plotProActiveResults

Plot read coverage of contigs/chunks with detected gaps and elevations and their
associated pattern-match.

Automate the detection of gaps and elevations in mapped sequencing
read coverage using a 2D pattern-matching algorithm. 'ProActive' detects, characterizes
and visualizes read coverage patterns in both genomes and metagenomes. Optionally,
users may provide gene annotations associated with their genome or metagenome
in the form of a .gff file. In this case, 'ProActive' will generate an additional
output table containing the gene annotations found within the detected regions of gapped
and elevated read coverage. Additionally, users can search for gene
annotations of interest in the output read coverage plots.

Jessie Maier

ProActive

Detect Elevations and Gaps in Mapped Sequencing Read Coverage

Manuel Kleiner

plotProActiveResults function

<dl><dt>pileup</dt>
<dd>A .txt file containing mapped sequencing read coverages averaged over
100 bp windows/bins.</dd>
<dt>ProActiveResults</dt>
<dd>The output from `ProActive()`.</dd>
<dt>elevFilter</dt>
<dd>Optional, only plot results with pattern-matches that achieved an
elevation ratio (max/min) greater than the specified values. Default is no filter.</dd>
<dt>saveFilesTo</dt>
<dd>Optional, Provide a path to the directory you wish to save
output to. A folder will be made within the provided directory to store
results.</dd></dl>

Arguments

Plot results of `ProActive()` pattern-matching — plotProActiveResults

<dl>

<dt>pileup</dt>
<dd>A .txt file containing mapped sequencing read coverages averaged over
100 bp windows/bins.</dd>


<dt>ProActiveResults</dt>
<dd>The output from `ProActive()`.</dd>


<dt>elevFilter</dt>
<dd>Optional, only plot results with pattern-matches that achieved an
elevation ratio (max/min) greater than the specified values. Default is no filter.</dd>


<dt>saveFilesTo</dt>
<dd>Optional, Provide a path to the directory you wish to save
output to. A folder will be made within the provided directory to store
results.</dd>

</dl>

plotProActiveResults: Plot results of `ProActive()` pattern-matching

Description

Usage

Value

Arguments

Examples