genome.plotter.to.pdf: Plot whole genome and single chromosome windows of...

In gkeele/miqtl: Suite of QTL Mapping Functions

Plot whole genome and single chromosome windows of haplotype-based genome scan in a PDF output document

Description

This function takes the genome scan output from scan.h2lmm() and plots the whole genome and single chromosome zoom-ins for all the specified chromosomes. When multiple imputations are used, includes the 95% confidence band on the median in the zoomed-in plots.

Usage

genome.plotter.to.pdf(
  scan.object,
  chr = c(1:19, "X"),
  use.lod = FALSE,
  scale = c("Mb", "cM"),
  main.col = "black",
  median.band.col = "gray88",
  main = "",
  no.title = FALSE,
  override.title = NULL,
  y.max.manual = NULL,
  hard.thresholds = NULL,
  thresholds.col = "red",
  thresholds.legend = NULL,
  pdf.output.path,
  pdf.height = 5,
  pdf.width = 9,
  ...
)

Arguments

scan.object	A scan.h2lmm() object (ROP or multiple imputations). If multiple imputations, median and confidence interval on median are plotted.
chr	DEFAULT: c(1:19, "X"). The chromosomes to be plotted. DEFAULT is all the mouse chromosomes.
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 are expected.
median.band.col	DEFAULT: "gray88". The color of the 95% confident band plotted around the median.
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 thresholds legend is used.
pdf.output.path	That path of the PDF file to be generated.
pdf.height	DEFAULT: 5. The height of an individual pages of the PDF.
pdf.width	DEFAULT: 9. The width of an individual pages of the PDF.
main.colors	DEFAULT: "black". The color of the main association score to be plotted.

Examples

genome.plotter.to.pdf()

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