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#
# This demo draw ribbon links between chromosomes
#
# Usage:
#
# library(RCircos);
# demo("RCircos.Tile.Plot.Demo");
#
# ______________________________________________________________________
# <RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO>
# Load RCircos library
# _________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
library(RCircos);
# Load human cytoband data and link data
# _________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
data(RCircos.Ribbon.Data);
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.Ribbon.Plot.Demo.pdf", height=8, width=8);
RCircos.Set.Plot.Area();
# Draw chromosome ideogram
# ________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
RCircos.Chromosome.Ideogram.Plot();
title("RCircos Ribbon Plot Demo");
# Link lines. Link data has only paired chromosome
# locations in each row and link lines are always
# drawn inside of chromosome ideogram.
# __________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
ribbon.data <- RCircos.Ribbon.Data;
ribbon.data["PlotColor"] <- c("red", "blue", "green", "cyan");
track.num <- 11;
RCircos.Ribbon.Plot(ribbon.data, track.num, FALSE);
# Close the graphic device and clear memory
# _________________________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
dev.off();
message("RCircos Ribbon Plot Demo Done!");
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