chromosome.plot: Manhattan plot

In CGEN: An R package for analysis of case-control studies in genetic epidemiology

Description

Creates a Manhattan plot

Usage

 Manhattan.plot(infile, plot.vars, locusMap.list, op=NULL)

Arguments

infile	Output file from GxE.scan. No default.
plot.vars	Character vector of the variables in infile to plot. These variables should p-values. No default.
locusMap.list	See locusMap.list. No default.
op	List of options (see details). The default is NULL.

Details

Plots p-values on a minus log base 10 scale versus the locations of the SNPs on each chromosome.

Options list op: Below are the names for the options list op. All names have default values if they are not specified.

• add A number to add spacing between the chromosomes. The default is 0.

• cex Magnification factor for the plotting symbol. The default is 1.

• cex.axis Magnification factor for the axes. The default is 1.

• cex.lab Magnification factor for the axes labels. The default is 1.

• cex.main Magnification factor for the title. The default is 1.

• colors Character vector of colors to use in the plot. See colors for all possible colors. The default is NULL.

• figs Two element vector for the number of rows and columns if length(plot.vars) > 1 and onePlot = 0. The default is NULL.

• min.p All p-values less than min.p will be set to min.p. The default is 1e-30.

• onePlot 0 or 1 to plot all of plot.vars on the same screen. The default is 0.

• pch Vector of plotting symbols to use. See points for the different plotting symbols.

• splitScreen 0 or 1 to split the plot into two seperate parts. The default is 0.

• subset Vector of chromosomes to plot. The default is NULL.

• tcl The length of tick marks as a fraction of the height of a line of text. The default is -0.5.

• x.las 0-3 for axis labels. 0=parallel, 1=horizontal, 2=perpendicular, 3=vertical The default is 2.

• yaxis.range Vector of length 2 to set the limits for the y-axis. The limits should be on the original scale. The default is NULL.

See Also

QQ.plot, locusMap.list

Examples

 
# Load the data containing the chromosomes and locations
data(LocusMapData, package="CGEN") 

# For illustrative purposes, add some hypothetical p-values to x
set.seed(123)
LocusMapData[, "pvalue"] <- runif(nrow(LocusMapData))

# Define the input list locusMap.list
locusList <- list(snp.var="SNP", chrm.var="CHROMOSOME", loc.var="LOCATION")

# Create the plot
Manhattan.plot(LocusMapData, "pvalue", locusList)

CGEN documentation built on April 28, 2020, 8:08 p.m.