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
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.
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...