manhattan: Creating a manhattan plot

Description

This function was designed to create a manhattan plot using a data frame with columns "Chrom" (Chromosome), "Position" and "p.val" (significance for the test).

Usage

manhattan(map, col=NULL, fdr.level=0.05, show.fdr=TRUE, PVCN=NULL, ylim=NULL, ...)

Value

If all parameters are correctly indicated the program will return:

$plot.data: a manhattan plot

Arguments

map: the data frame with 3 columns with names; "Chrom" (Chromosome), "Position" and "p.val" (significance for the test).
col: colors prefered by the user to be used in the manhattan plot. The default is NULL which will use the red-blue palette.
fdr.level: false discovery rate to be drawn in the plot.
show.fdr: a TRUE/FALSE value indicating if the FDR value should be shown in the manhattan plot or not. By default is TRUE meaning that will be displayed.
PVCN: In case the user wants to provide the name of the column that should be treated as the "p.val" column expected by the program in the 'map' argument.
ylim: the y axis limits for the manhattan plot if the user wants to customize it. By default the plot will reflect the minimum and maximum values found.
...: additional arguments to be passed to the plot function such as pch, cex, etc.

Author

Giovanny Covarrubias-Pazaran

References

Covarrubias-Pazaran G (2016) Genome assisted prediction of quantitative traits using the R package sommer. PLoS ONE 11(6): doi:10.1371/journal.pone.0156744

Examples

Run this code

#random population of 200 lines with 1000 markers
M <- matrix(rep(0,200*1000),1000,200)
for (i in 1:200) {
  M[,i] <- ifelse(runif(1000)<0.5,-1,1)
}
colnames(M) <- 1:200
set.seed(1234)
pp <- abs(rnorm(500,0,3));pp[23:34] <- abs(rnorm(12,0,20))
geno <- data.frame(Locus=paste("m",1:500, sep="."),Chrom=sort(rep(c(1:5),100)),
                   Position=rep(seq(1,100,1),5),
                   p.val=pp, check.names=FALSE)
geno$Locus <- as.character(geno$Locus)
## look at the data, 5LGs, 100 markers in each
## -log(p.val) value for simulated trait
head(geno)
tail(geno)
manhattan(geno)

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