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Metabolic network visualization using D3.js
Raw
README.md

My attempts to allow easier building of network maps using D3.js's force-directed layouts.

Nodes (and reactions) can be dragged into position, where they will remain fixed. Double-click a node (or reaction node) to unstick it.

Raw
force_directed_model.js
var width = 1024,
height = 768;
var color = d3.scale.category20();
var force = d3.layout.force()
.linkDistance(30)
.linkStrength(2)
.charge(-100)
.chargeDistance(400)
.gravity(.015)
.size([width, height])
var svg = d3.select("body").append("svg")
.attr("width", width)
.attr("height", height);
node_tip = d3.tip()
.attr('class', 'd3-tip')
.offset([10, 0])
.direction('s')
.html(function(d) {
return '<span>id: </span>' + d.id + "</br>" + '<span>x: </span>' + Math.round(d.x * 100)/100 + '</br>' + '<span>y: </span>' + Math.round(d.y * 100)/100 + '</br>' + '<span>fixed: </span>' + Boolean(d.fixed);
});
svg.call(node_tip);
$("#reactionbutton").click(function() {
var $this = $(this);
$this.toggleClass('btn-danger');
d3.selectAll(".node.rxn")
.classed("hidden", function (d, i) {
return !d3.select(this).classed("hidden");
});
if($this.hasClass('btn-danger')){
$this.text('Hide Reaction Nodes');
} else {
$this.text('Show Reaction Nodes');
}
});
function calc_imag_angle(x1, y1, x2, y2) {
var calcAngleVal = Math.atan2(x1-x2,y1-y2);
return math.exp(math.multiply(math.i, calcAngleVal));
}
function average_angles(rxn, rstoich, nodes) {
var angles = []
for (var n in rstoich) {
var angle = calc_imag_angle(rxn.x, rxn.y, nodes[n].x, nodes[n].y);
angles.push([math.multiply(angle, rstoich[n])]);
}
return math.mean(angles).toPolar().phi;
}
function average_dist(rxn, rstoich, nodes) {
var dist = []
for (var n in rstoich) {
var this_dist = math.sqrt(math.square(rxn.x - nodes[n].x)
+ math.square(rxn.y - nodes[n].y));
dist.push([this_dist]);
}
return math.mean(dist);
}
function calculate_path(d, force) {
var s = d.source,
t = d.target,
r = d.rxn,
cp = {};
var angle = average_angles(r, d.rstoich, force.nodes())
var dist = average_dist(r, d.rstoich, force.nodes())
cp["x"] = r.x - math.multiply(.5*dist, math.sin(angle));
cp["y"] = r.y - math.multiply(.5*dist, math.cos(angle));
// return "M" + s.x + "," + s.y + " L " + t.x + "," + t.y;
// return "M" + s.x + "," + s.y
// +" C" + s.x + "," + s.y
// + " " + cp.x + "," + cp.y
// + " " + r.x + "," + r.y
// +" S" + t.x + "," + t.y
// + " " + t.x + "," + t.y;
return "M" + s.x + "," + s.y
+ " Q" + cp.x + "," + cp.y
+ " " + r.x + "," + r.y
+" T" + t.x + "," + t.y
}
d3.json("model.json", function(error, model) {
if (error) throw error;
var metabolites = jQuery.extend(true, [], model.metabolites),
reactions = jQuery.extend(true, [], model.reactions),
nodes = [],
node_lookup = {},
links = [],
mlinks = [],
bilinks = []
rxn_stoich = {};
metabolites.forEach(function(metabolite) {
// Don't add hidden reactions
if ('notes' in metabolite) {
if ('map_info' in metabolite.notes) {
if (metabolite.notes.map_info.hidden) {
return;
}
}
}
// It's not hidden, add it to the nodes
nodes.push(metabolite);
});
var labelAnchors = [];
var labelAnchorLinks = [];
for (var i = 0, len = nodes.length; i < len; i++) {
var node = nodes[i]
node_lookup[node.id] = i;
labelAnchors.push({
node : node
});
labelAnchors.push({
node : node
});
labelAnchorLinks.push({
source : i * 2,
target : i * 2 + 1,
weight : 1
});
}
var fluxes = []
reactions.forEach(function(reaction) {
// Don't add hidden reactions
if ('notes' in reaction) {
if ('map_info' in reaction.notes) {
if (reaction.notes.map_info.hidden) {
return;
} else if ('flux' in reaction.notes.map_info) {
fluxes.push(Math.abs(reaction.notes.map_info.flux));
if (reaction.notes.map_info.flux < 0) {
// If the reaction is flowing in reverse, switch products and
// reactants.
for (var item in reaction.metabolites) {
reaction.metabolites[item] *= -1;
}
}
}
}
}
reaction['reactants'] = []
reaction['products'] = []
for (var item in reaction.metabolites) {
if (reaction.metabolites[item] > 0) {
if (item in node_lookup) {
// Only add if the node hasn't been hidden
reaction.products.push(item);
}
} else if (item in node_lookup) {
reaction.reactants.push(item);
}
}
var r_length = reaction.reactants.length,
p_length = reaction.products.length,
r_node = {
"id" : reaction.id,
"group" : "rxn"
};
// Add notes to reaction, if it exists (for map_info)
if ("notes" in reaction) {
r_node["notes"] = reaction.notes;
}
if (r_length == 0 || p_length == 0) {
return; // Don't add links on the boundary
}
nodes.push(r_node)
rindex = nodes.length - 1
if (r_length >= p_length) {
reaction.reactants.forEach(function (reactant, i) {
mlinks.push({
"source" : node_lookup[reactant],
"target" : node_lookup[reaction.products[i % p_length]],
"rxn" : rindex
});
});
} else {
reaction.products.forEach(function (product, i) {
mlinks.push({
"source" : node_lookup[reaction.reactants[i % r_length]],
"target" : node_lookup[product],
"rxn" : rindex
});
});
}
});
mlinks.forEach(function(link) {
if (link.rxn in rxn_stoich) {
rxn_stoich[link.rxn][link.source] = 1;
rxn_stoich[link.rxn][link.target] = -1;
} else {
rxn_stoich[link.rxn] = {};
rxn_stoich[link.rxn][link.source] = 1;
rxn_stoich[link.rxn][link.target] = -1;
}
});
mlinks.forEach(function(link) {
var s = nodes[link.source],
t = nodes[link.target],
r = nodes[link.rxn];
links.push({source: s, target: r}, {source: r, target: t});
bilinks.push({
"source" : s,
"target" : t,
"rxn" : r,
"rstoich" : rxn_stoich[link.rxn],
});
});
nodes.forEach( function (node) {
if ("notes" in node) {
if ("map_info" in node.notes) {
if (("x" in node.notes.map_info) && ("y" in node.notes.map_info)) {
node.x = node.notes.map_info.x;
node.y = node.notes.map_info.y;
node.fixed = 1;
}
}
}
});
force
.nodes(nodes)
.links(links)
.start();
svg.append("defs").selectAll("marker")
.data(reactions)
.enter()
.append("marker")
.attr("id", function (d) { return d.id; })
.attr("viewBox", "0 -5 10 10")
.attr("refX", 12)
.attr("refY", 0)
.attr("markerUnits", "userSpaceOnUse")
.attr("markerWidth", "8pt")
.attr("markerHeight", "8pt")
.attr("orient", "auto")
.attr("class", "endmarker")
.append("path")
.attr("d", "M0,-5L10,0L0,5");
var link = svg.append('g').selectAll(".link")
.data(bilinks)
.enter()
.append("path")
.attr("class", function (d) { return "link " + d.rxn.id; })
.attr("marker-end", function(d) {
return "url(#" + d.rxn.id + ")";
});
var node_drag = force.drag()
.on("dragstart", dragstart);
function dragstart(d) {
d3.select(this).classed("fixed", d.fixed = true);
}
function releasenode(d) {
// of course set the node to fixed so the force doesn't include the node in
// its auto positioning stuff
d.fixed = false;
force.resume();
}
// define the nodes
var node = svg.append("g").selectAll(".node")
.data(nodes)
.enter()
.append("g")
.on('dblclick', releasenode)
.on('mouseover', node_tip.show)
.on('mouseout', node_tip.hide)
.call(node_drag);
node.append("circle")
.attr("class", function(d) {
if (d.group == 'rxn') {
return "node " + d.group + " hidden";
} else return "node";})
.attr("id", function(d) { return d.id; })
.attr("r", 5)
.style("fill", function(d) {
if (d.group != 'rxn') {
return color(d.group);
} else return "";});
// add the text
node.append("text")
.attr("class", "nodelabel")
.attr("dx", "12")
.attr("dy", ".35em")
.text(function(d) { return d.name; });
var updateNode = function() {
this.attr("transform", function(d) {
return "translate(" + d.x + "," + d.y + ")";
});
}
var updateAnchorLink = function() {
this.attr("x1", function(d) {
return d.source.x;
}).attr("y1", function(d) {
return d.source.y;
}).attr("x2", function(d) {
return d.target.x;
}).attr("y2", function(d) {
return d.target.y;
});
}
var updateLink = function() {
this.attr("d", function(d) {
return calculate_path(d, force);
});
}
var updateAnchorNodes = function() {
this.each(function(d, i) {
if(i % 2 == 0) {
d.x = d.node.x;
d.y = d.node.y;
} else {
var b = this.childNodes[1].getBBox();
var diffX = d.x - d.node.x;
var diffY = d.y - d.node.y;
var dist = Math.sqrt(diffX * diffX + diffY * diffY);
var shiftX = b.width * (diffX - dist) / (dist * 2);
shiftX = Math.max(-b.width, Math.min(0, shiftX));
var shiftY = 5;
this.childNodes[1].setAttribute("transform", "translate(" + shiftX + "," + shiftY + ")");
}
});
}
force.on("tick", function() {
link.call(updateLink);
node.call(updateNode);
});
flux_scale = d3.scale.pow().exponent(1/3)
.domain([d3.min(fluxes), d3.max(fluxes)])
.range([1.5, 6]);
arrowhead_scale = d3.scale.linear()
.domain([1.5, 6])
.range([5, 10])
function get_flux_width (rxn) {
try {
return flux_scale(Math.abs(rxn.notes.map_info.flux));
}
catch(err) {
return 1.5; // Default linewidth
}
}
function get_flux_dasharray (d) {
try {
if (Math.abs(d.rxn.notes.map_info.flux) < 1E-6) {
return "5,5";
}
}
catch(err) {
return;
}
}
function get_flux_stroke (rxn) {
// For now, just keep the same color
return "#bbb"
}
function markerscale (d) {
return arrowhead_scale(get_flux_width(d)) + "pt";
}
svg.selectAll(".link")
.attr("stroke-width", function (d) {return get_flux_width(d.rxn);})
.attr("stroke", function (d) {return get_flux_stroke(d.rxn);})
.attr("stroke-dasharray", get_flux_dasharray);
svg.selectAll("marker")
.attr("markerWidth", markerscale)
.attr("markerHeight", markerscale)
.select("path")
.attr("fill", get_flux_stroke);
d3.select("#download")
.on("click", function () {
// Add position data to model nodes
force.nodes().forEach(function (node) {
if (node.fixed) {
if (node.group == "rxn") {
// Reaction object
obj = $.grep(model.reactions, function(e){ return e.id == node.id; })[0];
if (!("notes" in obj)) { obj.notes = {}; }
obj.notes['map_info'] = {
"x" : node.x,
"y" : node.y,
};
} else {
// Look in metabolites
obj = $.grep(model.metabolites, function(e){ return e.id == node.id; })[0];
if (!("notes" in obj)) { obj.notes = {}; }
obj.notes['map_info'] = {
"x" : node.x,
"y" : node.y,
};
}
}
});
var json = JSON.stringify(model);
var blob = new Blob([json], {type: "application/json"});
saveAs(blob, "model.json");
});
});
Raw
index.html
<!DOCTYPE html>
<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=UTF8">
<script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.6/d3.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjs/2.4.0/math.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/FileSaver.js/2014-11-29/FileSaver.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/2.1.4/jquery.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/d3-tip/0.6.7/d3-tip.min.js"></script>
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css">
<link rel="stylesheet" type="text/css" href="style.css">
<!-- <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjs/2.4.0/math.js"></script> -->
</head>
<body>
<div id="options">
<button type="button" id="download" class="btn btn-primary">Save JSON</button>
<button type="button" id="reactionbutton" class="btn btn-success ">Show Reaction Nodes</button>
</div>
<script src="force_directed_model.js"></script>
</body>
</html>
Raw
model.json
{
"genes": [
{
"id": "Asuc_0591",
"name": "Asuc_0591"
},
{
"id": "Asuc_1661",
"name": "Asuc_1661"
},
{
"id": "Asuc_0185",
"name": "Asuc_0185"
},
{
"id": "Asuc_1819",
"name": "fabG"
},
{
"id": "Asuc_0403",
"name": "Asuc_0403"
},
{
"id": "Asuc_0326",
"name": "Asuc_0326"
},
{
"id": "Asuc_0328",
"name": "Asuc_0328"
},
{
"id": "Asuc_2051",
"name": "fabG"
},
{
"id": "Asuc_0536",
"name": "Asuc_0536"
},
{
"id": "Asuc_0394",
"name": "fabG"
},
{
"id": "Asuc_1073",
"name": "Asuc_1073"
},
{
"id": "Asuc_1813",
"name": "Asuc_1813"
},
{
"id": "Asuc_1814",
"name": "Asuc_1814"
},
{
"id": "Asuc_0956",
"name": "fabG"
},
{
"id": "Asuc_0227",
"name": "Asuc_0227"
},
{
"id": "Asuc_1027",
"name": "Asuc_1027"
},
{
"id": "Asuc_0232",
"name": "Asuc_0232"
},
{
"id": "Asuc_1612",
"name": "Asuc_1612"
},
{
"id": "Asuc_0669",
"name": "Asuc_0669"
},
{
"id": "Asuc_1021",
"name": "fabG"
},
{
"id": "Asuc_1022",
"name": "fabG"
},
{
"id": "Asuc_0942",
"name": "fabG"
},
{
"id": "Asuc_0944",
"name": "Asuc_0944"
},
{
"id": "Asuc_0943",
"name": "fabG"
},
{
"id": "Asuc_0687",
"name": "Asuc_0687"
},
{
"id": "Asuc_0207",
"name": "Asuc_0207"
},
{
"id": "Asuc_1425",
"name": "fabG"
},
{
"id": "Asuc_0535",
"name": "fabG"
},
{
"id": "Asuc_0228",
"name": "Asuc_0228"
},
{
"id": "Asuc_0572",
"name": "fabG"
},
{
"id": "Asuc_1383",
"name": "Asuc_1383"
},
{
"id": "Asuc_0221",
"name": "Asuc_0221"
},
{
"id": "Asuc_1662",
"name": "Asuc_1662"
},
{
"id": "Asuc_1171",
"name": "Asuc_1171"
},
{
"id": "Asuc_0218",
"name": "Asuc_0218"
},
{
"id": "Asuc_1580",
"name": "Asuc_1580"
},
{
"id": "Asuc_1597",
"name": "Asuc_1597"
},
{
"id": "Asuc_1870",
"name": "Asuc_1870"
},
{
"id": "Asuc_0582",
"name": "Asuc_0582"
},
{
"id": "Asuc_0170",
"name": "Asuc_0170"
},
{
"id": "Asuc_0171",
"name": "Asuc_0171"
},
{
"id": "Asuc_0265",
"name": "Asuc_0265"
},
{
"id": "Asuc_0677",
"name": "fabG"
},
{
"id": "Asuc_1575",
"name": "Asuc_1575"
},
{
"id": "Asuc_1601",
"name": "Asuc_1601"
},
{
"id": "Asuc_0301",
"name": "Asuc_0301"
},
{
"id": "Asuc_0302",
"name": "Asuc_0302"
},
{
"id": "Asuc_0303",
"name": "Asuc_0303"
},
{
"id": "Asuc_1264",
"name": "Asuc_1264"
},
{
"id": "Asuc_1265",
"name": "Asuc_1265"
},
{
"id": "Asuc_1704",
"name": "Asuc_1704"
}
],
"id": "asuc_v1",
"metabolites": [
{
"compartment": "c",
"formula": "C3H4O10P2",
"id": "13dpg_c",
"name": "3-Phospho-D-glyceroyl phosphate",
"notes": {
"BRENDA": [
"BG18032",
"BG87317"
],
"BioPath": [
"1,3-Diphospho-D-glycerate"
],
"ChEBI": [
"16001",
"1658",
"20189",
"57604",
"11881"
],
"HMDB": [
"HMDB01270"
],
"KEGG": "C00236",
"MetaCyc": "DPG",
"PUBCHEM ID": [
"3535"
],
"Reactome": [
"29800"
],
"SEED": [
"cpd00203"
],
"UPA": [
"UPC00236"
]
}
},
{
"compartment": "c",
"formula": "C3H4O7P",
"id": "2pg_c",
"name": "D-Glycerate 2-phosphate",
"notes": {
"BRENDA": [
"BG17976",
"BG17975"
],
"BioPath": [
"2-Phospho-D-glycerate"
],
"ChEBI": [
"1267",
"58289",
"17835",
"21028",
"11651",
"12986",
"24344",
"39868"
],
"HMDB": [
"HMDB03391",
"HMDB00362"
],
"KEGG": "C00631",
"MetaCyc": "2-PG",
"PUBCHEM ID": [
"3904"
],
"Reactome": [
"30485"
],
"SEED": [
"cpd00482"
],
"UPA": [
"UPC00631"
]
}
},
{
"compartment": "c",
"formula": "C3H4O7P",
"id": "3pg_c",
"name": "3-Phospho-D-glycerate",
"notes": {
"BRENDA": [
"BG17981",
"BG17979"
],
"BioPath": [
"3-Phospho-D-glycerate"
],
"ChEBI": [
"40016",
"58272",
"57998",
"11879",
"1657",
"1659",
"17050",
"21029",
"11882",
"11880",
"12987",
"17794",
"24345"
],
"HMDB": [
"HMDB00807"
],
"KEGG": "C00197",
"MetaCyc": "G3P",
"PUBCHEM ID": [
"3497"
],
"Reactome": [
"29728"
],
"SEED": [
"cpd00169"
],
"UPA": [
"UPC00597",
"UPC00197"
]
}
},
{
"compartment": "c",
"formula": "C6H10O10P",
"id": "6pgc_c",
"name": "6-Phospho-D-gluconate",
"notes": {
"BRENDA": [
"BG22563"
],
"BioPath": [
"6-Phospho-D-gluconate"
],
"ChEBI": [
"2231",
"12232",
"48928",
"16863",
"58759",
"40282",
"33851"
],
"HMDB": [
"HMDB01316"
],
"KEGG": "C00345",
"MetaCyc": "CPD-2961",
"PUBCHEM ID": [
"3638"
],
"Reactome": [
"29996"
],
"SEED": [
"cpd00284"
],
"UPA": [
"UPC00345"
]
}
},
{
"compartment": "c",
"formula": "C6H9O9P",
"id": "6pgl_c",
"name": "6-phospho-D-glucono-1,5-lactone",
"notes": {
"BRENDA": [
"BG22089"
],
"BioPath": [
"D-Glucono-1,5-lactone_6-phosphate"
],
"ChEBI": [
"16938",
"12233",
"4160",
"20989",
"57955",
"12958"
],
"HMDB": [
"HMDB01127"
],
"KEGG": "C01236",
"MetaCyc": "D-6-P-GLUCONO-DELTA-LACTONE",
"PUBCHEM ID": [
"4457"
],
"Reactome": [
"31467"
],
"SEED": [
"cpd00911"
],
"UPA": [
"UPC01236"
]
}
},
{
"compartment": "c",
"formula": "C2H3O2",
"id": "ac_c",
"name": "Acetate",
"notes": {
"BRENDA": [
"BG15447"
],
"BioPath": [
"Acetate"
],
"CAS": [
"71-50-1"
],
"CASID": [
"71-50-1"
],
"ChEBI": [
"62947",
"62964",
"32029",
"22165",
"3310",
"2387",
"62984",
"63879",
"32138",
"15366",
"13704",
"63078",
"30089",
"40480",
"22169",
"40486",
"59199",
"63045",
"32954"
],
"HMDB": [
"HMDB00042"
],
"KEGG": "C00033",
"LIPIDMAPS": [
"LMFA01010000",
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Raw
style.css
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stroke-width: 1.5px;
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