grey highlight lines absent in the first two chromosomes

[mydongan]

Hi, thank you very much for developing CMplot, which we find extremely useful for multi-trait GWAS visualization.

I am using plot.type = "m" (multi-track Manhattan plot) with highlight.type = "l" to highlight SNPs that are significant in multiple traits. However, I consistently observe that no grey highlight lines are drawn on the first one or two chromosomes, even though those chromosomes do contain SNPs that are significant in multiple traits.

My understanding is that, in multi-track plots, grey highlight lines are drawn for SNPs included in the highlight vector, indicating shared SNP positions across traits. Please let me know if this interpretation is correct.

If so, could you clarify:

What exactly do the grey highlight lines represent in CMplot?

Under what conditions are they drawn?

Why might highlight lines be missing specifically on the first chromosomes when plotting all chromosomes together, but appear normally when chromosomes are plotted individually or subsets are used?

Thank you very much for your help.

`
SNPs <- data[
data$trait1 <=thresholds |
data$trait2 <=thresholds |
data$trait3 <=thresholds |
data$trait4<=thresholds |
data$trait5<=thresholds |
data$trait6<=thresholds |
data$trait7<=thresholds |
data$trait8<=thresholds , 1]

CMplot(data,type="p",plot.type="m",LOG10=TRUE,highlight=SNPs,highlight.type="l",
threshold=thresholds,threshold.col="black",threshold.lty=1,col=c("#0068B7","#90C31F"),
signal.cex=1.2, signal.col="red", highlight.col="grey",highlight.cex=0.7,
file="jpg",dpi=400,file.output=TRUE,verbose=TRUE,multracks=TRUE)
`