01plot_COSMIC.R

rm(list=ls());

library(OmicCircos)
## data set names
COSMIC_PHENOTYPE_ID  <- c("COSO29914830", "COSO32054826", "COSO29914826")
PRIMARY_SITE <- c("lung", "prostate", "lung")
## colors
cols  <- rainbow(10, alpha=0.8) 

for (p.i in 1:length(COSMIC_PHENOTYPE_ID)){
  tid    <- COSMIC_PHENOTYPE_ID[p.i]
  tname  <- PRIMARY_SITE[p.i]
  ## read input data sets
  cnv.f  <- paste0("../data_sets/COSMIC_CNV/", tid, "_", tname, ".txt")
  gexp.f <- paste0("../data_sets/COSMIC_EXP/", tid, "_", tname, ".txt")
  fus.f  <- paste0("../data_sets/COSMIC_FUSION/", tid, "_", tname, ".txt")
  cnv    <- read.table(cnv.f, header=T)
  gexp   <- read.table(gexp.f, header=T)
  fus    <- read.table(fus.f, header=T)
  ## output file name
  pdff <- paste0("../out/OC_", tid, "_", tname, ".pdf")
  pdf(pdff, 8, 8);
  par(mar=c(2, 2, 2, 2));
  plot(c(1,800), c(1,800), type="n", axes=F, xlab="", ylab="", main="");
  ## plot chromosome
  circos(R=400, cir="hg19", W=4, type="chr", print.chr.lab=T, scale=T);
  ## plot heatmap
  circos(R=260, cir="hg19", W=140, mapping=gexp[,c(1:20)],  col.v=4,  type="heatmap2", 
         lwd=0.1);
  ## plot CNV
  circos(R=110, cir="hg19", W=160,  mapping=cnv, col.v=4, type="b2", 
         B=F, lwd=1, cutoff=2, col=cols[c(2,7)]);
  ## plot fussion
  circos(R=120, cir="hg19", mapping=fus, type="link", lwd=1, col=cols[1]);
  dev.off()
}