The issue is fixed in the updated package.
rm(list=ls());
library(OmicCircos);
options(stringsAsFactors = FALSE);
set.seed(1234);
## get chromosome information
data("UCSC.hg19.chr", package="OmicCircos");
ref <- UCSC.hg19.chr;
ref[,1] <- gsub("chr", "", ref[,1]);
## initial values
cols <- rainbow(10, alpha=0.8);
lab.n <- 50;
cnv.n <- 200;
arc.n <- 30;
fus.n <- 10;
## make arc data
arc.d <- c();
for (i in 1:arc.n){
chr <- sample(1:19, 1);
chr.i <- which(ref[,1]==chr);
chr.arc <- ref[chr.i,];
arc.i <- sample(1:nrow(chr.arc), 2);
if (arc.i[1] > arc.i[2]){
arc.i <- arc.i[c(2,1)];
}
arc.d <- rbind(arc.d, c(chr.arc[arc.i[1],c(1,2)], chr.arc[arc.i[2],c(2,4)]));
}
colnames(arc.d) <- c("chr", "start", "end", "value");
## make fusion for link.pg
fus.d <- c();
for (i in 1:fus.n){
fus.i <- sample(1:nrow(arc.d), 2);
fus.d <- rbind(fus.d, c(arc.d[fus.i[1],c(1:3)], arc.d[fus.i[2],c(1:3)]));
}
colnames(fus.d) <- c("chr1", "po1.1", "p1.2", "chr2", "po2.1", "po2.2");
cnv.i <- sample(1:nrow(ref), cnv.n);
vale <- rnorm(cnv.n);
cnv.d <- data.frame(ref[cnv.i,c(1,2)], value=vale);
pdffile <- "2015_02_24.pdf";
pdf(pdffile, 8, 8);
par(mar=c(2, 2, 2, 2));
plot(c(1,800), c(1,800), type="n", axes=F, xlab="", ylab="");
circos(R=400, type="chr", cir="hg19", print.chr.lab=T, W=4, scale=T);
circos(R=340, cir="hg19", W=60, mapping=cnv.d, type="b3", B=T, col=cols[7]);
circos(R=340, cir="hg19", W=60, mapping=cnv.d, type="s2", B=F, col=cols[1], cex=0.5);
circos(R=280, cir="hg19", W=60, mapping=arc.d, type="arc2", B=F, col=cols, lwd=10, cutoff=0);
circos(R=220, cir="hg19", W=60, mapping=cnv.d, col.v=3, type="b2", B=T, cutoff=-0.2, col=cols[c(7,9)], lwd=2);
circos(R=160, cir="hg19", W=60, mapping=arc.d, col.v=4, type="arc", B=F, col=cols[c(1,7)], lwd=4, scale=T);
##
col2 <- rainbow(10, alpha=0.5);
circos(R=150, cir="hg19", W=10, mapping=fus.d, type="link.pg", lwd=2, col=col2[c(1,7,9)]);
dev.off();
In your code above
circos(R=150, cir="hg19", W=10, mapping=fus.d, type="link.pg", lwd=2, col=col2[c(1,7,9)]);
If type is changed to "link", then the link lines are all colored the same color (aqua). Setting the col parameter doesn't do anything.
Thanks!