15 RCircos zoomed heatmap, histogram, and points 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.

#   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);

## 
## RCircos.Core.Components initialized.
## Type ?RCircos.Reset.Plot.Parameters to see how to modify the core components.

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");

## Tiles plot may use more than one track. Please select correct area for next track if necessary.

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);

message("Zoom in plot demo done!")

## Zoom in plot demo done!

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

2025-06-05