plotReadFrequencies

Generates a barplot visualising the abundances of unique read count frequencies.

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

plotReadFrequencies function

<dl><dt>BC_dat</dt>
<dd>a BCdat object.</dd>
<dt>b</dt>
<dd>an integer value, defining the number of bins. Overridden by bw. Defaults to 30. (see `?ggplot2::geom_histogram`)</dd>
<dt>bw</dt>
<dd>an integer value, defining the width of the bins.</dd>
<dt>show_it</dt>
<dd>a logical vaue. If TRUE, the respective values are printed on the console?</dd>
<dt>log</dt>
<dd>a logical vaue. If TRUE, the y-axis will be on a log scale.</dd>
<dt>dens</dt>
<dd>a logical vaue. If TRUE, the density of the read frequencies will be plotted.</dd></dl>

Arguments

Plotting a Barplot — plotReadFrequencies

<dl>

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


<dt>b</dt>
<dd>an integer value, defining the number of bins. Overridden by bw. Defaults to 30. (see `?ggplot2::geom_histogram`)</dd>


<dt>bw</dt>
<dd>an integer value, defining the width of the bins.</dd>


<dt>show_it</dt>
<dd>a logical vaue. If TRUE, the respective values are printed on the console?</dd>


<dt>log</dt>
<dd>a logical vaue. If TRUE, the y-axis will be on a log scale.</dd>


<dt>dens</dt>
<dd>a logical vaue. If TRUE, the density of the read frequencies will be plotted.</dd>

</dl>

plotReadFrequencies: Plotting a Barplot

Description

Usage

Value

Arguments