genome.plotter.region: Plot user-specified windows of haplotype-based and snp-based...

In gkeele/miqtl: Suite of QTL Mapping Functions

Plot user-specified windows of haplotype-based and snp-based genome scans

Description

This function takes genome scan association outputs and plots the portion that corresponds to a region of a single chromosome. When multiple imputations are used, includes the 95% confidence band on the median.

Usage

genome.plotter.region(
  haplotype.association = NULL,
  snp.association = NULL,
  use.lod = FALSE,
  chr,
  region.min = NULL,
  region.max = NULL,
  scale = c("Mb", "cM"),
  haplotype.col = c("blue", "red"),
  haplotype.lwd = 3,
  haplotype.lty = 1,
  median.band.col = c("cyan", "pink"),
  snp.col = c("black", "gray"),
  snp.pch = 20,
  snp.cex = 0.9,
  main = "",
  no.title = FALSE,
  override.title = NULL,
  y.max.manual = NULL,
  use_bold_axis = FALSE,
  axis_lwd = 1,
  include_y_axis = TRUE,
  my.y.line = 2,
  my.y.axis.cex = 1,
  my.y.lab.cex = 0.5,
  my.x.line = 2,
  my.x.axis.cex = 1,
  my.xlab.cex = 1,
  x.padj = -0.3,
  my.x.labels = TRUE,
  override.xlab = NULL,
  include.x.ticks = TRUE,
  drop.x.tick = FALSE,
  my.title.line = 0.5,
  my.title.cex = 1,
  hard.thresholds = NULL,
  thresholds.col = "red",
  thresholds.legend = NULL,
  thresholds.lwd = 2,
  use.legend = TRUE,
  my.legend.cex = 0.6,
  my.legend.pos = "topright",
  my.bty = "n",
  rug.pos = NULL,
  rug.col = "gray50"
)

Arguments

haplotype.association	DEFAULT: NULL. A list of scan.h2lmm() objects (ROP or multiple imputations). If multiple imputations, median and confidence interval on median are plotted. If NULL, presumably only SNP scans will be plotted.
snp.association	DEFAULT: NULL. A list of imputed.snp.scan.h2lmm() objects. If NULL, presumably only haplotype-based scans will be plotted.
use.lod	DEFAULT: FALSE. Plots either the LOD score or the -log10 p-value.
chr	The chromosome to be plotted.
region.min	DEFAULT: NULL. The lower bound of the region to be plotted. Should match the scale. If NULL, defaults to the minimum of the specified chromosome.
region.max	DEFAULT: NULL. The upper bound of the region to be plotted. Should match the scale. If NULL, defaults to the maximum of the specified chromosome.
scale	DEFAULT: "Mb". Specifies the scale of genomic position to be plotted. Either Mb or cM can be used.
haplotype.col	DEFAULT: "black". The color of the haplotype-based association score to be plotted.
median.band.col	DEFAULT: "gray88". The color of the 95% confident band plotted around the median.
snp.col	DEFAULT: "black". The color of the SNP association score to be plotted.
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.
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.
use.legend	DEFAULT: TRUE. Include a legend for the different associations. If TRUE, the labels are the names of the non.mi.scan.list object.
my.legend.cex	DEFAULT: 0.6. Specifies the size of the text in the legend.
my.legend.pos	DEFAULT: "topright". Specifies where to put the legend, if specified in use.legend.

Examples

genome.plotter.region()

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