How to create an anchor for OmicCircos

Question

[Peter.Wood]

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.

Thanks.

Answer 1

[yhu]

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

The output file is at https://www.dropbox.com/s/pvudjol3s0wkde1/BioC_support01.pdf?dl=0

NOTE: Please use the updated version http://master.bioconductor.org/packages/3.1/bioc/html/OmicCircos.html

rm(list=ls());
library(OmicCircos);

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);

dev.off();

[tejaswi.iyyanki]

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

[IV]

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.