Hi, I am trying to generate bubble plot using Rgraphviz package to show fold changes of genes between two samples. In order to make things clear, I need show values of fold changes for each of the gene I am plotting. Therefore, adding x-axis and y-axis would be truly helpful to visualize. Does anyone knows if it is possible to do so and if yes, then how to do it? Thanks, Jiayi -- output of sessionInfo(): R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] Rgraphviz_1.28.0 graph_1.28.0 loaded via a namespace (and not attached): [1] tools_2.12.2 -- Sent via the guest posting facility at bioconductor.org.

On 07/02/2012 11:02 PM, Jiayi Hou [guest] wrote: > > Hi, > > I am trying to generate bubble plot using Rgraphviz package to show fold changes of genes between two samples. In order to make things clear, I need show values of fold changes for each of the gene I am plotting. Therefore, adding x-axis and y-axis would be truly helpful to visualize. Does anyone knows if it is possible to do so and if yes, then how to do it? Hi -- I'm not sure what 'bubble plot' is but perhaps Rgraphviz is not appropriate; maybe you want to use plot() and points(), the latter with different cex arguments? > plot(0, 0, xlim=c(0, 1), ylim=c(0, 1), type="n") > points(runif(30), runif(30), cex=runif(30) * 30) Martin > > Thanks, > > Jiayi > > -- output of sessionInfo(): > > R version 2.12.2 (2011-02-25) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Rgraphviz_1.28.0 graph_1.28.0 > > loaded via a namespace (and not attached): > [1] tools_2.12.2 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793