Plot Pedigrees
DESCRIPTION:
Plot objects created with the function pedigree.
USAGE:
plot.pedigree(x, id=x$id, sex=x$sex, status=x$status,
affected=as.matrix(x$affected), cex=1,
col=rep(1, length(x$id)), symbolsize=1,
branch=0.6, packed=T, align=packed, width=8,
density=c(-1, 50, 70, 90), angle=c(90, 70, 50, 0),
mar=c(4.1, 1, 4.1, 1), keep.par=F, ...)
REQUIRED ARGUMENTS:
- x
-
an object created by the function pedigree.
OPTIONAL ARGUMENTS:
- id
-
id variable - used for labeling.
- sex
-
sex variable - used to determine which symbols are plotted.
- status
-
can be missing.
If it exists, 0=alive/missing and 1=death.
- affected
-
variable, or matrix, of up to 4 columns representing 4 different
affected statuses.
- cex
-
controls text size.
Default=1.
- col
-
color for each id.
Default assigns the same color to everyone.
- symbolsize
-
controls symbol size.
Default=1.
- branch
-
defines how much angle is used to connect various levels of nuclear families.
- packed
-
default=T.
If T, uniform distance between all individuals at a given level.
- align
-
default=T.
Indicates extra effort should be spent trying to align parents and children.
Set to F to speed up plotting.
- width
-
default=8.
For a packed pedigree, the minimum width allowed in the realignment
of pedigrees.
- density
-
defines density used in the symbols.
Takes up to 4 different values.
- angle
-
defines angle used in the symbols.
Takes up to 4 different values.
- keep.par
-
default = F, allows user to keep the parameter settings the same as they
were for plotting (useful for adding extras to the plot).
- ...
-
extra options that feed into the plot function.
VALUE:
returns points for each plot plus original pedigree.
SIDE EFFECTS:
Creates a pedigree plot on the current plotting device.
SEE ALSO:
.
EXAMPLES:
d10 <- data.frame(upn=1:9, dadid=c(0,0,1,1,0,1,0,6,6),
momid=c(0,0,2,2,0,2,0,5,7),
sex=c(1,2,1,1,2,1,2,1,2),
affected=c(1,1,2,2,1,2,1,2,1))
ptemp <- pedigree(id=d10$upn, dadid=d10$dadid, momid=d10$momid,
sex=d10$sex, affected=d10$affect)
plot(ptemp)
col.founder <- rep(1,length(d10$affect))
col.founder[d10$id==1] <- 2
plot(ptemp, affected=cbind(d10$affect, d10$affect2, d10$affect3,
d10$affect4), col=col.founder, id=paste(ptemp$id,'\n',
'(',d10$post,')',sep=''), angle=c(90,80,70,60),
density=c(-1,90,70,50))