I'm building UI to visualize and edit graph which is present in a gremlin store.
Which framework is better Cytoscape.js vs Gephi.js Vs other?
Do these frameworks have Blueprints plugin available? I want to avoid writing module to convert the gremlin output to the framework compatible format.
Please advice. Thanks.
Answer from the Cytoscape development team...
Well, there are a number of ways you can use Cytoscape with TinkerPop, but I would think that the best way would be to use the REST interface to Cytoscape and inject your graph directly into it. You could save your graph as a Neo4j database and use the Neo4j app to pull it into Cytoscape or save your graph as a GraphML or some other common graph format and read it in that way. Neither Cytoscape or Gephi are UI frameworks, though -- both are standalone applications that are designed to import, visualize, analyze and manipulate very large graphs.
A good place to start is on the Cytoscape Automation topic in the Cytoscape manual: http://manual.cytoscape.org/en/stable/Programmatic_Access_to_Cytoscape_Features_Scripting.html
No matter which library you use for graphs on the web, you're going to have to convert your model to the JSON format used by the library (e.g. the Cytoscape JSON format if you use Cytoscape desktop or Cytoscape.js).
Related
I aim to "translate" GTFS files (non realtime) into directed graphs. Is there any API / tool that can do that easily ? I would like to create a graph per route in my GTFS, and then store it into a file.
So far I made a few tests using Python and pygtfs, or R and gtfsr, but none seems to be able to make that conversion.
You can try peartree. Their websites says: "peartree is a library for converting GTFS feed schedules into a representative directed network graph."
I am looking for a tool to automate making graphs with Gephi. I have dozens of similar graphs to prepare (only labels and figures in data differ), so need something able to automatically:
load nodes and edges from a file (e.g., csv)
set up layout (e.g., "type='force atlas 2', iterations=n, threads=m, scaling=p, gravity=q...")
apply selected laoyut
tune appearance (ranking: color, size)
export graph
I am aware of Gephi Toolkit, but it is for Java. Maybe there is some other way to automate Gephi? (or I will have to learn Java, which is not bad, but requires time)
I've also found Gephi Scripting Plugin, which is good but lacks some features, e.g. can't set up layout (only runs it with default settings).
Thanks in advance!
It is a bit tricky and haven't tried myself but if you don't want to get your feet wet with Java then you could try one of the automation frameworks that allow you to control a GUI application, e.g. Robot, PyAutoGUI or if you use Windows you can use pywinauto.
I know it not a complete answer but it might give you a lead.
Are there any beginner-friendly tutorials to display graphs in the way Knowledge graph has been done?
I have the data is JSON format presented from a graphdb
For eg:
The closest I have found so far is Gelphi. Which also can be integrated with unity to produce a 3d Graph like this one https://www.youtube.com/watch?v=h_arRCf73Kg.
Then there is https://cayley.io/
https://n0where.net/opengraphiti-data-visualization-engine/
There is also https://www.maana.io/knowledge-platform/platform-capabilities/#maana-knowledge-graph . However, i have not tried to use/download their platform.
https://en.wikipedia.org/wiki/Force-directed_graph_drawing
Finally, I am working myself on learning unity to build a simple GUI which a user can identify nodes and edges and entities easily and move them around. So instead of just reading from a data base, also write to it through a UI.
I am working on a web project for network visualization. I am writing my code in R using Shiny. And I want to display my graph using Cytoscape.js
I've searched the web for some kind of source code doing this. But I couldn't find anything. The webpage of Cytoscape.js is not enough for me cause I am not expert in js and can't use the examples.
Briefly, I have Adjacency matrix of my graph and want to use it with cytoscpae.js. Do you know any source code or a tutorial of the steps I should go through?
Cytoscape.js supports JSON for input, so as long as your R/Shiny code can produce that, you should be able to use Cytoscape.js. Here's the format described: http://cytoscape.github.io/cytoscape.js/#notation/elements-json
It looks like Shiny has a predefined set of widgets it supports, so there are a few options here:
(1) Shiny adds support for Cytoscape.js (e.g. https://github.com/cytoscape/r-cytoscape.js),
(2) A Cytoscape.js plugin is written for Shiny.
(3) You use JS for at least part of your app.
(1) and (2) will take more time than (3), so depending on your requirements, you may have to bite the bullet and use normal JS. When using a framework like R/Shiny without your own JS, you'll always be locked into whatever's supported and miss whatever's not -- so you lose on flexibility.
For very flexible and general interaction between R and Cytoscape.js, see the RCyjs project (docs)
I need to visualize a very large graph ( > 1 million ) in a website, the library should to receive a JSON and generate a png.
I've already tried graphviz with spfd but the waiting is too long, the user will not be able to interact with a GUI so Cytoscape or Gephi are not an option.
Another option could be maybe exporting a .dot to web, but I don't know how efficient this would be.
http://www.gnuplot.info/ and http://dygraphs.com/ are two of my favorite charting libraries for the web. Plotting a million data points I would probably use gnuplot. I would look at caching generated images as much as possible, perhaps even generating them in a batch rather than at the time of the request. I think you will run into performance issues trying to pass the data in via JSON and attempting to render the graph client side.