plotPedigree {BGmisc}

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,
  ...
)

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.

Value

A plot of the provided pedigree