allele.plotter.whole: Plot the regression coefficients or BLUPs as allele effects...

In gkeele/miqtl: Suite of QTL Mapping Functions

Plot the regression coefficients or BLUPs as allele effects for a genome scan (whole genomes or subset of chromosomes)

Description

This function takes a genome scan object from scan.h2lmm() and plots out allele effect estimates based on regression coefficients or BLUPs.

Usage

allele.plotter.whole(
  scan.object,
  just.these.chr = NULL,
  scale = "Mb",
  imp.confint.alpha = NULL,
  main.colors = c(rgb(240, 240, 0, maxColorValue = 255), rgb(128, 128, 128,
    maxColorValue = 255), rgb(240, 128, 128, maxColorValue = 255), rgb(16, 16, 240,
    maxColorValue = 255), rgb(0, 160, 240, maxColorValue = 255), rgb(0, 160, 0,
    maxColorValue = 255), rgb(240, 0, 0, maxColorValue = 255), rgb(144, 0, 224,
    maxColorValue = 255)),
  use.legend = TRUE,
  main = "",
  my.bty = "n",
  my.lwd = 1.25,
  set.plot.limit = c(-10, 10),
  my.legend.cex = 0.6,
  my.legend.pos = "topright",
  transparency = 0.6,
  y.max.manual = NULL,
  y.min.manual = NULL,
  my.y.line = 2,
  my.y.axis.cex = 1,
  my.y.lab.cex = 0.7,
  my.x.lab.cex = 0.7,
  no.title = FALSE,
  override.title = NULL,
  add.chr.to.label = FALSE,
  alternative.labels = NULL,
  axis.cram = TRUE,
  include.x.axis.line = TRUE
)

Arguments

scan.object	A scan.h2lmm() object that had return.allele.effects=TRUE.
just.these.chr	DEFAULT: NULL. Specifies a subset of the chromosomes to be plotted. NULL results in all chromosomes being plotted.
scale	DEFAULT: "Mb". Specifies the scale of genomic position to be plotted. Either Mb or cM are expected.
main.colors	DEFAULT: CC founder colors. The colors that correspond to the founder alleles.
use.legend	DEFAULT: TRUE. Include a legend for the different associations. If TRUE, the labels are the names of the non.mi.scan.list object.
main	DEFAULT: NULL. Adds a title above the model.
my.lwd	DEFAULT: rep(1.5, 8). Specifies the lwds for the alleles.
my.legend.cex	DEFAULT: 0.6. Specifies the size of the text in the legend.
my.legend.pos	DEFAULT: "topright". Specifies where to put the legend, if specified in use.legend.
transparency	DEFAULT: 0.6. The transparency level for the confidence bands. 0 is invisible, 1 is solid.
y.max.manual	DEFAULT: NULL. Manually adds a max y-value.
y.min.manual	DEFAULT: NULL. Manually adds a min y-value.
no.title	DEFAULT: FALSE. If TRUE, produces a plot with no title, not even the automatic title components like formula and sample size.
override.title	DEFAULT: NULL. If non-null, overrides automatic title components like formula and sample size.
add.chr.to.label	DEFAULT: FALSE. If TRUE, "chr" precedes integers on the x-axis.
alternative.labels	DEFAULT: NULL. If non-null, specifies alternative labels for the founder alleles.
axis.cram	DEFAULT: TRUE. This makes the plot much more likely to include all chromosome labels. With small plots, this could lead to overlapping labels.
include.x.axis.line	DEFAULT: TRUE. IF TRUE, this option adds an x-axis line with ticks between chromosomes.

Examples

allele.plotter.whole()

gkeele/miqtl documentation built on Sept. 13, 2024, 5:49 a.m.