R/AlleleCum.R

In kkeenan02/MsatAllele: Visualizes the scoring and binning of microsatellite fragment sizes

AlleleCum<-function(DataBase,loci,ymin=NULL,ymax=NULL,c1="black",c2="grey",ytsize=1,psize=1,pch=1){
  
  
  o<-order(DataBase[DataBase[,1]==loci,3])
  
  Frag<-DataBase[DataBase[,1]==loci,3]
  Frag<-Frag[o]
  
  
  Bin<-1:length(Frag)
  i<-1
  
  repeat{
    Bin[i]<-get.allele(DataBase,loci,Frag[i])
    i<-i+1
    if(i>length(Frag))break}
  
  
  
  
  
  Color.vect<-1:length(Frag)
  
  tempC<-c1
  
  Color.vect[1]<-c1
  i<-2
  
  
  repeat{
    if(Bin[i]==Bin[i-1])
    {Color.vect[i]<-tempC
     i<-i+1
    }else
    {ifelse(tempC==c1,tempC<-c2,ifelse(tempC==c2,tempC<-c1,tempC<-c1))
     Color.vect[i]<-tempC
     i<-i+1}
    if(i>length(Frag))break}
  
  
  
  plot(Frag,type="n",axes=FALSE,xlab="Number of observations",ylab="Allele size (bp)",main=loci,ylim=c(ymin,ymax))
  
  par(cex=psize)
  points(Frag,col=Color.vect,pch=pch)
  
  par(cex=1)
  axis(1,pos=min(Bin)-1)
  par(cex=ytsize)
  axis(2,pos=0,las=2,at=as.numeric(levels(as.factor(Bin))))
  par(cex=1)
}