plot.pedigree: plot pedigrees

In SaraMonts/kinship2_modified: Pedigree Functions. Modification of kinship2 package

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, age = NULL, number = NULL, cex = 1, col = 1, 
                 dist_text = 1.5, symbolsize = 1, branch = 0.6, 
                 packed = TRUE, align = c(1.5,2), width = 8, height = 4,
                 density = -1, mar = c(4.1, 1, 4.1, 1), angle = 45, 
                 keep.par = FALSE, subregion, pconnect= .5, 
                 consultand = NULL, info = NULL, adopted = NULL, ...)

Arguments

x	object created by the function pedigree.
id	id variable.
status	can be missing. If it exists, 0=alive/missing, 1=death and 2=pregnancy.
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). If values 2 or 3 are present in a matrix row and all the other values of the matrix row are 0, a dot or a vertical line is drawn inside the symbol (carriers and presymptomatics).
age	vector of ages of the subjects in the plot as character strings.
number	vector of number of subjects represented by every symbol. Possible values: 1, 2, 3, 4, 5, 6, 7, 8, 9 or "n" (unknown number).
cex	controls text size. Default=1.
col	color for each affected column. Default=1.
dist_text	distance between the symbols and the text below them. Default=1.5
symbolsize	controls symbolsize. Default=1.
branch	defines how much angle is used to connect various levels of nuclear families. Default=0.6.
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.
height	default=4. Height of the plot.
density	defines density used in the symbols for every affected column. Default=-1.
mar	margin parmeters, as in the par function
angle	defines angle used in the symbols for every affected column. Default=45.
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.
consultand	id of the consultand subjects.
info	matrix where every column is a field of information in the form of character strings.
adopted	vector that contains adoption information for every subject. Values can be: "in" (adopted inside the family), "out" (adopted outside the family) or NA (not adopted).
...	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)∑{i=1}{k} [(x_i - (p1+p2)/2)]^2

sum(x- mean(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 *(x1-x2)^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)
## Not run: 
plot(ped2)
legendPlot(ped2)

## End(Not run)

SaraMonts/kinship2_modified documentation built on Jan. 8, 2021, 9:20 p.m.