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YinLiLin / CMplot

📊 Circular and Rectangular Manhattan Plot
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Highlight one SNP but located in the wrong Chromosome #53

Open anglixue opened 2 years ago

anglixue commented 2 years ago

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: Circular-Manhattan trait1 trait2

Highlighting rs61805542 in CHR1:

Circular-Manhattan trait1 trait2

Cheers, Angli

YinLiLin commented 2 years ago

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 commented 2 years ago

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