manhattan {RAINBOWR}

Draw manhattan plot

Description

Draw manhattan plot

Usage

manhattan(
  input,
  sig.level = 0.05,
  method.thres = "BH",
  y.max = NULL,
  cex = 1,
  cex.lab = 1,
  lwd.thres = 1,
  plot.col1 = c("dark blue", "cornflowerblue"),
  cex.axis.x = 1,
  cex.axis.y = 1,
  plot.type = "p",
  plot.pch = 16
)

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

Significance level for the threshold. The default is 0.05.

method.thres

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

y.max

The maximum value for the vertical axis of manhattan plot. If NULL, automatically determined.

cex

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

cex.lab

The font size of the labels.

lwd.thres

The line width for the threshold.

plot.col1

This argument determines the color of the manhattan plot. You should substitute this argument as color vector whose length is 2. plot.col1[1] for odd chromosomes and plot.col1[2] for even chromosomes.

cex.axis.x

The font size of the x axis.

cex.axis.y

The font size of the y axis.

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".

Value

Draw manhttan plot