[BioC] problem getting setNodeColorRule from RCytoscape to work

[Burak Kutlu]

Same deal for "setEdgeColorRule" under the same settings..

# omitting the steps to load the simpleGraph example that comes with RCytoscape
>   setEdgeColorRule (cw, 'edgeType',  edgeType.values, colors, mode='lookup')
Error in convertToR(xmlParse(node, asText = TRUE)) : 
  faultCode: 1001 faultString: Attribute edgeType could not be found.



On Mar 17, 2012, at 10:13 AM, Burak Kutlu wrote:

> Hello, 
> Trying to replicate the example provided in the help page for setNodeColorRule, unfortunately it does not work for me.
> Any suggestions?
> thanks
> -burak
> 
> # example from the help page for setNodeColorRule
> 
>> cw <- new.CytoscapeWindow ('setNodeColorRule.test', graph=makeSimpleGraph())
>  control.points <- c (-3.0, 0.0, 3.0)   # typical range of log-fold-change ratio values
>    # paint negative values shades of green, positive values shades of
>    # red, out-of-range low values are dark green; out-of-range high
>    # values are dark red
>  node.colors <- c ("#00AA00", "#00FF00", "#FFFFFF", "#FF0000", "#AA0000")
>  setNodeColorRule (cw, node.attribute.name='lfc', control.points, node.colors, mode='interpolate')
>  redraw (cw)
>  data.values <- c ("kinase", "transcription factor", "glycoprotein")
>  node.colors <- c ("#0000AA", "#FFFF00", "#0000AA") 
>  setNodeColorRule (cw, node.attribute.name='type', data.values,   node.colors, mode='lookup', default.color='#AA0000')
>>  control.points <- c (-3.0, 0.0, 3.0)   # typical range of log-fold-change ratio values
>>    # paint negative values shades of green, positive values shades of
>>    # red, out-of-range low values are dark green; out-of-range high
>>    # values are dark red
>>  node.colors <- c ("#00AA00", "#00FF00", "#FFFFFF", "#FF0000", "#AA0000")
>>  setNodeColorRule (cw, node.attribute.name='lfc', control.points, node.colors, mode='interpolate')
> Error in convertToR(xmlParse(node, asText = TRUE)) : 
>  faultCode: 1001 faultString: Attribute lfc could not be found.
>>  redraw (cw)
>>  data.values <- c ("kinase", "transcription factor", "glycoprotein")
>>  node.colors <- c ("#0000AA", "#FFFF00", "#0000AA") 
>>  setNodeColorRule (cw, node.attribute.name='type', data.values,   node.colors, mode='lookup', default.color='#AA0000')
> Error in convertToR(xmlParse(node, asText = TRUE)) : 
>  faultCode: 1001 faultString: Attribute type could not be found.
>> 
> 
> 
> ## session info
> 
>> sessionInfo()
> R version 2.14.2 (2012-02-29)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] RCytoscape_1.5.2    XMLRPC_0.2-4        graph_1.32.0       
> [4] BiocInstaller_1.2.1
> 
> loaded via a namespace (and not attached):
> [1] RCurl_1.91-1 tools_2.14.2 XML_3.9-4