Highlight one SNP but located in the wrong Chromosome

[anglixue]

Dear LiLin,

I am plotting a circular plot and tried to hight one SNP (rs9906048), which is in CHR 17. However, the figure shows a different location (CHR 19) in the inner layer.

I also tried other SNPs (e.g. rs61805542 in CHR 1) and it seems it only appears certain SNPs.

Have you encountered this issue before?

---

Highlighting rs9906048 in CHR17:

Highlighting rs61805542 in CHR1:

Cheers, Angli

[YinLiLin]

Dear Angli,

Long time no see :smiley:. I haven't encountered this problem, thanks for pointing it out. From my first intuition, there may exist two SNPs located at CHR17 and CHR19 sharing the same name, did you check it? If it's not in this case, maybe there is an unknown potential bug in the script of CMplot, would you mind sending your data to me? i am pleasure to figure it out.

Best, Lilin

[anglixue]

Hi Lilin,

I also thought of that but double-checked if any duplicated SNP names.

I have sent you the data and below is the script I used

SNPs="rs9906048"
CMplot(data,type="p",plot.type="c",chr.labels=paste("Chr",c(1:22),sep=""),r=0.4,cir.legend=TRUE,ylim=c(0,20),
       outward=FALSE,cir.legend.col="black",cir.chr.h=1.3,chr.den.col="black",file="jpg",
       memo="",dpi=300,file.output=TRUE,verbose=TRUE,width=10,height=10,
       highlight=SNPs, highlight.text=SNPs, highlight.text.cex=2)

Thanks for your help！

Cheers, Angli