On Mon, Mar 28, 2011 at 3:05 PM, karena <dr.jz...@gmail.com> wrote: > I am using 'igraph' package to make some graphs of 'gene-gene interaction'. > > I can get a data.frame which has three columns. > gene1 gene2 pvalue > AGT MLR 1.2e-04 > MLR 11BHSD1 1.71e-05 > IFG2 11BHSD2 2.2e-07 > . . . > . . . > . . . > AGTR1 NPPA 3.2e-2 > > I have several questions: > 1) How can I make a plot in which the width of the edges can represent the > significance of the epistasis p values? I am thinking about getting another > column which is the -log(pvalue), so the larger the value is the more > significant the p value is.
epiG <- graph.data.frame(epitab) coords <- layout.fruchterman.reingold(epiG, weights=-log10(E(epiG)$pvalue)) plot(epiG, layout=coords, edge.width=-log10(E(epiG)$pvalue)) > 2) After I get the graph, how can I modify the image. Because all the nodes > in the image are numbers (0,1,.....,100), how can I add the gene name to > each node in the image? You cannot modify the image after the plotting. Well, you can, but it is a lot esier to specify all the parameters at the time of the plotting: plot(epiG, ..., vertex.label=V(epiG)$name, ...) See ?igraph.plotting for details. Best, Gabor > > -- > View this message in context: > http://r.789695.n4.nabble.com/Questions-about-igraph-package-tp3412734p3412734.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Gabor Csardi <csa...@rmki.kfki.hu> MTA KFKI RMKI ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
