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
0
votes
1 answer

Highlight actual path in tree as given data in Cytoscape

I am trying to Highlight all nodes and paths on click from a node to root. I found a partial example in this link - How to highlight the path between two nodes in CYTOSCAPE JS. The code in above link uses Dijkstra's algorithm to find the shortest…
Chirag A.M.
  • 131
  • 1
  • 8
0
votes
0 answers

Integrating Cytoscape in R Shiny Application

I am trying to integrate the code for generating a graph of LesMiserables network as a starting point to see if Cytoscape can be integrated with R shiny Please find the code here…
EricA
  • 403
  • 2
  • 14
0
votes
1 answer

Perform Centrality Functions on all Nodes using Cytoscape.js

I need to calculate degree, closeness and betweenness centrality for every node on a graph. I'm currently using the functions built into Cytoscape.js on each node after the cy.ready() event. However, as the graphs are quite large (250+ Nodes, 650+…
StudioLE
  • 656
  • 8
  • 13
0
votes
0 answers

Q: Cytoscape 3.4 How to import several attributes for all nodes and how to differentially represent them

I have already imported my whole dataset, around 6k nodes and 300k interactions, managed to format all the edges according to their type of interaction and now I am trying to import the metabolism of each gene into the network as node attributes.…
ThrowKudos
  • 1
0
votes
1 answer

Cytoscape JS: Catching graphs 'boxend' event

I have a cytoscape graph added to my web app. In the core's configuration I've set the boxSelectionEnabled to true. This is letting me draw a Box with holding Shift or Ctrl around graph elements. Now i am trying to read all these elements upon the…
Suraj
  • 451
  • 1
  • 9
  • 17
0
votes
1 answer

cytoscape.js compound nodes ignoring layout?

It appears that compound nodes don't obey layouts if they have connections between other parents, but children do not have connections. Best way to show is to modify their DAGRE example: http://jsbin.com/gist/e52c2fbc0b09edd6ec46?html,output by…
Jacob Garbe
  • 3
  • 4
0
votes
1 answer

how to open .cns file in cytoscape

I have used this command in R using Linkcomm package and generate this temp.cns file linkcomm2clustnsee(lc, file = "temp.cns", network.name = "network") I am trying to import temp.cns file into cytoscape for visualizing cluster.but i am unable to…
student123
  • 39
  • 9
0
votes
1 answer

With cytoscape.js how to show simultaneously arrows and custom labels for the arcs between nodes?

With cytoscape.js I want to get two effects at the same time: to show directed arrows for the arcs between nodes AND to show custom-made labels for the arcs between nodes. With the code available below I can only get arc labels shown but not…
KindRequestForHelp
  • 1
  • 1
0
votes
1 answer

cytoscape-qtip.js official demo example does not show tooltip; how to manage cytoscape qtip

The official demo example of cytoscape-qtip.js available at https://github.com/cytoscape/cytoscape.js-qtip/blob/master/demo.html does not show any tooltips like it should. This demo file does not seem to work correctly. I have tested various…
KindlyAskingThis
  • 11
  • 1
0
votes
1 answer

Defer, debounce or timeout an event

I have two events cy.on('mousedown touchstart', 'node', function (event) { // start }); cy.on('mouseover tapdragover', 'node', function (event) { // end }); The problem is that the second event is almost immediately fired since the first event…
Jamgreen
  • 10,329
  • 29
  • 113
  • 224
0
votes
1 answer

Cytoscape.js: precompute graph layout?

Cytoscape.js can calculate a layout for a graph file that does not have layout information, but being a JavaScript library, this calculation happens every time a user visits the web application and thus slows down the page load. Cytoscape Desktop…
Konrad Höffner
  • 11,100
  • 16
  • 60
  • 118
0
votes
1 answer

cytoscape.js not importing style

I use cytoscape.js 2.7.5 to display a graph exported by Cytoscape Desktop as graph.cyjs converted to a Javascript file graph.js containing "var graph = ... the content of the cyjs file ...;". With the following HTML I see the nodes and the edges but…
Konrad Höffner
  • 11,100
  • 16
  • 60
  • 118
0
votes
1 answer

cytoscape code not showing

I am trying to run some code that uses cytoscape.js. The problem is that after I run the file, sometimes it do show up the graph but most of the time it is not. I am currently using Eclipse Luna and this code is in a jsp file. Here is my code…
kaixas K
  • 111
  • 12
0
votes
1 answer

Implementing big data into Cytoscape

I am new to Cytoscape and need some advice. I have a file that has two columns named: source & destination (edge -> end node) For example, a sample starting from the top may look like this: src | dst 12.251.512 | 12.623.743 51.734.312 |…
Edon
  • 1,116
  • 2
  • 22
  • 47
0
votes
2 answers

[simple issue]: import .net file (word/occurences) into cytoscape...which attributes are which?

I took a corpus of text and put it into VosViewer to create a network for me. When I import this .net file into gephi, it works fine: I get a semantic network. Though I'm a little stuck for what attributes to select to import into cytoscape. Here is…
user5813071
1 2 3
…
35 36