ggPhenotypeByDegree: Plot correlation of genetic relatedness by phenotype

In ggpedigree: Visualizing Pedigrees with 'ggplot2' and 'plotly'

Plot correlation of genetic relatedness by phenotype

Description

This function plots the phenotypic correlation as a function of genetic relatedness.

Usage

ggPhenotypeByDegree(
  df,
  y_var,
  y_se = NULL,
  y_stem_se = NULL,
  y_ci_lb = NULL,
  y_ci_ub = NULL,
  config = list(),
  data_prep = TRUE,
  ...
)

Arguments

df	Data frame containing pairwise summary statistics. Required columns: addRel_min Minimum relatedness per group addRel_max Maximum relatedness per group n_pairs Number of pairs at that relatedness cnu Indicator for shared nuclear environment (1 = yes, 0 = no) mtdna Indicator for shared mitochondrial DNA (1 = yes, 0 = no)
y_var	Name of the y-axis variable column (e.g., "r_pheno_rho").
y_se	Name of the standard error column (e.g., "r_pheno_se").
y_stem_se	Optional; base stem used to construct SE ribbon bounds. (e.g., "r_pheno")
y_ci_lb	Optional; lower bound for confidence interval (e.g., "r_pheno_ci_lb").
y_ci_ub	Optional; upper bound for confidence interval (e.g., "r_pheno_ci_ub").
config	A list of configuration overrides. Valid entries include: filter_n_pairs Minimum number of pairs to include (default: 500) filter_degree_min Minimum degree of relatedness (default: 0) filter_degree_max Maximum degree of relatedness (default: 7) plot_title Plot title plot_subtitle Plot subtitle color_scale Paletteer color scale name (e.g., "ggthemes::calc") use_only_classic_kin If TRUE, only classic kin are shown group_by_kin If TRUE, use classic kin × mtDNA for grouping drop_classic_kin If TRUE, remove classic kin rows drop_non_classic_sibs If TRUE, remove non-classic sibs (default: TRUE) annotate_include If TRUE, annotate mother/father/sibling points annotate_x_shift Relative x-axis shift for annotations annotate_y_shift Relative y-axis shift for annotations point_size Size of geom_point points (default: 1) use_relative_degree If TRUE, x-axis uses degree-of-relatedness scaling grouping_column Grouping column name (default: mtdna_factor) value_rounding_digits Number of decimal places for rounding (default: 2) match_threshold_percent Tolerance % for matching known degrees max_degree_levels Maximum number of degrees to consider
data_prep	Logical; if TRUE, performs data preparation steps.
...	Additional arguments passed to 'ggplot2' functions.

Value

A ggplot object containing the correlation plot.

ggpedigree documentation built on Sept. 13, 2025, 1:08 a.m.