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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 write namespaced element attributes with LXML?

I'm using lxml (2.2.8) to create and write out some XML (specifically XGMML). The app which will be reading it is apparently fairly fussy and wants to see a top level element with:
timday
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Transfer layout from networkx to cytoscape

I want to use networkx to generate a layout for a graph. Is it possible to transfer this layout to cytoscape and draw it there? I tried to simply write a graph as import networkx as nx G =…
highBandWidth
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Hide and Show Child Nodes on Node Tap Cytoscape

I am trying to create a collapsible tree structure in Cytoscape using breadthfirst layout, to replicate the D3 collapsible tree. I am trying to replicate this type of click action on nodes, but adding restore functionality in addition - Images &…
Chirag A.M.
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cytoscape save graph as image by button

I saw in the cytoscape.js tutorial that there are ways to represent the graph as image (png, jpg), but there is a way to represent it as regular graph, and if the user would want he can save it as image by click on button or similar option? Didn't…
Avi
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Is it possible to get Dash-Cytoscape graph tooltips?

Here is an example cytoscape graph that I created using this site as reference here I was wondering if its possible to show the tooltips when hovering on each node in a graph in the same way that plotly can do to its graphs (like this)
xyiong
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How to integrate Cytoscape with JanusGraph 0.2?

JanusGraph official website provides some graph visualization tools. Cytoscape is one of them. I want to visualize my graph data with Cytoscape. I have no clue how to integrate Cytoscape with JanusGraph. Can someone provide some information how to…
jonyroy
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Visualization in pyqtgraph for node network?

I have a collection of network points stored as Nodes and Edges for use in networkx, but would like to impliment a more advanced visualzation tool into the pyqtgraph widget so that I can use it in a GUI designed in pyqt5. The problem with utilizing…
Jmegan042
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Replace all elements and redraw graph softly in cytoscape.js

Is there any one-command way to replace all elements of my graph with new data in cytoscape.js? In my case, after some operations on backend I have new graph-data and want to redraw my graph with this new data, but not to lose my camera settings,…
Alarmwolf
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How to wrap the text inside a shape using Cytoscape?

I'm trying to build tiles using Cytoscape. Basically, each rectangle (tile) has a title and I want it to be written within the limits of that rectangle. My code is: var cy = cytoscape({ container: document.getElementById('cy'), style: [ { …
user882670
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Is there a way to display a node label at the top inside the node?

I am creating a graph using cytoscape.js and I have compounded nodes which are inside the parent node. I would like to have the title of the main/parent node at the top of the node but inside the node. Is that possible in cytoscape? I have tried…
Learn AspNet
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cytoscape.js disable grab&moving nodes

I'm having trouble building a graph network with cytoscapeJS. I can add nodes and handle them which is quite easy, but I'm not able to configure cytospace to disable Dragging/Moving nodes. I have found a JSbin from somebody where you can try:…
ant45de
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How to load both html and javascript into webengine from loadContent()?

Could someone provide some suggestions on how to load the following onto webviewer from loadContent()? http://jsbin.com/aqupun/6/edit I was trying to do something like this, but it doesn't seem to work. Thanks! Scanner sc1 = new Scanner(new…
user2799603
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cytoscape.js with cola seems no longer to work

I'm trying the latest cytoscape with the latest cola and I get the following error: Uncaught TypeError: cola.adaptor is not a function for the cytoscape.js code snippet: var adaptor = layout.adaptor = cola.adaptor({ trigger: function( e ){ //…
Yeti
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Cytoscape.js large data performance vs sigma.js

I'm having a lot of trouble rendering a graph in cytoscape.js with ~1,000 nodes and ~5,000 edges (takes a very long time to render, once rendered impossible to interact with since browser is overloaded), however the same size graph appears to render…
Patrick DeVivo
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Change label of node within callback using Dash Cytoscape

I have created some nodes with Dash Cytoscapes. My final goal is that there should appear a Slider after clicking on a node. By selecting a value with this Slider the label of the node should be updated with the selected value. Since Im not able to…
Baflora
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