======简介======
客户需要进行全部染色体cnv的可视化。

目前流程不支持性染色体的可视化，需要补充。

======功能======
cnv的可视化。
======数据准备======
**1. cnv的检测结果：**

*ratio.txt.slim *BAF.txt.slim


**2. 可视化：**

<code>
Rscript cnv_profile.R
</code>

**cnv_profile.R ：**
<code>
## initializations and default values
setwd("./")
chrNum = 22
ploidy <- 2
# chromosome length, centromere position
chrLen<-c(249250621,243199373,198022430,191154276,180915260,171115067,159138663,146364022,141213431,135534747,135006516,133851895,115169878,107349540,102531392,90354753,81195210,78077248,59128983,63025520,48129895,51304566,155270560,59373566)
names(chrLen)<-c(1:chrNum,'X','Y')
centromere=c(125000000,93300000,91000000,50400000,48400000,61000000,59900000,45600000,49000000,40200000,53700000,35800000,17900000,17600000,19000000,36600000,24000000,17200000,26500000,27500000,13200000,14700000,60600000,12500000)
## execution
names(centromere)<-c(1:chrNum,'X','Y')
cumChrLen<-c(0,cumsum(chrLen))[-length(chrLen)]
names(cumChrLen)<-c(1:chrNum,'X','Y')
cumCen<-cumChrLen+centromere
names(cumCen)<-c(1:chrNum,'X','Y')

chrNum <- 24 #20210610
files <-read.table("./slim.config",sep="	")
png(filename = paste("ET203897",".CNV_profile.png",sep = ""),width=2400*2,height=nrow(files)*960*2,type="cairo-png",res=288*2)

par(mfrow=c(nrow(files)*2+2,1),mar=c(0.3,2,0.3,5))

plot(1:10,rep(0,10),col='white',bty='n',xaxt='n',yaxt='n',xlab='',ylab='',ylim=c(0,6))
text(5,2,"ET203897",cex=1.5)

#par(mfrow=c(2,1),mar=c(0.3,2,0.3,5))
for(j in 1:nrow(files)){
	### CNV profile
	par(mar=c(0,2,0.3,5))
	cat("Reading CNV file ...
")
	ratio <-read.table(as.character(files[j,2]), head=TRUE,sep="	")
	maxLevelToPlot <- 3

	for (i in c(1:length(ratio$Ratio))) {
		if (ratio$Ratio[i]>maxLevelToPlot) {
			ratio$Ratio[i]=maxLevelToPlot;
		}
	}
	ratio2<-subset(ratio,as.character(Chromosome) %in% c(1:chrNum,"X","Y"))#20210610
	ratio2$x<-cumChrLen[as.character(ratio2$Chromosome)]+ratio2$Start
	ratio2$color<-"darkolivegreen3"
	ratio2$color[ratio2$CopyNumber>2]<-"firebrick3"
	ratio2$color[ratio2$CopyNumber<2]<-"mediumblue"
        print(1)  #20210610
#	plot(ratio2$x,ratio2$Ratio*2,xlim = c(0,cumChrLen[chrNum+1]),ylim = c(0,maxLevelToPlot*ploidy),xlab = "",ylab = "",pch = ".",col = ratio2$color,bty='n',xaxt='n',yaxt='n')
	plot(ratio2$x,ratio2$Ratio*2,xlim = c(0,cumChrLen[chrNum]),ylim = c(0,maxLevelToPlot*ploidy),xlab = "",ylab = "",pch = ".",col = ratio2$color,bty='n',xaxt='n',yaxt='n') #20210610
        print(2) #20210610
	points(ratio2$x,ratio2$CopyNumber,cex=1.2,pch = ".",col = colors()[24])
	#plot(ratio2$x,ratio2$Ratio*2,ylim = c(0,maxLevelToPlot*ploidy),xlab = "",ylab = "",pch = ".",col = ratio2$color,bty=']',xaxt='n',yaxt='n')
	#axis(side=2,line=-0.95,at=0:6,labels=0:6,col='darkgrey',xpd=NA)
	segments(0,-0.1,0,6.1,lwd=1,xpd=T)
	for (i in 1:(chrNum)){  #20210610
		segments(cumChrLen[i],0.5,cumChrLen[i],5.5,lwd=1,lty=22,col="darkgrey")
	}
	for (i in 0:6){
		segments(-20000000,i,0,i,xpd=T)
		text(-10000000,i,i,pos=2,adj=0,xpd=T,cex=0.8,lwd=0.8)
	}
	## centromere
	text(cumCen[1:chrNum],rep(2,chrNum),labels=rep(".",chrNum),cex=2,adj=0)
	#text(cumCen[1:chrNum],rep(2,chrNum),labels=rep(".",chrNum),cex=2)
	text(cumCen[1:chrNum],rep(2.05,chrNum),labels=rep(".",chrNum),cex=2,adj=0)
	text(cumCen[1:chrNum],rep(2.03,chrNum),labels=rep(".",chrNum),cex=2,adj=0)
	text(cumCen[1:chrNum],rep(1.98,chrNum),labels=rep(".",chrNum),cex=2,adj=0)
	text(cumCen[1:chrNum],rep(1.95,chrNum),labels=rep(".",chrNum),cex=2,adj=0)
	mtext(side=2,line=0,"Copy Number",cex=0.5)
	### BAF
	BAF<-read.table(as.character(files[j,3]),head=TRUE,sep="	")
	BAF2<-subset(BAF,Chromosome %in% 1:chrNum)
	BAF2$x<-cumChrLen[as.character(BAF2$Chromosome)]+BAF2$Position
	BAF2$color<-colors()[1]
	BAF2$color[BAF2$A==0.5]<-colors()[92]
	BAF2$color[BAF2$A!=0.5 & BAF2$A>=0]<-colors()[62]

	par(mar=c(0.3,2,0,5))
	plot(BAF2$x,BAF2$BAF,ylim = c(-0.1,1.1),xlab = "",ylab = "",pch = ".",col = BAF2$color,bty='n',xaxt='n',yaxt='n')
	for (i in 1:chrNum){
     	  lBAF<-subset(BAF2,Chromosome==i)
        tt<-1
     	  pres<-1
        if (length(lBAF$FittedA)>4){
     	          for (n in c(2:(length(lBAF$FittedA)-pres-1))) {
           	            if (lBAF$FittedA[n]==lBAF$FittedA[n+pres]) {
                 	              tt[length(tt)+1] <- n
                        }
                }
                points(lBAF$x[tt],lBAF$FittedA[tt],pch = ".",col = colors()[24],cex=1.2)
                points(lBAF$x[tt],lBAF$FittedB[tt],pch = ".",col = colors()[24],cex=1.2)
        }
	}
	segments(0,-0.02,0,1.02,lwd=1,xpd=T)
	for (i in 2:(chrNum+1)){
		segments(cumChrLen[i],0,cumChrLen[i],1,lwd=1,lty=22,col="darkgrey")
	}
	for (i in seq(0,1,by=0.2)){
		segments(-20000000,i,0,i,xpd=T,lwd=0.8)
		text(-10000000,i,i,pos=2,adj=0,xpd=T,cex=0.8)
	}
	## sample label
	if(nrow(files)>1){
		text(cumChrLen[chrNum+1]*1,0.95,as.character(files[j,1]),xpd=T,cex=1.0,pos=4,adj=0)
	}
	mtext(side=2,line=0,"BAF",cex=0.5)
}
print(3) #20210610
#plot(cumChrLen[1:chrNum], rep(0,chrNum), xlim = c(0,cumChrLen[chrNum+1]),ylim = c(0,maxLevelToPlot*ploidy), col='white',bty='n',xaxt='n',yaxt='n',xlab='',ylab='')
plot(cumChrLen[1:chrNum], rep(0,chrNum), xlim = c(0,cumChrLen[chrNum]),ylim = c(0,maxLevelToPlot*ploidy), col='white',bty='n',xaxt='n',yaxt='n',xlab='',ylab='')#20210610
print(4) #20210610
#text(cumCen[1:chrNum],5.7+c(rep(0,12),rep(c(-0.1,-0.3),5)),labels=1:chrNum,xpd=T,cex=0.8)
text(cumCen[1:chrNum],5.7+c(rep(0,12),rep(c(-0.1,-0.3),5)),labels=names(chrLen),xpd=T,cex=0.8) #20210610
#cumChrLen
dev.off()
# pdf plot
pdf(paste("ET203897",".CNV_profile.pdf",sep = ""),width=600*7/480,height=nrow(files)*120*7/480)
par(mfrow=c(nrow(files)*2+2,1),mar=c(0.3,2,0.3,5))

plot(1:10,rep(0,10),col='white',bty='n',xaxt='n',yaxt='n',xlab='',ylab='',ylim=c(0,6))
text(5,2,"ET203897",cex=1.5)

#par(mfrow=c(2,1),mar=c(0.3,2,0.3,5))

for(j in 1:nrow(files)){
	### CNV profile
	par(mar=c(0,2,0.3,5))
	cat("Reading CNV file ...
")
	ratio <-read.table(as.character(files[j,2]), head=TRUE,sep="	")
	maxLevelToPlot <- 3

	for (i in c(1:length(ratio$Ratio))) {
		if (ratio$Ratio[i]>maxLevelToPlot) {
			ratio$Ratio[i]=maxLevelToPlot;
		}
	}
#	ratio2<-subset(ratio,Chromosome %in% 1:chrNum) 
	ratio2<-subset(ratio,as.character(Chromosome) %in% c(1:chrNum,"X","Y")) #add20210610
	ratio2$x<-cumChrLen[as.character(ratio2$Chromosome)]+ratio2$Start
	ratio2$color<-"darkolivegreen3"
	ratio2$color[ratio2$CopyNumber>2]<-"firebrick3"
	ratio2$color[ratio2$CopyNumber<2]<-"mediumblue"

#	plot(ratio2$x,ratio2$Ratio*2,xlim = c(0,cumChrLen[chrNum+1]),ylim = c(0,maxLevelToPlot*ploidy),xlab = "",ylab = "",pch = ".",col = ratio2$color,bty='n',xaxt='n',yaxt='n')
	plot(ratio2$x,ratio2$Ratio*2,xlim = c(0,cumChrLen[chrNum]),ylim = c(0,maxLevelToPlot*ploidy),xlab = "",ylab = "",pch = ".",col = ratio2$color,bty='n',xaxt='n',yaxt='n') #add20210610
	points(ratio2$x,ratio2$CopyNumber,cex=1.2,pch = ".",col = colors()[24])
	#plot(ratio2$x,ratio2$Ratio*2,ylim = c(0,maxLevelToPlot*ploidy),xlab = "",ylab = "",pch = ".",col = ratio2$color,bty=']',xaxt='n',yaxt='n')
#	axis(side=2,line=-0.95,at=0:6,labels=0:6,col='darkgrey',xpd=NA)
	segments(0,-0.1,0,6.1,lwd=1,xpd=T)
#	for (i in 2:(chrNum+1)){
	for (i in 1:(chrNum)){ #add20210610
		segments(cumChrLen[i],0.5,cumChrLen[i],5.5,lwd=1,lty=22,col="darkgrey")
	}
	for (i in 0:6){
		segments(-20000000,i,0,i,xpd=T)
		text(-10000000,i,i,pos=2,adj=0,xpd=T,cex=0.8,lwd=0.8)
	}
	## centromere
	text(cumCen[1:chrNum],rep(2,chrNum),labels=rep(".",chrNum),cex=2,adj=0)
	#text(cumCen[1:chrNum],rep(2,chrNum),labels=rep(".",chrNum),cex=2)
	text(cumCen[1:chrNum],rep(2.05,chrNum),labels=rep(".",chrNum),cex=2,adj=0)
	text(cumCen[1:chrNum],rep(2.03,chrNum),labels=rep(".",chrNum),cex=2,adj=0)
	text(cumCen[1:chrNum],rep(1.98,chrNum),labels=rep(".",chrNum),cex=2,adj=0)
	text(cumCen[1:chrNum],rep(1.95,chrNum),labels=rep(".",chrNum),cex=2,adj=0)
	mtext(side=2,line=0,"Copy Number",cex=0.5)
	### BAF
	BAF<-read.table(as.character(files[j,3]),head=TRUE,sep="	")
	BAF2<-subset(BAF,Chromosome %in% 1:chrNum)
	BAF2$x<-cumChrLen[as.character(BAF2$Chromosome)]+BAF2$Position
	BAF2$color<-colors()[1]
	BAF2$color[BAF2$A==0.5]<-colors()[92]
	BAF2$color[BAF2$A!=0.5 & BAF2$A>=0]<-colors()[62]

	par(mar=c(0.3,2,0,5))
	plot(BAF2$x,BAF2$BAF,ylim = c(-0.1,1.1),xlab = "",ylab = "",pch = ".",col = BAF2$color,bty='n',xaxt='n',yaxt='n')
	for (i in 1:chrNum){
     	  lBAF<-subset(BAF2,Chromosome==i)
        tt<-1
     	  pres<-1
        if (length(lBAF$FittedA)>4){
     	          for (n in c(2:(length(lBAF$FittedA)-pres-1))) {
           	            if (lBAF$FittedA[n]==lBAF$FittedA[n+pres]) {
                 	              tt[length(tt)+1] <- n
                        }
                }
                points(lBAF$x[tt],lBAF$FittedA[tt],pch = ".",col = colors()[24],cex=1.2)
                points(lBAF$x[tt],lBAF$FittedB[tt],pch = ".",col = colors()[24],cex=1.2)
        }
	}
	segments(0,-0.02,0,1.02,lwd=1,xpd=T)
	for (i in 2:(chrNum+1)){
		segments(cumChrLen[i],0,cumChrLen[i],1,lwd=1,lty=22,col="darkgrey")
	}
	for (i in seq(0,1,by=0.2)){
		segments(-20000000,i,0,i,xpd=T,lwd=0.8)
		text(-10000000,i,i,pos=2,adj=0,xpd=T,cex=0.8)
	}
	## sample label
	if(nrow(files)>1){
		text(cumChrLen[chrNum+1]*1,0.95,as.character(files[j,1]),xpd=T,cex=1.0,pos=4,adj=0)
	}
	mtext(side=2,line=0,"BAF",cex=0.5)
}

#plot(cumChrLen[1:(chrNum+1)], rep(0,chrNum+1), xlim = c(0,cumChrLen[chrNum+1]),ylim = c(0,maxLevelToPlot*ploidy), col='white',bty='n',xaxt='n',yaxt='n',xlab='',ylab='')
plot(cumChrLen[1:(chrNum+1)], rep(0,chrNum+1), xlim = c(0,cumChrLen[chrNum]),ylim = c(0,maxLevelToPlot*ploidy), col='white',bty='n',xaxt='n',yaxt='n',xlab='',ylab='') #20210610
#text(cumCen[1:chrNum],5.7+c(rep(0,12),rep(c(-0.1,-0.3),5)),labels=1:chrNum,xpd=T,cex=0.8)
text(cumCen[1:chrNum],5.7+c(rep(0,12),rep(c(-0.1,-0.3),5)),labels=names(chrLen),xpd=T,cex=0.8)
#cumChrLen
dev.off()
</code>
示例路径：

<code>
/TJNAS01/AFS_RESEQ/Proj/hongxiang/05.AFS/freec_visualization/test_X_Y
</code>