demo/RCircos.Histogram.Demo.R

In RCircos: Circos 2D Track Plot

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



    #   Load RCircos package and defined parameters
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    library(RCircos);


    #   Load human cytoband data and gene expression data
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    data(RCircos.Histogram.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, 10, 0);


    #   Open the graphic device (here a pdf file)
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    out.file <- "RCircos.Histogram.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 Histogram Plot Demo");


    #   Plot histogram Inside of chromosome ideogram
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    hist.data <- RCircos.Histogram.Data;
    hist.colors <- rep("blue", nrow(hist.data))
    rows <- which(hist.data$Data>0.4)
    hist.colors[rows] <- "red";
    hist.data["PlotColor"] <- hist.colors;

    data.col <- 4; 
    track.num <- 1;
    RCircos.Histogram.Plot(hist.data, data.col, track.num, "in");


    #   Close the graphic device and clear memory
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    dev.off();
    message("RCircos Histogram Demo Done!");