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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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How to make Cytoscape desktop interface font size larger?

How to change text size in Cytoscape 3? Not the font of the network labels, but the font of the GUI itself. I tried to look for it in preferences but there is nothing like it there.
Sashko Lykhenko
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How can I set a different color of Cytoscape network node center?

I have a network (figure A), (source: aacrjournals.org) . In this figure, every node center (I am confused, is it a sub-node?) has its color that is differential to node fill color, how can I do this? Thank you.
qiaozhi
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Cytoscape.js zigzag like edges

I am trying to create a zigzag like edges in cytoscape.js. I have found zigzag edges on github but I guess it's not yet implemented or it's abandoned, so I am trying to calculate the points but I am having some trouble. My graph looks like this: I…
Porjaz
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Convert correlation dataframe to dictionary {key = (sample_x,sample_y), value = correlation}

So I'm trying to do something very similar to these 2 posts but there a few differences. One, I don't want a csv file so no csv module and I want to get it done in Python not R. Convert Adjacency Matrix into Edgelist (csv file) for…
O.rka
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Drag event for nodes in Cytoscape.js

I'm looking for an event that fires as a node is being dragged. I thought that tapdrag looked like what I wanted, but tapdrag fires whenever the mouse moves over the node only when the mouse button is not down (so the node's not being dragged,…
TonyM
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Edges reflecting weight in Cytoscape

I just started looking into Cytoscape I was looking at the example here. My goal is to have a weighted directed graph (pretty much like a dendrogram, except weighted). I need to have the edges reflect the weight (either in terms of length, or color…
Bugaboo
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How to highlight the path between two nodes in CYTOSCAPE JS

i can create a graph using cytoscape js library . i am following the this tutorial and i implement like this. CODE: $(function(){ // on dom ready $('#cy').cytoscape({ style: cytoscape.stylesheet() .selector('node') .css({ …
Ramakrishna
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Point application to non-embedded JRE after installation

Is there a way to point the application to a different JRE after installation? The application installed and created a i4j_jres folder for its embedded java. does this program allow for it to have a different java location without needing to specify…
HighKingKwami
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On Google Colab, localhost access from Javascript fails

I have a Javascript snippet that my Jupyter Notebook installs into the browser page. It accesses a REST-enabled interactive application running on my PC (i.e., Cytoscape). An example of a Cytoscape call from Javascript is "GET…
bdemchak
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Unable to load Nodes table in Cytoscape from csv

I try to load a Node table from CSV (File -> Import -> Table from File) into an empty Network, in Cytoscape Version 3.8.0, Java 11.0.7 by Ubuntu. The problem is that I don't get anything in 'Node table' (right bottom corner - only the attributes…
Evgeni Marinov
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Is it possible to avoid overlapping of edges and nodes upon collapse/expand of compound nodes using klay layout from cytoscape?

I am quite new with the cytoscape and still need to learn a lot. I am working on providing a graph which contains simple nodes and compound nodes which can be collapsed or expanded. I would like to maintain spaces between every node…
Tom Reiner
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How to Import Javascript File - cytoscape/cytoscape-edgehandles.js

I have the following module in which I'm trying to add the cytoscape-edgehandles.js extension to my existing cytoscape-based project (trimmed unnecessary parts to illustrate the issue) - /* cytoscape import */ import…
Michael Di Felice
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Changing color when node is selected in Cytoscape JS

I would like to change the color of a selected node to a different color than the predefined background-color. However, as soon as I define a background color for the node in "style", the color does not change to blue (default behavior). Here is the…
Lazloo Xp
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py2cytoscape - automate saving view

I want to automate saving a view in cytoscape using the py2cytoscape package. from py2cytoscape import cyrest cytoscape =…
Mike
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How to change node's color individually in Cytoscape?

In Node's Style view, if I change the color in the label setting, it changes all the color of all nodes. I want to control the color of each individual node. How can I do that? Thanks for help.
user697911
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