Commit 05573d5c authored by Floreal Cabanettes's avatar Floreal Cabanettes
Browse files

Add dot plot documentation

parent c4c90511
# Dot plot
In bioinformatics a dot plot is a graphical method that allows the comparison of two biological sequences and identify regions of close similarity between them. It is a type of recurrence plot.
More details of dot plot [here](https://en.wikipedia.org/wiki/Dot_plot_(bioinformatics)). Below, some examples of events which can be detected by dot plots.
## Match
When two samples sequence are identical, it's a match.
![match](/static/images/dotplot/match.png)
## Gap
Dot plots can be used to detect a gap between two samples: small sequence which exists only in one sample, between two matching regions.
![gap](/static/images/dotplot/gap.png)
## Inversion
Sequence which exists in the two samples but not in the same order.
![inversion](/static/images/dotplot/inversion.png)
## Repeats
Dot plot can be used to detect repeated regions: a sequence which is repeated several times in a sample.
![repeats](/static/images/dotplot/repeat2.png)
\ No newline at end of file
......@@ -63,6 +63,7 @@
<ul class="dropdown-menu" role="menu">
<li><a href="/documentation/run">Launch a job</a></li>
<li><a href="/documentation/result">Results</a></li>
<li><a href="/documentation/dotplot">Dot plot</a></li>
<li><a href="/documentation/formats">File formats</a></li>
</ul>
</li>
......
......@@ -28,10 +28,17 @@
color: #ffffff;
font-weight: bold;
}
{% if toc %}
#body {
width: calc(100% - 300px);
margin-left: 295px !important;
}
{% else %}
#body {
width: calc(100% - 300px);
margin-left: 145px !important;
}
{% endif %}
</style>
<script type="text/javascript">
......@@ -42,11 +49,13 @@
{% endblock %}
{% block content %}
<div id="plan-back">
<div id="plan">
{{ toc }}
{% if toc %}
<div id="plan-back">
<div id="plan">
{{ toc }}
</div>
</div>
</div>
{% endif %}
<div id="body">
{{ content }}
......
......@@ -361,7 +361,7 @@ def documentation_result():
@app.route("/documentation/formats", methods=['GET'])
def documentation_formats():
with open(os.path.join(app_folder, "md", "formats.md"), "r",
with open(os.path.join(app_folder, "md", "doc_formats.md"), "r",
encoding='utf-8') as install_instr:
content = install_instr.read()
md = Markdown(extensions=[TocExtension(baselevel=1), TableExtension()])
......@@ -370,6 +370,17 @@ def documentation_formats():
return render_template("documentation.html", menu="documentation", content=content, toc=toc)
@app.route("/documentation/dotplot", methods=['GET'])
def documentation_dotplot():
with open(os.path.join(app_folder, "md", "doc_dotplot.md"), "r",
encoding='utf-8') as install_instr:
content = install_instr.read()
md = Markdown(extensions=[TocExtension(baselevel=1)])
content = Markup(md.convert(content))
toc = Markup(md.toc)
return render_template("documentation.html", menu="documentation", content=content, toc=toc)
@app.route("/install", methods=['GET'])
def install():
with open(os.path.join(app_folder, "md", "INSTALL.md"), "r", encoding='utf-8') as install_instr:
......
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