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=0.00001,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 <sokovic.anamar...@gmail.com> 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.