synbreed (version 0.12-9)

manhattanPlot: Manhattan plot for SNP effects

Description

Plot of SNP effects along the chromosome, e.g. for the visualization of marker effects generated by function gpMod.

Usage

manhattanPlot(b, gpData = NULL, colored = FALSE, add = FALSE,
              pch = 19, ylab = NULL, colP = NULL, ...)

Arguments

b

object of class gpMod with marker effects or numeric vector of marker effects to plot

gpData

object of class gpData with map position

colored

logical. Color the chromosomes?. The default is FALSE with chromosomes distinguished by grey tones.

add

If TRUE, the plot is added to an existing plot. The default is FALSE.

pch

a vector of plotting characters or symbols: see points. The default is an open circle.

ylab

a title for the y axis: see title.

colP

color for the different chromosomes and points.

…

further arguments for function plot

Examples

# NOT RUN {
library(synbreedData)
data(mice)
# plot only random noise
b <- rexp(ncol(mice$geno),3)
manhattanPlot(b,mice)
# }