demo/RCircos.Gene.Connector.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 area between 
    #   chromosomes, highlights, and chromosome names, label gene names 
    #   in the second data track and put connectors between chromosome 
    #   ideogram and gene names.
    #
    #   Usage:
    #
    #   library(RCircos);
    #   demo("RCircos.Gene.Connector.Demo");
    #   ______________________________________________________________________
    #   <RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO>



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


    #   Load gene label data and human cytoband data 
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    data(RCircos.Gene.Label.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, 5);


    #   Ready to make Circos plot. Open the graphic device (pdf file)
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    out.file <- "RCircos.Gene.Connector.Demo.pdf";
    pdf(file=out.file, height=8, width=8);

    RCircos.Set.Plot.Area();
    title("RCircos Gene and Connector Plot Demo");


    #   Draw chromosome ideogram
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    message("Draw chromosome ideogram ...\n");
    RCircos.Chromosome.Ideogram.Plot();


    #   Connectors in first track and gene names in the second track. 
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    message("Add Gene and connector tracks ...\n");
    data(RCircos.Gene.Label.Data);

    direction <- "in";
    track.num <- 1;
    RCircos.Gene.Connector.Plot(RCircos.Gene.Label.Data, 
                track.num, direction);

    gene.data <- RCircos.Gene.Label.Data;
    gene.colors <- rep("black", nrow(gene.data))
    gene.colors[which(gene.data$Gene=="TP53")] <- "red";
    gene.colors[which(gene.data$Gene=="BRCA2")] <- "red";
    gene.colors[which(gene.data$Gene=="RB1")] <- "red";
    gene.colors[which(gene.data$Gene=="JAK1")] <- "blue";
    gene.colors[which(gene.data$Gene=="JAK2")] <- "blue";

    gene.data["PlotColor"] <- gene.colors;

    name.col <- 4;
    track.num <- 2;
    RCircos.Gene.Name.Plot(gene.data, name.col, track.num, direction);
#

    track.num <- 1;
    direction <- "out";
    RCircos.Gene.Connector.Plot(RCircos.Gene.Label.Data, 
                track.num, direction);
    track.num <- 2;
    RCircos.Gene.Name.Plot(gene.data, name.col, track.num, direction);


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