preparePedigreeData: Prepare Pedigree Data
In ggpedigree: Visualizing Pedigrees with 'ggplot2' and 'plotly'

preparePedigreeData

R Documentation

Prepare Pedigree Data

Description

This function checks and prepares the pedigree data frame for use in ggPedigree.

Usage

preparePedigreeData(
  ped,
  famID = "famID",
  personID = "personID",
  momID = "momID",
  dadID = "dadID",
  matID = "matID",
  patID = "patID",
  config = list(focal_fill_include = TRUE, focal_fill_component = "maternal",
    recode_missing_ids = TRUE, add_phantoms = FALSE, code_male = "M", code_female = "F",
    code_na = NA),
  fill_group_paternal = c("paternal", "patID", "paternal line", "paternal lineages",
    "paternal lines"),
  fill_group_maternal = c("maternal", "matID", "maternal line", "maternal lineages",
    "maternal lines"),
  fill_group_family = c("family", "famID", "family line", "family lineages",
    "family lines"),
  status_column = NULL,
  focal_fill_column = NULL,
  sexVar = "sex"
)

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".
`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 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.
`fill_group_paternal`	A character vector specifying which paternal components to fill.
`fill_group_maternal`	A character vector specifying which maternal components to fill.
`fill_group_family`	A character vector specifying the family fill group names.
`status_column`	Character string specifying the column name for affected status. Defaults to NULL.
`focal_fill_column`	Character string specifying the column name for focal fill color.
`sexVar`	Character string specifying the column name for sex. Defaults to "sex".