How I Make QQ Plots Using ggplot

Introduction

Whenever I show my colleagues in the genetics group my results, the first things they say are “can you show me the Manhattan plots?” and “can you show me the QQ plots?”. I covered how to make Manhattan plots in ggplot before (click here) for a link. But now I want to go through how I make QQ plots. I’m aware that there’s a number of packages available that offer this funcionality, but I feel they’re for the most part a bit limiting compared to making the plot yourself using the {ggplot2} package. Another advantage I found of creating QQ plots myself, is that I got a better understanding of how GWAS summary statistics are projected on the QQ plot, and thus I got a better understanding of QQ plots. For this process, I’ll use the {tidyverse} package (which includes {ggplot2}) for all operations, the {ggtext} package for some fancy plot labels, and the {normentR} package to simulate some summary statistics and get some of my preferred color palettes. The code to calculate the confidence interval is based on code from Kamil Slowikowski (click here to go to the Gist).