ggpedigree (version 0.8.0)

ggPedigree: Plot a custom pedigree diagram

Description

Generates a ggplot2-based diagram of a pedigree using custom coordinate layout, calculated relationship connections, and flexible styling via `config`. It processes the data using `ped2fam()`. This function supports multiple families and optionally displays affected status and sex-based color/shape.

Usage

ggPedigree(
  ped,
  famID = "famID",
  personID = "personID",
  momID = "momID",
  dadID = "dadID",
  spouseID = "spouseID",
  matID = "matID",
  patID = "patID",
  twinID = "twinID",
  status_column = NULL,
  focal_fill_column = NULL,
  tooltip_columns = NULL,
  overlay_column = NULL,
  return_widget = FALSE,
  config = list(),
  debug = FALSE,
  hints = NULL,
  interactive = FALSE,
  phantoms = FALSE,
  ...
)
ggpedigree(
  ped,
  famID = "famID",
  personID = "personID",
  momID = "momID",
  dadID = "dadID",
  spouseID = "spouseID",
  matID = "matID",
  patID = "patID",
  twinID = "twinID",
  status_column = NULL,
  focal_fill_column = NULL,
  tooltip_columns = NULL,
  overlay_column = NULL,
  return_widget = FALSE,
  config = list(),
  debug = FALSE,
  hints = NULL,
  interactive = FALSE,
  phantoms = FALSE,
  ...
)

Value

A `ggplot` object rendering the pedigree diagram.

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".

spouseID

Character string specifying the column name for spouse IDs. Defaults to "spouseID".

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".

twinID

Character string specifying the column name for twin IDs. Defaults to "twinID".

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.

tooltip_columns

Character vector of column names to show when hovering. Defaults to c("personID", "sex"). Additional columns present in `ped` can be supplied – they will be added to the Plotly tooltip text. Defaults to NULL, which uses the default tooltip columns.

overlay_column

Character string specifying the column name for overlay alpha values.

return_widget

Logical; if TRUE (default) returns a plotly htmlwidget. If FALSE, returns the underlying plotly object (useful for further customization before printing).

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.

debug

Logical. If TRUE, prints debugging information. Default: FALSE.

hints

Data frame with hints for layout adjustments. Default: NULL.

interactive

Logical. If TRUE, generates an interactive plot using `plotly`. Default: FALSE.

phantoms

Logical. If TRUE, adds phantom parents for individuals without parents.

...

Additional arguments passed to `ggplot2` functions.

Examples

library(BGmisc)
data("potter")
ggPedigree(potter, famID = "famID", personID = "personID")

data("hazard")
ggPedigree(hazard, famID = "famID", personID = "ID", config = list(code_male = 0))