MDSplot

Generate a multidimensional scaling (MDS) plot from genetic distance data.

Analyzing genetic data obtained from pooled samples.
This package can read in Fragment Analysis output files, process the data,
and score peaks, as well as facilitate various analyses, including cluster
analysis, calculation of genetic distances and diversity indices,
as well as bootstrap resampling for statistical inference. Specifically
tailored to handle genetic data efficiently, researchers can explore
population structure, genetic differentiation, and genetic relatedness
among samples. We updated some functions from Covarrubias-Pazaran et al.
(2016) <doi:10.1186/s12863-016-0365-6> to allow for the use of new file formats
and referenced the following to write our genetic analysis functions:
Long et al. (2022) <doi:10.1038/s41598-022-04776-0>, Jost (2008)
<doi:10.1111/j.1365-294x.2008.03887.x>, Nei (1973)
<doi:10.1073/pnas.70.12.3321>, Foulley et al. (2006)
<doi:10.1016/j.livprodsci.2005.10.021>, Chao et al. (2008)
<doi:10.1111/j.1541-0420.2008.01010.x>.

Kathleen Kuesters

pooledpeaks

Genetic Analysis of Pooled Samples

Jeffrey Long

Jessica Blanton

Walter Blank

Jeffrey Kovach

Ronald Blanton

MDSplot function

<dl><dt>distance</dt>
<dd>A matrix containing the genetic distance data.</dd>
<dt>pcs</dt>
<dd>A numeric vector specifying the principal coordinates to plot.</dd>
<dt>PF</dt>
<dd>A factor vector specifying population labels.</dd>
<dt>y</dt>
<dd>A character vector specifying colors for population labels.</dd></dl>

Arguments

Multi Dimensional Scaling (MDS) Plot — MDSplot

<dl>

<dt>distance</dt>
<dd>A matrix containing the genetic distance data.</dd>


<dt>pcs</dt>
<dd>A numeric vector specifying the principal coordinates to plot.</dd>


<dt>PF</dt>
<dd>A factor vector specifying population labels.</dd>


<dt>y</dt>
<dd>A character vector specifying colors for population labels.</dd>

</dl>

MDSplot: Multi Dimensional Scaling (MDS) Plot

Description

Usage

Value

Arguments

Examples