plotSE.R

plotSE<-function(seFile, seCol="red", teCol="black", mark="H3K27ac", bg=TRUE){
  
  dat=read.delim(seFile, comment.char = '&', nrows=3)
  colnames(dat)<-"V1"
  se.signal.cut=as.character(dat$V1[3])
  se.signal.cut=as.numeric(strsplit(se.signal.cut, " ")[[1]][4])
  
  se=read.delim(seFile, comment.char = '#', header = TRUE)
  se.count.cut=dim(subset(se, se$isSuper==1))[1]
  
  subData=if(bg) subset(se, select = c(7,9,10)) else subset(se, select=c(7,8,9))
  
  colnames(subData)<-paste("V", 1:ncol(subData), sep="")
  
  suppressPackageStartupMessages(require(dplyr))
  subData=mutate(subData, type=ifelse(subData$V3==1, "SE", "TE"))
  
  suppressPackageStartupMessages(require(ggplot2))
  suppressPackageStartupMessages(require(scales))
  ggplot(subData, aes(V2, V1))+geom_line()+
    geom_point(aes(col=type, size=0.01))+
    scale_color_manual(values = c(seCol, teCol))+
    theme_classic(base_size = 16)+scale_y_continuous(labels=comma)+
    xlab("Enhancer Rank")+ylab(paste(mark, "Normalized read density", sep=" "))+
    theme(legend.position = "none")+
    geom_hline(yintercept = se.signal.cut, linetype=2, color="gray")+
    geom_vline(xintercept = se.count.cut, linetype=2, color="gray")
}

The code was throwing error. I did below mentioned modification
line no. 13 -- colnames(subData)<-paste("V1", 1:ncol(subData), sep="")
line no. 16 -- subData=mutate(subData, type=ifelse(subData$V13==1, "SE", "TE"))
line no. 20 -- ggplot(subData, aes(V12, V11))+geom_line()+