paramlink (version 0.7-0)

plot.linkdat: Plot pedigrees with genotypes

Description

Plots a medical pedigree with genotypes for a single marker, or (for power analysis) indicating which individuals are available for genotyping.

Usage

## S3 method for class 'linkdat':
plot(x, marker = NULL, alleles = NULL, sep = "", missing = "-", 
                       id.labels = x$orig.ids, title = paste("Family", x$famid), 
                       available = FALSE, col =1, deceased = numeric(0), 
                       starred = numeric(0), aff2 = NULL, margins = c(4.1, 1, 4.1, 1), ...)

Arguments

x

a linkdat object.

marker

NULL, or a single integer.

alleles

a character vector with allele names.

sep

a character of length 1 separating alleles for diploid markers.

missing

the symbol (integer or character) for missing alleles.

id.labels

a vector with labels/names of the pedigree members.

title

the plot title. If NULL or "", no title is added to the plot.

available

if TRUE, the available individuals are drawn in red.

col

a vector with color indicators for the pedigree members. Recycled if necessary. By default everyone is drawn black.

deceased

a numeric containing ID's of deceased pedigree members.

starred

a numeric containing ID's of pedigree members that should be marked with a star in the pedigree plot.

aff2

NULL, or a numeric with affection statuses (2=affected, 1=unaffected, 0=unknown) for a second trait.

margins

a numeric of length 4 indicating the plot margins.

...

arguments to plot.pedigree from the kinship package. In particular symbolsize is useful.

Details

Uses the plot.pedigree from the kinship package.

See Also

plot.pedigree

Examples

data(toyped)
x = linkdat(toyped)
plot(x, marker=1, alleles=c("a1","a2"), sep="| ", deceased=2)