Javascript – Adding new nodes to Force-directed layout

d3.jsforce-layoutjavascript

First question on Stack Overflow, so bear with me! I am new to d3.js, but have been consistently amazed by what others are able to accomplish with it… and almost as amazed by how little headway I've been able to make with it myself! Clearly I'm not grokking something, so I hope that the kind souls here can show me the light.

My intention is to make a reusable javascript function which simply does the following:

Creates a blank force-directed graph in a specified DOM element
Allows you to add and delete labeled, image-bearing nodes to that graph, specifying connections between them

I've taken http://bl.ocks.org/950642 as a starting point, since that's essentially the kind of layout I want to be able to create:

enter image description here

Here's what my code looks like:

<!DOCTYPE html>
<html>
<head>
    <script type="text/javascript" src="jquery.min.js"></script>
    <script type="text/javascript" src="underscore-min.js"></script>
    <script type="text/javascript" src="d3.v2.min.js"></script>
    <style type="text/css">
        .link { stroke: #ccc; }
        .nodetext { pointer-events: none; font: 10px sans-serif; }
        body { width:100%; height:100%; margin:none; padding:none; }
        #graph { width:500px;height:500px; border:3px solid black;border-radius:12px; margin:auto; }
    </style>
</head>
<body>
<div id="graph"></div>
</body>
<script type="text/javascript">

function myGraph(el) {

    // Initialise the graph object
    var graph = this.graph = {
        "nodes":[{"name":"Cause"},{"name":"Effect"}],
        "links":[{"source":0,"target":1}]
    };

    // Add and remove elements on the graph object
    this.addNode = function (name) {
        graph["nodes"].push({"name":name});
        update();
    }

    this.removeNode = function (name) {
        graph["nodes"] = _.filter(graph["nodes"], function(node) {return (node["name"] != name)});
        graph["links"] = _.filter(graph["links"], function(link) {return ((link["source"]["name"] != name)&&(link["target"]["name"] != name))});
        update();
    }

    var findNode = function (name) {
        for (var i in graph["nodes"]) if (graph["nodes"][i]["name"] === name) return graph["nodes"][i];
    }

    this.addLink = function (source, target) {
        graph["links"].push({"source":findNode(source),"target":findNode(target)});
        update();
    }

    // set up the D3 visualisation in the specified element
    var w = $(el).innerWidth(),
        h = $(el).innerHeight();

    var vis = d3.select(el).append("svg:svg")
        .attr("width", w)
        .attr("height", h);

    var force = d3.layout.force()
        .nodes(graph.nodes)
        .links(graph.links)
        .gravity(.05)
        .distance(100)
        .charge(-100)
        .size([w, h]);

    var update = function () {

        var link = vis.selectAll("line.link")
            .data(graph.links);

        link.enter().insert("line")
            .attr("class", "link")
            .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; });

        link.exit().remove();

        var node = vis.selectAll("g.node")
            .data(graph.nodes);

        node.enter().append("g")
            .attr("class", "node")
            .call(force.drag);

        node.append("image")
            .attr("class", "circle")
            .attr("xlink:href", "https://d3nwyuy0nl342s.cloudfront.net/images/icons/public.png")
            .attr("x", "-8px")
            .attr("y", "-8px")
            .attr("width", "16px")
            .attr("height", "16px");

        node.append("text")
            .attr("class", "nodetext")
            .attr("dx", 12)
            .attr("dy", ".35em")
            .text(function(d) { return d.name });

        node.exit().remove();

        force.on("tick", function() {
          link.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; });

          node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
        });

        // Restart the force layout.
        force
          .nodes(graph.nodes)
          .links(graph.links)
          .start();
    }

    // Make it all go
    update();
}

graph = new myGraph("#graph");

// These are the sort of commands I want to be able to give the object.
graph.addNode("A");
graph.addNode("B");
graph.addLink("A", "B");

</script>
</html>

Every time I add a new node, it re-labels all of the existing nodes; these pile on top of each other and things start to get ugly. I understand why this is: because when I call the update() function function upon adding a new node, it does a node.append(...) to the entire data set. I can't figure out how to do this for only the node I'm adding… and I can only apparently use node.enter() to create a single new element, so that doesn't work for the additional elements I need bound to the node. How can I fix this?

Thank you for any guidance that you're able to give on any of this issue!

Edited because I quickly fixed a source of several other bugs that were previously mentioned

Best Answer

After many long hours of being unable to get this working, I finally stumbled across a demo that I don't think is linked any of the documentation: http://bl.ocks.org/1095795:

enter image description here

This demo contained the keys which finally helped me crack the problem.

Adding multiple objects on an enter() can be done by assigning the enter() to a variable, and then appending to that. This makes sense. The second critical part is that the node and link arrays must be based on the force() -- otherwise the graph and model will go out of synch as nodes are deleted and added.

This is because if a new array is constructed instead, it will lack the following attributes:

index - the zero-based index of the node within the nodes array.

x - the x-coordinate of the current node position.

y - the y-coordinate of the current node position.

px - the x-coordinate of the previous node position.

py - the y-coordinate of the previous node position.

fixed - a boolean indicating whether node position is locked.

weight - the node weight; the number of associated links.

These attributes are not strictly needed for the call to force.nodes(), but if these are not present, then they would be randomly initialised by force.start() on the first call.

If anybody is curious, the working code looks like this:

<script type="text/javascript">

function myGraph(el) {

    // Add and remove elements on the graph object
    this.addNode = function (id) {
        nodes.push({"id":id});
        update();
    }

    this.removeNode = function (id) {
        var i = 0;
        var n = findNode(id);
        while (i < links.length) {
            if ((links[i]['source'] === n)||(links[i]['target'] == n)) links.splice(i,1);
            else i++;
        }
        var index = findNodeIndex(id);
        if(index !== undefined) {
            nodes.splice(index, 1);
            update();
        }
    }

    this.addLink = function (sourceId, targetId) {
        var sourceNode = findNode(sourceId);
        var targetNode = findNode(targetId);

        if((sourceNode !== undefined) && (targetNode !== undefined)) {
            links.push({"source": sourceNode, "target": targetNode});
            update();
        }
    }

    var findNode = function (id) {
        for (var i=0; i < nodes.length; i++) {
            if (nodes[i].id === id)
                return nodes[i]
        };
    }

    var findNodeIndex = function (id) {
        for (var i=0; i < nodes.length; i++) {
            if (nodes[i].id === id)
                return i
        };
    }

    // set up the D3 visualisation in the specified element
    var w = $(el).innerWidth(),
        h = $(el).innerHeight();

    var vis = this.vis = d3.select(el).append("svg:svg")
        .attr("width", w)
        .attr("height", h);

    var force = d3.layout.force()
        .gravity(.05)
        .distance(100)
        .charge(-100)
        .size([w, h]);

    var nodes = force.nodes(),
        links = force.links();

    var update = function () {

        var link = vis.selectAll("line.link")
            .data(links, function(d) { return d.source.id + "-" + d.target.id; });

        link.enter().insert("line")
            .attr("class", "link");

        link.exit().remove();

        var node = vis.selectAll("g.node")
            .data(nodes, function(d) { return d.id;});

        var nodeEnter = node.enter().append("g")
            .attr("class", "node")
            .call(force.drag);

        nodeEnter.append("image")
            .attr("class", "circle")
            .attr("xlink:href", "https://d3nwyuy0nl342s.cloudfront.net/images/icons/public.png")
            .attr("x", "-8px")
            .attr("y", "-8px")
            .attr("width", "16px")
            .attr("height", "16px");

        nodeEnter.append("text")
            .attr("class", "nodetext")
            .attr("dx", 12)
            .attr("dy", ".35em")
            .text(function(d) {return d.id});

        node.exit().remove();

        force.on("tick", function() {
          link.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; });

          node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
        });

        // Restart the force layout.
        force.start();
    }

    // Make it all go
    update();
}

graph = new myGraph("#graph");

// You can do this from the console as much as you like...
graph.addNode("Cause");
graph.addNode("Effect");
graph.addLink("Cause", "Effect");
graph.addNode("A");
graph.addNode("B");
graph.addLink("A", "B");

</script>

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Javascript – the ‘new’ keyword in JavaScript

It does 5 things:

It creates a new object. The type of this object is simply object.
It sets this new object's internal, inaccessible, [[prototype]] (i.e. __proto__) property to be the constructor function's external, accessible, prototype object (every function object automatically has a prototype property).
It makes the this variable point to the newly created object.
It executes the constructor function, using the newly created object whenever this is mentioned.
It returns the newly created object, unless the constructor function returns a non-null object reference. In this case, that object reference is returned instead.

Note: constructor function refers to the function after the new keyword, as in

new ConstructorFunction(arg1, arg2)

Once this is done, if an undefined property of the new object is requested, the script will check the object's [[prototype]] object for the property instead. This is how you can get something similar to traditional class inheritance in JavaScript.

The most difficult part about this is point number 2. Every object (including functions) has this internal property called [[prototype]]. It can only be set at object creation time, either with new, with Object.create, or based on the literal (functions default to Function.prototype, numbers to Number.prototype, etc.). It can only be read with Object.getPrototypeOf(someObject). There is no other way to set or read this value.

Functions, in addition to the hidden [[prototype]] property, also have a property called prototype, and it is this that you can access, and modify, to provide inherited properties and methods for the objects you make.

Here is an example:

ObjMaker = function() {this.a = 'first';};
// ObjMaker is just a function, there's nothing special about it that makes 
// it a constructor.

ObjMaker.prototype.b = 'second';
// like all functions, ObjMaker has an accessible prototype property that 
// we can alter. I just added a property called 'b' to it. Like 
// all objects, ObjMaker also has an inaccessible [[prototype]] property
// that we can't do anything with

obj1 = new ObjMaker();
// 3 things just happened.
// A new, empty object was created called obj1.  At first obj1 was the same
// as {}. The [[prototype]] property of obj1 was then set to the current
// object value of the ObjMaker.prototype (if ObjMaker.prototype is later
// assigned a new object value, obj1's [[prototype]] will not change, but you
// can alter the properties of ObjMaker.prototype to add to both the
// prototype and [[prototype]]). The ObjMaker function was executed, with
// obj1 in place of this... so obj1.a was set to 'first'.

obj1.a;
// returns 'first'
obj1.b;
// obj1 doesn't have a property called 'b', so JavaScript checks 
// its [[prototype]]. Its [[prototype]] is the same as ObjMaker.prototype
// ObjMaker.prototype has a property called 'b' with value 'second'
// returns 'second'

It's like class inheritance because now, any objects you make using new ObjMaker() will also appear to have inherited the 'b' property.

If you want something like a subclass, then you do this:

SubObjMaker = function () {};
SubObjMaker.prototype = new ObjMaker(); // note: this pattern is deprecated!
// Because we used 'new', the [[prototype]] property of SubObjMaker.prototype
// is now set to the object value of ObjMaker.prototype.
// The modern way to do this is with Object.create(), which was added in ECMAScript 5:
// SubObjMaker.prototype = Object.create(ObjMaker.prototype);

SubObjMaker.prototype.c = 'third';  
obj2 = new SubObjMaker();
// [[prototype]] property of obj2 is now set to SubObjMaker.prototype
// Remember that the [[prototype]] property of SubObjMaker.prototype
// is ObjMaker.prototype. So now obj2 has a prototype chain!
// obj2 ---> SubObjMaker.prototype ---> ObjMaker.prototype

obj2.c;
// returns 'third', from SubObjMaker.prototype

obj2.b;
// returns 'second', from ObjMaker.prototype

obj2.a;
// returns 'first', from SubObjMaker.prototype, because SubObjMaker.prototype 
// was created with the ObjMaker function, which assigned a for us

I read a ton of rubbish on this subject before finally finding this page, where this is explained very well with nice diagrams.

Javascript – Open a URL in a new tab (and not a new window)

This is a trick,

function openInNewTab(url) {
 window.open(url, '_blank').focus();
}

//or just
window.open(url, '_blank').focus();

In most cases, this should happen directly in the onclick handler for the link to prevent pop-up blockers, and the default "new window" behavior. You could do it this way, or by adding an event listener to your DOM object.

<div onclick="openInNewTab('www.test.com');">Something To Click On</div>

http://www.tutsplanet.com/open-url-new-tab-using-javascript/

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