From 9b1aecdbb51c7cb843ca79ab430d8dc2b9d3767e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 24 Jun 2020 15:35:47 -0500
Subject: Fixed issue where scatterplot had different N than correlation
 results + fixed some aesthetic issues with correlatoin results table

---
 wqflask/wqflask/correlation/corr_scatter_plot.py | 23 ++++++++++++++++-------
 wqflask/wqflask/templates/correlation_page.html  | 24 ++++++++----------------
 2 files changed, 24 insertions(+), 23 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 04ec427d..819836b1 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -4,7 +4,7 @@ import math
 
 from flask import g
 
-from base.trait import create_trait
+from base.trait import create_trait, retrieve_sample_data
 from base import data_set
 from utility import corr_result_helpers
 from scipy import stats
@@ -17,12 +17,21 @@ class CorrScatterPlot(object):
     """Page that displays a correlation scatterplot with a line fitted to it"""
 
     def __init__(self, params):
-        self.data_set_1 = data_set.create_dataset(params['dataset_1'])
-        self.data_set_2 = data_set.create_dataset(params['dataset_2'])
-        #self.data_set_3 = data_set.create_dataset(params['dataset_3'])
-        self.trait_1 = create_trait(name=params['trait_1'], dataset=self.data_set_1)
-        self.trait_2 = create_trait(name=params['trait_2'], dataset=self.data_set_2)
-        #self.trait_3 = create_trait(name=params['trait_3'], dataset=self.data_set_3)
+        self.dataset_1 = data_set.create_dataset(params['dataset_1'])
+        self.dataset_2 = data_set.create_dataset(params['dataset_2'])
+        #self.dataset_3 = data_set.create_dataset(params['dataset_3'])
+        self.trait_1 = create_trait(name=params['trait_1'], dataset=self.dataset_1)
+        self.trait_2 = create_trait(name=params['trait_2'], dataset=self.dataset_2)
+        #self.trait_3 = create_trait(name=params['trait_3'], dataset=self.dataset_3)
+
+        primary_samples = self.dataset_1.group.samplelist
+        if self.dataset_1.group.parlist != None:
+            primary_samples += self.dataset_1.group.parlist
+        if self.dataset_1.group.f1list != None:
+            primary_samples += self.dataset_1.group.f1list
+
+        self.trait_1 = retrieve_sample_data(self.trait_1, self.dataset_1, primary_samples)
+        self.trait_2 = retrieve_sample_data(self.trait_2, self.dataset_2, primary_samples)
 
         samples_1, samples_2, num_overlap = corr_result_helpers.normalize_values_with_samples(self.trait_1.data, self.trait_2.data)
 
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 71705390..f429948d 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -4,6 +4,7 @@
     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
+    <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
 {% endblock %}
 {% block content %}
     <div class="container" style="min-width: 1250px;">
@@ -114,8 +115,8 @@
         <div style="margin-bottom: 5px;">
             <b>Show/Hide Columns:</b>
         </div>
-        <div style="width: {% if target_dataset.type == "ProbeSet" %}1600px{% elif target_dataset.type == "Publish" %}1400px{% else %}800px{% endif %};">
-            <table id="trait_table" class="display dataTable nowrap" style="font-size: 12px; float: left;">
+        <div style="width: 100%; min-width: {% if target_dataset.type == "ProbeSet" %}1700px{% elif target_dataset.type == "Publish" %}1600px{% else %}600px{% endif %};">
+            <table id="trait_table" class="table-hover table-striped cell-border" style="float: left;">
                 <thead>
                     <tr>
                         <th></th>
@@ -143,7 +144,7 @@
                         <td data-export="{{ trait.description_display }}">{{ trait.description_display }}</TD>
                         <td data-export="{{ trait.location_repr }}" style="white-space: nowrap;">{{ trait.location_repr }}</td>
                         <td data-export="{{ '%0.3f' % trait.mean|float }}" align="right">{{ '%0.3f' % trait.mean|float }}</td>
-                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }} align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
+                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
                         <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td>
                         <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td>
                         {% if trait.lit_corr == "" or trait.lit_corr == 0.000 %}
@@ -167,8 +168,8 @@
                         {% else %}
                         <TD data-export="N/A">N/A</TD>
                         {% endif %}
-                        <td data-export="{{ trait.description_display }}">{% if trait.description_display|length > 50 %}{{ trait.description_display[:50] }}...{% else %}{{ trait.description_display }}{% endif %}</td>
-                        <td data-export="{{ trait.authors }}">{{ trait.authors }}</td>
+                        <td data-export="{{ trait.description_display }}">{% if trait.description_display|length > 70 %}{{ trait.description_display[:70] }}...{% else %}{{ trait.description_display }}{% endif %}</td>
+                        <td data-export="{{ trait.authors }}">{% if trait.authors.split(',') > 6 %}{{ trait.authors.split(',')[:6]|join(', ') }}, et al.{% else %}{{ trait.authors }}{% endif %}</td>
                         <td data-export="{{ trait.pubmed_text }}">
                             <a href="{{ trait.pubmed_link }}">
                                 {{ trait.pubmed_text }}
@@ -211,7 +212,6 @@
     </script>
 
     <script type="text/javascript" charset="utf-8">
-
         $.fn.dataTable.ext.order['dom-innertext'] = function (settings, col) {
           return this.api().column(col, { order: 'index' }).nodes().map(function (td, i) {
             return Math.abs(parseFloat($('a', td).text()));
@@ -424,16 +424,8 @@
                     { "type": "natural" }
                 ],
                 "createdRow": function ( row, data, index ) {
-                    $('td', row).eq(3).attr('title', $('td', row).eq(3).text());
-                    if ($('td', row).eq(3).text().length > 50) {
-                        $('td', row).eq(3).text($('td', row).eq(3).text().substring(0, 50));
-                        $('td', row).eq(3).text($('td', row).eq(3).text() + '...')
-                    }
-                    $('td', row).eq(4).attr('title', $('td', row).eq(4).text());
-                    if ($('td', row).eq(4).text().length > 40) {
-                        $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 40));
-                        $('td', row).eq(4).text($('td', row).eq(4).text() + '...')
-                    }
+                    $('td', row).eq(4).text(decodeURIComponent(escape($('td', row).eq(4).text())));
+                    $('td', row).eq(5).text(decodeURIComponent(escape($('td', row).eq(5).text())));
                 },
                 "order": [[9, "asc" ]],
                 "sDom": "Btir",
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