Re: [R] how to change manhattan plot code to get a different color per chromosome
Hi Jim,
thank you so much for this elaborate code I will definitely use some
hacks from it in the future.
For now, for the purpose of compactness of the code I just set
manually colors which I want to be there:
manhattan(results_log,chr="CHR",bp="POS",p="META_pval",snp="MARKER",suggestiveline
= F, genomewideline = F,main = "Gokind old",col = c("red2", "orange",
"gold1","springgreen4", "dodgerblue",
"darkorchid1","orchid1"),ylim=c(0,9),cex = 0.6)
in this qqman function.
Cheers,
Ana
On Tue, Jun 16, 2020 at 4:00 AM Jim Lemon wrote:
>
> Hi Ana,
> Your attached image seems to have bailed out before landing in the
> list. Here's how to do it using a simple manhattan plot with the data
> from:
>
> https://reneshbedre.github.io//assets/posts/mhat/gwas_res_sim.csv
>
> gwas<-read.csv("gwas_res_sim.csv",stringsAsFactors=FALSE)
> # get the data into chromosome order
> gwas<-gwas[order(gwas$chr,gwas$SNP),]
> gwas$BP<-rep(NA,dim(gwas)[1]
> # fake some base positions
> for(chromosome in 1:20) {
> snporder<-order(as.numeric(gsub("rs","",gwas[gwas$chr == chromosome,"SNP"])))
> gwas$BP[gwas$chr == chromosome]<-
> as.numeric(paste(chromosome,snporder,sep="."))
> }
> library(plotrix)
> # set the chromosome colors here - be more creative than me
> chrcol<-color.scale(1:10,extremes=c("red","blue"))
>
> # simple manhattan plot function
> manhattan<-function(x,CHR="CHR",BP="BP",SNP="SNP",p="p",
> main="Manhattan Plot",xlab="Chromosome",ylab="-log10(p)",
> pch=".",cex=1,siglevel=0.1,sigcol="green",sigcex=2,
> chrlab=NULL,chrcol=NULL,annotate=FALSE) {
>
> par(xaxs="i",yaxs="i")
> nchr<-length(unique(x[,CHR]))
> if(is.null(chrlab)) chrlab<-1:nchr
> ypos<--log10(x[,p])
> plot(x[,BP],ypos,ylim=c(0,max(ypos,na.rm=TRUE)*1.05),
> main=main,xlab=xlab,ylab=ylab,
> pch=pch,col=chrcol[x[,CHR]],cex=4,xaxt="n")
> abline(h=-log10(siglevel),lty=2)
> staxlab(1,at=(1:nchr) + 0.5,labels=chrlab)
> sigindx<-which(ypos >= -log10(siglevel))
> sigSNP<-unique(x[sigindx,SNP])
> cat(length(sigindx),"sig\n")
> points(x[sigindx,BP],ypos[sigindx],
> pch=pch,col=sigcol,cex=sigcex)
> if(annotate) text(x[sigindx,BP],ypos[sigindx]*1.03,x[sigindx,SNP])
> return(sigSNP=sigSNP)
> }
>
> manhattan(gwas,CHR="chr",p="pvalue",cex=4,sigcex=6,
> chrcol=chrcol,annotate=TRUE)
>
> Jim
>
> On Tue, Jun 16, 2020 at 8:06 AM Ana Marija
> wrote:
> >
> > Hello,
> >
> > Is there is a way to set colors in this plot to look like this one in
> > attach (different color for each CHR-there is 22 of them)?
> >
> >
> > library(qqman)
> > results_log <- read.table("meta_p_pos_chr.F",
> > head=TRUE,stringsAsFactors=FALSE)
> > png("META.png")
> > manhattan(results_log,chr="CHR",bp="POS",p="META_pval",snp="MARKER",ylim
> > = c(0, 10))
> > dev.off()
> >
> > Thanks
> > Ana
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > 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-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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] how to change manhattan plot code to get a different color per chromosome
Hi Ana,
Your attached image seems to have bailed out before landing in the
list. Here's how to do it using a simple manhattan plot with the data
from:
https://reneshbedre.github.io//assets/posts/mhat/gwas_res_sim.csv
gwas<-read.csv("gwas_res_sim.csv",stringsAsFactors=FALSE)
# get the data into chromosome order
gwas<-gwas[order(gwas$chr,gwas$SNP),]
gwas$BP<-rep(NA,dim(gwas)[1]
# fake some base positions
for(chromosome in 1:20) {
snporder<-order(as.numeric(gsub("rs","",gwas[gwas$chr == chromosome,"SNP"])))
gwas$BP[gwas$chr == chromosome]<-
as.numeric(paste(chromosome,snporder,sep="."))
}
library(plotrix)
# set the chromosome colors here - be more creative than me
chrcol<-color.scale(1:10,extremes=c("red","blue"))
# simple manhattan plot function
manhattan<-function(x,CHR="CHR",BP="BP",SNP="SNP",p="p",
main="Manhattan Plot",xlab="Chromosome",ylab="-log10(p)",
pch=".",cex=1,siglevel=0.1,sigcol="green",sigcex=2,
chrlab=NULL,chrcol=NULL,annotate=FALSE) {
par(xaxs="i",yaxs="i")
nchr<-length(unique(x[,CHR]))
if(is.null(chrlab)) chrlab<-1:nchr
ypos<--log10(x[,p])
plot(x[,BP],ypos,ylim=c(0,max(ypos,na.rm=TRUE)*1.05),
main=main,xlab=xlab,ylab=ylab,
pch=pch,col=chrcol[x[,CHR]],cex=4,xaxt="n")
abline(h=-log10(siglevel),lty=2)
staxlab(1,at=(1:nchr) + 0.5,labels=chrlab)
sigindx<-which(ypos >= -log10(siglevel))
sigSNP<-unique(x[sigindx,SNP])
cat(length(sigindx),"sig\n")
points(x[sigindx,BP],ypos[sigindx],
pch=pch,col=sigcol,cex=sigcex)
if(annotate) text(x[sigindx,BP],ypos[sigindx]*1.03,x[sigindx,SNP])
return(sigSNP=sigSNP)
}
manhattan(gwas,CHR="chr",p="pvalue",cex=4,sigcex=6,
chrcol=chrcol,annotate=TRUE)
Jim
On Tue, Jun 16, 2020 at 8:06 AM Ana Marija wrote:
>
> Hello,
>
> Is there is a way to set colors in this plot to look like this one in
> attach (different color for each CHR-there is 22 of them)?
>
>
> library(qqman)
> results_log <- read.table("meta_p_pos_chr.F",
> head=TRUE,stringsAsFactors=FALSE)
> png("META.png")
> manhattan(results_log,chr="CHR",bp="POS",p="META_pval",snp="MARKER",ylim
> = c(0, 10))
> dev.off()
>
> Thanks
> Ana
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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] how to change manhattan plot code to get a different color per chromosome
Hello,
Is there is a way to set colors in this plot to look like this one in
attach (different color for each CHR-there is 22 of them)?
library(qqman)
results_log <- read.table("meta_p_pos_chr.F", head=TRUE,stringsAsFactors=FALSE)
png("META.png")
manhattan(results_log,chr="CHR",bp="POS",p="META_pval",snp="MARKER",ylim
= c(0, 10))
dev.off()
Thanks
Ana
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.
