[BioC] 5000 nodes RCytoscape

[Paul Shannon]

Hi Ruben,

Please send me the results of your sessionInfo() as well as the version numbers of Cytoscape and the CytoscapeRPC plugin.

It would also help to see the precise code you used, presented in order, statement by statement, so that I can confidently recreate the error you see.

Thanks,

 - Paul

On Mar 19, 2013, at 10:42 PM, rubens at andrew.cmu.edu wrote:

> Hi Paul Shannon,
> 
> I used the code pasted below (posted by you in a thread) to create a 5000
> nodes graph (using an adjacency matrix). But it outputs the next errors:
> 
>> cw = CytoscapeWindow (window.name, g)
> Error in convertToR(xmlParse(node, asText = TRUE)) :
>  faultCode: 0 faultString: Failed to invoke method createNetwork in class
> tudelft.CytoscapeRPC.CytoscapeRPCCallHandler: minimum bounding rectangle
> of movable nodes and edge anchors not free to rotate within
> MutableGraphLayout boundaries
>> displayGraph (cw)
> entering RCytoscape::displayGraph
> sending 625 nodes
> Error in convertToR(xmlParse(node, asText = TRUE)) :
>  faultCode: 1001 faultString: Network 3 not found
>> redraw (cw)
> Error in convertToR(xmlParse(node, asText = TRUE)) :
>  faultCode: 1001 faultString: Network 3 not found
>> layout (cw, 'jgraph-spring')
> Error in convertToR(xmlParse(node, asText = TRUE)) :
>  faultCode: 1001 faultString: Network 3 not found
> 
> 
> I try the same code with 1875 nodes and it works perfectly. I try it with
> 2500 and it outputs the same errors.
> 
> I will be very grateful if you help me to solve this problem.
> 
> Thanks
> 
> Ruben Sanchez
> CMU
> 
> 
> 
> 
> 
> 
> 
> 
> 
> R CODE USED
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> 
> library (RCytoscape)
> 
> 
>  # if you want to remove self-loops, enable this line
> #diag (m) = 0   # remove any self-loops
> 
>  # now create a Bioconductor graph of subclass 'graphAM'
> g = new ('graphAM', adjMat=m, edgemode='directed')
> 
>  # these next few lines are useful if you run this script repetetively,
> since RCy requires that all window names are unique,
>  # these lines allows you to detect and then delete any pre-existing
> window with the same name
> 
> if (!exists ('cy'))   # get access to application-level Cytoscape operations.
>  cy = CytoscapeConnection ()
> 
> window.name = 'adjacency matrix graph simple demo'
> 
> if (window.name %in% as.character (getWindowList (cy)))
>  deleteWindow (cy, window.name)
> 
>  # now create a window, send the graph, render it, lay it out
> 
> cw = CytoscapeWindow (window.name, g)
> displayGraph (cw)
> redraw (cw)
> layout (cw, 'jgraph-spring')
>