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Add AMR accumulation/rarefaction plot view. #46

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merged 6 commits into from
Jan 19, 2024
Merged

Add AMR accumulation/rarefaction plot view. #46

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de7a89b
Add plot_heatmap view for AMR genes.
njohner Jan 18, 2024
79195f7
Cleanup pan_genome.html template.
njohner Jan 18, 2024
368850f
Fix pan_genome title for orthogroups.
njohner Jan 18, 2024
1b5350a
Add AMR accumulation/rarefaction plot view.
njohner Jan 18, 2024
693849b
Add accumulation/rarefaction box to AMR comparison index view.
njohner Jan 18, 2024
ee89b56
Add accumulation/rarefaction to AMR navigation tabs.
njohner Jan 18, 2024
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1 change: 1 addition & 0 deletions docs/CHANGELOG.md
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Expand Up @@ -16,6 +16,7 @@ to [Common Changelog](https://common-changelog.org)

### Added

- Add AMR accumulation/rarefaction plot view. ([#46](https://github.com/metagenlab/zDB/pull/46)) (Niklaus Johner)
- Add AMR heatmap view. ([#45](https://github.com/metagenlab/zDB/pull/45)) (Niklaus Johner)
- Add AMR details view. ([#44](https://github.com/metagenlab/zDB/pull/44)) (Niklaus Johner)
- Add AMR Venn diagram view. ([#41](https://github.com/metagenlab/zDB/pull/41)) (Niklaus Johner)
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41 changes: 26 additions & 15 deletions testing/webapp/test_views.py
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Expand Up @@ -74,6 +74,7 @@
'/module_comparison/',
'/orthogroup/group_85',
'/orthogroup_comparison',
'/pan_genome/amr',
'/pan_genome/cog',
'/pan_genome/ko',
'/pan_genome/orthogroup',
Expand Down Expand Up @@ -188,21 +189,6 @@ def test_cog_barchart(self):
self.assertPlot(resp)
self.assertContains(resp, "Distribution of COGs within COG categories")

def test_pan_genome_cog(self):
resp = self.client.get("/pan_genome/cog")
self.assertEqual(200, resp.status_code)
self.assertTemplateUsed(resp, 'chlamdb/pan_genome.html')
self.assertEqual("cog", resp.context["type"])
self.assertTitle(resp, "Comparisons: Clusters of Orthologous groups (COGs)")
self.assertNoPlot(resp)

resp = self.client.post("/pan_genome/cog", data={"targets": ["0", "1"]})
self.assertEqual(200, resp.status_code)
self.assertTemplateUsed(resp, 'chlamdb/pan_genome.html')
self.assertEqual("cog", resp.context["type"])
self.assertTitle(resp, "Comparisons: Clusters of Orthologous groups (COGs)")
self.assertPlot(resp)


class ComparisonViewsTestMixin():

Expand All @@ -215,6 +201,7 @@ class ComparisonViewsTestMixin():
table_html = '<table class="hover" id="mytable" style="padding-top: 1em;">'
venn_html = '<div id="venn_diagram" '
heatmap_html = '<div id="heatmap" '
rarefaction_plot_html = 'id="rarefaction_plot"'

def assertPageTitle(self, resp, title):
self.assertContains(
Expand Down Expand Up @@ -254,6 +241,14 @@ def assertHeatmap(self, resp):
self.assertTrue(resp.context.get("envoi_heatmap", False))
self.assertContains(resp, self.heatmap_html)

def assertNoRarefactionPlot(self, resp):
self.assertFalse(resp.context.get("envoi", False))
self.assertNotContains(resp, self.rarefaction_plot_html)

def assertRarefactionPlot(self, resp):
self.assertTrue(resp.context.get("envoi", False))
self.assertContains(resp, self.rarefaction_plot_html)

@property
def tab_comp_view(self):
return f"/{self.view_type}_comparison"
Expand Down Expand Up @@ -347,6 +342,22 @@ def test_plot_heatmap_view(self):
self.assertHeatmap(resp)
self.assertNav(resp)

def test_pan_genome_view(self):
resp = self.client.get(f"/pan_genome/{self.view_type}")
self.assertEqual(200, resp.status_code)
self.assertTemplateUsed(resp, 'chlamdb/pan_genome.html')
self.assertEqual(self.view_type, resp.context["type"])
self.assertPageTitle(resp, self.page_title)
self.assertNoRarefactionPlot(resp)

resp = self.client.post(f"/pan_genome/{self.view_type}",
data={"targets": ["0", "1"]})
self.assertEqual(200, resp.status_code)
self.assertTemplateUsed(resp, 'chlamdb/pan_genome.html')
self.assertEqual(self.view_type, resp.context["type"])
self.assertPageTitle(resp, self.page_title)
self.assertRarefactionPlot(resp)


class TestPfamViews(SimpleTestCase, ComparisonViewsTestMixin):

Expand Down
1 change: 1 addition & 0 deletions webapp/templates/chlamdb/extract_nav_tabs_template.html
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Expand Up @@ -75,6 +75,7 @@
<li class={% if active_tab == "venn" %}"active"{%endif%}><a href="{% url 'venn_amr' %}">Venn</a></li>
<li class={% if active_tab == "comp" %}"active"{%endif%}><a href="{% url 'amr_comparison' %}">Presence/absence table</a></li>
<li class={% if active_tab == "heat" %}"active"{%endif%}><a href="{% url 'plot_heatmap' 'amr' %}">Heatmaps</a></li>
<li class={% if active_tab == "pan" %}"active"{%endif%}><a href="{% url 'pan_genome' 'amr' %}">Accumulation/rarefaction plot </a></li>
</ul>
</nav>
{% endif %}
Expand Down
150 changes: 78 additions & 72 deletions webapp/templates/chlamdb/pan_genome.html
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Expand Up @@ -7,89 +7,95 @@
{% include "chlamdb/header.html" %}
</head>
<script src="https://d3js.org/d3.v4.js"></script>

<div class="container-fluid" id="main_container">
<div class="row">
<div id="wrapper">
<div id="page-content-wrapper">
<div class="row">
<div class="col-lg-12">
{% include "chlamdb/menu.html" %}
{% include "chlamdb/extract_nav_tabs_template.html" with type=type active_tab="pan" %}

<br>
<p class="page-title"><b>Accumulation/rarefaction plot of
{% if type == 'pfam' %}
Pfam domains
{% elif type == 'cog' %}
COG categories
{% elif type == 'interpro'%}
Interpro Entries.
{% elif type == 'EC' %}
EC numbers. Based on PRIAM data. Partial EC are not considered.
{% elif type == 'ko' %}
Kegg orthologous groups (KO)
{% elif type == 'orthology' %}
orthologous groups
{% endif %}</b><a href="https://zdb.readthedocs.io/en/latest/tutorial/website.html#comparisons" id="show-option"
target="_blank" ><i class="fab fa-info-circle " style="size: 5em;" ></i></a></p>
<div id="page-content-wrapper">
<div class="row">
<div class="col-lg-12">
{% include "chlamdb/menu.html" %}
{% include "chlamdb/extract_nav_tabs_template.html" with type=type active_tab="pan" %}

<br>
<p class="page-title">
<b>
Accumulation/rarefaction plot of
{% if type == 'pfam' %}
Pfam domains
{% elif type == 'cog' %}
COG categories
{% elif type == 'interpro'%}
Interpro Entries.
{% elif type == 'EC' %}
EC numbers. Based on PRIAM data. Partial EC are not considered.
{% elif type == 'ko' %}
Kegg orthologous groups (KO)
{% elif type == 'orthogroup' %}
orthologous groups
{% elif type == 'amr' %}
Antimicrobial resistance genes
{% endif %}
</b>
<a href="https://zdb.readthedocs.io/en/latest/tutorial/website.html#comparisons" id="show-option" target="_blank" >
<i class="fab fa-info-circle " style="size: 5em;" ></i>
</a>
</p>



<form action='{% url "pan_genome" type %}' method="post">
{% csrf_token %}
{{ form.as_p }}
<input type="submit" value="Submit" />
</form>
<form action='{% url "pan_genome" type %}' method="post">
{% csrf_token %}
{{ form.as_p }}
<input type="submit" value="Submit" />
</form>


</div>
</div>
{% if envoi %}
<div class="row" style="padding-top:30px; background-color: rgba(245, 245, 245, 0.986); margin-top: 2em">
<div class="panel panel-success" style="margin: 1em;" >
<div class="panel-heading" style="width:100%">
<h5 class="panel-title">Help to interpret the results</h5>
</div>

{% if envoi %}
<div class="row" style="padding-top:30px; background-color: rgba(245, 245, 245, 0.986); margin-top: 2em">
<div class="panel panel-success" style="margin: 1em;" >
<div class="panel-heading" style="width:100%">
<h5 class="panel-title">Help to interpret the results
</div>
<p style="margin: 10px 10px 10px 10px">
This plot shows the relationship between the number of {{type_txt}} and the number of genomes considered.

<br>The <span style="color: #69b3a2;"><b>green</b></span> and the <span style="color: #5499c7;"><b>blue</b></span> lines are both based on a single random permutation of the selected genomes. The <span style="color: #69b3a2;"><b>green</b></span> line represent the total number of {{type_txt}} present in the first n genomes of the permutation. The <span style="color: #5499c7;"><b>blue</b></span> represents the number of {{type_txt}} shared by the first n genomes of the permutation.

<br>The <span style="color:#FF6347;"><b>red</b></span> line shows the number of {{type_txt}} present in exactly n genomes. This plot do not depend on a permutation and it is possible to click on the points to get more detailed information.
<br>

</p>
</div>
<p style="margin: 10px 10px 10px 10px">
This plot shows the relationship between the number of {{type_txt}} and the number of genomes considered.
<br>
The <span style="color: #69b3a2;"><b>green</b></span> and the <span style="color: #5499c7;"><b>blue</b></span> lines are both based on a single random permutation of the selected genomes. The <span style="color: #69b3a2;"><b>green</b></span> line represent the total number of {{type_txt}} present in the first n genomes of the permutation. The <span style="color: #5499c7;"><b>blue</b></span> represents the number of {{type_txt}} shared by the first n genomes of the permutation.
<br>
The <span style="color:#FF6347;"><b>red</b></span> line shows the number of {{type_txt}} present in exactly n genomes. This plot do not depend on a permutation and it is possible to click on the points to get more detailed information.
<br>
</p>
</div>


<div class="tab-pane active" id="tab1" style="margin: 1em;">
<div class="panel panel-success" style="width:100%; top: 200px; ">
<div style="width: 1000px;" id="rarefaction_plot">
</div>

<div id="plot_type" style="display: flex; justify-content: space-around; width: 900px;">
<div>
<input style="margin-left" value="pangenome" type="radio" id="pangenome" name="plot_type" checked>
<label for="pangenome">Total number of {{type_txt}}</label>
</div>

<div>
<input style="center" type="radio" value="coregenome" id="coregenome" name="plot_type">
<label for="coregenome">Number of shared {{type_txt}}</label>
</div>

<div>
<input style="margin-right" type="radio" value="ortho_distrib" id="ortho_distrib" name="plot_type">
<label for="ortho_distrib">Distribution of {{type_txt}}</label>
</div>
</div>
</div>
</div>

<div id="download_svg">
</div>

{% endif %}
<div class="tab-pane active" id="tab1" style="margin: 1em;">
<div class="panel panel-success" style="width:100%; top: 200px; ">
<div style="width: 1000px;" id="rarefaction_plot"></div>

<div id="plot_type" style="display: flex; justify-content: space-around; width: 900px;">
<div>
<input style="margin-left" value="pangenome" type="radio" id="pangenome" name="plot_type" checked>
<label for="pangenome">Total number of {{type_txt}}</label>
</div>

<div>
<input style="center" type="radio" value="coregenome" id="coregenome" name="plot_type">
<label for="coregenome">Number of shared {{type_txt}}</label>
</div>

<div>
<input style="margin-right" type="radio" value="ortho_distrib" id="ortho_distrib" name="plot_type">
<label for="ortho_distrib">Distribution of {{type_txt}}</label>
</div>
</div>
</div>
</div>

<div id="download_svg"></div>
</div>
{% endif %}
</div>
</div>
</div>
Expand Down
2 changes: 1 addition & 1 deletion webapp/views/utils.py
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Expand Up @@ -14,7 +14,7 @@ def safe_replace(string, search_string, replace_string):
'COG Ortholog': ['fam_cog'],
'Comparisons: Antimicrobial Resistance': [
'amr_comparison', 'index_comp_amr', 'entry_list_amr', 'extract_amr',
'plot_heatmap_amr', 'venn_amr'],
'plot_heatmap_amr', 'pan_genome_amr', 'venn_amr'],
'Comparisons: Clusters of Orthologous groups (COGs)': [
'cog_barchart', 'index_comp_cog', 'cog_phylo_heatmap',
'cog_comparison', 'entry_list_cog', 'extract_cog', 'heatmap_COG',
Expand Down
8 changes: 4 additions & 4 deletions webapp/views/views.py
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Expand Up @@ -177,10 +177,7 @@ class ComparisonIndexView(View, ComparisonViewMixin):
def boxes(self):
boxes = ["entry-list", "extraction", "venn",
"tabular-comparison", "heatmap", "accumulation-rarefaction"]
if self.comp_type == "amr":
boxes = ["entry-list", "extraction", "venn",
"tabular-comparison", "heatmap"]
elif self.comp_type == "orthogroup":
if self.comp_type == "orthogroup":
boxes.remove("entry-list")
elif self.comp_type == "ko":
boxes.append("barcharts")
Expand Down Expand Up @@ -2060,6 +2057,9 @@ def pan_genome(request, type):
elif type == "pfam":
df_hits = db.get_pfam_hits(taxids, search_on="taxid")
type_txt = "PFAM domains"
elif type == "amr":
df_hits = db.get_amr_hit_counts(taxids, search_on="taxid")
type_txt = "AMR genes"
else:
form = venn_form_class()
return render(request, 'chlamdb/pan_genome.html', my_locals(locals()))
Expand Down