alignPedigreeWithRelations

This function aligns a pedigree object using relations if provided, or
defaults to the default alignment settings.

internal

Provides plotting functions for visualizing pedigrees and family trees. The package complements a behavior genetics package 'BGmisc' [Garrison et al. (2024) <doi:10.21105/joss.06203>] by rendering pedigrees using the 'ggplot2' framework. Features include support for duplicated individuals, complex mating structures, integration with simulated pedigrees, and layout customization. Due to the impending deprecation of kinship2, version 1.0 incorporates the layout helper functions from kinship2. The pedigree alignment algorithms are adapted from 'kinship2' [Sinnwell et al. (2014) <doi:10.1159/000363105>]. We gratefully acknowledge the original authors: Jason Sinnwell, Terry Therneau, Daniel Schaid, and Elizabeth Atkinson for their foundational work.

S. Mason Garrison

ggpedigree

Visualizing Pedigrees with 'ggplot2' and 'plotly'

alignPedigreeWithRelations function

<dl><dt>ped</dt>
<dd>A data frame containing the pedigree data. Needs personID, momID, dadID, and sex columns.</dd>
<dt>personID</dt>
<dd>Character string specifying the column name for individual IDs. Defaults to "personID".</dd>
<dt>dadID</dt>
<dd>Character string specifying the column name for father IDs. Defaults to "dadID".</dd>
<dt>momID</dt>
<dd>Character string specifying the column name for mother IDs. Defaults to "momID".</dd>
<dt>code_male</dt>
<dd>Value used to indicate male sex. Defaults to NULL.</dd>
<dt>sexVar</dt>
<dd>Character. Name of the column in `ped` for the sex variable.</dd>
<dt>config</dt>
<dd>List of configuration options:<dl>
 <dt>code_male</dt>
<dd>Default is 1. Used by BGmisc::recodeSex().</dd></dl></dd> <dt>ped_packed</dt>
<dd>Logical, default TRUE. Passed to `kinship2_align.pedigree`.</dd> <dt>ped_align</dt>
<dd>Logical, default TRUE. Align generations.</dd> <dt>ped_width</dt>
<dd>Numeric, default 15. Controls spacing.</dd>
</dl>

Arguments

Align pedigree with additional relations — alignPedigreeWithRelations

<dl>

<dt>ped</dt>
<dd>A data frame containing the pedigree data. Needs personID, momID, dadID, and sex columns.</dd>


<dt>personID</dt>
<dd>Character string specifying the column name for individual IDs. Defaults to "personID".</dd>


<dt>dadID</dt>
<dd>Character string specifying the column name for father IDs. Defaults to "dadID".</dd>


<dt>momID</dt>
<dd>Character string specifying the column name for mother IDs. Defaults to "momID".</dd>


<dt>code_male</dt>
<dd>Value used to indicate male sex. Defaults to NULL.</dd>


<dt>sexVar</dt>
<dd>Character. Name of the column in `ped` for the sex variable.</dd>


<dt>config</dt>
<dd>List of configuration options:<dl>
 <dt>code_male</dt>
<dd>Default is 1. Used by BGmisc::recodeSex().</dd>

 <dt>ped_packed</dt>
<dd>Logical, default TRUE. Passed to `kinship2_align.pedigree`.</dd>

 <dt>ped_align</dt>
<dd>Logical, default TRUE. Align generations.</dd>

 <dt>ped_width</dt>
<dd>Numeric, default 15. Controls spacing.</dd>


</dl></dd>

</dl>

alignPedigreeWithRelations: Align pedigree with additional relations

Description

Usage

Value

Arguments