vasturiano/three-forcegraph

Force-directed graph as a ThreeJS 3d object

ThreeJS Force-Directed Graph

A ThreeJS WebGL class to represent a graph data structure in a 3-dimensional space using a force-directed iterative layout. Uses either d3-force-3d or ngraph for the underlying physics engine.

See also the standalone version.

Quick start

import ThreeForceGraph from 'three-forcegraph';

or using a script tag

<script src="//unpkg.com/three-forcegraph"></script>

then

const myGraph = new ThreeForceGraph()
  .graphData(myData);

const myScene = new THREE.Scene();
myScene.add(myGraph);

...

// on animation frame
myGraph.tickFrame();

API reference

Method	Description	Default
graphData([data])	Getter/setter for graph data structure (see below for syntax details). Can also be used to apply incremental updates.	{ nodes: [], links: [] }
jsonUrl([url])	URL of JSON file to load graph data directly from, as an alternative to specifying graphData directly.
numDimensions([int])	Getter/setter for number of dimensions to run the force simulation on (1, 2 or 3).	3
dagMode([str])	Apply layout constraints based on the graph directionality. Only works correctly for DAG graph structures (without cycles). Choice between td (top-down), bu (bottom-up), lr (left-to-right), rl (right-to-left), zout (near-to-far), zin (far-to-near), radialout (outwards-radially) or radialin (inwards-radially).
dagLevelDistance([num])	If dagMode is engaged, this specifies the distance between the different graph depths.	auto-derived from the number of nodes
dagNodeFilter([fn])	Node accessor function to specify nodes to ignore during the DAG layout processing. This accessor method receives a node object and should return a boolean value indicating whether the node is to be included. Excluded nodes will be left unconstrained and free to move in any direction.	node => true
onDagError([fn])	Callback to invoke if a cycle is encountered while processing the data structure for a DAG layout. The loop segment of the graph is included for information, as an array of node ids. By default an exception will be thrown whenever a loop is encountered. You can override this method to handle this case externally and allow the graph to continue the DAG processing. Strict graph directionality is not guaranteed if a loop is encountered and the result is a best effort to establish a hierarchy.	throws exception
nodeRelSize([num])	Getter/setter for the ratio of node sphere volume (cubic px) per value unit.	4
nodeId([str])	Node object accessor attribute for unique node id (used in link objects source/target).	id
nodeVal([num, str or fn])	Node object accessor function, attribute or a numeric constant for the node numeric value (affects sphere volume).	val
nodeResolution([num])	Getter/setter for the geometric resolution of each node, expressed in how many slice segments to divide the circumference. Higher values yield smoother spheres.	8
nodeVisibility([boolean, str or fn])	Node object accessor function, attribute or a boolean constant for whether to display the node.	true
nodeColor([str or fn])	Node object accessor function or attribute for node color (affects sphere color).	color
nodeAutoColorBy([str or fn])	Node object accessor function (fn(node)) or attribute (e.g. 'type') to automatically group colors by. Only affects nodes without a color attribute.
nodeOpacity([num])	Getter/setter for all the nodes sphere opacity, between [0,1].	0.75
nodeThreeObject([Object3d, str or fn])	Node object accessor function or attribute for generating a custom 3d object to render as graph nodes. Should return an instance of ThreeJS Object3d. If a falsy value is returned, the default 3d object type will be used instead for that node.	default node object is a sphere, sized according to val and styled according to color.
nodeThreeObjectExtend([bool, str or fn])	Node object accessor function, attribute or a boolean value for whether to replace the default node when using a custom nodeThreeObject (false) or to extend it (true).	false
nodePositionUpdate([fn(nodeObject, coords, node)])	Getter/setter for the custom function to call for updating the position of nodes at every render iteration. It receives the respective node ThreeJS Object3d, the coordinates of the node ({x,y,z} each), and the node's data. If the function returns a truthy value, the regular position update function will not run for that node.
linkSource([str])	Link object accessor attribute referring to id of source node.	source
linkTarget([str])	Link object accessor attribute referring to id of target node.	target
linkVisibility([boolean, str or fn])	Link object accessor function, attribute or a boolean constant for whether to display the link line. A value of false maintains the link force without rendering it.	true
linkColor([str or fn])	Link object accessor function or attribute for line color.	color
linkAutoColorBy([str or fn])	Link object accessor function (fn(link)) or attribute (e.g. 'type') to automatically group colors by. Only affects links without a color attribute.
linkOpacity([num])	Getter/setter for line opacity of all the links, between [0,1].	0.2
linkWidth([num, str or fn])	Link object accessor function, attribute or a numeric constant for the link line width. A value of zero will render a ThreeJS Line whose width is constant (1px) regardless of distance. Values are rounded to the nearest decimal for indexing purposes.	0
linkResolution([num])	Getter/setter for the geometric resolution of each link, expressed in how many radial segments to divide the cylinder. Higher values yield smoother cylinders. Applicable only to links with positive width.	6
linkCurvature([num, str or fn])	Link object accessor function, attribute or a numeric constant for the curvature radius of the link line. Curved lines are represented as 3D bezier curves, and any numeric value is accepted. A value of 0 renders a straight line. 1 indicates a radius equal to half of the line length, causing the curve to approximate a semi-circle. For self-referencing links (source equal to target) the curve is represented as a loop around the node, with length proportional to the curvature value. Lines are curved clockwise for positive values, and counter-clockwise for negative values. Note that rendering curved lines is purely a visual effect and does not affect the behavior of the underlying forces.	0
linkCurveRotation([num, str or fn])	Link object accessor function, attribute or a numeric constant for the rotation along the line axis to apply to the curve. Has no effect on straight lines. At 0 rotation, the curve is oriented in the direction of the intersection with the XY plane. The rotation angle (in radians) will rotate the curved line clockwise around the "start-to-end" axis from this reference orientation.	0
linkMaterial([Material, str or fn])	Link object accessor function or attribute for specifying a custom material to style the graph links with. Should return an instance of ThreeJS Material. If a falsy value is returned, the default material will be used instead for that link.	default link material is MeshLambertMaterial styled according to color and opacity.
linkThreeObject([Object3d, str or fn])	Link object accessor function or attribute for generating a custom 3d object to render as graph links. Should return an instance of ThreeJS Object3d. If a falsy value is returned, the default 3d object type will be used instead for that link.	default link object is a line or cylinder, sized according to width and styled according to material.
linkThreeObjectExtend([bool, str or fn])	Link object accessor function, attribute or a boolean value for whether to replace the default link when using a custom linkThreeObject (false) or to extend it (true).	false
linkPositionUpdate([fn(linkObject, { start, end }, link)])	Getter/setter for the custom function to call for updating the position of links at every render iteration. It receives the respective link ThreeJS Object3d, the start and end coordinates of the link ({x,y,z} each), and the link's data. If the function returns a truthy value, the regular position update function will not run for that link.
linkDirectionalArrowLength([num, str or fn])	Link object accessor function, attribute or a numeric constant for the length of the arrow head indicating the link directionality. The arrow is displayed directly over the link line, and points in the direction of source > target. A value of 0 hides the arrow.	0
linkDirectionalArrowColor([str or fn])	Link object accessor function or attribute for the color of the arrow head.	color
linkDirectionalArrowRelPos([num, str or fn])	Link object accessor function, attribute or a numeric constant for the longitudinal position of the arrow head along the link line, expressed as a ratio between 0 and 1, where 0 indicates immediately next to the source node, 1 next to the target node, and 0.5 right in the middle.	0.5
linkDirectionalArrowResolution([num])	Getter/setter for the geometric resolution of the arrow head, expressed in how many slice segments to divide the cone base circumference. Higher values yield smoother arrows.	8
linkDirectionalParticles([num, str or fn])	Link object accessor function, attribute or a numeric constant for the number of particles (small spheres) to display over the link line. The particles are distributed equi-spaced along the line, travel in the direction source > target, and can be used to indicate link directionality.	0
linkDirectionalParticleSpeed([num, str or fn])	Link object accessor function, attribute or a numeric constant for the directional particles speed, expressed as the ratio of the link length to travel per frame. Values above 0.5 are discouraged.	0.01
linkDirectionalParticleWidth([num, str or fn])	Link object accessor function, attribute or a numeric constant for the directional particles width. Values are rounded to the nearest decimal for indexing purposes.	0.5
linkDirectionalParticleColor([str or fn])	Link object accessor function or attribute for the directional particles color.	color
linkDirectionalParticleResolution([num])	Getter/setter for the geometric resolution of each directional particle, expressed in how many slice segments to divide the circumference. Higher values yield smoother particles.	4
emitParticle(link)	An alternative mechanism for generating particles, this method emits a non-cyclical single particle within a specific link. The emitted particle shares the styling (speed, width, color) of the regular particle props. A valid link object that is included in graphData should be passed as a single parameter.
getGraphBbox([nodeFilterFn])	Returns the current bounding box of the nodes in the graph, formatted as { x: [<num>, <num>], y: [<num>, <num>], z: [<num>, <num>] }. If no nodes are found, returns null. Accepts an optional argument to define a custom node filter: node => <boolean>, which should return a truthy value if the node is to be included. This can be useful to calculate the bounding box of a portion of the graph.
forceEngine([str])	Getter/setter for which force-simulation engine to use (d3 or ngraph).	d3
d3ReheatSimulation()	Reheats the force simulation engine, by setting the alpha value to 1. Only applicable if using the d3 simulation engine.
d3AlphaMin([num])	Getter/setter for the simulation alpha min parameter, only applicable if using the d3 simulation engine.	0
d3AlphaDecay([num])	Getter/setter for the simulation intensity decay parameter, only applicable if using the d3 simulation engine.	0.0228
d3AlphaTarget([num])	Getter/setter for the simulation alpha target parameter, only applicable if using the d3 simulation engine.	0
d3VelocityDecay([num])	Getter/setter for the nodes' velocity decay that simulates the medium resistance, only applicable if using the d3 simulation engine.	0.4
d3Force(str, [fn])	Getter/setter for the internal forces that control the d3 simulation engine. Follows the same interface as d3-force-3d's simulation.force. Three forces are included by default: 'link' (based on forceLink), 'charge' (based on forceManyBody) and 'center' (based on forceCenter). Each of these forces can be reconfigured, or new forces can be added to the system. This method is only applicable if using the d3 simulation engine.
ngraphPhysics([object])	Specify custom physics configuration for ngraph, according to its configuration object syntax. This method is only applicable if using the ngraph simulation engine.	ngraph default
warmupTicks([int])	Getter/setter for number of layout engine cycles to dry-run at ignition before starting to render.	0
cooldownTicks([int])	Getter/setter for how many build-in frames to render before stopping and freezing the layout engine.	Infinity
cooldownTime([num])	Getter/setter for how long (ms) to render for before stopping and freezing the layout engine.	15000
resetCountdown()	Resets the engine countdown timer to the initial value. Useful when you want to keep the engine ticking for a while after the last user interaction.
onEngineTick(fn)	Callback function invoked at every tick of the simulation engine.	-
onEngineStop(fn)	Callback function invoked when the simulation engine stops and the layout is frozen.	-
onLoading(fn)	Callback function for notification that data is being loaded asynchronously based on jsonUrl.	-
onFinishLoading(fn)	Callback function for notification that the component has finished loading data asynchronously.	-
onUpdate(fn)	Callback function for notification that the component has started updating and the simulation engine is temporarily paused.	-
onFinishUpdate(fn)	Callback function for notification that the component has finished updating, done iterating through the warmup phase (if needed) and the simulation engine has been resumed.	-
tickFrame()	This method should be called on each cycle of the global renderer to iterate the underlying force simulation engine and update the nodes/links objects' positions.
resetProps()	Reset all object properties to their default value.
refresh()	Redraws all the nodes/links.

Input JSON syntax

{
    "nodes": [
        {
            "id": "id1",
            "name": "name1",
            "val": 1
        },
        {
            "id": "id2",
            "name": "name2",
            "val": 10
        },
        ...
    ],
    "links": [
        {
            "source": "id1",
            "target": "id2"
        },
        ...
    ]
}

Giving Back

If this project has helped you and you'd like to contribute back, you can always buy me a ☕!

three-forcegraph's Issues

Cannot scale or move graph

Hi there, nice work on this graph visualization. I'm trying to get it to work with an existing THREE Scene containing other objects and a camera, but the graph is really large compared to my camera point-of-view (and I should not change the camera).

I would like to do something like this:

var myGraph = new ThreeForceGraph()
    .graphData(myData);

myGraph.scale.set(0.1, 0.1, 0.1);

var myScene = new THREE.Scene();
myScene.add(myGraph);

However, even setting the scale to 0.5 disconnects the links from the nodes, like this:

It gets worse with smaller scale or larger position.

The same happens if I try to set the position of the graph object.

I also tried wrapping it in another Object3D:

var wrapper = new Object3D();
wrapper.add(myGraph);
wrapper.scale.set(0.1, 0.1, 0.1);
myScene.add(wrapper);

but unfortunately this gives the same results.

Finally, I tried changing the node sizes, link sizes, link forces, etc etc, but I cannot manage to get the right results.

Is there a proper way to scale the graph as a whole, or is a current limitation?

Any help would be much appreciated!

Performance: draw all lines in a single buffer geometry

Is your feature request related to a problem? Please describe.
drawing graphs with many links has poor performance on constrained devices

Describe the solution you'd like
option to render all lines as part of a single buffer geometry

Describe alternatives you've considered
not drawing the lines at all 😿

Additional context
example of many line segments in a buffer geometry

each is 1500 line segments
https://github.com/mrdoob/three.js/blob/master/examples/webgl_lines_sphere.html#L112-L128

primary challenge seems to be the expectation of 1 link matches 1 three object

Issue with node color and opacity

First of all, I want to point out how valuable is the work that you have done.

Please, allow me a question (maybe it is a dummy one). My issue is that I cannot change the 'color' and 'opacity' attributes for the nodes. I read the API, and especially for the color attribute I have used all the possible variations.

Here is a snippet of my data.json.

 "nodes": [
                {
                    "id": "id1",
                    "name": "name1",
                    "node-color": '0xff0000',
                    "color": 'red', // another approach 0xff0000 // another ff0000 // I tried RGB as well
                    "opacity": 1, // same thing for opacity when I change the values between [0,1]
                    "val": 1
                }
],
"links": [
                {
                    "source": "id1",
                    "target": "id2",
                    "opacity": 1,
                    "color": "#ff0000"
                }
            ]

Same thing applies for links. All of them present with a 'default ' grey color.
I do not know, if I misread something or it is a bug.

Thanks in advance for your help.
Pan

Sudden displaying error...

All of the sudden, I am facing an error with imports

import ThreeForceGraph from 'three-forcegraph';

Could not find a declaration file for module 'three-forcegraph'. /node_modules/three-forcegraph/dist/three-forcegraph.common.js' implicitly has an 'any' type.
Try npm install @types/three-forcegraph if it exists or add a new declaration (.d.ts) file containing declare module 'three-forcegraph';

All my nodes are displayed in the center stacked on one after another (I have visual representation but not the correct one)

Has something changed with the library? Also when I used to click on ThreeForceGraph it redirected to the component. No, it does nothing.

I much appreciate your help.

turn off force engine

Hi vasturiano, great lib!!! I must say it.
I am just wondering how do you turn off force engine since my project already have it in the serverside.
My goal is basically render nodes and links that already have coordinates.
Can you tell me specifically which function is about switching force engine on and off?
Cheers.

Figured out by myself.

d3ForceLayout: d3ForceSimulation() .force('link',null) .force('charge', null) .force('center', null) .stop(),

addAttribute change to setAttribute in latest release (@1.29.2) throws error

Feel free to close it. I did not complete the issue template

ReferenceError: window is not defined

Describe the bug
I installed this library, latest version as of now (1.41.5), but getting ReferenceError: window is not defined error.

To Reproduce
Steps to reproduce the behavior:

1. Go to https://codesandbox.io/s/step-15-trackball-controls-fixed-xdrgv?from-embed=&file=/src/initializeScene.js
2. This tutorial was originally written by https://dev.to/pahund/adding-trackball-controls-to-a-three-js-scene-with-sprites-48hp
3. Use the same code example from codesandbox website example into the existing nextjs project.
4. Run the project
5. See error

Expected behavior
A mind map graph to be visible just like in the example

Screenshots

Desktop (please complete the following information):

• OS: Mac Ventura 13.3
• Browser: Chrome
• Version: 111.0.5563.146

Support passing request options to fetch() call in jsonUrl()

I found this issue while playing with 3d-force-graph. I was trying to load a JSON file with my own data, following the async-load example, and it was failing in my environment with the following error (URL redacted).

Cross-Origin Read Blocking (CORB) blocked cross-origin response https://identity.XXX.com/adfs/ls/IdpInitiatedSignon.aspx?RelayState=RPID%3Dhttps%253A%252F%252FXXXX.XXX.com%252Fopensso&goto=http%3A%2F%2FYYY.ZZZcom%2...%2Fdata%2Fgraph.json with MIME type text/html. See https://www.chromestatus.com/feature/5629709824032768 for more details.

It looks like our intranet redirects requests through a proxy for identity checking, thus the CORS error.

The following code, an adaptation from the example in https://developer.mozilla.org/en-US/docs/Web/API/Fetch_API/Using_Fetch, is able to retrieve the same JSON file without error.

  const getData = (url = ``, data = {}) => {
  // Default options are marked with *
    return fetch(url, {
        method: "GET", // *GET, POST, PUT, DELETE, etc.
        mode: "cors", // no-cors, cors, *same-origin
        cache: "no-cache", // *default, no-cache, reload, force-cache, only-if-cached
        credentials: "same-origin", // include, same-origin, *omit
        headers: {
            "Content-Type": "application/json; charset=utf-8",
            // "Content-Type": "application/x-www-form-urlencoded",
        },
        redirect: "follow", // manual, *follow, error
        referrer: "no-referrer", // no-referrer, *client
        //body: JSON.stringify(data), // body data type must match "Content-Type" header
    })
    .then(response => response.json()) // parses response to JSON
    .catch(error => console.error(`Fetch Error =\n`, error));
};

getData(`./data/graph.json`)
  .then(data => console.log(data)) // JSON from `response.json()` call
  .catch(error => console.error(error));

So exposing the second argument of the fetch() call through the jsonUrl wrapper would help in these let's-be-paranoid-and-check-our-own-files scenarios. I am afraid they might be common inside enterprise intranets.

Node radius is not properly calculated

I just realized that the radius of the node is calculated as the cube root of the volume, but it should be calculated as the cube root of (3 times the volume divided by 4 times pi) (Math.cbrt((3 * state.nodeRelSize) / (4 * Math.PI)))

Is this a mistake or is this intended?

No issue

First, I want to give you positive feedback. Your work is very valuable.
Please allow me a question. Is it possible to assign arrow heads to the links of a graph? If it is possible, could you post a small example. I have seen that the arrow helper is available, but frozen.
Best regards
Tom Schaefer

add gitignore

add gitignore

Add Full 2D Support

I am currently developing my own modifications of this for my project, but I think having full native support for setting numDimensions to 2 would be nice, considering I've found it to be more performant than using the regular 2D Force Graph, at least with my medium-large dataset. By 'full support', I mean disabling rotation, using an orthographic camera instead of a perspective one, making zoom relative to mouse position rather than the viewport center, and similar functionalities that make it act more like the 2D version of Force Graph while also using ThreeJS.

This is the app I am currently using Force Graph in. It has a 2D mode that uses the regular Force Graph, and a 3D mode that uses the 3D one. On my phone, 2D mode is so slow it's unusable, while 3D runs just fine. Both could be further optimized, but I believe there are definitely some advantages to the way the ThreeJS implementation is rendered that can make it more performant for larger datasets.

Interacting with nodes

Hi there again,

Is there any "easy way" to interact with the graph nodes like in this example?

https://github.com/vasturiano/3d-force-graph/blob/master/example/click-to-focus/index.html

Functions such as onNodeHover and onNodeClick are not included in this npm package

My goal is to have something like a hover text tooltip on each Mesh and later on an interaction when someone clicks on a node.

I found a work around for the onNodeHover by adding document.addEventListener("mousemove"), but I was wondering if there is more elegant solution from the API perspective.

Although I am able to retrieve the node (as 3D object presented as follows) when hovering, my actual data (__data field) presented as

uuid: "999D36DF-CB74-4860-9577-D414845BC8F3"
castShadow: false
...
.__data : { 
color: "#1f78b4",
description: "Quadtree 1"
group: 2
id: "id4"
index: 3
name :"name4" 
val:1}
...

inside the object and I cannot find a way to retrieve, let say the name for example.

Do you have any insights?

Thank you in advance for your help.

UPDATE:
object['__data'].name did the trick, but I just wondering if there is more elegant solution.

Example with drei (React-Three-Drei)?

Is your feature request related to a problem? Please describe.
Hi!! We were wondering, what the easiest way to add a 3d-force-graph inside a R3F Canvas to use it alongside react-three-drei and R3Fcomponents 🤩

Describe the solution you'd like
Something similar to this:

<Canvas style={{ position: "fixed" }}>
    <Suspense fallback={null}>
      {/* Camera */}
      <PerspectiveCamera makeDefault position={[0, 0.5, 10]}/>
      {/* Lighting */}
      <ambientLight args={[ambientLight.color, ambientLight.opacity]}/>
      {/* Objects */}
      <ForceGraph3D graphData={data}/>
      {/* Orbit Controls */}
      <OrbitControls ref={orbitControlsRef}/>
    </Suspense>
</Canvas>

Describe alternatives you've considered

• We tried passing something like {new ThreeForceGraph().graphData(myData)} as a component, as well as the ForceGraph3D component itself, but none worked.

Additional context
We are looking to work with more models than just the 3d-graph inside the canvas, and for this we would need to treat it as one more component of our Canvas, but as far as we understand the ForceGraph3D component is a Canvas itself.

How would you tackle this challenge? Thank you so very much! 🤩

Setting link width greatly slows model - possible fix?

First off, huge thanks for sharing your amazing work!

Issue
I found that setting a link width to any number caused the animation loop to slow down 10x. I was using this through react-force-graph, but found a fix/workaround in three-forcegraph.module.js

The slowdown happened whenever I set ForceGraph3D's linkWidth prop to a number, even a constant. Model would slow from a locked 30fps to ~3.

Fix?
The fix/workaround I found is at line 308 of https://github.com/vasturiano/three-forcegraph/blob/d02d90c5b489497a08b9f91cc33a96325a35cf46/src/forcegraph-kapsule.js That's where the link's object check/assign logic is
if (line.geometry.type !== 'CylinderBufferGeometry') { [removed] const geometry = new three.CylinderBufferGeometry(r, r, 1, state.linkResolution, 1, false); [removed] line.geometry = geometry; }

I looked at the type actually being returned at time-of-check and it was just CylinderGeometry.

Changing the check string to 'CylinderGeometry' fixed the slowdown and allowed the widths to be varied.

I tried to see if there was a difference/downside to this type, but it appears CylinderBufferGeometry is just an alias of CylinderGeometry, which itself inherits from BufferGeometry.
https://github.com/mrdoob/three.js/blob/20a41d2a4ff9ca170154a900dc2fe5eb983c1a6a/src/geometries/CylinderGeometry.js

Looks like a change may have come in this commit?

I hope this is helpful! Again, many thanks!!

Reposition nodes in the graph

Is your feature request related to a problem? Please describe.

Hey! We would like to implement the feature of repositioning the nodes by dragging them, just as in this example: https://vasturiano.github.io/3d-force-graph/example/fix-dragged-nodes/

We are using the library with R3F so it is not possible for us to use 3d-force-graph as they use their own renderer and scene.

How hard would be to implement this feature? Is there an easy way on doing so or any guidance you could provide 🙏 ?

Really appreciate the work you have done with this library, is very valuable.

Thank you in advance 🚀

NodePositionUpdate running multiple times

Describe the bug

I have noticed that the method nodePositionUpdate runs multiple times. In my case it runs 6000 - 6300 times as shown in the screenshot below. In this case, I'm just console logging the coords inside the method.

To Reproduce

1. Invoke the method nodePositionUpdate inside the ThreeForceGraph class.
2. Write a console.log() inside of it to see how many times it is called.

Expected behavior

I don't know if I'm missing something and this is the expected behavior! But I believe that after the coords have been settled it should stop calling the function.

Screenshots

Desktop

• OS: macOS Ventura 13.1
• Browser: Google Chrome
• Version 110

Face Coloring for Cluster Visualization

Is your feature request related to a problem? Please describe.
I want to visualize clusters by coloring the space between the nodes that belong to that cluster.

Describe the solution you'd like
I want to provide an array of node arrays that represent the different clusters, potentially but not necessarily overlapping. Then the space inbetween these nodes should be colored using distinct colors (basically color the faces between edges/links between the nodes, the convex hull).

My call would look like that:

const Graph = ForceGraph3D()(document.getElementById("3d-graph"));
Graph.resetProps();
Graph.cooldownTicks(200)
        .nodeLabel('name')
        .enableClusterVisualization(true)
        .jsonUrl('some-data.json')

with the json in the form of:

{
    "nodes": [
        {
            "id": "id1",
            "name": "name1",
            "val": 1
        },
        {
            "id": "id2",
            "name": "name2",
            "val": 10
        },
        (...)
    ],
    "links": [
        {
            "source": "id1",
            "target": "id2"
        },
        (...)
    ],
    "clusters": [
        ["id1", "id2"],
        ["id3", "id4"],
        (...)
    ]
}

Describe alternatives you've considered
Just coloring the nodes is not enough (e.g. for overlapping clusters).

Only recompute part of the graph

Is there a way to add edges to the graph, recompute the part of the graph, and then re-render? I am working with a graph with tons of nodes and edges so to speed up the process I am joining going to add the edges of a node when they are clicked on. The problem with this is that the whole graph is recomputed and thus takes a long time.