11 RCircos scatter plot with CNV data

Authors: Hongen Zhang  Reviser: Tianze Cao

2025-06-05

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

#   Load RCircos library

library(RCircos);

#   Load human cytoband data and scatterplot data

data(RCircos.Scatter.Data);
    if(length(grep("chr", RCircos.Scatter.Data$chromosome)) == 0)
        RCircos.Scatter.Data$chromosome <- paste0("chr", 
    RCircos.Scatter.Data$chromosome);

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


#   Setup RCircos core components:

RCircos.Set.Core.Components(cyto.info, NULL, 1, 0);

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

RCircos.Set.Plot.Area();

#   Draw chromosome ideogram

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

#   Scatterplot 

scatter.data <- RCircos.Scatter.Data;
scatter.colors <- rep("cyan", nrow(scatter.data));
scatter.colors[which(scatter.data$seg.mean>=1)] <- "green";
scatter.colors[which(scatter.data$seg.mean<=1)] <- "blue";
scatter.data["PlotColor"] <- scatter.colors;

RCircos.Scatter.Plot(scatter.data, data.col = 5, track.num = 1, "in");