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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
## S3 method for class 'linkdat'
plot(x, marker = NULL, alleles = NULL, sep = "/", missing = "-", 
     skip.empty.genotypes = FALSE, id.labels = x$orig.ids, 
     title = paste("Family", x$famid), available = FALSE, col = 1, 
     deceased = numeric(0), starred = numeric(0), aff2 = NULL, 
     margins = c(0.6, 1, 4.1, 1), ...)
                       
## S3 method for class 'singleton'
plot(x, marker = NULL, alleles = NULL, sep = "/", missing = "-", 
     id.labels = x$orig.ids, title = paste("Family", x$famid), 
     available = FALSE, col = 1, starred = numeric(0), 
     margins = c(4.1, 1, 4.1, 1), symbolsize=4, offset=0.5+0.2*symbolsize, 
     textsize=1, ...)

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/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. (Not implemented for singletons.)

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. (Not implemented for singletons.)

margins

a numeric of length 4 indicating the plot margins.

symbolsize

numeric controlling the size of pedigree symbols (squares for males, circles for females). NB: This works differently in plot.linkdat and plot.singleton.

offset

a numeric controlling the vertical distance between the symbol and text label in singleton plots.

textsize

a numeric controlling the text label size in singleton plots.

...

in plot.linkdat: Arguments passed on to plot.pedigree in the kinship2 package. In particular symbolsize and cex can be useful.

Details

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

Author(s)

Magnus Dehli Vigeland, Guro Doerum

See Also

plot.pedigree

Examples

1
2
3
4
5
6
7
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)

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.