Hello,

I am a new user to the OmicCircos package and the R code. For a little while I have been trying to create a circos plot to show the expression of a gene set. However, after constructing data frames with gene names and segment sizes, the segAnglePo and sim.circos functions consistently revert to the hg19/hg18 genome to form the anchor of the figure. If someone please explain how to construct an anchor for the circos plot using a set of genes rather than the entire human genome it would be much appreciated.

Kind regards,

Peter.

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();

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