.addAnnotate

Add annotates to ggplot Pedigree Plot

internal

Provides plotting functions for visualizing pedigrees in behavior genetics and kinship research. The package complements 'BGmisc' [Garrison et al. (2024) <doi:10.21105/joss.06203>] by rendering pedigrees using the 'ggplot2' framework and offers a modern alternative to the base-graphics pedigree plot in 'kinship2' [Sinnwell et al. (2014) <doi:10.1159/000363105>]. Features include support for duplicated individuals, complex mating structures, integration with simulated pedigrees, and layout customization.

S. Mason Garrison

ggpedigree

Visualizing Pedigrees with 'ggplot2' and 'plotly'

.addAnnotate function

<dl><dt>config</dt>
<dd>A list of configuration overrides. Valid entries include:<dl>
 <dt>filter_n_pairs</dt>
<dd>Minimum number of pairs to include (default: 500)</dd></dl></dd> <dt>filter_degree_min</dt>
<dd>Minimum degree of relatedness (default: 0)</dd> <dt>filter_degree_max</dt>
<dd>Maximum degree of relatedness (default: 7)</dd> <dt>plot_title</dt>
<dd>Plot title</dd> <dt>plot_subtitle</dt>
<dd>Plot subtitle</dd> <dt>color_scale</dt>
<dd>Paletteer color scale name (e.g., "ggthemes::calc")</dd> <dt>use_only_classic_kin</dt>
<dd>If TRUE, only classic kin are shown</dd> <dt>group_by_kin</dt>
<dd>If TRUE, use classic kin × mtDNA for grouping</dd> <dt>drop_classic_kin</dt>
<dd>If TRUE, remove classic kin rows</dd> <dt>drop_non_classic_sibs</dt>
<dd>If TRUE, remove non-classic sibs (default: TRUE)</dd> <dt>annotate_include</dt>
<dd>If TRUE, annotate mother/father/sibling points</dd> <dt>annotate_x_shift</dt>
<dd>Relative x-axis shift for annotations</dd> <dt>annotate_y_shift</dt>
<dd>Relative y-axis shift for annotations</dd> <dt>point_size</dt>
<dd>Size of geom_point points (default: 1)</dd> <dt>use_relative_degree</dt>
<dd>If TRUE, x-axis uses degree-of-relatedness scaling</dd> <dt>grouping_column</dt>
<dd>Grouping column name (default: mtdna_factor)</dd> <dt>value_rounding_digits</dt>
<dd>Number of decimal places for rounding (default: 2)</dd> <dt>match_threshold_percent</dt>
<dd>Tolerance % for matching known degrees</dd> <dt>max_degree_levels</dt>
<dd>Maximum number of degrees to consider</dd>
</dl>

Arguments

Add annotates to ggplot Pedigree Plot — .addAnnotate

<dl>

<dt>config</dt>
<dd>A list of configuration overrides. Valid entries include:<dl>
 <dt>filter_n_pairs</dt>
<dd>Minimum number of pairs to include (default: 500)</dd>

 <dt>filter_degree_min</dt>
<dd>Minimum degree of relatedness (default: 0)</dd>

 <dt>filter_degree_max</dt>
<dd>Maximum degree of relatedness (default: 7)</dd>

 <dt>plot_title</dt>
<dd>Plot title</dd>

 <dt>plot_subtitle</dt>
<dd>Plot subtitle</dd>

 <dt>color_scale</dt>
<dd>Paletteer color scale name (e.g., "ggthemes::calc")</dd>

 <dt>use_only_classic_kin</dt>
<dd>If TRUE, only classic kin are shown</dd>

 <dt>group_by_kin</dt>
<dd>If TRUE, use classic kin × mtDNA for grouping</dd>

 <dt>drop_classic_kin</dt>
<dd>If TRUE, remove classic kin rows</dd>

 <dt>drop_non_classic_sibs</dt>
<dd>If TRUE, remove non-classic sibs (default: TRUE)</dd>

 <dt>annotate_include</dt>
<dd>If TRUE, annotate mother/father/sibling points</dd>

 <dt>annotate_x_shift</dt>
<dd>Relative x-axis shift for annotations</dd>

 <dt>annotate_y_shift</dt>
<dd>Relative y-axis shift for annotations</dd>

 <dt>point_size</dt>
<dd>Size of geom_point points (default: 1)</dd>

 <dt>use_relative_degree</dt>
<dd>If TRUE, x-axis uses degree-of-relatedness scaling</dd>

 <dt>grouping_column</dt>
<dd>Grouping column name (default: mtdna_factor)</dd>

 <dt>value_rounding_digits</dt>
<dd>Number of decimal places for rounding (default: 2)</dd>

 <dt>match_threshold_percent</dt>
<dd>Tolerance % for matching known degrees</dd>

 <dt>max_degree_levels</dt>
<dd>Maximum number of degrees to consider</dd>


</dl></dd>

</dl>

.addAnnotate: Add annotates to ggplot Pedigree Plot

Description

Usage

Value

Arguments