demo/RCircos.Chromosome.Tick.Demo.R

In RCircos: Circos 2D Track Plot

    #
    #   This demo draw human chromosome ideogram with ticks. Since in most 
    #   cases ticks are not necessary for data presentation, we add ticks  
    #   to existing ideogram instead of plotting an ideogram with ticks.
    #
    #   Set 20 tracks inside of chromosome ideogram to get enough space 
    #   for all chromosomes with ticks in 5MB interval
    #
    #   ______________________________________________________________________
    #   <RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO> 


    #   Load RCircos package
    #   ==============================================================

    library(RCircos);


    #   Load human cytoband data 
    #   ==============================================================

    data(UCSC.HG19.Human.CytoBandIdeogram);
    hg19.cyto <- UCSC.HG19.Human.CytoBandIdeogram;


    #   Set 10 tracks in outside of chromosome ideogram to get enough 
    #   space for all chromosomes ticks in 10 MB interval
    #   ==============================================================

    RCircos.Set.Core.Components(cyto.info=hg19.cyto, chr.exclude=NULL, 
            tracks.inside=10, tracks.outside=5);


    #   Open the graphic device (here a png image file)
    #   ==============================================================
    pdf(file="RCircos.Demo.Chromosome.Ticks.pdf", height=8, width=8);
    RCircos.Set.Plot.Area();
    title("RCircos Tick Demo")

    #   Draw chromosome ideogram with ticks in 10 mb interval
    #   ==============================================================
    RCircos.Chromosome.Ideogram.Plot(tick.interval=10);


    #   Close the graphic device and clear memory
    #   ==============================================================
    dev.off();
    message("R Circos Tick Demo Done ...\n\n");