9 RCircos polygon plot

This demo draw chromosome ideogram with padding between chromosomes, highlights, chromosome names, and histogram.

#  Load RCircos package and defined parameters

library(RCircos);

#  Load human cytoband data and gene expression data

data(RCircos.Polygon.Data);
data(UCSC.HG19.Human.CytoBandIdeogram);
cyto.info <- UCSC.HG19.Human.CytoBandIdeogram;

#  Setup RCircos core components:

RCircos.Set.Core.Components(cyto.info, NULL, 10, 10);

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

RCircos.Set.Plot.Area();


#  Draw chromosome ideogram

message("Draw chromosome ideogram ...\n");

## Draw chromosome ideogram ...

RCircos.Chromosome.Ideogram.Plot();
title("RCircos Polygon Plot Demo");


#  Plot histogram Inside of chromosome ideogram

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

message("RCircos Polygon Plot Demo Done!");

## RCircos Polygon Plot Demo Done!

2025-06-05