plotClusterTree

Generates a tree plot based on a herachical clustering of the complete distance matrix.

Provides the necessary functions to identify and extract a selection of already available barcode constructs (Cornils, K. et al. (2014) <doi:10.1093/nar/gku081>) and freely choosable barcode designs from next generation sequence (NGS) data. Furthermore, it offers the possibility to account for sequence errors, the calculation of barcode similarities and provides a variety of visualisation tools (Thielecke, L. et al. (2017) <doi:10.1038/srep43249>).

Lars Thielecke

genBaRcode

Analysis and Visualization Tools for Genetic Barcode Data

plotClusterTree function

<dl><dt>BC_dat</dt>
<dd>a BCdat object.</dd>
<dt>tree_est</dt>
<dd>a character string, indicating the particular cluster algorithm, possible algorithms are "Neighbor-Joining" ("NJ") and "Unweighted Pair Group Method" ("UPGMA").</dd>
<dt>type</dt>
<dd>a character string, the graph layout style ("unrooted", "phylogram", "cladogram", "fan", "radial").</dd>
<dt>tipLabel</dt>
<dd>a logical value, indicating the use of labeled tree leaves.</dd>
<dt>m</dt>
<dd>a character string, Method for distance calculation, default value is Hamming distance. Possible values
are "osa", "lv", "dl", "hamming", "lcs", "qgram", "cosine", "jaccard", "jw", "soundex" (see stringdist function
of the stringdist-package for more information).</dd></dl>

Arguments

Plotting a Cluster Tree — plotClusterTree

<dl>

<dt>BC_dat</dt>
<dd>a BCdat object.</dd>


<dt>tree_est</dt>
<dd>a character string, indicating the particular cluster algorithm, possible algorithms are "Neighbor-Joining" ("NJ") and "Unweighted Pair Group Method" ("UPGMA").</dd>


<dt>type</dt>
<dd>a character string, the graph layout style ("unrooted", "phylogram", "cladogram", "fan", "radial").</dd>


<dt>tipLabel</dt>
<dd>a logical value, indicating the use of labeled tree leaves.</dd>


<dt>m</dt>
<dd>a character string, Method for distance calculation, default value is Hamming distance. Possible values
are "osa", "lv", "dl", "hamming", "lcs", "qgram", "cosine", "jaccard", "jw", "soundex" (see stringdist function
of the stringdist-package for more information).</dd>

</dl>

plotClusterTree: Plotting a Cluster Tree

Description

Usage

Arguments