Hello ,
Thank you very much , I will look in these links .

Kind Regards
-Amit Kumar



On Mon, Jun 11, 2012 at 2:42 PM, Paul Shannon <pshannon@fhcrc.org> wrote:

> 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@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
> >>
> >>       [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
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> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> > Bioconductor@r-project.org
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>
>

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