Manhattan.plot {CGEN} | R Documentation

## Manhattan plot

### 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)

[Package CGEN version 3.18.0 Index]