demo/OmicCircos4vignette4.R

In CBIIT-CGBB/OmicCircos2: High-quality circular visualization of omics data

rm(list=ls());
options(stringsAsFactors = FALSE);
library(OmicCircos2);

data(UCSC.hg18);
data("TCGA.PAM50_genefu_hg18");
data("TCGA.BC.fus");
data("TCGA.BC.cnv.2k.60");
data("TCGA.BC.gene.exp.2k.60");
data("TCGA.BC.sample60");
data("TCGA.BC_Her2_cnv_exp");

pvalue <- -1 * log10(TCGA.BC_Her2_cnv_exp[,5]);
pvalue <- cbind(TCGA.BC_Her2_cnv_exp[,c(1:3)], pvalue);

Her2.i <- which(TCGA.BC.sample60[,2] == "Her2");
Her2.n <- TCGA.BC.sample60[Her2.i,1];

Her2.j <- which(colnames(TCGA.BC.cnv.2k.60) %in% Her2.n);
cnv    <- TCGA.BC.cnv.2k.60[,c(1:3,Her2.j)]; 
cnv.m  <- cnv[,c(4:ncol(cnv))];
cnv.m[cnv.m >  2] <- 2;
cnv.m[cnv.m < -2] <- -2;
cnv <- cbind(cnv[,1:3], cnv.m);

Her2.j   <- which(colnames(TCGA.BC.gene.exp.2k.60) %in% Her2.n);
gene.exp <- TCGA.BC.gene.exp.2k.60[,c(1:3,Her2.j)]; 

TCGA.PAM50_genefu_hg18[,1] <- paste0("chr", TCGA.PAM50_genefu_hg18[,1]);
cnv[,1]      <- paste0("chr", cnv[,1]);
gene.exp[,1] <- paste0("chr", gene.exp[,1]);
pvalue[,1]   <- paste0("chr", pvalue[,1]);
TCGA.BC.fus[,1]   <- paste0("chr", TCGA.BC.fus[,1]);
TCGA.BC.fus[,4]   <- paste0("chr", TCGA.BC.fus[,4]);

colors <- rainbow(10, alpha=0.5);

pdffile  <- "OmicCircos4vignette4.pdf";
pdf(pdffile, 8, 8);
par(mar=c(2, 2, 2, 2));
plot(c(1,800), c(1,800), type="n", axes=FALSE, xlab="", ylab="", xpd=1);

#circos(R=385, cir=UCSC.hg18, mapping=UCSC.hg18.chr, type="chr.label.h", cex=1.3);
circos(R=350, cir=UCSC.hg18, mapping=UCSC.hg18.chr, type="chr.scale", lwd=0.001, cex=0.3);
circos(R=345, cir=UCSC.hg18, mapping=UCSC.hg18.chr, type="chr2", W=10)
circos(R=380, cir=UCSC.hg18, W=20, mapping=TCGA.PAM50_genefu_hg18, type="label", side="out", col="black", cex=0.6);
circos(R=250, cir=UCSC.hg18, W=50, mapping=cnv, col.v=4, type="ml3", B=FALSE, col=colors[7], cutoff=0, scale=TRUE, cex=0.4);
circos(R=200, cir=UCSC.hg18, W=50, mapping=gene.exp, col.v=4, type="ml3", B=TRUE, col=colors[3], cutoff=0, scale=TRUE, cex=0.4);
circos(R=140, cir=UCSC.hg18, W=50, mapping=pvalue, col.v=4, type="l", B=FALSE, col=colors[1], scale=TRUE, cex=0.4);
circos(R=132, cir=UCSC.hg18, W=50, mapping=TCGA.BC.fus, type="link", lwd=2);

plot(c(1,800), c(1,800), type="n", axes=FALSE, xlab="", ylab="");
#circos(R=385, cir=UCSC.hg18, mapping=UCSC.hg18.chr, type="chr.label.h", cex=1.3);
circos(R=350, cir=UCSC.hg18, mapping=UCSC.hg18.chr, type="chr.scale", lwd=0.001, cex=0.3);
circos(R=345, cir=UCSC.hg18, mapping=UCSC.hg18.chr, type="chr2", W=10)
circos(R=300, cir=UCSC.hg18, W=20, mapping=TCGA.PAM50_genefu_hg18, col.v=3, type="label", side="in", col="blue", cex=0.6);
circos(R=310, cir=UCSC.hg18, W=50, mapping=cnv, col.v=4, type="ml3", B=TRUE, col=colors[7], cutoff=0, scale=TRUE, cex=0.4);
circos(R=150, cir=UCSC.hg18, W=50, mapping=gene.exp, col.v=4, type="ml3", B=TRUE, col=colors[3], cutoff=0, scale=TRUE, cex=0.4);
circos(R=90,  cir=UCSC.hg18, W=50, mapping=pvalue, col.v=4, type="l", B=FALSE, col=colors[1], scale=TRUE, cex=0.4);
circos(R=82, cir=UCSC.hg18, W=50, mapping=TCGA.BC.fus, type="link", lwd=2);

dev.off();