addFocalFillColumn: Add Focal Fill Column to Pedigree Data

Description

Adds a `focal_fill` column to the pedigree data based on configuration input. Supports additive, mitochondrial, and line-based modes. If `focal_fill_column` is specified, it takes priority over inferred modes.

Usage

addFocalFillColumn(
  ds_ped,
  config,
  focal_fill_column = NULL,
  famID = "famID",
  matID = "matID",
  patID = "patID",
  personID = "personID",
  fill_group_family = c("famID", "family", "family lineages", "family lines",
    "family line"),
  fill_group_maternal = c("maternal", "matID", "maternal line", "maternal lineages",
    "maternal lines"),
  fill_group_paternal = c("paternal", "patID", "paternal line", "paternal lineages",
    "paternal lines")
)

Value

A data frame with a `focal_fill` column added if applicable.

Arguments

ds_ped

A data frame already processed by `transformPed()`.

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.

focal_fill_column

Character string specifying the column name for focal fill color.

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".

personID

Character string specifying the column name for individual IDs. Defaults to "personID".

fill_group_family

Character vector specifying fill types for family lineage.

fill_group_maternal

Character vector specifying fill types for maternal lineage.

fill_group_paternal

Character vector specifying fill types for paternal lineage.