Generate Plotting Information for a Pedigree

DESCRIPTION:

Given a pedigree, this function creates helper matrices that describe the layout of a plot of the pedigree.

USAGE:

align.pedigree(ped, packed=T, hints=ped$hints, width=6, align=T)

REQUIRED ARGUMENTS:

ped
a pedigree object

OPTIONAL ARGUMENTS:

packed
should the pedigree be compressed, i.e., to allow diagonal lines connecting parents to children in order to have a smaller overall width for the plot.
hints
two column hints matrix. The first column determines the relative order of subjects within a sibship, as well as the relative order of processing for the founder couples. (For this latter, the female founders are ordered as though they were sisters). The second column contains spouse information, e.g., if hints[2,6] = 17, then subject number 17 of the pedigree is a spouse of number 2, and is preferentially plotted to the right of number 2. Negative numbers plot the spouse preferentially to the left.
width
for a packed output, the minimum width
align
should iterations of the springs algorithm be used to improve the plotted output. If TRUE, a default number of iterations is used. If numeric, this specifies the number of iterations.

VALUE:

a structure with components

ARGUMENTS:

n
a vector giving the number of subjects on each horizontal level of the plot
nid
a matrix with one row for each level, giving the numeric id of each subject plotted. A value of 17 means the 17th subject in the pedigree.
pos
a matrix giving the horizontal position of each plot point.
fam
a matrix giving the family id of each plot point. A value of "3" would mean that the two subjects in positions 3 and 4, in the row above, are this subject's parents.
spouse
a matrix with values 1= subject plotted to the immediate right is a spouse, 2= subject plotted to the immediate right is an inbred spouse, 0= not a spouse.
twins
optional matrix which will only be present if the pedigree contains twins. It has values 1= sibling to the right is a monozygotic twin, 2= sibling to the right is a dizygotic twin, 3= sibling to the right is a twin of unknown zygosity, 0= not a twin.

DETAILS:

This is an internal routine, used almost exclusively by plot.pedigree . The subservient functions alignped1, alignped2 , alignped3 , and alignped4 contain the bulk of the computation.

SEE ALSO: