cytoscape | open source platform for network analysis

by cytoscape Shell Version: 3.9.1 License: No License

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | cytoscape Summary

cytoscape is a Shell library typically used in User Interface applications. cytoscape has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

Cytoscape is a fairly complex application and its core distribution has multiple repositories for managing its code. This repository contains top-level pom file and utility script for building Cytoscape core distribution. Most App developers won't need to clone this repository. Keep reading below to learn about how to work with Cytoscape's source code.

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Support

cytoscape has a low active ecosystem.

It has 405 star(s) with 111 fork(s). There are 83 watchers for this library.

It had no major release in the last 12 months.

cytoscape has no issues reported. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of cytoscape is 3.9.1

Quality

cytoscape has 0 bugs and 0 code smells.

Security

cytoscape has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

cytoscape code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

cytoscape does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

cytoscape releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

It has 17 lines of code, 0 functions and 1 files.

It has low code complexity. Code complexity directly impacts maintainability of the code.

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cytoscape Key Features

No Key Features are available at this moment for cytoscape.

cytoscape Examples and Code Snippets

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Community Discussions

Trending Discussions on cytoscape

Cytoscape Desktop: Order of source nodes if group attributes layout is applied by target node attribute

Reading the List of Open Networks in Cytoscape

Dash Cytoscape from python networks graph not honouring the nodes coordinates

Cytoscape graph automove (with animation) when dragging a node

Changing the color of node-labels using Python Dash Cytoscapes

Change label of node within callback using Dash Cytoscape

Add in URL hyperlink to text returned upon click in plotly dash

Dash_table: SyntaxError: positional argument follows keyword argument

How to export a Cytoscape.js graph to image?

Cytoscape.js combine multiple edges into one (thicker) edge

QUESTION

Cytoscape Desktop: Order of source nodes if group attributes layout is applied by target node attribute

Asked 2022-Mar-17 at 15:12

I am using the Group Attributes Layout on a target node column in Cytoscape Desktop. All target nodes are grouped and sorted as expected. The source nodes are also grouped in a circle which is desired, I just cannot figure out how to get those (source nodes) in a custom order.

Thanks in advance! Chris

...

ANSWER

Answered 2022-Mar-17 at 15:12

It's pretty easy -- just start by selecting your target nodes, then doing the layout using "Selected Only". That will only layout your target nodes. Then repeat the process for your source nodes.

-- scooter

Source https://stackoverflow.com/questions/71496415

QUESTION

Reading the List of Open Networks in Cytoscape

Asked 2022-Mar-17 at 15:09

I am trying to get a CyNetwork[] containing all of the networks open in the Cytoscape network tab. My understanding is that I need a CyNetworkReader to call CyNetworkReader.getNetworks() and to get a CyNetworkReader I need a CyNetworkReaderManager. However, I don't know how to get a CyNetworkReaderManager, nor do I know the proper InputStream or input name to use CyNetworkReaderManager.getReader(). Any help would be much appreciated.

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ANSWER

Answered 2022-Mar-17 at 15:09

Close. Actually, you would need a CyNetworkReader to read in a new network from disk. If you want to get the list of currently loaded networks, you would need to use the CyNetworkManager.getNetworkSet() method. To get a handle on the CyNetworkManager, you just need to get it from OSGi, so in your CyActivator, you would do something like:

Source https://stackoverflow.com/questions/71498227

QUESTION

Dash Cytoscape from python networks graph not honouring the nodes coordinates

Asked 2022-Mar-15 at 09:07

I am trying to learn Dash Cytoscape and wanted to perform the following: generate a graph with network, apply a fruchterman-reingold algorithm to position the nodes, convert the data to the cytoscape format and display it in a Dash app. Here is the code:

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ANSWER

Answered 2022-Mar-15 at 09:07

Did you tried

n["position"] = {"x": int(p[0] * SCALING_FACTOR), "y": int(p[1] * SCALING_FACTOR)}

in step 5?

Source https://stackoverflow.com/questions/71428375

QUESTION

Cytoscape graph automove (with animation) when dragging a node

Asked 2022-Feb-05 at 16:45

I was looking to this example of cola.js in which, when dragging a specific node, the other nodes have the capability to automove according to the new position of the node I'm dragging, and the thing I'm interested in is that you can see the graph transition to the new position in a sort of animation. I noticed that cytoscape does this with cytoscape-automove extention, but in every example I found there's no animation and no delay performed when nodes automove. Could you suggest any way to do this with cytoscape?

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ANSWER

Answered 2022-Feb-05 at 16:45

There is cytoscape.js-cola which does more or less what cola does. The option infinite: true animates the graph while moving nodes as seen in your example.

You simply would need to add the cola layout to the cy instance – after installing the cytoscape.js-cola-module with npm install cytoscape-cola f.e.

Source https://stackoverflow.com/questions/70931143

QUESTION

Changing the color of node-labels using Python Dash Cytoscapes

Asked 2021-Nov-10 at 11:03

I want to change the color of the labels of nodes and did that the way the documentation describes it. However, if I add a stylesheet element for the labels they are disappearing of my cytoscapes element. What do I miss? Im using a seperate .css file for styling purposes. Do I have to add this part to the .css file too?

...

ANSWER

Answered 2021-Nov-10 at 11:03

Cytoscape selectors and styling are a bit "different" : since the label content is a style, you need to specify it (again) in the style dictionary, otherwise it looses its content when applying styles.

This sounds like a bug to me, because any little override requires to reapply the whole styles for the elements, and we don't necessarily know these styles.

There is another buggy thing in my opinion which is that 'label', '[label]' and 'node' selectors seems to behave exactly the same (that is applying to 'node' as described in the doc).

Anyway, once you know that you can do :

Source https://stackoverflow.com/questions/69910236

QUESTION

Change label of node within callback using Dash Cytoscape

Asked 2021-Nov-07 at 17:23

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 display the slider after clicking a node I made it be displayed permanently below the nodes. Hopefully you got some ideas to reach my desire.

...

ANSWER

Answered 2021-Nov-07 at 17:23

You can wrap the slider in a div element, which you can hide by default using the hidden property :

Source https://stackoverflow.com/questions/69865157

QUESTION

Add in URL hyperlink to text returned upon click in plotly dash

Asked 2021-Oct-24 at 18:53

This code generates a network as expected using plotly dash:

...

ANSWER

Answered 2021-Oct-24 at 18:53

Returning active URL links upon node selection

You can just use the Dash html.A component, no?:

Source https://stackoverflow.com/questions/69697072

QUESTION

Dash_table: SyntaxError: positional argument follows keyword argument

Asked 2021-Oct-24 at 07:57

I want to build a network using dash.

I have this data frame (called final_net):

...

ANSWER

Answered 2021-Oct-24 at 07:57

Well for one, you forgot, as the error says, the keyword for the parameter (i.e., "elements"):

Source https://stackoverflow.com/questions/69688826

QUESTION

How to export a Cytoscape.js graph to image?

Asked 2021-Sep-24 at 12:12

I am learning Cytoscape.js. I successfully make a HTML file containing this basic graph. I try to export the graph to image using:

...

ANSWER

Answered 2021-Sep-24 at 12:12

If you have the following (make sure the DOM is loaded before trying to query for elements):

HTML:

Source https://stackoverflow.com/questions/69304985

QUESTION

Cytoscape.js combine multiple edges into one (thicker) edge

Asked 2021-Sep-07 at 08:09

I'm using cytoscape.js 3.19.1 and I cannot figure out how to combine multiple edges into one, and have the weight increased of that one edge.

Current view

I am now looking for a solution where 2 edges get combined into one with a width of 2, 3 edges combined into one with a width of 3, etc.

I am changing the color of the nodes with this code:

...

ANSWER

Answered 2021-Sep-07 at 08:09

Actually, you might achieve this using some different styles on the edges. "haystack" or "straight" might be useful. Check them https://js.cytoscape.org/demos/edge-types/

Or you might use https://github.com/iVis-at-Bilkent/cytoscape.js-expand-collapse

Check its demo and collapse the edges.

Source https://stackoverflow.com/questions/68995868

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install cytoscape

To test changes, simply install the JAR using the App Manager or copy to the ~/CytoscapeConfiguration/3/apps/installed directory.
You can set up a Travis CI. You need to be registered with Travis to setup a new job, and have a username and password for https://nrnb-nexus.ucsd.edu/ to deploy to nexus.
Go to https://travis-ci.com/github/cytoscape
Find and select the relevant repository in the repositories list
Follow the steps to enable Travis CI for that repository
You can use the Travis CI setup as well as the .travis.yml from the cytoscape build as a guide to building and deploying your app.
Now you can build Cytoscape. Run the new version and make sure your app is part of the distribution.
These are general instructions on how to build a Cytoscape release locally. The Cytoscape Build Server (https://cytoscape-builds.ucsd.edu/) contains scripts to automate this process and should be used to generate releases. However, the general steps of the release build are outlined here for reference.
Make sure you have already installed install4j
CD to Cytoscape project's top directory
Switch to release branch: cy switch release/3.x.x
Run cy pull to synchronize local repository to remote
Run mvn clean install -U to make sure you can build all bundles without problems
CD to gui-distribution/packaging
Run mvn clean install -U
CD to target/install4j and check you have installers for each platform
(Optional you need Apple developer account and Mac to do this!) CD to gui-distribution/packaging and run sign-dmg.sh 'your account' and check you have signed dmg in signed directory
https://github.com/cytoscape/cytoscape-scripts/blob/develop/deploy_installers.sh

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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