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genocrunch-2.1/app/assets/javascripts/correlationNetwork.js
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correlationNetwork.js
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function correlationNetwork(id, legend_id, json, W = 600, H = 600, font_family = "verdana, arial, helvetica, sans-serif", color_palette = d3.schemeCategory10) {
// Size
var margin = {top: 10, right: 10, bottom: 40, left: 10},
width = W - margin.left - margin.right,
height = H - margin.top - margin.bottom;
// Restrictions
drag_size_limit = 80;
// Colors, symbols and scaling
var colors = d3.scaleOrdinal(color_palette),
link_color = [["#999999", "Pos. correlation"],
["#ff3385", "Neg. correlation"]],
symbols = d3.scaleOrdinal([d3.symbolCircle,
d3.symbolSquare,
d3.symbolTriangle,
d3.symbolStar,
d3.symbolDiamond,
d3.symbolCross]),
legend_svg_symsize = 15,
rRange = [6, 24],
size_legend_data = [15, 10, 5],
wRange = [0.1*rRange[0], 0.9*rRange[0]],
sizeScale = d3.scaleLinear()
.range(rRange),
widthScale = d3.scaleLinear()
.range(wRange),
attractionScale = d3.scaleLinear()
.range([100, 50]),
repulsionScale = d3.scaleLinear()
.range([50, 100]),
chargeScale = d3.scaleLinear()
.range([-100, -200]),
sizeOptions = [{"text":"", "value":"", "title":""},
{"text":"Degree", "value":"degree", "title":"Node degree"},
{"text":"Mean abundance", "value":"mean", "title":"Mean abundance"},
{"text":"Max abundance", "value":"max", "title":"Max abundance"},
{"text":"Min abundance", "value":"min", "title":"Min abundance"}
];
oRange = [0.1, 0.3],
p_value_legend_data = [[0.001, "***"],
[0.01, "**"],
[0.05, "*"],
[1, "ns"],
["NA", "na"]],
stat_settings = {"range":[0.2, 0.6, 0.8, 1],
"domain":[1, 0.05, 0.01, 0.001],
"text":["ns", "*", "**", "***"]},
opacity = d3.scaleLinear()
.range(stat_settings.range)
.domain(stat_settings.domain),
colorBarSize = 10;
// General functions
function getSizeExtrema(json, fun, extrema="max", absolute=false) {
var values = json.map(function(d){
if (absolute) {
return Math.abs(d[fun]);
}
return d[fun];
})
if (extrema == "max") {
return Math.max.apply(null, values);
} else if (extrema == "min") {
return Math.min.apply(null, values);
};
};
function getNodeDegree(links, nodes) {
var degree = {};
links.forEach(function (d, i) {
if (Object.keys(degree).indexOf(d.target.toString()) == -1) {
degree[d.target.toString()] = 1;
} else {
degree[d.target.toString()] = degree[d.target.toString()]+1;
};
if (Object.keys(degree).indexOf(d.source.toString()) == -1) {
degree[d.source.toString()] = 1;
} else {
degree[d.source.toString()] = degree[d.source.toString()]+1;
};
});
nodes.forEach(function (d) {
if (Object.keys(degree).indexOf(d.id) != -1) {
d["degree"] = degree[d.id];
} else {
d["degree"] = 0; // Just to avoid scale domain to start at 0...
}
});
};
function unique(value, index, self) {
return self.indexOf(value) === index;
}
// Buttons
var buttons = d3.select("#d3-buttons")
buttons.html("");
//$.getJSON(data, function(json) {
//////////////// Simulation ////////////////
var simulation = d3.forceSimulation()
.force("center", d3.forceCenter(width / 2, height / 2))
.force("y", d3.forceY())
.force("x", d3.forceX());
var ticked = function() {
link
.attr("x1", function(d) { return Math.max(0, Math.min(d.source.x, width)); })
.attr("y1", function(d) { return Math.max(0, Math.min(d.source.y, height)); })
.attr("x2", function(d) { return Math.max(0, Math.min(d.target.x, width)); })
.attr("y2", function(d) { return Math.max(0, Math.min(d.target.y, height)); });
node
.attr("transform", function(d) {
return "translate(" + Math.max(0, Math.min(d.x, width)) + "," + Math.max(0, Math.min(d.y, height)) + ")"; });
nodeLabel
.attr("transform", function(d, i) {
return "translate(" + Math.max(0, Math.min(d.x, width)) + "," + Math.max(0, Math.min(d.y, height)) + ")"; });
};
function dragstarted(d) {
if (!d3.event.active) simulation.alphaTarget(0.25).restart();
d.fx = d.x;
d.fy = d.y;
}
function dragged(d) {
d.fx = d3.event.x;
d.fy = d3.event.y;
}
function dragended(d) {
if (!d3.event.active) simulation.alphaTarget(0);
d.fx = null;
d.fy = null;
}
//////////////// Draw links and nodes ////////////////
var legendContainer = d3.select("#"+legend_id).append("div")
.attr('class', 'columns-2')
var svgContainer = d3.select("#"+id)
.style("height", (height + margin.top + margin.bottom)+"px")
var svg = svgContainer.append("svg")
.attr("id", "svg-figure")
.attr("class", "svg-figure network-well")
.attr("width", (width + margin.left + margin.right)+"px")
.attr("height",(height + margin.top + margin.bottom)+"px")
.style("pointer-events", "all")
.call(d3.zoom()
.scaleExtent([1, 4])
.duration(1000)
.translateExtent([[margin.left, margin.top], [width + margin.right, height + margin.top + margin.bottom]])
.on("zoom", zoomed));
var g = svg.append("g")
.attr("transform", "translate(" + margin.left + "," + margin.top + ")");
function zoomed() {
g.attr("transform", d3.event.transform);
};
// Draw links
var link = g.append("g")
.selectAll();
// Draw Nodes
var node = g.append("g")
.selectAll("g");
var nodeLabel = g.append("g")
.selectAll("g");
// Add legend
var legend = legendContainer.append("div")
.attr("id", "svg-legend")
.style("font-family", font_family)
var colorLegend = legend.append("ul")
.style("list-style-type", "none")
.style("padding-top", "25px")
.selectAll("ul");
legend.append("div")
.style("border-top", "solid #ccc 1px")
var symbolLegend = legend.append("ul")
.style("list-style-type", "none")
.selectAll("ul");
legend.append("div")
.style("border-top", "solid #ccc 1px")
var linkLegend = legend.append("ul")
.style("list-style-type", "none")
.selectAll("ul");
//////////////// NODES COLORS ////////////////
var setSymbolColor = function() {
var selected_model = $('#modelSelect').val(),
selected_effect = $('#effectSelect').val(),
color_domain = json.nodes.map(function (d){return d.stat[selected_model][selected_effect]['highest-mean'];}).filter(unique);
if (selected_model != '')
colors.domain(color_domain);
// Update symbols color
d3.selectAll(".coloured-symbol")
.style("fill", function (d){
if (selected_model != '')
return colors(d.stat[selected_model][selected_effect]['highest-mean']);
return colors('');
})
.attr("fill-opacity", function (d){
if (selected_model != '')
return opacity(d.stat[selected_model][selected_effect]['p-value']);
return 1;
});
// Update color legend
colorLegend = colorLegend.data([]);
colorLegend.exit().remove();
colorLegend = colorLegend
.data(color_domain)
.enter().append("li")
.attr("id", function(d) { return d;})
.attr("class", "legend legend-no-interaction")
.attr("selected", 0)
.attr("title", function(d) { return d;})
colorLegendSpan = colorLegend.append("span")
var legend_svg_width = legend_svg_symsize*p_value_legend_data.length;
colorLegendSpanSvg = colorLegendSpan.append("svg")
.attr("width", legend_svg_width+"px")
.attr("height", legend_svg_symsize+"px")
.style("margin-right", "5px")
.style("overflow", "visible")
for (var i = 0; i < p_value_legend_data.length; i++) {
// (V)(°,,,°)(V)
colorLegendSpanSvg.append("g")
.attr("transform", "translate("+(i*legend_svg_width/p_value_legend_data.length)+", -2)")
.append("text")
.attr("transform", "rotate(-90)")
.attr("y", legend_svg_symsize)
.text(function(d, j){
if (j == 0 && color_domain.length > 0)
return p_value_legend_data[i][1];
})
colorLegendSpanSvg.append("rect")
.attr("transform", "translate("+(i*legend_svg_width/p_value_legend_data.length)+", 0)")
.attr("width", legend_svg_symsize)
.attr("height", legend_svg_symsize)
.attr("stroke", "none")
.attr("fill", function (d, j){
if (p_value_legend_data[i][0] == "NA") {
return "lightgrey";
};
return colors(d);
})
.attr("fill-opacity", function (d, j){
if (p_value_legend_data[i][0] == "NA") {
return 1;
};
return opacity(p_value_legend_data[i][0]);
})
};
colorLegendSpan.append("span")
.html(function(d) { return d;})
};
//////////////// NODES SHAPE AND SIZE ////////////////
var setSymbolSize = function() {
var selected_size_factor = $("#sizeSelect").val(),
symbols_domain = json.nodes.map(function (d){return d['data-type'];}).filter(unique),
size = {};
symbols.domain(symbols_domain);
if (selected_size_factor != '') {
for (var i = 0; i < symbols_domain.length; i++) {
size[symbols_domain[i]] = {value:json.nodes.filter(function (d){return d['data-type'] == symbols_domain[i];}).map(function(d){return Number(d[selected_size_factor]);})};
size[symbols_domain[i]]['min'] = Math.min.apply(null, size[symbols_domain[i]]['value']);
size[symbols_domain[i]]['max'] = Math.max.apply(null, size[symbols_domain[i]]['value']);
}
}
// Set symbols size
d3.selectAll(".symbol")
.transition().duration(400)
.attr("d", d3.symbol()
.type(function (d){ return symbols(d['data-type']);})
.size(function (d){
if (selected_size_factor != '') {
sizeScale.domain([size[d['data-type']]['min'], size[d['data-type']]['max']]);
d.r = sizeScale(d[selected_size_factor]);
} else {
d.r = 20;
}
return d.r*d.r;
}))
.attr('radius', function(d){return d.r;});
// Set size-dependent simulation variables
var symbol_data = [];
d3.selectAll(".symbol").each(function(){return symbol_data.push(d3.select(this).attr("radius"));});
var force_size_factor = (Math.log2(symbol_data.length+1)+1)/2;
chargeScale.domain([Math.min.apply(null, symbol_data), Math.max.apply(null, symbol_data)]);
if (force_size_factor == 0) {
force_size_factor = 1;
};
simulation
.force("collide", d3.forceCollide()
.radius(function (d){
return d.r;
})
.iterations(2)
.strength(1/force_size_factor))
.force("charge", d3.forceManyBody()
.strength(function (d){
return chargeScale(d.r)/force_size_factor;
}));
// Update symbol legend
symbolLegend = symbolLegend.data([]);
symbolLegend.exit().remove();
symbolLegend = symbolLegend
.data(symbols_domain)
.enter().append("li")
.attr("id", function(d) { return d;})
.attr("class", "legend legend-no-interaction")
.attr("selected", 0)
.attr("title", function(d) { return d;})
symbolLegendSpan = symbolLegend.append("span")
var legend_svg_width = legend_svg_symsize*size_legend_data.length;
symbolLegendSpanSvg = symbolLegendSpan.append("svg")
.attr("width", legend_svg_width+"px")
.attr("height", legend_svg_symsize+"px")
.style("margin-right", "5px")
.style("overflow", "visible")
for (var i = 0; i < size_legend_data.length; i++) {
// (V)(°,,,°)(V)
symbolLegendSpanSvg.append("path")
.attr("transform", "translate("+(i*legend_svg_width/size_legend_data.length)+", "+legend_svg_symsize/2+")")
.attr("d", d3.symbol()
.type(function (d){ return symbols(d);})
.size(size_legend_data[i]*size_legend_data[i]))
.attr("stroke", "#333")
.attr("fill-opacity", 0)
};
symbolLegendSpan.append("span")
.html(function(d) { return d;})
}
//////////////// RESTART ////////////////
var restart = function() {
var weight_thres = [$("#pThresRange").val(), $("#nThresRange").val()],
weight_p_value_thres = $("#weightPvalThres").val(),
link_data = JSON.parse(JSON.stringify(json.links.filter(function(d){
if (d.weight >= 0) {
return (d.weight >= weight_thres[0] && d['p-value'] <= weight_p_value_thres);
}
return (d.weight < -weight_thres[1] && d['p-value'] <= weight_p_value_thres);
})));
getNodeDegree(link_data, json.nodes);
var kept_node = link_data.map(function(d){return d['source'];}).concat(link_data.map(function(d){return d['target'];})).filter(unique),
node_data = JSON.parse(JSON.stringify(json.nodes.filter(function(d){return kept_node.indexOf(d.id) != -1;}))),
link_width = {weight:link_data.map(function(d){return d.weight;})};
link_width['min'] = Math.min.apply(null, link_width.weight.map(Math.abs));
link_width['max'] = Math.max.apply(null, link_width.weight.map(Math.abs));
widthScale.domain([link_width['min'], link_width['max']]);
attractionScale.domain([link_width['min'], link_width['max']]);
// Update links
link = link.data([]);
link.exit().remove();
link = link
.data(link_data);
link = link.enter()
.append("line")
.attr("class", "link-line")
.attr("stroke-linecap", "round")
.attr("stroke", function (d) {
if (Number(d.weight) >= 0) {
return link_color[0][0];
} else {
return link_color[1][0];
};
})
.attr("stroke-width", function (d) {
return widthScale(Math.abs(d.weight));
});
// Update nodes
node = node.data([]);
node.exit().remove();
node = node
.data(node_data);
node = node.enter()
.append("g")
.append("path")
.attr("class", "coloured-symbol symbol")
.attr("stroke", "white");
// Update nodes labels
nodeLabel = nodeLabel.data([]);
nodeLabel.exit().remove();
nodeLabel = nodeLabel
.data(node_data);
nodeLabel = nodeLabel.enter()
.append("g")
.attr('class', 'node-label');
nodeLabel.append("path")
.attr("class", "symbol")
.attr("stroke", "#333333")
.attr("fill-opacity", 0)
.attr("stroke-opacity", 0);
nodeLabel.append("text")
.text(function (d) {
var label = d.name.split(";");
if (label.length > 1)
return label[label.length-2] +";"+ label[label.length-1];
return label[0];
})
.attr("text-anchor", "start")
.attr("font-family", font_family)
.attr("display", "none")
.attr("selected", false);
// Add interactive option if not too many nodes
//if (node_data.length < drag_size_limit) {
node.call(d3.drag()
.on("start", dragstarted)
.on("drag", dragged)
.on("end", dragended));
nodeLabel.call(d3.drag()
.on("start", dragstarted)
.on("drag", dragged)
.on("end", dragended));
//};
setSymbolSize();
setSymbolColor();
displayLabels();
showLabels();
// Restart simulation
simulation = simulation
.nodes(node_data)
.on("tick", ticked);
var data_size_factor = 1+node_data.length*node_data.length;
simulation
.force("link", d3.forceLink()
.id(function(d) { return d.id;})
.distance(function(d) {
if (d.weight >= 0) {
return attractionScale(Math.abs(d.weight))/data_size_factor;
} else {
return repulsionScale(Math.abs(d.weight))/data_size_factor;
};
})
.strength(function(d) {
if (d.weight >= 0) {
return repulsionScale(Math.abs(d.weight))/100;
} else {
return attractionScale(Math.abs(d.weight))/100;
};
}));
simulation.force("link")
.links(link_data);
simulation.alpha(0.5).restart();
// Update links legend
linkLegend = linkLegend.data([]);
linkLegend.exit().remove();
linkLegend = linkLegend
.data(link_color)
.enter().append("li")
.attr("id", function(d) { return d[1];})
.attr("class", "legend legend-no-interaction")
.attr("selected", 0)
.attr("title", function(d) { return d[1];})
linkLegendSpan = linkLegend.append("span")
linkLegendSpanSvg = linkLegendSpan.append("svg")
.attr("width", "25px")
.attr("height", "10px")
.style("margin-right", "5px")
.style("overflow", "visible")
linkLegendSpanSvg.append("rect")
.attr("width", 25)
.attr("height", 5)
.attr("y", 2.5)
.attr("stroke", "none")
.attr("fill", function(d){return d[0]})
linkLegendSpan.append("span")
.html(function(d, i) { return ['Coeff. > ', 'Coeff. < -'][i]+weight_thres[i];})
}
// Nodes labels functions
function displayLabels () {
var selected_label = $(".node-label");
selected_label.on("mouseenter", function() {
d3.select(this.childNodes[1]).attr("display", "inline");
d3.select(this.childNodes[0]).attr("stroke-opacity", 1);
});
selected_label.on("mouseleave", function() {
if (this.childNodes[1].getAttribute("selected") == "false") {
d3.select(this.childNodes[1]).attr("display", "none");
};
d3.select(this.childNodes[0]).attr("stroke-opacity", 0);
});
selected_label.on("click", function() {
if (this.childNodes[1].getAttribute("selected") == "false") {
d3.select(this.childNodes[1]).attr("display", "inline");
d3.select(this.childNodes[1]).attr("selected", true);
} else {
d3.select(this.childNodes[1]).attr("display", "none");
d3.select(this.childNodes[1]).attr("selected", false);
}
});
};
// Model update function
var updateEffect = function() {
var keys = Object.keys(json.legend[$('#modelSelect').val()])
new_data = [...Array(keys.length)];
for (var i = 0; i < keys.length; i++) {
new_data[i] = {label:keys[i], value:keys[i]}
}
$('#effectSelect').multiselect('dataprovider', new_data)
.multiselect("refresh");
setSymbolColor();
}
// Display labels button
var showLabels = function() {
var label_text = d3.selectAll(".node-label").select(function(){ return this.childNodes[1];});
if ($("#labelButton").is(':checked')) {
label_text.attr("display", "inline");
label_text.attr("selected", true);
} else {
label_text.attr("display", "none");
label_text.attr("selected", false);
};
};
// Search in labels
var searchLabels = function() {
$("#labelButton").attr("checked", false);
var key = $("#searchInput").val().toUpperCase();
if (key != '') {
var selected = d3.selectAll(".node-label").filter(function(){return this.__data__.name.toUpperCase().indexOf(key.toUpperCase()) != -1 });
non_selected = d3.selectAll(".node-label").filter(function(){return this.__data__.name.toUpperCase().indexOf(key.toUpperCase()) == -1 });
selected.select(function(){ return this.childNodes[1];}).attr("display", "inline");
selected.select(function(){ return this.childNodes[1];}).attr("selected", true);
non_selected.select(function(){ return this.childNodes[1];}).attr("display", "none");
non_selected.select(function(){ return this.childNodes[1];}).attr("selected", false);
} else {
to_free = d3.selectAll(".node-label");
to_free.select(function(){return this.childNodes[1];}).attr("display", "none");
to_free.select(function(){return this.childNodes[1];}).attr("selected", false);
};
};
// Label button and search
appendLabelCheckBox(buttons, "Show labels", "Labels", "labelButton", showLabels)
appendSearchInput(buttons, "Search", "searchInput", searchLabels);
// Select model
var modelSelect = buttons.append("div")
.attr("title", "Chose model")
.attr("class", "form-group")
modelSelect.append("label")
.html("Color (model)")
modelSelect.append("div")
.attr("class", "multiselect-btn-container figtool-multiselect-btn-container")
.append("select")
.attr("id", "modelSelect")
.attr("class", "form-control multiselect figtool-multiselect")
.selectAll("option")
.data(Object.keys(json.legend))
.enter().append("option")
.text(function (d){ return d;});
$('#modelSelect').on('change', updateEffect);
// Select effect
var effectSelect = buttons.append("div")
.attr("title", "Chose effect")
.attr("class", "form-group")
effectSelect.append("label")
.html("Color (effect)")
effectSelect.append("div")
.attr("class", "multiselect-btn-container figtool-multiselect-btn-container")
.append("select")
.attr("id", "effectSelect")
.attr("class", "form-control multiselect figtool-multiselect")
.selectAll("option")
.data(Object.keys(json.legend[$('#modelSelect').val()]))
.enter().append("option")
.text(function (d){ return d;});
$('#effectSelect').on('change', setSymbolColor);
// Select size
var sizeSelect = buttons.append("div")
.attr("title", "Chose size variable")
.attr("class", "form-group")
sizeSelect.append("label")
.html("Radius")
sizeSelect.append("div")
.attr("class", "multiselect-btn-container figtool-multiselect-btn-container")
.append("select")
.attr("id", "sizeSelect")
.attr("class", "form-control multiselect figtool-multiselect")
.selectAll("option")
$('#sizeSelect').on('change', setSymbolSize);
// Button for link weight threshold
var weightPvalThres = buttons.append("div")
.attr("title", "Set a p-value cutoff for links.")
.attr("class", "form-group")
weightPvalThres.append("label")
.html("Links p-value cutoff")
weightPvalThres.append("input")
.attr("id", "weightPvalThres")
.attr("type", "number")
.attr("class", "form-control form-number-field")
.attr("min", 0)
.attr("max", 1)
.attr("step", 0.001)
.attr("value", 1)
.on("change", restart);
var pThresRange = buttons.append("span")
.attr("title", "Cut-off for positive correlations.")
pThresRange.append("label")
.append("p")
.html("Pos. corr. cut-off <span style='white-space: nowrap'>(<i style='color:"+link_color[0][0]+"' class='fa fa-window-minimize icon-sim-link'></i>).</span>")
pThresRange.append("input")
.attr("id", "pThresRange")
.attr("type", "range")
.attr("class", "full-width")
.attr("min", 0)
.attr("max", 1)
.attr("step", 0.05)
.on("change", restart);
$("#pThresRange").val('0.75')
var nThresRange = buttons.append("span")
.attr("title", "Cut-off for negative correlations.")
nThresRange.append("label")
.append("p")
.html("Neg. corr. cut-off <span style='white-space: nowrap'>(<i style='color:"+link_color[1][0]+"' class='fa fa-window-minimize icon-sim-link'></i>).</span>")
nThresRange.append("input")
.attr("id", "nThresRange")
.attr("type", "range")
.attr("class", "full-width")
.attr("min", 0)
.attr("max", 1)
.attr("step", 0.05)
.on("change", restart);
$("#nThresRange").val('0.75')
setMultiselect('.figtool-multiselect');
//resizeMultiselect('#d3-buttons', 1, '#d3-buttons', false);
$('#sizeSelect').multiselect('dataprovider', sizeOptions)
.multiselect("refresh");
restart();
//});
};
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