Question: How to create an anchor for OmicCircos
gravatar for Peter.Wood
5.4 years ago by
Peter.Wood0 wrote:

Could someone please explain how to create an anchor in the OmicCircos package from a data frame. My previous attempts have failed with the OmicCircos package uploading the hg18/hg19 genome rather than my gene set.


ADD COMMENTlink modified 5.2 years ago by yhu50 • written 5.4 years ago by Peter.Wood0
gravatar for yhu
5.2 years ago by
United States
yhu50 wrote:

You maybe wanted one gene on one segment. Please try the code as the following. 

The output file is at

NOTE: Please use the updated version


gene.n  <- 200;
chr     <- paste0("Gene", 1:gene.n);
val     <- rnorm(gene.n);
seg.dat <- data.frame(chr=chr, start=rep(1, gene.n), end=rep(1,gene.n)+1, name=chr, value=val);
seg.c   <- segAnglePo(seg.dat, seg=chr);

cols    <- rainbow(10, alpha=0.8);

pdf("BioC_support01.pdf", 8,8);
par(mar=c(2, 2, 2, 2))
plot(c(1,800), c(1,800), type="n", axes=FALSE, xlab="", ylab="");

circos(R=350, type="chr", cir=seg.c, print.chr.lab=TRUE, W=8)
circos(R=270, cir=seg.c, W=80, mapping=seg.dat, type="s", col.v=5, col=cols, B=T, cex=abs(seg.dat[,5])*1.5);
circos(R=190, cir=seg.c, W=80, mapping=seg.dat, type="b", col.v=5, col=cols, B=F, lwd=abs(seg.dat[,5])*1.5);
circos(R=110, cir=seg.c, W=80, mapping=seg.dat, type="b2", col.v=5, col=cols[c(1,7)], cutoff=0, B=T, lwd=2);;
ADD COMMENTlink modified 4.7 years ago by Sukhdeep Singh10k • written 5.2 years ago by yhu50

This was very helpful! Thank you. Very simple and elegant. I was able to customize my circos plot easily!

ADD REPLYlink written 4.0 years ago by tejaswi.iyyanki0

In this example, line tracks (e.g. if tracks using type "l", "lh", "ls", etc, are included) do not seem to function properly regardless of the lwd utilized.

ADD REPLYlink written 3.4 years ago by IV1.3k
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