I would like to draw a simple graph with d3.js like this one
I failed to find out the graph layout in both in v5 API documentation and on the Internet.
All examples use d3.force layout from d3-force. Although it looks impressive, I am not looking for a graph layout with physicall simulation.
Is there a simpler layout or is the best way to use d3.force layout with switched off physics ?
There isn't any need to use the d3.forceSimulation, that ultimately is just one of the many D3 layouts that are on offer. If you look at Mike Bostocks example Force Directed Graph then the modifications you need are as follows:
Define a set of nodes - basically an array of things to represent the circles
Append the svg:circle elements to the DOM using .data(nodes)
Defined a set of links
Append the svg:line elements to the DOM using .data(links)
This is essentially using D3 for it's pure DOM data binding, and not using a pre-built layout.
You can copy any of the force example really - all it's doing underneath is setting an x and a y position underneath. If you've already got those, just position your circles at those points.
All the parts to do with simulation and the ticked event you can remove from the example.
Here is an example providing a static layout:
var svg = d3.select("svg"),
width = +svg.attr("width"),
height = +svg.attr("height");
var color = d3.scaleOrdinal(d3.schemeCategory20);
const layout = (graph) => {
return new Promise((resolve) => {
var simulation = d3
.forceSimulation()
.alphaMin(0.3)
.force("link", d3.forceLink().id(function(d) {
return d.id;
}))
.force("charge", d3.forceManyBody())
.force("center", d3.forceCenter(width / 2, height / 2))
.on("end", resolve(graph));
simulation.nodes(graph.nodes);
simulation.force("link").links(graph.links);
});
};
const render = (graph) => {
var link = d3.select("#target").append("g")
.attr("class", "links")
.selectAll("line")
.data(graph.links)
.enter().append("line")
.attr("stroke-width", function(d) { return Math.sqrt(d.value); })
.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 node = d3.select("#target").append("g")
.attr("class", "nodes")
.selectAll("circle")
.data(graph.nodes)
.enter().append("circle")
.attr("r", 5)
.attr("cx", function(d) { return d.x; })
.attr("cy", function(d) { return d.y; })
.attr("fill", function(d) { return color(d.group); });
}
d3.json("https://gist.githubusercontent.com/mbostock/4062045/raw/5916d145c8c048a6e3086915a6be464467391c62/miserables.json", function(error, graph) {
if (error) throw error;
layout(graph)
.then((graph) => render(graph));
});
.links line {
stroke: #999;
stroke-opacity: 0.6;
}
.nodes circle {
stroke: #fff;
stroke-width: 1.5px;
}
<script src="https://d3js.org/d3.v4.min.js"></script>
<svg width="960" height="600">
<g id="target" transform="translate(480, 300)">
</g>
</svg>
EDIT
To change the distance between the nodes you need to change some of the forces in play. The docs are really good - specifically what you want to change is https://github.com/d3/d3-force#many-body
So modify the charge force to read:
.force("charge", d3.forceManyBody().strength(-charge))
You'll need to define the charge, and tweak it a little until the force gives you a good layout.
How to apply force repulsion on map's labels so they find their right places automatically ?
Bostock' "Let's Make a Map"
Mike Bostock's Let's Make a Map (screenshot below). By default, labels are put at the point's coordinates and polygons/multipolygons's path.centroid(d) + a simple left or right align, so they frequently enter in conflict.
Handmade label placements
One improvement I met requires to add an human made IF fixes, and to add as many as needed, such :
.attr("dy", function(d){ if(d.properties.name==="Berlin") {return ".9em"} })
The whole become increasingly dirty as the number of labels to reajust increase :
//places's labels: point objects
svg.selectAll(".place-label")
.data(topojson.object(de, de.objects.places).geometries)
.enter().append("text")
.attr("class", "place-label")
.attr("transform", function(d) { return "translate(" + projection(d.coordinates) + ")"; })
.attr("dy", ".35em")
.text(function(d) { if (d.properties.name!=="Berlin"&&d.properties.name!=="Bremen"){return d.properties.name;} })
.attr("x", function(d) { return d.coordinates[0] > -1 ? 6 : -6; })
.style("text-anchor", function(d) { return d.coordinates[0] > -1 ? "start" : "end"; });
//districts's labels: polygons objects.
svg.selectAll(".subunit-label")
.data(topojson.object(de, de.objects.subunits).geometries)
.enter().append("text")
.attr("class", function(d) { return "subunit-label " + d.properties.name; })
.attr("transform", function(d) { return "translate(" + path.centroid(d) + ")"; })
.attr("dy", function(d){
//handmade IF
if( d.properties.name==="Sachsen"||d.properties.name==="Thüringen"|| d.properties.name==="Sachsen-Anhalt"||d.properties.name==="Rheinland-Pfalz")
{return ".9em"}
else if(d.properties.name==="Brandenburg"||d.properties.name==="Hamburg")
{return "1.5em"}
else if(d.properties.name==="Berlin"||d.properties.name==="Bremen")
{return "-1em"}else{return ".35em"}}
)
.text(function(d) { return d.properties.name; });
Need for better solution
That's just not manageable for larger maps and sets of labels. How to add force repulsions to these both classes: .place-label and .subunit-label?
This issue is quite a brain storming as I haven't deadline on this, but I'am quite curious about it. I was thinking about this question as a basic D3js implementation of Migurski/Dymo.py. Dymo.py's README.md documentation set a large set of objectives, from which to select the core needs and functions (20% of the work, 80% of the result).
Initial placement: Bostock give a good start with left/right positionning relative to the geopoint.
Inter-labels repulsion: different approach are possible, Lars & Navarrc proposed one each,
Labels annihilation: A label annihilation function when one label's overall repulsion is too intense, since squeezed between other labels, with the priority of annihilation being either random or based on a population data value, which we can get via NaturalEarth's .shp file.
[Luxury] Label-to-dots repulsion: with fixed dots and mobile labels. But this is rather a luxury.
I ignore if label repulsion will work across layers and classes of labels. But getting countries labels and cities labels not overlapping may be a luxury as well.
In my opinion, the force layout is unsuitable for the purpose of placing labels on a map. The reason is simple -- labels should be as close as possible to the places they label, but the force layout has nothing to enforce this. Indeed, as far as the simulation is concerned, there is no harm in mixing up labels, which is clearly not desirable for a map.
There could be something implemented on top of the force layout that has the places themselves as fixed nodes and attractive forces between the place and its label, while the forces between labels would be repulsive. This would likely require a modified force layout implementation (or several force layouts at the same time), so I'm not going to go down that route.
My solution relies simply on collision detection: for each pair of labels, check if they overlap. If this is the case, move them out of the way, where the direction and magnitude of the movement is derived from the overlap. This way, only labels that actually overlap are moved at all, and labels only move a little bit. This process is iterated until no movement occurs.
The code is somewhat convoluted because checking for overlap is quite messy. I won't post the entire code here, it can be found in this demo (note that I've made the labels much larger to exaggerate the effect). The key bits look like this:
function arrangeLabels() {
var move = 1;
while(move > 0) {
move = 0;
svg.selectAll(".place-label")
.each(function() {
var that = this,
a = this.getBoundingClientRect();
svg.selectAll(".place-label")
.each(function() {
if(this != that) {
var b = this.getBoundingClientRect();
if(overlap) {
// determine amount of movement, move labels
}
}
});
});
}
}
The whole thing is far from perfect -- note that some labels are quite far away from the place they label, but the method is universal and should at least avoid overlap of labels.
One option is to use the force layout with multiple foci. Each foci must be located in the feature's centroid, set up the label to be attracted only by the corresponding foci. This way, each label will tend to be near of the feature's centroid, but the repulsion with other labels may avoid the overlapping issue.
For comparison:
M. Bostock's "Lets Make a Map" tutorial (resulting map),
my gist for an Automatic Labels Placement version (resulting map) implementing the foci's strategy.
The relevant code:
// Place and label location
var foci = [],
labels = [];
// Store the projected coordinates of the places for the foci and the labels
places.features.forEach(function(d, i) {
var c = projection(d.geometry.coordinates);
foci.push({x: c[0], y: c[1]});
labels.push({x: c[0], y: c[1], label: d.properties.name})
});
// Create the force layout with a slightly weak charge
var force = d3.layout.force()
.nodes(labels)
.charge(-20)
.gravity(0)
.size([width, height]);
// Append the place labels, setting their initial positions to
// the feature's centroid
var placeLabels = svg.selectAll('.place-label')
.data(labels)
.enter()
.append('text')
.attr('class', 'place-label')
.attr('x', function(d) { return d.x; })
.attr('y', function(d) { return d.y; })
.attr('text-anchor', 'middle')
.text(function(d) { return d.label; });
force.on("tick", function(e) {
var k = .1 * e.alpha;
labels.forEach(function(o, j) {
// The change in the position is proportional to the distance
// between the label and the corresponding place (foci)
o.y += (foci[j].y - o.y) * k;
o.x += (foci[j].x - o.x) * k;
});
// Update the position of the text element
svg.selectAll("text.place-label")
.attr("x", function(d) { return d.x; })
.attr("y", function(d) { return d.y; });
});
force.start();
While ShareMap-dymo.js may work, it does not appear to be very well documented. I have found a library that works for the more general case, is well documented and also uses simulated annealing: D3-Labeler
I've put together a usage sample with this jsfiddle.The D3-Labeler sample page uses 1,000 iterations. I have found this is rather unnecessary and that 50 iterations seems to work quite well - this is very fast even for a few hundred data points. I believe there is room for improvement both in the way this library integrates with D3 and in terms of efficiency, but I wouldn't have been able to get this far on my own. I'll update this thread should I find the time to submit a PR.
Here is the relevant code (see the D3-Labeler link for further documentation):
var label_array = [];
var anchor_array = [];
//Create circles
svg.selectAll("circle")
.data(dataset)
.enter()
.append("circle")
.attr("id", function(d){
var text = getRandomStr();
var id = "point-" + text;
var point = { x: xScale(d[0]), y: yScale(d[1]) }
var onFocus = function(){
d3.select("#" + id)
.attr("stroke", "blue")
.attr("stroke-width", "2");
};
var onFocusLost = function(){
d3.select("#" + id)
.attr("stroke", "none")
.attr("stroke-width", "0");
};
label_array.push({x: point.x, y: point.y, name: text, width: 0.0, height: 0.0, onFocus: onFocus, onFocusLost: onFocusLost});
anchor_array.push({x: point.x, y: point.y, r: rScale(d[1])});
return id;
})
.attr("fill", "green")
.attr("cx", function(d) {
return xScale(d[0]);
})
.attr("cy", function(d) {
return yScale(d[1]);
})
.attr("r", function(d) {
return rScale(d[1]);
});
//Create labels
var labels = svg.selectAll("text")
.data(label_array)
.enter()
.append("text")
.attr("class", "label")
.text(function(d) {
return d.name;
})
.attr("x", function(d) {
return d.x;
})
.attr("y", function(d) {
return d.y;
})
.attr("font-family", "sans-serif")
.attr("font-size", "11px")
.attr("fill", "black")
.on("mouseover", function(d){
d3.select(this).attr("fill","blue");
d.onFocus();
})
.on("mouseout", function(d){
d3.select(this).attr("fill","black");
d.onFocusLost();
});
var links = svg.selectAll(".link")
.data(label_array)
.enter()
.append("line")
.attr("class", "link")
.attr("x1", function(d) { return (d.x); })
.attr("y1", function(d) { return (d.y); })
.attr("x2", function(d) { return (d.x); })
.attr("y2", function(d) { return (d.y); })
.attr("stroke-width", 0.6)
.attr("stroke", "gray");
var index = 0;
labels.each(function() {
label_array[index].width = this.getBBox().width;
label_array[index].height = this.getBBox().height;
index += 1;
});
d3.labeler()
.label(label_array)
.anchor(anchor_array)
.width(w)
.height(h)
.start(50);
labels
.transition()
.duration(800)
.attr("x", function(d) { return (d.x); })
.attr("y", function(d) { return (d.y); });
links
.transition()
.duration(800)
.attr("x2",function(d) { return (d.x); })
.attr("y2",function(d) { return (d.y); });
For a more in depth look at how D3-Labeler works, see "A D3 plug-in for automatic label placement using simulated
annealing"
Jeff Heaton's "Artificial Intelligence for Humans, Volume 1" also does an excellent job at explaining the simulated annealing process.
You might be interested in the d3fc-label-layout component (for D3v5) that is designed exactly for this purpose. The component provides a mechanism for arranging child components based on their rectangular bounding boxes. You can apply either a greedy or simulated annealing strategy in order to minimise overlaps.
Here's a code snippet which demonstrates how to apply this layout component to Mike Bostock's map example:
const labelPadding = 2;
// the component used to render each label
const textLabel = layoutTextLabel()
.padding(labelPadding)
.value(d => d.properties.name);
// a strategy that combines simulated annealing with removal
// of overlapping labels
const strategy = layoutRemoveOverlaps(layoutGreedy());
// create the layout that positions the labels
const labels = layoutLabel(strategy)
.size((d, i, g) => {
// measure the label and add the required padding
const textSize = g[i].getElementsByTagName('text')[0].getBBox();
return [textSize.width + labelPadding * 2, textSize.height + labelPadding * 2];
})
.position(d => projection(d.geometry.coordinates))
.component(textLabel);
// render!
svg.datum(places.features)
.call(labels);
And this is a small screenshot of the result:
You can see a complete example here:
http://bl.ocks.org/ColinEberhardt/389c76c6a544af9f0cab
Disclosure: As discussed in the comment below, I am a core contributor of this project, so clearly I am somewhat biased. Full credit to the other answers to this question which gave us inspiration!
For 2D case
here are some examples that do something very similar:
one http://bl.ocks.org/1691430
two http://bl.ocks.org/1377729
thanks Alexander Skaburskis who brought this up here
For 1D case
For those who search a solution to a similar problem in 1-D i can share my sandbox JSfiddle where i try to solve it. It's far from perfect but it kind of doing the thing.
Left: The sandbox model, Right: an example usage
Here is the code snippet which you can run by pressing the button in the end of the post, and also the code itself. When running, click on the field to position the fixed nodes.
var width = 700,
height = 500;
var mouse = [0,0];
var force = d3.layout.force()
.size([width*2, height])
.gravity(0.05)
.chargeDistance(30)
.friction(0.2)
.charge(function(d){return d.fixed?0:-1000})
.linkDistance(5)
.on("tick", tick);
var drag = force.drag()
.on("dragstart", dragstart);
var svg = d3.select("body").append("svg")
.attr("width", width)
.attr("height", height)
.on("click", function(){
mouse = d3.mouse(d3.select(this).node()).map(function(d) {
return parseInt(d);
});
graph.links.forEach(function(d,i){
var rn = Math.random()*200 - 100;
d.source.fixed = true;
d.source.px = mouse[0];
d.source.py = mouse[1] + rn;
d.target.y = mouse[1] + rn;
})
force.resume();
d3.selectAll("circle").classed("fixed", function(d){ return d.fixed});
});
var link = svg.selectAll(".link"),
node = svg.selectAll(".node");
var graph = {
"nodes": [
{"x": 469, "y": 410},
{"x": 493, "y": 364},
{"x": 442, "y": 365},
{"x": 467, "y": 314},
{"x": 477, "y": 248},
{"x": 425, "y": 207},
{"x": 402, "y": 155},
{"x": 369, "y": 196},
{"x": 350, "y": 148},
{"x": 539, "y": 222},
{"x": 594, "y": 235},
{"x": 582, "y": 185}
],
"links": [
{"source": 0, "target": 1},
{"source": 2, "target": 3},
{"source": 4, "target": 5},
{"source": 6, "target": 7},
{"source": 8, "target": 9},
{"source": 10, "target": 11}
]
}
function tick() {
graph.nodes.forEach(function (d) {
if(d.fixed) return;
if(d.x<mouse[0]) d.x = mouse[0]
if(d.x>mouse[0]+50) d.x--
})
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 dblclick(d) {
d3.select(this).classed("fixed", d.fixed = false);
}
function dragstart(d) {
d3.select(this).classed("fixed", d.fixed = true);
}
force
.nodes(graph.nodes)
.links(graph.links)
.start();
link = link.data(graph.links)
.enter().append("line")
.attr("class", "link");
node = node.data(graph.nodes)
.enter().append("circle")
.attr("class", "node")
.attr("r", 10)
.on("dblclick", dblclick)
.call(drag);
.link {
stroke: #ccc;
stroke-width: 1.5px;
}
.node {
cursor: move;
fill: #ccc;
stroke: #000;
stroke-width: 1.5px;
opacity: 0.5;
}
.node.fixed {
fill: #f00;
}
<script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.4.11/d3.min.js"></script>
<body></body>
Summary
Using the example below I've created a database driven tree view with blocks of information instead of the circle nodes.
Interactive d3.js tree diagram
Please see the example screenshot below:
The idea is for the lines to start from where the block ends. I assume it's something to do with the following function:
// Custom projection
var linkProjection = d3.svg.diagonal()
.source(function (d) {
return { "y": d.source.y, "x": d.source.x };
})
.target(function (d) {
return { "y": d.target.y, "x": d.target.x };
})
.projection(function (d) {
return [d.y, d.x];
});
// Enter any new links at the parent's previous position.
link.enter().insert("path", "g")
.attr("class", "link")
.style("fill", "none")
.style("stroke", "#d1d6da")
.style("stroke-width", "1")
.attr("d", function (d) {
var s = { x: source.x0, y: source.y0 };
var t = { x: source.x0, y: source.y0 };
return linkProjection({ source: s, target: t });
});
I have tried adding the block width to the y coordinate but although it starts from the correct position with the drawing it ends at the start of the block again.
Any suggestions?
Without more code it's hard to say, but I think it has to do with the coordinate system. x,y point to the center of the object I think. So you'll have to translate y to the the right by half the length of your box.
i.e. The parents previous position (x,y) points to the center of the parent.
Given a datum containing multiple data elements, such as an object or array, is it possible to set multiple attributes on a selection with a single value function?
E.g. something like:
var data = [{ 'x': 10, 'y': 20, 'r': 5 }];
d3.select('body').append('svg').selectAll('circle')
.data(data)
.enter().append('circle')
.attr('cx cy r', function (d) {
return [d.x, d.y, d.r];
});
instead of:
var data = [{ 'x': 10, 'y': 20, 'r': 5 }];
d3.select('body').append('svg').selectAll('circle')
.data(data)
.enter().append('circle')
.attr('cx', function (d) {
return d.x;
});
.attr('cy', function (d) {
return d.y;
});
.attr('r', function (d) {
return d.r;
});
UPDATE (July 8th 2016) This answer applies to d3 v3.x — NOT v4.x. For the latter version, see Tim Hayes's answer, also on this page. Or... just swap attr with attrs in my answer below, and don't forget to require/import/script-embed d3-selection-multi. And... don't miss the bit about using .each, which may be useful to you.
Yeah, it's possible by passing in a hash (like jQuery's css() method):
d3.select('body').append('svg').selectAll('circle')
.data(data)
.enter().append('circle')
.attr({
cx: function (d) { return d.x; },
cy: function (d) { return d.y; },
r: function (d) { return d.r; }
});
This works for style() as well.
If the reoccurring function (d) {} start to feel like too much, this is another approach:
d3.select('body').append('svg').selectAll('circle')
.data(data)
.enter().append('circle')
.each(function (d) {
d3.select(this).attr({
cx: d.x,
cy: d.y,
r: d.r
});
})
NOTE: this feature only exists in d3.js v2.10.0 or higher
This is an old post, but I found it while Googling around for an answer. The accepted answer no longer works in D3 v4.0.
Moving forward, you can do the same by using the attrs() method. But attrs() is only supported if you load the optional d3-selection-multi script.
So using the example above, it would look like this in D3 v4.0:
// load d3-selection-multi as separate script
<script src="https://d3js.org/d3-selection-multi.v0.4.min.js"></script>
d3.select('body').append('svg').selectAll('circle')
.data(data)
.enter().append('circle')
.attrs({
cx: function (d) { return d.x; },
cy: function (d) { return d.y; },
r: function (d) { return d.r; }
});
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.