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#
# This demo draw chromosome ideogram with padding between
# chromosomes, highlights, chromosome names, and tile plot.
#
# Usage:
#
# library(RCircos);
# demo("RCircos.Tile.Plot.Demo");
# ______________________________________________________________________
# <RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO>
# Load RCircos library
# _________________________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
library(RCircos);
# Load human cytoband data and gene expression data
# _________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
data(RCircos.Tile.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.Tile.Plot.Demo.pdf", height=8, width=8);
RCircos.Set.Plot.Area();
# Draw chromosome ideogram
# _________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
RCircos.Chromosome.Ideogram.Plot();
title("RCircos Tile Plot Demo");
# Tile plot. Note: tile plot data have chromosome
# locations only and each data file is for one track
# ________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
tile.data <- RCircos.Tile.Data;
tile.colors <- rainbow(nrow(tile.data));
tile.data["PlotColor"] <- tile.colors;
track.num <- 9;
RCircos.Tile.Plot(tile.data, track.num, "in");
# Close the graphic device and clear memory
# ________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
dev.off();
message("RCircos Tile Plot Demo Done!");
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