multitrack slow

[rb643]

Following the example on the website I'm trying to generate a multitrack manhattan plot of 3 traits this is however taking well over 2 hours and seems to simply be stuck.. The stacked circular plot only takes a minute or two so I am wondering whether I am missing something or if there is a bug in the code. This is was I used:

A dataframe with columns: SNP, chr, pos and 3 traits T1, T2 and T3 with that hold p-values for around 10m SNP's

SNPs <- list( data$SNP[data$T1<1e-8], data$SNP[data$T2<1e-8], data$SNP[data$T3<1e-8] ) CMplot(data, plot.type="m",multracks=TRUE,threshold=c(1e-8,1e-6),threshold.lty=c(1,2), threshold.lwd=c(1,1), threshold.col=c("black","grey"), amplify=TRUE,bin.size=1e6, chr.den.col=c("darkgreen", "yellow", "red"), signal.col=c("red","green","blue"), signal.cex=1, file="jpg",memo="",dpi=300,file.output=TRUE,verbose=TRUE, highlight=SNPs, highlight.text=SNPs, highlight.text.cex=1.4)

It print to the command window that its plotting T1 and generates an empty jpeg, but then it just seems to stall...

[YinLiLin]

Thanks for using CMplot. This problem may happen if there are massive highlighted SNPs, which would result in much more time cost to assign all highlighted SNPs in a limited region without overlap.