mygeno.image: image of genotypes

In byandell/qtlview: Visualization of QTL Scans for Multiple Traits

Description

image of genotypes

Usage

mygeno.image(x, chr, reorder = TRUE, id = "MouseNum",
  sex = c("both", "male", "female"), genotypes, xlim,
  use.cM = FALSE, reorder.by.genotype, recomb.only = FALSE,
  keep.missing = TRUE, ...)
## S3 method for class 'mygeno.image'
plot(x, xlim, use.cM = FALSE, equal.spacing = FALSE,
  zscale = TRUE, normal.score = TRUE, main = "", ...)
## S3 method for class 'mygeno.image'
summary(object, ...)
## S3 method for class 'mygeno.image'
print(x, ...)

Arguments

x	object of class cross (see read.cross)
chr	vector of chromosome names for object x
reorder	character vector of traits to align with genotype
id	name used to match individual identifiers
sex	choice of both, male or female sex
genotypes	character vector of genotype names for summary (see below)
xlim	range on chr to consider (ignored if length(chr) > 1)
use.cM	use cM map if TRUE; otherwise use Mb map
reorder.by.genotype	reorder by average genotype if TRUE (see below)
recomb.only	only show recombinant individuals if TRUE
equal.spacing	use equal spacing for markers if TRUE
keep.missing	keep individuals with missing genotypes if TRUE
zscale	include Z gray scale if TRUE
normal.score	use normal scores of phenotypes if TRUE
main	main label for plot
...	additional arguments to subset.cross

Details

Produces an image map of genotypes. Individuals are sorted by average genotype (e.g. number of B alleles) if reorder is TRUE. Genotypes are color-coded as blue (AA), green (AB), red (BB). If non-segregating markers are included, regions spanned by them are colored lightgray. Gray scale on right is mean genotype across markers (black = AA, white = BB).

If names of phenotypes are provided with reorder, these are visually shown next to genotype bar on right as smooth and raw forms. In addition, a second plot of genotype vs. phenotype shows the relationship in detail.

byandell/qtlview documentation built on May 13, 2019, 9:53 a.m.