manhattan: Mannhattan Plot

In isglobal-brge/dsOmicsClient: DataSHIELD client site Omics association functions.

Mannhattan Plot

Description

Performs Mannhattan plot for GWAS, DGE or EWAS analysis

Usage

manhattan(
  x,
  featureCol = 1,
  chrCol = 2,
  posCol = 3,
  pvalCol = 4,
  sig = 5e-08,
  sugg = 1e-06,
  threshold = NA,
  hlight = NA,
  col = c("#E2709A", "#CB4577", "#BD215B", "#970F42", "#75002B"),
  ylims = c(1.5, 9),
  title = "Manhattan plot",
  ...
)

Arguments

x	an object of class dsGWAS
featureCol	column having feature name (e.g. SNP, CpG, gene, ..)
chrCol	column having chromosome name
sig	genome-wide significant level. Default 5x10-8
sugg	suggestive significant level. Default 1x10-6
threshold	numeric value or NA for no label; label snps with pvalue < threshold. Default is NA
hlight	list of features names to highlight. For no SNP higlighting, use NA (default)
col	vector listing color/colors desired for manhattan plot. Default c("#E2709A", "#CB4577", "#BD215B", "#970F42", "#75002B")
ylims	y limits to be visualized in -log10 scale. Default is c(1.5,9)
title	plot title, with quotations (e.g. "My Manhattan Plot")
...	additional ggplot arguments (ylim, cex, etc. can be altered within the plot section of the function)
positionCol	column having basepair position

Value

a ggplot object having the Manhattan plot

Author(s)

modified from here: https://github.com/pcgoddard/Burchardlab_Tutorials/wiki/GGplot2-Manhattan-Plot-Function

isglobal-brge/dsOmicsClient documentation built on March 20, 2023, 3:52 p.m.