# ________________________________________________________________________________________
# <><RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO><>
#
#	This demo draw chromosome ideogram with padding area between chromosomes, 
#	highlights, and chromosome names, label gene names in the second data track
#	and put connectors between chromosome ideogram and gene names.
#
#	Usage:
#
#	library(RCircos);
#	demo("RCircos.Gene.Connector.Demo");
#
# ________________________________________________________________________________________
# <><RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO><RCircos DEMO><>




	#	Load RCircos package and defined parameters
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	library(RCircos);


	#	Load gene label data and human cytoband data 
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	data(RCircos.Gene.Label.Data);
	data(UCSC.HG19.Human.CytoBandIdeogram);
	cyto.info <- UCSC.HG19.Human.CytoBandIdeogram;


	#	Setup RCircos core components:
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	RCircos.Set.Core.Components(cyto.info, NULL, 5, 0);


	#	Ready to make Circos plot image. Open the graphic device (pdf file)	
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	out.file <- "RCircos.Gene.Connector.Demo.pdf";
	pdf(file=out.file, height=8, width=8);

	RCircos.Set.Plot.Area();
	title("RCircos Gene and Connector Plot Demo");


	#	Draw chromosome ideogram
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	cat("Draw chromosome ideogram ...\n");
	RCircos.Chromosome.Ideogram.Plot();


	#	Connectors in first track and gene names in the second track. 
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	cat("Add Gene and connector tracks ...\n");
	data(RCircos.Gene.Label.Data);

	direction <- "in";
	track.num <- 1;
	RCircos.Gene.Connector.Plot(RCircos.Gene.Label.Data, 
			track.num, direction);

	gene.data <- RCircos.Gene.Label.Data;
	gene.colors <- rep("black", nrow(gene.data))
	gene.colors[which(gene.data$Gene=="TP53")] <- "red";
	gene.colors[which(gene.data$Gene=="BRCA2")] <- "red";
	gene.colors[which(gene.data$Gene=="RB1")] <- "red";
	gene.colors[which(gene.data$Gene=="JAK1")] <- "blue";
	gene.colors[which(gene.data$Gene=="JAK2")] <- "blue";

	gene.data["PlotColor"] <- gene.colors;

	name.col <- 4;
	track.num <- 2;
	RCircos.Gene.Name.Plot(gene.data, name.col, track.num, direction);


	#	Close the graphic device and clear memory
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	dev.off();
	cat("R Circos Demo Done ...\n\n");
	rm(list=ls(all=T));