I'm trying to create Q-Q plots with GWAS p-values using R but it hasn't really been working out. I need for them to be on a -log10 scale, and for them to have a confidence band/interval.
I tried out:
- qqman - works great and it's simple but it does not provide a confidence interval function>
- snpStats - has the confidence interval but the X and Y axis are chi-squared values. I'm not sure if there's a way to get -log10 P-values? The plots look great though.
qq.chisq(-2 * log(*P-values*), df = 2, pvals= TRUE, conc=c(0.05, 0.95))
- car - the plot looks a little....odd. Maybe I'm just using it wrong but I don't like the distribution of the dots. Why does the X-axis start at -4 instead of 0?
I'm hoping the colorful examples would help me get a detailed answer lol