RCircos.Track.Outline.Simple.R

RCircos.Track.Outline.Simple<-function(out.pos, in.pos)
{
	RCircos.Cyto <- RCircos.Get.Plot.Ideogram();
	RCircos.Pos <- RCircos.Get.Plot.Positions();
	RCircos.Par <- RCircos.Get.Plot.Parameters();

	chroms <- unique(RCircos.Cyto$Chromosome);
	for(a.chr in 1:length(chroms))
	{
		the.chr  <- RCircos.Cyto[RCircos.Cyto$Chromosome==chroms[a.chr],];
		start <- the.chr$Location[1]- the.chr$Unit[1] + 1;
		end   <- the.chr$Location[nrow(the.chr)];

		polygon.x<- c(RCircos.Pos[start:end,1]*out.pos, 
				RCircos.Pos[end:start,1]*in.pos);
		polygon.y<- c(RCircos.Pos[start:end,2]*out.pos, 
				RCircos.Pos[end:start,2]*in.pos);
		polygon(polygon.x, polygon.y, col="white");

	}
}