ggPedigree {ggpedigree} | R Documentation |
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,
...
)
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:
|
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. |
Value
A 'ggplot' object rendering the pedigree diagram.
Examples
library(BGmisc)
data("potter")
ggPedigree(potter, famID = "famID", personID = "personID")
data("hazard")
ggPedigree(hazard, famID = "famID", personID = "ID", config = list(code_male = 0))