[Bioc-devel] Replacement for CytoscapeWindowClass from devel RCy3

Alex Pico alex.pico at gladstone.ucsf.edu
Sat Mar 31 00:50:15 CEST 2018

Hi Robert,

Indeed, lots of changes being made in this major version bump to RCy3. The goals are to align better with the rapid development of Cytoscape’s REST API. A description of how to “upgrade” existing scripts is provided here:
https://github.com/cytoscape/RCy3/wiki/Upgrading-Existing-Scripts <https://github.com/cytoscape/RCy3/wiki/Upgrading-Existing-Scripts>

In the case you pointed to the upgrade is not too bad (see attached):
 * Replace all instances/references to CyWindow Objects with a simple numeric, the network SUID. 
	Note: that even this reference is now optional for all functions, i.e., you can leave it out completely if you know that you are operating on the “current” network in Cytoscape. If you’re not sure, then this is how you specify networks now.
 * Replaced getAllEdgeAttributes with getTableColumns(‘edge’)

That’s it!  If you have any more questions, please ask.
 - Alex

> On Mar 30, 2018, at 9:13 AM, Robert M. Flight <rflight79 at gmail.com> wrote:
> My package, categoryCompare, is failing in Bioc devel.
> The reason appears to be exports in previous versions of RCy3 no longer being exported, namely the "CytoscapeWindowClass".
> I had some methods where behavior was defined based on being passed an object of "CytoscapeWindowClass" (see https://github.com/rmflight/categoryCompare/blob/7305185a65f80b108d50971b350c165a4e0cbe47/R/outCytoscape.r#L37 <https://github.com/rmflight/categoryCompare/blob/7305185a65f80b108d50971b350c165a4e0cbe47/R/outCytoscape.r#L37> for an example).
> It appears this class no longer exists in the devel version of RCy3, and what is noted as a replacement for the deprecated function that created it (example being createNetworkFromGraph), has no specific class outside of returning a "function".
> I could use some advice on how I should modify my method signature to handle this for the next version of RCy3, or if the object returned will indeed have a "class" attached to them that can be checked via method signatures.
> Thanks,
> -Robert
> Robert M Flight, PhD
> Bioinformatics Research Associate
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