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
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