plot_manhattan_gwas: Plot a Manhattan plot for GWAS results
In rmgpanw/ukbwranglrextra: Exploring UKB Data - Extra

plot_manhattan_gwas

R Documentation

Plot a Manhattan plot for GWAS results

Description

Plot a Manhattan plot for GWAS results

Usage

plot_manhattan_gwas(
  df,
  chr = "CHR",
  minuslog10_p = "P",
  text = "SNP",
  order_idx = "ORDER_IDX",
  geom_point_args = list(alpha = 1, size = 2),
  labs_args = list(x = "Chromosome", y = "-log10(p value)"),
  col_manual = c("blue4", "orange3")
)

Arguments

`df`	A data frame.
`chr`	Name of chromosome column. Should be type character or factor.
`minuslog10_p`	Name of -log10(p value) column. Should be on -log10 scale.
`text`	Name of column with text annotation.
`order_idx`	Name of column with order to arrange SNPs. Should be type integer.
`geom_point_args`	A named list of arguments to be passed to `ggplot2::geom_point()`.
`labs_args`	List of arguments to be passed to `ggplot2::labs()`.
`col_manual`	Character vector of colours