Plot Pedigrees

This function is used to plot a Pedigree object.

It is a wrapper for plot_fromdf() and ped_to_plotdf() as well as ped_to_legdf() if legend = TRUE.

Usage

# S4 method for class 'Pedigree,missing'
plot(
  x,
  aff_mark = TRUE,
  id_lab = "id",
  label = NULL,
  ggplot_gen = FALSE,
  cex = 1,
  symbolsize = 1,
  branch = 0.6,
  packed = TRUE,
  align = c(1.5, 2),
  align_parents = TRUE,
  force = FALSE,
  width = 6,
  title = NULL,
  subreg = NULL,
  pconnect = 0.5,
  fam_to_plot = 1,
  legend = FALSE,
  leg_cex = 0.8,
  leg_symbolsize = 0.5,
  leg_loc = NULL,
  leg_adjx = 0,
  leg_adjy = 0,
  precision = 2,
  lwd = par("lwd"),
  ped_par = list(),
  leg_par = list(),
  tips = NULL
)

Arguments

x: A Pedigree object.
aff_mark: If TRUE, add a aff_mark to each box corresponding to the value of the affection column for each filling scale.
id_lab: The column name of the id for each individuals.
label: If not NULL, add a label to each box under the id corresponding to the value of the column given.
ggplot_gen: If TRUE add the segments to the ggplot object
cex: Character expansion of the text
symbolsize: Size of the symbols
branch: defines how much angle is used to connect various levels of nuclear families.
packed: Should the Pedigree be compressed. (i.e. allow diagonal lines connecting parents to children in order to have a smaller overall width for the plot.)
align: For a packed Pedigree, align children under parents TRUE, to the extent possible given the page width, or align to to the left margin FALSE. This argument can be a two element vector, giving the alignment parameters, or a logical value. If TRUE, the default is c(1.5, 2), or if numeric the routine alignped4() will be called.
align_parents: If align_parents = TRUE, go one step further and try to make both parents of each child have the same depth. (This is not always possible). It helps the drawing program by lining up pedigrees that 'join in the middle' via a marriage.
force: If force = TRUE, the function will return the depth minus min(depth) if depth reach a state with no founders is not possible.
width: For a packed output, the minimum width of the plot, in inches.
title: The title of the plot.
subreg: A 4-element vector for (min x, max x, min depth, max depth), used to edit away portions of the plot coordinates returned by ped_to_plotdf(). This is useful for zooming in on a particular region of the Pedigree.
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.
fam_to_plot: default=1. If the Pedigree contains multiple families, this parameter can be used to select which family to plot. It can be a numeric value or a character value. If numeric, it is the index of the family to plot returned by unique(x$ped$famid). If character, it is the family id to plot.
legend: default=FALSE. If TRUE, a legend will be added to the plot.
leg_cex: default=0.8. Controls the size of the legend text.
leg_symbolsize: default=0.5. Controls the size of the legend symbols.
leg_loc: default=NULL. If NULL, the legend will be placed in the upper right corner of the plot. Otherwise, a 4-element vector of the form (x0, x1, y0, y1) can be used to specify the location of the legend. The legend will be fitted to the specified and might be distorted if the aspect ratio of the legend is different from the aspect ratio of the specified location.
leg_adjx: default=0. Controls the horizontal labels adjustment of the legend.
leg_adjy: default=0. Controls the vertical labels adjustment of the legend.
precision: The number of decimal places to round the solution to.
lwd: default=par("lwd"). Controls the line width of the segments, arcs and polygons.
ped_par: default=list(). A list of parameters to use as graphical parameteres for the main plot.
leg_par: default=list(). A list of parameters to use as graphical parameters for the legend.
tips: A character vector of the column names of the data frame to use as tooltips. If NULL, no tooltips are added.

Value

an invisible list containing

df : the data.frame used to plot the Pedigree
par_usr : the user coordinates used to plot the Pedigree
ggplot : the ggplot object if ggplot_gen = TRUE

Details

Two important parameters control the looks of the result. One is the user specified maximum width. The smallest possible width is the maximum number of subjects on a line, if the user's suggestion is too low it is increased to 1 + that amount (to give just a little wiggle room).

To make a Pedigree where all children are centered under parents simply make the width large enough, however, the symbols may get very small.

The second is align, a vector of 2 alignment parameters a and b. For each set of siblings at a set of locations x and with parents at p=c(p1,p2) the alignment penalty is

$$(1/k^a)\sum{i=1}{k} [(x_i - (p1+p2)/2)]^2$$

$$\sum(x- \overline(p))^2/(k^a)$$

Where k is the number of siblings in the set.

When a = 1 moving a sibship with k sibs one unit to the left or right of optimal will incur the same cost as moving one with only 1 or two sibs out of place.

If a = 0 then large sibships are harder to move than small ones, with the default value a = 1.5 they are slightly easier to move than small ones. The rationale for the default is as long as the parents are somewhere between the first and last siblings the result looks fairly good, so we are more flexible with the spacing of a large family. By tethering all the sibs to a single spot they are kept close to each other. The alignment penalty for spouses is $b(x_1 - x_2)^2$, which tends to keep them together. The size of b controls the relative importance of sib-parent and spouse-spouse closeness.

Side Effects

Creates plot on current plotting device.

Examples