Many thanks Peter. I have uploaded 1.0-23 which should have this fixed. Jing Hua
-----Original Message----- From: Peter Ehlers [mailto:ehl...@ucalgary.ca] Sent: 28 June 2010 15:47 To: vaneet Cc: r-help@r-project.org; Jing Hua Zhao Subject: Re: [R] mhplot error with test example: "ylim not found" It seems to me that gap::mhtplot needs a fix. You might want to contact the maintainer (cc'd). In the meantime, you should be able to place an object ylim in your workspace before calling the function: ylim <- c(0, 10) mhtplot(test, ylim = c(0, 10)) Of course, you could also just fixt the function (it's short and the fix is easy). -Peter Ehlers On 2010-06-23 8:47, vaneet wrote: > > Hello all, > > I am trying to make a genome association plot for p-values related to SNPs > and was fortunate to find that R contains a package that produces Manhattan > plots which is what's preferred for my current project. The function > mhtplot() is found in the 'gap' package which I installed in R 2.11.1 on > Windows. I thought I'd test out the function first with the examples they > give in the documentation: > > # foo example > test<- matrix(c(1,1,4,1,1,6,1,10,3,2,1,5,2,2,6,2,4,8),byrow=TRUE,6) > mhtplot(test) > mhtplot(test,logscale=F) > > # fake example with Affy500k data > affy<-c(40220, 41400, 33801, 32334, 32056, 31470, 25835, 27457, 22864, > 28501, 26273, > 24954, 19188, 15721, 14356, 15309, 11281, 14881, 6399, 12400, 7125, > 6207) > CM<- cumsum(affy) > n.markers<- sum(affy) > n.chr<- length(affy) > test<- data.frame(chr=rep(1:n.chr,affy),pos=1:n.markers,p=runif(n.markers)) > > # to reduce size of the plot > # bitmap("mhtplot.bmp",res=72*5) > oldpar<- par() > par(las="2",cex=0.6) > colors<- rep(c("blue","green"),11) > mhtplot(test,colors=colors,pch=19,bg=colors) > title("A simulated example according to EPIC-Norfolk QCed SNPs") > > When I run either of the examples the following results: > > Error in mhtplot(........) : object 'ylim' not found > > Even though I'm not sure why it would require this parameter, when I tried > to fill in the parameter (ylim = c(0,10)) the same error results. I am not > sure how to get around this. > > Vaneet ______________________________________________ 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.
