score_plot

<code>"score_plot"</code> plots the projection of the individuals onto the 
first two principal components.

internal

Methods to detect genetic markers involved in biological
adaptation. 'pcadapt' provides statistical tools for outlier detection based on
Principal Component Analysis. Implements the method described in (Luu, 2016)
<DOI:10.1111/1755-0998.12592> and later revised in (Privé, 2020)
<DOI:10.1093/molbev/msaa053>.

Florian Privé

pcadapt

Fast Principal Component Analysis for Outlier Detection

Keurcien Luu

Michael Blum

Eric Bazin

Nicolas Duforet-Frebourg

score_plot function

<dl><dt>x</dt>
<dd>an output from <code>pcadapt</code> containing the scores.</dd>
<dt>i</dt>
<dd>an integer indicating onto which principal component the individuals
 are projected when the "scores" option is chosen.
Default value is set to <code>1</code>.</dd>
<dt>j</dt>
<dd>an integer indicating onto which principal component the individuals 
are projected when the "scores" option is chosen.
Default value is set to <code>2</code>.</dd>
<dt>pop</dt>
<dd>a list of integers or strings specifying which subpopulation the 
individuals belong to.</dd>
<dt>plt.pkg</dt>
<dd>a character string specifying the package to be used to 
display the graphical outputs. Use <code>"plotly"</code> for interactive plots, or 
<code>"ggplot"</code> for static plots.</dd></dl>

Arguments

Principal Components Analysis Scores Plot — score_plot

<dl>

<dt>x</dt>
<dd>an output from <code>pcadapt</code> containing the scores.</dd>


<dt>i</dt>
<dd>an integer indicating onto which principal component the individuals
 are projected when the "scores" option is chosen.
Default value is set to <code>1</code>.</dd>


<dt>j</dt>
<dd>an integer indicating onto which principal component the individuals 
are projected when the "scores" option is chosen.
Default value is set to <code>2</code>.</dd>


<dt>pop</dt>
<dd>a list of integers or strings specifying which subpopulation the 
individuals belong to.</dd>


<dt>plt.pkg</dt>
<dd>a character string specifying the package to be used to 
display the graphical outputs. Use <code>"plotly"</code> for interactive plots, or 
<code>"ggplot"</code> for static plots.</dd>

</dl>

score_plot: Principal Components Analysis Scores Plot

Description

Usage

Arguments