.preparePhenotypeByDegreeData: Prepare data for ggPhenotypeByDegree This function prepares the data frame for plotting by calculating necessary columns and ensuring required columns are present.

Description

Prepare data for ggPhenotypeByDegree This function prepares the data frame for plotting by calculating necessary columns and ensuring required columns are present.

Usage

.preparePhenotypeByDegreeData(
  df,
  y_var,
  y_se = NULL,
  y_stem_se = NULL,
  y_ci_lb = NULL,
  y_ci_ub = NULL,
  config = list()
)

Value

A modified data frame with additional columns for plotting.

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