Merge pull request #22 from Clinical-Genomics/tresholds

inserting tresholds mm

NIPTool/server/templates/batch/header.html

@@ -79,13 +79,13 @@ <h5>Batch Warnings </h5>
                 href="{{ url_for('server.batch', batch_id = batch._id) }}">NCV Table</a>
         </li>
         <li {% if page_id =='batches_NCV13' %} class="active" {% endif %}><a
-                href="{{ url_for('server.NCV13', batch_id = batch._id) }}">NCV13</a>
+                href="{{ url_for('server.NCV', batch_id = batch._id, ncv = '13') }}">NCV13</a>
         </li>
         <li {% if page_id =='batches_NCV18' %} class="active" {% endif %}><a
-                href="{{ url_for('server.NCV18', batch_id = batch._id) }}">NCV18</a>
+                href="{{ url_for('server.NCV', batch_id = batch._id, ncv = '18') }}">NCV18</a>
         </li>
         <li {% if page_id =='batches_NCV21' %} class="active" {% endif %}><a
-                href="{{ url_for('server.NCV21', batch_id = batch._id) }}">NCV21</a>
+                href="{{ url_for('server.NCV', batch_id = batch._id, ncv = '21') }}">NCV21</a>
         </li>
         <li {% if page_id =='batches_FF' %} class="active" {% endif %}><a
                 href="{{ url_for('server.fetal_fraction', batch_id = batch._id) }}">FF</a>

NIPTool/server/templates/batch/plots/NCV.html

@@ -1,84 +1,107 @@
 {% block scripts %}
-<script>
-    {% for chrom, cases  in ncv_chrom_data.items() %}
-    $(function chrom_plot() {
-    var data = []
-    var layout = {
-        legend:{hovermode:'closest' },
-        hovermode:'closest',
-        annotations : [],
-        xaxis :{showline: true,
-                ticktext : {{cases['names']|tojson}},
-                tickvals : {{cases['x_axis']}},
-                tickangle : 20,
-                linecolor: '#636363',
-                linewidth: 5,
-                showgrid: true,
-                gridcolor: '#bdbdbd'
-                },
-
-        yaxis :{range: [-10,],
-                zeroline: false,
-                showline: true,
-                showgrid: false,
-                linecolor: '#636363',
-                linewidth: 5,
-                title : 'NCV{{chrom}}'
-                }};
+    <script>
+        {% for chrom, cases  in ncv_chrom_data.items() %}
+            $(function chrom_plot() {
+                var data = []
+                var layout = {
+                    legend: {hovermode: 'closest'},
+                    hovermode: 'closest',
+                    annotations: [],
+                    xaxis: {
+                        showline: true,
+                        ticktext: {{cases['names']|tojson}},
+                        tickvals: {{cases['x_axis']}},
+                        tickangle: 20,
+                        linecolor: '#636363',
+                        linewidth: 5,
+                        showgrid: true,
+                        gridcolor: '#bdbdbd'
+                    },
 
-    var cases = {name: "Current batch (N ="+ "{{cases['count']}}" +")" ,
-                 y: {{cases['values']}},
-                x: {{cases['x_axis']}},
-                text: {{cases['names']|tojson}},
-                mode: 'markers',
-                type: 'scatter',
+                    yaxis: {
+                        range: [-10,],
+                        zeroline: false,
+                        showline: true,
+                        showgrid: false,
+                        linecolor: '#636363',
+                        linewidth: 5,
+                        title: 'NCV{{chrom}}'
+                    }
                 };
-    data.push(cases)
 
-    var box = {
-        y: {{ normal_data['values'] }},
-        pointpos: 30,
-        type: 'box',
-        marker: {
-            color: '#ccccb3'},
-            name: 'Negative (N='+{{normal_data['count']}}+')',
-            hoverinfo:'none'}
-    data.push(box)
+                var cases = {
+                    name: "Current batch (N =" + "{{cases['count']}}" + ")",
+                    y: {{cases['values']}},
+                    x: {{cases['x_axis']}},
+                    text: {{cases['names']|tojson}},
+                    mode: 'markers',
+                    type: 'scatter',
+                };
+                data.push(cases)
+
+                var box = {
+                    y: {{ normal_data['values'] }},
+                    pointpos: 30,
+                    type: 'box',
+                    marker: {
+                        color: '#ccccb3'
+                    },
+                    name: 'Negative (N='+{{normal_data['count']}}+')',
+                    hoverinfo: 'none'
+                }
+                data.push(box)
+
+
+                {% for line  in tris_thresholds %}
+                    var line = {
+                        x: [{{cases['x_axis'][0]}}, {{cases['x_axis'][-1]}}],
+                        y: [{{tris_thresholds[line]['NCV']}}, {{tris_thresholds[line]['NCV']}}],
+                        mode: 'lines',
+                        text: "{{tris_thresholds[line]['text']}}",
+                        showlegend: false,
+                        line: {
+                            dash: "dot",
+                            color: "{{tris_thresholds[line]["color"]}}",
+                            width: 1
+                        },
+                        name: "{{line}}"
+                    };
+                    data.push(line);
+                {% endfor %}
 
-
+                {% for status  in abnormal_data.keys() %}
+                    var verif = {
+                        name: "{{status}} T{{chrom}} (N="+{{abnormal_data[status]['count']}}+")",
+                        y: {{abnormal_data[status]['values']}},
+                        x: {{abnormal_data[status]['x_axis']}},
+                        text: {{abnormal_data[status]['names']|tojson}},
+                        mode: 'markers',
+                        type: 'scatter'
+                    };
+                    data.push(verif);
+                {% endfor %}
 
-    {% for status  in abnormal_data.keys() %}
-        var verif = {                                                                  
-            name: "{{status}} T{{chrom}} (N="+{{abnormal_data[status]['count']}}+")",
-            y: {{abnormal_data[status]['values']}},                                        
-            x: {{abnormal_data[status]['x_axis']}} ,
-            text: {{abnormal_data[status]['names']|tojson}},                                       
-            mode: 'markers',                                             
-            type: 'scatter'}; 
-        data.push(verif);
-    {% endfor %}
 
-
-    Plotly.newPlot('NCV{{chrom}}_plot', data, layout);
-    });
-    {% endfor %}
-</script>
+                Plotly.newPlot('NCV{{chrom}}_plot', data, layout);
+            });
+        {% endfor %}
+    </script>
 
 
-<script>
-$(document).ready(function() {
-    var table = $('#batch_table').DataTable( {
-        lengthChange: false,
-        paging:     false,
-        info: false,
-        searching:  false
-    } );
-} );
-</script>
+    <script>
+        $(document).ready(function () {
+            var table = $('#batch_table').DataTable({
+                lengthChange: false,
+                paging: false,
+                info: false,
+                searching: false
+            });
+        });
+    </script>
 
 
-<script>
-var d = new Date();
-document.getElementById("demo").innerHTML = d.toDateString();
-</script>
+    <script>
+        var d = new Date();
+        document.getElementById("demo").innerHTML = d.toDateString();
+    </script>
 {% endblock %}

NIPTool/server/templates/batch/report.html

@@ -54,7 +54,9 @@ <h2 class="page-header"><strong>NIPT Results </strong><br><small>Batch:
                     </table>
                 </footer>
                 <footer>
+                    {% if coverage=="1" %}
                     <div id="cov_plot" style="min-width:400px; height:800px; "></div>
+                    {% endif %}
                 </footer>
                 <footer>
                     <div id="NCV13_plot" style="min-width:400px; height:800px; "></div>

NIPTool/server/utils.py

@@ -12,17 +12,17 @@ def get_sample_info(sample):
     sample_info_keys = ["Zscore_13", "Zscore_18", "Zscore_21", "CNVSegment", "FF_Formatted", "FFX", "FFY", "Zscore_X"]
     for key in sample_info_keys:
         val = sample.get(key)
-        if isinstance(val,(float,int)):
+        if isinstance(val, (float, int)):
             sample[key] = round(val, 2)
         else:
             sample[key] = ""
-        
+
     return {
         "sample_id": sample.get("_id"),
         "FF": {"value": sample.get("FF_Formatted"), "warn": sample_warnings.get("FF_Formatted")},
-        "CNVSegment": {"value": sample.get("CNVSegment"), "warn": "default",},
-        "FFX": {"value": sample.get("FFX"), "warn": "default",},
-        "FFY": {"value": sample.get("FFY"), "warn": "default",},
+        "CNVSegment": {"value": sample.get("CNVSegment"), "warn": "default", },
+        "FFX": {"value": sample.get("FFX"), "warn": "default", },
+        "FFY": {"value": sample.get("FFY"), "warn": "default", },
         "Zscore_13": {"value": sample.get("Zscore_13"), "warn": sample_warnings.get("Zscore_13")},
         "Zscore_18": {"value": sample.get("Zscore_18"), "warn": sample_warnings.get("Zscore_18")},
         "Zscore_21": {"value": sample.get("Zscore_21"), "warn": sample_warnings.get("Zscore_21")},
@@ -47,32 +47,31 @@ def _get_status(sample):
 
 def _get_ff_warning(fetal_fraction):
     """Get fetal fraction warning based on preset treshold"""
-    if fetal_fraction is "":
+    if fetal_fraction == "":
         return "default"
 
-    try:
-        fetal_fraction = fetal_fraction
-    except:
-        fetal_fraction = None
     if fetal_fraction and fetal_fraction <= FF_TRESHOLD:
         return "danger"
     else:
         return "default"
 
+
 def get_sample_warnings(sample):
+    """"""
+
     sample_warnings = {}
     fetal_fraction = sample.get('FF_Formatted')
     sample_warnings["FF_Formatted"] = _get_ff_warning(fetal_fraction)
     for key in ["Zscore_13", "Zscore_18", "Zscore_21"]:
         z_score = sample.get(key)
         sample_warnings[key] = _get_tris_warning(z_score, fetal_fraction)
-
-    return sample_warnings
 
+    return sample_warnings
 
 
 def _get_tris_warning(z_score: float, fetal_fraction):
     """Get automated trisomi warning, based on preset Zscore thresholds"""
+
     if fetal_fraction is None or z_score is None:
         return "default"
 
@@ -112,6 +111,7 @@ def get_scatter_data_for_coverage_plot(samples):
             data[sample_id]["x"].append(chr)
     return data
 
+
 def get_box_data_for_coverage_plot(samples):
     """Coverage Ratio data for Coverage Plot."""
     data = {}
@@ -202,8 +202,12 @@ def get_ff_cases(adapter, batch_id):
             }
         },
     ]
-    data = list(adapter.sample_aggregate(pipe))[0]
+    aggregation = list(adapter.sample_aggregate(pipe))
+
     massaged_data = {}
+    if not aggregation:
+        return massaged_data
+    data = aggregation[0]
     for i, sample_id in enumerate(data["names"]):
         massaged_data[sample_id] = {
             "FFY": data["FFY"][i],
@@ -345,14 +349,14 @@ def get_last_batches(adapter, nr: int) -> list:
     batch_sort_aggregation = [{'$sort': {'SequencingDate': -1}}]
     sorted_batches = list(adapter.batch_aggregate(batch_sort_aggregation))
     if len(sorted_batches) > nr:
-        sorted_batches = sorted_batches[0:nr] 
+        sorted_batches = sorted_batches[0:nr]
 
-    return(sorted_batches)
+    return (sorted_batches)
 
 
 # Statistics
 
-def get_statistics_for_scatter_plot(batches: list, fields: list)-> dict:
+def get_statistics_for_scatter_plot(batches: list, fields: list) -> dict:
     """Formating data for scatter plot"""
 
     scatter_plot_data = {}
@@ -371,24 +375,20 @@ def get_statistics_for_box_plot(adapter, batches: list, fields: list):
 
     match = {'$match': {'SampleProject': {'$in': batches}}}
     lookup = {'$lookup': {
-                'from': 'batch', 
-                'localField': 'SampleProject', 
-                'foreignField': '_id', 
-                'as': 'batch'}} 
+        'from': 'batch',
+        'localField': 'SampleProject',
+        'foreignField': '_id',
+        'as': 'batch'}}
     unwind = {'$unwind': {'path': '$batch'}}
     group = {'$group': {'_id': {
-                            'batch': '$SampleProject', 
-                            'date': '$batch.SequencingDate'}}}
+        'batch': '$SampleProject',
+        'date': '$batch.SequencingDate'}}}
 
     for field in fields:
         group['$group'][field] = {'$push': f"${field}"}
 
     pipe = [match, lookup, unwind, group]
-            #maybe add a fina sort to the pipe
+    # maybe add a fina sort to the pipe
     box_plot_data = list(adapter.sample_aggregate(pipe))
-
-    return box_plot_data
-
-
-
 
+    return box_plot_data