demo/RCircos.Demo.Mouse.And.Rat.R

In RCircos: Circos 2D Track Plot

    #   ______________________________________________________________________
    #   <RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO>
    #
    #   This demo draws a heatmap with both mouse and rat gene expresion 
    #   data and links between same genes. 
    #
    #   We will put mouse data on right side and rat data on left side.  
    #   Since we are going to draw the image with both mouse and rat  
    #   chromosome ideogram, we deduct total points of each ideogram by 
    #   half. This is done by modify the base.per.unit from 3000 to 
    #   30000. Chromosome padding will be automatically modified if we do 
    #   not give it new value.
    #
    #   Last revised on June 9, 2016
    #
    #   ______________________________________________________________________
    #   <RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO>




    #   Load RCircos package and defined parameters. 
    #   __________________________________________________
    #   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

    library(RCircos);


    #   Load chromosome cytoband data. We will generate 
    #   a pseudo karyotype by concatenating the second 
    #   ideogram data to the first one.
    #   __________________________________________________
    #   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

    message("Read in cytoband data ...\n");

    data(UCSC.Mouse.GRCm38.CytoBandIdeogram);
    data(UCSC.Baylor.3.4.Rat.cytoBandIdeogram);


    #   Load mouse and rat gene expression data
    #   __________________________________________________
    #   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

    message("Read in gene expression data ...\n");

    data(RCircos.Mouse.Expr.Data);
    data(RCircos.Rat.Expr.Data);


    #   Generate link data from the two datasets. These
    #   lines are regular R script code.
    #   __________________________________________________
    #   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

    mouse.data <- RCircos.Mouse.Expr.Data;
    rat.data <- RCircos.Rat.Expr.Data;

    mouse.gene <- as.character(mouse.data$Gene);
    rat.gene   <- as.character(rat.data$Gene);

    mouse.set <- mouse.data[mouse.gene %in% rat.gene,];
    mouse.set <- mouse.set[order(mouse.set$Expr.Mean),];
    last <- nrow(mouse.set);
    first <- last - 49;
    mouse.set <- mouse.set[first:last,];

    mouse.set.gene <- as.character(mouse.set$Gene);
    rat.set <- rat.data[rat.gene %in% mouse.set.gene,];

    mouse.set <- mouse.set[order(mouse.set$Gene),];
    rat.set <- rat.set[order(rat.set$Gene),];

    link.data <- data.frame(mouse.set[,1:3], rat.set[,1:3]);


    #   Modify the datasets and ideogram so that they have
    #   same chromosome names. Please make sure the items
    #   in the two lists have same order.
    #   __________________________________________________
    #   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

    species.list <- c("M", "R");

    cyto.list <- list(UCSC.Mouse.GRCm38.CytoBandIdeogram, 
                    UCSC.Baylor.3.4.Rat.cytoBandIdeogram);
    RCircos.Multiple.Species.Core.Components(cyto.list, 
                    species.list, NULL, 5, 5);

    data.list <- list(RCircos.Mouse.Expr.Data, 
                    RCircos.Rat.Expr.Data);
    expr.data <- RCircos.Multiple.Species.Dataset(data.list, 
                    species.list);

    link.data[,1] <- paste(species.list[1], link.data[,1], sep="");
    link.data[,4] <- paste(species.list[2], link.data[,4], sep="");


    #   Setup RCircos core components then change the
    #   base.per.unit to 30000 for fast drawing
    #   __________________________________________________
    #   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

    params <- RCircos.Get.Plot.Parameters();
    params$base.per.unit <- 30000;
    RCircos.Reset.Plot.Parameters(params);


    #   Initialize graphic device (GUI or image file)
    #
    #   tiff(file="RCircos.Demo.Mouse.And.Rat.tif", height=8,
    #       width=9, unit="in", type="cairo", res=300);
    #
    #   png(file="RCircos.Demo.Mouse.And.Rat.png", height=8,
    #       width=9, unit="in", type="cairo", res=300);
    #   __________________________________________________
    #   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

    message("Initialize graphic device ...\n");

    pdf(file="RCircos.Demo.Mouse.And.Rat.pdf", height=8, width=8);
    RCircos.Set.Plot.Area();


    #   Plot chromosome ideogram, heatmap, and link lines
    #   __________________________________________________
    #   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

    RCircos.Chromosome.Ideogram.Plot();

    data.col <- 5;
    track.num <- 1;
    RCircos.Heatmap.Plot(expr.data, data.col, track.num, "in");

    track.num <- 3;
    RCircos.Link.Plot(link.data, track.num, FALSE);


    #   Add a title and a legend
    #   __________________________________________________
    #   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

    title("RCircos Demo: Mouse and Rat Gene Expression");
    legend(0.6, 2, legend=c("Right: GSE42081 Mouse", 
                "Left:  GSE42081 Rat"), cex=0.8);


    #   Add a color key
    #   __________________________________________________
    #   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

    RCircos.Plot.Heatmap.Color.Scale(max.value=3, min.value=-3,
        color.type="BlueWhiteRed", scale.location=1, 
        scale.width=2, scale.height=0.2) 



    #   Done. Close the device if plot to image file...
    #   _______________________________________________
    #   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

    dev.off();
    message("R Circos Demo with mouse and Rat data done ...\n\n");