manhattan: Draw manhattan plot

In RAINBOWR: Genome-Wide Association Study with SNP-Set Methods

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

RAINBOWR documentation built on Sept. 12, 2023, 9:08 a.m.