plot.HaploFreq {optiSel} | R Documentation |
Plots Frequencies of Haplotype Segments in Specified Breeds
Description
For a particular haplotype from thisBreed
and each marker m
the frequency of the segment containing marker m
in a specified reference breed is plotted.
Usage
## S3 method for class 'HaploFreq'
plot(x, ID=1, hap=1, refBreed=NULL, Chr=NULL, show.maxFreq=FALSE, ...)
Arguments
x |
This is either an R-Object obtained with function haplofreq or a list obtained with function freqlist. |
ID |
Either the ID of the animal from this breed to be plotted, or the position of the animal in R-Object |
hap |
Number of the haplotype to be plotted ( |
refBreed |
Breed name. The frequencies the haplotype segments have in this reference breed will be plotted. Parameter |
Chr |
Vector with chromosomes to be plotted. The default means that all chromosomes will be plotted. |
show.maxFreq |
If |
... |
Arguments to be passed to methods, such as graphical parameters. |
Details
For a particular haplotype from thisBreed
and each marker m
from chromosomes Chr
the frequency of the segment containing marker m
in reference breed refBreed
is plotted (red line), as well as the maximum frequency the segment has in one of the evaluated breeds (black line), and the maximum frequency a segment from thisBreed
has in one of the evaluated breeds (grey area, if show.maxFreq=TRUE
).
Value
No return value, called for plotting.
Author(s)
Robin Wellmann
Examples
data(map)
data(Cattle)
dir <- system.file("extdata", package="optiSel")
files <- paste(dir, "/Chr", 1:2, ".phased", sep="")
Freq <- freqlist(
haplofreq(files, Cattle, map, thisBreed="Angler", refBreeds="Rotbunt", minSNP=20),
haplofreq(files, Cattle, map, thisBreed="Angler", refBreeds="Holstein", minSNP=20),
haplofreq(files, Cattle, map, thisBreed="Angler", refBreeds="Fleckvieh", minSNP=20)
)
names(Freq)
plot(Freq, ID=1, hap=2, refBreed="Rotbunt")
Freq <- haplofreq(files, Cattle, map, thisBreed="Angler", refBreeds="others", minSNP=20)
plot(Freq, ID=1, hap=2)
plot(Freq, ID=1, hap=2, show.maxFreq=TRUE)
Freq <- haplofreq(files, Cattle, map, thisBreed="Angler", refBreeds="Angler", minSNP=20)
plot(Freq, ID=1, hap=2)