Question: Kegg pathways overlay with log fold change values
0
gravatar for Amit Kumar Kashyap
7.3 years ago by
Amit Kumar Kashyap50 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+36 73+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]]
pathways limma spia • 1.5k views
ADD COMMENTlink modified 7.3 years ago by alessandro brozzi120 • written 7.3 years ago by Amit Kumar Kashyap50
Answer: Kegg pathways overlay with log fold change values
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gravatar for alessandro brozzi
7.3 years ago by
European Union
alessandro brozzi120 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+906 3+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]] > > _______________________________________________ > Bioconductor mailing list > 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]]
ADD COMMENTlink written 7.3 years ago by alessandro brozzi120
With RCytoscape http://bioconductor.org/packages/2.10/bioc/html/RCytoscape.html http://db.systemsbiology.net:8080/cytoscape/RCytoscape/versions/curr ent/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/fendtY east/ - 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+90 63+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]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 7.3 years ago by Paul Shannon750
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/curr ent/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/fendt Yeast/ > > - 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+906 3+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]] > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> 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]] > > > > _______________________________________________ > > Bioconductor mailing list > > 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]]
ADD REPLYlink written 7.3 years ago by Amit Kumar Kashyap50
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