Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

FCOSE demo & misc. docs fixes for 3.31.0 #3303

Merged
merged 3 commits into from
Dec 17, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
247 changes: 247 additions & 0 deletions documentation/demos/fcose-gene/code.js
Original file line number Diff line number Diff line change
@@ -0,0 +1,247 @@
/* global Promise, fetch, window, cytoscape, document, tippy, _ */

Promise.all([
fetch('cy-style.json')
.then(function(res) {
return res.json();
}),
fetch('data.json')
.then(function(res) {
return res.json();
})
])
.then(function(dataArray) {
var h = function(tag, attrs, children){
var el = document.createElement(tag);

Object.keys(attrs).forEach(function(key){
var val = attrs[key];

el.setAttribute(key, val);
});

children.forEach(function(child){
el.appendChild(child);
});

return el;
};

var t = function(text){
var el = document.createTextNode(text);

return el;
};

var $ = document.querySelector.bind(document);

var cy = window.cy = cytoscape({
container: document.getElementById('cy'),
style: dataArray[0],
elements: dataArray[1],
layout: { name: 'grid' } // fixed, non-equal positions ensure deterministic fcose results
});

// values modified by sliders
var nodeRepulsionVal = 4500;
var idealEdgeLengthVal = 1;

var params = {
name: 'fcose',
nodeRepulsion: n => nodeRepulsionVal,
idealEdgeLength: e => idealEdgeLengthVal / e.data('weight'),
animate: true,
randomize: false
};
var layout = makeLayout({ animate: false });

layout.run();

var $btnParam = h('div', {
'class': 'param'
}, []);

var $config = $('#config');

$config.appendChild( $btnParam );

var sliders = [
{
label: 'Edge length',
update: sliderVal => idealEdgeLengthVal = sliderVal,
initVal: idealEdgeLengthVal,
min: 1,
max: 5,
step: 0.1
},

{
label: 'Node repulsion',
update: sliderVal => nodeRepulsionVal = sliderVal,
initVal: nodeRepulsionVal,
min: 4500,
max: 1000000,
step: 1
}
];

var buttons = [
{
label: h('span', { 'class': 'fa fa-random' }, []),
layoutOpts: {
randomize: true,
animate: true
},
tooltip: 'Randomise'
},

{
label: h('span', { 'class': 'fa fa-play' }, []),
layoutOpts: {
randomize: false,
animate: true
},
tooltip: 'Step'
}
];

sliders.forEach( makeSlider );

buttons.forEach( makeButton );

function makeLayout( opts ){
params.randomize = (opts || {}).randomize || false;

for( var i in opts ){
params[i] = opts[i];
}

return cy.layout( Object.assign({}, params) );
}

function makeSlider( opts ){
var $input = h('input', {
id: 'slider-'+opts.param,
type: 'range',
min: opts.min,
max: opts.max,
step: opts.step,
value: opts.initVal,
'class': 'slider'
}, []);

var $param = h('div', { 'class': 'param' }, []);

var $label = h('label', { 'class': 'label label-default', for: 'slider-'+opts.param }, [ t(opts.label) ]);

$param.appendChild( $label );
$param.appendChild( $input );

$config.appendChild( $param );

var update = _.throttle(function(){
opts.update(parseFloat($input.value));

layout.stop();
layout = makeLayout({ animate: true });
layout.run();
}, 1000/4, { trailing: true });

$input.addEventListener('input', update);
$input.addEventListener('change', update);
}

function makeButton( opts ){
var $button = h('button', { 'class': 'btn btn-default', title: opts.tooltip }, [ opts.label ]);

$btnParam.appendChild( $button );

$button.addEventListener('click', function(){
layout.stop();

layout = makeLayout( opts.layoutOpts );
layout.run();
});

return tippy( $button, {
content: opts.tooltip,
arrow: true,
placement: 'right'
} );
}

var makeTippy = function(node, html){
return tippy( node.popperRef(), {
html: html,
trigger: 'manual',
arrow: true,
placement: 'bottom',
hideOnClick: false,
interactive: true
} ).tooltips[0];
};

var hideTippy = function(node){
var tippy = node.data('tippy');

if(tippy != null){
tippy.hide();
}
};

var hideAllTippies = function(){
cy.nodes().forEach(hideTippy);
};

cy.on('tap', function(e){
if(e.target === cy){
hideAllTippies();
}
});

cy.on('tap', 'edge', function(e){
hideAllTippies();
});

cy.on('zoom pan', function(e){
hideAllTippies();
});

cy.nodes().forEach(function(n){
var g = n.data('name');

var $links = [
{
name: 'GeneCard',
url: 'http://www.genecards.org/cgi-bin/carddisp.pl?gene=' + g
},
{
name: 'UniProt search',
url: 'http://www.uniprot.org/uniprot/?query='+ g +'&fil=organism%3A%22Homo+sapiens+%28Human%29+%5B9606%5D%22&sort=score'
},
{
name: 'GeneMANIA',
url: 'http://genemania.org/search/human/' + g
}
].map(function( link ){
return h('a', { target: '_blank', href: link.url, 'class': 'tip-link' }, [ t(link.name) ]);
});

var tippy = makeTippy(n, h('div', {}, $links));

n.data('tippy', tippy);

n.on('click', function(e){
tippy.show();

cy.nodes().not(n).forEach(hideTippy);
});
});

$('#config-toggle').addEventListener('click', function(){
$('body').classList.toggle('config-closed');

cy.resize();
});

});
144 changes: 144 additions & 0 deletions documentation/demos/fcose-gene/cy-style.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,144 @@
[{
"selector": "core",
"style": {
"selection-box-color": "#AAD8FF",
"selection-box-border-color": "#8BB0D0",
"selection-box-opacity": "0.5"
}
}, {
"selector": "node",
"style": {
"width": "mapData(score, 0, 0.006769776522008331, 20, 60)",
"height": "mapData(score, 0, 0.006769776522008331, 20, 60)",
"content": "data(name)",
"font-size": "12px",
"text-valign": "center",
"text-halign": "center",
"background-color": "#555",
"text-outline-color": "#555",
"text-outline-width": "2px",
"color": "#fff",
"overlay-padding": "6px",
"z-index": "10"
}
}, {
"selector": "node[?attr]",
"style": {
"shape": "rectangle",
"background-color": "#aaa",
"text-outline-color": "#aaa",
"width": "16px",
"height": "16px",
"font-size": "6px",
"z-index": "1"
}
}, {
"selector": "node[?query]",
"style": {
"background-clip": "none",
"background-fit": "contain"
}
}, {
"selector": "node:selected",
"style": {
"border-width": "6px",
"border-color": "#AAD8FF",
"border-opacity": "0.5",
"background-color": "#77828C",
"text-outline-color": "#77828C"
}
}, {
"selector": "edge",
"style": {
"curve-style": "haystack",
"haystack-radius": "0.5",
"opacity": "0.4",
"line-color": "#bbb",
"width": "mapData(weight, 0, 1, 1, 8)",
"overlay-padding": "3px"
}
}, {
"selector": "node.unhighlighted",
"style": {
"opacity": "0.2"
}
}, {
"selector": "edge.unhighlighted",
"style": {
"opacity": "0.05"
}
}, {
"selector": ".highlighted",
"style": {
"z-index": "999999"
}
}, {
"selector": "node.highlighted",
"style": {
"border-width": "6px",
"border-color": "#AAD8FF",
"border-opacity": "0.5",
"background-color": "#394855",
"text-outline-color": "#394855"
}
}, {
"selector": "edge.filtered",
"style": {
"opacity": "0"
}
}, {
"selector": "edge[group=\"coexp\"]",
"style": {
"line-color": "#d0b7d5"
}
}, {
"selector": "edge[group=\"coloc\"]",
"style": {
"line-color": "#a0b3dc"
}
}, {
"selector": "edge[group=\"gi\"]",
"style": {
"line-color": "#90e190"
}
}, {
"selector": "edge[group=\"path\"]",
"style": {
"line-color": "#9bd8de"
}
}, {
"selector": "edge[group=\"pi\"]",
"style": {
"line-color": "#eaa2a2"
}
}, {
"selector": "edge[group=\"predict\"]",
"style": {
"line-color": "#f6c384"
}
}, {
"selector": "edge[group=\"spd\"]",
"style": {
"line-color": "#dad4a2"
}
}, {
"selector": "edge[group=\"spd_attr\"]",
"style": {
"line-color": "#D0D0D0"
}
}, {
"selector": "edge[group=\"reg\"]",
"style": {
"line-color": "#D0D0D0"
}
}, {
"selector": "edge[group=\"reg_attr\"]",
"style": {
"line-color": "#D0D0D0"
}
}, {
"selector": "edge[group=\"user\"]",
"style": {
"line-color": "#f0ec86"
}
}]
Loading
Loading