Plot correlation of genetic relatedness by phenotype — ggPhenotypeByDegree • ggpedigree

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.