R: function to plot 2D scan results

plot.scan.gwaa.2D {GenABEL} | R Documentation

## function to plot 2D scan results

### Description

Plots results of 2D analysis produced by `scan.glm.2D` or `scan.haplo.2D`

### Usage

    	## S3 method for class 'scan.gwaa.2D'
    plot(x, y, ..., df=1)

### Arguments

`x` | object of type `scan.gwaa.2D-class`, as returned by `scan.glm.2D` or `scan.haplo.2D`
`y` | this argument is not used
`...` | additional arguments to be passed to plot
`df` | Whether 1, 2, or "all" d.f.s should be plotted. Note that for `scan.haplo.2D` 1 and 2 d.f. list the same values.

### Details

Now plots only "allelelic" results. This is fine for `scan.haplo.2D`as only alleic tests are produced; however, `scan.glm.2D` also produces "genotypic" results.

### Value

No value returned.

### Author(s)

Yurii Aulchenko

### See Also

`scan.gwaa.2D-class`, `scan.glm.2D`, `scan.haplo.2D`

### Examples

    require(GenABEL.data)
    data(srdta)
    a <- scan.glm.2D("qt3~CRSNP",data=srdta,snps=c(1:10))
    # "allelic" results
    plot(a)
    # to plot "genotypic" results:
    filled.contour(x=a$map,y=a$map,z=-log10(a$P2df))

[Package GenABEL version 1.8-0 Index]