Help with the choice of a program for evaluating the connection of nodes

Question

big data

Help with choosing a program for evaluating the connection of nodes
Hello, I'm sure someone has come across a solution to the problem:
Let's say there are 200 nodes (participants), there are different connections between them
1. each node is connected to several others
2. there are coordinates of these nodes in space. those. there are distances from the node to all the others.

The task is to create 3D clusters (distribution) of these nodes in space, given these two parameters.

I am sure there must be algorithms/platforms for analyzing connections in the same social networks.
While I deal with such a platform www.cytoscape.org/

Who faced a similar problem, tell me where to dig.
Thanks

Answer 1

It looks like you're referring to graph stacking by "creating clusters".
To begin with, decide what you still have: the coordinates of the vertices (why then laying, its purpose is just to determine the coordinates for the vertices), pairwise distances (between all vertices, or only between connected ones), or only connections.
Any styling is based on a binary metric for vertices. The simplest metric: 1 - there is a connection, 0 - there is no connection. Depending on the available information and goals, more complex metrics can be invented. If you have pairwise distances between vertices, it makes sense to apply them in the metric.
The most common laying methods are: physical (pseudo-physical) modeling. Ribs are springs. See en.wikipedia.org/wiki/Force-directed_graph_drawing. There are at least a dozen specific algorithms, and even more implementations, from the systems listed on the Wikipedia page by reference to libraries in any language.
Personally, I used the Gephi program, the Sigma.js library (for laying the graph in the browser) and implemented the algorithms myself. Gephi seemed inconvenient to me. I don't remember if there is 3D. The impression is that ready-made programs in this area tend to be tailored for a specific use case, so if you don’t have some simple case, I recommend looking more towards libraries (this does not apply to Sigma, the styling is also almost not customizable there). ).
Regarding social networks:
2D graph of Vkontakte friends on WebGL: habrahabr.ru/post/144758/
VK application for building a 2D graph of friends:vk.com/app2353824_14882053
2D friends map (FB app: apps.facebook.com/challenger_meurs )

Answer 2

I recommend to look at the materials of this course www.coursera.org/course/sna
all the basic metrics were shown there and there was an overview of gephi

Answer 3

ORA can do this sort of thing in 3D:
simmons-fan.livejournal.com/276282.html
More recent versions should be able to export this as a video.