plot.pedigree {kinship2}

plot pedigrees

Description

plot objects created with the pedigree function

Usage

## S3 method for class 'pedigree'
plot(x, id = x$id, status = x$status, 
                        affected = x$affected, 
                        cex = 1, col = 1,
                        symbolsize = 1, branch = 0.6, 
                        packed = TRUE, align = c(1.5,2), width = 8, 
                        density=c(-1, 35,65,20), #mar=c(3.1, 1, 3.1, 1),
                        angle=c(90,65,40,0), keep.par=FALSE,
                        subregion, pconnect=.5, ...)

Arguments

x

object created by the function pedigree.

id

id variable - used for labeling.

status

can be missing. If it exists, 0=alive/missing and 1=death.

affected

vector, or matrix with up to 4 columns for affected indicators. Subject's symbol is divided into sections for each status, shaded if indicator is 1, not-shaded for 0, and symbol "?" if missing (NA)

cex

controls text size. Default=1.

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)

subregion

4-element vector for (min x, max x, min depth, max depth), used to edit away portions of the plot coordinates returned by align.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.

...

Extra options that feed into the plot function.

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

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.

Value

an invisible list containing

plist

a list that contains all the position information for plotting the pedigree. This will useful for further functions (yet unwritten) for manipulating the plot, but likely not to an ordinary user.

x, y

the x an and y plot coordinates of each subject in the plot. The coordinate is for the top of the plotted symbol. These will be in the same order as the input pedigree. If someone in the pedigree does not appear in the plot their coordinates will be NA. If they appear multiple times one of the instances is chosen. (Which one is a function of the order in which the pedigree was constructed.)

boxh

the height of the symbol, in user coordinates

boxw

the width of the symbol

call

a copy of the call that generated the plot

Side Effects

creates plot on current plotting device.

See Also

pedigree

Examples

data(sample.ped)

pedAll <- pedigree(sample.ped$id, sample.ped$father, sample.ped$mother, 
       sample.ped$sex,  #affected=sample.ped$affected,
       affected=cbind(sample.ped$affected, sample.ped$avail), 
       famid=sample.ped$ped)

ped2 <- pedAll['2']

print(ped2)


## plot(ped2)