[BioC] problem getting setNodeColorRule from RCytoscape to work

[Paul Shannon]

Hi Tony,

It looks like a version problem.   Could you send the results of sessionInfo ()?  Include, too, please, the version of Cytoscape you are running, and which version of Jan Bot's CytoscapeRPC plugin.  I'll bet we can figure it out quickly.

- Paul


On Apr 2, 2012, at 2:20 PM, Tony wrote:

> Paul Shannon <pshannon at ...> writes:
> 
>>> cw = new.CytoscapeWindow (title = 'bug?', graph=g)
>>> displayGraph (cw)
>>   entering RCytoscape::displayGraph
>>   sending 3 nodes
>>   sending 3 edges
>>   adding node attributes...
>>   [1] "type"
>>   [1] "lfc"
>>   [1] "label"
>>   [1] "count"
>>   adding edge attributes...
>>   [1] "edgeType"
>>   entering setEdgeAttributesDirect, edgeType, with 3 names and 3 values
>>   [1] "score"
>>   entering setEdgeAttributesDirect, score, with 3 names and 3 values
>>   [1] "misc"
>> 
>>> noa (cw <at> graph, 'lfc')
>>   A  B  C
>>  -3  0  3
>> 
>>> control.points <- c (-3.0, 0.0, 3.0)   # typical range of log-fold-change 
> ratio values
>>> node.colors <- c ("#00AA00", "#00FF00", "#FFFFFF", "#FF0000", "#AA0000")
>>> noa (cw <at> graph, 'lfc')  # do this again, just to be sure
>>   A  B  C
>>  -3  0  3
>>> setNodeColorRule (cw, node.attribute.name='lfc', control.points, 
> node.colors, mode='interpolate')
>>> redraw (cw)
>> 
>> 
> 
> 
> Hi Paul,
> 
> I searched the archive and found this thread, my setNodeColorRule is not
> working but with a different reason. When I run your example code, I got:
> 
> Error in convertToR(xmlParse(node, asText = TRUE)) : 
>  faultCode: 0 faultString: Failed to invoke method 
> createContinuousNodeVisualStyle in class 
> tudelft.CytoscapeRPC.CytoscapeRPCCallHandler: 
> cytoscape.visual.mappings.ContinuousMapping.<init>
> (Ljava/lang/Class;Ljava/lang/String;)V
> 
> Any idea of what part is wrong with my side? Thanks so much!
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor