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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: Node Background Image Issue

i have issues setting an svg image as background of a node. When i start dragging it, it always rescales the image in Chrome (even with fixed background height) and firefox doesnt even show it. I have tested lots of properties to solve it and didnt…
Donskelle
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How to let Cytoscape.js automatically create a layout like what Cytoscape creates?

I used Cytoscape for biological network visualization before using Cytoscape.js. Cytoscape is able to create an automatic layout from our network file using its internal placement algorithm. The layout placement is very reasonable--- nodes that are…
qcx
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Multiple Root Nodes in Cytoscape

I am creating a tree with Breadthfirst layout in Cytoscape. In layout options, I have set a node as root. But is there a way that I can have 2 nodes as root nodes? I see in cytoscape reference has layout options in following way: var options = { …
Chirag A.M.
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Cytoscape dynamically style last added node only

I'm in the beginning phase of using Cytoscape.js and I'm trying to style the last added node to my dagre-layout tree. For context, I'm trying to visualize the Git workflow as I make a Git commit. The current nodes on the tree are colored green. When…
binhxn89
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Using yFiles layouts in cytoscape.js

I am new to cytoscape.js. I want to use hierarchical layout from yFiles layouts in cytoscape. Is there a way to specify this layout in json file? Thanks, Rtut
Rtut
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How do I configure graph to show downward pointing edges without hardcoding node positions?

I am trying to achieve this effect using cytoscape.js and the cytoscope-cola.js extension. I want to make the edges of my graph direct downwards like in this picture: Instead of the unconstrained graph that shows up by default. I'm using the cola…
Louis93
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undo remove nodes operation in Cytoscape JS

When you remove nodes in cytoscape JS (using cy.remove()), the edges attached to these nodes are also deleted from the graph. The description for cy.remove() says it removes elements from the graph and returns them. However, the data that is…
Waldorf
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Convert Adjacency Matrix into Edgelist (csv file) for Cytoscape

I have a large (200 columns/rows) adjacency matrix in a csv file. This details interactions between individuals. I would like to convert this file into an edgelist, it can be done manually, but would take an enormous amount of time. A small subset…
Workhorse
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Increase width of selected edges only (cytoscape.js)

How can I predefine when I select a few nodes that are connected or simply edges, to make the width of the selected edges be bigger, without affecting the rest of edges of the entire network or the node's width? I predefined this when the nodes or…
DanielBoloc
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How can I set the start position of nodes in cytoscape.js with cy.load?

I am trying to set the start position of my nodes manually but loading them from a JSON structure. If I put the position within the 'nodes' structure it works, however I am trying to add a seperate structure called 'positions:'which I thought…
user1768233
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how to make a satisfied layout for my data(complex network) using networkx or something else

I want to visualize my data. my data is like: my data file is :https://gist.github.com/anonymous/5568836 4556 5092 0.7000 4556 4785 0.7500 4556 5397 0.7000 4556 5139 0.7500 4556 5937 0.8333 4556 6220 0.7000…
kuafu
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How to automate [load + export] operation in Cytoscape?

I have ~100 *.xgmml files each specifying a different network. How can I automate the process of generating PNG image files through Cytoscape for each of these input files? (The Cytoscape command-line options include some to load files, but I don't…
kjo
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R WGCNA Cytoscape hub genes

I have the following problem with WGCNA - http://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/ Working on Section 1.6, Export of networks to external software (Cytoscape) I'm currently trying to perform WGCNA…
Derek
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Cytoscapejs: Background image in cytoscape loads with delay in Angular App

I have defined all style in a separate 'nodeselector.ts' file Eg: export const styles = [{ "selector": "node", "style": { "text-valign": "bottom", "text-halign": "center", "text-margin-y": "5px", …
Lisa
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networkx position (biggest) nodes in the middle of a graph

I've been creating graphs with the networkx package and everything works fine. I would like to make the graphs even better by placing the bigger nodes in the middle of the graph and the layout functions from networkx does not seem to do the job. The…
fuzzysocks
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