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d3js continuous node color network - not able to figure out the problem [duplicate]

This question already has answers here:
Code within d3.json() callback is not executed
(2 answers)
Closed 4 years ago.
I am not able to figure out what I am doing wrong in the following html code. I have a JSON file with a "cohesive" attribute which is a continuous variable. I want to draw a force directed graph on D3JS using the JSON file with the node color reflecting the difference in cohesive energy. When I run this script, I don't get any errors but there is no output as well. I just started with HTML scripting so please forgive me if I am making a very silly error but I would really appreciate if someone could point out what I am doing wrong.
function convertRange(value, r1, r2) {
return (value - r1[0]) * (r2[1] - r2[0]) / (r1[1] - r1[0]) + r2[0];
}
var svg = d3.select("svg"),
width = +svg.attr("width"),
height = +svg.attr("height");
var colorScale = d3.scaleLinear(d3.interpolateViridis);
var simulation = d3.forceSimulation()
.force("link", d3.forceLink().id(function(d) {
return d.id;
}))
.force("charge", d3.forceManyBody())
.force("center", d3.forceCenter(width / 2, height / 2));
d3.json("Perovskite_info.json", function(error, graph) {
if (error) throw error;
var link = svg.append("g")
.attr("class", "links")
.selectAll("line")
.data(graph.links)
.enter().append("line")
.attr("stroke-width", function(d) {
return Math.sqrt(d.value);
});
var node = svg.append("g")
.attr("nodes")
.selectAll("circle")
.data(graph.nodes)
.enter().append("circle")
.attr("r", 5)
.attr("fill", function(d) {
return colorScale(convertRange(d.cohesive_en, [1.6, 7.2], [0, 1]));
})
.call(d3.drag()
.on("start", dragstarted)
.on("drag", dragged)
.on("end", dragended));
node.append("title")
.text(function(d) {
return d.id;
});
simulation
.nodes(graph.nodes)
.on("tick", ticked);
simulation.force("link")
.links(graph.links);
function ticked() {
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;
});
}
});
function dragstarted(d) {
if (!d3.event.active) simulation.alphaTarget(0.3).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;
}
.links line {
stroke: #999;
stroke-opacity: 0.6;
}
.nodes circle {
stroke: black;
stroke-width: 1.5px;
}
<script src="https://d3js.org/d3.v5.min.js"></script>
<h1>Cohesive Energy Calculation</h1>
<svg width="1060" height="800"></svg>
This is how one my json begins:
{"directed": false, "multigraph": false, "graph": {}, "nodes": [{"pos": [-37.50340668168362, -0.6442713601030169], "cohesive_en": 5.752120797750001, "cohesive": 5.752120797750001, "cluster": 1, "similarity": 0.6371195466189876, "id": "PrCoO3"},
For the full JSON please follow this link: https://api.myjson.com/bins/m3gd8
Edit: So I figured out what the problems were:
First off, as one of the answers stated, I was using d3.v5 but using the d3v4 api to import data. Secondly, I also needed to import the d3 interpolate module which I hadn't done. So the code wasn't working. This question was asked at a point where I had done d3 for 2 days so the quality of the code is low.

you use a D3v4 API of loading a file.
D3v5 use the Fetch API
// d3.json("Perovskite_info.json", function(error, graph) {
d3.json("Perovskite_info.json").then( function(graph) {
//if (error) throw error;
Then there is a problem in how you add the nodes compared to the links but you will find that.
Why do the colorScale Math yourself in convertRange?
There is no color yet but that is a different problem.

force-directed d3.js add edge labels

I want to visualize a graph in d3js with the force-directed layout. I have been following this question, but I don't get it to work.
I created an jsfiddle, which can be found here.
However, now the lines are not working, but the labels are how they should be. Oddly, when I execute it locally it is working but someday lines are shown twice, like this:
<g class="link-g">
<line class="link" x1="297.0210832552382" y1="122.48446414068198" x2="245.8066880510027" y2="240.1061616356794"></line>
<text>interaction</text>
<text x="271.4138856531205" y="181.2953128881807">interaction</text>
</g>
Anyway, what I do is the following. First the link and linktext.
var link = svg.selectAll(".link")
.data(links, function(d) {
return d.source.id + '-' + d.target.id;
});
link.enter()
.append("g")
.attr("class","link-g")
.append("line")
.attr("class", "link");
link.exit().remove();
var linktext = svg.selectAll(".link-g")
.append("text")
.text("label");
Then in the 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;
});
What am I doing wrong? Thanks.

You add attributes x1, x2, y1, y2 on the svg:g element instead of the line, that's why there is no visible links.
If you check the code : svg:g elements have good values, and line got no attribute.
Create a new variable to store your links, and add attributes on this variable:
var linkLine = link.enter()
.append("g")
.attr("class","link-g")
.append("line")
.attr("class", "link");
And update tick function
function tick(){
linkLine.attr("x1", function(d) {
return d.source.x;
})
/* ... (others attr) ... */
}

D3 Multiple Force Directed Graphs

I can't multiple D3 force directed graphs to appear on one page, as they all pile into the same svg for whatever reason. I am out of ideas, and I have tried the top ideas online, which generally center around making sure you have a unique div to place each in, which I do.
I have divs with ids occurrences5, occurrences5...etc. So the loop should correctly find each div. The names of the JSON files are the same as the ids for each div.
var color = d3.scale.category20();
var occurences = ["occurrences3", "occurrences5", "occurrences10","occurrences20"];
for (var i = 0; i < occurences.length; i++) {
var occurence = occurences[i];
var svg = d3.select("#" + occurence).append("svg")
.attr("width", width)
.attr("height", height)
.attr("id", "#" + occurence + "svg");
d3.json(occurence + ".json", function(error, graph) {
if (error) throw error;
var force = d3.layout.force()
.charge(-120)
.linkDistance(30)
.size([width, height]);
force
.nodes(graph.nodes)
.links(graph.links)
.start();
var link = svg.selectAll(".link")
.data(graph.links)
.enter().append("line")
.attr("class", "link")
.style("stroke-width", function(d) { return Math.sqrt(d.value); });
var node = svg.selectAll(".node")
.data(graph.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; });
});
});
}})

You need to set svg within the callback function(error, graph) you pass to d3.json and not outside it
Reason: the callback function you pass to d3.json is called asynchronously i.e. it won't run nicely once per iteration as you're looping through the occurrences array. It appears all 4 callbacks are returning after that loop has finished and thus svg is set to the last value it had in that loop, thus everything's getting added to that svg element.

If I separate the creation of each chart into their own function() blocks, it works. I got my answer from: D3 Dimple - How to show multiple dimple charts on same page?
However, you can separate into a function like so:
var occurences = ["occurrences3", "occurrences5", "occurrences10","occurrences20"];
occurences.forEach(function(entry) {
draw(entry);
});
function draw(occurence) {...

Create radial network diagram with non-hierarchical data in D3.js

I am trying to create a diagram similar to this one in D3.js:
http://mbostock.github.io/d3/talk/20111116/bundle.html
This example uses hierarchical edge bundling. However, my data is not hierarchical in nature and I want to represent a relatively simple network structure. I have a bunch of nodes divided into groups, and connected through a simple connectivity matrix. I am able to generate a force-directed network diagram in D3.js similar to this:
http://bl.ocks.org/mbostock/4062045
var width = 500,
height = 500;
var color = d3.scale.category20();
var force = d3.layout.force()
.charge(-120)
.linkDistance(30)
.size([width, height]);
var svg = d3.select("body").append("svg")
.attr("width", width)
.attr("height", height);
var graph = getData();
force
.nodes(graph.nodes)
.links(graph.links)
.start();
var link = svg.selectAll(".link")
.data(graph.links)
.enter()
.append("line")
.attr("class", "link")
.style("stroke-width", function(d) { return Math.sqrt(d.value); });
var node = svg.selectAll(".node")
.data(graph.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; });
});
function getData() {
return {
"nodes":[
{"name":"Myriel","group":1},
{"name":"Napoleon","group":1},
{"name":"Mlle.Baptistine","group":1},
{"name":"Mme.Magloire","group":1},
{"name":"CountessdeLo","group":1},
{"name":"Geborand","group":1},
{"name":"Champtercier","group":1},
{"name":"Cravatte","group":1},
{"name":"Count","group":1},
{"name":"OldMan","group":1},
{"name":"Labarre","group":2},
{"name":"Valjean","group":2},
{"name":"Marguerite","group":3},
{"name":"Mme.deR","group":2},
{"name":"Isabeau","group":2},
{"name":"Gervais","group":2},
{"name":"Tholomyes","group":3},
{"name":"Listolier","group":3},
{"name":"Fameuil","group":3},
{"name":"Blacheville","group":3},
{"name":"Favourite","group":3},
{"name":"Dahlia","group":3},
{"name":"Zephine","group":3},
{"name":"Fantine","group":3},
{"name":"Mme.Thenardier","group":4},
{"name":"Thenardier","group":4},
{"name":"Cosette","group":5},
{"name":"Javert","group":4},
{"name":"Fauchelevent","group":0},
{"name":"Bamatabois","group":2},
{"name":"Perpetue","group":3},
{"name":"Simplice","group":2},
{"name":"Scaufflaire","group":2},
{"name":"Woman1","group":2},
{"name":"Judge","group":2},
{"name":"Champmathieu","group":2},
{"name":"Brevet","group":2},
{"name":"Chenildieu","group":2},
{"name":"Cochepaille","group":2},
{"name":"Pontmercy","group":4},
{"name":"Boulatruelle","group":6},
{"name":"Eponine","group":4},
{"name":"Anzelma","group":4},
{"name":"Woman2","group":5},
{"name":"MotherInnocent","group":0},
{"name":"Gribier","group":0},
{"name":"Jondrette","group":7},
{"name":"Mme.Burgon","group":7},
{"name":"Gavroche","group":8},
{"name":"Gillenormand","group":5},
{"name":"Magnon","group":5},
{"name":"Mlle.Gillenormand","group":5},
{"name":"Mme.Pontmercy","group":5},
{"name":"Mlle.Vaubois","group":5},
{"name":"Lt.Gillenormand","group":5},
{"name":"Marius","group":8},
{"name":"BaronessT","group":5},
{"name":"Mabeuf","group":8},
{"name":"Enjolras","group":8},
{"name":"Combeferre","group":8},
{"name":"Prouvaire","group":8},
{"name":"Feuilly","group":8},
{"name":"Courfeyrac","group":8},
{"name":"Bahorel","group":8},
{"name":"Bossuet","group":8},
{"name":"Joly","group":8},
{"name":"Grantaire","group":8},
{"name":"MotherPlutarch","group":9},
{"name":"Gueulemer","group":4},
{"name":"Babet","group":4},
{"name":"Claquesous","group":4},
{"name":"Montparnasse","group":4},
{"name":"Toussaint","group":5},
{"name":"Child1","group":10},
{"name":"Child2","group":10},
{"name":"Brujon","group":4},
{"name":"Mme.Hucheloup","group":8}
],
"links":[
{"source":1,"target":0,"value":1},
{"source":2,"target":0,"value":8},
{"source":3,"target":0,"value":10},
{"source":3,"target":2,"value":6},
{"source":4,"target":0,"value":1},
{"source":5,"target":0,"value":1},
{"source":6,"target":0,"value":1},
{"source":7,"target":0,"value":1},
{"source":8,"target":0,"value":2},
{"source":9,"target":0,"value":1},
{"source":11,"target":10,"value":1},
{"source":11,"target":3,"value":3},
{"source":11,"target":2,"value":3},
{"source":11,"target":0,"value":5},
{"source":12,"target":11,"value":1},
{"source":13,"target":11,"value":1},
{"source":14,"target":11,"value":1},
{"source":15,"target":11,"value":1},
{"source":17,"target":16,"value":4},
{"source":18,"target":16,"value":4},
{"source":18,"target":17,"value":4},
{"source":19,"target":16,"value":4},
{"source":19,"target":17,"value":4},
{"source":19,"target":18,"value":4},
{"source":20,"target":16,"value":3},
{"source":20,"target":17,"value":3},
{"source":20,"target":18,"value":3},
{"source":20,"target":19,"value":4},
{"source":21,"target":16,"value":3},
{"source":21,"target":17,"value":3},
{"source":21,"target":18,"value":3},
{"source":21,"target":19,"value":3},
{"source":21,"target":20,"value":5},
{"source":22,"target":16,"value":3},
{"source":22,"target":17,"value":3},
{"source":22,"target":18,"value":3},
{"source":22,"target":19,"value":3},
{"source":22,"target":20,"value":4},
{"source":22,"target":21,"value":4},
{"source":23,"target":16,"value":3},
{"source":23,"target":17,"value":3},
{"source":23,"target":18,"value":3},
{"source":23,"target":19,"value":3},
{"source":23,"target":20,"value":4},
{"source":23,"target":21,"value":4},
{"source":23,"target":22,"value":4},
{"source":23,"target":12,"value":2},
{"source":23,"target":11,"value":9},
{"source":24,"target":23,"value":2},
{"source":24,"target":11,"value":7},
{"source":25,"target":24,"value":13},
{"source":25,"target":23,"value":1},
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{"source":27,"target":23,"value":5},
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{"source":27,"target":24,"value":1},
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{"source":29,"target":11,"value":2},
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{"source":72,"target":26,"value":2},
{"source":72,"target":27,"value":1},
{"source":72,"target":11,"value":1},
{"source":73,"target":48,"value":2},
{"source":74,"target":48,"value":2},
{"source":74,"target":73,"value":3},
{"source":75,"target":69,"value":3},
{"source":75,"target":68,"value":3},
{"source":75,"target":25,"value":3},
{"source":75,"target":48,"value":1},
{"source":75,"target":41,"value":1},
{"source":75,"target":70,"value":1},
{"source":75,"target":71,"value":1},
{"source":76,"target":64,"value":1},
{"source":76,"target":65,"value":1},
{"source":76,"target":66,"value":1},
{"source":76,"target":63,"value":1},
{"source":76,"target":62,"value":1},
{"source":76,"target":48,"value":1},
{"source":76,"target":58,"value":1}
]
}
}
.node {
stroke: #fff;
stroke-width: 1.5px;
}
.link {
stroke: #999;
stroke-opacity: .6;
}
<script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.4.11/d3.min.js"></script>
However, I can't figure out how to generate the radial graph above when the structure is not hierarchical. In the example given here
https://gist.github.com/mbostock/7607999
they use the bundle() and cluster.nodes() functions which require a hierarchical data structure. Can I use the same json data structure that I use for the force-directed graph for this type of radial graph? If yes, how?
EDIT: Here is a (non-working) JSFiddle http://jsfiddle.net/12sb8jxg/
I added
nested = d3.nest()
.key(function (d) {
return d.group;
})
.entries(graph.nodes);
but
cluster.nodes(nested)
still doesn't append the .x, .y, .parent etc. necessary for the bundle function to work.

d3.js force-directed issues, significance of "d"?

I'm having a bit of trouble getting a something to work with D3.js. Namely, I'm trying to make a tree of nodes, using the basic code from http://bl.ocks.org/mbostock/1021953.
I switched it to load the data inline, as opposed to loading from file, because I'm using it with a Rails application and don't want to have repetitive information. I switched the line so that you could see the format of my data.
Anyways, here's the bulk of my code:
<%= javascript_tag do %>
var nodes = [{"title":"Duncan's Death","id":"265"},{"title":"Nature Thrown Off","id":"266"},{"title":"Cows Dead","id":"267"},{"title":"Weather Bad","id":"268"},{"title":"Lighting kills man","id":"269"},{"title":"Macbeth's Rise","id":"270"}];
var links = [{"source":"265","target":"266","weight":"1"},{"source":"266","target":"267","weight":"1"},{"source":"266","target":"268","weight":"1"},{"source":"268","target":"269","weight":"1"}];
var firstelement = +links[0].source;
links.forEach(function(l) {
l.source = +l.source;
l.source = l.source-firstelement;
l.target = +l.target
l.target = l.target-firstelement;
});
var width = 960,
height = 500;
var color = d3.scale.category20();
var force = d3.layout.force()
.charge(-1000)
.linkDistance(300)
.size([width, height]);
var svg = d3.select("body").append("svg")
.attr("width", width)
.attr("height", height);
force
.nodes(nodes)
.links(links)
.start();
var link = svg.selectAll(".link")
.data(links)
.enter().append("line")
.attr("class", "link")
.style("stroke-width", function(d) { return Math.sqrt(d.weight); });
var node = svg.selectAll(".node")
.data(nodes)
.enter().append("g")
.attr("class", "node")
.call(force.drag);
node.append("circle")
.attr("class", "circle_node")
.attr("r", 50)
.style("fill", function(d) { return color(d.id); })
node.append("title")
.text(function(d) { return d.title; });
node.append("text")
.attr("x", function(d) { return d.x; } )
.attr("y", function(d) { return d.y; })
.text(function(d) { return d.title; });
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("x", function(a) { return a.x; })
.attr("y", function(a) { return a.y; });
});
<% end %>
This seems like it should work to me, but I can seem to manage it. The links work, but the nodes all remain in the top left corner. I've tried just entering the circles directly and appending the text to them (staying close to the source code I listed above,) but while the circles behave properly, it doesn't display the text. I'd like the title to be centered in the nodes.
More generally, I'm kind of confused by how this is working. What does "d" refer to within lines like
function(d) { return d.source.x; }
It seems to be declaring a function and calling it simultaneously. I know that it doesn't have to be specifically the character "d," (for instance, switching the "d" to an "a" seems to make no difference as long as it's done both in the declaration and within the function.) But what is it referring to? The data entered into the object that's being modified? For instance, if I wanted to print that out, (outside of the attribute,) how would I do it?
Sorry, I'm new to D3 (and fairly new to JavaScript in general,) so I have a feeling the answer is obvious, but I've been looking it up and through tutorials and I'm still lost. Thanks in advance.

First, there's a simple problem with your code that is causing all your nodes to stay in the top left corner. You are trying to position each node using the code:
node.attr("x", function(a) { return a.x; })
.attr("y", function(a) { return a.y; });
However, node is a selection of gs which do not take x and y attributes. Instead, you can move each node using translate transform, e.g.
node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
Making this change should allow the nodes to move around.
Next, moving to your question about "d", I think the first thing you need to understand is what you can do with a selection of elements in D3. From the docs: a selection (such as nodes) "is an array of elements pulled from the current document." Once you have a selection of elements, you can apply operators to change the attributes or style of the elements. You can also bind data to each element.
In your case, you are binding data to a selection of gs (nodes):
var node = svg.selectAll(".node")
.data(nodes)
.enter().append("g")
You are then using attr to change the position of each node. However, instead of setting the x and y attributes of each element to the same value, you are passing attr an anonymous function that will return a (presumably different) position for each node:
node.attr("x", function(a) { return a.x; })
.attr("y", function(a) { return a.y; });
This behavior is also explained in the docs for attr:
Attribute values and such are specified as either constants or
functions; the latter are evaluated for each element.
Thus, d represents an individual element (Object) in nodes.
So going back to your code, on each tick two things are happening:
The position of each node (data) is being recalculated by force.
Each corresponding element is then being moved to its new location by the anonymous function you pass to force.on.