demo/RCircos.Zoom.Plot.Demo.R

In RCircos: Circos 2D Track Plot

    #
    #   RCircos Zoom Plot Demo
    #
    #   This demo plot human chromosome ideogram with zoomed heatmap plot,  
    #   zoomed hitogram plot, and zoomed scatter(points) plot on outside 
    #   of chromosome ideogram.
    #
    #   Usage:
    #
    #   library(RCircos);
    #   demo("RCircos.Zoom.Plot.Demo");
    #   ______________________________________________________________________
    #   <RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO> 


    #   Initialize the plot objects
    #   ==================================================================
    
    library(RCircos);
    data(UCSC.HG19.Human.CytoBandIdeogram);

    cyto <- UCSC.HG19.Human.CytoBandIdeogram;
    RCircos.Set.Core.Components(cyto.info=cyto, chr.exclude=NULL, 
            tracks.inside=10, tracks.outside=5);

    pdf(file="RCircos.ZoomIn.Plot.Demo.pdf", width=10, height=10);
    RCircos.Set.Plot.Area();
    RCircos.Chromosome.Ideogram.Plot();


    #    Zoom heatmap plot with defined track number
    #    ================================================================

    data(RCircos.Heatmap.Data);
    min.value <- min(as.matrix(RCircos.Heatmap.Data[,5:10]));
    max.value <- max(as.matrix(RCircos.Heatmap.Data[,5:10]));

    RCircos.Heatmap.Plot(RCircos.Heatmap.Data, data.col=5, 
            side="in", track.num=1);

    zoom.data <- RCircos.Get.Zoom.Data(RCircos.Heatmap.Data, name.col=4, 
            genomic.columns=3, target.gene="SP5", neighbor.genes=5);
    zoom.range <- RCircos.Get.Zoom.Range(zoom.data, genomic.columns=3);
    zoom.pos <- RCircos.Set.Zoom.Plot.Positions(zoom.range, total.genes=11, 
            area.length=0.25, fixed.width=TRUE, gene.width=NULL);

    RCircos.Plot.Zoomed.Heatmap(zoom.data, data.col=5, zoom.pos=zoom.pos, 
            track.num=2, outside.pos=NULL, inside.pos=NULL, 
            min.value, max.value);

    RCircos.Mark.Zoom.Area(zoom.range, track.num=2, zoom.pos=zoom.pos, 
            fill.color="red", inside.pos=NULL, outside.pos=NULL);

    RCircos.Label.Zoom.Region(zoom.data, name.col=4, zoom.pos=zoom.pos, 
            text.size=0.6, track.num=3, outside.pos=NULL, inside.pos=NULL);

    rm(zoom.data); rm(zoom.range); rm(zoom.pos);
    rm(min.value); rm(max.value);  rm(RCircos.Heatmap.Data);


    #    Zoom histogram plot with defined inside.pos and outside.pos
    #    =================================================================

    data(RCircos.Histogram.Data);
    RCircos.Histogram.Plot(RCircos.Histogram.Data, data.col=4, 
            side="in", track.num=2);

    data.rows <- which(RCircos.Histogram.Data$Chromosome=="chr4");
    zoom.data <- RCircos.Histogram.Data[data.rows[1:11], ];

    zoom.range <- RCircos.Get.Zoom.Range(zoom.data,  genomic.columns=3);
    zoom.pos <- RCircos.Set.Zoom.Plot.Positions(zoom.range, total.genes=11, 
            area.length=0.25, fixed.width=TRUE, gene.width=NULL);

    track.pos <- RCircos.Get.Track.Positions("out", 2);
    track.height <- track.pos[1] - track.pos[2];
    in.pos <- track.pos[2];
    out.pos <- in.pos + track.height*2;

    RCircos.Plot.Zoomed.Histogram(zoom.data, data.col=4, zoom.pos=zoom.pos, 
            track.num=NULL, inside.pos=in.pos, outside.pos=out.pos);

    RCircos.Mark.Zoom.Area(zoom.range, track.num=NULL, zoom.pos=zoom.pos, 
            fill.color="green", outside.pos=out.pos, inside.pos=in.pos);

    rm(zoom.data); rm(zoom.range); rm(zoom.pos);
    rm(data.rows); rm(track.pos); rm(track.height);
    rm(in.pos); rm(out.pos); rm(RCircos.Histogram.Data);


    #   Zoom point(scatter) plot  with defined inside.pos and outside.pos
    #   =================================================================

    data(RCircos.Scatter.Data);
    RCircos.Scatter.Plot(RCircos.Scatter.Data, data.col=5, track.num=3,
            side="in", by.fold=1);

    data.col <- 5;
    min.value <- min(as.matrix(RCircos.Scatter.Data[, data.col]));
    max.value <- max(as.matrix(RCircos.Scatter.Data[, data.col]));

    data.rows <- which(RCircos.Scatter.Data$Chromosome=="chr5");
    zoom.data <- RCircos.Scatter.Data[1160:1171, ];
    zoom.data["PlotColors"] <- rainbow(nrow(zoom.data));

    zoom.range <- RCircos.Get.Zoom.Range(zoom.data, genomic.columns=3);
    zoom.pos <- RCircos.Set.Zoom.Plot.Positions(zoom.range, total.genes=11, 
            area.length=0.25, fixed.width=TRUE, gene.width=NULL);

    #   Manually move zoome area a little forward to avoid overlap
    #
    zoom.pos <- zoom.pos + 1500;

    track.pos <- RCircos.Get.Track.Positions(side="out", track.num=3);
    track.height <- track.pos[1] - track.pos[2];
    in.pos <- track.pos[2];
    out.pos <- in.pos + track.height * 2;

    RCircos.Plot.Zoomed.Scatters(zoom.data, data.col=5, 
            track.num=NULL, zoom.pos=zoom.pos, 
            min.value=min.value, max.value=max.value, 
            point.type=19, with.size=TRUE, point.scale=1,
            inside.pos=in.pos, outside.pos=out.pos);

    RCircos.Mark.Zoom.Area(zoom.range, track.num=NULL, zoom.pos=zoom.pos, 
            fill.color="yellow", inside.pos=in.pos, outside.pos=out.pos);

    rm(zoom.data); rm(zoom.range); rm(zoom.pos);
    rm(data.col);  rm(min.value);  rm(max.value);
    rm(data.rows); rm(track.pos);  rm(track.height);
    rm(in.pos);    rm(out.pos);    rm(RCircos.Scatter.Data);




    #   Zoomed-in gene connectors and gene labels with defined track number
    #   ===================================================================

    data(RCircos.Heatmap.Data);
    data.rows <- which(RCircos.Heatmap.Data$Chromosome=="chr7");
    zoom.data <- RCircos.Heatmap.Data[5580:5590, 1:4];
    zoom.range <- RCircos.Get.Zoom.Range(zoom.data, genomic.columns=3);
    zoom.pos <- RCircos.Set.Zoom.Plot.Positions(zoom.range, total.genes=11, 
            area.length=0.25, fixed.width=TRUE, gene.width=NULL);
            
    RCircos.Plot.Zoomed.Gene.Connectors(zoom.data, zoom.pos=zoom.pos, 
            track.num=1, line.width=1, outside.pos=NULL, inside.pos=NULL);
        
    #   Zoomed gene connector will use three tracks so next track number
    #   must be three more
    RCircos.Label.Zoom.Region(zoom.data, name.col=4, zoom.pos=zoom.pos, 
            text.size=0.7, track.num=4, outside.pos=NULL, inside.pos=NULL);

    rm(zoom.data); rm(zoom.range); rm(zoom.pos); rm(data.rows);
    rm(RCircos.Heatmap.Data);


    #   Zoomed-in parallel line plot with defined in and out plot positions
    #   ===================================================================
    
    data(RCircos.Tile.Data);
    RCircos.Tile.Plot(RCircos.Tile.Data, track.num=4, side="in");

    data.rows <- which(RCircos.Tile.Data$Chromosome=="chr18");
    zoom.data <- RCircos.Tile.Data[data.rows, ];
    zoom.range <- RCircos.Get.Zoom.Range(zoom.data,  genomic.columns=3)
    zoom.pos <- RCircos.Set.Zoom.Plot.Positions(zoom.range,  
            total.genes=5, area.length=0.06, gene.width=NULL);

    track.pos <- RCircos.Get.Track.Positions(side="out", track.num=3);
    track.height <- track.pos[1] - track.pos[2];
    in.pos <- track.pos[2];
    out.pos <- in.pos + track.height * 2;

    RCircos.Plot.Zoomed.Parallel.Lines(zoom.data, zoom.pos=zoom.pos, 
            track.num=NULL, genomic.cols=3, line.width=3, 
            inside.pos=in.pos, outside.pos=out.pos, outline=TRUE);

    RCircos.Mark.Zoom.Area(zoom.range, track.num=NULL, zoom.pos=zoom.pos, 
            fill.color="yellow", inside.pos=in.pos, outside.pos=out.pos)

    rm(zoom.data); rm(zoom.range);   rm(zoom.pos); rm(data.rows); 
    rm(track.pos); rm(track.height); rm(in.pos);   rm(out.pos);
    rm(RCircos.Tile.Data);


    #   Zoomed-in tile plot with defined inside and outside plot positions
    #   ===================================================================

    data(RCircos.Tile.Data);
    data.rows <- which(RCircos.Tile.Data$Chromosome=="chrX");
    zoom.data <- RCircos.Tile.Data[data.rows, ];
    
    zoom.range <- RCircos.Get.Zoom.Range(zoom.data,  genomic.columns=3);
    zoom.pos <- RCircos.Set.Zoom.Plot.Positions(zoom.range, 
            total.genes=length(data.rows), area.length=0.08, 
            fixed.width=FALSE, gene.width=NULL);

    track.pos <- RCircos.Get.Track.Positions(side="out", track.num=3);
    track.height <- track.pos[1] - track.pos[2];
    in.pos <- track.pos[2];
    out.pos <- in.pos + track.height * 3;

    layers <- RCircos.Get.Plot.Layers(RCircos.Tile.Data, genomic.columns=3);
    RCircos.Plot.Zoomed.Tiles(zoom.data, zoom.pos=zoom.pos, 
            genomic.cols=3, layers=max(layers), track.num=NULL, 
            inside.pos=in.pos, outside.pos=out.pos, border.col=NULL);

    RCircos.Mark.Zoom.Area(zoom.range, track.num=NULL, zoom.pos=zoom.pos, 
            fill.color="green", inside.pos=in.pos, outside.pos=out.pos);

    rm(zoom.data); rm(zoom.range);   rm(zoom.pos); rm(data.rows); 
    rm(track.pos); rm(track.height); rm(in.pos);   rm(out.pos);
    rm(RCircos.Tile.Data);


    #   Zoomed-in chromosome ideogram tick plot with defined 
    #   inside and outside plot positions
    #   ===================================================================

    zoom.range <- c("chr15", 56828384, 71672845);
    zoom.pos <- RCircos.Set.Zoom.Plot.Positions(zoom.range, total.genes=11, 
            area.length=0.06, fixed.width=FALSE, gene.width=NULL);
    
    track.pos <- RCircos.Get.Track.Positions(side="out", track.num=3);
    track.height <- track.pos[1] - track.pos[2];
    in.pos <- track.pos[2];
    out.pos <- in.pos + track.height * 3;
    
    RCircos.Plot.Zoomed.Ideogram.Ticks(zoom.info=zoom.range, 
            zoom.pos=zoom.pos, tick.interval=2, track.num=NULL, 
            inside.pos=in.pos, outside.pos=out.pos);
    RCircos.Mark.Zoom.Area(zoom.range, track.num=NULL, zoom.pos=zoom.pos, 
            fill.color="green", inside.pos=in.pos, outside.pos=out.pos);

    rm(zoom.range); rm(zoom.pos); 
    rm(track.pos);  rm(track.height); rm(in.pos); rm(out.pos);

  
    #   Zoomed-in polygon plot with defined plot positions
    #   ===================================================================

    data(RCircos.Polygon.Data);
    data.col <- 4;
    
    rows <- seq(1, 77, by=2)
    plot.colors <- rep("red", nrow(RCircos.Polygon.Data))
    plot.colors[rows] <- "green"
    RCircos.Polygon.Data["PlotColor"] <- plot.colors
    RCircos.Polygon.Data$Data[rows] <- RCircos.Polygon.Data$Data[rows]*-1

    RCircos.Polygon.Plot(RCircos.Polygon.Data, track.num=5, 
            data.col=data.col, side="in")
 
    data.rows <- which(RCircos.Polygon.Data$Chromosome=="chr9");
    zoom.data <- RCircos.Polygon.Data[data.rows, ];

    zoom.range <- RCircos.Get.Zoom.Range(zoom.data,  genomic.columns=3);
    zoom.pos <- RCircos.Set.Zoom.Plot.Positions(zoom.range, 
            total.genes=length(data.rows), area.length=0.08, 
            fixed.width=FALSE, gene.width=NULL);

    track.pos <- RCircos.Get.Track.Positions(side="out", track.num=3)
    track.height <- track.pos[1] - track.pos[2];
    in.pos <- track.pos[2];
    out.pos <- in.pos + track.height * 3;

    min.value <- min(RCircos.Polygon.Data$Data)
    max.value <- max(RCircos.Polygon.Data$Data)
    
    RCircos.Plot.Zoomed.Polygons(zoom.data, data.col=data.col, 
            track.num=NULL, zoom.pos=zoom.pos, genomic.cols=3, 
            min.value=min.value, max.value=max.value, border.col=NULL, 
            inside.pos=in.pos, outside.pos=out.pos, outline=TRUE);

    RCircos.Mark.Zoom.Area(zoom.range, track.num=NULL, zoom.pos=zoom.pos, 
            fill.color="green", inside.pos=in.pos, outside.pos=out.pos);

    dev.off()
    message("Zoom in plot demo done!")




    #   End of RCircos.Zoom.Plot.Demo.R
    #   =============================================================