snp.genome.plotter.w.r2: Plot a single chromosome window of a SNP-based genome scan...

In gkeele/miqtl: Suite of QTL Mapping Functions

Plot a single chromosome window of a SNP-based genome scan overlayed with r^2 information

Description

This function takes the outputs from imputed.snp.scan.h2lmm() and pairwise.cor.snp.scan() and plots the SNP association for a single chromosome, overlayed with r^2 information for a specified SNP.

Usage

snp.genome.plotter.w.r2(
  snp.scan,
  r2.object,
  scale = "Mb",
  zoom.in = FALSE,
  zoom.in.by = 0.1,
  y.max.manual = NULL,
  my.y.line = 2,
  my.y.axis.cex = 1,
  my.ylab.cex = 1,
  title = "",
  override.title = NULL,
  my.title.line = NA,
  title.cex = 1,
  alt.col = NULL,
  this.cex = 1,
  hard.thresholds = NULL,
  thresholds.col = "red",
  thresholds.legend = NULL,
  my.legend.cex = 0.6,
  my.legend.pos = "topleft",
  thresholds.lty = 2,
  thresholds.lwd = 1,
  my.bty = "n",
  r2.bounds = NULL,
  bounds.col = "gray",
  high.color = "red",
  low.color = "blue",
  add.outline = FALSE,
  include.ramp = TRUE,
  ramp.cex = 0.7
)

Arguments

snp.scan	An imputed.snp.scan.h2lmm() object.
r2.object	A pairwise.cor.snp.scan() object.
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.
this.cex	DEFAULT: 1. Allows for the adjustment of the cex value for the main plot.
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.
r2.bounds	DEFAULT: NULL. If NULL, no interval is depicted on the plot. If set to a value in [0,1], will include interval based on the given r2 on the plot.

Examples

snp.genome.plotter.w.r2()

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