manhattan: 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
)

Value

Draw manhttan plot

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".