qtlbim: QTL Bayesian Interval Mapping

Description Usage Arguments Details Value Author(s) References See Also Examples

Plots joint LOD for chromosomes on a two dimensional grid.

## S3 method for class 'qb.scantwo'
plot(x, chr, smooth = 3, main, offset,
  nodiag, slice = NULL, show.locus = TRUE,
  weight = c("sqrt","count","none","atten","ratten"), verbose = FALSE,
  split.chr, ...)

`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.

The offset is used only if 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).