ggGWAS

An R-Package (work-in-progress) that contains ggplot2-extensions of data visualisations used with GWAS data.

Mainly, these are Q-Q plot and Manhattan plot that both use P-values from GWASs as input.

An inspiration for ggGWAS has been the R-package qqman, except that ggGWAS aims to have the look and functionality of ggplot2.

Installation

You can install the development version from GitHub with:

# install.packages("remotes")
remotes::install_github("sinarueeger/ggGWAS")

Install including vignettes:

remotes::install_github("sinarueeger/ggGWAS", 
build = TRUE, 
build_opts = c("--no-resave-data", "--no-manual"))

vignette("gggwas-reasoning")
vignette("gggwas-internals")

Install the dev branch:

remotes::install_github("sinarueeger/ggGWAS", ref = "dev")

Basic usage

library(ggGWAS)
library(ggplot2)
#> Warning: package 'ggplot2' was built under R version 3.5.2

theme_set(theme_bw())
## Generate some random data
n <- 1000
n_chr <- 4

df <-
  data.frame(
    POS = rep(1:(n/n_chr), n_chr),
    CHR = rep(1:n_chr, rep(n/n_chr, n_chr)),
    SNP = paste0("rs", 1:n),
    P = runif(n),
    GWAS = sample(c("a", "b"), n, replace = TRUE)
  )

Q-Q plot

Lightweight Q-Q plot (with hex tiles)

library(ggGWAS)
ggplot(data = df) + 
  stat_gwas_qq_hex(aes(y = P)) + 
  geom_abline(intercept = 0, slope = 1, linetype = 3)

?stat_gwas_qq_hex ## for more examples

Conventional Q-Q plot

ggplot(data = df) +
  stat_gwas_qq(aes(y = P)) + 
  geom_abline(intercept = 0, slope = 1, linetype = 3)

?stat_gwas_qq ## for more examples

Manhattan plot

Currently working on stat_gwas_manhattan() that should at one point look like this:

ggplot(data = df) + stat_gwas_manhattan(aes(pos = POS, y = -log10(P), chr = CHR))

Till then, use the ggman::ggmanhattan function from the ggman package:

library(dplyr)
library(ggman)
ggman::ggmanhattan(data = df, SNP = "SNP", chr = "CHR", bp = "POS", P = "P", sparsify = FALSE, theme_base = theme_bw(), build = 'hg18', highlight = df %>% slice(which.min(P)) %>% pull(SNP)) +
  labs(title = "MHTPLOT" )

##Contributing lease note that the ‘ggGWAS’ project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.