plot.scanonevar: plot.scanonevar

In rcorty/vqtl: Genome Scans to Accommodate and Target Genetic and Non-Genetic Effects on Trait Variance in Test Crosses

Description

plot.scanonevar implements the plot generic for objects of class 'scanonevar'. Because scanonevar objects can be viewed in terms of LODs or empirical p-values, this plotting function checks the 'units' attribute to determine which to plot.

Usage

## S3 method for class 'scanonevar'
plot(x, y = NULL,
  chrs = unique(x[["result"]][["chr"]]), tests_to_plot = c("mQTL",
  "vQTL", "mvQTL"), plotting.units = if (any(grepl(pattern = "empir.p", x
  = names(x[["result"]])))) {     "empir.p" } else {     "LOD" },
  plot.title = x[["meta"]][["scan.formulae"]][["mean.alt.formula"]][[2]],
  marker.rug = TRUE, ymax = NULL, legend_pos = NULL,
  alpha_pos = c("left", "right", "none"), alpha_chr = 1,
  alpha_size = 2, ...)

Arguments

x	the scanonevar object to be plotted
y	Optionally, a scanone object to be plotting for comparison to the scanonevar object.
chrs	Optionally, the subset of the chromosomes to plot
tests_to_plot	which one or ones of the three possible tests to plot ('mQTL', 'vQTL', and 'mvQTL')
plotting.units	One of 'LOD', 'asymp.p', or 'empir.p', implying whether LOD scores, asymptotic p-values, or empirical p-values should be plotted. Defaults to 'LOD'
plot.title	the title of the plot
marker.rug	Should a marker rug be plotted? Defaults to TRUE.
ymax	the top of the y axis
legend_pos	the position of the legend
alpha_pos	the position of the alpha values (false positive rate)
alpha_chr	which chromosome to put the alphas (FPRs) on
alpha_size	size of annotations for alpha=0.05 and alpha=0.01 lines
...	additional plotting arguments

Details

If such a strong signal was observed that the empirical p-value underflows R's float type, this function produces an error. The author is open to suggestions on how to deal with this situation better.

These plots look better when both x (the scanonevar object) and y (optional scanone for comparison) are in units p values than when they are in LOD units.

none

Value

Returns the plot.

Author(s)

Robert Corty [e-mail]

Examples

set.seed(27599)
test.cross <- qtl::sim.cross(map = qtl::sim.map(len = rep(20, 3), n.mar = 5), n.ind = 50)
test.sov <- scanonevar(cross = test.cross)
plot(x = test.sov)

rcorty/vqtl documentation built on May 27, 2019, 3:04 a.m.