plot.LDdf: Plot function for class 'LDdf'

In synbreed: Framework for the Analysis of Genomic Prediction Data using R

Description

The function visualises wheter the LD between adjacent values or visualization of pairwise Linkage Disequilibrium (LD) estimates generated by function pairwiseLD versus marker distance. A single plot is generated for every chromosome.

Usage

## S3 method for class 'LDdf'
plot(
  x,
  gpData,
  plotType = "dist",
  dense = FALSE,
  nMarker = TRUE,
  centr = NULL,
  chr = NULL,
  type = "p",
  breaks = NULL,
  n = NULL,
  file = NULL,
  fileFormat = "pdf",
  onefile = TRUE,
  colL = 2,
  colD = 1,
  ...
)

Arguments

x	Object of class LDdf, i.e the output of function pairwiseLD with argument type="data.frame".
gpData	Object of class gpData with object map
plotType	You can decide, if you like to have a plot with the LD of the neighbouring markers (option "neighbour"), or you like to have a scatter plot of distance and LD (default option "dist").
dense	For plotType="neighbour", logical. Should density visualization for high-density genetic maps be used?
nMarker	For plotType="neighbour", logical. Print number of markers for each chromosome?
centr	For plotType="neighbour", numeric vector. Positions for the centromeres in the same order as chromosomes in map. If "maize", centromere positions of maize in Mbp are used.
chr	For plotType="dist", numeric scalar or vector. Return value is a plot for each chromosome in chr. Note: Remember to add in a batch-script one empty line for each chromosome, if you use more than one chromosome!
type	For plotType="dist", character string to specify the type of plot. Use "p" for a scatterplot, "bars" for stacked bars or "nls" for scatterplot together with nonlinear regression curve according to Hill and Weir (1988).
breaks	For plotType="dist", list containing breaks for stacked bars (optional, only for type="bars"). Components are dist with breaks for distance on x-axis and r2 for breaks on for r2 on y-axis. By default, 5 equal spaced categories for dist and r2 are used.
n	For plotType="dist", numeric. Number of observations used to estimate LD. Only required for type="nls".
file	Optionally a path to a file where the plot is saved to
fileFormat	character. At the moment two file formats are supported: pdf and png. Default is "pdf".
onefile	logical. If fileFormat = "pdf" you can decide, if you like to have all graphics in one file or in multiple files.
colL	The color for the line if type="nls" is used. In other cases without a meaning.
colD	The color for the dots in the plot of type="nls" and type="p"
...	further graphical arguments for function plot

Details

For more Details see at plotNeighbourLD or LDDist

Author(s)

Hans-Juergen Auinger

See Also

plotNeighbourLD, LDDist, plotGenMap, pairwiseLD

synbreed documentation built on March 12, 2021, 3:01 a.m.