Mercurial > repos > richjp > cloudmap_zebrafish_hom_mapping

<tool id="cloudmap_zf_hom_mapping" name="cloudmap_zf_hom_mapping" version="0.01">
<description>Map a zebrafish mutant using bulk sergeant homozygosity mapping</description>
<requirements>
      <requirement type="package" version="9.10">ghostscript</requirement>
      <requirement type="package" version="1.3.18">graphicsmagick</requirement>
  </requirements>
<command interpreter="python">

        cloudmap_zf_hom_mapping.py --script_path "$runMe" --interpreter "Rscript"
            --tool_name "cloudmap_zf_hom_mapping" --input_tab "$input1"   --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
</command>
<inputs>
<param name="input1"  type="data" format="vcf" label="Select a suitable input file from your history"/>
<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="cloudmap_zf_hom_mapping"/>

</inputs>
<outputs>
 <data format="html" name="html_file" label="${job_name}.html"/>

</outputs>
<configfiles>
<configfile name="runMe">
#homozygosity-mapping script
#input file: Q200 variants no wildtype
ourargs = commandArgs(TRUE)
inf = ourargs[1]
outf = ourargs[2]
Q200var = read.table(inf)


het &lt;- Q200var[grep("AF=0.5",Q200var\$V8), ]
hom &lt;- Q200var[grep("AF=1.0",Q200var\$V8), ]

get_hom1 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr1")
  het &lt;- subset(x2,x2\$V1=="chr1")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom2 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr2")
  het &lt;- subset(x2,x2\$V1=="chr2")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom3 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr3")
  het &lt;- subset(x2,x2\$V1=="chr3")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom4 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr4")
  het &lt;- subset(x2,x2\$V1=="chr4")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom5 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr5")
  het &lt;- subset(x2,x2\$V1=="chr5")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom6 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr6")
  het &lt;- subset(x2,x2\$V1=="chr6")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom7 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr7")
  het &lt;- subset(x2,x2\$V1=="chr7")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom8 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr8")
  het &lt;- subset(x2,x2\$V1=="chr8")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom9 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr9")
  het &lt;- subset(x2,x2\$V1=="chr9")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom10 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr10")
  het &lt;- subset(x2,x2\$V1=="chr10")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom11 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr11")
  het &lt;- subset(x2,x2\$V1=="chr11")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom12 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr12")
  het &lt;- subset(x2,x2\$V1=="chr12")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom13 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr13")
  het &lt;- subset(x2,x2\$V1=="chr13")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom14 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr14")
  het &lt;- subset(x2,x2\$V1=="chr14")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom15 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr15")
  het &lt;- subset(x2,x2\$V1=="chr15")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom16 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr16")
  het &lt;- subset(x2,x2\$V1=="chr16")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom17 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr17")
  het &lt;- subset(x2,x2\$V1=="chr17")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom18 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr18")
  het &lt;- subset(x2,x2\$V1=="chr18")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom19 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr19")
  het &lt;- subset(x2,x2\$V1=="chr19")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom20 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr20")
  het &lt;- subset(x2,x2\$V1=="chr20")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom21 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr21")
  het &lt;- subset(x2,x2\$V1=="chr21")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom22 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr22")
  het &lt;- subset(x2,x2\$V1=="chr22")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom23 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr23")
  het &lt;- subset(x2,x2\$V1=="chr23")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom24 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr24")
  het &lt;- subset(x2,x2\$V1=="chr24")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

get_hom25 &lt;- function(x1,x2){
  hom &lt;- subset(x1,x1\$V1=="chr25")
  het &lt;- subset(x2,x2\$V1=="chr25")
  d1 &lt;- density(hom\$V2)
  d2 &lt;- density(het\$V2)
  return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
}

h1 &lt;- get_hom1(hom,het)
h2 &lt;- get_hom2(hom,het)
h3 &lt;- get_hom3(hom,het)
h4 &lt;- get_hom4(hom,het)
h5 &lt;- get_hom5(hom,het)
h6 &lt;- get_hom6(hom,het)
h7 &lt;- get_hom7(hom,het)
h8 &lt;- get_hom8(hom,het)
h9 &lt;- get_hom9(hom,het)
h10 &lt;- get_hom10(hom,het)
h11 &lt;- get_hom11(hom,het)
h12 &lt;- get_hom12(hom,het)
h13 &lt;- get_hom13(hom,het)
h14 &lt;- get_hom14(hom,het)
h15 &lt;- get_hom15(hom,het)
h16 &lt;- get_hom16(hom,het)
h17 &lt;- get_hom17(hom,het)
h18 &lt;- get_hom18(hom,het)
h19 &lt;- get_hom19(hom,het)
h20 &lt;- get_hom20(hom,het)
h21 &lt;- get_hom21(hom,het)
h22 &lt;- get_hom22(hom,het)
h23 &lt;- get_hom23(hom,het)
h24 &lt;- get_hom24(hom,het)
h25 &lt;- get_hom25(hom,het)


#Extracting maxima (homozygosity-mapping)

zero_crossings_maxima &lt;- function(x,y){

  dy &lt;- diff(y)
  xn &lt;- x[2:length(x)]

  n &lt;- length(dy)
  t1 &lt;- dy[1:n-1];
  t2 &lt;- dy[2:n];
  tt &lt;- t1*t2
  ind &lt;- which(tt &lt; 0)

  # print out the maxima
  d2y &lt;- diff(dy)
  vind &lt;- c()
  vy &lt;- c()
  vxn &lt;- c()

  xnn &lt;- x[3:length(x)]
  for(i in 1:length(ind)){
    ### cat( ind[i], d2y[ind[i]], '\n')
    if( d2y[ind[i]] &lt; 0 ){
      ### cat(ind[i], y[ind[i]], xn[ind[i]], "\n" )
      vind &lt;- c(vind, ind[i])
      vy &lt;- c(vy, y[ind[i]])
      vxn &lt;- c(vxn, xn[ind[i]])
    }
  }

  maxima &lt;- data.frame(ind=vind, y=vy, x=vxn)
  maxima &lt;- maxima[order(maxima\$y),]

  #print( maxima )

  results &lt;- list()
  results\$dy &lt;- dy
  results\$xn &lt;- xn
  results\$maxima &lt;- maxima[ order(maxima\$y, decreasing=T), ]

  return(results)
}

res1 &lt;- zero_crossings_maxima(h1\$x,h1\$ratio)
res2 &lt;- zero_crossings_maxima(h2\$x,h2\$ratio)
res3 &lt;- zero_crossings_maxima(h3\$x,h3\$ratio)
res4 &lt;- zero_crossings_maxima(h4\$x,h4\$ratio)
res5 &lt;- zero_crossings_maxima(h5\$x,h5\$ratio)
res6 &lt;- zero_crossings_maxima(h6\$x,h6\$ratio)
res7 &lt;- zero_crossings_maxima(h7\$x,h7\$ratio)
res8 &lt;- zero_crossings_maxima(h8\$x,h8\$ratio)
res9 &lt;- zero_crossings_maxima(h9\$x,h9\$ratio)
res10 &lt;- zero_crossings_maxima(h10\$x,h10\$ratio)
res11 &lt;- zero_crossings_maxima(h11\$x,h11\$ratio)
res12 &lt;- zero_crossings_maxima(h12\$x,h12\$ratio)
res13 &lt;- zero_crossings_maxima(h13\$x,h13\$ratio)
res14 &lt;- zero_crossings_maxima(h14\$x,h14\$ratio)
res15 &lt;- zero_crossings_maxima(h15\$x,h15\$ratio)
res16 &lt;- zero_crossings_maxima(h16\$x,h16\$ratio)
res17 &lt;- zero_crossings_maxima(h17\$x,h17\$ratio)
res18 &lt;- zero_crossings_maxima(h18\$x,h18\$ratio)
res19 &lt;- zero_crossings_maxima(h19\$x,h19\$ratio)
res20 &lt;- zero_crossings_maxima(h20\$x,h20\$ratio)
res21 &lt;- zero_crossings_maxima(h21\$x,h21\$ratio)
res22 &lt;- zero_crossings_maxima(h22\$x,h22\$ratio)
res23 &lt;- zero_crossings_maxima(h23\$x,h23\$ratio)
res24 &lt;- zero_crossings_maxima(h24\$x,h24\$ratio)
res25 &lt;- zero_crossings_maxima(h25\$x,h25\$ratio)


#plotting (including maxima and adjusting to max ratio)
# all on one plot
pdf("allchrs.pdf",height=10, width=20)
library(Hmisc)
ymax &lt;- 1.05*max( c(h1\$ratio,h2\$ratio,h3\$ratio,h4\$ratio,h5\$ratio,h6\$ratio,h7\$ratio,h8\$ratio,h9\$ratio,h10\$ratio,h11\$ratio,h12\$ratio,h13\$ratio,h14\$ratio,h15\$ratio,h16\$ratio,h17\$ratio,h18\$ratio,h19\$ratio,h20\$ratio,h21\$ratio,h22\$ratio,h23\$ratio,h24\$ratio,h25\$ratio))
par(mfrow=c(5,5))
plot(h1\$x, h1\$ratio,type="l", lwd=3, col="red", xlim=c(0,61000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 1")
points( res1\$maxima\$x[1], res1\$maxima\$y[1], col="red", pch=19 )
abline(v=res1\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res1\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h2\$x, h2\$ratio,type="l", lwd=3, col="red", xlim=c(0,61000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 2")
points( res2\$maxima\$x[1], res2\$maxima\$y[1], col="red", pch=19 )
abline(v=res2\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res2\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h3\$x, h3\$ratio,type="l", lwd=3, col="red", xlim=c(0,64000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 3")
points( res3\$maxima\$x[1], res3\$maxima\$y[1], col="red", pch=19 )
abline(v=res3\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res3\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h4\$x, h4\$ratio,type="l", lwd=3, col="red",, xlim=c(0,64000000),ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 4")
points( res4\$maxima\$x[1], res4\$maxima\$y[1], col="red", pch=19 )
abline(v=res4\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res4\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h5\$x, h5\$ratio,type="l", lwd=3, col="red",, xlim=c(0,76000000),ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 5")
points( res5\$maxima\$x[1], res5\$maxima\$y[1], col="red", pch=19 )
abline(v=res5\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res5\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h6\$x, h6\$ratio,type="l", lwd=3, col="red",, xlim=c(0,60000000),ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 6")
points( res6\$maxima\$x[1], res6\$maxima\$y[1], col="red", pch=19 )
abline(v=res6\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res6\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h7\$x, h7\$ratio,type="l", lwd=3, col="red",, xlim=c(0,78000000),ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio" , main="Chromosome 7")
points( res7\$maxima\$x[1], res7\$maxima\$y[1], col="red", pch=19 )
abline(v=res7\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res7\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h8\$x, h8\$ratio,type="l", lwd=3, col="red",, xlim=c(0,57000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio" , main="Chromosome 8")
points( res8\$maxima\$x[1], res8\$maxima\$y[1], col="red", pch=19 )
abline(v=res8\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res8\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h9\$x, h9\$ratio,type="l", lwd=3, col="red",, xlim=c(0,59000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio" , main="Chromosome 9")
points( res9\$maxima\$x[1], res9\$maxima\$y[1], col="red", pch=19 )
abline(v=res9\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res9\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h10\$x, h10\$ratio,type="l", lwd=3, col="red",, xlim=c(0,47000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 10")
points( res10\$maxima\$x[1], res10\$maxima\$y[1], col="red", pch=19 )
abline(v=res10\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res10\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h11\$x, h11\$ratio,type="l", lwd=3, col="red",, xlim=c(0,47000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 11")
points( res11\$maxima\$x[1], res11\$maxima\$y[1], col="red", pch=19 )
abline(v=res11\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res11\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h12\$x, h12\$ratio,type="l", lwd=3, col="red",, xlim=c(0,51000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 12")
points( res12\$maxima\$x[1], res12\$maxima\$y[1], col="red", pch=19 )
abline(v=res12\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res12\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h13\$x, h13\$ratio,type="l", lwd=3, col="red",, xlim=c(0,55000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 13")
points( res13\$maxima\$x[1], res13\$maxima\$y[1], col="red", pch=19 )
abline(v=res13\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res13\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h14\$x, h14\$ratio,type="l", lwd=3, col="red",, xlim=c(0,54000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 14")
points( res14\$maxima\$x[1], res14\$maxima\$y[1], col="red", pch=19 )
abline(v=res14\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res14\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h15\$x, h15\$ratio,type="l", lwd=3, col="red",, xlim=c(0,48000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 15")
points( res15\$maxima\$x[1], res15\$maxima\$y[1], col="red", pch=19 )
abline(v=res15\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res15\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h16\$x, h16\$ratio,type="l", lwd=3, col="red",, xlim=c(0,59000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 16")
points( res16\$maxima\$x[1], res16\$maxima\$y[1], col="red", pch=19 )
abline(v=res16\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res16\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h17\$x, h17\$ratio,type="l", lwd=3, col="red",, xlim=c(0,54000000),, ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 17")
points( res17\$maxima\$x[1], res17\$maxima\$y[1], col="red", pch=19 )
abline(v=res17\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res17\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h18\$x, h18\$ratio,type="l", lwd=3, col="red", xlim=c(0,50000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 18")
points( res18\$maxima\$x[1], res18\$maxima\$y[1], col="red", pch=19 )
abline(v=res18\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res18\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h19\$x, h19\$ratio,type="l", lwd=3, col="red",, xlim=c(0,51000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", , main="Chromosome 19")
points( res19\$maxima\$x[1], res19\$maxima\$y[1], col="red", pch=19 )
abline(v=res19\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res19\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h20\$x, h20\$ratio,type="l", lwd=3, col="red",, xlim=c(0,56000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 20")
points( res20\$maxima\$x[1], res20\$maxima\$y[1], col="red", pch=19 )
abline(v=res20\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res20\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h21\$x, h21\$ratio,type="l", lwd=3, col="red",, xlim=c(0,45000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 21")
points( res21\$maxima\$x[1], res21\$maxima\$y[1], col="red", pch=19 )
abline(v=res21\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res21\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h22\$x, h22\$ratio,type="l", lwd=3, col="red",, xlim=c(0,43000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 22")
points( res22\$maxima\$x[1], res22\$maxima\$y[1], col="red", pch=19 )
abline(v=res22\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res22\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h23\$x, h23\$ratio,type="l", lwd=3, col="red",, xlim=c(0,47000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 23")
points( res23\$maxima\$x[1], res23\$maxima\$y[1], col="red", pch=19 )
abline(v=res23\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res23\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h24\$x, h24\$ratio,type="l", lwd=3, col="red",, xlim=c(0,44000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 24")
points( res24\$maxima\$x[1], res24\$maxima\$y[1], col="red", pch=19 )
abline(v=res24\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res24\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
plot(h25\$x, h25\$ratio,type="l", lwd=3, col="red",, xlim=c(0,39000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 25")
points( res25\$maxima\$x[1], res25\$maxima\$y[1], col="red", pch=19 )
abline(v=res25\$maxima\$x[1], lwd=1)
legend("topleft", bty="n",  paste(format(round(res25\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(10)
dev.off()

# seperate plots
pdf("chr1.pdf",height=5, width=10)
plot(h1\$x, h1\$ratio,type="l", lwd=3, col="red", xlim=c(0,61000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 1")
points( res1\$maxima\$x[1], res1\$maxima\$y[1], col="red", pch=19 )
abline(v=res1\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res1\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr2.pdf",height=5, width=10)
plot(h2\$x, h2\$ratio,type="l", lwd=3, col="red", xlim=c(0,61000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 2")
points( res2\$maxima\$x[1], res2\$maxima\$y[1], col="red", pch=19 )
abline(v=res2\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res2\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr3.pdf",height=5, width=10)
plot(h3\$x, h3\$ratio,type="l", lwd=3, col="red", xlim=c(0,64000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 3")
points( res3\$maxima\$x[1], res3\$maxima\$y[1], col="red", pch=19 )
abline(v=res3\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res3\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr4.pdf",height=5, width=10)
plot(h4\$x, h4\$ratio,type="l", lwd=3, col="red",, xlim=c(0,64000000),ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 4")
points( res4\$maxima\$x[1], res4\$maxima\$y[1], col="red", pch=19 )
abline(v=res4\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res4\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr5.pdf",height=5, width=10)
plot(h5\$x, h5\$ratio,type="l", lwd=3, col="red",, xlim=c(0,76000000),ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 5")
points( res5\$maxima\$x[1], res5\$maxima\$y[1], col="red", pch=19 )
abline(v=res5\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res5\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr6.pdf",height=5, width=10)
plot(h6\$x, h6\$ratio,type="l", lwd=3, col="red",, xlim=c(0,60000000),ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 6")
points( res6\$maxima\$x[1], res6\$maxima\$y[1], col="red", pch=19 )
abline(v=res6\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res6\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr7.pdf",height=5, width=10)
plot(h7\$x, h7\$ratio,type="l", lwd=3, col="red",, xlim=c(0,78000000),ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio" , main="Chromosome 7")
points( res7\$maxima\$x[1], res7\$maxima\$y[1], col="red", pch=19 )
abline(v=res7\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res7\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr8.pdf",height=5, width=10)
plot(h8\$x, h8\$ratio,type="l", lwd=3, col="red",, xlim=c(0,57000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio" , main="Chromosome 8")
points( res8\$maxima\$x[1], res8\$maxima\$y[1], col="red", pch=19 )
abline(v=res8\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res8\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr9.pdf",height=5, width=10)
plot(h9\$x, h9\$ratio,type="l", lwd=3, col="red",, xlim=c(0,59000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio" , main="Chromosome 9")
points( res9\$maxima\$x[1], res9\$maxima\$y[1], col="red", pch=19 )
abline(v=res9\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res9\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr10.pdf",height=5, width=10)
plot(h10\$x, h10\$ratio,type="l", lwd=3, col="red",, xlim=c(0,47000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 10")
points( res10\$maxima\$x[1], res10\$maxima\$y[1], col="red", pch=19 )
abline(v=res10\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res10\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr11.pdf",height=5, width=10)
plot(h11\$x, h11\$ratio,type="l", lwd=3, col="red",, xlim=c(0,47000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 11")
points( res11\$maxima\$x[1], res11\$maxima\$y[1], col="red", pch=19 )
abline(v=res11\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res11\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr12.pdf",height=5, width=10)
plot(h12\$x, h12\$ratio,type="l", lwd=3, col="red",, xlim=c(0,51000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 12")
points( res12\$maxima\$x[1], res12\$maxima\$y[1], col="red", pch=19 )
abline(v=res12\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res12\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr13.pdf",height=5, width=10)
plot(h13\$x, h13\$ratio,type="l", lwd=3, col="red",, xlim=c(0,55000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 13")
points( res13\$maxima\$x[1], res13\$maxima\$y[1], col="red", pch=19 )
abline(v=res13\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res13\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr14.pdf",height=5, width=10)
plot(h14\$x, h14\$ratio,type="l", lwd=3, col="red",, xlim=c(0,54000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 14")
points( res14\$maxima\$x[1], res14\$maxima\$y[1], col="red", pch=19 )
abline(v=res14\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res14\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr15.pdf",height=5, width=10)
plot(h15\$x, h15\$ratio,type="l", lwd=3, col="red",, xlim=c(0,48000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 15")
points( res15\$maxima\$x[1], res15\$maxima\$y[1], col="red", pch=19 )
abline(v=res15\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res15\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr16.pdf",height=5, width=10)
plot(h16\$x, h16\$ratio,type="l", lwd=3, col="red",, xlim=c(0,59000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 16")
points( res16\$maxima\$x[1], res16\$maxima\$y[1], col="red", pch=19 )
abline(v=res16\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res16\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr17.pdf",height=5, width=10)
plot(h17\$x, h17\$ratio,type="l", lwd=3, col="red",, xlim=c(0,54000000),, ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 17")
points( res17\$maxima\$x[1], res17\$maxima\$y[1], col="red", pch=19 )
abline(v=res17\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res17\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr18.pdf",height=5, width=10)
plot(h18\$x, h18\$ratio,type="l", lwd=3, col="red", xlim=c(0,50000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 18")
points( res18\$maxima\$x[1], res18\$maxima\$y[1], col="red", pch=19 )
abline(v=res18\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res18\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr19.pdf",height=5, width=10)
plot(h19\$x, h19\$ratio,type="l", lwd=3, col="red",, xlim=c(0,51000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", , main="Chromosome 19")
points( res19\$maxima\$x[1], res19\$maxima\$y[1], col="red", pch=19 )
abline(v=res19\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res19\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr20.pdf",height=5, width=10)
plot(h20\$x, h20\$ratio,type="l", lwd=3, col="red",, xlim=c(0,56000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 20")
points( res20\$maxima\$x[1], res20\$maxima\$y[1], col="red", pch=19 )
abline(v=res20\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res20\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr21.pdf",height=5, width=10)
plot(h21\$x, h21\$ratio,type="l", lwd=3, col="red",, xlim=c(0,45000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 21")
points( res21\$maxima\$x[1], res21\$maxima\$y[1], col="red", pch=19 )
abline(v=res21\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res21\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr22.pdf",height=5, width=10)
plot(h22\$x, h22\$ratio,type="l", lwd=3, col="red",, xlim=c(0,43000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 22")
points( res22\$maxima\$x[1], res22\$maxima\$y[1], col="red", pch=19 )
abline(v=res22\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res22\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr23.pdf",height=5, width=10)
plot(h23\$x, h23\$ratio,type="l", lwd=3, col="red",, xlim=c(0,47000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 23")
points( res23\$maxima\$x[1], res23\$maxima\$y[1], col="red", pch=19 )
abline(v=res23\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res23\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr24.pdf",height=5, width=10)
plot(h24\$x, h24\$ratio,type="l", lwd=3, col="red",, xlim=c(0,44000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 24")
points( res24\$maxima\$x[1], res24\$maxima\$y[1], col="red", pch=19 )
abline(v=res24\$maxima\$x[1], lwd=1)
legend("topleft", bty="n", legend=paste(format(round(res24\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(nx=10)
dev.off()
pdf("chr25.pdf",height=5, width=10)
plot(h25\$x, h25\$ratio,type="l", lwd=3, col="red",, xlim=c(0,39000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 25")
points( res25\$maxima\$x[1], res25\$maxima\$y[1], col="red", pch=19 )
abline(v=res25\$maxima\$x[1], lwd=1)
legend("topleft", bty="n",  paste(format(round(res25\$maxima\$x[1] ,0),nsmall=0) ) )
minor.tick(10)
dev.off()
</configfile>
</configfiles>


        <tests>
        <test>
        <param name="input1" value="cloudmap_zf_hom_mapping_test1_input.xls" ftype="vcf"/>
        <param name="job_name" value="test1"/>
        <param name="runMe" value="$runMe"/>
        <output name="html_file" file="cloudmap_zf_hom_mapping_test1_output.html" ftype="html" lines_diff="5"/>
        </test>
        </tests>


<help>


**What it Does**

This tool is part of an update to the CloudMap pipeline (Minevich et al. 2012) to incorporate homozygosity mapping in zebrafish. This tool facilitates the mapping of zebrafish mutants from WGS or RNA-Seq data using bulk segregant homozygosity mapping. As input it takes a VCF list of variants (usually quality filtered for Q200 with WT SNPs/indels removed). This file is produced when running the CloudMap zebrafish pipeline. It plots an adjusted homozygosity ratio such that a high ratio indicates mapping region. It outputs an HTML file with combined and individual chromosome plots as PDFs. The adjusted homozygosity ratio is calculated as described in:

IN SUBMISSION

**Script**
Pressing execute will run the following code over your input file and generate some outputs in your history::


 #homozygosity-mapping script
 #input file: Q200 variants no wildtype
 ourargs = commandArgs(TRUE)
 inf = ourargs[1]
 outf = ourargs[2]
 Q200var = read.table(inf)


 het &lt;- Q200var[grep("AF=0.5",Q200var\$V8), ]
 hom &lt;- Q200var[grep("AF=1.0",Q200var\$V8), ]

 get_hom1 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr1")
   het &lt;- subset(x2,x2\$V1=="chr1")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom2 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr2")
   het &lt;- subset(x2,x2\$V1=="chr2")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom3 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr3")
   het &lt;- subset(x2,x2\$V1=="chr3")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom4 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr4")
   het &lt;- subset(x2,x2\$V1=="chr4")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom5 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr5")
   het &lt;- subset(x2,x2\$V1=="chr5")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom6 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr6")
   het &lt;- subset(x2,x2\$V1=="chr6")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom7 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr7")
   het &lt;- subset(x2,x2\$V1=="chr7")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom8 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr8")
   het &lt;- subset(x2,x2\$V1=="chr8")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom9 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr9")
   het &lt;- subset(x2,x2\$V1=="chr9")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom10 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr10")
   het &lt;- subset(x2,x2\$V1=="chr10")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom11 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr11")
   het &lt;- subset(x2,x2\$V1=="chr11")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom12 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr12")
   het &lt;- subset(x2,x2\$V1=="chr12")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom13 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr13")
   het &lt;- subset(x2,x2\$V1=="chr13")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom14 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr14")
   het &lt;- subset(x2,x2\$V1=="chr14")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom15 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr15")
   het &lt;- subset(x2,x2\$V1=="chr15")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom16 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr16")
   het &lt;- subset(x2,x2\$V1=="chr16")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom17 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr17")
   het &lt;- subset(x2,x2\$V1=="chr17")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom18 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr18")
   het &lt;- subset(x2,x2\$V1=="chr18")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom19 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr19")
   het &lt;- subset(x2,x2\$V1=="chr19")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom20 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr20")
   het &lt;- subset(x2,x2\$V1=="chr20")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom21 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr21")
   het &lt;- subset(x2,x2\$V1=="chr21")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom22 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr22")
   het &lt;- subset(x2,x2\$V1=="chr22")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom23 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr23")
   het &lt;- subset(x2,x2\$V1=="chr23")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom24 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr24")
   het &lt;- subset(x2,x2\$V1=="chr24")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 get_hom25 &lt;- function(x1,x2){
   hom &lt;- subset(x1,x1\$V1=="chr25")
   het &lt;- subset(x2,x2\$V1=="chr25")
   d1 &lt;- density(hom\$V2)
   d2 &lt;- density(het\$V2)
   return(list( x=d1\$x, ratio=(d1\$y/d2\$y)*(nrow(hom)/nrow(het))))
 }

 h1 &lt;- get_hom1(hom,het)
 h2 &lt;- get_hom2(hom,het)
 h3 &lt;- get_hom3(hom,het)
 h4 &lt;- get_hom4(hom,het)
 h5 &lt;- get_hom5(hom,het)
 h6 &lt;- get_hom6(hom,het)
 h7 &lt;- get_hom7(hom,het)
 h8 &lt;- get_hom8(hom,het)
 h9 &lt;- get_hom9(hom,het)
 h10 &lt;- get_hom10(hom,het)
 h11 &lt;- get_hom11(hom,het)
 h12 &lt;- get_hom12(hom,het)
 h13 &lt;- get_hom13(hom,het)
 h14 &lt;- get_hom14(hom,het)
 h15 &lt;- get_hom15(hom,het)
 h16 &lt;- get_hom16(hom,het)
 h17 &lt;- get_hom17(hom,het)
 h18 &lt;- get_hom18(hom,het)
 h19 &lt;- get_hom19(hom,het)
 h20 &lt;- get_hom20(hom,het)
 h21 &lt;- get_hom21(hom,het)
 h22 &lt;- get_hom22(hom,het)
 h23 &lt;- get_hom23(hom,het)
 h24 &lt;- get_hom24(hom,het)
 h25 &lt;- get_hom25(hom,het)


 #Extracting maxima (homozygosity-mapping)

 zero_crossings_maxima &lt;- function(x,y){

   dy &lt;- diff(y)
   xn &lt;- x[2:length(x)]

   n &lt;- length(dy)
   t1 &lt;- dy[1:n-1];
   t2 &lt;- dy[2:n];
   tt &lt;- t1*t2
   ind &lt;- which(tt &lt; 0)

   # print out the maxima
   d2y &lt;- diff(dy)
   vind &lt;- c()
   vy &lt;- c()
   vxn &lt;- c()

   xnn &lt;- x[3:length(x)]
   for(i in 1:length(ind)){
     ### cat( ind[i], d2y[ind[i]], '\n')
     if( d2y[ind[i]] &lt; 0 ){
       ### cat(ind[i], y[ind[i]], xn[ind[i]], "\n" )
       vind &lt;- c(vind, ind[i])
       vy &lt;- c(vy, y[ind[i]])
       vxn &lt;- c(vxn, xn[ind[i]])
     }
   }

   maxima &lt;- data.frame(ind=vind, y=vy, x=vxn)
   maxima &lt;- maxima[order(maxima\$y),]

   #print( maxima )

   results &lt;- list()
   results\$dy &lt;- dy
   results\$xn &lt;- xn
   results\$maxima &lt;- maxima[ order(maxima\$y, decreasing=T), ]

   return(results)
 }

 res1 &lt;- zero_crossings_maxima(h1\$x,h1\$ratio)
 res2 &lt;- zero_crossings_maxima(h2\$x,h2\$ratio)
 res3 &lt;- zero_crossings_maxima(h3\$x,h3\$ratio)
 res4 &lt;- zero_crossings_maxima(h4\$x,h4\$ratio)
 res5 &lt;- zero_crossings_maxima(h5\$x,h5\$ratio)
 res6 &lt;- zero_crossings_maxima(h6\$x,h6\$ratio)
 res7 &lt;- zero_crossings_maxima(h7\$x,h7\$ratio)
 res8 &lt;- zero_crossings_maxima(h8\$x,h8\$ratio)
 res9 &lt;- zero_crossings_maxima(h9\$x,h9\$ratio)
 res10 &lt;- zero_crossings_maxima(h10\$x,h10\$ratio)
 res11 &lt;- zero_crossings_maxima(h11\$x,h11\$ratio)
 res12 &lt;- zero_crossings_maxima(h12\$x,h12\$ratio)
 res13 &lt;- zero_crossings_maxima(h13\$x,h13\$ratio)
 res14 &lt;- zero_crossings_maxima(h14\$x,h14\$ratio)
 res15 &lt;- zero_crossings_maxima(h15\$x,h15\$ratio)
 res16 &lt;- zero_crossings_maxima(h16\$x,h16\$ratio)
 res17 &lt;- zero_crossings_maxima(h17\$x,h17\$ratio)
 res18 &lt;- zero_crossings_maxima(h18\$x,h18\$ratio)
 res19 &lt;- zero_crossings_maxima(h19\$x,h19\$ratio)
 res20 &lt;- zero_crossings_maxima(h20\$x,h20\$ratio)
 res21 &lt;- zero_crossings_maxima(h21\$x,h21\$ratio)
 res22 &lt;- zero_crossings_maxima(h22\$x,h22\$ratio)
 res23 &lt;- zero_crossings_maxima(h23\$x,h23\$ratio)
 res24 &lt;- zero_crossings_maxima(h24\$x,h24\$ratio)
 res25 &lt;- zero_crossings_maxima(h25\$x,h25\$ratio)


 #plotting (including maxima and adjusting to max ratio)
 # all on one plot
 pdf("allchrs.pdf",height=10, width=20)
 library(Hmisc)
 ymax &lt;- 1.05*max( c(h1\$ratio,h2\$ratio,h3\$ratio,h4\$ratio,h5\$ratio,h6\$ratio,h7\$ratio,h8\$ratio,h9\$ratio,h10\$ratio,h11\$ratio,h12\$ratio,h13\$ratio,h14\$ratio,h15\$ratio,h16\$ratio,h17\$ratio,h18\$ratio,h19\$ratio,h20\$ratio,h21\$ratio,h22\$ratio,h23\$ratio,h24\$ratio,h25\$ratio))
 par(mfrow=c(5,5))
 plot(h1\$x, h1\$ratio,type="l", lwd=3, col="red", xlim=c(0,61000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 1")
 points( res1\$maxima\$x[1], res1\$maxima\$y[1], col="red", pch=19 )
 abline(v=res1\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res1\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h2\$x, h2\$ratio,type="l", lwd=3, col="red", xlim=c(0,61000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 2")
 points( res2\$maxima\$x[1], res2\$maxima\$y[1], col="red", pch=19 )
 abline(v=res2\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res2\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h3\$x, h3\$ratio,type="l", lwd=3, col="red", xlim=c(0,64000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 3")
 points( res3\$maxima\$x[1], res3\$maxima\$y[1], col="red", pch=19 )
 abline(v=res3\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res3\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h4\$x, h4\$ratio,type="l", lwd=3, col="red",, xlim=c(0,64000000),ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 4")
 points( res4\$maxima\$x[1], res4\$maxima\$y[1], col="red", pch=19 )
 abline(v=res4\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res4\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h5\$x, h5\$ratio,type="l", lwd=3, col="red",, xlim=c(0,76000000),ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 5")
 points( res5\$maxima\$x[1], res5\$maxima\$y[1], col="red", pch=19 )
 abline(v=res5\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res5\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h6\$x, h6\$ratio,type="l", lwd=3, col="red",, xlim=c(0,60000000),ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 6")
 points( res6\$maxima\$x[1], res6\$maxima\$y[1], col="red", pch=19 )
 abline(v=res6\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res6\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h7\$x, h7\$ratio,type="l", lwd=3, col="red",, xlim=c(0,78000000),ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio" , main="Chromosome 7")
 points( res7\$maxima\$x[1], res7\$maxima\$y[1], col="red", pch=19 )
 abline(v=res7\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res7\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h8\$x, h8\$ratio,type="l", lwd=3, col="red",, xlim=c(0,57000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio" , main="Chromosome 8")
 points( res8\$maxima\$x[1], res8\$maxima\$y[1], col="red", pch=19 )
 abline(v=res8\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res8\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h9\$x, h9\$ratio,type="l", lwd=3, col="red",, xlim=c(0,59000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio" , main="Chromosome 9")
 points( res9\$maxima\$x[1], res9\$maxima\$y[1], col="red", pch=19 )
 abline(v=res9\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res9\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h10\$x, h10\$ratio,type="l", lwd=3, col="red",, xlim=c(0,47000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 10")
 points( res10\$maxima\$x[1], res10\$maxima\$y[1], col="red", pch=19 )
 abline(v=res10\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res10\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h11\$x, h11\$ratio,type="l", lwd=3, col="red",, xlim=c(0,47000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 11")
 points( res11\$maxima\$x[1], res11\$maxima\$y[1], col="red", pch=19 )
 abline(v=res11\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res11\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h12\$x, h12\$ratio,type="l", lwd=3, col="red",, xlim=c(0,51000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 12")
 points( res12\$maxima\$x[1], res12\$maxima\$y[1], col="red", pch=19 )
 abline(v=res12\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res12\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h13\$x, h13\$ratio,type="l", lwd=3, col="red",, xlim=c(0,55000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 13")
 points( res13\$maxima\$x[1], res13\$maxima\$y[1], col="red", pch=19 )
 abline(v=res13\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res13\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h14\$x, h14\$ratio,type="l", lwd=3, col="red",, xlim=c(0,54000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 14")
 points( res14\$maxima\$x[1], res14\$maxima\$y[1], col="red", pch=19 )
 abline(v=res14\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res14\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h15\$x, h15\$ratio,type="l", lwd=3, col="red",, xlim=c(0,48000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 15")
 points( res15\$maxima\$x[1], res15\$maxima\$y[1], col="red", pch=19 )
 abline(v=res15\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res15\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h16\$x, h16\$ratio,type="l", lwd=3, col="red",, xlim=c(0,59000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 16")
 points( res16\$maxima\$x[1], res16\$maxima\$y[1], col="red", pch=19 )
 abline(v=res16\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res16\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h17\$x, h17\$ratio,type="l", lwd=3, col="red",, xlim=c(0,54000000),, ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 17")
 points( res17\$maxima\$x[1], res17\$maxima\$y[1], col="red", pch=19 )
 abline(v=res17\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res17\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h18\$x, h18\$ratio,type="l", lwd=3, col="red", xlim=c(0,50000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 18")
 points( res18\$maxima\$x[1], res18\$maxima\$y[1], col="red", pch=19 )
 abline(v=res18\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res18\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h19\$x, h19\$ratio,type="l", lwd=3, col="red",, xlim=c(0,51000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", , main="Chromosome 19")
 points( res19\$maxima\$x[1], res19\$maxima\$y[1], col="red", pch=19 )
 abline(v=res19\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res19\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h20\$x, h20\$ratio,type="l", lwd=3, col="red",, xlim=c(0,56000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 20")
 points( res20\$maxima\$x[1], res20\$maxima\$y[1], col="red", pch=19 )
 abline(v=res20\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res20\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h21\$x, h21\$ratio,type="l", lwd=3, col="red",, xlim=c(0,45000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 21")
 points( res21\$maxima\$x[1], res21\$maxima\$y[1], col="red", pch=19 )
 abline(v=res21\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res21\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h22\$x, h22\$ratio,type="l", lwd=3, col="red",, xlim=c(0,43000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 22")
 points( res22\$maxima\$x[1], res22\$maxima\$y[1], col="red", pch=19 )
 abline(v=res22\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res22\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h23\$x, h23\$ratio,type="l", lwd=3, col="red",, xlim=c(0,47000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 23")
 points( res23\$maxima\$x[1], res23\$maxima\$y[1], col="red", pch=19 )
 abline(v=res23\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res23\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h24\$x, h24\$ratio,type="l", lwd=3, col="red",, xlim=c(0,44000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 24")
 points( res24\$maxima\$x[1], res24\$maxima\$y[1], col="red", pch=19 )
 abline(v=res24\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res24\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 plot(h25\$x, h25\$ratio,type="l", lwd=3, col="red",, xlim=c(0,39000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 25")
 points( res25\$maxima\$x[1], res25\$maxima\$y[1], col="red", pch=19 )
 abline(v=res25\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n",  paste(format(round(res25\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(10)
 dev.off()

 # seperate plots
 pdf("chr1.pdf",height=5, width=10)
 plot(h1\$x, h1\$ratio,type="l", lwd=3, col="red", xlim=c(0,61000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 1")
 points( res1\$maxima\$x[1], res1\$maxima\$y[1], col="red", pch=19 )
 abline(v=res1\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res1\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr2.pdf",height=5, width=10)
 plot(h2\$x, h2\$ratio,type="l", lwd=3, col="red", xlim=c(0,61000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 2")
 points( res2\$maxima\$x[1], res2\$maxima\$y[1], col="red", pch=19 )
 abline(v=res2\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res2\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr3.pdf",height=5, width=10)
 plot(h3\$x, h3\$ratio,type="l", lwd=3, col="red", xlim=c(0,64000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 3")
 points( res3\$maxima\$x[1], res3\$maxima\$y[1], col="red", pch=19 )
 abline(v=res3\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res3\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr4.pdf",height=5, width=10)
 plot(h4\$x, h4\$ratio,type="l", lwd=3, col="red",, xlim=c(0,64000000),ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 4")
 points( res4\$maxima\$x[1], res4\$maxima\$y[1], col="red", pch=19 )
 abline(v=res4\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res4\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr5.pdf",height=5, width=10)
 plot(h5\$x, h5\$ratio,type="l", lwd=3, col="red",, xlim=c(0,76000000),ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 5")
 points( res5\$maxima\$x[1], res5\$maxima\$y[1], col="red", pch=19 )
 abline(v=res5\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res5\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr6.pdf",height=5, width=10)
 plot(h6\$x, h6\$ratio,type="l", lwd=3, col="red",, xlim=c(0,60000000),ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 6")
 points( res6\$maxima\$x[1], res6\$maxima\$y[1], col="red", pch=19 )
 abline(v=res6\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res6\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr7.pdf",height=5, width=10)
 plot(h7\$x, h7\$ratio,type="l", lwd=3, col="red",, xlim=c(0,78000000),ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio" , main="Chromosome 7")
 points( res7\$maxima\$x[1], res7\$maxima\$y[1], col="red", pch=19 )
 abline(v=res7\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res7\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr8.pdf",height=5, width=10)
 plot(h8\$x, h8\$ratio,type="l", lwd=3, col="red",, xlim=c(0,57000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio" , main="Chromosome 8")
 points( res8\$maxima\$x[1], res8\$maxima\$y[1], col="red", pch=19 )
 abline(v=res8\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res8\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr9.pdf",height=5, width=10)
 plot(h9\$x, h9\$ratio,type="l", lwd=3, col="red",, xlim=c(0,59000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio" , main="Chromosome 9")
 points( res9\$maxima\$x[1], res9\$maxima\$y[1], col="red", pch=19 )
 abline(v=res9\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res9\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr10.pdf",height=5, width=10)
 plot(h10\$x, h10\$ratio,type="l", lwd=3, col="red",, xlim=c(0,47000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 10")
 points( res10\$maxima\$x[1], res10\$maxima\$y[1], col="red", pch=19 )
 abline(v=res10\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res10\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr11.pdf",height=5, width=10)
 plot(h11\$x, h11\$ratio,type="l", lwd=3, col="red",, xlim=c(0,47000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 11")
 points( res11\$maxima\$x[1], res11\$maxima\$y[1], col="red", pch=19 )
 abline(v=res11\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res11\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr12.pdf",height=5, width=10)
 plot(h12\$x, h12\$ratio,type="l", lwd=3, col="red",, xlim=c(0,51000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 12")
 points( res12\$maxima\$x[1], res12\$maxima\$y[1], col="red", pch=19 )
 abline(v=res12\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res12\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr13.pdf",height=5, width=10)
 plot(h13\$x, h13\$ratio,type="l", lwd=3, col="red",, xlim=c(0,55000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 13")
 points( res13\$maxima\$x[1], res13\$maxima\$y[1], col="red", pch=19 )
 abline(v=res13\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res13\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr14.pdf",height=5, width=10)
 plot(h14\$x, h14\$ratio,type="l", lwd=3, col="red",, xlim=c(0,54000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 14")
 points( res14\$maxima\$x[1], res14\$maxima\$y[1], col="red", pch=19 )
 abline(v=res14\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res14\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr15.pdf",height=5, width=10)
 plot(h15\$x, h15\$ratio,type="l", lwd=3, col="red",, xlim=c(0,48000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 15")
 points( res15\$maxima\$x[1], res15\$maxima\$y[1], col="red", pch=19 )
 abline(v=res15\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res15\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr16.pdf",height=5, width=10)
 plot(h16\$x, h16\$ratio,type="l", lwd=3, col="red",, xlim=c(0,59000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 16")
 points( res16\$maxima\$x[1], res16\$maxima\$y[1], col="red", pch=19 )
 abline(v=res16\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res16\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr17.pdf",height=5, width=10)
 plot(h17\$x, h17\$ratio,type="l", lwd=3, col="red",, xlim=c(0,54000000),, ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 17")
 points( res17\$maxima\$x[1], res17\$maxima\$y[1], col="red", pch=19 )
 abline(v=res17\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res17\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr18.pdf",height=5, width=10)
 plot(h18\$x, h18\$ratio,type="l", lwd=3, col="red", xlim=c(0,50000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 18")
 points( res18\$maxima\$x[1], res18\$maxima\$y[1], col="red", pch=19 )
 abline(v=res18\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res18\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr19.pdf",height=5, width=10)
 plot(h19\$x, h19\$ratio,type="l", lwd=3, col="red",, xlim=c(0,51000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", , main="Chromosome 19")
 points( res19\$maxima\$x[1], res19\$maxima\$y[1], col="red", pch=19 )
 abline(v=res19\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res19\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr20.pdf",height=5, width=10)
 plot(h20\$x, h20\$ratio,type="l", lwd=3, col="red",, xlim=c(0,56000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 20")
 points( res20\$maxima\$x[1], res20\$maxima\$y[1], col="red", pch=19 )
 abline(v=res20\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res20\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr21.pdf",height=5, width=10)
 plot(h21\$x, h21\$ratio,type="l", lwd=3, col="red",, xlim=c(0,45000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 21")
 points( res21\$maxima\$x[1], res21\$maxima\$y[1], col="red", pch=19 )
 abline(v=res21\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res21\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr22.pdf",height=5, width=10)
 plot(h22\$x, h22\$ratio,type="l", lwd=3, col="red",, xlim=c(0,43000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 22")
 points( res22\$maxima\$x[1], res22\$maxima\$y[1], col="red", pch=19 )
 abline(v=res22\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res22\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr23.pdf",height=5, width=10)
 plot(h23\$x, h23\$ratio,type="l", lwd=3, col="red",, xlim=c(0,47000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 23")
 points( res23\$maxima\$x[1], res23\$maxima\$y[1], col="red", pch=19 )
 abline(v=res23\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res23\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr24.pdf",height=5, width=10)
 plot(h24\$x, h24\$ratio,type="l", lwd=3, col="red",, xlim=c(0,44000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 24")
 points( res24\$maxima\$x[1], res24\$maxima\$y[1], col="red", pch=19 )
 abline(v=res24\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n", legend=paste(format(round(res24\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(nx=10)
 dev.off()
 pdf("chr25.pdf",height=5, width=10)
 plot(h25\$x, h25\$ratio,type="l", lwd=3, col="red",, xlim=c(0,39000000), ylim=c(0,ymax), xlab="Location (Mb)", ylab="Adjusted homozygosity ratio", main="Chromosome 25")
 points( res25\$maxima\$x[1], res25\$maxima\$y[1], col="red", pch=19 )
 abline(v=res25\$maxima\$x[1], lwd=1)
 legend("topleft", bty="n",  paste(format(round(res25\$maxima\$x[1] ,0),nsmall=0) ) )
 minor.tick(10)
 dev.off()

**Attribution**
This Galaxy tool was created by r.poole@ucl.ac.uk at 13/10/2014 13:41:11
using the Galaxy Tool Factory.

See https://bitbucket.org/fubar/galaxytoolfactory for details of that project
Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team.
Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573


</help>
<citations>
    <citation type="doi">10.1534/genetics.112.144204</citation>
    <citation type="doi">10.1093/bioinformatics/bts573</citation>
</citations>
</tool>
author	richjp
date	Mon, 13 Oct 2014 08:42:19 -0400
parents
children	9b60d5a2c313