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 'qb.scantwo':
plot(x, chr, smooth = 3, main, offset,
  nodiag, slice = NULL, show.locus = TRUE,
  weight = c("sqrt","count","none"), verbose = FALSE,
  split.chr, ...)

Arguments

x An object of class qb.scantwo.
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.
weight Weights to use for nearest neighbor smoothing. sqrt is square root of count per locus. Used only if smooth > 0.
verbose Give verbose feedback if TRUE.
split.chr Split summary by multiple QTL per chromosome (see details for plot.qb.scanone).
... 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 1.9.3 Index]