how to call an app from Cytoscape using R?
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adR ▴ 20
@do-it-23093
Last seen 3 days ago
Germany, M√ľnchen

hi everyone,

I would like to call a Cytoscape app installed on my local computer and want to call a specific app and use some of the functions in the called app using R programing language. For example, I want to visualize and do clustering for my graph object currently present in my R studio. How I am supposed to call one of the clusterings algorithms from Cytoscape using R?

something like in the code below,


    CytoscapeApp(graphObject, "Community Detection (Louvain)")

Thanks!

RCy3 • 54 views
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alex.pico • 0
@alexpico-15339
Last seen 9 days ago
United States

App developers can choose to implement CyREST Commands (or not). The easiest way to check is to open the Swagger docs when you have Cytoscape running: Help > Automation > CyREST Commands API: http://localhost:1234/v1/swaggerUI/swagger-ui/index.html?url=http%3A%2F%2Flocalhost%3A1234%2Fv1%2Fcommands%2Fswagger.json#/

This will show you the namespaces, commands and parameters that are available, depending on which apps you have installed.

In the case of the cluterMaker2 app, you'll find really good support for most of their algorithms, including quite a few community clustering algos, such as glay, leiden, Newman's leading eigenvector, and others.

You run command-based functions using the same pattern, e.g., http://cytoscape.org/RCy3/reference/commandsPOST.html

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