Mannhattan Plot

Performs Mannhattan plot for GWAS, DGE or EWAS analysis

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

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