Question: How to adjust the position of chromosome or gene labels in OmicCircos
0
gravatar for camgrisdale
22 months ago by
camgrisdale0 wrote:

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
omiccircos circos R • 1.1k views
ADD COMMENTlink modified 14 months ago by linouhao0 • written 22 months ago by camgrisdale0
0
gravatar for theobroma22
21 months ago by
theobroma221.1k
theobroma221.1k wrote:

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

ADD COMMENTlink written 21 months ago by theobroma221.1k

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

Any other idea how to adjust positions?

ADD REPLYlink written 21 months ago by camgrisdale0
0
gravatar for linouhao
14 months ago by
linouhao0
linouhao0 wrote:

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

ADD COMMENTlink written 14 months ago by linouhao0
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