Thanks for your help, Rui! That works and will save me a lot of trouble. --Kelly
-----Original Message----- From: Rui Barradas [mailto:ruipbarra...@sapo.pt] Sent: Tuesday, July 10, 2012 2:24 AM To: Vining, Kelly Cc: r-help@r-project.org Subject: Re: [R] boxplot with "cut" Hello, Maybe this iss what you're looking for. GD is your data.frame. multi.boxplot <- function(x, by, ...){ x <- as.data.frame(x) sp <- split(x, by) len <- length(sp) - 1 n <- ncol(x) n1 <- n + 1 boxplot(x[[ 1 ]] ~ by, at = 0:len*n1 + 1, xlim = c(0, (len + 1)*n1), ylim = range(unlist(x)), xaxt = "n", ...) for(i in seq_len(n)[-1]) boxplot(x[[i]] ~ by, at = 0:len*n1 + i, xaxt = "n", add = TRUE, ...) axis(1, at = 0:len*n1 + n1/2, labels = names(sp), tick = TRUE) } cols <- grep("ReadCount", names(GD)) multi.boxplot(GD[, cols], cut(GD$GeneDensity, breaks=10)) If this is it and you don't like those x-axis tick lables, use as.integer(cut(...etc...)). Hope this helps, Rui Barradas Em 09-07-2012 20:51, Vining, Kelly escreveu: > Dear UseRs, > I'm making box plots from a data set that looks like this: > > > Chr Start End GeneDensity ReadCount_Explant ReadCount_Callus > ReadCount_Regen > 1 1 1 10000 107.82 1.243 1.047 > 1.496 > 2 1 10001 20000 202.50 0.835 0.869 > 0.456 > 3 1 20001 30000 158.80 1.813 1.529 > 1.131 > 4 1 30001 40000 100.53 1.731 1.752 > 1.610 > 5 1 40001 50000 100.53 3.056 2.931 > 3.631 > 6 1 50001 60000 100.53 1.960 2.013 > 2.459 > > I'm breaking the "GeneDensity" column into deciles, then making a box plot of > the relationship between the GeneDensity parameter and each of the three > "ReadCount" columns. Here's an example of one of my boxplot commands: > > boxplot(GeneDensity$ReadCount_Explant ~ > cut(GeneDensitySorted$GeneDensity, breaks=10), ylim=c(0,40), > ylab="RPKM", xlab="GENE DENSITY (LOW -> HIGH)", main="INTERNODE > EXPLANT") > > Right now, I'm making three separate graphs: one for each of the three > "ReadCount" columns. I'd like to put all three sets on one graph, so that > each decile is represented by three boxes, one for each ReadCount category, > but don't know how to make that work. I tried this: > > boxplot(GeneDensitySorted$ReadCount_Explant ~ > cut(GeneDensitySorted$GeneDensity, breaks=10), > GeneDensitySorted$ReadCount_Callus ~ > cut(GeneDensitySorted$GeneDensity, breaks=10), > GeneDensitySorted$ReadCount_Regen ~ cut(GeneDensitySorted$GeneDensity, > breaks=10), ylim=c(0,40), ylab="RPKM", xlab="GENE DENSITY (LOW -> > HIGH)") > > Not surprisingly, I got this error: > > Error in as.data.frame.default(data) : > cannot coerce class '"formula"' into a data.frame > > Does anyone know how to accomplish this box plot? > > Any help is much appreciated. > > --Kelly V. > ______________________________________________ > 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. > ______________________________________________ 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.
