[BioC] Kegg pathways overlay with log fold change values

[Paul Shannon]

With RCytoscape 

  http://bioconductor.org/packages/2.10/bioc/html/RCytoscape.html
  http://db.systemsbiology.net:8080/cytoscape/RCytoscape/versions/current/index.html

it is straightforward to 

  1) Display a KEGG network retrieved by Jitao David Zhang's KEGGgraph package
  2) control all visual attributes of the graph, using simple 'vizmap' rules and data (e.g., from limma and SPIA)

For instance, to control node color:

 cw <- new.CytoscapeWindow ('setNodeColorRule.test', graph=makeSimpleGraph())
 displayGraph (cw)
 layoutNetwork (cw, 'jgraph-spring')
 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)   # applies all current vizmap rules

Reproducing the original KEGG layout can be a bit of work.  In principle, we could obtain the coordinates from the kgml file, and apply them with repeated calls to RCytoscape's setNodePosition method.  In practice, I usually use a combination of automatic layout, and manual layout, saving the result via a call to the saveLayout method.

For a fully worked up example, see 

  http://rcytoscape.systemsbiology.net/versions/current/gallery/fendtYeast/

 - Paul

On Jun 11, 2012, at 5:24 AM, alessandro brozzi wrote:

> hi,
> you might try this:
> 
> http://bioinformatics.oxfordjournals.org/content/25/11/1470.short
> http://bioc.ism.ac.jp/2.8/bioc/html/KEGGgraph.html
> 
> Alex
> On Mon, Jun 11, 2012 at 2:18 PM, Amit Kumar Kashyap <amitonbiochem at gmail.com
>> wrote:
> 
>> Hello all,
>> 
>> does anyone  knows how we can overlay expression data { coloring with up
>> and down genes } in pathways using R package or any other script.
>> 
>> Especially the results from SPIA package , we get the  kegg link like this
>> ...
>> 
>> 
>> http://www.genome.jp/dbget-bin/show_pathway?hsa05200+999+22798+3915+3673+3675+6776+4233+2260+2263+7039+3082+5899+5337+5579+112399+2034+9063+1029+355+650+5743+596+7188+1612+2113+4254
>> 
>> 
>> Now I would like to color up and down regulated genes according to
>> differentially expressed genes from limma package results.
>> 
>> 
>> Thanks in advance.
>> 
>> Kind Regards
>> -Amit Kumar
>> 
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>> 
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