Re: [R] mhplot error with test example: "ylim not found"
Thank you, everyone. The function works fine now.
Vaneet
-Original Message-
From: Jing Hua Zhao [mailto:jinghua.z...@mrc-epid.cam.ac.uk]
Sent: Monday, June 28, 2010 2:46 PM
To: Peter Ehlers; Lotay, Vaneet
Cc: r-help@r-project.org
Subject: RE: [R] mhplot error with test example: "ylim not found"
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.
Re: [R] mhplot error with test example: "ylim not found"
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.
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.
[R] mhplot error with test example: "ylim not found"
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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