[R] mhplot error with test example: "ylim not found"

[Jing Hua Zhao]

Many thanks Peter. I have uploaded 1.0-23 which should have this fixed.
Jing Hua

-----Original Message-----
From: Peter Ehlers [mailto:ehlers at ucalgary.ca] 
Sent: 28 June 2010 15:47
To: vaneet
Cc: r-help at 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