transformPed: Process Pedigree Data
In ggpedigree: Visualizing Pedigrees with 'ggplot2' and 'plotly'

transformPed

R Documentation

Process Pedigree Data

Description

This function processes the pedigree data frame to ensure it is in the correct format for ggPedigree. It checks for the presence of family, paternal, and maternal IDs, and fills in missing components based on the configuration.

Usage

transformPed(
  ped,
  famID = "famID",
  personID = "personID",
  momID = "momID",
  dadID = "dadID",
  matID = "matID",
  patID = "patID",
  config = list(focal_fill_include = TRUE, focal_fill_component = "maternal"),
  fill_group_paternal = c("paternal", "patID", "paternal line", "paternal lineages",
    "paternal lines"),
  fill_group_maternal = c("maternal", "matID", "maternal line", "maternal lineages",
    "maternal lines")
)

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".
`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".
`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.
`fill_group_paternal`	A character vector specifying which paternal components to fill.
`fill_group_maternal`	A character vector specifying which maternal components to fill.