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

Value

A data frame