Nothing
# ______________________________________________________________________
# <RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO>
#
# This demo draw chromosome ideogram with padding between chromosomes,
# highlights, chromosome names, and histogram.
#
# Usage:
#
# library(RCircos);
# demo("RCircos.Polygon.Demo");
# ______________________________________________________________________
# <RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO>
# Load RCircos package and defined parameters
# ________________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
library(RCircos);
# Load human cytoband data and gene expression data
# ________________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
data(RCircos.Polygon.Data);
data(UCSC.HG19.Human.CytoBandIdeogram);
cyto.info <- UCSC.HG19.Human.CytoBandIdeogram;
# Setup RCircos core components:
# _________________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
RCircos.Set.Core.Components(cyto.info, NULL, 10, 10);
# Open the graphic device (here a pdf file)
# _________________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
pdf(file="RCircos.Polygon.Demo.pdf", height=8, width=8);
RCircos.Set.Plot.Area();
# Draw chromosome ideogram
# _________________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
message("Draw chromosome ideogram ...\n");
RCircos.Chromosome.Ideogram.Plot();
title("RCircos Polygon Plot Demo");
# Plot histogram Inside of chromosome ideogram
# _________________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
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
# _________________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
dev.off();
message("RCircos Polygon Plot Demo Done!");
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