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<div id="content">
<h1 class="title">Some utilities for visualization of RepeatExplorer output</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org2c08df2">1. Requirements</a></li>
<li><a href="#org36d88a4">2. Visualization of comparative clustering</a>
<ul>
<li><a href="#org93bce99">2.1. Visualization examples:</a>
<ul>
<li><a href="#orgba14f34">2.1.1. Example 1</a></li>
<li><a href="#org9596a2d">2.1.2. Example 2</a></li>
<li><a href="#org89300ae">2.1.3. Example 3</a></li>
</ul>
</li>
<li><a href="#org3e3de47">2.2. Complete command line options:</a></li>
</ul>
</li>
</ul>
</div>
</div>
<p>
Utilities for visualization of RepeatExplorer2 outputs
</p>
<div id="outline-container-org2c08df2" class="outline-2">
<h2 id="org2c08df2"><span class="section-number-2">1</span> Requirements</h2>
<div class="outline-text-2" id="text-1">
<ul class="org-ul">
<li>R programming environment with optparse package is required. In Ubuntu based distribution this can be installed using:</li>
</ul>
<div class="org-src-container">
<pre class="src src-bash">sudo apt-get install r-base-core r-cran-optparse
</pre>
</div>
</div>
</div>
<div id="outline-container-org36d88a4" class="outline-2">
<h2 id="org36d88a4"><span class="section-number-2">2</span> Visualization of comparative clustering</h2>
<div class="outline-text-2" id="text-2">
<p>
Visualization can be created with script <code>plot_comparative_clustering_summary.R</code>
using two output files from RepeatExplorer pipeline:
</p>
<p>
File <code>CLUSTER_TABLE.csv</code> contains automatic annotation, information about
cluster sizes and the total number of reads used for analysis:
</p>
<p>
Example of <code>CLUSTER_TABLE.csv</code>:
</p>
<pre class="example">
"Number_of_reads_in_clusters" 3002
"Number_of_clusters" 895
"Number_of_superclusters" 895
"Number_of_singlets" 6998
"Number_of_analyzed_reads" 10000
"Cluster" "Supercluster" "Size" "Size_adjusted" "Automatic_annotation" "TAREAN_classification" "Final_annotation"
1 1 61 61 "All" "Other"
2 2 59 59 "All/repeat/satellite" "Putative satellites (high confidence)"
3 3 45 45 "All/repeat/satellite" "Putative satellites (low confidence)"
4 4 38 38 "All" "Other"
5 5 32 32 "All" "Other"
6 6 28 28 "All" "Other"
7 7 25 25 "All" "Other"
8 8 24 24 "All" "Other"
9 9 23 23 "All" "Other"
10 10 22 22 "All/repeat/mobile_element/Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre" "Other"
11 11 20 20 "All" "Other"
12 12 20 20 "All" "Other"
</pre>
<p>
In the output file from RepeatExplorer pipeline, the last column
<code>Final_annotation</code> is empty - <b>this column is supposed to be completed manually</b>! Visualization is created based on the <code>Final_annotation</code> column. If the
data in <code>Final_annotation</code> is missing <code>Automatic_annotation</code> column is used instead.
</p>
<p>
Species specific composition of clusters is provided in tab delimited file <code>COMPARATIVE_ANALYSIS_COUNTS.csv</code> file:
</p>
<pre class="example">
# Total counts: 2544 2522 2494 2440
#
"cluster" "supercluster" "LAS" "PFL" "PST" "VML"
1 1 61 0 0 0
2 2 0 23 36 0
3 3 45 0 0 0
4 4 0 0 0 38
5 5 32 0 0 0
6 6 0 13 15 0
...
</pre>
</div>
<div id="outline-container-org93bce99" class="outline-3">
<h3 id="org93bce99"><span class="section-number-3">2.1</span> Visualization examples:</h3>
<div class="outline-text-3" id="text-2-1">
</div>
<div id="outline-container-orgba14f34" class="outline-4">
<h4 id="orgba14f34"><span class="section-number-4">2.1.1</span> Example 1</h4>
<div class="outline-text-4" id="text-2-1-1">
<p>
Simple visualization without genome size normalization:
</p>
<div class="org-src-container">
<pre class="src src-bash">./plot_comparative_clustering_summary.R <span style="color: #008000;">\</span>
--cluster_table=example_data/example_1_CLUSTER_TABLE.csv <span style="color: #008000;">\</span>
--comparative_counts=example_data/example_1_COMPARATIVE_ANALYSIS_COUNTS.csv <span style="color: #008000;">\</span>
--output=figs/example1.pdf
</pre>
</div>
<div class="figure">
<p><img src="./figs/example1.png" alt="example1.png" />
</p>
</div>
<p>
Blocks show the proportion of species within the clusters. Barplot shows the
total cluster sizes. By default, maximum 10 most abundant annotated categories are colored and
shown on legend. The number of colored categories can be specified by option
<code>-N</code>, maximum number of colors is 20.
</p>
</div>
</div>
<div id="outline-container-org9596a2d" class="outline-4">
<h4 id="org9596a2d"><span class="section-number-4">2.1.2</span> Example 2</h4>
<div class="outline-text-4" id="text-2-1-2">
<p>
It is possible to create visualization based on the nuclear genomic sequences only.
Two images below show the visualization with and without organele and
contaminated clusters (using option <code>-n</code>).
</p>
<div class="org-src-container">
<pre class="src src-bash"><span style="color: #8D8D84;"># </span><span style="color: #8D8D84; font-style: italic;">organel and contamination included</span>
./plot_comparative_clustering_summary.R <span style="color: #008000;">\</span>
--cluster_table=example_data/example_2_CLUSTER_TABLE.csv <span style="color: #008000;">\</span>
--comparative_counts=example_data/example_2_COMPARATIVE_ANALYSIS_COUNTS.csv <span style="color: #008000;">\</span>
--number_of_colors <span style="color: #D0372D;">10</span> <span style="color: #008000;">\</span>
--output=figs/example_with_contamination.pdf
<span style="color: #8D8D84;"># </span><span style="color: #8D8D84; font-style: italic;">clusters containing organelle and contamination were removed (option -n)</span>
./plot_comparative_clustering_summary.R <span style="color: #008000;">\</span>
--cluster_table=example_data/example_2_CLUSTER_TABLE.csv <span style="color: #008000;">\</span>
--comparative_counts=example_data/example_2_COMPARATIVE_ANALYSIS_COUNTS.csv <span style="color: #008000;">\</span>
--number_of_colors <span style="color: #D0372D;">10</span> -n <span style="color: #008000;">\</span>
--output=figs/example_nuclear_only.pdf
</pre>
</div>
<p>
The clusters with plastid are included:
<img src="./figs/example_with_contamination.png" alt="example_with_contamination.png" />
</p>
<p>
The clusters annotated as plastid are removed:
<img src="./figs/example_nuclear_only.png" alt="example_nuclear_only.png" />
</p>
</div>
</div>
<div id="outline-container-org89300ae" class="outline-4">
<h4 id="org89300ae"><span class="section-number-4">2.1.3</span> Example 3</h4>
<div class="outline-text-4" id="text-2-1-3">
<p>
If you want to visualize genomic abundances of repetitive sequences, you must
provide also tab delimited file with genome sizes of analyzed species in the
folowing format:
</p>
<pre class="example">
VCR 2.9
VVL 2.04
VGR 3.78
</pre>
<p>
Example command to visualize genomic abundances, option <code>-g</code> is used to specify
file with genome sizes:
</p>
<div class="org-src-container">
<pre class="src src-bash">./plot_comparative_clustering_summary.R <span style="color: #008000;">\</span>
--cluster_table=example_data/example_2_CLUSTER_TABLE.csv <span style="color: #008000;">\</span>
--comparative_counts=example_data/example_2_COMPARATIVE_ANALYSIS_COUNTS.csv <span style="color: #008000;">\</span>
--number_of_colors <span style="color: #D0372D;">10</span> -g example_data/example_2_GS.csv <span style="color: #008000;">\</span>
--output=figs/example_genomic_abundances.pdf
</pre>
</div>
<p>
Note that if option <code>-g</code> is used, non-nuclear sequences are always removed.
</p>
<div class="figure">
<p><img src="./figs/example_genomic_abundances.png" alt="example_genomic_abundances.png" />
</p>
</div>
<p>
Size of block is directly proportional to the amount of repeat in nuclear DNA. When genome sizes are provided, scale legend is then included in the output.
</p>
</div>
</div>
</div>
<div id="outline-container-org3e3de47" class="outline-3">
<h3 id="org3e3de47"><span class="section-number-3">2.2</span> Complete command line options:</h3>
<div class="outline-text-3" id="text-2-2">
<div class="org-src-container">
<pre class="src src-bash">Usage: ./plot_comparative_clustering_summary.R <span style="color: #707183;">[</span>options<span style="color: #707183;">]</span>
Options:
-c CLUSTER_TABLE, --cluster_table=CLUSTER_TABLE
file from RepeatExplorer2 clustering - CLUSTER_TABLE.csv
-m COMPARATIVE_COUNTS, --comparative_counts=COMPARATIVE_COUNTS
file from RepeatExplorer2 output - COMPARATIVE_ANALYSIS_COUNTS.csv
-o OUTPUT, --output=OUTPUT
File name for output figures <span style="color: #707183;">(</span>pdf document<span style="color: #707183;">)</span>
-N NUMBER_OF_COLORS, --number_of_colors=NUMBER_OF_COLORS
Number of unique colors used from plotting <span style="color: #707183;">(</span><span style="color: #D0372D;">2-20,</span> default is <span style="color: #D0372D;">10</span><span style="color: #707183;">)</span>
-g GENOME_SIZE, --genome_size=GENOME_SIZE
file from genome sizes of species provided<span style="color: #0000FF;"> in</span> tab delimited file<span style="color: #0000FF;"> in</span> the format:
species_code1 GenomeSize1
species_code2 GenomeSize2
species_code3 GenomeSize3
species_code4 GenomeSize4
provide the same codes for species as<span style="color: #0000FF;"> in</span> file COMPARATIVE_ANALYSIS_COUNTS.csv. The use of genome
sizes file imply the --nuclear_only option.
-n, --nuclear_only
remove all non-nuclear sequences <span style="color: #707183;">(</span>organelle and contamination<span style="color: #707183;">)</span><span style="color: #006FE0;">.</span>
-h, --help
Show this help message and exit
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<div id="postamble" class="status">
<p class="author">Author: Petr Novak</p>
<p class="date">Created: 2020-01-17 Pá 11:13</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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