recodeMissingIDs: Recode Missing IDs in Pedigree Data
In ggpedigree: Visualizing Pedigrees with 'ggplot2' and 'plotly'

recodeMissingIDs

R Documentation

Recode Missing IDs in Pedigree Data

Description

This function recodes missing IDs in the pedigree data frame to NA. It checks for specified missing codes (both numeric and character) in their respective columns.

Usage

recodeMissingIDs(
  ped,
  momID = "momID",
  dadID = "dadID",
  personID = "personID",
  famID = "famID",
  matID = "matID",
  patID = "patID",
  missing_code_numeric = 0,
  missing_code_character = c("0", "NA", "na", ""),
  config = list()
)

Arguments

`ped`	A data frame containing the pedigree data. Needs personID, momID, dadID, and sex columns.
`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".
`personID`	Character string specifying the column name for individual IDs. Defaults to "personID".
`famID`	Character string specifying the column name for family IDs. Defaults to "famID".
`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".
`missing_code_numeric`	Numeric code representing missing IDs (default is 0).
`missing_code_character`	Character vector representing missing IDs (default is c("0", "NA", "na", "")).
`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.