plot.R

setwd("C:\\Users\\xuwenhao\\Desktop\\bwa output\\nwe_bwa\\polu_length_count\\3p_and_5p")
library(ggplot2)
library(gridExtra)
files=list.files(getwd())
files <- files[grepl("w*\\.txt$", files)]
ways=unlist(strsplit(getwd(),"/"))
pdf(paste(ways[length(ways)],".pdf",seq=""),family="GB1")#改后缀

plot_c <- list()
for (f in files)
{

  #b<-regexpr(".txt", f)#匹配
  #key <- substr(f, 0, b[1]-1)#抓取
  #mine=paste(key, ".pdf", sep = "")
  #Villabruna_leng_tag_nhpolu-aln1024-n0.03-low-uni-5p1-3p1-leng-of-ancester-count.txt
  samplenames=unlist(strsplit(f,"_"))
  elements=unlist(strsplit(f,"-"))
  name=paste(samplenames[1],elements[length(elements)-1],seq="-")
  #do something...
  #f = 'JK2911_S0_L002_R1_001.fastq.merged.fq.sorted.cleaned_rmdup_leng_tag_nhpolu-aln1024-n0.03-low-uni-3p-1-leng-of-ancester-count.txt'
  #print(f)
  M=read.table(f)
  colnames(M) <- c("length", "number")
  Length=M$length
  Number=M$number
  p=ggplot2::qplot(Length,data=M,geom="histogram",binwidth=3,weight=Number,
                   colour=I("white"),size=I(0.5),
                   fill=I("lightblue"))
  
  p=p+ggplot2::labs(x="read length",y="number",title=name)
  p=p+ggplot2::scale_x_continuous(limits=c(0,201),breaks=seq(0,200,20))
  #print(p)
  #automatically save the plots
  #dev.off()
  plot_c <- c(plot_c, list(p))  
}
do.call(grid.arrange, c(plot_c, nrow=2))

dev.off()