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#
# This demo draw chromosome ideogram with padding between
# chromosomes, highlights, chromosome names, and scatters.
#
# Usage:
#
# library(RCircos);
# demo("RCircos.Scatter.Plot.Demo");
# ______________________________________________________________________
# <RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO>
# Load RCircos library
# ________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
library(RCircos);
# Load human cytoband data and scatterplot data
# ________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
data(RCircos.Scatter.Data);
if(length(grep("chr", RCircos.Scatter.Data$chromosome)) == 0)
RCircos.Scatter.Data$chromosome <- paste0("chr",
RCircos.Scatter.Data$chromosome);
data(UCSC.HG19.Human.CytoBandIdeogram);
cyto.info <- UCSC.HG19.Human.CytoBandIdeogram;
# Setup RCircos core components:
# ________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
RCircos.Set.Core.Components(cyto.info, NULL, 10, 0);
# Open the graphic device (here a pdf file)
# ________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
pdf(file="RCircos.Scatter.Plot.Demo.pdf", height=8, width=8);
RCircos.Set.Plot.Area();
# Draw chromosome ideogram
# ________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
RCircos.Chromosome.Ideogram.Plot();
title("RCircos Scatter Plot Demo");
# Scatterplot
# _________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
scatter.data <- RCircos.Scatter.Data;
scatter.colors <- rep("cyan", nrow(scatter.data));
scatter.colors[which(scatter.data$seg.mean>=2)] <- "red";
scatter.colors[which(scatter.data$seg.mean<=-2)] <- "blue";
scatter.data["PlotColor"] <- scatter.colors;
data.col <- 5;
track.num <- 6;
RCircos.Scatter.Plot(scatter.data, data.col, track.num, "in", 1);
# Close the graphic device
# ___________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
dev.off();
message("RCircos Scatter Plot Demo Done!");
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