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$GeneDensity, breaks=10))
If this is it and you don't like those x-axis tick lables, use
as.integer(cut(...etc...)).
Hope this helps,
Rui Barradas
Em 09-07-2012 20:51, Vining, Kelly escreveu:
Dear UseRs,
I'm making box plots from a data set that looks like this:
Chr Start End GeneDensity ReadCount_Explant ReadCount_Callus
ReadCount_Regen
1 1 1 1 107.82 1.2431.047 1.496
2 1 10001 2 202.50 0.8350.869 0.456
3 1 20001 3 158.80 1.8131.529 1.131
4 1 30001 4 100.53 1.7311.752 1.610
5 1 40001 5 100.53 3.0562.931 3.631
6 1 50001 6 100.53 1.9602.013 2.459
I'm breaking the GeneDensity column into deciles, then making a box plot of the
relationship between the GeneDensity parameter and each of the three ReadCount columns.
Here's an example of one of my boxplot commands:
boxplot(GeneDensity$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.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
