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

In gkeele/kqtl: Suite of QTL Mapping Functions

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 = "",
  y.max.manual = NULL, my.legend.cex = 0.6, hard.thresholds = NULL,
  thresholds.col = "red", thresholds.legend = NULL)

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.
median.band.col	DEFAULT: "gray88". The color of the 95% confident band plotted around the median.
main	DEFAULT: "". Adds a title above the model.
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.
main.colors	DEFAULT: "black". The color of the main association score to be plotted.

Examples

genome.plotter.chr()

gkeele/kqtl documentation built on May 17, 2019, 6:06 a.m.