plotPedigree: plotPedigree A wrapped function to plot simulated pedigree from function `simulatePedigree`. This function require the installation of package `kinship2`.

Description

plotPedigree A wrapped function to plot simulated pedigree from function simulatePedigree. This function require the installation of package kinship2.

Usage

plotPedigree(
  ped,
  code_male = NULL,
  verbose = FALSE,
  affected = NULL,
  cex = 0.5,
  col = 1,
  symbolsize = 1,
  branch = 0.6,
  packed = TRUE,
  align = c(1.5, 2),
  width = 8,
  density = c(-1, 35, 65, 20),
  mar = c(2.1, 1, 2.1, 1),
  angle = c(90, 65, 40, 0),
  keep.par = FALSE,
  pconnect = 0.5,
  ...
)

Value

A plot of the provided pedigree

Arguments

ped: The simulated pedigree data.frame from function simulatePedigree. Or a pedigree dataframe with the same colnames as the dataframe simulated from function simulatePedigree.
code_male: This optional input allows you to indicate what value in the sex variable codes for male. Will be recoded as "M" (Male). If NULL, no recoding is performed.
verbose: logical If TRUE, prints additional information. Default is FALSE.
affected: This optional parameter can either be a string specifying the column name that indicates affected status or a numeric/logical vector of the same length as the number of rows in 'ped'. If NULL, no affected status is assigned.
cex: The font size of the IDs for each individual in the plot.
col: color for each id. Default assigns the same color to everyone.
symbolsize: controls symbolsize. Default=1.
branch: defines how much angle is used to connect various levels of nuclear families.
packed: default=T. If T, uniform distance between all individuals at a given level.
align: these parameters control the extra effort spent trying to align children underneath parents, but without making the pedigree too wide. Set to F to speed up plotting.
width: default=8. For a packed pedigree, the minimum width allowed in the realignment of pedigrees.
density: defines density used in the symbols. Takes up to 4 different values.
mar: margin parmeters, as in the par function
angle: defines angle used in the symbols. Takes up to 4 different values.
keep.par: Default = F, allows user to keep the parameter settings the same as they were for plotting (useful for adding extras to the plot)
pconnect: when connecting parent to children the program will try to make the connecting line as close to vertical as possible, subject to it lying inside the endpoints of the line that connects the children by at least pconnect people. Setting this option to a large number will force the line to connect at the midpoint of the children.
...: Extra options that feed into the plot function.