ggPedigree.core: Core Function for ggPedigree
In ggpedigree: Visualizing Pedigrees with 'ggplot2' and 'plotly'

ggPedigree.core

R Documentation

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,
  overlays = NULL,
  status_column = NULL,
  code_male = NULL,
  config = list(),
  debug = FALSE,
  hints = NULL,
  sexVar = "sex",
  function_name = "ggPedigree",
  affected_fill_column = NULL,
  outline_color_column = NULL
)

Arguments

`ped`	A data frame containing the pedigree data. Needs personID, momID, dadID, and sex 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. For a single overlay, this is the simplest interface. For multiple overlays, use the `overlays` parameter instead.
`overlays`	A list of overlay specifications for adding multiple independent overlay layers. Each element should be a list with at minimum a `column` entry, plus optional entries: `code_affected`, `shape`, `color`, `size`, `stroke`, `mode`. Unspecified entries inherit from the `overlay_*` config defaults. When `overlays` is provided, `overlay_column` is ignored. Example: `overlays = list(list(column = "DECES", shape = "cross"), list(column = "PROBAND", shape = 8, color = "red"))`
`status_column`	Character string specifying the column name for affected status. Defaults to NULL.
`code_male`	Integer or string. Value identifying males in the sex column. (typically 0 or 1) Default: 1
`config`	A list of configuration options for customizing the plot. See getDefaultPlotConfig for details of each option. 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.
`sexVar`	Character string specifying the column name for sex. Defaults to "sex".
`affected_fill_column`	Character string specifying the column name for conditional affected fill. When provided, individuals matching the 'affected_fill_code_affected' config will have their symbols filled. Default is NULL.
`outline_color_column`	Character string specifying the column name for outline color control. When provided, individuals matching 'outline_color_code_affected' config will have colored outlines (e.g., blue for included). Default is NULL.