plot.linkdat: Plot pedigrees with genotypes

Description

This is the main function for pedigree plotting, with many options for controlling the appearance of pedigree symbols, labels and marker genotypes. Most of the work is done by the plotting functionality in the 'kinship2' package.

Usage

# S3 method for linkdat
plot(
  x,
  marker = NULL,
  alleles = NULL,
  sep = "/",
  missing = "-",
  skip.empty.genotypes = FALSE,
  id.labels = NULL,
  title = NULL,
  available = FALSE,
  col = 1,
  deceased = numeric(0),
  starred = numeric(0),
  aff2 = NULL,
  margins = c(0.6, 1, 4.1, 1),
  ...
)
# S3 method for singleton
plot(
  x,
  marker = NULL,
  alleles = NULL,
  sep = "/",
  missing = "-",
  skip.empty.genotypes = FALSE,
  id.labels = NULL,
  title = NULL,
  available = FALSE,
  col = 1,
  deceased = numeric(0),
  starred = numeric(0),
  aff2 = NULL,
  margins = c(8, 0, 0, 0),
  ...
)

Arguments

x: a linkdat object.
marker: either NULL, a vector of positive integers, a marker object, or a list of marker objects. If NULL, no genotypes are plotted. If a marker object (or a list of such), the genotypes are written below each individual in the pedigree, in the format determined by alleles, sep and missing. If a vector of integers is given, the corresponding marker objects are extracted from x$markerdata.
alleles: a character vector with allele names.
sep: a character of length 1 separating alleles for diploid markers.
missing: the symbol (integer or character) for missing alleles.
skip.empty.genotypes: a logical. If TRUE, and marker is non-NULL, empty genotypes (which by default looks like '-/-') are not printed.
id.labels: a vector with labels for each pedigree member. This defaults to x$plot.labels is this is set (see setPlotLabels), otherwise to as.character(x$orig.ids).
title: the plot title. If NULL or '', no title is added to the plot.
available: either a logical, a colour name, or the word 'shaded'. If a colour name is given, the available individuals (as defined by x$available) are plotted in this colour. If available=F no colouring is used, while (for backwards compatibility) available=T is equivalent to available='red'. The 'shaded' option results in diagonal shading.
col: a vector with colour 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. For singletons only the first element (the 'bottom' margin) is used.
...: arguments passed on to plot.pedigree in the kinship2 package. In particular symbolsize and cex can be useful.

Author

Magnus Dehli Vigeland, Guro Doerum

Details

plot.linkdat is in essence a wrapper for `plot.pedigree()` in the kinship2 package.

Examples

Run this code


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

y = singleton(id=1)
m = marker(y, 1, c('A',0), alleles=c('A','B'))
plot(y, marker=m, id='indiv 1', title='Singleton', available=TRUE)