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Report view #18

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merged 6 commits into from Nov 17, 2020
Merged

Report view #18

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4c36482
building report view
mayabrandi Nov 11, 2020
255db33
Merge branch 'coverage_plot' of https://github.com/Clinical-Genomics/…
mayabrandi Nov 13, 2020
185eeb4
merging
mayabrandi Nov 13, 2020
a2fcacb
sample project and ratio corection
mayabrandi Nov 13, 2020
4401b23
finally
mayabrandi Nov 16, 2020
e0e7533
Merge branch 'master' of https://github.com/Clinical-Genomics/NIPTool…
mayabrandi Nov 16, 2020
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23 changes: 0 additions & 23 deletions ...erver/templates/batch/fetal_fraction.html → NIPTool/server/templates/batch/plots/FF.html
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@@ -1,26 +1,3 @@
{% extends 'layout/layout.html' %}



{% block body %}
{% include 'layout/navigation.html' %}
<div class="container-fluid">
{% include 'batch/header.html' %}
<div class="tab-content">
<div class="tab-pane active" id='NCV_XY'>
<div class="panel panel-default">
<div class="panel-body">
<div id="FFY" style="min-width:400px; height:800px; ">
</div>
<div id="FFX" style="min-width:400px; height:800px; ">
</div>
</div>
</div>
</div>
</div>
</div>
{% endblock %}

{% block scripts %}
<script>
var XY_plot = document.getElementById('FFY')
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25 changes: 1 addition & 24 deletions ...er/templates/batch/fetal_fraction_XY.html → ...l/server/templates/batch/plots/FF_XY.html
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@@ -1,23 +1,3 @@
{% extends 'layout/layout.html' %}



{% block body %}
{% include 'layout/navigation.html' %}
<div class="container-fluid">
{% include 'batch/header.html' %}
<div class="tab-content">
<div class="tab-pane active" id='NCV_XY'>
<div class="panel panel-default">
<div class="panel-body">
<div id="FFXY" style="min-width:400px; height:800px; ">
</div>
</div>
</div>
</div>
</div>
</div>
{% endblock %}
{% block scripts %}
<script>
var XY_plot = document.getElementById('FFXY')
Expand Down Expand Up @@ -89,7 +69,4 @@

Plotly.newPlot('FFXY', data, layout);
</script>
{% endblock %}



{% endblock %}
19 changes: 3 additions & 16 deletions NIPTool/server/templates/batch/NCV.html → ...ool/server/templates/batch/plots/NCV.html
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@@ -1,20 +1,6 @@
{% extends 'layout/layout.html' %}
{% block body %}
{% include 'layout/navigation.html' %}
<div class="container-fluid">
{% include 'batch/header.html' %}
<div class="tab-pane active" id='NCV_{{chrom}}'>
<div class="panel panel-default">
<div class="panel-body">
<div id="NCV_plot" style="min-width:400px; height:800px; "></div><br><br>
</div>
</div>
</div>
</div>
{% endblock %}

{% block scripts %}
<script>
{% for chrom, cases in ncv_chrom_data.items() %}
$(function chrom_plot() {
var data = []
var layout = {
Expand Down Expand Up @@ -73,8 +59,9 @@
{% endfor %}


Plotly.newPlot('NCV_plot', data, layout);
Plotly.newPlot('NCV{{chrom}}_plot', data, layout);
});
{% endfor %}
</script>


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16 changes: 0 additions & 16 deletions NIPTool/server/templates/batch/coverage.html → ...erver/templates/batch/plots/coverage.html
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@@ -1,19 +1,3 @@
{% extends 'layout/layout.html' %}

{% block body %}
{% include 'layout/navigation.html' %}
<div class="container-fluid">
{% include 'batch/header.html' %}
<div class="tab-pane active" id='norm_cov'>
<div class="panel panel-default">
<div class="panel-body">
<div id="cov_plot" style="min-width:400px; height:800px; "></div>
</div>
</div>
</div>
</div>
{% endblock %}

{% block scripts %}
<script>
var XY_plot = document.getElementById('cov_plot')
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85 changes: 83 additions & 2 deletions NIPTool/server/templates/batch/report.html
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@@ -1,7 +1,88 @@
{% extends 'layout/layout.html' %}



{% block body %}
{% include 'layout/navigation.html' %}
<div class="container-fluid">
<div class="tab-pane active" id='NCV_{{chrom}}'>
<div class="panel panel-default">
<div class="panel-body">
<h2 class="page-header"><strong>NIPT Results </strong><br><small>Batch:
{{batch._id}}</small><small>
<p align="right" id="demo"></p>
</small></h2>
<footer>
<table id="batch_table" class="table table-bordered">
<thead>
<tr>
<th>Sample Name</th>
<th>NCV13</th>
<th>NCV18</th>
<th>NCV21</th>
<th>NCVX</th>
<th>FF(%)</th>
<th>FFX(%)</th>
<th>FFY(%)</th>
<th>CNVSegment</th>
<th>Warning</th>
<th>Status</th>
<th>Comment</th>
</tr>
</thead>
<tbody>
{% for sample in sample_info %}
<input type=text name="samples" value="{{ sample.sample_id }}" hidden>
<tr>
<td width="20%">{{ sample.sample_id }}</td>
<td width="4%" class="{{ sample.Zscore_13.warn}}">{{ sample.Zscore_13.value }}</td>
<td width="4%" class="{{ sample.Zscore_18.warn}}">{{ sample.Zscore_18.value }}</td>
<td width="4%" class="{{ sample.Zscore_21.warn}}">{{ sample.Zscore_21.value }}</td>
<td width="4%" class="{{ sample.Zscore_X.warn}}">{{ sample.Zscore_X.value }}</td>
<td width="4%" class="{{sample.FF.warn}}">{{sample.FF.value}}</td>
<td width="4%" class="{{sample.FFX.warn}}">{{sample.FFX.value}}</td>
<td width="4%" class="{{sample.FFY.warn}}">{{sample.FFY.value}}</td>
<td width="4%" class="{{sample.CNVSegment.warn}}">{{sample.CNVSegment.value}}</td>
<th>
<p> <small></small></p>
</th>
<th>
<p> <small>{{ sample.Status }}</small></p>
</th>
<td width="18%">{{sample.Comment}}</td>
</tr>
{% endfor %}
</tbody>
</table>
</footer>
<footer>
<div id="cov_plot" style="min-width:400px; height:800px; "></div>
</footer>
<footer>
<div id="NCV13_plot" style="min-width:400px; height:800px; "></div>
</footer>
<footer>
<div id="NCV18_plot" style="min-width:400px; height:800px; "></div>
</footer>
<footer>
<div id="NCV21_plot" style="min-width:400px; height:800px; "></div>
</footer>
<footer>
<div id="FFXY" style="min-width:400px; height:800px; "></div>
</footer>
<footer>
<div id="FFY" style="min-width:400px; height:800px; "></div>
</footer>
<footer>
<div id="FFX" style="min-width:400px; height:800px; "></div>
</footer>
</div>
</div>
</div>
</div>
{% endblock %}
{% block scripts %}
{% include 'batch/plots/NCV.html' %}
{% include 'batch/plots/FF_XY.html' %}
{% include 'batch/plots/FF.html' %}
{% include 'batch/plots/coverage.html' %}

{% endblock %}
25 changes: 25 additions & 0 deletions NIPTool/server/templates/batch/tabs/FF.html
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@@ -0,0 +1,25 @@
{% extends 'layout/layout.html' %}



{% block body %}
<div class="container-fluid">
{% include 'batch/header.html' %}
<div class="tab-content">
<div class="tab-pane active" id='NCV_XY'>
<div class="panel panel-default">
<div class="panel-body">
<div id="FFY" style="min-width:400px; height:800px; ">
</div>
<div id="FFX" style="min-width:400px; height:800px; ">
</div>
</div>
</div>
</div>
</div>
</div>
{% endblock %}

{% block scripts %}
{% include 'batch/plots/FF.html' %}
{% endblock %}
22 changes: 22 additions & 0 deletions NIPTool/server/templates/batch/tabs/FF_XY.html
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@@ -0,0 +1,22 @@
{% extends 'layout/layout.html' %}
{% block body %}
<div class="container-fluid">
{% include 'batch/header.html' %}
<div class="tab-content">
<div class="tab-pane active" id='NCV_XY'>
<div class="panel panel-default">
<div class="panel-body">
<div id="FFXY" style="min-width:400px; height:800px; ">
</div>
</div>
</div>
</div>
</div>
</div>
{% endblock %}
{% block scripts %}
{% include 'batch/plots/FF_XY.html' %}
{% endblock %}



17 changes: 17 additions & 0 deletions NIPTool/server/templates/batch/tabs/NCV.html
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@@ -0,0 +1,17 @@
{% extends 'layout/layout.html' %}
{% block body %}
<div class="container-fluid">
{% include 'batch/header.html' %}
<div class="tab-pane active" id='NCV_{{chr}}'>
<div class="panel panel-default">
<div class="panel-body">
<div id="NCV{{chr}}_plot" style="min-width:400px; height:800px; "></div><br><br>
</div>
</div>
</div>
</div>
{% endblock %}

{% block scripts %}
{% include 'batch/plots/NCV.html' %}
{% endblock %}
18 changes: 18 additions & 0 deletions NIPTool/server/templates/batch/tabs/coverage.html
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@@ -0,0 +1,18 @@
{% extends 'layout/layout.html' %}

{% block body %}
<div class="container-fluid">
{% include 'batch/header.html' %}
<div class="tab-pane active" id='norm_cov'>
<div class="panel panel-default">
<div class="panel-body">
<div id="cov_plot" style="min-width:400px; height:800px; "></div>
</div>
</div>
</div>
</div>
{% endblock %}

{% block scripts %}
{% include 'batch/plots/coverage.html' %}
{% endblock %}
3 changes: 1 addition & 2 deletions NIPTool/server/templates/batch/batch.html → ...ol/server/templates/batch/tabs/table.html
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Expand Up @@ -3,7 +3,7 @@


{% block body %}
{% include 'layout/navigation.html' %}

<div class="container-fluid">
{% include 'batch/header.html' %}
<div class="tab-content">
Expand All @@ -28,7 +28,6 @@
</tr>
</tbody>
</table>
<div class="table-responsive">

<table id="batch_table" class="table table-bordered table-hover table-wrapper-scroll-y" >
<thead>
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1 change: 0 additions & 1 deletion NIPTool/server/templates/batches.html
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@@ -1,6 +1,5 @@
{% extends 'layout/layout.html' %}
{% block body %}
{% include 'layout/navigation.html' %}
<div class="container-fluid">
<div class="jumbotron vertical-center">
<div class="row">
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4 changes: 3 additions & 1 deletion NIPTool/server/templates/layout/layout.html
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Expand Up @@ -50,7 +50,9 @@

<body>
<div id="wrapper">
{% block body %}{% endblock %}
{% include 'layout/navigation.html' %}
{% block body %}
{% endblock %}
</div> <!--wrapper-->


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1 change: 0 additions & 1 deletion NIPTool/server/templates/sample/sample.html
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@@ -1,6 +1,5 @@
{% extends 'layout/layout.html' %}
{% block body %}
{% include 'layout/navigation.html' %}
<div class="container-fluid">
{% include 'sample/header.html' %}
<ul class="nav nav-tabs" id="myTab">
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1 change: 0 additions & 1 deletion NIPTool/server/templates/sample/sample_tris.html
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@@ -1,7 +1,6 @@
{% extends 'layout/layout.html' %}

{% block body %}
{% include 'layout/navigation.html' %}
<div class="container-fluid">
{% include 'sample/header.html' %}
<ul class="nav nav-tabs" id="myTab">
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1 change: 0 additions & 1 deletion NIPTool/server/templates/statistics.html
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@@ -1,6 +1,5 @@
{% extends 'layout/layout.html' %}
{% block body %}
{% include 'layout/navigation.html' %}
<div class="container-fluid">
<div class="jumbotron vertical-center">
<div class="row">
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2 changes: 2 additions & 0 deletions NIPTool/server/utils.py
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Expand Up @@ -350,6 +350,8 @@ def get_last_batches(adapter, nr: int) -> list:
return(sorted_batches)


# Statistics

def get_statistics_for_scatter_plot(batches: list, fields: list)-> dict:
"""Formating data for scatter plot"""

Expand Down