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var default_style = [ // the stylesheet for the graph
{
selector: 'node',
style: {
'background-color': '#666',
'label': 'data(label)',
'font-size': 10
}
},
{
selector: 'edge',
style: {
'width': 'data(width)',
'line-color': 'data(color)',
'target-arrow-color': '#ccc',
'target-arrow-shape': 'triangle',
'font-size': 8
}
}
]
var default_layout = { name: 'circle',
fit: true, // whether to fit the viewport to the graph
padding: 30 // the padding on fit
//idealEdgeLength: function( edge ){ return edge.data['correlation']*10; },
}
window.onload=function() {
// id of Cytoscape Web container div
//var div_id = "cytoscapeweb";
var cy = cytoscape({
container: $('#cytoscapeweb'), // container to render in
elements: elements_list,
style: default_style,
zoom: 12,
layout: default_layout,
zoomingEnabled: true,
userZoomingEnabled: true,
panningEnabled: true,
userPanningEnabled: true,
boxSelectionEnabled: false,
selectionType: 'single',
// rendering options:
styleEnabled: true
});
var eles = cy.$() // var containing all elements, so elements can be restored after being removed
var defaults = {
zoomFactor: 0.05, // zoom factor per zoom tick
zoomDelay: 45, // how many ms between zoom ticks
minZoom: 0.1, // min zoom level
maxZoom: 10, // max zoom level
fitPadding: 30, // padding when fitting
panSpeed: 10, // how many ms in between pan ticks
panDistance: 10, // max pan distance per tick
panDragAreaSize: 75, // the length of the pan drag box in which the vector for panning is calculated (bigger = finer control of pan speed and direction)
panMinPercentSpeed: 0.25, // the slowest speed we can pan by (as a percent of panSpeed)
panInactiveArea: 8, // radius of inactive area in pan drag box
panIndicatorMinOpacity: 0.5, // min opacity of pan indicator (the draggable nib); scales from this to 1.0
zoomOnly: false, // a minimal version of the ui only with zooming (useful on systems with bad mousewheel resolution)
fitSelector: undefined, // selector of elements to fit
animateOnFit: function(){ // whether to animate on fit
return false;
},
fitAnimationDuration: 1000, // duration of animation on fit
// icon class names
sliderHandleIcon: 'fa fa-minus',
zoomInIcon: 'fa fa-plus',
zoomOutIcon: 'fa fa-minus',
resetIcon: 'fa fa-expand'
};
cy.panzoom( defaults );
function create_qtips(cy){
cy.nodes().qtip({
content: function(){
qtip_content = ''
gn_link = '<b>'+'<a href="' + gn2_url + '/show_trait?trait_id=' + this.data().id.split(":")[0] + '&dataset=' + this.data().id.split(":")[1] + '" >'+this.data().id +'</a>'+'</b><br>'
qtip_content += gn_link
if (typeof(this.data().geneid) !== 'undefined'){
ncbi_link = '<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=' + this.data().geneid + '" >NCBI<a>'+'<br>'
qtip_content += ncbi_link
}
if (typeof(this.data().omim) !== 'undefined'){
omim_link = '<a href="http://www.ncbi.nlm.nih.gov/omim/' + this.data().omim + '" >OMIM<a>'+'<br>'
qtip_content += omim_link
}
return qtip_content
},
position: {
my: 'top center',
at: 'bottom center'
},
style: {
classes: 'qtip-bootstrap',
tip: {
width: 16,
height: 8
}
}
});
cy.edges().qtip({
content: function(){
correlation_line = '<b>Sample r: ' + this.data().correlation + '</b><br>'
p_value_line = 'Sample p(r): ' + this.data().p_value + '<br>'
overlap_line = 'Overlap: ' + this.data().overlap + '<br>'
scatter_plot = '<a href="' + gn2_url + '/corr_scatter_plot?method=pearson&dataset_1=' + this.data().source.split(":")[1] + '&dataset_2=' + this.data().target.split(":")[1] + '&trait_1=' + this.data().source.split(":")[0] + '&trait_2=' + this.data().target.split(":")[0] + '" >View Scatterplot</a>'
return correlation_line + p_value_line + overlap_line + scatter_plot
},
position: {
my: 'top center',
at: 'bottom center'
},
style: {
classes: 'qtip-bootstrap',
tip: {
width: 16,
height: 8
}
}
});
}
create_qtips(cy)
$('#neg_slide').change(function() {
eles.restore()
pos_slide_val = $('#pos_slide').val();
cy.$("node[max_corr > " + $(this).val() + "][max_corr < " + pos_slide_val + "]").remove();
cy.$("edge[correlation > " + $(this).val() + "][correlation < " + pos_slide_val + "]").remove();
cy.layout({ name: $('select[name=layout_select]').val(),
fit: true, // whether to fit the viewport to the graph
padding: 25 // the padding on fit
}).run();
});
$('#pos_slide').change(function() {
eles.restore()
neg_slide_val = $('#neg_slide').val();
cy.$("node[max_corr > " + neg_slide_val +"][max_corr < " + $(this).val() + "]").remove();
cy.$("edge[correlation > " + neg_slide_val +"][correlation < " + $(this).val() + "]").remove();
cy.layout({ name: $('select[name=layout_select]').val(),
fit: true, // whether to fit the viewport to the graph
padding: 25 // the padding on fit
}).run();
});
$('#reset_graph').click(function() {
eles.restore()
$('#pos_slide').val(0)
$('#neg_slide').val(0)
cy.layout({ name: $('select[name=layout_select]').val(),
fit: true, // whether to fit the viewport to the graph
padding: 25 // the padding on fit
}).run();
});
$('select[name=focus_select]').change(function() {
focus_trait = $(this).val()
eles.restore()
cy.$('edge[source != "' + focus_trait + '"][target != "' + focus_trait + '"]').remove()
cy.layout({ name: $('select[name=layout_select]').val(),
fit: true, // whether to fit the viewport to the graph
padding: 25 // the padding on fit
}).run();
});
$('select[name=layout_select]').change(function() {
layout_type = $(this).val()
cy.layout({ name: layout_type,
fit: true, // whether to fit the viewport to the graph
padding: 25 // the padding on fit
}).run();
});
$('select[name=font_size]').change(function() {
font_size = $(this).val()
new_style = default_style
new_style[0]['style']['font-size'] = parseInt(font_size)
cy.style().fromJson(new_style).update()
});
$('select[name=edge_width]').change(function() {
//eles.restore()
//ZS: This is needed, or else it alters the original object
orig_elements = JSON.parse(JSON.stringify(elements_list));
width_multiplier = $(this).val()
updated_elements = []
for (i=0; i < orig_elements.length; i++){
this_element = orig_elements[i]
if ('source' in this_element['data']) {
orig_width = this_element['data']['width']
this_element['data']['width'] = orig_width * width_multiplier
}
updated_elements.push(this_element)
}
cy.remove(eles)
cy.add(updated_elements)
cy.layout({ name: $('select[name=layout_select]').val(),
fit: true, // whether to fit the viewport to the graph
padding: 25 // the padding on fit
}).run();
});
$('select[name=edge_width]').change(function() {
//eles.restore()
//ZS: This is needed, or else it alters the original object
orig_elements = JSON.parse(JSON.stringify(elements_list));
width_multiplier = $(this).val()
updated_elements = []
for (i=0; i < orig_elements.length; i++){
this_element = orig_elements[i]
if ('source' in this_element['data']) {
orig_width = this_element['data']['width']
this_element['data']['width'] = orig_width * width_multiplier
}
updated_elements.push(this_element)
}
cy.remove(eles)
cy.add(updated_elements)
cy.layout({ name: $('select[name=layout_select]').val(),
fit: true, // whether to fit the viewport to the graph
padding: 25 // the padding on fit
}).run();
});
$("a#image_link").click(function(e) {
var pngData = cy.png();
$(this).attr('href', pngData);
$(this).attr('download', 'network_graph.png');
});
};
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