plot.pedigree {kinship}R Documentation

plot pedigrees

Description

plot objects created with the function pedigree

Usage

## S3 method for class 'pedigree':
plot(x, id=x$id, sex=x$sex, status=x$status,
affected=x$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), mar=c(4.1,1,4.1,1), angle=c(90, 70, 50, 0), keep.par=F, ...)

Arguments

x object created by the function pedigree.
id id variable - used for labelling.
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 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 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.
mar no comment(s)
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 plot on current plotting device.

See Also

pedigree

Examples

## Not run: 
# The original example
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))

# The example to R News and Bioinformatics
# pedigree 10081 in GAW14
p1 <- scan(nlines=16,what=list(0,0,0,0,0,"",""))
 1   2   3  2  2  7/7  7/10 
 2   0   0  1  1  -/-  -/-  
 3   0   0  2  2  7/9  3/10 
 4   2   3  2  2  7/9  3/7  
 5   2   3  2  1  7/7  7/10 
 6   2   3  1  1  7/7  7/10 
 7   2   3  2  1  7/7  7/10 
 8   0   0  1  1  -/-  -/-  
 9   8   4  1  1  7/9  3/10 
10   0   0  2  1  -/-  -/- 
11   2  10  2  1  7/7  7/7 
12   2  10  2  2  6/7  7/7 
13   0   0  1  1  -/-  -/- 
14  13  11  1  1  7/8  7/8 
15   0   0  1  1  -/-  -/- 
16  15  12  2  1  6/6  7/7 

p2 <- as.data.frame(p1)
names(p2) <- c("id","fid","mid","sex","aff","GABRB1","D4S1645")
attach(p2)
sex <- sex-1
p3 <- pedigree(id,fid,mid,sex,aff)
pdf("10081.pdf")
par(xpd=TRUE)
plot(p3)
dev.off()
## End(Not run)

[Package kinship version 1.1.0-21 Index]