autohint: Align a pedigree to print well

In kinship2: Pedigree Functions

Align a pedigree to print well

Description

A pedigree structure can contain a hints object which helps to reorder the pedigree (e.g. left-to-right order of children within family) so as to plot with minimal distortion. This routine is used to create an initial version of the hints. They can then be modified if desired.

Usage

autohint(ped, hints, packed=TRUE, align=FALSE)

Arguments

ped	a pedigree structure
hints	optional hints object. Only the order component is used.
packed	If TRUE, 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 FALSE to speed up plotting.

Details

This routine would not normally be called by a user. It moves children within families, so that marriages are on the "edge" of a set children, closest to the spouse. For pedigrees that have only a single connection between two families this simple-minded approach works surprisingly well. For more complex structures hand-tuning of the hints matrix may be required.

The pedigree in the example below is one where rearranging the founders greatly decreases the number of extra connections. When autohint is called with a a vector of numbers as the second argument, the values for the founder females are used to order the founder families left to right across the plot. The values within a sibship are used as the preliminary order of siblings within a family; this may be changed to move one of them to the edge so as to match up with a spouse. The actual values in the vector are not important, only their order.

Value

a list containing components order and spouse

See Also

pedigree, besthint

Examples

data(testped1)
ped1 <- with(testped1, pedigree(id, father, mother, sex))
plot(ped1, cex=.7, symbolsize=.7)

# rearrange some founders
temp <- 1:nrow(testped1)
temp[76] <- .1
temp[77] <- .2
temp[74] <- .3
temp[60] <- .4
temp[30] <- temp[8] + .1
temp[65] <- temp[4] + .1
temp[14] <- temp[3] + .1
ped1$hints <- autohint(ped1, temp)
plot(ped1, cex=.7)

kinship2 documentation built on May 29, 2024, 11:14 a.m.