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Merge pull request #30 from metagenlab/nj/fix_og_comp
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Fix orthogroup comparison view navigation tabs.
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@njohner
njohner authored Jan 5, 2024
2 parents a550458 + 6d42a0d commit 22e032c
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4 changes: 4 additions & 0 deletions docs/CHANGELOG.md
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Expand Up @@ -18,6 +18,10 @@ to [Common Changelog](https://common-changelog.org)
- Add unitesting for pipelines. ([#26](https://github.com/metagenlab/zDB/pull/26)) (Niklaus Johner)
- Add antimicrobial resistance annotations. ([#23](https://github.com/metagenlab/zDB/pull/23)) (Niklaus Johner)

### Fixed

- Fix orthogroup comparison view navigation tabs. ([#30](https://github.com/metagenlab/zDB/pull/30)) (Niklaus Johner)


## 1.2.1 - 2023-10-16

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6 changes: 5 additions & 1 deletion webapp/chlamdb/views.py
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Expand Up @@ -4099,7 +4099,7 @@ def first_coloured_row(self):

class OrthogroupComparisonView(TabularComparisonViewBase):

view_type = "orthogroup"
view_type = "orthology"
base_info_headers = ["Orthogroup", "Annotaion"]

table_help = """
Expand All @@ -4113,6 +4113,10 @@ class OrthogroupComparisonView(TabularComparisonViewBase):

compared_obj_name = "orthogroups"

@property
def view_name(self):
return "orthogroup_comparison"

def get_table_rows(self):
og_count = self.db.get_og_count(self.targets)
annotations = self.db.get_genes_from_og(
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118 changes: 59 additions & 59 deletions webapp/templates/chlamdb/extract_nav_tabs_template.html
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@@ -1,71 +1,71 @@


{% if type == "COG" %}
<nav>
<ul id="tabs_main" class="nav nav-tabs">
<li class={% if active_tab == "index" %}"active"{%endif%}><a href="{% url 'entry_list_cog' %}">Index</a></li>
<li class={% if active_tab == "det" %}"active"{%endif%}><a href="{% url 'extract_cog' %}">Extract form</a></li>
<li class={% if active_tab == "venn" %}"active"{%endif%}><a href="{% url 'venn_cog' %}">Venn</a></li>
<li class={% if active_tab == "comp" %}"active"{%endif%}><a href="{% url 'cog_comparison' %}">Presence/absence table</a></li>
<li class={% if active_tab == "heat" %}"active"{%endif%}><a href="{% url 'plot_heatmap' 'COG' %}">Heatmap</a></li>
<li class={% if active_tab == "pan" %}"active"{%endif%}><a href="{% url 'pan_genome' 'COG' %}">Accumulation/rarefaction plot</a></li>
<li class={% if active_tab == "bar" %}"active"{%endif%}><a href="{% url 'cog_barchart' %}">Categories barchart</a></li>
<li class={% if active_tab == "COG_freq" %}"active"{%endif%}><a href="{% url 'COG_phylo_heatmap' True %}">Cat. heatmap freq.</a></li>
<li class={% if active_tab == "COG_counts" %}"active"{%endif%}><a href="{% url 'COG_phylo_heatmap' False %}">Cat. heatmap counts</a></li>
</ul>
</nav>
<nav>
<ul id="tabs_main" class="nav nav-tabs">
<li class={% if active_tab == "index" %}"active"{%endif%}><a href="{% url 'entry_list_cog' %}">Index</a></li>
<li class={% if active_tab == "det" %}"active"{%endif%}><a href="{% url 'extract_cog' %}">Extract form</a></li>
<li class={% if active_tab == "venn" %}"active"{%endif%}><a href="{% url 'venn_cog' %}">Venn</a></li>
<li class={% if active_tab == "comp" %}"active"{%endif%}><a href="{% url 'cog_comparison' %}">Presence/absence table</a></li>
<li class={% if active_tab == "heat" %}"active"{%endif%}><a href="{% url 'plot_heatmap' 'COG' %}">Heatmap</a></li>
<li class={% if active_tab == "pan" %}"active"{%endif%}><a href="{% url 'pan_genome' 'COG' %}">Accumulation/rarefaction plot</a></li>
<li class={% if active_tab == "bar" %}"active"{%endif%}><a href="{% url 'cog_barchart' %}">Categories barchart</a></li>
<li class={% if active_tab == "COG_freq" %}"active"{%endif%}><a href="{% url 'COG_phylo_heatmap' True %}">Cat. heatmap freq.</a></li>
<li class={% if active_tab == "COG_counts" %}"active"{%endif%}><a href="{% url 'COG_phylo_heatmap' False %}">Cat. heatmap counts</a></li>
</ul>
</nav>
{% elif type == "ko" %}
<nav>
<ul id="tabs_main" class="nav nav-tabs">
<li class={% if active_tab == "index" %}"active"{%endif%}><a href="{% url 'entry_list_ko' %}">Index</a></li>
<li class={% if active_tab == "det" %}"active"{%endif%}><a href="{% url 'extract_ko' %}">Extract form</a></li>
<li class={% if active_tab == "venn" %}"active"{%endif%}><a href="{% url 'venn_ko' %}">Venn</a></li>
<li class={% if active_tab == "comp" %}"active"{%endif%}><a href="{% url 'ko_comparison' %}">Presence/absence table</a></li>
<li class={% if active_tab == "heat" %}"active"{%endif%}><a href="{% url 'plot_heatmap' 'ko' %}">Heatmap</a></li>
<li class={% if active_tab == "pan" %}"active"{%endif%}><a href="{% url 'pan_genome' 'ko' %}">Accumulation/rarefaction plot </a></li>
<li class={% if active_tab == "bar" %}"active"{%endif%}><a href="{% url 'module_barchart' %}">Categories barchart</a></li>
</ul>
</nav>
<nav>
<ul id="tabs_main" class="nav nav-tabs">
<li class={% if active_tab == "index" %}"active"{%endif%}><a href="{% url 'entry_list_ko' %}">Index</a></li>
<li class={% if active_tab == "det" %}"active"{%endif%}><a href="{% url 'extract_ko' %}">Extract form</a></li>
<li class={% if active_tab == "venn" %}"active"{%endif%}><a href="{% url 'venn_ko' %}">Venn</a></li>
<li class={% if active_tab == "comp" %}"active"{%endif%}><a href="{% url 'ko_comparison' %}">Presence/absence table</a></li>
<li class={% if active_tab == "heat" %}"active"{%endif%}><a href="{% url 'plot_heatmap' 'ko' %}">Heatmap</a></li>
<li class={% if active_tab == "pan" %}"active"{%endif%}><a href="{% url 'pan_genome' 'ko' %}">Accumulation/rarefaction plot </a></li>
<li class={% if active_tab == "bar" %}"active"{%endif%}><a href="{% url 'module_barchart' %}">Categories barchart</a></li>
</ul>
</nav>

{% elif type == "Pfam" %}
<nav>
<ul id="tabs_main" class="nav nav-tabs">
<li class={% if active_tab == "index" %}"active"{%endif%}><a href="{% url 'entry_list_pfam' %}">Index</a></li>
<li class={% if active_tab == "det" %}"active"{%endif%}><a href="{% url 'extract_pfam' %}">Extract form</a></li>
<li class={% if active_tab == "venn" %}"active"{%endif%}><a href="{% url 'venn_pfam' %}">Venn</a></li>
<li class={% if active_tab == "comp" %}"active"{%endif%}><a href="{% url 'pfam_comparison' %}">Presence/absence table</a></li>
<li class={% if active_tab == "heat" %}"active"{%endif%}><a href="{% url 'plot_heatmap' 'Pfam' %}">Heatmaps</a></li>
<li class={% if active_tab == "pan" %}"active"{%endif%}><a href="{% url 'pan_genome' 'Pfam' %}">Accumulation/rarefaction plot </a></li>
</ul>
</nav>
<nav>
<ul id="tabs_main" class="nav nav-tabs">
<li class={% if active_tab == "index" %}"active"{%endif%}><a href="{% url 'entry_list_pfam' %}">Index</a></li>
<li class={% if active_tab == "det" %}"active"{%endif%}><a href="{% url 'extract_pfam' %}">Extract form</a></li>
<li class={% if active_tab == "venn" %}"active"{%endif%}><a href="{% url 'venn_pfam' %}">Venn</a></li>
<li class={% if active_tab == "comp" %}"active"{%endif%}><a href="{% url 'pfam_comparison' %}">Presence/absence table</a></li>
<li class={% if active_tab == "heat" %}"active"{%endif%}><a href="{% url 'plot_heatmap' 'Pfam' %}">Heatmaps</a></li>
<li class={% if active_tab == "pan" %}"active"{%endif%}><a href="{% url 'pan_genome' 'Pfam' %}">Accumulation/rarefaction plot </a></li>
</ul>
</nav>

{% elif type == "EC" %}
<nav>
<ul id="tabs_main" class="nav nav-tabs">
<li class={% if active_tab == "det" %}"active"{%endif%}><a href="{% url 'extract_EC' %}">Extract form</a></li>
<li class={% if active_tab == "venn" %}"active"{%endif%}><a href="{% url 'venn_EC' %}">Venn diagram</a></li>
<li class={% if active_tab == "heat" %}"active"{%endif%}><a href="{% url 'plot_heatmap' 'EC' %}">Heatmaps</a></li>
<li class={% if active_tab == "pan" %}"active"{%endif%}><a href="{% url 'pan_genome' 'EC' %}">Accumulation/rarefaction plot </a></li>
</ul>
</nav>
<nav>
<ul id="tabs_main" class="nav nav-tabs">
<li class={% if active_tab == "det" %}"active"{%endif%}><a href="{% url 'extract_EC' %}">Extract form</a></li>
<li class={% if active_tab == "venn" %}"active"{%endif%}><a href="{% url 'venn_EC' %}">Venn diagram</a></li>
<li class={% if active_tab == "heat" %}"active"{%endif%}><a href="{% url 'plot_heatmap' 'EC' %}">Heatmaps</a></li>
<li class={% if active_tab == "pan" %}"active"{%endif%}><a href="{% url 'pan_genome' 'EC' %}">Accumulation/rarefaction plot </a></li>
</ul>
</nav>
{% elif type == "interpro" %}
<nav>
<ul id="tabs_main" class="nav nav-tabs">
<li class={% if active_tab == "det" %}"active"{%endif%}><a href="{% url 'extract_interpro' %}">Extract form</a></li>
<li class={% if active_tab == "venn" %}"active"{%endif%}><a href="{% url 'venn_interpro' %}">Venn</a></li>
<li class={% if active_tab == "heat" %}"active"{%endif%}><a href="{% url 'plot_heatmap' 'interpro' %}">Heatmaps</a></li>
<li class={% if active_tab == "pan" %}"active"{%endif%}><a href="{% url 'pan_genome' 'interpro' %}">Accumulation/rarefaction plot </a></li>
</ul>
</nav>
<nav>
<ul id="tabs_main" class="nav nav-tabs">
<li class={% if active_tab == "det" %}"active"{%endif%}><a href="{% url 'extract_interpro' %}">Extract form</a></li>
<li class={% if active_tab == "venn" %}"active"{%endif%}><a href="{% url 'venn_interpro' %}">Venn</a></li>
<li class={% if active_tab == "heat" %}"active"{%endif%}><a href="{% url 'plot_heatmap' 'interpro' %}">Heatmaps</a></li>
<li class={% if active_tab == "pan" %}"active"{%endif%}><a href="{% url 'pan_genome' 'interpro' %}">Accumulation/rarefaction plot </a></li>
</ul>
</nav>
{% elif type == 'orthology' %}
<nav>
<ul id="tabs_main" class="nav nav-tabs">
<li class={% if active_tab == "det" %}"active"{%endif%}><a href="{% url 'extract_orthogroup' %}">Extract form</a></li>
<li class={% if active_tab == "venn" %}"active"{%endif%}><a href="{% url 'venn_orthogroup' %}">Venn</a></li>
<li class={% if active_tab == "comp" %}"active"{%endif%}><a href="{% url 'orthogroup_comparison' %}">Presence/absence table</a></li>
<li class={% if active_tab == "heat" %}"active"{%endif%}><a href="{% url 'plot_heatmap' 'orthology' %}">Heatmap</a></li>
<li class={% if active_tab == "pan" %}"active"{%endif%}><a href="{% url 'pan_genome' 'orthology' %}">Accumulation/rarefaction plot </a></li>
</ul>
</nav>
<nav>
<ul id="tabs_main" class="nav nav-tabs">
<li class={% if active_tab == "det" %}"active"{%endif%}><a href="{% url 'extract_orthogroup' %}">Extract form</a></li>
<li class={% if active_tab == "venn" %}"active"{%endif%}><a href="{% url 'venn_orthogroup' %}">Venn</a></li>
<li class={% if active_tab == "comp" %}"active"{%endif%}><a href="{% url 'orthogroup_comparison' %}">Presence/absence table</a></li>
<li class={% if active_tab == "heat" %}"active"{%endif%}><a href="{% url 'plot_heatmap' 'orthology' %}">Heatmap</a></li>
<li class={% if active_tab == "pan" %}"active"{%endif%}><a href="{% url 'pan_genome' 'orthology' %}">Accumulation/rarefaction plot </a></li>
</ul>
</nav>
{% endif %}

137 changes: 67 additions & 70 deletions webapp/templates/chlamdb/tabular_comparison.html
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Expand Up @@ -18,85 +18,82 @@
<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=view_type active_tab="comp" %}

<br>
<p class="page-title"><b>{{form_title}} </b><a href="/docs/index.html" id="show-option" title="{{form_help}}"><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=view_type active_tab="comp" %}
<br>
<p class="page-title"><b>{{form_title}} </b><a href="/docs/index.html" id="show-option" title="{{form_help}}"><i class="fab fa-info-circle " style="size: 5em;" ></i></a></p>
</div>

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

{% if show_comparison_table %}
<div class="row" style="padding-top:10px ;background-color: rgba(245, 245, 245, 0.986); margin-top: 1em;" >

<h4>{{table_title|safe}}</h4>
<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>
<p style="margin: 10px 10px 10px 10px">
{{table_help|safe}}
</p>
</div>
<form action='{% url view_name %}' method="post">
{% csrf_token %}
{{ form.as_p }}
<input type="submit" value="Submit" />

</form>

{% if show_comparison_table %}


<div class="row" style="padding-top:10px ;background-color: rgba(245, 245, 245, 0.986); margin-top: 1em;" >

<h4>{{table_title|safe}}</h4>
<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>
<p style="margin: 10px 10px 10px 10px">
{{table_help|safe}}
</p>
</div>
</div>
</div>

<br>
<div class="col-lg-12">
<table class="hover" id="mytable" style="padding-top: 1em;">
<style>
table {
table-layout: fixed;
} </style>
<thead>
<tr>
{% for title in table_headers %}
<th>{{title}}</th>
{% endfor %}
</tr>
</thead>
<tbody>
{% for row in table_rows %}
<tr>
{% for value in row|slice_up_to:n_data_columns %}
{% if forloop.counter0 < first_coloured_row %}
<td>{{value|safe}}</td>
{% else %}
{% with color_i=forloop.counter0|add:hist_colour_index_shift %}
{% with colour=row|return_item:color_i %}
{% if colour != 0 %}
<td data-hist="{{colour}}">{{value}}</td>
{% else %}
<td>{{value}}</td>
{% endif %}
{% endwith %}
{% endwith %}
{% endif %}
{% endfor %}
</tr>
{% endfor %}
</tbody>
</table>
</div>
{% endif %}
<br>
<div class="col-lg-12">
<table class="hover" id="mytable" style="padding-top: 1em;">
<style>
table {
table-layout: fixed;
}
</style>
<thead>
<tr>
{% for title in table_headers %}
<th>{{title}}</th>
{% endfor %}
</tr>
</thead>
<tbody>
{% for row in table_rows %}
<tr>
{% for value in row|slice_up_to:n_data_columns %}
{% if forloop.counter0 < first_coloured_row %}
<td>{{value|safe}}</td>
{% else %}
{% with color_i=forloop.counter0|add:hist_colour_index_shift %}
{% with colour=row|return_item:color_i %}
{% if colour != 0 %}
<td data-hist="{{colour}}">{{value}}</td>
{% else %}
<td>{{value}}</td>
{% endif %}
{% endwith %}
{% endwith %}
{% endif %}
{% endfor %}
</tr>
{% endfor %}
</tbody>
</table>
</div>
{% endif %}

</div>
</div>
</div>
</div>
</div>


</body>

<script src="{% static 'js/jquery.hottie.js' %}"></script>
<script>
$(function(){
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