demo/RCircos.Heatmap.Demo.R

In RCircos: Circos 2D Track Plot

    #
    #   This demo draw chromosome ideogram with padding between 
    #   chromosomes, highlights, chromosome names, and heatmap 
    #   with gene expression data.
    #
    #   Usage:
    #
    #   library(RCircos);
    #   demo("RCircos.Heatmap.Demo");
    #   ______________________________________________________________________
    #   <RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO>



    #   Load RCircos library
    #   _________________________________________________________________
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    library(RCircos);


    #   Load human cytoband data and gene expression data
    #   _________________________________________________________________
    #   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

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


    #   Setup RCircos core components:
    #   _________________________________________________________________
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    RCircos.Set.Core.Components(cyto.info, NULL, 5, 0);


    #   Open the graphic device (here a pdf file)
    #   _________________________________________________________________
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    out.file <- "RCircos.Heatmap.Demo.pdf";
    pdf(file=out.file, height=8, width=8);

    RCircos.Set.Plot.Area();


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

    RCircos.Chromosome.Ideogram.Plot();
    title("RCircos Heatmap Plot Demo");



    #   Plot five tracks of heatmap
    #   _________________________________________________________________
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    total.track <- 5;
    for(a.track in 1:total.track)
    {
        data.col <- a.track + 4;
        RCircos.Heatmap.Plot(RCircos.Heatmap.Data, data.col, a.track, "in");
    }


    #   Close the graphic device
    #   _________________________________________________________________
    #   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

    dev.off();
    message("RCircos Heatmap demo done!\n");