对结构变异分布的圈图的R脚本

if (!require(pacman)){
    install.packages("pacman")
    library(pacman)
}
### Load packages
pacman::p_load(circlize)
### Data prep
df=data.frame(name="chr8",start=11000,end=13000)
pbDELsp=read.delim("fastq.list.spots.DEL.target.bed",header=FALSE)
pbINS=read.delim("fastq.list.spots.INS.target.bed",header=FALSE)
pbDELta=read.delim("fastq.list.tails.DEL.target.bed",header=FALSE)
pbINV=read.delim("astq.list.tails.INV.target.bed",header=FALSE)
sfDEL=read.delim("fastq.list.sniffles.vcf.DEL.target.bed",header=FALSE)
sfINS=read.delim("fastq.list.sniffles.vcf.INS.target.bed",header=FALSE)
sfDUP=read.delim("fastq.list.sniffles.vcf.DUP.target.bed",header=FALSE)
sfINV=read.delim("fastq.list.sniffles.vcf.INV.target.bed",header=FALSE)
pbDEL=rbind(pbDELsp,pbDELta)
pbsv_list=list(pbDEL, pbINS, pbINV)
dflen1=length(pbsv_list)
cols_to_keep=c(TRUE,TRUE,TRUE,FALSE,FALSE,FALSE)
for (i in 1:dflen1) {
  pbsv_list[[i]] = pbsv_list[[i]][,cols_to_keep]
  colnames(pbsv_list[[i]]) = c("chr","start","end")
  pbsv_list[[i]]$chr=paste("chr",pbsv_list[[i]]$chr,sep="")
}
pbsv_combine=rbind(pbDEL, pbINS, pbINV)
pbsv_combine=pbsv_combine[,cols_to_keep]
colnames(pbsv_combine)=c("chr","start","end")
pbsv_combine$chr=paste("chr",pbsv_combine$chr,sep="")
sfsv_list=list(sfDEL, sfINS, sfINV, sfDUP)
dflen2=length(sfsv_list)
for (i in 1:dflen2) {
  sfsv_list[[i]] = sfsv_list[[i]][,cols_to_keep]
  colnames(sfsv_list[[i]]) = c("chr","start","end")
  sfsv_list[[i]]$chr=paste("chr",sfsv_list[[i]]$chr,sep="")
}
sfsv_combine=rbind(sfDEL, sfINS, sfINV, sfDUP)
sfsv_combine=sfsv_combine[,cols_to_keep]
colnames(sfsv_combine)=c("chr","start","end")
sfsv_combine$chr=paste("chr",sfsv_combine$chr,sep="")
### Figure
pdf(file="sequel_density_trial.pdf",width=7,height=7)
circos.genomicInitialize(df,tickLabelsStartFromZero = FALSE)
#circos.genomicRainfall(pbsv_list, col = c("red", "darkblue", "cyan"),cex=0.3,bg.border = "gray")
#circos.genomicRainfall(sfsv_list, col = c("red", "darkblue", "cyan", "darkgreen"),cex=0.3,bg.border = "gray")
circos.genomicDensity(pbsv_list, window.size = 1e5, col = c("#1f1a4f","#c82027","#E69F00"), bg.border = "gray")
circos.genomicDensity(sfsv_list, window.size = 1e5, col = c("#1f1a4f","#c82027","#E69F00","#999999"), bg.border = "gray")
       
circos.clear()
dev.off()