[BioC] RCytoscape: object 'graph' not found error

[Paul Shannon]

Hi Christopher,

In a moment I will work this through step-by-step, but the solution is almost certain to change

  g <<- initEdgeAttribute (g, "edgeInteger", "integer", 0)

to 

  g <- initEdgeAttribute (g, "edgeInteger", "integer", 0)

The use of the global assignment operator is an old bad habit of mine, which you probably picked up from my documentation.  I will seek those out, and expunge them!

One would expect global assignment, however inelegant, to work in this case.  But I have seen that in some occasional circumstances the scoping rules and environment traversal behave oddly.   I think that is what you have encountered here.   Using the normal assignment operator is the right thing to do.

Please let me know how this goes.

 - Paul
  
On Dec 31, 2013, at 10:33 AM, Christopher T Gregg wrote:

> Hi,
> 
> I have encountered an error with RCytoscape that is unclear to me.  I have attached our script and data file and sessionInfo (at the bottom of the script) below.
> 
> Our data is an adjacency matrix and we wish to construct a weighted network graph in Cytoscape.  I am able to generate the graph object ('g'), which contains the gene names in the @adjMat slot from the adjacency matrix and it will generate a graph in Cytoscape.  However, when I attempt to add node and edge attributes to the g object, I get the following error:
> 
>> g <<- initEdgeAttribute (g, "edgeInteger", "integer", 0)
>> edgeData (g, from, to, "edgeInteger") <<- edgeInteger
> Error in edgeData(g, from, to, "edgeInteger") <<- edgeInteger :
>  object 'g' not found
> 
> The edgeInteger, from and to variables have the data of interest and the g object is successfully generated (see below), so I can't understand where the error lies.  Thank you for any and all help.
> 
> best wishes,
> Chris
> 
> #SUCCESSFUL GENERATION OF GRAPH OBJECT and EDGE INTEGER
> g <<- new ("graphAM", adjMat = dataNetR, edgemode="weighted")
>> g
> A graphAM graph with weighted edges
> Number of Nodes = 6
> Number of Edges = 7.5
>> str(g)
> Formal class 'graphAM' [package "graph"] with 5 slots
>  ..@ adjMat    : num [1:6, 1:6] 0 0 0 0 0 0 1 0 0 0 ...
>  .. ..- attr(*, "dimnames")=List of 2
>  .. .. ..$ : NULL
>  .. .. ..$ : chr [1:6] "ENSMUSG00000000037" "ENSMUSG00000004267" "ENSMUSG00000016757" "ENSMUSG00000019849" ...
>  ..@ edgeData  :Formal class 'attrData' [package "graph"] with 2 slots
>  .. .. ..@ data    : list()
>  .. .. ..@ defaults: list()
>  ..@ nodeData  :Formal class 'attrData' [package "graph"] with 2 slots
>  .. .. ..@ data    : list()
>  .. .. ..@ defaults:List of 1
>  .. .. .. ..$ nodeChar:Class 'STRING'  chr ""
>  ..@ renderInfo:Formal class 'renderInfo' [package "graph"] with 4 slots
>  .. .. ..@ nodes: list()
>  .. .. ..@ edges: list()
>  .. .. ..@ graph: list()
>  .. .. ..@ pars : list()
>  ..@ graphData :List of 1
>  .. ..$ edgemode: chr "weighted"
> 
>> edgeInteger
> [1] 0.13080159 0.14678129 0.10697558 0.12109223 0.14722505 0.19004585 0.08775686 0.15081269 0.04768105 0.21863816 0.19299134 0.17825061
> [13] 0.18689388 0.10821313 0.14221187
> 
> Christopher Gregg, PhD.
> New York Stem Cell Foundation-Robertson Investigator
> Assistant Professor, Neurobiology and Anatomy
> Adjunct Assistant Professor, Human Genetics
> 323 Wintrobe Bldg 530
> University of Utah, School of Medicine
> 20 North 1900 East
> Salt Lake City, Utah 84132-3401
> 
> phone: (801) 581-8212
> fax: (801) 585-9736
> ------------------------------------
> Gregg Lab Website: www.neuro.utah.edu/labs/gregg/index.html<http://www.neuro.utah.edu/labs/gregg/index.html>
> 
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