Skip to contents

Align a Pedigree object

Source: R/align.R
align.Rd

Given a Pedigree, this function creates helper matrices that describe the layout of a plot of the Pedigree.

Usage

# S4 method for class 'Pedigree'
align(
  obj,
  packed = TRUE,
  width = 10,
  align = TRUE,
  hints = NULL,
  missid = "NA_character_",
  align_parents = TRUE,
  force = FALSE,
  precision = 2
)

Arguments

obj

A Pedigree object

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.)

width

For a packed output, the minimum width of the plot, in inches.

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.

hints

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

missid

A character vector with the missing values identifiers. All the id, dadid and momid corresponding to those values will be set to NA_character_.

align_parents

If align_parents = TRUE, go one step further and try to make both parents of each child have the same depth. (This is not always possible). It helps the drawing program by lining up pedigrees that 'join in the middle' via a marriage.

force

If force = TRUE, the function will return the depth minus min(depth) if depth reach a state with no founders is not possible.

precision

The number of decimal places to round the solution to.

Value

A list with components

  • n: A vector giving the number of subjects on each horizonal level of the plot

  • nid: A matrix with one row for each level, giving the numeric id of each subject plotted. (A value of 17 means the 17th subject in the Pedigree).

  • pos: A matrix giving the horizontal position of each plot point

  • fam: A matrix giving the family id of each plot point. A value of 3 would mean that the two subjects in positions 3 and 4, in the row above, are this subject's parents.

  • spouse: A matrix with values

    • 0 = not a spouse

    • 1 = subject plotted to the immediate right is a spouse

    • 2 = subject plotted to the immediate right is an inbred spouse

  • twins: Optional matrix which will only be present if the Pedigree contains twins :

    • 0 = not a twin

    • 1 = sibling to the right is a monozygotic twin

    • 2 = sibling to the right is a dizygotic twin

    • 3 = sibling to the right is a twin of unknown zygosity

Details

This is an internal routine, used almost exclusively by ped_to_plotdf().

The subservient functions auto_hint(), alignped1(), alignped2(), alignped3(), and alignped4() contain the bulk of the computation.

If the hints are missing the auto_hint() routine is called to supply an initial guess.

If multiple families are present in the obj Pedigree, this routine is called once for each family, and the results are combined in the list returned.

For more information you can read the associated vignette: vignette("pedigree_alignment").

See also

alignped1(), alignped2(), alignped3(), alignped4(), auto_hint()

Examples

data(sampleped)
ped <- Pedigree(sampleped)
align(ped)
#> $`1`
#> $`1`$n
#> [1]  2 10 16 14
#> 
#> $`1`$nid
#>      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
#> [1,]   35   36    0    0    0    0    0    0    0     0     0     0     0     0
#> [2,]    1    2    3    4   37   38    5    6    7     8     0     0     0     0
#> [3,]    9   10   11   12   14   39   40   41   14    15    12    18    17    16
#> [4,]   21   22   23   24   27   28   25   26   29    30    31    32    33    34
#>      [,15] [,16]
#> [1,]     0     0
#> [2,]     0     0
#> [3,]    19    20
#> [4,]     0     0
#> 
#> $`1`$pos
#>      [,1] [,2] [,3] [,4] [,5] [,6]  [,7]  [,8]  [,9] [,10] [,11] [,12] [,13]
#> [1,]  3.8  4.8  0.0  0.0 0.00 0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00
#> [2,]  0.0  1.0  2.8  3.8 4.80 5.80 11.25 12.25 14.01 15.01  0.00  0.00  0.00
#> [3,]  0.0  1.0  2.0  3.0 4.00 5.00  6.00  7.00  8.00  9.00 10.00 11.00 12.00
#> [4,]  0.0  1.0  2.0  3.0 6.01 7.01  8.01  9.01 10.01 11.01 12.01 13.01 14.01
#>      [,14] [,15] [,16]
#> [1,]  0.00     0     0
#> [2,]  0.00     0     0
#> [3,] 13.00    14    15
#> [4,] 15.01     0     0
#> 
#> $`1`$fam
#>      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
#> [1,]    0    0    0    0    0    0    0    0    0     0     0     0     0     0
#> [2,]    0    0    1    0    0    1    0    0    0     0     0     0     0     0
#> [3,]    1    3    3    3    3    5    5    5    0     7     0     7     0     7
#> [4,]    1    1    1    1    9    9   11   11   13    15    15    15    15    15
#>      [,15] [,16]
#> [1,]     0     0
#> [2,]     0     0
#> [3,]     7     9
#> [4,]     0     0
#> 
#> $`1`$spouse
#>      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
#> [1,]    1    0    0    0    0    0    0    0    0     0     0     0     0     0
#> [2,]    1    0    1    0    1    0    1    0    1     0     0     0     0     0
#> [3,]    1    0    0    0    0    0    0    0    1     0     1     0     1     0
#> [4,]    0    0    0    0    0    0    0    0    0     0     0     0     0     0
#>      [,15] [,16]
#> [1,]     0     0
#> [2,]     0     0
#> [3,]     1     0
#> [4,]     0     0
#> 
#> 
#> $`2`
#> $`2`$n
#> [1] 2 7 5
#> 
#> $`2`$nid
#>      [,1] [,2] [,3] [,4] [,5] [,6] [,7]
#> [1,]    1    2    0    0    0    0    0
#> [2,]    3    4    5    6    7    9    8
#> [3,]   10   11   12   13   14    0    0
#> 
#> $`2`$pos
#>      [,1] [,2] [,3] [,4] [,5] [,6] [,7]
#> [1,]  2.7  3.7  0.0  0.0  0.0    0    0
#> [2,]  0.0  1.0  2.0  3.0  4.0    5    6
#> [3,]  0.0  1.0  4.5  5.5  6.5    0    0
#> 
#> $`2`$fam
#>      [,1] [,2] [,3] [,4] [,5] [,6] [,7]
#> [1,]    0    0    0    0    0    0    0
#> [2,]    0    1    1    1    1    0    1
#> [3,]    1    1    6    6    6    0    0
#> 
#> $`2`$spouse
#>      [,1] [,2] [,3] [,4] [,5] [,6] [,7]
#> [1,]    1    0    0    0    0    0    0
#> [2,]    1    0    0    0    0    1    0
#> [3,]    0    0    0    0    0    0    0
#> 
#>