plot.qb.scantwo {qtlbim} | R Documentation

## Two dimensional LOD Plot of Epistasis/joint

### Description

Plots joint LOD for chromosomes on a two dimensional grid.

### Usage

    ## S3 method for class 'summary.qb.scantwo':
    print(x, digits = 3, ...)
    ## S3 method for class 'qb.scantwo':
    print(x, digits = 3, ...)
    ## S3 method for class 'qb.scantwo':
    plot(x, chr, smooth = 3, main, offset,
      nodiag, slice = NULL, show.locus = TRUE, verbose = FALSE, ...)

### Arguments

`x` | An object of class `qb.scantwo`.
`digits` | Significant digits to round with print.
`chr` | Vector of chromosomes to plot. Must be integer.
`smooth` | Perform smoothing if > 0 using weighted average over `smooth` adjacent points.
`main` | Main title.
`offset` | Offset to make all values non-negative (see below).
`nodiag` | If `TRUE` do not include diagonal in plot.
`slice` | Take 1-D slice through 2-D surface is not `NULL` (see below).
`show.locus` | If a `slice`, show locus estimate if `TRUE`.
`verbose` | Give verbose feedback if `TRUE`.
`...` | Other parameters passed to generic plot function.

### Details

The `offset` is used only if `\line{qb.scantwo}` used `type` = "estimate" to make values for plotting all non-negative. Values are rescaled by `offset` so that the origin is at 1 and, by default, the min and max are at 0 and 2, respectively, for each half of the plot. We need this at this time because `plot.scantwo` does not allow negative values.

The `plot.scantwo` argument `nodiag` is set to ensure values are all shown and not modified by `plot.scantwo`. Plots with different values for `nodiag` or `lower` than the defauls may be non-sensical. For instance, passing `lower = "cond-int"` produces much white area on the image.

A non-null `slice` yields a 1-D view of the 2-D surface. The plots for slices use `plot.scantwo`. The elements of the slice vector are:

chr
  Chromosome number to slice on.
upper
  Focus on upper triangle of 2-D if `TRUE`.
start
  Start position in chromosome `chr` (default = 0).
end
  End position in chromosome `chr` (default = end of chromosome).
weight
  Type of weighted mean across `chr` by number of MCMC samples: 0 = unweigthed; 1 = uniform weighting; 2 = position-specific weighting (default).

### Value

The scantwo object being plotted.

### Author(s)

Brian S. Yandell, yandell@stat.wisc.edu

### References

http://www.qtlbim.org

### See Also

`qb.scantwo`, `plot.scantwo`

### Examples

    example(qb.scantwo)

[Package qtlbim version 1.6.5 Index]