manhattan2 {RAINBOWR}

Draw manhattan plot (another method)

Description

Draw manhattan plot (another method)

Usage

manhattan2(
  input,
  sig.level = 0.05,
  method.thres = "BH",
  cex = 1,
  plot.col2 = 1,
  plot.type = "p",
  plot.pch = 16,
  cum.pos = NULL,
  lwd.thres = 1,
  cex.lab = 1,
  cex.axis = 1
)

Arguments

input

Data frame of GWAS results where the first column is the marker names, the second and third column is the chromosome amd map position, and the forth column is -log10(p) for each marker.

sig.level

Siginifincance level for the threshold. The default is 0.05.

method.thres

Method for detemining threshold of significance. "BH" and "Bonferroni are offered.

cex

A numerical value giving the amount by which plotting text and symbols should be magnified relative to the default.

plot.col2

Color of the manhattan plot. color changes with chromosome and it starts from plot.col2 + 1 (so plot.col2 = 1 means color starts from red.)

plot.type

This argument determines the type of the manhattan plot. See the help page of "plot".

plot.pch

This argument determines the shape of the dot of the manhattan plot. See the help page of "plot".

cum.pos

Cumulative position (over chromosomes) of each marker

lwd.thres

The line width for the threshold.

cex.lab

The font size of the labels.

cex.axis

The font size of the axes.

Value

Draw manhttan plot