[BioC] problem getting setNodeColorRule from RCytoscape to work

[Paul Shannon]

Hi Tony,

Thanks for sending the session and version info.

Please see comments inline below...

> Hi Paul,
> 
> Thanks so much for your timely response. Here is the sessioninfo():
> 
>> sessionInfo ()
> R version 2.14.2 (2012-02-29)
> Platform: x86_64-pc-linux-gnu (64-bit)
> 
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
> [7] LC_PAPER=C                 LC_NAME=C                 
> [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] RCytoscape_1.4.4 XMLRPC_0.2-4     graph_1.32.0    
> 
> loaded via a namespace (and not attached):
> [1] RCurl_1.6-7  tools_2.14.2 XML_3.9-4   
>> 
> 
> My Cytoscape version is 2.7.0, CytoscapeRPC is version 1.8 downloaded from 
> http://chianti.ucsd.edu/cyto_web/plugins/displayplugininfo.php?name=CytoscapeRPC
> 
> Thank you for your help!

There are updates for a few of your packages, and for Cytoscape itself.  One plausible cause is RCurl.  Your version 1.6-7, and the current release is 1.91-1.  

May I suggest the following?  Upgrade RCurl (see http://www.omegahat.org/RCurl/) and then, if you don't mind, restart R, and send me the exact transcript of your R session, the few lines of code needed to reproduce the error.  When I see them in context (if the RCurl update does not fix the problem) then I could do a better job of figuring things out.  Meanwhile: I am sorry that you are running into trouble.

Also, I should warn you!  We have a new release of R, of Bioconductor, and RCytoscape.  Though it can be a little painful to make the transition, we generally encourage everyone to stay current.  Since the release happened only yesterday, finding the fix for your problem should be something we can do separately form the upgrade we might soon recommend.

 - 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!
> 
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