6,
"Degree" : 1,
"PartnerOfMultiEdgedNodePairs" : 0,
"ClusteringCoefficient" : 0.0,
"Radiality" : 0.66666667,
"Stress" : 0,
"BetweennessCentrality" : 0.0,
"NumberOfUndirectedEdges" : 0,
"gal1RGexp" : -0.242,
"name" : "YLR293C",
"COMMON" : "GSP1",
"gal4RGexp" : -0.247,
"IsSingleNode" : false,
"NeighborhoodConnectivity" : 3.0
}
}, {
"data" : {
"id" : "383",
"degree_layout" : 1,
"gal80Rexp" : -0.151,
"gal1RGsig" : 0.30844,
"Eccentricity" : 19,
"gal4RGsig" : 0.0085173,
"shared_name" : "YMR146C",
"TopologicalCoefficient" : 0.0,
"SUID" : 383,
"SelfLoops" : 0,
"NumberOfDirectedEdges" : 1,
"AverageShortestPathLength" : 10.81048387,
"selected" : false,
"gal80Rsig" : 0.072007,
"ClosenessCentrality" : 0.0925028,
"Degree" : 1,
"PartnerOfMultiEdgedNodePairs" : 0,
"ClusteringCoefficient" : 0.0,
"Radiality" : 0.63664875,
"Stress" : 0,
"BetweennessCentrality" : 0.0,
"NumberOfUndirectedEdges" : 0,
"gal1RGexp" : -0.05,
"name" : "YMR146C",
"COMMON" : "TIF34",
"gal4RGexp" : -0.143,
"IsSingleNode" : false,
"NeighborhoodConnectivity" : 3.0
}
}, {
"data" : {
"id" : "382",
"degree_layout" : 3,
"gal80Rexp" : 0.354,
"gal1RGsig" : 0.072655,
"Eccentricity" : 18,
"gal4RGsig" : 0.0011724,
"shared_name" : "YDR429C",
"TopologicalCoefficient" : 0.33333333,
"SUID" : 382,
"SelfLoops" : 0,
"NumberOfDirectedEdges" : 3,
"AverageShortestPathLength" : 9.81451613,
"selected" : false,
"gal80Rsig" : 1.6643E-5,
"ClosenessCentrality" : 0.10188989,
"Degree" : 3,
"PartnerOfMultiEdgedNodePairs" : 0,
"ClusteringCoefficient" : 0.0,
"Radiality" : 0.67353644,
"Stress" : 4106,
"BetweennessCentrality" : 0.02250902,
"NumberOfUndirectedEdges" : 0,
"gal1RGexp" : 0.078,
"name" : "YDR429C",
"COMMON" : "TIF35",
"gal4RGexp" : -0.209,
"IsSingleNode" : false,
"NeighborhoodConnectivity" : 3.0
}
}, {
"data" : {
"id" : "381",
"degree_layout" : 5,
"gal80Rexp" : 0.124,
"gal1RGsig" : 0.0017854,
"Eccentricity" : 19,
"gal4RGsig" : 0.0055302,
"shared_name" : "YFL017C",
"TopologicalCoefficient" : 0.2,
"SUID" : 381,
"SelfLoops" : 0,
"NumberOfDirectedEdges" : 5,
"AverageShortestPathLength" : 9.45564516,
"selected" : false,
"gal80Rsig" : 0.050323,
"ClosenessCentrality" : 0.10575693,
"Degree" : 5,
"PartnerOfMultiEdgedNodePairs" : 0,
"ClusteringCoefficient" : 0.0,
"Radiality" : 0.68682796,
"Stress" : 6282,
"BetweennessCentrality" : 0.0426128,
"NumberOfUndirectedEdges" : 0,
"gal1RGexp" : 0.131,
"name" : "YFL017C",
"COMMON" : "GNA1",
"gal4RGexp" : 0.122,
"IsSingleNode" : false,
"NeighborhoodConnectivity" : 1.6
}
}, {
"data" : {
"id" : "380",
"degree_layout" : 2,
"gal80Rexp" : -0.146,
"gal1RGsig" : 0.0018696,
"Eccentricity" : 2,
"gal4RGsig" : 6.2814E-4,
"shared_name" : "YAL003W",
"TopologicalCoefficient" : 1.0,
"SUID" : 380,
"SelfLoops" : 0,
"NumberOfDirectedEdges" : 2,
"AverageShortestPathLength" : 1.33333333,
"selected" : false,
"gal80Rsig" : 0.013062,
"ClosenessCentrality" : 0.75,
"Degree" : 2,
"PartnerOfMultiEdgedNodePairs" : 0,
"ClusteringCoefficient" : 0.0,
"Radiality" : 0.83333333,
"Stress" : 2,
"BetweennessCentrality" : 0.16666667,
"NumberOfUndirectedEdges" : 0,
"gal1RGexp" : -0.157,
"name" : "YAL003W",
"COMMON" : "EFB1",
"gal4RGexp" : -0.2,
"IsSingleNode" : false,
"NeighborhoodConnectivity" : 2.0
}
}, {
"data" : {
"id" : "379",
"degree_layout" : 2,
"gal80Rexp" : -0.036,
"gal1RGsig" : 9.8446E-6,
"Eccentricity" : 26,
"gal4RGsig" : 0.0050114,
"shared_name" : "YOL123W",
"TopologicalCoefficient" : 0.5,
"SUID" : 379,
"SelfLoops" : 0,
"NumberOfDirectedEdges" : 2,
"AverageShortestPathLength" : 15.36290323,
"selected" : false,
"gal80Rsig" : 0.59496,
"ClosenessCentrality" : 0.06509186,
"Degree" : 2,
"PartnerOfMultiEdgedNodePairs" : 0,
"ClusteringCoefficient" : 0.0,
"Radiality" : 0.46804062,
"Stress" : 1970,
"BetweennessCentrality" : 0.00806452,
"NumberOfUndirectedEdges" : 0,
"gal1RGexp" : 0.245,
"name" : "YOL123W",
"COMMON" : "HRP1",
"gal4RGexp" : 0.126,
"IsSingleNode" : false,
"NeighborhoodConnectivity" : 2.0
}
}, {
"data" : {
"id" : "378",
"degree_layout" : 1,
"gal80Rexp" : 0.281,
"gal1RGsig" : 0.0013639,
"Eccentricity" : 27,
"gal4RGsig" : 0.0040902,
"shared_name" : "YGL044C",
"TopologicalCoefficient" : 0.0,
"SUID" : 378,
"SelfLoops" : 0,
"NumberOfDirectedEdges" : 1,
"AverageShortestPathLength" : 16.35887097,
"selected" : false,
"gal80Rsig" : 0.0057448,
"ClosenessCentrality" : 0.06112891,
"Degree" : 1,
"PartnerOfMultiEdgedNodePairs" : 0,
"ClusteringCoefficient" : 0.0,
"Radiality" : 0.43115293,
"Stress" : 0,
"BetweennessCentrality" : 0.0,
"NumberOfUndirectedEdges" : 0,
"gal1RGexp" : 0.162,
"name" : "YGL044C",
"COMMON" : "RNA15",
"gal4RGexp" : -0.211,
"IsSingleNode" : false,
"NeighborhoodConnectivity" : 2.0
}
}, {
"data" : {
"id" : "377",
"degree_layout" : 1,
"gal80Rexp" : 0.623,
"gal1RGsig" : 0.0019352,
"Eccentricity" : 3,
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"shared_name" : "YPL211W",
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"source" : "80",
"target" : "328",
"EdgeBetweenness" : 2.0,
"shared_name" : "YLR197W (pp) YOR310C",
"shared_interaction" : "pp",
"name" : "YLR197W (pp) YOR310C",
"interaction" : "pp",
"SUID" : 407,
"selected" : false
}
}, {
"data" : {
"id" : "406",
"source" : "79",
"target" : "78",
"EdgeBetweenness" : 4.0,
"shared_name" : "YGL202W (pp) YGR074W",
"shared_interaction" : "pp",
"name" : "YGL202W (pp) YGR074W",
"interaction" : "pp",
"SUID" : 406,
"selected" : false
}
}, {
"data" : {
"id" : "405",
"source" : "78",
"target" : "64",
"EdgeBetweenness" : 4.0,
"shared_name" : "YGR074W (pp) YBR043C",
"shared_interaction" : "pp",
"name" : "YGR074W (pp) YBR043C",
"interaction" : "pp",
"SUID" : 405,
"selected" : false
}
}, {
"data" : {
"id" : "404",
"source" : "77",
"target" : "186",
"EdgeBetweenness" : 4.0,
"shared_name" : "YBR170C (pp) YGR048W",
"shared_interaction" : "pp",
"name" : "YBR170C (pp) YGR048W",
"interaction" : "pp",
"SUID" : 404,
"selected" : false
}
}, {
"data" : {
"id" : "403",
"source" : "76",
"target" : "267",
"EdgeBetweenness" : 496.0,
"shared_name" : "YDL023C (pp) YJL159W",
"shared_interaction" : "pp",
"name" : "YDL023C (pp) YJL159W",
"interaction" : "pp",
"SUID" : 403,
"selected" : false
}
}, {
"data" : {
"id" : "402",
"source" : "75",
"target" : "284",
"EdgeBetweenness" : 496.0,
"shared_name" : "YGR136W (pp) YGR058W",
"shared_interaction" : "pp",
"name" : "YGR136W (pp) YGR058W",
"interaction" : "pp",
"SUID" : 402,
"selected" : false
}
}, {
"data" : {
"id" : "401",
"source" : "69",
"target" : "211",
"EdgeBetweenness" : 496.0,
"shared_name" : "YLR345W (pp) YLR321C",
"shared_interaction" : "pp",
"name" : "YLR345W (pp) YLR321C",
"interaction" : "pp",
"SUID" : 401,
"selected" : false
}
}, {
"data" : {
"id" : "400",
"source" : "68",
"target" : "81",
"EdgeBetweenness" : 6.0,
"shared_name" : "YBL079W (pp) YDL088C",
"shared_interaction" : "pp",
"name" : "YBL079W (pp) YDL088C",
"interaction" : "pp",
"SUID" : 400,
"selected" : false
}
}, {
"data" : {
"id" : "399",
"source" : "67",
"target" : "103",
"EdgeBetweenness" : 5236.0,
"shared_name" : "YBR045C (pp) YIL045W",
"shared_interaction" : "pp",
"name" : "YBR045C (pp) YIL045W",
"interaction" : "pp",
"SUID" : 399,
"selected" : false
}
}, {
"data" : {
"id" : "398",
"source" : "67",
"target" : "179",
"EdgeBetweenness" : 2962.0,
"shared_name" : "YBR045C (pp) YOR178C",
"shared_interaction" : "pp",
"name" : "YBR045C (pp) YOR178C",
"interaction" : "pp",
"SUID" : 398,
"selected" : false
}
}, {
"data" : {
"id" : "397",
"source" : "66",
"target" : "180",
"EdgeBetweenness" : 3174.0,
"shared_name" : "YER054C (pp) YER133W",
"shared_interaction" : "pp",
"name" : "YER054C (pp) YER133W",
"interaction" : "pp",
"SUID" : 397,
"selected" : false
}
}, {
"data" : {
"id" : "396",
"source" : "66",
"target" : "67",
"EdgeBetweenness" : 2746.0,
"shared_name" : "YER054C (pp) YBR045C",
"shared_interaction" : "pp",
"name" : "YER054C (pp) YBR045C",
"interaction" : "pp",
"SUID" : 396,
"selected" : false
}
}, {
"data" : {
"id" : "395",
"source" : "65",
"target" : "84",
"EdgeBetweenness" : 496.0,
"shared_name" : "YPR145W (pp) YMR117C",
"shared_interaction" : "pp",
"name" : "YPR145W (pp) YMR117C",
"interaction" : "pp",
"SUID" : 395,
"selected" : false
}
}, {
"data" : {
"id" : "394",
"source" : "63",
"target" : "365",
"EdgeBetweenness" : 988.0,
"shared_name" : "YDR277C (pp) YJR022W",
"shared_interaction" : "pp",
"name" : "YDR277C (pp) YJR022W",
"interaction" : "pp",
"SUID" : 394,
"selected" : false
}
}, {
"data" : {
"id" : "393",
"source" : "63",
"target" : "62",
"EdgeBetweenness" : 496.0,
"shared_name" : "YDR277C (pp) YDL194W",
"shared_interaction" : "pp",
"name" : "YDR277C (pp) YDL194W",
"interaction" : "pp",
"SUID" : 393,
"selected" : false
}
} ]
}
================================================
FILE: benchmark/graphs/random.js
================================================
var def = function( specdVal, defVal ){
return specdVal !== undefined ? specdVal : defVal;
};
module.exports = function( opts ){
opts = opts || {};
var nNodes = def( opts.nodes, 2 );
var nEdges = def( opts.edges, 1 );
var generateNode = def( opts.generateNode, function(){
return {};
} );
var generateEdge = def( opts.generateEdge, function( src, tgt ){
return {
data: { source: src.data.id, target: tgt.data.id }
};
} );
var nodes = [];
var edges = [];
var i;
var src, tgt;
var randNode = function(){
var index = Math.round( Math.random() * ( nNodes - 1 ) );
return nodes[ index ];
};
for( i = 0; i < nNodes; i++ ){
nodes.push( generateNode() );
}
for( i = 0; i < nEdges; i++ ){
src = randNode();
tgt = randNode();
edges.push( generateEdge( src, tgt ) );
}
return {
nodes: nodes,
edges: edges
};
};
================================================
FILE: benchmark/has-class.js
================================================
var Suite = require('./suite');
var a;
var suite = new Suite('eles.hasClass()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal'), styleEnabled: false });
a = cy.nodes();
return cy;
}
});
suite
.add( function( cy ) {
a.hasClass('foo');
})
;
module.exports = suite;
================================================
FILE: benchmark/id-selector.js
================================================
var Suite = require('./suite');
var suite = new Suite('#id selector', {
setup: function( cytoscape ){
return cytoscape({ elements: require('./graphs/gal') });
}
});
suite
.add( function( cy ) {
cy.$('#381');
})
;
module.exports = suite;
================================================
FILE: benchmark/init.js
================================================
var Suite = require('./suite');
var Cytoscape;
var eles;
var suite = new Suite('new Cytoscape()', {
setup: function( cytoscapeImpl ){
Cytoscape = cytoscapeImpl;
eles = JSON.parse( JSON.stringify( require('./graphs/gal') ) );
}
});
suite
.add( function() {
return new Cytoscape({ elements: eles });
})
;
module.exports = suite;
================================================
FILE: benchmark/is.js
================================================
var Suite = require('./suite');
var a;
var suite = new Suite('eles.is()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal') });
a = cy.nodes();
return cy;
}
});
suite
.add( function( cy ) {
a.is('node');
})
;
module.exports = suite;
================================================
FILE: benchmark/karger-stein.js
================================================
var eles;
var Suite = require('./suite');
var suite = new Suite('eles.kargerStein()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal') });
eles = cy.elements().components()[0]; // Karger-Stein can run only on connected (sub)graphs
return cy;
}
});
suite
.add( function( cy ) {
eles.kargerStein({});
})
;
module.exports = suite;
================================================
FILE: benchmark/kruskal.js
================================================
var eles;
var Suite = require('./suite');
var suite = new Suite('eles.kruskal()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal') });
eles = cy.elements();
return cy;
}
});
suite
.add( function( cy ) {
eles.kruskal();
})
;
module.exports = suite;
================================================
FILE: benchmark/page-rank.js
================================================
var eles;
var Suite = require('./suite');
var suite = new Suite('eles.pageRank()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal') });
eles = cy.elements();
return cy;
}
});
suite
.add( function( cy ) {
eles.pageRank({});
})
;
module.exports = suite;
================================================
FILE: benchmark/same.js
================================================
var Suite = require('./suite');
var a, b;
var suite = new Suite('eles.same()', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal') });
a = cy.nodes();
b = cy.nodes();
return cy;
}
});
suite
.add( function( cy ) {
a.same(b);
})
;
module.exports = suite;
================================================
FILE: benchmark/selector-filter.js
================================================
var Suite = require('./suite');
var eles;
var suite = new Suite('eles.filter(selector)', {
setup: function( cytoscape ){
var cy = cytoscape({ elements: require('./graphs/gal') });
eles = cy.nodes();
return cy;
}
});
suite
.add( function( cy ) {
// n.b.
// - use a selector that matches all nodes so we really compare the selector matching rather than letting the matches exit early
// - only create one selector : compare matching perf, not creation perf
eles.filter('node:unselected:grabbable[gal80Rexp > 0][SUID > 0][Stress >= 5][AverageShortestPathLength > 0]');
})
;
module.exports = suite;
================================================
FILE: benchmark/single/index.js
================================================
// set this to run just a single suite via `npm run benchmark:single`
// (useful when working on a specific function)
var suite = require('../collection-creation');
suite.run({ async: true });
================================================
FILE: benchmark/suite/index.js
================================================
var Benchmark = require('benchmark');
var newCytoscape = require('../../build/cytoscape.cjs.js');
var oldCytoscape = require('../../build/cytoscape.benchmark.js');
global.newCytoscape = newCytoscape;
global.oldCytoscape = oldCytoscape;
function Suite( name, suiteOpts ){
suiteOpts = suiteOpts || {};
var suite = new Benchmark.Suite( name, suiteOpts );
var suiteAdd = suite.add;
suite.on('start', function(){
console.log('Starting benchmark:', suite.name); // eslint-disable-line no-console
});
suite.on('cycle', function(event) {
console.log(String(event.target)); // eslint-disable-line no-console
});
suite.on('complete', function(){
console.log( 'Fastest is:' ,this.filter('fastest').map('name')[0] ); // eslint-disable-line no-console
});
suite.add = function( fn ){
global.setup = suiteOpts.setup || function( cytoscape ){
return cytoscape();
};
global.teardown = suiteOpts.teardown || function( cy ){
if( cy && cy.destroy ){ cy.destroy(); }
};
global.fn = fn;
suiteAdd.apply( suite, [ name + '::old', function(){ return fn( global.cy ); }, {
setup: function(){
global.cy = setup( oldCytoscape );
},
teardown: function(){
teardown( global.cy );
}
} ] );
suiteAdd.apply( suite, [ name + '::new', function(){ return fn( global.cy ); }, {
setup: function(){
global.cy = setup( newCytoscape );
},
teardown: function(){
teardown( global.cy );
}
} ] );
return this; // chaining
};
return suite;
}
module.exports = Suite;
================================================
FILE: bower.json
================================================
{
"name": "cytoscape",
"license": "MIT",
"description": "Graph theory (a.k.a. network) library for analysis and visualisation",
"homepage": "http://js.cytoscape.org",
"repository": {
"type": "git",
"url": "https://github.com/cytoscape/cytoscape.js.git"
},
"authors": [
{
"name": "Max Franz",
"email": "maxkfranz@gmail.com",
"homepage": "http://maxfranz.com"
},
{
"name": "Christian Lopes",
"email": "chrtannus@gmail.com"
},
{
"name": "Yue Dong",
"email": "oryato@gmail.com"
},
{
"name": "Onur Sumer",
"email": "s.onur.sumer@gmail.com"
},
{
"name": "Gerardo Huck",
"email": "gerardohuck@gmail.com"
},
{
"name": "Alexandr Truhin (bumbu)",
"email": "bmbalex@gmail.com"
}
],
"keywords": [
"graph",
"graph-theory",
"network",
"node",
"edge",
"vertex",
"link",
"analysis",
"visualisation",
"visualization",
"requirejs",
"amd",
"commonjs",
"node",
"npm",
"nodejs",
"bower",
"jquery"
],
"main": "dist/cytoscape.umd.js",
"ignore": [
"documentation",
"src",
"test",
"debug",
"gulpfile.js",
"package.json",
"CONTRIBUTING.md",
"build",
"node_modules"
]
}
================================================
FILE: debug/FileSaver.js
================================================
(function (global, factory) {
if (typeof define === "function" && define.amd) {
define([], factory);
} else if (typeof exports !== "undefined") {
factory();
} else {
var mod = {
exports: {}
};
factory();
global.FileSaver = mod.exports;
}
})(this, function () {
"use strict";
/*
* FileSaver.js
* A saveAs() FileSaver implementation.
*
* By Eli Grey, http://eligrey.com
*
* License : https://github.com/eligrey/FileSaver.js/blob/master/LICENSE.md (MIT)
* source : http://purl.eligrey.com/github/FileSaver.js
*/
// The one and only way of getting global scope in all environments
// https://stackoverflow.com/q/3277182/1008999
var _global = typeof window === 'object' && window.window === window ? window : typeof self === 'object' && self.self === self ? self : typeof global === 'object' && global.global === global ? global : void 0;
function bom(blob, opts) {
if (typeof opts === 'undefined') opts = {
autoBom: false
};else if (typeof opts !== 'object') {
console.warn('Deprecated: Expected third argument to be a object');
opts = {
autoBom: !opts
};
} // prepend BOM for UTF-8 XML and text/* types (including HTML)
// note: your browser will automatically convert UTF-16 U+FEFF to EF BB BF
if (opts.autoBom && /^\s*(?:text\/\S*|application\/xml|\S*\/\S*\+xml)\s*;.*charset\s*=\s*utf-8/i.test(blob.type)) {
return new Blob([String.fromCharCode(0xFEFF), blob], {
type: blob.type
});
}
return blob;
}
function download(url, name, opts) {
var xhr = new XMLHttpRequest();
xhr.open('GET', url);
xhr.responseType = 'blob';
xhr.onload = function () {
saveAs(xhr.response, name, opts);
};
xhr.onerror = function () {
console.error('could not download file');
};
xhr.send();
}
function corsEnabled(url) {
var xhr = new XMLHttpRequest(); // use sync to avoid popup blocker
xhr.open('HEAD', url, false);
xhr.send();
return xhr.status >= 200 && xhr.status <= 299;
} // `a.click()` doesn't work for all browsers (#465)
function click(node) {
try {
node.dispatchEvent(new MouseEvent('click'));
} catch (e) {
var evt = document.createEvent('MouseEvents');
evt.initMouseEvent('click', true, true, window, 0, 0, 0, 80, 20, false, false, false, false, 0, null);
node.dispatchEvent(evt);
}
}
var saveAs = _global.saveAs || // probably in some web worker
typeof window !== 'object' || window !== _global ? function saveAs() {}
/* noop */
// Use download attribute first if possible (#193 Lumia mobile)
: 'download' in HTMLAnchorElement.prototype ? function saveAs(blob, name, opts) {
var URL = _global.URL || _global.webkitURL;
var a = document.createElement('a');
name = name || blob.name || 'download';
a.download = name;
a.rel = 'noopener'; // tabnabbing
// TODO: detect chrome extensions & packaged apps
// a.target = '_blank'
if (typeof blob === 'string') {
// Support regular links
a.href = blob;
if (a.origin !== location.origin) {
corsEnabled(a.href) ? download(blob, name, opts) : click(a, a.target = '_blank');
} else {
click(a);
}
} else {
// Support blobs
a.href = URL.createObjectURL(blob);
setTimeout(function () {
URL.revokeObjectURL(a.href);
}, 4E4); // 40s
setTimeout(function () {
click(a);
}, 0);
}
} // Use msSaveOrOpenBlob as a second approach
: 'msSaveOrOpenBlob' in navigator ? function saveAs(blob, name, opts) {
name = name || blob.name || 'download';
if (typeof blob === 'string') {
if (corsEnabled(blob)) {
download(blob, name, opts);
} else {
var a = document.createElement('a');
a.href = blob;
a.target = '_blank';
setTimeout(function () {
click(a);
});
}
} else {
navigator.msSaveOrOpenBlob(bom(blob, opts), name);
}
} // Fallback to using FileReader and a popup
: function saveAs(blob, name, opts, popup) {
// Open a popup immediately do go around popup blocker
// Mostly only avalible on user interaction and the fileReader is async so...
popup = popup || open('', '_blank');
if (popup) {
popup.document.title = popup.document.body.innerText = 'downloading...';
}
if (typeof blob === 'string') return download(blob, name, opts);
var force = blob.type === 'application/octet-stream';
var isSafari = /constructor/i.test(_global.HTMLElement) || _global.safari;
var isChromeIOS = /CriOS\/[\d]+/.test(navigator.userAgent);
if ((isChromeIOS || force && isSafari) && typeof FileReader === 'object') {
// Safari doesn't allow downloading of blob urls
var reader = new FileReader();
reader.onloadend = function () {
var url = reader.result;
url = isChromeIOS ? url : url.replace(/^data:[^;]*;/, 'data:attachment/file;');
if (popup) popup.location.href = url;else location = url;
popup = null; // reverse-tabnabbing #460
};
reader.readAsDataURL(blob);
} else {
var URL = _global.URL || _global.webkitURL;
var url = URL.createObjectURL(blob);
if (popup) popup.location = url;else location.href = url;
popup = null; // reverse-tabnabbing #460
setTimeout(function () {
URL.revokeObjectURL(url);
}, 4E4); // 40s
}
};
_global.saveAs = saveAs.saveAs = saveAs;
if (typeof module !== 'undefined') {
module.exports = saveAs;
}
});
================================================
FILE: debug/add-remove.js
================================================
/* global $, cy, */
(function(){
var idCounter = 0;
function makeId(){
return 'ele' + ( ++idCounter );
}
function number(group){
var input = $('#' + group + '-number');
var val = parseInt( input.value );
if( isNaN(val) ){
return 0;
}
return val;
}
function time(callback){
var start = new Date();
callback();
var end = new Date();
$('#add-remove-time').innerHTML = ( (end - start) + ' ms' );
}
$('#add-elements-button').addEventListener('click', function(){
var n = number('nodes');
var e = number('edges');
var width = cy.width();
var height = cy.height();
var nodes = [];
for(var i = 0; i < n; i++){
nodes.push({
group: 'nodes',
data: { id: makeId(), weight: Math.round( Math.random() * 100 ) },
position: { x: Math.random() * width, y: Math.random() * height }
});
}
function randNodeId(){
return nodes[ Math.round(Math.random() * (nodes.length - 1)) ].data.id;
}
var edges = [];
for(var i = 0; i < e; i++){
edges.push({
group: 'edges',
data: {
id: makeId(),
weight: Math.round( Math.random() * 100 ),
source: randNodeId(),
target: randNodeId()
}
});
}
var eles = {
nodes: nodes,
edges: edges
};
time(function(){
cy.add( eles );
});
});
$('#remove-selected-button').addEventListener('click', function(){
var eles = cy.elements(':selected');
time(function(){
eles.remove();
});
});
})();
================================================
FILE: debug/bind.js
================================================
/* global $, notify, cy */
$("#bind-button").addEventListener('click', function(){
var action = $("#bind-type-select").value;
var event = $("#bind-event-select").value;
var selector = $("#bind-selector").value;
var delegate = $("#bind-delegate").value;
notify('Binding applied',
action + ' on `' + selector + '` for `' + event + '` with delegate `' + delegate + '`'
);
var callback = function(){
var title = 'Event triggered for ' + this.data("id");
var text = action + ' on `' + selector + '` for ' + event + '` with delegate `' + delegate + '`';
notify(
title,
text
);
};
if( action == "unbind" || action == "off" ){
callback = undefined;
}
if( event == "" ){
event = undefined;
}
var args = [];
if( event ){ args.push(event); }
if( delegate ){ args.push(delegate); }
if( callback ){ args.push(callback); }
var eles = cy.elements(selector);
eles[action].apply( eles, args );
});
$("#core-bind-button").addEventListener('click', function(){
var action = $("#core-bind-type-select").value;
var event = $("#core-bind-event-select").value;
var delegate = $("#core-bind-delegate").value;
var target = "core";
notify(
'Binding applied',
action + ' on ' + target + ' for `' + event + '`' + '` with delegate `' + delegate + '`'
);
var callback = function(){
var title = 'Event triggered for core';
var text = '`' + action + '` on ' + target + ' for `' + event + '`' + '` with delegate `' + delegate + '`';
notify(
title,
text
);
};
if( action == "unbind" || action == "off" ){
callback = undefined;
}
if( event == "" ){
event = undefined;
}
var args = [];
if( event ){ args.push(event); }
if( delegate ){ args.push(delegate); }
if( callback ){ args.push(callback); }
cy[action].apply( cy, args );
});
================================================
FILE: debug/compound.js
================================================
/* global cy, loadCompoundGraph, $ */
var loadCompoundGraph = function(){
cy.elements().remove();
cy.add({
nodes: [{ data: { id: 'n8', parent: 'n4' } },
{ data: { id: 'n9', parent: 'n4' } },
{ data: { id: 'n4', parent: 'n1' } },
{ data: { id: 'n5', parent: 'n1', shape: 'triangle' } },
{ data: { id: 'n1' } },
{ data: { id: 'n2' } },
{ data: { id: 'node-really-long-name-6', parent: 'n2' } },
{ data: { id: 'n7', parent: 'n2', shape: 'square' } },
{ data: { id: 'n3', parent: 'non-auto', shape: 'rectangle' } },
{ data: { id: 'non-auto'}}],
edges: [ { data: { id: 'e1', source: 'n1', target: 'n3' } },
{ data: { id: 'e2', source: 'n3', target: 'n7' } },
{ data: { id: 'e3', source: 'node-really-long-name-6', target: 'n7' } },
{ data: { id: 'e4', source: 'node-really-long-name-6', target: 'n9' } },
{ data: { id: 'e5', source: 'n8', target: 'n9' } },
{ data: { id: 'e6', source: 'n5', target: 'n8' } },
{ data: { id: 'e7', source: 'n2', target: 'n4' } },
{ data: { id: 'e8', source: 'n8', target: 'n8' } },
{ data: { id: 'e9', source: 'n1', target: 'n1' } },
{ data: { id: 'e10', source: 'n1', target: 'n9' } },
{ data: { id: 'e11', source: 'n4', target: 'n1' } }
]
});
cy.layout({ name: 'grid', cols: 3 }).run();
};
$('#load-compound').addEventListener('click', loadCompoundGraph);
================================================
FILE: debug/filter.js
================================================
/* global $, cy */
(function(){
function selectFromFilter(){
var selector = $("#filter-selector").value;
var toSelect = cy.elements(selector);
toSelect.select();
cy.elements().not(toSelect).unselect();
}
$("#filter-button").addEventListener('click', function(){
selectFromFilter();
});
$("#filter-selector").addEventListener("keydown", function(e){
if( e.which == 13 ){
selectFromFilter();
}
});
})();
================================================
FILE: debug/gal.json
================================================
{
"nodes" : [ {
"data" : {
"id" : "392",
"degree_layout" : 1,
"gal80Rexp" : 0.292,
"gal1RGsig" : 9.1177E-4,
"Eccentricity" : 26,
"gal4RGsig" : 3.5692E-6,
"shared_name" : "YKR026C",
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"SelfLoops" : 0,
"NumberOfDirectedEdges" : 1,
"AverageShortestPathLength" : 15.37096774,
"selected" : false,
"gal80Rsig" : 0.011229,
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"Degree" : 1,
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"COMMON" : "GCN3",
"gal4RGexp" : -0.501,
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}
}, {
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"SelfLoops" : 0,
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"selected" : false,
"gal80Rsig" : 0.0059966,
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"name" : "YGL122C",
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}
}, {
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}
}, {
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"gal80Rsig" : 0.93826,
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}
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}
}, {
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}
}, {
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"NumberOfDirectedEdges" : 2,
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"selected" : false,
"gal80Rsig" : 6.7798E-4,
"ClosenessCentrality" : 0.75,
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}
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"name" : "YBR118W",
"COMMON" : "TEF2",
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}
}, {
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}
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"COMMON" : "TIF35",
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}
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"name" : "YPL211W",
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}
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"gal1RGexp" : -0.066,
"name" : "YGR014W",
"COMMON" : "MSB2",
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}
}, {
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}
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}
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}
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