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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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534 questions
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cytoscape.js - how to merge attributes of the same node from different sources

I have a working graph which displays some nodes & their attributes. Then I get a JSON with different data, where some nodes may already exist on my graph. How to combine both data sources, to make them both visible on the same graph - BUT nodes…
Alexey
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How to change sizes of selected nodes in Cytoscape?

I would like to change the sizes of the selected nodes in Cytoscape app. Also, for large networks when manual selection is very tedious, then is it also possible to set the sizes of source and target nodes differently?
Wasim Aftab
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How to add attribute to node's data field in cytoscape.js?

I am trying to dynamically update nodes of my cy object with the "parent" field. When the elements are first loaded in from a json file, they do not have a parent field. The documentation says I should be able to set a particular data field simply…
Ellen Wang
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Call an app in a loop with different parameters in Cytoscape

I'm new in Cytoscape. I want to know how can I run an app (for example MCL clustering algorithm) multiple times with different parameters in Cytoscape. Is there any way to write an script to do that instead of running manually multiple times for…
SaRa
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Conversion from pairwise matrix to Cytoscape edge table is too slow

My code is similar to this. Given a matrix like this: a b c d a 1 NA 3 4 b NA 2 NA 4 c NA NA NA NA d NA NA NA 4 It converts it to this: a a 1 a c 3 a d 4 b b 2 b d 4 d d 4 The relevant code is as below: 2 pears <-…
psdanielxu
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conversion newick to graphml using python

I would like to convert a tree from newick to a format like graphml, that I can open with cytoscape. So, I have a file "small.newick" that contain: ((raccoon:1,bear:6):0.8,((sea_lion:11.9, seal:12):7,((monkey:100,cat:47):20,…
Gildas
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Cytsocape.js can not create edge with nonexistant target

I try to create an edge after I created the nodes using an AJAX request. My code: success: function(data) { $.each(data['kids'], function(i, value) { cy.add({ group: 'nodes', data: { id: value['id'] }, …
user8980530
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Cytoscape.js - Highlight all paths from the selected node

Here I tried to highlight all paths from the selected node but It dose not work with the bfs Algorithm, who can I solve this ? I want to highlight all the paths and nodes from the selected node. cy.on('click', 'node', function (event) { …
Raul Martin
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How to Get All Nodes With a Specific Value?

I am just began to develop cytoscape plugin. I am trying to hide all nodes which has "pronaliz:status" statement in its "shared name" column. I saw the link below and i tryed it but could not make it. It is not hiding any…
Erkan
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Visual Neo4J DB on Cytoscape Plugin

Good afternoon, We are working on a tool, that would be needed to use Neo4J, a graph database. Also there are a lot of plugins which we can visualize the nodes, think we are going for Cytoscape.js. The Neo4J database was created but at the moment we…
Yanu312
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Cytoscape set node data in Ember

I am trying to add a node data to a Cytoscape instance set as a component property. But ember throws an error to use Ember.set. Any ideas?
Rony Varghese
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How do I get a reference to Cytoscape Canvas Context?

I need a reference to Cytoscape Canvas Object and it's 2D context. How can I do this? I don't see any "id" attribute on the canvas. Thanks
Aravind
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Cytoscape JS - Modifying Container Height After Initialization

I initialize Cytoscape with something that looks like the following: var cy = cytoscape({ container: $('#my-element'), height: 500px }); I would like to change the height of the container element to something other than the original 500px…
Lloyd Banks
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Cytoscape js create custom renderer (renderer extension)

Please can anyone help me with creation of a renderer extension for cytoscape js lib. Here is how it is working now: let CanvasRenderer = cytoscape('renderer', 'canvas'); CanvasRenderer.prototype.drawPolygonPath = function(context, x, y, width,…
Станислав Голембивский
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Finding unique pairs between nodes in Cytoscape.js

I am using Cytoscape.js. I have some nodes connected with edges. I want to loop through each connection between two nodes. The problem is that in some cases, two nodes have multiple edges between them, so I cannot just say cy.edges().forEach()…
Jamgreen
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