Handle Effect Size plots on the scatterplot page

Added a new parameter to the scatterplot page ('effect') that causes the figures to be drawn differently. For example:
- The plot width is different
- Spearman Rank plot isn't displayed/generated
- The number of X-axis ticks is explicitly set to 3, with no decimal places

4 files changed, 106 insertions, 95 deletions

diff --git a/gn2/wqflask/correlation/corr_scatter_plot.py b/gn2/wqflask/correlation/corr_scatter_plot.py
index ab130cc5..79905cc2 100644
--- a/gn2/wqflask/correlation/corr_scatter_plot.py
+++ b/gn2/wqflask/correlation/corr_scatter_plot.py
@@ -45,6 +45,8 @@ class CorrScatterPlot:
         if self.dataset_1.group.f1list != None:
             primary_samples += self.dataset_1.group.f1list
 
+        self.effect_plot = True if 'effect' in params else False
+
         if 'dataid' in params:
             trait_data_dict = json.loads(Redis.get(params['dataid']))
             trait_data = {key:webqtlCaseData.webqtlCaseData(key, float(trait_data_dict[key])) for (key, value) in trait_data_dict.items() if trait_data_dict[key] != "x"}
@@ -116,6 +118,7 @@ class CorrScatterPlot:
 
         self.js_data = dict(
             data=self.data,
+            effect_plot=self.effect_plot,
             rdata=self.rdata,
             indIDs=self.indIDs,
             trait_1=self.trait_1.dataset.name + ": " + str(self.trait_1.name),
diff --git a/gn2/wqflask/static/new/javascript/draw_corr_scatterplot.js b/gn2/wqflask/static/new/javascript/draw_corr_scatterplot.js
index f883c0d9..9a6d317d 100644
--- a/gn2/wqflask/static/new/javascript/draw_corr_scatterplot.js
+++ b/gn2/wqflask/static/new/javascript/draw_corr_scatterplot.js
@@ -24,8 +24,6 @@ if (y_val_range >= 2 && y_val_range < 8){
   y_tick_digits = 'f'
 }
 
-console.log("y_digits:", y_tick_digits)
-
 var layout = {
     height: 700,
     width: 800,
@@ -140,12 +138,8 @@ var modebar_options = {
 
 cofactor1_dict = {}
 ranked_cofactor1_dict = {}
-//cofactor1_values = []
-//ranked_cofactor1_values = []
 cofactor2_dict = {}
 ranked_cofactor2_dict = {}
-//cofactor2_values = []
-//ranked_cofactor2_values = []
 cofactor3_dict = {}
 ranked_cofactor3_dict = {}
 
@@ -176,6 +170,15 @@ function drawg() {
       }
     }
 
+    // Change some plot settings if the plot is an Effect Size plot
+    if (js_data.effect_plot) {
+      layout['width'] = 500
+      layout['xaxis']['nticks'] = 3
+      layout['xaxis']['tickformat'] = '.0f'
+      layout['yaxis']['nticks'] = 3
+      layout['yaxis']['tickformat'] = '.0f'
+    }
+
     Plotly.newPlot('scatterplot2', [trace2, trace1], layout, modebar_options)
 
 }
@@ -760,7 +763,9 @@ function chartupdatedata() {
 }
 
 drawg();
-srdrawg();
+if (!js_data.effect_plot) {
+  srdrawg();
+}
 
 $(".chartupdatewh").change(function () {
     chartupdatewh();
diff --git a/gn2/wqflask/templates/corr_scatterplot.html b/gn2/wqflask/templates/corr_scatterplot.html
index c2586bc0..9532726c 100644
--- a/gn2/wqflask/templates/corr_scatterplot.html
+++ b/gn2/wqflask/templates/corr_scatterplot.html
@@ -126,18 +126,20 @@
     <li {% if method == 'pearson' %}class="active"{% endif %}>
       <a href="#tp1" data-toggle="tab">Pearson</a>
     </li>
+    {% if effect_plot == false %}
     <li {% if method == 'spearman' %}class="active"{% endif %}>
       <a href="#tp2" data-toggle="tab">Spearman Rank</a>
     </li>
+    {% endif %}
   </ul>
 
-  <div class="tab-content" style="width: 800px;">
+  <div class="tab-content" style="width: {% if effect_plot %}500{% else %}800{% endif %}px;">
 
     <div class="tab-pane {% if method == 'pearson' %}active{% endif %}" id="tp1">
       <br>
       <div id="scatterplot2"></div>
       <br>
-      <div style="min-width: 700px; overflow: hidden;">
+      <div style="width: {% if effect_plot %}500{% else %}800{% endif %}px; overflow: hidden;">
       <div style="margin-left: 50px; min-width: 300px;">
         {% if trait_1.dataset.type == "ProbeSet" %}
         <div>
@@ -248,101 +250,102 @@
       </div>
     </div>
 
+    {% if effect_plot == false %}
     <div class="tab-pane {% if method == 'spearman' %}active{% endif %}" id="tp2">
       <br>
       <div id="srscatterplot2"></div>
       <br>
-      <div class="row" style="min-width: 700px; overflow: hidden;">
-      <div style="margin-left: 50px; min-width: 300px;">
-        {% if trait_1.dataset.type == "ProbeSet" %}
-        <div>
-          X axis:
-          <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
-            {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.tissue + " "  + trait_1.dataset.name + ": " + trait_1.name|string}}
-          </a>
-        </div>
-        <div>
-          [{{trait_1.symbol}} on {{trait_1.location_repr}} Mb]
-          {{trait_1.description_display}}
-        </div>
-        {% elif trait_1.dataset.type == "Publish" %}
-        <div>
-          X axis:
-          <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
-            {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.name + ": " + trait_1.name|string}}
-          </a>
-        </div>
-        <div>
-          <a href="{{trait_1.pubmed_link}}">PubMed: {{trait_1.pubmed_text}}</a>
+      <div class="row" style="width: 800px; overflow: hidden;">
+        <div style="margin-left: 50px; min-width: 300px;">
+          {% if trait_1.dataset.type == "ProbeSet" %}
+          <div>
+            X axis:
+            <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
+              {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.tissue + " "  + trait_1.dataset.name + ": " + trait_1.name|string}}
+            </a>
+          </div>
+          <div>
+            [{{trait_1.symbol}} on {{trait_1.location_repr}} Mb]
             {{trait_1.description_display}}
-        </div>
-        {% endif %}
+          </div>
+          {% elif trait_1.dataset.type == "Publish" %}
+          <div>
+            X axis:
+            <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
+              {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.name + ": " + trait_1.name|string}}
+            </a>
+          </div>
+          <div>
+            <a href="{{trait_1.pubmed_link}}">PubMed: {{trait_1.pubmed_text}}</a>
+              {{trait_1.description_display}}
+          </div>
+          {% endif %}
 
-        <br/>
+          <br/>
 
-        {% if trait_2.dataset.type == "ProbeSet" %}
-        <div>
-          Y axis:
-          <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
-            {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.tissue + " "  + trait_2.dataset.name + ": " + trait_2.name|string}}
-          </a>
-        </div>
-        <div>
-          [{{trait_2.symbol}} on {{trait_2.location_repr}} Mb]
-          {{trait_2.description_display}}
-        </div>
-        {% elif trait_2.dataset.type == "Publish" %}
-        <div>
-          Y axis:
-          <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
-            {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.name + ": " + trait_2.name|string}}
-          </a>
-        </div>
-        <div>
-          <a href="{{trait_2.pubmed_link}}">PubMed: {{trait_2.pubmed_text}}</a>
+          {% if trait_2.dataset.type == "ProbeSet" %}
+          <div>
+            Y axis:
+            <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
+              {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.tissue + " "  + trait_2.dataset.name + ": " + trait_2.name|string}}
+            </a>
+          </div>
+          <div>
+            [{{trait_2.symbol}} on {{trait_2.location_repr}} Mb]
             {{trait_2.description_display}}
+          </div>
+          {% elif trait_2.dataset.type == "Publish" %}
+          <div>
+            Y axis:
+            <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
+              {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.name + ": " + trait_2.name|string}}
+            </a>
+          </div>
+          <div>
+            <a href="{{trait_2.pubmed_link}}">PubMed: {{trait_2.pubmed_text}}</a>
+              {{trait_2.description_display}}
+          </div>
+          {% endif %}
+        </div>
+        <div style="float: left; margin-top: 30px;">
+          <table class="table table-hover table-striped table-bordered" style="width: 80%; margin-left: 60px; text-align: right;">
+            <thead>
+              <tr><th style="text-align: right;">Statistic</th><th style="text-align: right;">Value</th></tr>
+            </thead>
+            <tbody>
+              <tr>
+                <td>Number</td>
+                <td>{{jsdata.num_overlap}}</td>
+              </tr>
+              <tr>
+                <td>Slope</td>
+                <td>{{ jsdata.srslope_string }}</td>
+              </tr>
+              <tr>
+                <td>Intercept</td>
+                <td>{{'%0.3f' % jsdata.srintercept}}</td>
+              </tr>
+              <tr>
+                <td>r value</td>
+                <td>{{'%0.3f' % jsdata.srr_value}}</td>
+              </tr>
+        <tr>
+                <td>P value</td>
+                <td>{% if jsdata.srp_value < 0.001 %}{{'%0.3e' % jsdata.srp_value}}{% else %}{{'%0.3f' % jsdata.srp_value}}{% endif %}</td>
+              </tr>
+              <tr>
+                <td style="text-align: left;" colspan="2">
+                  Regression Line
+                  <br>
+                  y = {{ jsdata.srslope_string }} * x {% if jsdata.srintercept < 0 %}- {{'%0.3f' % (jsdata.srintercept * -1)}}{% else %}+ {{'%0.3f' % jsdata.srintercept}}{% endif %}
+                </td>
+              </tr>
+            </tbody>
+          </table>
         </div>
-        {% endif %}
-      </div>
-      <div style="float: left; margin-top: 30px;">
-        <table class="table table-hover table-striped table-bordered" style="width: 80%; margin-left: 60px; text-align: right;">
-          <thead>
-            <tr><th style="text-align: right;">Statistic</th><th style="text-align: right;">Value</th></tr>
-          </thead>
-          <tbody>
-            <tr>
-              <td>Number</td>
-              <td>{{jsdata.num_overlap}}</td>
-            </tr>
-            <tr>
-              <td>Slope</td>
-              <td>{{ jsdata.srslope_string }}</td>
-            </tr>
-            <tr>
-              <td>Intercept</td>
-              <td>{{'%0.3f' % jsdata.srintercept}}</td>
-            </tr>
-            <tr>
-              <td>r value</td>
-              <td>{{'%0.3f' % jsdata.srr_value}}</td>
-            </tr>
-	    <tr>
-              <td>P value</td>
-              <td>{% if jsdata.srp_value < 0.001 %}{{'%0.3e' % jsdata.srp_value}}{% else %}{{'%0.3f' % jsdata.srp_value}}{% endif %}</td>
-            </tr>
-            <tr>
-              <td style="text-align: left;" colspan="2">
-                Regression Line
-                <br>
-                y = {{ jsdata.srslope_string }} * x {% if jsdata.srintercept < 0 %}- {{'%0.3f' % (jsdata.srintercept * -1)}}{% else %}+ {{'%0.3f' % jsdata.srintercept}}{% endif %}
-              </td>
-            </tr>
-          </tbody>
-        </table>
-      </div>
       </div>
-  </div>
-
+    </div>
+    {% endif %}
 </div>
 
 {% endblock %}
diff --git a/gn2/wqflask/templates/mapping_results.html b/gn2/wqflask/templates/mapping_results.html
index 2b1660fd..c27de85e 100644
--- a/gn2/wqflask/templates/mapping_results.html
+++ b/gn2/wqflask/templates/mapping_results.html
@@ -416,7 +416,7 @@
                 'data': null,
                 'render': function(data, type, row, meta) {
                   {% if geno_db_exists == "True" %}
-                  return '<a target"_blank" href="corr_scatter_plot?method=pearson&dataset_1={{ dataset.group.name }}Geno&dataset_2={{ dataset.name }}&trait_1=' + data.name + '&trait_2={{ this_trait.name }}&cached_trait=trait_2&dataid={{ dataid }}">' + String(parseFloat(data.additive).toFixed(3)) + '</a>'
+                  return '<a target"_blank" href="corr_scatter_plot?method=pearson&dataset_1={{ dataset.group.name }}Geno&dataset_2={{ dataset.name }}&trait_1=' + data.name + '&trait_2={{ this_trait.name }}&cached_trait=trait_2&dataid={{ dataid }}&effect=True">' + String(parseFloat(data.additive).toFixed(3)) + '</a>'
                   {% else %}
                   return String(parseFloat(data.additive).toFixed(3))
                   {% endif %}