dot-preparePhenotypeByDegreeData: Prepare data for ggPhenotypeByDegree This function prepares...
In ggpedigree: Visualizing Pedigrees with 'ggplot2' and 'plotly'

.preparePhenotypeByDegreeData

R Documentation

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()
)

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

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