[BioC] problem getting setNodeColorRule from RCytoscape to work

[Tony]

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!