how to call an app from Cytoscape using R?

Hi everyone,

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

something like in the code below,

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


If running R4.2 try

if (!require("BiocManager", quietly = TRUE))



Thanks for the help. I have RCy3, but my question was how to call the apps of Cytoscape in R. Means, let's say the CytoscapeApp is a function in the RCy3 package to call a Cytoscape app.
So, I am asking if it's possible to play, for example, to apply different clustering algorithms for my graph using the RCy3 package in R and see the effect on Cytoscape.


It’s possible to call functions from source in C/C+, Python and Haskell and Julia, although the last two don’t seem well-established.

If Cytoscape can be shell scripted you could call through System(), except on Ventura currently (bug in current RStudio).

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