setwd("/mnt/fix/b/dimopoulos/home/solenn/megahit/stats")



#list.files(pattern = "stats","../")[grep("txt",list.files(pattern = "stats","../"))]
#pdf("MappingRate.pdf",width=640,height = 480)
#pdf("MappingRate.pdf")
tiff(filename ="MappingRate.tiff",width = 1024*2,height = 768*2,pointsize=22,compression = "lzw")
par(mfrow=c(2,4))

ymax=0
for (FN in list.files(pattern = "stats*"))
{
  
  data=read.table(FN,as.is = T)
  ymax=max(ymax,max(data[,2]))
  
}
ymax=round(ymax*1.1)

k=1

for (FN in list.files(pattern = "stats*"))
{
data=read.table(FN,as.is = T)

colnames(data)=c("kmer size","overall alignment rate")
if (k%%4!=0)
plot(data,type="l",main=paste(unlist(strsplit(FN,"\\."))[c(2,3)],collapse = " "),ylim=c(0,ymax)) else
  plot(data,type="l",main=paste(unlist(strsplit(FN,"\\."))[c(2)],collapse = " "),ylim=c(0,ymax)) 
  
k=k+1
}
dev.off()



ymax3=0
for (FN in list.files(pattern = "contigs*")[1:4])
{
  
  data=read.table(FN,as.is = T)[,c(1,6)]
  ymax3=max(ymax3,max(data[,2]))
  
}
ymax3=round(ymax3*1.1)

ymax4=0
for (FN in list.files(pattern = "contigs*")[5:8])
{
  
  data=read.table(FN,as.is = T)[,c(1,6)]
  ymax4=max(ymax4,max(data[,2]))
  
}
ymax4=round(ymax4*1.1)



k=1
#FN=list.files(pattern = "contigs*")[1]
#pdf("Contigsize.pdf")
tiff(filename ="Contigsize.tiff",width = 1024*2,height = 768*2,pointsize=22,compression = "lzw")
par(mfrow=c(2,4))
for (FN in list.files(pattern = "contigs*"))
{
data=read.table(FN,as.is = T)[,c(1,6)]

colnames(data)=c("kmer size","number of sequences")
if (k<5)
{if (k%%4!=0)
  plot(data,type="l",main=paste(unlist(strsplit(FN,"\\."))[c(2,3)],collapse = " "),ylim=c(0,ymax3)) else
    plot(data,type="l",main=paste(unlist(strsplit(FN,"\\."))[c(2)],collapse = " "),ylim=c(0,ymax3))
  } else
  {
    if (k%%4!=0)
      plot(data,type="l",main=paste(unlist(strsplit(FN,"\\."))[c(2,3)],collapse = " "),ylim=c(0,ymax4)) else
        plot(data,type="l",main=paste(unlist(strsplit(FN,"\\."))[c(2)],collapse = " "),ylim=c(0,ymax4))
  }
    
k=k+1
}
dev.off()