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

In gkeele/miqtl: Suite of QTL Mapping Functions

Plot whole genome and single chromosome windows of a SNP-based genome scan

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,
  point.col = "black",
  point.cex = 0.5,
  scale = "Mb",
  distinguish.chr.type = c("color", "box"),
  distinguish.box.col = "gray88",
  distinguish.snp.col = "gray60",
  y.max.manual = NULL,
  my.y.line = 2,
  my.y.axis.cex = 1,
  title = "",
  override.title = NULL,
  my.title.line = NA,
  title.cex = 1,
  alt.col = NULL,
  hard.thresholds = NULL,
  thresholds.col = "red",
  thresholds.legend = NULL,
  thresholds.lty = 2,
  thresholds.lwd = 1,
  my.legend.cex = 0.6,
  my.legend.pos = "topright",
  my.bty = "n",
  my.x.labels = TRUE,
  add.chr.to.label = FALSE,
  axis.cram = TRUE,
  include.x.axis.line = TRUE
)

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.
add.chr.to.label	DEFAULT: FALSE. If TRUE, adds "Chr" before every chromosome label. If FALSE, "Chr" is added as an axis label under the y-axis.
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

snp.genome.plotter.whole()

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