6 RCircos plot showing data track layout

Authors: Hongen Zhang  Reviser: Tianze Cao

2025-06-05

This demo draw chromosome ideogram with padding between
chromosomes, highlights, chromosome names, and three empty tracks inside and outside of chromosome ideogram.

#   Load RCircos library

library(RCircos);

#   Load human cytoband data 

data(UCSC.HG19.Human.CytoBandIdeogram);
cyto.info <- UCSC.HG19.Human.CytoBandIdeogram;

#   Setup RCircos core components:

RCircos.Set.Core.Components(cyto.info, NULL, 5, 5);

## 
## RCircos.Core.Components initialized.
## Type ?RCircos.Reset.Plot.Parameters to see how to modify the core components.

#   Open the graphic device (here a pdf file)

RCircos.Set.Plot.Area();

#   Draw chromosome ideogram

message("Draw chromosome ideogram ...\n");

## Draw chromosome ideogram ...

RCircos.Chromosome.Ideogram.Plot();
title("R Circos Layout Demo");

#   Marking plot areas both inside and outside of
#   chromosome ideogram ( 3 for each)
#   ********************************************
total.track <- 3;
subtrack <- 5;

#   Outside of chromosome ideogram

RCircos.Par <- RCircos.Get.Plot.Parameters();
one.track <- RCircos.Par$track.height + RCircos.Par$track.padding;

for(a.track in 1:total.track)
{   
    in.pos    <- RCircos.Par$track.out.start  + (a.track-1)*one.track;
    out.pos <- in.pos + RCircos.Par$track.height;
    RCircos.Track.Outline(out.pos, in.pos, subtrack);
}

#   Inside of chromosome ideogram

for(a.track in 1:total.track)
{
    out.pos <- RCircos.Par$track.in.start  - (a.track-1)*one.track;
    in.pos    <- out.pos - RCircos.Par$track.height;
    RCircos.Track.Outline(out.pos, in.pos, subtrack);
}

message("RCircos Layout Demo Done!");

## RCircos Layout Demo Done!