demo/RCircos.Polygon.Plot.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.Polygon.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.Polygon.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, 10);


    #   Open the graphic device (here a pdf file)
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    pdf(file="RCircos.Polygon.Demo.pdf", 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 Polygon Plot Demo");


    #   Plot histogram Inside of chromosome ideogram
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    polygon.data <- RCircos.Polygon.Data;
    RCircos.Polygon.Plot(polygon.data, track.num=NULL, data.col=4,
        genomic.columns=3, side="in", inside.pos=1.6, outside.pos=1.8, 
        border.col="black", polygon.col="red", is.sorted=TRUE)

    polygon.data$Data <- polygon.data$Data*-1
    RCircos.Polygon.Plot(polygon.data, track.num=NULL, data.col=4,
        genomic.columns=3, side="in", inside.pos=1.3, outside.pos=1.5, 
        border.col="black", polygon.col="green", is.sorted=TRUE)

    rows <- seq(1, 77, by=2)

    plot.colors <- rep("red", nrow(polygon.data))
    plot.colors[rows] <- "green"
    polygon.data["PlotColor"] <- plot.colors
    polygon.data$Data[rows] <- polygon.data$Data[rows]*-1

    RCircos.Polygon.Plot(polygon.data, track.num=NULL, data.col=4,
        genomic.columns=3, side="in", inside.pos=0.8, outside.pos=1.2, 
        border.col="black", polygon.col=NULL, is.sorted=TRUE)

    title("RCircos Polygon Plot Demo")



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