ggPedigree.core: Core Function for ggPedigree

Description

This function is the core implementation of the ggPedigree function. It handles the data preparation, layout calculation, and plotting of the pedigree diagram. It is not intended to be called directly by users.

Usage

ggPedigree.core(
  ped,
  famID = "famID",
  personID = "personID",
  momID = "momID",
  dadID = "dadID",
  spouseID = "spouseID",
  matID = "matID",
  patID = "patID",
  twinID = "twinID",
  focal_fill_column = NULL,
  overlay_column = NULL,
  status_column = NULL,
  config = list(),
  debug = FALSE,
  hints = NULL,
  function_name = "ggPedigree",
  phantoms = FALSE,
  ...
)

Arguments

ped

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

famID

Character string specifying the column name for family IDs. Defaults to "famID".

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 string specifying the column name for spouse IDs. Defaults to "spouseID".

matID

Character string specifying the column name for maternal lines Defaults to "matID".

patID

Character string specifying the column name for paternal lines Defaults to "patID".

twinID

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

focal_fill_column

Character string specifying the column name for focal fill color.

overlay_column

Character string specifying the column name for overlay alpha values.

status_column

Character string specifying the column name for affected status. Defaults to NULL.

config

A list of configuration options for customizing the plot. See getDefaultPlotConfig for details. The list can include:

code_male: Integer or string. Value identifying males in the sex column. (typically 0 or 1) Default: 1.

segment_spouse_color, segment_self_color

Character. Line colors for respective connection types.

segment_sibling_color, segment_parent_color, segment_offspring_color

Character. Line colors for respective connection types.

label_text_size, point_size, segment_linewidth

Numeric. Controls text size, point size, and line thickness.

generation_height

Numeric. Vertical spacing multiplier between generations. Default: 1.

shape_unknown, shape_female, shape_male, status_shape_affected

Integers. Shape codes for plotting each group.

sex_shape_labels

Character vector of labels for the sex variable. (default: c("Female", "Male", "Unknown"))

unaffected, affected

Values indicating unaffected/affected status.

sex_color_include

Logical. If TRUE, uses color to differentiate sex.

label_max_overlaps

Maximum number of overlaps allowed in repelled labels.

label_segment_color

Color used for label connector lines.

debug

Logical. If TRUE, prints debugging information. Default: FALSE.

hints

Data frame with hints for layout adjustments. Default: NULL.

phantoms

Logical. If TRUE, adds phantom parents for individuals without parents.

...

Additional arguments passed to `ggplot2` functions.