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# RCircos area plot demo
#
# This demo draw chromosome ideogram with ticks, and use histogram
# data to make histogram plot and area plots ("mountain", "curtain",
# and "band").
# ______________________________________________________________________
# <RCircos Demo><RCircos Demo><RCircos Demo><RCircos Demo><RCircos Demo>
# Load RCircos package
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library(RCircos);
# Load chromosome ideogram data and histogram plot data then
# set up RCircos core components
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data("UCSC.HG19.Human.CytoBandIdeogram");
data("RCircos.Histogram.Data");
RCircos.Set.Core.Components(UCSC.HG19.Human.CytoBandIdeogram,
chr.exclude=NULL, tracks.inside=10, tracks.outside=5);
# Open graphic device (here a pdf file)
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pdf("RCircos.Area.Plot.Demo.pdf", height=8, width=8);
RCircos.Set.Plot.Area();
# plot chromosome ideogram and histogram
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RCircos.Chromosome.Ideogram.Plot(20)
RCircos.Histogram.Plot(RCircos.Histogram.Data, data.col=4,
inside.pos=1.59, outside.pos=1.89);
# Area plot (mountain, curtain, and band)
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area.data <- RCircos.Histogram.Data;
adj.value <- runif(nrow(area.data), 0, 0.4)
area.data["DataT"] <- 0.5 + adj.value
area.data["DataB"] <- 0.5 - adj.value
RCircos.Area.Plot(area.data, data.col=4, plot.type="mountain",
inside.pos=1.2, outside.pos=1.5, is.sorted=FALSE);
RCircos.Area.Plot(area.data, data.col=4, plot.type="curtain",
inside.pos=0.9, outside.pos=1.1, is.sorted=FALSE);
RCircos.Area.Plot(area.data, data.col=c(5,6), plot.type="band",
inside.pos=0.4, outside.pos=0.7, is.sorted=FALSE);
title("RCircos Area Plot Demo");
# Close the graphic device
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dev.off();
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