LDDist {synbreed} | R Documentation |
LD versus distance Plot
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)
[Package
synbreed version 0.12-12
Index]