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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.

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cytoscape.js for PPI jsmol. Main difference between cytoscape.js and cytoscape

I want to implement a web application for PPI and 3D strucutres. Anyone know if cytoscape.js is better than cytoscape ?
albertgeorge253
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JavaScript access to Angular scope returning "undefined" - Asynchronous issue?

Problem: I'm trying to get some data from a server to populate a cytoscape graph. When i access the scope from javascript its undefined. Despite their being quite a few posts with this / similar issue. I'm having trouble finding an explanation about…
geoff whitehead
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Is it possible to make hyperlinks inside nodes in Cytoscape.js?

I want users to be able to click on some text inside the node and do some action, like show some dialog or open some other window. Is this possible? In the documentation there is something like : text-events : Whether events should occur on an…
paul_n
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Cytoscape- Selecting directed edges

In Cytoscape, I have bi-directional edges from a reference node. How do I select only those edges that have a particular directionality. For example selecting all the outward directed edges from the reference node.
user3392665
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Cytoscape : Add element in setTimeout doesn't get rendered

In the following code , I add a node to the graph in setTimout but it's not rendered. When I move the code out of setTimeout it's drawn. Any reason ? var cytoscape = require('cytoscape'); var cy = cytoscape({ container:…
Arian
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Cytoscape Graph is not showing

I am trying to show a cytoscape graph in an ext window. Everything is working well, until i add the ext-all.css, the graph is no longer displayed. This is the panel were the graph is supposed to be shown ( the #cy div) var formPanel2 = new…
Khouloud
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Cytoscape.js, nodes aren't getting selected with Chrome

In cytoscape.js I have a network, and when I select a node, normally the color of the inner circle, which is green, should turn black, like this in Mozilla Browser: But when I try the same network in Google Chrome it doesn't work, I just get this,…
DanielBoloc
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How to show compiler errors in problems pane when using Maven in Eclipse?

The way that I see compiler errors is right clicking my pom.xml and clicking "run as --> maven install" and a console output shows compiler errors. Is it possible to make eclipse detect compiler errors in real-time and show them in the problems pane…
Murd
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MySQL: Output rows created from columns containing delimited data

Assuming I have the following data in a MySQL: **bond** | **node** | **edges** foo | 1 | 2,3 hak | 2 | 1 wat | 3 | 1,2 I wish to return results to create data suitable for visualisation in Cytoscape. It…
ZBM 2
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Need to pass node object created in loop to edges

I am reading in and looping through a json file to create a graph with nodes and edges using a JavaScript library cytoscape, but am having some newbie problems. Here is my pseudo code w/pseudo bugs. 1) Create new node for each node with label…
tjustbecause
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concate string with data(id) in cytoscape

I use cytoscape to present a structure with image in each node. The node content is appear, but the image is not. Is there a way to concate string path with the data(id) ? style:cytoscape.stylesheet() .selector('node') …
user3117522
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Numeric column in cytoscape

I'm new to cytoscape. I want to make the width of edges in my network according to a certain number. my file looks like this: node1 node2 34.04 node3 node2 56.89 node4 node5 8.09 node1 node4 10.54 when I import my network file I choose column 3 to…
user2335015
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Building .sif file from microarray ,tab file with expression valuses and gene id only

How to generate a .sif (simple interaction) file from gene micro array expression .tab file containing only gene expression values and gene names? I use Expander software and MeV and want to build an input file for Cytoscape and Spike software. Is…
Matthew Sprindzuk
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Displaying qTip hover on outer nodes of Cytoscape.js graph?

When hovering over the outer nodes of graph in Cytoscape.js, the qTip dialog is not displayed. Is there anyway to display the qTip bubbles upon hovering on an outer node? I can have the qtip popup on nodes in the upper half but not much along the…
Mango Web Design
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Quick example of Cytoscape being used with Primefaces

I am looking for an example (complete xhtml) of a simple graph created with cytoscape.js in a webapplication using Primefaces. Right now, I am unsure of how to integrate the jquery with primefaces.
Nick
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