generateKirchenplot

Generates a barplot based on read counts. If <code>ori_BCs</code> is provided the bar color reflects the
distance between a particular barcode to one of the provided barcode sequences.

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

generateKirchenplot function

<dl><dt>BC_dat</dt>
<dd>a BCdat object.</dd>
<dt>ori_BCs</dt>
<dd>a vector of character strings containing known barcode sequences (without the fixed positions of the barcode construct).</dd>
<dt>ori_BCs2</dt>
<dd>a vector of character strings containing a 2nd set of known barcode sequences (also without the fixed positions).</dd>
<dt>loga</dt>
<dd>a logical value, indicating the use or non-use of logarithmic read count values.</dd>
<dt>col_type</dt>
<dd>character string, choosing one of the availabe color palettes ("rainbow", "heat.colors", "topo.colors", "greens", "wild" - see package "grDevices")</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). If neither `ori_BCs` nor `ori_BCs2` are provided with input the choice of `m` does not matter.</dd>
<dt>setLabels</dt>
<dd>a character vector, containing three strings serving as plot labels.</dd></dl>

Arguments

Plotting a Kirchenplot — generateKirchenplot

<dl>

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


<dt>ori_BCs</dt>
<dd>a vector of character strings containing known barcode sequences (without the fixed positions of the barcode construct).</dd>


<dt>ori_BCs2</dt>
<dd>a vector of character strings containing a 2nd set of known barcode sequences (also without the fixed positions).</dd>


<dt>loga</dt>
<dd>a logical value, indicating the use or non-use of logarithmic read count values.</dd>


<dt>col_type</dt>
<dd>character string, choosing one of the availabe color palettes ("rainbow", "heat.colors", "topo.colors", "greens", "wild" - see package "grDevices")</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). If neither `ori_BCs` nor `ori_BCs2` are provided with input the choice of `m` does not matter.</dd>


<dt>setLabels</dt>
<dd>a character vector, containing three strings serving as plot labels.</dd>

</dl>

generateKirchenplot: Plotting a Kirchenplot

Description

Usage

Value

Arguments