Stack Overflow
Stack Overflow

Questions tagged [cytoscape]

Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. Various apps are available for different problem domains, including bioinformatics, social network analysis, and semantic web.

Cytoscape (not to be confused with the JavaScript library ) is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization.

Related tags :

534 questions
2
votes
0 answers

Getting Node Ranks/Levels in Cytoscape.js Dagre Layout

I am trying to add styling to cytoscape.js nodes based on their level/rank in the graph. For example, the root node is rank 1, the children of the root node are of rank 2, and so on. Is there a function that returns the node's rank or return a…
HadiHammoud2000
  • 31
  • 5
2
votes
1 answer

Cytoscape 2.8.2 Launch With Errors

I am very new to Cytoscape, which I need for my thesis and I need to use this specific version. I installed it on my Laptop and on the installation instructions said to install the Java 2 Runtime Environment, version 1.4.2 or higher. I could not…
Mema Stamataki
  • 25
  • 4
2
votes
0 answers

Dash Cytoscape: Is it possible to make colors of nodes change upon click by user?

I currently have the following Network Graph. The blue nodes belong to class 'mNodes' and the pink node belongs to class 'vNodes'. Is there a way to change the colour of any node dynamically when the user clicks on it? (e.g. When user clicks on node…
ta.ng
  • 55
  • 1
  • 8
2
votes
1 answer

Cytoscape.js combine multiple edges into one (thicker) edge

I'm using cytoscape.js 3.19.1 and I cannot figure out how to combine multiple edges into one, and have the weight increased of that one edge. Current view I am now looking for a solution where 2 edges get combined into one with a width of 2, 3 edges…
JohnnyMaccarone
  • 23
  • 3
2
votes
1 answer

Dash Plotly Cytoscape initial zoom isn't working

I'm trying to create a Cytoscape on Plotly Dash. The zoom value I gave in Cytoscape props does not affect. cyto.Cytoscape( id='my-cytoscape', zoom=500, layout={"name": "preset"}, style={"width": "100%", "height": "600px"}, …
ebubekir
  • 58
  • 6
2
votes
1 answer

Cytoscape - Adding Dynamic Height and then using fit function

I have a graph where I set the dynamic height for the graph because the graph can have different height based on the data we receive from the backend so I am calculating the height based on the number of nodes. Also, I am using Dagre layout with…
Nike Star Overflow
  • 21
  • 1
2
votes
1 answer

How to set the concentric circle layout parameters in python dash_cytoscape?

I have my elements defined like where level refers to the circle layer I want that node. elements = [{'data': {'id': 'a', 'label': 'a', 'level': 1}, {'data': {'id': 'b', 'label': 'b', 'level': 1}, {'data': {'id': 'c',…
qazwsxedc111
  • 21
  • 1
2
votes
0 answers

Focus/Zoom in on part of the graph or a specific set of nodes or a single node

I am currently using Cytoscape to create a large graph with 500 nodes. I am using Dagre for the hierarchical layout. Currently the graph is small on the screen because of number of nodes which makes sense but Is there a way to focus on a single node…
Learn AspNet
  • 1,192
  • 3
  • 34
  • 74
2
votes
1 answer

Multiple data values for label text in cytoscape.js

I am trying to add multiple values to a label in cytoscape.js like so - { "selector": "edge", "style": { "curve-style": "haystack", "text-wrap": "wrap", "label": "data(count)" + "data(edgevalue)", "font-size":…
Ebikeneser
  • 2,582
  • 13
  • 57
  • 111
2
votes
1 answer

How do you specify edgeLength for each edge using Dash Cytoscape cola.js but in Python

I am trying to create a physics direct network graph using Dash Cytoscape. I have tried using Cose, Cose-Bilkent and now Cola, but my issue is that I cannot get the edge lengths to be cleary directly proportional to the weight. In JS in Cola you can…
spike4848
  • 21
  • 1
2
votes
1 answer

How to get javafx WebView to load resources from a jar file

I'm trying to get a javafx.scene.web.WebView to load resources from a jar file, but it doesn't want to do it, and doesn't produce any meaningful error. The jar file is an OSGi bundle, specifically a cytoscape app (plugin) bundle. Here's my code: (it…
Lawrence D'Anna
  • 2,998
  • 2
  • 22
  • 25
2
votes
2 answers

Change individual node size using Dash-Cytoscape

I've been using Dash-Cytoscape for two days now and I tried a lot of things to change the node size individually. I tried this but it didn't work: import dash import dash_cytoscape as cyto import dash_html_components as html app =…
Juan Carlos Jchr
  • 119
  • 1
  • 8
2
votes
2 answers

cytoscape.js graph, shows/draws only with few nodes and edges

I am creating a graph with Cytoscape.js on my website, to show admins the connections among users. Everything is fine, but some graph are not drawn down. No errors in console, but the canvas seems empty. For example, a graph that is not drawn has 20…
DeLac
  • 1,068
  • 13
  • 43
2
votes
1 answer

how to use Cytoscape from igraph

How can we reflect Fruchterman-Reingold layout using Cytoscape? I cannot replicate the Fruchterman-Reingold layout figure from igraph using Cytoscape. library(RCy3) library(igraph) library(ggraph) library(tidygraph) …
user224050
  • 317
  • 3
  • 10
2
votes
1 answer

What is the 'container' node create on merging multiple networks in Cytoscape?

I merged 190 networks obtained from KEGG using Cytoscape. The merged network has a node called 'container' that is very highly connected to several other nodes. The node 'container' does not come from the original pathway files. What does this node…
Sara Ibrahim Omar
  • 23
  • 4
1 2 3
…
35 36