Develop Reference

(d3.js) How to combine dynamic force directed graph with collapsible force directed graph?

I'm trying to combine two different force directed graphs.
One is dynamic force directed graph (code from here) where I can set the thickness of the lines between nodes (and the data is defined inline); the other is collapsible force directed graph (code from a SO answer here, that uses non-tree data) where I can click the nodes to hide the children (and the data is defined from a JSON file).
I thought this should be clear enough, but I keep having problems. The JS console said that the propertyforce is undefined even though I have set its variable.
Here is the Plunker: http://plnkr.co/edit/MtOB9PGnXlNwlNj6P5NY?p=preview
And here is the collapsible graph part (full code is in Plunker)
// Combined script //
var root,
force = d3.layout.force()
.size([width, height])
.on("tick", tick);
var link = svg.selectAll(".link"),
node = svg.selectAll(".node");
d3.json("data.json", function(json) {
root = json;
//Give nodes ids and initialize variables
for(var i=0; i<root.nodes.length; i++) {
var node = root.nodes[i];
node.id = i;
node.collapsing = 0;
node.collapsed = false;
}
//Give links ids and initialize variables
for(var i=0; i<root.links.length; i++) {
var link = root.links[i];
link.source = root.nodes[link.source];
link.target = root.nodes[link.target];
link.id = i;
}
update();
});
function update() {
//Keep only the visible nodes
var nodes = root.nodes.filter(function(d) {
return d.collapsing == 0;
});
var links = root.links;
//Keep only the visible links
links = root.links.filter(function(d) {
return d.source.collapsing == 0 && d.target.collapsing == 0;
});
force
.nodes(nodes)
.links(links)
.start();
// Update the links…
link = link.data(links, function(d) { return d.id; });
// Exit any old links.
link.exit().remove();
// Enter any new links.
link.enter().insert("line", ".node")
.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; })
.attr("marker-end", "url(#arrow)");
// Update the nodes…
node = node.data(nodes, function(d){ return d.id; }).style("fill", color);
// Exit any old nodes.
node.exit().remove();
// Enter any new nodes.
node.enter().append("circle")
.attr("class", "node")
.attr("cx", function(d) { return d.x; })
.attr("cy", function(d) { return d.y; })
.attr("r", function(d) { return Math.sqrt(d.size) / 10 || 4.5; })
.style("fill", color)
.on("click", click)
.call(force.drag);
}
function tick() {
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("cx", function(d) { return d.x; })
.attr("cy", function(d) { return d.y; });
}
// Toggle children on click.
function click(d) {
if (!d3.event.defaultPrevented) {
//check if link is from this node, and if so, collapse
root.links.forEach(function(l) {
if(l.source.id == d.id) {
if(d.collapsed){
l.target.collapsing--;
} else {
l.target.collapsing++;
}
}
});
d.collapsed = !d.collapsed;
}
update();
}
// Combined end //
Without combining the two codes, it's working fine, as shown in this fiddle: https://jsfiddle.net/Lrrepn0c/
Any ideas?

D3js force duplicate nodes on enter()

I am having some issues with d3js and I can't figure out what is going on. The idea is to draw initial graph from some endpoint data (first img), that's fine works well. Each node is clickable, on click ajax call is made for that node and data is returned, based on some criteria at that point nodes.push(xx), links.push(xx) happens to add new nodes and restart() is called to draw new nodes and links. The issue is that the main graph is doing the correct thing (Not showed on screenshots as I had to put fake data on the first graph i.e. calling an endpoint /record/id/first doesn't return a data) but there are bunch of random nodes showing up in the right bottom corner.
You can also see on the example below, even if the data doesn't change after clicking on first/second/third something wrong goes with node.enter() after restart() with the same data passed in...
JS FIDDLE: http://jsfiddle.net/5754j86e/
var w = 1200,
h = 1200;
var nodes = [];
var links = [];
var node;
var link;
var texts;
var ids = [];
var circleWidth = 10;
var initialIdentifier = "marcin";
nodes = initialBuildNodes(initialIdentifier, sparql);
links = initialBuildLinks(sparql);
//Add SVG
var svg = d3.select('#chart').append('svg')
.attr('width', w)
.attr('height', h);
var linkGroup = svg.append("svg:g").attr("id", "link-group");
var nodeGroup = svg.append("svg:g").attr("id", "node-group");
var textGroup = svg.append("svg:g").attr("id", "text-group");
//Add Force Layout
var force = d3.layout.force()
.size([w, h])
.gravity(.05)
.charge(-1040);
force.linkDistance(120);
restart();
function restart() {
force.links(links)
console.log("LINKS ARE: ", links)
link = linkGroup.selectAll(".link").data (links);
link.enter().append('line')
.attr("class", "link");
link.exit().remove();
force.nodes(nodes)
console.log("NODES ARE: ", nodes)
node = nodeGroup.selectAll(".node").data (nodes);
node.enter().append("svg:g")
.attr("class", "node")
.call(force.drag);
node.append('circle')
.attr('cx', function(d) { return d.x; })
.attr('cy', function(d) { return d.y; })
.attr('r', circleWidth )
.attr('fill', function(d, i) {
if (i>0) { return palette.pink }
else { return palette.blue }
})
.on("click", function(d) {
nodeClicked (d);
})
.on('mouseenter', function(d){
nodeMouseEnter(d)
})
.on('mouseout', function(d){
nodeMouseOut(d)
});
node.exit().remove();
var annotation = textGroup.selectAll(".annotation").data (nodes);
annotation.enter().append("svg:g")
.attr("class", "annotation")
.append("text")
.attr("x", function(d) { return d.radius + 4 })
.attr("y", ".31em")
.attr("class", "label")
.text(function(d) { return d.name; });
annotation.exit().remove();
force.start();
}
function nodeClicked (d) {
// AJAX CALL happens here and bunch of nodes.push({name: "new name"}) happen
}
force.on('tick', function(e) {
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, i) {
return 'translate('+ d.x +', '+ d.y +')';
})
svg.selectAll(".annotation").attr("transform", function(d) {
var labelx = d.x + 13;
return "translate(" + labelx + "," + d.y + ")";
})
});

Okay I got it, based on the docs (https://github.com/mbostock/d3/wiki/Selections#enter):
var update_sel = svg.selectAll("circle").data(data)
update_sel.attr(/* operate on old elements only */)
update_sel.enter().append("circle").attr(/* operate on new elements only */)
update_sel.attr(/* operate on old and new elements */)
update_sel.exit().remove() /* complete the enter-update-exit pattern */
From my code you can see I do enter() and then once again I add circle on node in a separate statement.
node = nodeGroup.selectAll(".node").data (nodes);
node.enter().append("svg:g")
.attr("class", "node")
.call(force.drag);
node.append('circle')
.attr('cx', function(d) { return d.x; })
.attr('cy', function(d) { return d.y; })
.attr('r', circleWidth )
.attr('fill', function(d, i) {
if (i>0) { return palette.pink }
else { return palette.blue }
});
Adding circle should be within the scope of enter() otherwise it happens to all nodes not only the new nodes therefore it should be :
node.enter().append("svg:g")
.attr("class", "node")
.call(force.drag)
.append('circle')
.attr('cx', function(d) { return d.x; })
.attr('cy', function(d) { return d.y; })
.attr('r', circleWidth )
.attr('fill', function(d, i) {
if (i>0) { return palette.pink }
else { return palette.blue }
});

D3.js - unable to add lines to a static network

I'm not an expert in d3 (as many of you know) however I am attempting to modify a working force network so that the nodes are fixed. So far I have been able to get the nodes to work but haven't been able to get the lines between them to work.
I've created a fiddle at http://jsfiddle.net/PatriciaW/Dnnve/
Any help will be very welcome.
var width = 960,
height = 700,
n = 100;
var categoryColour = {
"community group": "red",
"volunteer": "blue",
"organization": "green",
"air": "transparent"
};
var json2 = {"nodes":[{"node":{"name":"TCAN","x2":1,"y2":2,"description":"A network of organizations in Toronto devoted to climate change mitigation and adaptation.","category":"organization","size":3,"URL":"http:\/\/localhost:8888\/mydrupal\/groups\/tcan"}},{"node":{"name":"Rita ","x2":5,"y2":3,"description":"Rita is devoted to mitigating climate change and participates in many organizations.","category":"volunteer","size":2,"URL":"http:\/\/localhost:8888\/mydrupal\/groups\/rita"}},{"node":{"name":"Green 13","x2":5,"y2":4,"description":"Green 13","category":"community group","size":2,"URL":"http:\/\/localhost:8888\/mydrupal\/groups\/green-13"}},{"node":{"name":"ZCO","x2":3,"y2":1,"description":"Zero Carbon Ontario","category":"organization","size":2,"URL":"http:\/\/localhost:8888\/mydrupal\/groups\/zco"}},{"node":{"name":"Resilient Toronto","x2":3,"y2":5,"description":"","category":"organization","size":3,"URL":"http:\/\/localhost:8888\/mydrupal\/groups\/resilient-toronto"}},{"node":{"name":"City of Toronto","x2":3,"y2":3,"description":"","category":"organization","size":5,"URL":"http:\/\/localhost:8888\/mydrupal\/groups\/city-toronto"}}]};
var nodes=json2.nodes.map(function(json2) {
return json2.node;
});
var i = 0;
while (i < nodes.length) {
nodes[i].fixed=true;
nodes[i].x = (nodes[i].x2)*100;
nodes[i].y = (nodes[i].y2)*100;
i = i+ 1;
}
var json = {"connections":[{"connection":{"source":"Rita","target":"Resilient Toronto"}},{"connection":{"source":"TCAN","target":"Resilient Toronto"}},{"connection":{"source":"Resilient Toronto","target":"City of Toronto"}},{"connection":{"source":"Rita","target":"ZCO"}},{"connection":{"source":"Rita","target":"Green 13"}},{"connection":{"source":"Green 13","target":"TCAN"}},{"connection":{"source":"ZCO","target":"TCAN"}}]};
var links=json.connections.map(function(json) {
return json.connection;
});
var force = d3.layout.force()
.nodes(nodes)
.links(links)
.size([width, height])
.linkDistance(60)
.charge(-300)
.on("tick", tick)
.start();
svg = d3.select("#network")
.append("svg")
.attr("width", width)
.attr("height", height);
var link = svg.selectAll(".link")
.data(force.links())
.enter().append("line")
.attr("class", "link");
var node = svg.selectAll(".node")
.data(force.nodes())
.enter().append("g")
.attr("class", "node")
.call(force.drag);
node.append("circle") // this is OK if use nodes or links below but defaults to links
.attr("r", 8)
.style("fill", function(nodes) {
return categoryColour [nodes.category];
})
node.append("text") // OK
.attr("x", 12)
.attr("dy", ".35em")
.text(function(d) {
return d.name; });
function tick() {
link
.attr("x1", function(d) {
// console.log("d"); console.log(d); has source and target but not .x and y values?
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 + ")";
});
};
// Use a timeout to allow the rest of the page to load first.
setTimeout(function() {
force.tick();
console.log("timeout nodes "); console.log(nodes); //
svg.selectAll("line")
.data(links)
.enter().append("line")
.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; });
svg.selectAll("circle")
.data(nodes)
.enter().append("circle")
.attr("cx", function(d) { return d.x; })
.attr("cy", function(d) { return d.y; })
.attr("r", 4.5);
}, 10);

I'm not an expert either but I think you are having issues because the source and target values in your connections should be referencing the respective positional array index for the node (not the name of the node).
A simple example, in your fiddle just change the first connection from...
{"connection":{"source":"Rita","target":"Resilient Toronto"}}
to...
{"connection":{"source":1,"target":4}}
1 and 4 being the index of the elements in the nodes array. Hope this is what you are looking for.

I updated the jsfiddle with the working code. Needs improvement but demonstrates the principle.

D3 Collapsible Force Layout Mixing up Children and Parents

I'm working on the example located on jsfiddle, here.
It appears that I have everything structured properly, as the children are properly associated with their parents and the proper text is displayed.
The problems I've run into are as follows...
The main node (in the center) is not collapsible. The overall behavior of the graph is somewhat glitchy when compared to the example located here.
Colors do not change when nodes are collapsed, children of the parent node are displayed when the parent is collapsed. After several clicks on various nodes, children and parents seem to get switched.
My question is what section of code could be causing this and why?
Here's the code that I'm using to generate the chart. Data is missing, but is provided by the jsfiddle. Any help is appreciated, thanks in advance.
var width = 960,
height = 500,
root;
var force = d3.layout.force()
.charge(-220)
.size([width, height])
.on("tick", tick);
var svg = d3.select("body").append("svg")
.attr("width", width)
.attr("height", height);
var link = svg.selectAll(".link");
function update() {
var nodes = flatten(root);
var links = d3.layout.tree().links(nodes);
console.log(nodes);
// Restart the force layout.
force.nodes(nodes)
.links(links)
.linkDistance(55)
.start();
var link = svg.selectAll(".link")
.data(links, function(d) { return d.target.id; });
link.enter().append("line")
.attr("class", "link");
link.exit().remove();
var node = svg.selectAll("g.node")
.data(nodes)
var groups = node.enter().append("g")
.attr("class", "node")
.attr("id", function (d) {
return d.id
})
.on('click', click)
.call(force.drag);
groups.append("circle")
.attr("class","node")
.attr("x", -8)
.attr("y",-8)
.attr("r", function(d) { return d.children ? 4.5 : 10 })
.style("fill", color)
.on("click", click)
.call(force.drag);
groups.append("text")
.attr("dx", 12)
.attr("dy", "0.35em")
.style("font-size", "10px")
.style("color", "#000000")
.style("font-family", "Arial")
.text(function (d) {
console.log(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 + ")";
});
});
}
function tick() {
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 + ")";
});
}
// Color leaf nodes orange, and packages white or blue.
function color(d) {
return d._children ? "#3182bd" // collapsed package
: d.children ? "#c6dbef" // expanded package
: "#fd8d3c"; // leaf node
}
// Toggle children on click.
function click(d) {
if (!d3.event.defaultPrevented) {
if (d.children) {
d._children = d.children;
d.children = null;
} else {
d.children = d._children;
d._children = null;
}
update();
}
}
// Returns a list of all nodes under the root.
function flatten(root) {
var nodes = [], i = 0;
function recurse(node) {
if (node.children) node.children.forEach(recurse);
if (!node.id) node.id = ++i;
nodes.push(node);
}
recurse(root);
return nodes;
}

Ok, there are two things going on here.
First, by default, d3 uses the index of each datum as its ID (to determine when the item enters/exits the selection). This is your issue with parent/children moving around, when the element at index X is replaced by a new element, d3 thinks they are the same. You need to provide a function to return the id:
var node = svg.selectAll("g.node")
.data(nodes, function(d) { return d.id; });
Second, you're only setting the fill color of the circle when an item enters the selection. You should extract the bit that is assigning the style out of the enter() block, so it will be executed each time you call update().
node.selectAll('circle').style('fill', color);
I copied and hacked together your fiddle into plunker, because jsFiddle was running really slow for me:
http://plnkr.co/edit/7AJlQub6uCGQ3VSvq4pa?p=preview

Setting up D3 force directed graph

To the esteemed readers. I'm reasonably new in javascript and I have come across this problem. I'm trying to implement a modified version of this force directed graph:
http://mbostock.github.com/d3/ex/force.html
The json data is generated on the fly from a php script. The idea is to color all lines connecting to one specific node ( defined in a php script) in one color and all the others in shades of gray. I'm attempting to do it by matching the source variable in the json file to the variable from the php script and changing color when that is true like this:
var link = svg.selectAll("line.link")
.data(json.links)
.enter().append("line")
.attr("class", "link")
.style("stroke-width", function(d) { return Math.sqrt(d.value);})
.style("stroke-opacity", function(d) { return d.value/10;})
.style("stroke", function(d) {
x = (tested == d.source) ? return '#1f77b4' : '#707070';// <-- Attempt to change the color of the link when this is true.
})
however this does not work. The script works fine but without the color change if I just do this
var link = svg.selectAll("line.link")
.data(json.links)
.enter().append("line")
.attr("class", "link")
.style("stroke-width", function(d) { return Math.sqrt(d.value);})
.style("stroke-opacity", function(d) { return d.value/10;})
.style("stroke", function(d) {
return '#707070';
})
I've been staring at this for days trying to figure out to get this done and I'm stuck. Any help would be greatly appreciated!!
Here is my complete script
<script type="text/javascript">
var width = 1200,
height = 1200;
var color = d3.scale.category20();
var tested=<?php echo $tested_source;?>; //<-- the variable from php
var svg = d3.select("#chart").append("svg")
.attr("width", width)
.attr("height", height);
d3.json("data.json", function(json) {
var force = d3.layout.force()
.charge(-130)
.linkDistance(function(d) { return 500-(50*d.value);})
.size([width, height]);
force
.nodes(json.nodes)
.links(json.links)
.start();
var link = svg.selectAll("line.link")
.data(json.links)
.enter().append("line")
.attr("class", "link")
.style("stroke-width", function(d) { return Math.sqrt(d.value);})
.style("stroke-opacity", function(d) { return d.value/10;})
.style("stroke", function(d) {
x = (tested == d.source) ? return '#1f77b4' : '#707070'; //<-- Attempt to change the color of the link when this is true. But is is not working... :(
})
var node = svg.selectAll("circle.node")
.data(json.nodes)
.enter().append("circle")
.attr("class", "node")
.attr("r", 12)
.style("fill", function(d) { return color(d.group); })
.call(force.drag);
node.append("title")
.text(function(d) { return d.name; });
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("cx", function(d) { return d.x; })
.attr("cy", function(d) { return d.y; });
});
});
</script>

d.source is an object, you can't use == to determine if tested is a similar object. Have a look at this answer for more details on object equality.
If you want to test for a specific value of the d.source object described below, which I assume you want, you need to specify it.
Here is the source object architecture : (I'm using the example you pointed so the data comes from the miserables.json)
source: Object
group: 4
index: 75
name: "Brujon"
px: 865.6440689638284
py: 751.3426708796574
weight: 7
x: 865.9584580575608
y: 751.2658636251376
Now, here is the broken part in your code :
x = (tested == d.source) ? return '#1f77b4' : '#707070';// <-- Attempt to change the color of the link when this is true.
It doesn't work because the return is misplaced.
You're mixing ternary and return statements but you don't put them in the right order :
return test ? value_if_true : value_if_false;
if you want to assign the value to x anyway, you can do
x = test ? value_if_true : value_if_false;
return x;
You should do something like this :
return (tested == d.source) ? '#1f77b4' : '#707070';// <-- Attempt to change the color of the link when this is true.
That's for the general syntax, but this won't work as is You need to pick one of the value for your test for example :
return (tested === d.source.name) ? '#1f77b4' : '#707070';
Also, if the variable from PHP is a string you should do
var tested="<?php echo $tested_source;?>"; //<-- the variable from php
and in most cases you should use json_encode to map PHP variables into javascript ones.
As a final note, I would recommend using console functions coupled with Firebug's console panel if you're using Firefox, or the Chrome Developer Tool's console panel if you're using a Chromium based browser. It would allow you to debug your code more easily.
Working code
var width = 960,
height = 500;
var color = d3.scale.category20();
var force = d3.layout.force().charge(-120).linkDistance(30).size([width, height]);
var svg = d3.select("#chart").append("svg").attr("width", width).attr("height", height);
var tested = 20;
d3.json("miserables.json", function (json) {
force.nodes(json.nodes).links(json.links).start();
var link = svg.selectAll("line.link")
.data(json.links)
.enter()
.append("line")
.attr("class", "link")
.style("stroke-width", function (d) {
return Math.sqrt(d.value);
}).style("stroke-opacity", function (d) {
return d.value / 10;
}).style("stroke", function (d) {
return (tested == d.source.index) ? '#ee3322' : '#707070'; //'#1f77b4'
});
var node = svg.selectAll("circle.node")
.data(json.nodes)
.enter()
.append("circle")
.attr("class", "node")
.attr("r", 5)
.style("fill", function (d) {
return color(d.group);
}).call(force.drag);
node.append("title").text(function (d) {
return d.name;
});
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("cx", function (d) {
return d.x;
}).attr("cy", function (d) {
return d.y;
});
});
});