recodeMissingIDs: 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()
)

Value

A data frame with missing IDs recoded to NA.

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.