manhattan_plot

<code>manhattan_plot</code> displays a Manhattan plot which represents the p-values 
for each SNP for a particular test statistic.

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

manhattan_plot function

<dl><dt>x</dt>
<dd>an object of class "pcadapt" generated with <code>pcadapt</code> 
containing the p-values of interest.</dd>
<dt>chr.info</dt>
<dd>a list containing the chromosome information for each marker.</dd>
<dt>snp.info</dt>
<dd>a list containing the names of all genetic markers present in
the input.</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>
<dt>K</dt>
<dd>an integer specifying which principal component to display when 
<code>method="componentwise"</code>.</dd></dl>

Arguments

Manhattan Plot — manhattan_plot

<dl>

<dt>x</dt>
<dd>an object of class "pcadapt" generated with <code>pcadapt</code> 
containing the p-values of interest.</dd>


<dt>chr.info</dt>
<dd>a list containing the chromosome information for each marker.</dd>


<dt>snp.info</dt>
<dd>a list containing the names of all genetic markers present in
the input.</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>


<dt>K</dt>
<dd>an integer specifying which principal component to display when 
<code>method="componentwise"</code>.</dd>

</dl>

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manhattan_plot: Manhattan Plot

Description

Usage

Arguments