Thanks again Alex! Copying bioc-devel list in case anyone else has similar issues.
On Fri, Mar 30, 2018, 8:15 PM Alex Pico <alex.p...@gladstone.ucsf.edu> wrote: > I think that’s correct. A few tips based on looking at your particular > usage… > > 1) cw <- CytoscapeWindow(graphName, graph=ccGraph, …) > > ...becomes > > net.suid <- createNetworkFromGraph(graph=ccGraph,title=graphName, ...) > > 2) You don’t need `displayGraph(cw)` anymore > > 3) You can simply delete `cw` from all subsequent functions. Optionally, > you can replace it with `network=net.suid` > > 4) You don’t need `redraw(cw)` anymore > > 5) Your “Rule” functions become... > > setNodeTooltipMapping(nodeAtts[toolTipLoc[1]]) > > setNodeColorMapping(‘fillcolor’, tmpCols, tmpCols, ‘d’, default.color=' > #FF0000’) > # or, if you have a column of hex colors already, try this: > setNodeColorMapping(‘fillcolor’, tmpCols, mapping.type= ‘p’, > default.color='#FF0000’) > > setNodeShapeMapping(‘shape’, nodeShapes, nodeShapes, ‘d’, default.shape=' > ellipse' ) > # again, if you have a column of hex colors already, try this: > setNodeShapeMapping(‘shape’, nodeShapes, mapping.type= ‘p’, default.shape= > 'ellipse') > > > Ok. Hope that helps! > - Alex > > On Mar 30, 2018, at 4:54 PM, Robert M. Flight <rfligh...@gmail.com> wrote: > > OK, I'll have to try out some of the examples and see if it works. In most > of my methods it would just mean removing that part of the signature, I > think. > > Robert > > On Fri, Mar 30, 2018, 7:44 PM Alex Pico <alex.p...@gladstone.ucsf.edu> > wrote: > >> Correct. This simplification comes at the cost of Object types. The >> advantages, however, include avoiding a false sense of state when CyREST is >> stateless. There was an whole class of errors and user issues based on >> breaks between the R Object and the Cytoscape network. Now, you can even >> restart R and pick right up in the middle of script (as far as RCy3 is >> concerned). >> >> Also, since in most cases you are working with one network at a time, you >> can actually ignore the SUID and let the default behavior (of working with >> the “current” network) take over and greatly simplify your scripts. >> >> - Alex >> >> On Mar 30, 2018, at 4:05 PM, Robert M. Flight <rfligh...@gmail.com> >> wrote: >> >> Alex, >> >> That makes sense. Appreciate the info on SUID. Again this is only a >> simple numeric though, right?? No class attribrute or formal class with it?? >> >> I like the fact that currently my methods know they are operating on a >> cytoscape network object, this breaks that paradigm. >> >> Will have to think about the best way to handle this. >> >> Robert >> >> On Fri, Mar 30, 2018, 6:50 PM Alex Pico <alex.p...@gladstone.ucsf.edu> >> wrote: >> >>> 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 >>> >>> >>> 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 <rfligh...@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 >>> 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 >>> Puller of Rabbits from Hats >>> Research Parasite >>> Resource Center for Stable Isotope Resolved Metabolomics >>> Manager, Systems Biology and Omics Integration Journal Club >>> Markey Cancer Center >>> CC434 Roach Building >>> University of Kentucky >>> Lexington, KY >>> >>> Twitter: @rmflight >>> Web: rmflight.github.io >>> ORCID: http://orcid.org/0000-0001-8141-7788 >>> EM rfligh...@gmail.com >>> PH 502-509-1827 <(502)%20509-1827> >>> >>> To call in the statistician after the experiment is done may be no more >>> than asking him to perform a post-mortem examination: he may be able to say >>> what the experiment died of. - Ronald Fisher >>> >>> >>> >> > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
