Initial hint for a Pedigree alignment

Compute an initial guess for the alignment of a Pedigree

Usage

# S4 method for class 'Pedigree'
auto_hint(obj, hints = NULL, packed = TRUE, align = FALSE, reset = FALSE)

Arguments

obj

A Pedigree object

hints

A Hints object or a named list containing horder and spouse. If NULL then the Hints stored in obj will be used.

packed

Should the Pedigree be compressed. (i.e. allow diagonal lines connecting parents to children in order to have a smaller overall width for the plot.)

align

For a packed Pedigree, align children under parents TRUE, to the extent possible given the page width, or align to to the left margin FALSE. This argument can be a two element vector, giving the alignment parameters, or a logical value. If TRUE, the default is c(1.5, 2), or if numeric the routine alignped4() will be called.

reset

If TRUE, then even if the Ped object has Hints, reset them to the initial values.

Value

The initial Hints object.

Details

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.

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 may be required.

When auto_hint() is called with a a vector of numbers as the hints 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.

See also

align(), best_hint()

Hints

Examples

data(sampleped)
ped <- Pedigree(sampleped[sampleped$famid == 1, ])
auto_hint(ped)
#> An object of class "Hints"
#> Slot "horder":
#> 1_101 1_102 1_103 1_104 1_105 1_106 1_107 1_108 1_109 1_110 1_111 1_112 1_113 
#>     1     2     3     4     5     6     7     8     1     1     2     3     1 
#> 1_114 1_115 1_116 1_117 1_118 1_119 1_120 1_121 1_122 1_123 1_124 1_125 1_126 
#>     4     1     3     9     2     4    10     1     2     3     4     5     6 
#> 1_127 1_128 1_129 1_130 1_131 1_132 1_133 1_134 1_135 1_136 1_137 1_138 1_139 
#>     7     8     9    10    11    12    13    14     2     3    10    11    11 
#> 1_140 1_141 
#>    12    13 
#> 
#> Slot "spouse":
#>     idl   idr anchor
#> 1 1_112 1_118  right
#> 2 1_114 1_115  right
#> 3 1_109 1_110   left
#>