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Calculate coordinates for plotting individuals in a pedigree

Source: R/calcCoordinates.R
calculateCoordinates.Rd

Extracts and modifies the x and y positions for each individual in a pedigree data frame using the align.pedigree function from the `kinship2` package. It returns a data.frame with positions for plotting.

Usage

calculateCoordinates(
  ped,
  personID = "personID",
  momID = "momID",
  dadID = "dadID",
  spouseID = "spouseID",
  sexVar = "sex",
  twinID = "twinID",
  code_male = NULL,
  config = list()
)

Arguments

ped

A data frame containing the pedigree data. Needs personID, momID, dadID, and sex columns.

personID

Character string specifying the column name for individual IDs. Defaults to "personID".

momID

Character string specifying the column name for mother IDs. Defaults to "momID".

dadID

Character string specifying the column name for father IDs. Defaults to "dadID".

spouseID

Character. Name of the column in `ped` for the spouse ID variable.

sexVar

Character. Name of the column in `ped` for the sex variable.

twinID

Character string specifying the column name for twin IDs. Defaults to "twinID".

code_male

Value used to indicate male sex. Defaults to NULL.

config

List of configuration options:

code_male

Default is 1. Used by BGmisc::recodeSex().

ped_packed

Logical, default TRUE. Passed to `kinship2_align.pedigree`.

ped_align

Logical, default TRUE. Align generations.

ped_width

Numeric, default 15. Controls spacing.

Value

A data frame with one or more rows per person, each containing:

  • `x_order`, `y_order`: Grid indices representing layout rows and columns.

  • `x_pos`, `y_pos`: Continuous coordinate positions used for plotting.

  • `nid`: Internal numeric identifier for layout mapping.

  • `extra`: Logical flag indicating whether this row is a secondary appearance.

Examples

# Load example data
data(potter, package = "BGmisc")

# Calculate coordinates for the pedigree
coords <- calculateCoordinates(
  ped = potter,
  personID = "personID",
  momID = "momID",
  dadID = "dadID",
  code_male = 1
)

# View the coordinates
head(coords)
#>   personID famID             name first_name surname gen momID dadID spouseID
#> 1        1     1   Vernon Dursley     Vernon Dursley   1   101   102        3
#> 2        2     1 Marjorie Dursley   Marjorie Dursley   1   101   102       NA
#> 3        3     1    Petunia Evans    Petunia   Evans   1   103   104        1
#> 4        4     1       Lily Evans       Lily   Evans   1   103   104        5
#> 5        5     1     James Potter      James  Potter   1    NA    NA        4
#> 6        6     1   Dudley Dursley     Dudley Dursley   2     3     1       NA
#>   sex twinID zygosity nid x_pos x_order y_order y_pos parent_fam spousehint
#> 1   1     NA     <NA>   1   1.0       2       2     2          1          1
#> 2   0     NA     <NA>   2   0.0       1       2     2          1          0
#> 3   0     NA     <NA>   3   2.0       3       2     2          3          0
#> 4   0     NA     <NA>   4   4.0       5       2     2          3          0
#> 5   1     NA     <NA>   5   3.0       4       2     2          0          1
#> 6   1     NA     <NA>   6   1.5       1       3     3          2          0
#>   y_fam extra x_fam
#> 1     1 FALSE   0.5
#> 2     1 FALSE   0.5
#> 3     1 FALSE   3.0
#> 4     1 FALSE   3.0
#> 5    NA FALSE    NA
#> 6     2 FALSE   1.5

# Example with custom configuration
coords_custom <- calculateCoordinates(
  ped = potter,
  personID = "personID",
  momID = "momID",
  dadID = "dadID",
  code_male = 1,
  config = list(
    ped_packed = FALSE,
    ped_width = 20
  )
)
# Load example data
data(potter, package = "BGmisc")

# Calculate coordinates for the pedigree
coords <- calculateCoordinates(
  ped = potter,
  personID = "personID",
  momID = "momID",
  dadID = "dadID",
  config = list(
    code_male = 1
  )
)

# View the coordinates
head(coords)
#>   personID famID             name first_name surname gen momID dadID spouseID
#> 1        1     1   Vernon Dursley     Vernon Dursley   1   101   102        3
#> 2        2     1 Marjorie Dursley   Marjorie Dursley   1   101   102       NA
#> 3        3     1    Petunia Evans    Petunia   Evans   1   103   104        1
#> 4        4     1       Lily Evans       Lily   Evans   1   103   104        5
#> 5        5     1     James Potter      James  Potter   1    NA    NA        4
#> 6        6     1   Dudley Dursley     Dudley Dursley   2     3     1       NA
#>   sex twinID zygosity nid x_pos x_order y_order y_pos parent_fam spousehint
#> 1   1     NA     <NA>   1   1.0       2       2     2          1          1
#> 2   0     NA     <NA>   2   0.0       1       2     2          1          0
#> 3   0     NA     <NA>   3   2.0       3       2     2          3          0
#> 4   0     NA     <NA>   4   4.0       5       2     2          3          0
#> 5   1     NA     <NA>   5   3.0       4       2     2          0          1
#> 6   1     NA     <NA>   6   1.5       1       3     3          2          0
#>   y_fam extra x_fam
#> 1     1 FALSE   0.5
#> 2     1 FALSE   0.5
#> 3     1 FALSE   3.0
#> 4     1 FALSE   3.0
#> 5    NA FALSE    NA
#> 6     2 FALSE   1.5

# Example with custom configuration
coords_custom <- calculateCoordinates(
  ped = potter,
  personID = "personID",
  momID = "momID",
  dadID = "dadID",
  config = list(
    ped_packed = FALSE,
    ped_width = 20
  )
)