R语言制作GWAS 曼哈顿图 自编教程.pdf

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1、R语言制作曼哈顿图-自编教程一、TXT文件格式（1）在excel格式（带表）头如下：（2）“另存为”“文本文件（制表符分割）（*.txt）”二、R语言制图1、改变所在R语言工作目录（所在文件目录）2、更改所编程语言的检验水平线（P=0.05和P=0.01）在“1”和“2”处的取值分别代表着显著水平（P<0.05）和极显著水平（P<0.01），分别取值为：0.05÷SNP数目。3、更改导入的“TXT”文件和保存的“pdf”文件名：程序语言如下：（只输入双虚线中间的语言部分）===============================================

2、===========manhattan<-function(dataframe,pchsize=19,colors=c("gray10","gray100"),ymax="max",limitchromosomes=1:19,suggestiveline=-log10(1.78916E-08),genomewideline=-log10(8.94582E-08),annotate=NULL,...){d=dataframeif(!("CHR"%in%names(d)&"BP"%in%names(d)&"P"%in%names(d)))stop("Makesure

3、yourdataframecontainscolumnsCHR,BP,andP")if(any(limitchromosomes))d=d[d$CHR%in%limitchromosomes,]d=subset(na.omit(d[order(d$CHR,d$BP),]),(P>0&P<=1))#removena's,sort,andkeeponly0

4、")ymax<-ceiling(max(d$logp))if(ymax<8)ymax<-8numchroms=length(unique(d$CHR))if(numchroms==1){d$pos=d$BPticks=floor(length(d$pos))/2+1}else{for(iinunique(d$CHR)){if(i==1){d[d$CHR==i,]$pos=d[d$CHR==i,]$BP}else{lastbase=lastbase+tail(subset(d,CHR==i-1)$BP,1)d[d$CHR==i,]$pos=d[d$CHR==i,]$

5、BP+lastbase}ticks=c(ticks,d[d$CHR==i,]$pos[floor(length(d[d$CHR==i,]$pos)/2)+1])}}if(numchroms==1){with(d,plot(pos,logp,ylim=c(0,ymax),ylab=expression(-log[10](italic(p))),xlab=paste("Chromosome",unique(d$CHR),"position"),...))}else{with(d,plot(pos,logp,ylim=c(0,ymax),ylab=expression(

6、-log[10](italic(p))),xlab="Chromosome",xaxt="n",type="n",...))axis(1,at=ticks,lab=unique(d$CHR),...)icol=1for(iinunique(d$CHR)){with(d[d$CHR==i,],points(pos,pch=pchsize,logp,col=colors[icol],...))icol=icol+1}}if(!is.null(annotate)){d.annotate=d[which(d$SNP%in%annotate),]with(d.annotat

7、e,points(pos,logp,col="green3",...))}if(suggestiveline)abline(h=suggestiveline,col="blue")if(genomewideline)abline(h=genomewideline,col="red")}d=read.table(file="GLM_眼肌面积_胴体重协变量.txt",header=TRUE)pdf("GLM_眼肌面积_胴体重协变量.pdf");manhattan(d,limitchromosomes=1:30,colors=c("#234589","red","#43

8、1287"