demo/OmicCircos4vignette8.R

In OmicCircos: High-quality circular visualization of omics data

rm(list=ls());

library(OmicCircos);
options(stringsAsFactors = FALSE);

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

## gene expression data for PCA
exp.m <- TCGA.BC.gene.exp.2k.60[,c(4:ncol(TCGA.BC.gene.exp.2k.60))];

cnv   <- TCGA.BC.cnv.2k.60;

## PCA
type.n  <- unique(TCGA.BC.sample60[,2]);
colors  <- rainbow(length(type.n), alpha=0.5);

pca.col <- rep(NA, nrow(TCGA.BC.sample60));
for (i in 1:length(type.n)){
  n   <- type.n[i];
  n.i <- which(TCGA.BC.sample60[,2] == n);
  n.n <- TCGA.BC.sample60[n.i,1];
  g.i <- which(colnames(exp.m) %in% n.n);
  pca.col[g.i] <- colors[i];
}

exp.m   <- na.omit(exp.m);
pca.out <- prcomp(t(exp.m), scale = TRUE);

## subtype cnv
cnv.i <- c();
for (i in 1:length(type.n)){
  n     <- type.n[i];
  n.i   <- which(TCGA.BC.sample60[,2] == n);
  n.n   <- TCGA.BC.sample60[n.i,1];
  cnv.i <- which(colnames(cnv) %in% n.n);
}

## main
pdf("OmicCircos4vignette8.pdf", 8,8);
par(mar=c(5, 5, 5, 5));

plot(c(1,800), c(1,800), type="n", axes=FALSE, xlab="", ylab="", main="");

legend(680,800, c("Basal","Her2","LumA","LumB"), pch=19, col=colors[c(2,4,1,3)], cex=0.5, 
     title ="Gene Expression (PCA)", box.col="white");

legend(5,800, c("1 Basal", "2 Her2", "3 LumA", "4 LumB", "(center)"), cex=0.5, 
     title ="CNV (OmicCircos)", box.col="white");

circos(xc=400, yc=400, R=390, cir="hg18", W=4,  type="chr", print.chr.lab=TRUE, scale=TRUE);
R.v <- 330;
for (i in 1:length(type.n)){
  n     <- type.n[i];
  n.i   <- which(TCGA.BC.sample60[,2] == n);
  n.n   <- TCGA.BC.sample60[n.i,1];
  cnv.i <- which(colnames(cnv) %in% n.n);
  cnv.v <- cnv[,cnv.i];
  cnv.v[cnv.v > 2]  <- 2;
  cnv.v[cnv.v < -2] <- -2;
  cnv.m <- cbind(cnv[,c(1:3)], cnv.v);
  if (i%%2==1){
    circos(xc=400, yc=400, R=R.v, cir="hg18", W=60, mapping=cnv.m, col.v=4,  
           type="ml3", B=TRUE, lwd=1, cutoff=0, scale=TRUE);
  } else {
    circos(xc=400, yc=400, R=R.v, cir="hg18", W=60, mapping=cnv.m, col.v=4,  
           type="ml3", B=FALSE, lwd=1, cutoff=0, scale=TRUE);
  }
  R.v <- R.v - 60;
}

points(pca.out$x[,1]*6+410, pca.out$x[,2]*6+400, pch=19, col=pca.col, cex=2);

dev.off() 

## detach(package:OmicCircos, unload=TRUE)