[BioC] problem getting setNodeColorRule from RCytoscape to work
Tony
tonyatvt at gmail.com
Mon Apr 2 23:20:39 CEST 2012
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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