LLRplot

Plot LLR(rely/U) against LLR(relx/U), for one combination of
 relationships, colour coded by fcl &amp; top.

internal

Multi-generational pedigree inference from incomplete data on
hundreds of SNPs, including parentage assignment and sibship clustering.
See Huisman (2017) (<DOI:10.1111/1755-0998.12665>) for more information.

Jisca Huisman

sequoia

Pedigree Inference from SNPs

LLRplot function

<dl><dt>relx</dt>
<dd>relationship to plot on the x-axis. One of 'PO', 'FS', 'HS',
'GP', 'FA', or 'HA'.</dd>
<dt>rely</dt>
<dd>relationship to plot on the y-axis; as <code>relx</code>.</dd>
<dt>LLRU</dt>
<dd>matrix with log10-likelihoods, already scaled by LL(U) for each
pair.</dd>
<dt>fcl</dt>
<dd>focal relationship, sets outer circle colour of points.</dd>
<dt>top</dt>
<dd>most likely relationship, sets inner filling colour of points.</dd>
<dt>RelCol</dt>
<dd>named character vector with colours to use per relationship.</dd>
<dt>bgcol</dt>
<dd>do background colour TRUE/FALSE.</dd>
<dt>Tassign</dt>
<dd>assignment threshold, shown as grey square in bottom-left
corner and band along the diagonal.</dd>
<dt>Tfilter</dt>
<dd>filter threshold, shown as dark grey square in bottom-left.</dd></dl>

Arguments

Scatter Plot of Pair LLRs — LLRplot

<dl>

<dt>relx</dt>
<dd>relationship to plot on the x-axis. One of 'PO', 'FS', 'HS',
'GP', 'FA', or 'HA'.</dd>


<dt>rely</dt>
<dd>relationship to plot on the y-axis; as <code>relx</code>.</dd>


<dt>LLRU</dt>
<dd>matrix with log10-likelihoods, already scaled by LL(U) for each
pair.</dd>


<dt>fcl</dt>
<dd>focal relationship, sets outer circle colour of points.</dd>


<dt>top</dt>
<dd>most likely relationship, sets inner filling colour of points.</dd>


<dt>RelCol</dt>
<dd>named character vector with colours to use per relationship.</dd>


<dt>bgcol</dt>
<dd>do background colour TRUE/FALSE.</dd>


<dt>Tassign</dt>
<dd>assignment threshold, shown as grey square in bottom-left
corner and band along the diagonal.</dd>


<dt>Tfilter</dt>
<dd>filter threshold, shown as dark grey square in bottom-left.</dd>

</dl>

LLRplot: Scatter Plot of Pair LLRs

Description

Usage

Arguments

Details