how to call an app from Cytoscape using R?

[amare]

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)")

Thanks!

[technocrat]

If running R4.2 try

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RCy3")

[amare]

@technocrat

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.

[technocrat]

(facepalm)

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).