legendPlot: Legend Pedigree Plot

In mayoverse/kinship2: Pedigree Functions

Legend Pedigree Plot

Description

Pedigree plot with ready-made legend along the bottom of the page to represent colors and affection statuses

Usage

legendPlot(
  x,
  id = x$id,
  affected = x$affected,
  affected.label = NULL,
  col = 1,
  col.label = NULL,
  symbolsize = 0.75,
  cex = 0.5,
  ...
)

Arguments

x	Pedigree data frame with ped (pedigree id), id (id of individual), father (id of father), mother (id of mother), sex, affected (affection status), and avail (DNA availability).
id	Optional, a character string to replace the correspinding id for persons in the pedigree
affected	A variable indicating affection status. A multi-column matrix can be used to give the status with respect to multiple traits. Logical, factor, and integer types are converted to 0/1 representing unaffected and affected, respectively. NAs are considered missing.
affected.label	Set labels for affection statuses
col	Colors for the plot symbol for each individual
col.label	Named vector, with elements matching the unique color codes, the names are the labels used in the legend.
symbolsize	Size of symbols (circle/square/triangle). Default is 1.0
cex	Character expansion size for labels and ids. Default is 1.0
...	Character expansion size for labels and ids. Default is 1.0

Value

A pedigree plot with a legend

Author(s)

Jason Sinnwell, code contributed by Sara Achenbach

See Also

pedigree, plot.pedigree

Examples

## Not run: 
data(sample.ped)
pedAll <- with(sample.ped, pedigree(id, father, mother, sex,
               affected=cbind(affected, avail), famid=ped)
ped1 <- pedAll["1"]
legendPlot(ped1,  affected.label=c("cancer","available"))

## End(Not run)

mayoverse/kinship2 documentation built on July 4, 2023, 1:11 a.m.