From b158f11588afc4c93c5daf17ed0195f392e2e2d7 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Fri, 18 Mar 2022 14:56:57 +0300
Subject: integrate scree plot

---
 wqflask/wqflask/templates/correlation_matrix.html | 6 ++++++
 wqflask/wqflask/templates/pca_scree_plot.html     | 6 +++---
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 3da6981c..e90accf2 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -71,6 +71,12 @@
   <button class="btn btn-default" id="export">Download <span class="glyphicon glyphicon-download"></span></button>
 </form>
 <br>
+
+<div style="margin:20x;">
+  {% include 'pca_scree_plot.html' %}
+  
+</div>
+
 {% if pca_works == "True" %}
 <h2>PCA Traits</h2>
 <div style="margin-bottom: 20px; overflow:hidden; width: 450px;">
diff --git a/wqflask/wqflask/templates/pca_scree_plot.html b/wqflask/wqflask/templates/pca_scree_plot.html
index 41036333..b0ef78d0 100644
--- a/wqflask/wqflask/templates/pca_scree_plot.html
+++ b/wqflask/wqflask/templates/pca_scree_plot.html
@@ -15,11 +15,11 @@
 </body>
 <script type="text/javascript" src="{{ url_for('js', filename='plotly/plotly.min.js') }}"></script>
 <script type="text/javascript">
-js_data = { { js_data | safe } }
-
+js_data = {{ js_data | safe }}
 
 let { x_coord, y_coord } = js_data["scree_data"]
 
+
 const layout = {
 
     title: {
@@ -87,7 +87,7 @@ let custom_configs = (filename, download_format, modebar = true) => {
 
 }
 
-Plotly.newPlot(document.getElementById(), data, layout,
+Plotly.newPlot(document.getElementById("scree_plot"), data, layout,
 	custom_configs(file_name = "scree_plot", download_format = "svg"));
 </script>
 
-- 
cgit v1.2.3


From 0964e2563a96130e306edd31cd91fee4b378697d Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Fri, 18 Mar 2022 14:57:25 +0300
Subject: code to fetch scree data from gn3

---
 wqflask/wqflask/correlation_matrix/show_corr_matrix.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 88d62045..cf37b9e9 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -37,6 +37,7 @@ from gn3.computations.pca import compute_pca
 from gn3.computations.pca import process_factor_loadings_tdata
 from gn3.computations.pca import generate_pca_temp_traits
 from gn3.computations.pca import cache_pca_dataset
+from gn3.computations.pca import generate_scree_plot_data
 
 
 class CorrelationMatrix:
@@ -169,6 +170,7 @@ class CorrelationMatrix:
                 pca = self.calculate_pca()
                 self.loadings_array = process_factor_loadings_tdata(
                     factor_loadings=self.loadings, traits_num=len(self.trait_list))
+
             else:
                 self.pca_works = "False"
         except:
@@ -176,6 +178,7 @@ class CorrelationMatrix:
 
         self.js_data = dict(traits=[trait.name for trait in self.traits],
                             groups=groups,
+                            scree_data = self.scree_data,
                             cols=list(range(len(self.traits))),
                             rows=list(range(len(self.traits))),
                             samples=self.all_sample_list,
@@ -187,6 +190,7 @@ class CorrelationMatrix:
 
         self.loadings = pca["components"]
         self.scores = pca["scores"]
+        self.pca_obj = pca["pca"]
 
         this_group_name = self.trait_list[0][1].group.name
         temp_dataset = create_dataset(
@@ -205,6 +209,13 @@ class CorrelationMatrix:
 
         self.pca_trait_ids = list(pca_temp_traits.keys())
 
+        x_coord, y_coord = generate_scree_plot_data(
+            list(self.pca_obj.explained_variance_ratio_))
+
+        self.scree_data = {
+            "x_coord": x_coord,
+            "y_coord": y_coord
+        }
         return pca
 
 
-- 
cgit v1.2.3


From 11c94876a376539030d9645a1779abff62858c65 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Fri, 18 Mar 2022 16:32:28 +0300
Subject: fixes for ImageButtonOptions

---
 wqflask/wqflask/templates/pca_scree_plot.html | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/wqflask/wqflask/templates/pca_scree_plot.html b/wqflask/wqflask/templates/pca_scree_plot.html
index b0ef78d0..e0b854fa 100644
--- a/wqflask/wqflask/templates/pca_scree_plot.html
+++ b/wqflask/wqflask/templates/pca_scree_plot.html
@@ -9,7 +9,7 @@
 
 <body>
     <div>
-        pca scree plot
+        
         <div id="scree_plot" style="width:700px;height:600px;"></div>
     </div>
 </body>
@@ -23,7 +23,7 @@ let { x_coord, y_coord } = js_data["scree_data"]
 const layout = {
 
     title: {
-        text: "<b>Scree Plot</b>",
+        text: "<b>Pca Scree Plot</b>",
         font: {
             "size": 24,
             "family": "Arial",
@@ -77,8 +77,8 @@ let custom_configs = (filename, download_format, modebar = true) => {
         displayModeBar: modebar,
         scrollZoom: false,
         toImageButtonOptions: {
-            download_format,
             filename,
+            format:download_format,
             height: 600,
             width: 700,
             scale: 1
-- 
cgit v1.2.3


From 5c941a9872f70d9be4d54badb536dc5ef04a0223 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Fri, 18 Mar 2022 16:49:00 +0300
Subject: remove correlation test button

---
 wqflask/wqflask/templates/show_trait_calculate_correlations.html | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 16a819fa..2f98f14e 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -119,9 +119,6 @@
               <div class="col-xs-3 controls">
                   <input type="button" class="btn corr_compute submit_special btn-success" data-url="/corr_compute" title="Compute Correlation" value="Compute">
               </div>
-                  <div class="col-xs-3 controls">
-                  <input type="button" class="btn test_corr_compute submit_special btn-success" data-url="/test_corr_compute" title="Compute Correlation" value="Test Compute">
-              </div>
           </div>
       </div>
     </div>
-- 
cgit v1.2.3


From 33605e355b7335138dd75ef3ffe29d095533933d Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Fri, 18 Mar 2022 16:51:30 +0300
Subject: add uniform font for title

---
 wqflask/wqflask/templates/pca_scree_plot.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wqflask/wqflask/templates/pca_scree_plot.html b/wqflask/wqflask/templates/pca_scree_plot.html
index e0b854fa..11bfebff 100644
--- a/wqflask/wqflask/templates/pca_scree_plot.html
+++ b/wqflask/wqflask/templates/pca_scree_plot.html
@@ -27,7 +27,7 @@ const layout = {
         font: {
             "size": 24,
             "family": "Arial",
-            "color": "#FF0000"
+            "color": "#000000"
         }
     },
 
-- 
cgit v1.2.3