How to adjust the position of chromosome or gene labels in OmicCircos

Question

[camgrisdale]

Does anyone know if it's possible to change the position of labels (ie. type="label") in the R package OmicCircos? For some reason the labels are all being pushed to the bottom of the circle with lines (that connect them to their genomic position) running through the circle from the other side where those labels should be. I can run example data and labels map right next to their genomic position, but with my custom gene position (see below) things start to go awry.

Thanks for any help.

Here is an example workflow:

library(OmicCircos)
egfrregion<-data.frame(chrom="chr7",chromStart=c(55085793),chromEnd=c(55280322),name="EGFR",gieStain="na") #EGFR gene region
seg.d<-egfrregion
seg.name<-"chr7"
db7<-segAnglePo(seg.dat=seg.d, seg=seg.name)
egfr.pos<-data.frame(chr=c(rep("chr7",3)),po=c(55085793,55086793,55087059),NAME=c("5UTR","exon1","intron1")) #first few exon/intron positions, should be located just after 12 o'clock position on circle
par(mar=c(2, 2, 2, 2))
plot(c(1,800), c(1,800), type="n", axes=FALSE, xlab="", ylab="");
circos(R=330, cir=db7, type="chr", W=40, scale=TRUE, print.chr.lab=FALSE) #chromosome 7 region
circos(R=340, cir=db7,type="label",W=20,mapping=egfr.pos,cex=0.7,side="out") #gene position annotation

[amyruthvandiver]

Did you ever come up with a solution for this? I am having the same issue when I try to plot a single chromosome.

Answer 1

[theobroma22]

Did you try adjusting the positions? Did you try setting scale=FALSE in the 330 radius?

[camgrisdale]

I just tried setting scale=FALSE and there was no change.

Any other idea how to adjust positions?

Answer 2

[linouhao]

let us send mails for the authors, I do not think the doc of omicscircos is nice.