genome.plotter.chr: Plot single chromosome windows of haplotype-based genome scan

In gkeele/miqtl: Suite of QTL Mapping Functions

Plot single chromosome windows of haplotype-based genome scan

Description

This function takes the genome scan output from scan.h2lmm() and plots the portion that corresponds to a single chromosome. When multiple imputations are used, includes the 95% confidence band on the median.

Usage

genome.plotter.chr(
  scan.object,
  chr,
  use.lod = FALSE,
  scale = c("Mb", "cM"),
  main.col = "black",
  median.band.col = "gray88",
  main = "",
  no.title = FALSE,
  override.title = NULL,
  my.y.line = 2,
  my.y.axis.cex = 1,
  y.max.manual = NULL,
  make.y.axis.sparse = FALSE,
  my.ylab.cex = 1,
  my.x.line = 3,
  my.x.axis.cex = 1,
  my.xlab.cex = 1,
  x.padj = 1,
  my.x.axis.at = NULL,
  my.x.labels = TRUE,
  override.xlab = NULL,
  my.title.line = 0.5,
  title.cex = 1,
  my.lwd = 1.5,
  override.ylab = NULL,
  my.legend.cex = 0.6,
  my.type = "l",
  point.cex = 0.5,
  hard.thresholds = NULL,
  thresholds.col = "red",
  thresholds.legend = NULL,
  include.qtl.rug = FALSE,
  rug.pos = NULL,
  rug.col = "gray50",
  physical.dist.is.Mb = TRUE,
  use.frame.plot = FALSE
)

Arguments

scan.object	A scan.h2lmm() object (ROP or multiple imputations). If multiple imputations, median and confidence interval on median are plotted.
chr	The chromosome to be plotted.
use.lod	DEFAULT: FALSE. Plots either the LOD score or the -log10 p-value.
scale	DEFAULT: "Mb". Specifies the scale of genomic position to be plotted. Either Mb or cM can be used.
main.col	DEFAULT: "black". The color of the main association score to be plotted.
median.band.col	DEFAULT: "gray88". The color of the 95% confident band plotted around the median.
main	DEFAULT: "". Adds a title above the model.
no.title	DEFAULT: FALSE. If TRUE, no title is printed.
override.title	DEFAULT: NULL. If a string is specified, it is included on plot without any of the default automated title.
y.max.manual	DEFAULT: NULL. Manually adds a max y-value. Allows multiple genome scans to easily be on the same scale.
my.legend.cex	DEFAULT: 0.6. Specifies the size of the text in the legend.
hard.thresholds	DEFAULT: NULL. Specify one or more horizontal threshold lines.
thresholds.col	DEFAULT: "red". Set the colors of the specified thresholds.
thresholds.legend	DEFAULT: NULL. If non-NULL, string arguments used as labels in thresholds legend. If NULL, no threshols legend is used.

Examples

genome.plotter.chr()

gkeele/miqtl documentation built on June 13, 2022, 4:20 p.m.