[BioC] problem getting setNodeColorRule from RCytoscape to work

[Paul Shannon]

Thanks, Burak.  

So far so good.  Now try, if you will --  just to step through this slow and easy:

> 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)

 - Paul


On Mar 17, 2012, at 11:04 AM, Burak Kutlu wrote:

> Hi Paul
> Thanks for the prompt response!!
> 
> Here's the output which looks identical to yours. 
> 
>> noa.names (cw at graph)
> [1] "type"  "lfc"   "label" "count"
>> noa (cw at graph, 'lfc')
> A  B  C 
> -3  0  3 
> 
> -burak
> 
> On Mar 17, 2012, at 11:02 AM, Paul Shannon wrote:
> 
>> noa.names (cw at graph)
>> noa (cw at graph, 'lfc')
>