plot.relationshipMatrix: Heatmap for relationship Matrix

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

Description

Visualization for objects of class relationshipMatrix using a heatmap of pairwise relatedness coefficients.

Usage

## S3 method for class 'relationshipMatrix'
plot(x, y=NULL, levelbreaks=NULL, axes=TRUE, cols=NULL, groupLines = NULL, ...)

Arguments

x	Object of class relationshipMatrix
y	Optional for comparisons of objects of class relationshipMatrix
levelbreaks	list with one element for x andy. Define breaks in the color scheme of the plot. If you make to many breaks, the color scheme repeats! If y=NULL this can be an vector. If you like to have the same breaks or both relationship matrices, you can also use just one vector.
axes	a logical value indicating whether axes should be drawn on the plot. Default is TRUE.
cols	a list with one element for each relationship matrix. Colors and the number of levelbreaks should fit. But also if not, a plot is drawn. In case option y=NULL, cols can bei a vector.
groupLines	add positions to make groups more visible
...	further graphical arguments passed to function levelplot in package lattice. To create equal colorkeys for two heatmaps, use at=seq(from,to,length=9).

Author(s)

Valentin Wimmer and Hans-Juergen Auinger

Examples

# small pedigree
ped <- simul.pedigree(gener=4,7)
gp <- create.gpData(pedigree=ped)
A <- kin(gp,ret="add")
plot(A)

# big pedigree
## Not run: 
library(synbreedData)
data(maize)
K <- kin(maize,ret="kin")
U <- kin(codeGeno(maize),ret="realized")/2
# equal colorkeys
plot(K,levelbreaks=seq(0,2,length=9))
plot(U,levelbreaks=seq(0,2,length=9))

## End(Not run)

synbreed documentation built on May 2, 2019, 3:23 a.m.