LDDist: LD versus distance Plot

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

Description

Visualization of pairwise Linkage Disequilibrium (LD) estimates generated by function pairwiseLD versus marker distance. A single plot is generated for every chromosome.

Usage

LDDist(
  LDdf,
  chr = NULL,
  type = "p",
  breaks = NULL,
  n = NULL,
  file = NULL,
  fileFormat = "pdf",
  onefile = TRUE,
  colL = 2,
  colD = 1,
  ...
)

Arguments

LDdf	object of class LDdf which is the output of function pairwiseLD and argument type="data.frame"
chr	numeric scalar or vector. Return value is a plot for each chromosome in chr. To plot the complete LD within Chromosomes in a single plot use "all". Note: This includes no values for between chromosom LD! The default is NULL. This givs a single plot for each chromosome. Note: Remember to add one empty line for each chromosome in batch-scripts , if you use more than one chromosome!
type	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	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	numeric. Number of observations used to estimate LD. Only required for type="nls".
file	character. path to a file where plot is saved to (optional).
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 arguments for plot

Author(s)

Valentin Wimmer, Hans-Juergen Auinger and Theresa Albrecht

References

For nonlinear regression curve: Hill WG, Weir BS (1988) Variances and covariances of squared linkage disequilibria in finite populations. Theor Popul Biol 33:54-78.

See Also

pairwiseLD, LDMap

Examples

## Not run: 
library(synbreedData)
# maize data example
data(maize)
maizeC <- codeGeno(maize)

# LD for chr 1
maizeLD <- pairwiseLD(maizeC, chr = 1, type = "data.frame")
# scatterplot
LDDist(maizeLD, type = "p", pch = 19, colD = hsv(alpha = 0.1, v = 0))

# stacked bars  with default categories
LDDist(maizeLD, type = "bars")

# stacked bars  with user-defined categories
LDDist(maizeLD, type = "bars", breaks = list(
  dist = c(0, 10, 20, 40, 60, 180),
  r2 = c(1, 0.6, 0.4, 0.3, 0.1, 0)
))

## End(Not run)

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