ggPhenotypeByDegree: 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,
  ...
)

Value

A ggplot object containing the correlation plot.

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.