On 02/28/2012 08:13 AM, aishsk wrote:
Hi I am using the ggplot2 package for the volcano plot and I am using the following code for the same:g = ggplot(data=data, aes(x=data[11], y=-log10(data[12]), colour=threshold)) + + geom_point(alpha=0.4, size=1.75) + + opts(legend.position = "none") + + xlim(c(-10, 10)) + ylim(c(0, 15)) + + xlab("log2 fold change") + ylab("-log10 p-value") data[11] is a column of the fold change values and data[12] contains the P values and I am getting a following error: Error: geom_point requires the following missing aesthetics: x, y What can be done for the same ? And if not what other package may I use for the same in which I don't have to use a lmfit model?
Have you tried, if 'data' is a data.frame, simply plot(data[[1]], -log10(data[[12]])) ?
Martin
Thanks -- View this message in context: http://r.789695.n4.nabble.com/Volcano-Plot-tp4428622p4428622.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.
-- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 ______________________________________________ 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.
