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!

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

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! > > _______________________________________________ > 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

Paul Shannon <pshannon at="" ...=""> writes: > > 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 > 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=Cy toscapeRPC Thank you for your help!

Paul Shannon <pshannon at="" ...=""> writes: > > Hi Tony, > > Thanks for sending the session and version info. > > Please see comments inline below... > > > 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 > Hi Paul, Problem solved! I followed your suggestions to upgrade all the packages, R, RCurl, RCytoscape, Rcytoscaperpc, still not working, then I also upgraded Cytoscape itself to 2.8.2, them everything work charmingly! Indeed, stay current! Thank you for your help and your wonderful software! Also attach my new sessionInfo in case someone need to check against. > sessionInfo() R version 2.15.0 (2012-03-30) 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_1.6.1 XMLRPC_0.2-4 graph_1.34.0 loaded via a namespace (and not attached): [1] BiocGenerics_0.2.0 RCurl_1.91-1 tools_2.15.0 XML_3.9-4 >