R/drawChromosomeZoom.R

In gada: Genome Alteration Detection Algorithm (GADA)

drawChromosomeZoom<-function(chr, size=0.05, chromStart, chromEnd , print.names=TRUE, ...)
 {
  on.exit(par("xpd"=TRUE))
  par(xpd=FALSE)

  if (chr==23)
      chr <- "X"
  if (chr == 24)
      chr <- "Y"

  chromName<-paste("chr",chr,sep="")
  limits<-c(chromStart, chromEnd)
  tamany<-chromEnd-chromStart

  plot(0, axes = FALSE, xlab = "", type = "n", col = "gray", xlim = limits, ...)

  pp<-par("usr")
  ytop <- pp[3]
  ybottom <- pp[3]+size
  ymig <- (ytop+ybottom)/2

  segments(0,ymig,tamany,ymig,col="gray",cex=2) ### pintem ratlles horitzontals pels cromosomes
  bandes<-ideogram[ideogram$chrom==chromName, ]
  bandes$posGrafic <- bandes$chromStart+(bandes$chromEnd-bandes$chromStart)/2
  numBandes<-dim(bandes)[1]
  gieStain<-levels(bandes$gieStain) ### [1] "acen" "gneg" "gpos100" "gpos25" "gpos50" "gpos75" "gvar" "stalk"
  colorsBandes<-c("red","gray100","black","gray25","gray50","gray75","gray50","gray50")
  japintat<-0

  for(h in 1:numBandes)
   {
   chromStart<-bandes$chromStart[h]
   chromEnd<-bandes$chromEnd[h]
   giemsaBand<-bandes$gieStain[h]
   colorBanda<-colorsBandes[giemsaBand]
   if(giemsaBand == "acen")
    {
     segments(chromStart,ybottom,chromStart,ytop,col="black")
    } 
   else
    {
     if(giemsaBand == "gvar")
      {
       rect(chromStart,ybottom,chromEnd,ytop,col=colorBanda,angle=90,density=0.9)
       cylindrect(chromStart,ybottom,chromEnd,ytop,col=colorBanda,gradient="y",nslices=50)
      } 
     else
      {
       rect(chromStart,ybottom,chromEnd,ytop,col=colorBanda,border="gray50")
       cylindrect(chromStart,ybottom,chromEnd,ytop,col=colorBanda,gradient="y",nslices=50)
      } 
    }
   if(japintat==0 & giemsaBand == "acen")
    {
     japintat <- 1
     points(chromEnd, ymig, pch=19, col = "gray", xpd = TRUE, cex=0.8)
    }
   }
# Noms de les bandes
  if (print.names)
    text(bandes$posGrafic,rep(ybottom-1.5*size,numBandes),bandes$name,srt=-90,adj=0,cex=0.6,xpd=TRUE)
}