snp.genome.plotter.whole: Plot whole genome and single chromosome windows of a...

In gkeele/kqtl: Suite of QTL Mapping Functions

Description

This function takes the genome scan output from imputed.snp.scan.h2lmm() and plots the whole genome or single chromosome zoom-ins.

Usage

snp.genome.plotter.whole(snp.scan, just.these.chr = NULL, scale = "Mb",
  y.max.manual = NULL, title = "", alt.col = NULL,
  hard.thresholds = NULL, thresholds.col = "red",
  thresholds.legend = NULL, my.legend.cex = 0.6,
  my.legend.pos = "topright")

Arguments

snp.scan	An imputed.snp.scan.h2lmm() object.
just.these.chr	DEFAULT: NULL. The chromosomes to be plotted. NULL leads to all chromosomes being plotted.
scale	DEFAULT: "Mb". Specifies the scale of genomic position to be plotted. Either Mb or cM are expected.
y.max.manual	DEFAULT: NULL. Manually adds a max y-value. Allows multiple genome scans to easily be on the same scale.
title	DEFAULT: "". Manually adds a max ylim to the plot. Allows multiple genome scans to easily be on the same scale.
alt.col	DEFAULT: NULL. Allows for a custom color vector for individual SNPs.
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,
my.legend.cex	DEFAULT: 0.6. Specifies the size of the text in the legend.
my.legend.pos	DEFAULT: "topright". Specified position of the legend on the plot.

Examples

snp.genome.plotter.whole()

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