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TreeScaperNetworks.html
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TreeScaperNetworks.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Display TreeScaper Networks</title>
<!-- d3 library for data visualization and animation -->
<script type="text/javascript" src="https://d3js.org/d3.v4.min.js"></script>
<!-- jstat library for probability distributions -->
<script type="text/javascript" src="https://cdn.jsdelivr.net/npm/jstat@latest/dist/jstat.min.js"></script>
<!-- phyleaux library for phylogenetic objects and functions -->
<script type="text/javascript" src="https://jembrown.github.io/phyleaux.js"></script>
<style type="text/css">
@font-face { font-family: Glober; font-weight: semibold; src: url('Glober-SemiBold.otf'); }
h1 {
font-family: Glober;
font-size: 24px;
}
h2 {
font-family: Glober;
font-size: 18px;
}
label {
font-size: 16px;
}
/* Set slider width (% of window width) */
input {
width: 50%
}
/* Dropdown Button */
.dropbtn {
background-color: white;
color: black;
padding: 4px;
font-size: 14px;
border: 1px solid grey;
border-radius: 5px;
cursor: pointer;
}
/* Dropdown button on hover & focus */
.dropbtn:hover, .dropbtn:focus {
background-color: "#f1f1f1";
}
/* The container <div> - needed to position the dropdown content */
.dropdown {
position: relative;
display: inline-block;
}
/* Dropdown Content (Hidden by Default) */
.dropdown-content {
display: none;
position: absolute;
background-color: #f1f1f1;
min-width: 70px;
width: 100%;
box-shadow: 0px 8px 16px 0px rgba(0,0,0,0.2);
z-index: 1;
}
/* Links inside the dropdown */
.dropdown-content a, button {
color: black;
padding: 12px 16px;
text-decoration: none;
display: block;
}
/* Change color of dropdown links on hover */
.dropdown-content a:hover {background-color: #ddd}
/* Show the dropdown menu (use JS to add this class to the .dropdown-content container when the user clicks on the dropdown button) */
.show {display:block;}
</style>
</head>
<body>
<h1>Plot Bipartition and Tree Networks from TreeScaper</h1>
<script>
var dataset = {};
var nodeColor = "grey";
var posEdgeColor = "blue";
var negEdgeColor = "red";
var nodeStyle = "circles";
/* Functions called by options from the Node Color dropdown */
var changeNodeColorRed = function(){
nodeColor = "red";
refreshNetwork();
}
var changeNodeColorOrange = function(){
nodeColor = "orange";
refreshNetwork();
}
var changeNodeColorBlue = function(){
nodeColor = "blue";
refreshNetwork();
}
var changeNodeColorGreen = function(){
nodeColor = "green";
refreshNetwork();
}
var changeNodeColorGrey = function(){
nodeColor = "grey";
refreshNetwork();
}
var changeNodeColorBlack = function(){
nodeColor = "black";
refreshNetwork();
}
/* Functions called by options from the Edge Color (Positive) dropdown */
var changePosEdgeColorRed = function(){
posEdgeColor = "red";
refreshNetwork();
}
var changePosEdgeColorOrange = function(){
posEdgeColor = "orange";
refreshNetwork();
}
var changePosEdgeColorBlue = function(){
posEdgeColor = "blue";
refreshNetwork();
}
var changePosEdgeColorGreen = function(){
posEdgeColor = "green";
refreshNetwork();
}
var changePosEdgeColorGrey = function(){
posEdgeColor = "grey";
refreshNetwork();
}
var changePosEdgeColorBlack = function(){
posEdgeColor = "black";
refreshNetwork();
}
/* Functions called by options from the Edge Color (Negative) dropdown */
var changeNegEdgeColorRed = function(){
negEdgeColor = "red";
refreshNetwork();
}
var changeNegEdgeColorOrange = function(){
negEdgeColor = "orange";
refreshNetwork();
}
var changeNegEdgeColorBlue = function(){
negEdgeColor = "blue";
refreshNetwork();
}
var changeNegEdgeColorGreen = function(){
negEdgeColor = "green";
refreshNetwork();
}
var changeNegEdgeColorGrey = function(){
negEdgeColor = "grey";
refreshNetwork();
}
var changeNegEdgeColorBlack = function(){
negEdgeColor = "black";
refreshNetwork();
}
var changeNodesToCircles = function(){
nodeStyle = "circles";
refreshNetwork();
}
var changeNodesToNumbers = function(){
nodeStyle = "numbers";
refreshNetwork();
}
// Function to quickly replot network after changing a display parameter
var refreshNetwork = function() {
d3.select("svg").selectAll("line").remove();
d3.select("svg").selectAll("circle").remove();
d3.select("svg").selectAll("text").remove();
plotNetwork( svg = d3.select("svg"),
w = 600,
h = 600,
r = d3.select("#nodeRadius").property("value"),
edgeScaling = (parseFloat(d3.select("#fineEdgeScaling").property("value")) +
parseFloat(d3.select("#grossEdgeScaling").property("value"))),
edgeForceScaling = d3.select("#edgeForceScaling").property("value"),
nodeForceScaling = -1*d3.select("#nodeForceScaling").property("value"));
}
// Function to read in file of covariances or affinities
// Expects this file to contain values along and below the diagonal (not above)
var handleFiles = function(files){
var reader = new FileReader(); // Instantiates file reader
reader.onload = function(event) { // Defines what happens when file is done loading
parseMatrix(reader.result);
refreshNetwork();
/*d3.select("svg").selectAll("line").remove();
d3.select("svg").selectAll("circle").remove();
plotNetwork( svg = d3.select("svg"),
w = 600,
h = 600,
r = d3.select("#nodeRadius").property("value"),
edgeScaling = (parseFloat(d3.select("#fineEdgeScaling").property("value")) +
parseFloat(d3.select("#grossEdgeScaling").property("value"))),
edgeForceScaling = d3.select("#edgeForceScaling").property("value"),
nodeForceScaling = -1*d3.select("#nodeForceScaling").property("value"));*/
};
reader.readAsText(files[0]); // Begins reading in the file - will only accept one file.
}
// The parseMatrix() function can read in either an affinity or a covariance network from TreeScaper
// and create the network format expected by d3 (see default example below).
var parseMatrix = function(matrixText){
// Make array out of lines of file
var lines = matrixText.split("\n");
// For the header line, remove starting and trailing whitespace
lines[0] = lines[0].trim();
// Split the line by whitespace
var IDs = lines[0].split(/[ \t]+/);
// Remove the first element of the header line - "trees"
if (IDs[0] === "trees"){
IDs.splice(0,1); // Removes first element
}
// Create nodes element and add it to dataset
var nodes = [];
for (var i = 0; i < IDs.length; i++){
var newNode = { name: IDs[i] };
nodes.push(newNode);
}
dataset.nodes = nodes;
// Then parse additional lines to populate edges
var edges = [];
for (var lineNum = 2; lineNum < lines.length; lineNum++){
lines[lineNum] = lines[lineNum].trim();
var covs = lines[lineNum].split(/[ \t]+/);
covs.splice(0,1);
covs.splice(covs.length-1,1);
for (var cov = 0; cov < covs.length; cov++){
var newEdge = {};
newEdge.source = lineNum - 1;
newEdge.target = cov;
newEdge.weight = covs[cov];
edges.push(newEdge);
}
}
dataset.edges = edges;
}
// Creates the default network of only two equally frequent 5-taxon trees.
dataset = {
// 5-taxon bipartition descriptions
nodes:[
{ name: "OA|BCD" },
{ name: "OB|ACD" },
{ name: "OC|ABD" },
{ name: "OD|ABC" },
{ name: "AB|OCD" },
{ name: "AC|OBD" },
{ name: "AD|OBC" },
{ name: "BC|OAD" },
{ name: "BD|OAC" },
{ name: "CD|OAB" },
],
// Edges between all bipartitions, with weights as covariances from the
// example tree set.
edges: [
{ source: 0, target: 1, weight: 0.0 }, // 1
{ source: 0, target: 2, weight: 0.0 }, // 2
{ source: 0, target: 3, weight: 0.0 }, // 3
{ source: 0, target: 4, weight: 0.0 }, // 4
{ source: 0, target: 5, weight: 0.0 }, // 5
{ source: 0, target: 6, weight: -0.25 }, // 6
{ source: 0, target: 7, weight: -0.25 }, // 7
{ source: 0, target: 8, weight: 0.0 }, // 8
{ source: 0, target: 9, weight: 0.25 }, // 9
{ source: 1, target: 2, weight: 0.0 }, // 10
{ source: 1, target: 3, weight: 0.0 }, // 11
{ source: 1, target: 4, weight: 0.0 }, // 12
{ source: 1, target: 5, weight: 0.0 }, // 13
{ source: 1, target: 6, weight: 0.0 }, // 14
{ source: 1, target: 7, weight: 0.0 }, // 15
{ source: 1, target: 8, weight: 0.0 }, // 16
{ source: 1, target: 9, weight: 0.0 }, // 17
{ source: 2, target: 3, weight: 0.0 }, // 18
{ source: 2, target: 4, weight: 0.0 }, // 19
{ source: 2, target: 5, weight: 0.0 }, // 20
{ source: 2, target: 6, weight: 0.0 }, // 21
{ source: 2, target: 7, weight: 0.0 }, // 22
{ source: 2, target: 8, weight: 0.0 }, // 23
{ source: 2, target: 9, weight: 0.0 }, // 24
{ source: 3, target: 4, weight: 0.0 }, // 25
{ source: 3, target: 5, weight: 0.0 }, // 26
{ source: 3, target: 6, weight: 0.0 }, // 27
{ source: 3, target: 7, weight: 0.0 }, // 28
{ source: 3, target: 8, weight: 0.0 }, // 29
{ source: 3, target: 9, weight: 0.0 }, // 30
{ source: 4, target: 5, weight: 0.0 }, // 31
{ source: 4, target: 6, weight: 0.0 }, // 32
{ source: 4, target: 7, weight: 0.0 }, // 33
{ source: 4, target: 8, weight: 0.0 }, // 34
{ source: 4, target: 9, weight: 0.0 }, // 35
{ source: 5, target: 6, weight: 0.0 }, // 36
{ source: 5, target: 7, weight: 0.0 }, // 37
{ source: 5, target: 8, weight: 0.0 }, // 38
{ source: 5, target: 9, weight: 0.0 }, // 39
{ source: 6, target: 7, weight: 0.25 }, // 40
{ source: 6, target: 8, weight: 0.0 }, // 41
{ source: 6, target: 9, weight: -0.25 }, // 42
{ source: 7, target: 8, weight: 0.0 }, // 43
{ source: 7, target: 9, weight: -0.25 }, // 44
{ source: 8, target: 9, weight: 0.0 }, // 45
]
}
// Function to plot the network on a new or an existing svg
var plotNetwork = function( svg = null, // by default, no existing svg is provided
w = 600, // svg width
h = 600, // svg height
r = 3, // node radius
edgeScaling = 5.5, // Scaling factor for edge width display
edgeForceScaling = 0, // Scaling factor for force of weighted edges (turned off by default)
nodeForceScaling = -100){ // Scaling factor for repelling force of nodes (low, by default)
// Creating the svg to hold the covariance network
if (svg === null){
svg = d3.select("body")
.append("svg")
.attr("width",w)
.attr("height",h);
}
// Setting up the force simulation to arrange nodes in the covariance network
var force = d3.forceSimulation(dataset.nodes)
.force("charge", d3.forceManyBody().strength(nodeForceScaling))
.force("link", d3.forceLink(dataset.edges).strength(function(d){
// return (Math.abs(d.weight) * edgeForceScaling)+0.01
return (d.weight * edgeForceScaling)+0.01
}))
.force("center", d3.forceCenter().x(w/2).y(h/2));
// Define plotting parameters for covariance edges
var edges = svg.selectAll("line")
.data(dataset.edges)
.enter()
.append("line")
.style("stroke", function(d){
if (d.weight > 0){ // + covariances
return posEdgeColor;
} else if (d.weight < 0){ // - covariances
return negEdgeColor;
} // Ignores edges with 0 weights
})
.style("stroke-width", function(d){ // Edge weights proportional to magnitude of covariance
return Math.abs(d.weight) * edgeScaling
});
if (nodeStyle == "circles"){
// Define plotting parameters for bipartition nodes
var nodes = svg.selectAll("circle")
.data(dataset.nodes)
.enter()
.append("circle")
.attr("r", r)
.style("fill",function(d,i){
return nodeColor;
})
.call(d3.drag() //Define what to do on drag events
.on("start", dragStarted)
.on("drag", dragging)
.on("end", dragEnded));
} else if (nodeStyle == "numbers"){
var nodes = svg.selectAll("text")
.data(dataset.nodes)
.enter()
.append("text")
.text(function(d,i){
return d.name;
})
.call(d3.drag() //Define what to do on drag events
.on("start", dragStarted)
.on("drag", dragging)
.on("end", dragEnded));
}
// Next 3 functions define behavior of node dragging
function dragStarted(d) {
if (!d3.event.active) force.alphaTarget(0.3).restart();
d.fx = d.x;
d.fy = d.y;
}
function dragging(d) {
d.fx = d3.event.x;
d.fy = d3.event.y;
}
function dragEnded(d) {
if (!d3.event.active) force.alphaTarget(0);
d.fx = null;
d.fy = null;
}
// Tooltip for nodes to show node description
// For default TreeScaper matrices, these are just indices
nodes.append("title")
.text(function(d) {
return d.name;
});
// Tooltip for edges to show edge weights (covariances or affinities)
edges.append("title")
.text(function(d) {
return d.weight;
});
// Defining behavior of nodes and edges during physical simulation
force.on("tick", function() {
edges.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; });
if (nodeStyle == "circles"){
nodes.attr("cx", function(d) { return d.x; })
.attr("cy", function(d) { return d.y; });
} else if (nodeStyle == "numbers"){
nodes.attr("x", function(d) { return d.x; })
.attr("y", function(d) { return d.y; });
}
});
// Adds a scale bar with a default value of 0.1 in the bottom-right corner
svg.append("line")
.attr("x1",w-50)
.attr("x2",w-100)
.attr("y1",h-100)
.attr("y2",h-100)
.attr("stroke","black")
.attr("stroke-width",edgeScaling * 0.1);
}
// Initial display of default network
plotNetwork();
</script>
<br>
Choose the covariance (bipartition) or affinity (tree) matrix from TreeScaper you wish to display.<br><br>
<!-- Input selection for file containing network -->
<input type="file" id="input" class="fileIn" onchange="handleFiles(this.files)"><br><br>
Adjust the display of the network using the controls. Notes and description of these options are provided below.<br><br>
<!-- Dropdown menu to change node color -->
<!-- Functions called by all color dropdown menus are defined above -->
<div class="dropdown">
<button onclick="toggleNodeColorDropdown()" class="dropbtn">Node Color</button>
<div id="nodeColor" class="dropdown-content">
<a onclick="changeNodeColorRed()">Red</a>
<a onclick="changeNodeColorOrange()">Orange</a>
<a onclick="changeNodeColorBlue()">Blue</a>
<a onclick="changeNodeColorGreen()">Green</a>
<a onclick="changeNodeColorGrey()">Grey</a>
<a onclick="changeNodeColorBlack()">Black</a>
</div>
</div>
<!-- Dropdown menu to change the color of positive edges -->
<div class="dropdown">
<button onclick="togglePosEdgeColorDropdown()" class="dropbtn">Edge Color (Positive Weights)</button>
<div id="posEdgeColor" class="dropdown-content">
<a onclick="changePosEdgeColorRed()">Red</a>
<a onclick="changePosEdgeColorOrange()">Orange</a>
<a onclick="changePosEdgeColorBlue()">Blue</a>
<a onclick="changePosEdgeColorGreen()">Green</a>
<a onclick="changePosEdgeColorGrey()">Grey</a>
<a onclick="changePosEdgeColorBlack()">Black</a>
</div>
</div>
<!-- Dropdown menu to change the color of negative edges -->
<div class="dropdown">
<button onclick="toggleNegEdgeColorDropdown()" class="dropbtn">Edge Color (Negative Weights)</button>
<div id="negEdgeColor" class="dropdown-content">
<a onclick="changeNegEdgeColorRed()">Red</a>
<a onclick="changeNegEdgeColorOrange()">Orange</a>
<a onclick="changeNegEdgeColorBlue()">Blue</a>
<a onclick="changeNegEdgeColorGreen()">Green</a>
<a onclick="changeNegEdgeColorGrey()">Grey</a>
<a onclick="changeNegEdgeColorBlack()">Black</a>
</div>
</div>
<div class="dropdown">
<button onclick="toggleNodeCirclesNumbers()" class="dropbtn">Node Style</button>
<div id="nodeCircleNum" class="dropdown-content">
<a onclick="changeNodesToCircles()">Circles</a>
<a onclick="changeNodesToNumbers()">Numbers</a>
</div>
</div>
<br><br>
<!-- Input slider for node radius -->
<label for="nodeRadius"
style="display: inline-block; width: 150px; text-align: center">
Node Radius <span id="nodeRadius-value"></span>
</label>
<input type="range" min="0" max="10" id="nodeRadius" step="0.1" value="3">
<br><br>
<!-- Input slider for fine-grained control of edge thicknesses (scales edge weights) -->
<label for="fineEdgeScaling"
style="display: inline-block; width: 150px; text-align: center">
Edge Weight Scaling (Fine Control) <span id="fineEdgeScaling-value"></span>
</label>
<input type="range" min="0" max="1" id="fineEdgeScaling" step="0.01" value="0.5">
<br><br>
<!-- Input slider for rough control of edge thicknesses (scales edge weights) -->
<label for="grossEdgeScaling"
style="display: inline-block; width: 150px; text-align: center">
Edge Weight Scaling (Gross Control) <span id="grossEdgeScaling-value"></span>
</label>
<input type="range" min="0" max="25" id="grossEdgeScaling" step="0.5" value="5">
<br><br>
<!-- Input slider to modulate the force of weighted edges -->
<!-- Positive edges attract and negative edges repel -->
<label for="edgeForceScaling"
style="display: inline-block; width: 150px; text-align: center">
Edge Force Scaling <span id="edgeForceScaling-value"></span>
</label>
<input type="range" min="0" max="0.3" id="edgeForceScaling" step="0.01" value="0">
<br><br>
<!-- Input slider to modulate the repelling force of nodes -->
<label for="nodeForceScaling"
style="display: inline-block; width: 150px; text-align: center">
Node Force Scaling <span id="nodeForceScaling-value"></span>
</label>
<input type="range" min="100" max="1500" id="nodeForceScaling" step="10" value="100">
<br><br>
<script>
/* When the user clicks on the button,
toggle between hiding and showing the dropdown content */
function toggleNodeColorDropdown() {
document.getElementById("nodeColor").classList.toggle("show");
}
function togglePosEdgeColorDropdown() {
document.getElementById("posEdgeColor").classList.toggle("show");
}
function toggleNegEdgeColorDropdown() {
document.getElementById("negEdgeColor").classList.toggle("show");
}
function toggleNodeCirclesNumbers() {
document.getElementById("nodeCircleNum").classList.toggle("show");
}
// Close the dropdown menu if the user clicks outside of it
window.onclick = function(event) {
if (!event.target.matches('.dropbtn')) {
var dropdowns = document.getElementsByClassName("dropdown-content");
var i;
for (i = 0; i < dropdowns.length; i++) {
var openDropdown = dropdowns[i];
if (openDropdown.classList.contains('show')) {
openDropdown.classList.remove('show');
}
}
}
}
// Replotting the network when fine control of edge weights is changed
d3.select("#fineEdgeScaling")
.on("input",function(){
refreshNetwork();
})
// Replotting the network when rough control of edge weights is changed
d3.select("#grossEdgeScaling")
.on("input",function(){
refreshNetwork();
})
// Replotting the network when the forces of edges are changed
d3.select("#edgeForceScaling")
.on("input",function(){
refreshNetwork();
})
// Replotting the network when the forces of nodes are changed
d3.select("#nodeForceScaling")
.on("input",function(){
refreshNetwork();
})
// Replotting the network when the radius of nodes is changed
d3.select("#nodeRadius")
.on("input",function(){
refreshNetwork();
})
</script>
<h2> Notes </h2>
<p>
The position of nodes in the network can be changed interactively by clicking and dragging.
Depending on the size of the network, it may take some time to return to equilibrium. Changing
any of the options below may also perturb the network, requiring time for it to return to equilibrium.
</p>
<p>
Network plots are created as SVGs. To export these figures, and allow editing in other software, try using
<a href="https://nytimes.github.io/svg-crowbar/">SVG crowbar</a> in a Chrome browser.
</p>
<p>
<i>Node Color</i> - Changes the color of the nodes, which are displayed as circles.
</p>
<p>
<i>Edge Color (Positive Weights)</i> - Changes the color of edges whose weights are positive.
Positively weighted edges pull nodes towards each other. By default, these edges are colored blue.
</p>
<p>
<i>Edge Color (Negative Weights)</i> - Changes the color of edges whose weights are negative.
Negatively weighted edges repel nodes. By default, these edges are colored red.
</p>
<p>
<i>Node Radius</i> - Changes the size of the circles that represent the nodes in the network.
The minimum is 0 and the maximum is 10 pixels.
</p>
<p>
<i>Edge Weight Scaling (Fine Control)</i> - In combination with the slider below (gross control), this slider
adjusts the width of lines representing edges in the network. The minimum value is 0 and the maximum is 1. Covariance
(bipartition) networks often have larger values and may require use of this control.
</p>
<p>
<i>Edge Weight Scaling (Gross Control)</i> - In combination with the slider above (fine control), this slider
adjusts the width of lines representing edges in the network. The minimum value is 0 and the maximum is 25. Affinity
(tree) networks often have smaller values and may require use of this control.
</p>
<p>
<i>Edge Force Scaling</i> - Adjusts the strength of attraction or repulsion provided by the edges. Edges with
positive weights attract, while those with negative weights repel.
</p>
<p>
<i>Node Force Scaling</i> - Adjusts the strength of repulsion among the nodes. The minimum is weak repulsion and
the maximum is very strong repulsion.
</p>
</body>
</html>