plot.pedigree: Visualization of pedigree

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

Description

A function to visualize pedigree structure by a graph using the igraph package. Each genotype is represented as vertex and direct offsprings are linked by an edge.

Usage

## S3 method for class 'pedigree'
plot(x, effect = NULL, ...)

Arguments

x	object of class pedigree or object of class gpData with element pedigree
effect	vector of length nrow(pedigree) with effects to plot on the x axis
...	Other arguments for function igraph.plotting

Details

The pedigree is structured top to bottom. The first generation is printed in the first line. Links over more than one generation are possible as well as genotypes with only one (known) parent. Usually, no structure in one generation is plotted. If an effect is given, the genotypes are ordered by this effect in the horizontal direction and a labeled axis is plotted at the bottom.

Value

A named graph visualizing the pedigree structure. Color is used to distinguish sex.

Note

This function uses the plotting method for graphs in the library igraph

Author(s)

Valentin Wimmer and Hans-Juergen Auinger

See Also

create.pedigree, simul.pedigree

Examples

id <- paste("ID", 1:9, sep = "0")
par1 <- paste("ID", c("", "", "", "", 1, 1, 1, 4, 7), sep = "0")
par2 <- paste("ID", c("", "", "", "", 2, 3, 2, 5, 8), sep = "0")
ped1 <- create.pedigree(id, par1, par2, unknown = "ID0")
ped1
plot(ped1)

# create 2nd pedigree object
Id <- paste("ID", 10:16, sep = "")
Par1 <- paste("ID", c("", "", 1, 1, 6, 7, 7), sep = "0")
Par2 <- paste("ID", c("", "", 10, "08", "09", 11, 14), sep = "")
ped2 <- create.pedigree(Id, Par1, Par2, unknown = c("ID0", "ID"))
ped2

ped <- add.pedigree(ped1, ped2)
plot(ped)

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