demo/OmicCircos4vignette3.R

In OmicCircos: High-quality circular visualization of omics data

rm(list=ls());

library(OmicCircos);
options(stringsAsFactors = FALSE);
set.seed(1234);

## initial values for simulation data 
seg.num     <- 10;
ind.num     <- 20;
seg.po      <- c(20:50);
link.num    <- 10;
link.pg.num <- 4;
## output simulation data
sim.out <- sim.circos(seg=seg.num, po=seg.po, ind=ind.num, link=link.num, 
  link.pg=link.pg.num);

seg.f     <- sim.out$seg.frame;
seg.v     <- sim.out$seg.mapping;
link.v    <- sim.out$seg.link
link.pg.v <- sim.out$seg.link.pg
seg.num   <- length(unique(seg.f[,1]));

## select segments
seg.name <- paste("chr", 1:seg.num, sep="");
db       <- segAnglePo(seg.f, seg=seg.name);

colors   <- rainbow(seg.num, alpha=0.5);
pdffile  <- "OmicCircos4vignette3.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="", main="");

circos(R=400, type="chr", cir=db, col=colors, print.chr.lab=TRUE, W=4, scale=TRUE);
circos(R=360, cir=db, W=40, mapping=seg.v, col.v=8, type="quant90", B=FALSE, col=colors, lwd=2, scale=TRUE);
circos(R=320, cir=db, W=40, mapping=seg.v, col.v=3, type="sv", B=TRUE, col=colors[7],  scale=TRUE);
circos(R=280, cir=db, W=40, mapping=seg.v, col.v=3, type="ss", B=FALSE, col=colors[3],  scale=TRUE);
circos(R=240, cir=db, W=40, mapping=seg.v, col.v=8, type="heatmap", lwd=3);
circos(R=200, cir=db, W=40, mapping=seg.v, col.v=3, type="s.sd", B=FALSE, col=colors[4]);
circos(R=160, cir=db, W=40, mapping=seg.v, col.v=3, type="ci95", B=TRUE, col=colors[4], lwd=2);
circos(R=150, cir=db, W=40, mapping=link.v, type="link", lwd=2, col=colors[c(1,7)]);
circos(R=150, cir=db, W=40, mapping=link.pg.v, type="link.pg", lwd=2, col=sample(colors,link.pg.num));

the.col1=rainbow(10, alpha=0.5)[3];
highlight <- c(160, 410, 6, 2, 6, 10, the.col1, the.col1);
circos(R=110, cir=db, W=40, mapping=highlight, type="hl", lwd=1);

the.col1=rainbow(10, alpha=0.1)[3];
the.col2=rainbow(10, alpha=0.5)[1];
highlight <- c(160, 410, 3, 12, 3, 20, the.col1, the.col2);
circos(R=110, cir=db, W=40, mapping=highlight, type="hl", lwd=2);

dev.off()

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