gg.manhattan: Manhattan plot function for gwas (stolen from pcgoddard)

In thomasbattram/usefunc: Personal repository for useful functions

Manhattan plot function for gwas (stolen from pcgoddard)

Description

Generates a Manhattan plot using gwas data

Usage

gg.manhattan(
  df,
  hlight,
  col = "default",
  title = "Manhattan",
  SNP = "SNP",
  CHR = "CHR",
  BP = "BP",
  P = "P",
  sig = 5e-08,
  sugg = 1e-05,
  lab = FALSE,
  colour = TRUE,
  remove_chr_labs = NULL
)

Arguments

df	data.frame containing your results
hlight	a vector containing any SNPs that need highlighting
col	colours for the plot (default = RColorBrewer::brewer.pal(9, "Greys")[c(5,9)])
title	title of the plot
SNP	name of the column corresponding to SNPs
CHR	name of the column corresponding to chromosome number
BP	name of the column corresponding to base pair
P	name of the column corresponding to p value
sig	the "significance threshold"
sugg	the "suggestive significance threshold"
lab	whether or not to add labels to the sites on the plot
colour	coloured plot?
remove_chr_labs	chromosome labels to remove from the x-axis. default = NULL

Value

manhattan plot

thomasbattram/usefunc documentation built on April 24, 2023, 1:46 p.m.