RCytoscape: unable to find an inherited method for function ‘nodeData<-’
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vmanem ▴ 10
@vmanem-8250
Last seen 9.4 years ago
Canada

Dear Cytoscape users,

I am using Cytoscape (V 2.8.1) with CytoscapeRPC plugin to view large scalenetworks. I am getting the following error.

g <- new ("graphAM", adjMat = adjmat, edgemode="undirected")
cw <- new.CytoscapeWindow ('vignette', graph=g, overwriteWindow=TRUE)

nodes have no label attribute -- adding default labels
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘nodeData<-’ for
signature ‘"graphAM", "matrix", "character"’

Can someone advise me in fixing this error. Thanks... !

 

rcytoscape • 1.4k views
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pshannon ▴ 100
@pshannon-6931
Last seen 9.0 years ago
United States

The best course -- which we have discussed off-line, and which I believe seems promising to you -- is to switch to the new RCy3 package, currently submitted to Bioc, available on github, and for which we are actively soliciting testers.

If you will send me some more information I will try to reproduce the error you see.  Please send the results of

traceback()   # when the error ocurrs

sessionInfo() 

 - Paul

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Paul, where is the proper forum to discuss potential bugs and possibly contribution for RCy3? The github repo?

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