Fixed the path for the json file in gen_select_dataset.py since it was wrong and uncommented simplejson import

Added "Reset" option to network graph that returns all the nodes/edges

Made the visualization options area in the network graph a little wider

6 files changed, 128 insertions, 83 deletions

diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 23adc4f9..542c0d83 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -49,7 +49,7 @@ from utility.tools import locate, locate_ignore_error, TEMPDIR, SQL_URI
 
 import MySQLdb
 
-# import simplejson as json
+import simplejson as json
 import urlparse
 
 
@@ -289,7 +289,7 @@ def main():
 
     #print("data:", data)
 
-    output_file = """./wqflask/wqflask/static/new/javascript/dataset_menu_structure.json"""
+    output_file = """./wqflask/static/new/javascript/dataset_menu_structure.json"""
 
     with open(output_file, 'w') as fh:
         json.dump(data, fh, indent="   ", sort_keys=True)
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index 1d725c4c..cebe5c03 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -167,9 +167,9 @@ class NetworkGraph(object):
                     if abs(sample_r) > max_corr:
                         max_corr = abs(sample_r)
  
-                    edge_data = {'id' : this_trait.name + '_to_' + target_trait.name,
-                                 'source' : this_trait.name + ":" + this_trait.dataset.name,
-                                 'target' : target_trait.name + ":" + target_trait.dataset.name,
+                    edge_data = {'id' : str(this_trait.name) + '_to_' + str(target_trait.name),
+                                 'source' : str(this_trait.name) + ":" + str(this_trait.dataset.name),
+                                 'target' : str(target_trait.name) + ":" + str(target_trait.dataset.name),
                                  'correlation' : round(sample_r, 3),
                                  'abs_corr' : abs(round(sample_r, 3)),
                                  'p_value' : round(sample_p, 3),
@@ -181,8 +181,9 @@ class NetworkGraph(object):
                                  
                     self.edges_list.append(edge_dict)
       
-            node_dict = { 'data' : {'id' : this_trait.name + ":" + this_trait.dataset.name, 
+            node_dict = { 'data' : {'id' : str(this_trait.name) + ":" + str(this_trait.dataset.name), 
                                     'label' : this_trait.name,
+                                    'symbol' : this_trait.symbol,
                                     'geneid' : this_trait.geneid,
                                     'omim' : this_trait.omim,
                                     'max_corr' : max_corr } }
diff --git a/wqflask/wqflask/static/new/css/network_graph.css b/wqflask/wqflask/static/new/css/network_graph.css
index c01c0d24..1cba546a 100644
--- a/wqflask/wqflask/static/new/css/network_graph.css
+++ b/wqflask/wqflask/static/new/css/network_graph.css
@@ -13,7 +13,7 @@
 #secondaryContent {
     position: relative;
     float: left;
-    width: 16.5em;
+    width: 18.5em;
     padding: 1em 1em 1em 1em;
     background: #fff url('/static/new/images/a1.gif') top right repeat-y;
 }
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 750a9118..d3db1853 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -317,6 +317,30 @@
             ]
          },
          "GTEx": {
+            "Adipose tissue, subcutaneous mRNA": [
+               [
+                  "580",
+                  "GTEx_log2_Subcu_0314",
+                  "GTEx Human Subcutaneous (Mar14) RPKM Log2"
+               ],
+               [
+                  "530",
+                  "GTEx_Subcu_0414",
+                  "GTEx Human Subcutaneous (Apr14) RPKM"
+               ]
+            ],
+            "Adipose tissue, visceral mRNA": [
+               [
+                  "587",
+                  "GTEx_log2_Visce_0314",
+                  "GTEx Human Visceral (Mar14) RPKM Log2"
+               ],
+               [
+                  "537",
+                  "GTEx_Visce_0414",
+                  "GTEx Human Visceral (Apr14) RPKM"
+               ]
+            ],
             "Adrenal Gland mRNA": [
                [
                   "545",
@@ -773,18 +797,6 @@
                   "GTEx Human Stomach (Apr14) RPKM"
                ]
             ],
-            "Subcutaneous mRNA": [
-               [
-                  "580",
-                  "GTEx_log2_Subcu_0314",
-                  "GTEx Human Subcutaneous (Mar14) RPKM Log2"
-               ],
-               [
-                  "530",
-                  "GTEx_Subcu_0414",
-                  "GTEx Human Subcutaneous (Apr14) RPKM"
-               ]
-            ],
             "Substantia Nigra mRNA": [
                [
                   "581",
@@ -857,18 +869,6 @@
                   "GTEx Human Vagina (Apr14) RPKM"
                ]
             ],
-            "Visceral mRNA": [
-               [
-                  "587",
-                  "GTEx_log2_Visce_0314",
-                  "GTEx Human Visceral (Mar14) RPKM Log2"
-               ],
-               [
-                  "537",
-                  "GTEx_Visce_0414",
-                  "GTEx Human Visceral (Apr14) RPKM"
-               ]
-            ],
             "Whole Blood mRNA": [
                [
                   "588",
@@ -883,6 +883,20 @@
             ]
          },
          "GTEx_v5": {
+            "Adipose tissue, subcutaneous mRNA": [
+               [
+                  "718",
+                  "GTEXv5_AdipSub_0915",
+                  "GTEXv5 Human Adipose Subcutaneous RefSeq (Sep15) RPKM log2"
+               ]
+            ],
+            "Adipose tissue, visceral mRNA": [
+               [
+                  "719",
+                  "GTEXv5_AdiVis_0915",
+                  "GTEXv5 Human Adipose Visceral Omentum RefSeq (Sep15) RPKM log2"
+               ]
+            ],
             "Adrenal Gland mRNA": [
                [
                   "720",
@@ -1191,13 +1205,6 @@
                   "GTEXv5 Human Stomach RefSeq (Sep15) RPKM log2"
                ]
             ],
-            "Subcutaneous mRNA": [
-               [
-                  "718",
-                  "GTEXv5_AdipSub_0915",
-                  "GTEXv5 Human Adipose Subcutaneous RefSeq (Sep15) RPKM log2"
-               ]
-            ],
             "Substantia Nigra mRNA": [
                [
                   "737",
@@ -1240,13 +1247,6 @@
                   "GTEXv5 Human Vagina RefSeq (Sep15) RPKM log2"
                ]
             ],
-            "Visceral mRNA": [
-               [
-                  "719",
-                  "GTEXv5_AdiVis_0915",
-                  "GTEXv5 Human Adipose Visceral Omentum RefSeq (Sep15) RPKM log2"
-               ]
-            ],
             "Whole Blood mRNA": [
                [
                   "770",
@@ -1609,9 +1609,30 @@
                ]
             ]
          },
+         "B6D2": {
+            "Phenotypes": [
+               [
+                  "None",
+                  "B6D2Publish",
+                  "B6D2 Published Phenotypes"
+               ]
+            ],
+            "Retina mRNA": [
+               [
+                  "803",
+                  "UTHSC_mm9_B6D2_Ret_0916",
+                  "UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Gene Level RMA"
+               ]
+            ]
+         },
          "B6D2F2": {
             "Brain mRNA": [
                [
+                  "78",
+                  "BRF2_M_0805_P",
+                  "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN"
+               ],
+               [
                   "77",
                   "BRF2_M_0805_R",
                   "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA"
@@ -1622,11 +1643,6 @@
                   "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5"
                ],
                [
-                  "78",
-                  "BRF2_M_0805_P",
-                  "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN"
-               ],
-               [
                   "33",
                   "BRF2_M_0304_P",
                   "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN"
@@ -2306,16 +2322,16 @@
             ],
             "Kidney mRNA": [
                [
-                  "239",
-                  "MA_M2F_0706_R",
-                  "Mouse kidney M430v2 Female (Aug06) RMA"
-               ],
-               [
                   "240",
                   "MA_M2M_0706_R",
                   "Mouse kidney M430v2 Male (Aug06) RMA"
                ],
                [
+                  "239",
+                  "MA_M2F_0706_R",
+                  "Mouse kidney M430v2 Female (Aug06) RMA"
+               ],
+               [
                   "118",
                   "MA_M2_0806_R",
                   "Mouse kidney M430v2 Sex Balanced (Aug06) RMA"
@@ -2495,16 +2511,16 @@
             ],
             "Neocortex mRNA": [
                [
-                  "375",
-                  "DevNeocortex_ILM6.2P14RInv_1111",
-                  "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv"
-               ],
-               [
                   "374",
                   "DevNeocortex_ILM6.2P3RInv_1111",
                   "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv"
                ],
                [
+                  "375",
+                  "DevNeocortex_ILM6.2P14RInv_1111",
+                  "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv"
+               ],
+               [
                   "284",
                   "HQFNeoc_1210v2_RankInv",
                   "HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv"
@@ -3017,6 +3033,11 @@
             ],
             "Hippocampus mRNA": [
                [
+                  "214",
+                  "Illum_LXS_Hipp_NOE_1008",
+                  "Hippocampus Illumina NOE (Oct08) RankInv beta"
+               ],
+               [
                   "211",
                   "Illum_LXS_Hipp_RSS_1008",
                   "Hippocampus Illumina RSS (Oct08) RankInv beta"
@@ -3037,11 +3058,6 @@
                   "Hippocampus Illumina RSE (Oct08) RankInv beta"
                ],
                [
-                  "214",
-                  "Illum_LXS_Hipp_NOE_1008",
-                  "Hippocampus Illumina NOE (Oct08) RankInv beta"
-               ],
-               [
                   "143",
                   "Illum_LXS_Hipp_loess0807",
                   "Hippocampus Illumina (Aug07) LOESS"
@@ -3472,6 +3488,10 @@
             "B6BTBRF2"
          ],
          [
+            "B6D2",
+            "Glaucoma and Aged Retina, UTHSC"
+         ],
+         [
             "B6D2F2",
             "B6D2F2"
          ],
@@ -3793,6 +3813,14 @@
          ],
          "GTEx": [
             [
+               "Adipose tissue, subcutaneous mRNA",
+               "Adipose tissue, subcutaneous mRNA"
+            ],
+            [
+               "Adipose tissue, visceral mRNA",
+               "Adipose tissue, visceral mRNA"
+            ],
+            [
                "Adrenal Gland mRNA",
                "Adrenal Gland mRNA"
             ],
@@ -3945,10 +3973,6 @@
                "Stomach mRNA"
             ],
             [
-               "Subcutaneous mRNA",
-               "Subcutaneous mRNA"
-            ],
-            [
                "Substantia Nigra mRNA",
                "Substantia Nigra mRNA"
             ],
@@ -3973,16 +3997,20 @@
                "Vagina mRNA"
             ],
             [
-               "Visceral mRNA",
-               "Visceral mRNA"
-            ],
-            [
                "Whole Blood mRNA",
                "Whole Blood mRNA"
             ]
          ],
          "GTEx_v5": [
             [
+               "Adipose tissue, subcutaneous mRNA",
+               "Adipose tissue, subcutaneous mRNA"
+            ],
+            [
+               "Adipose tissue, visceral mRNA",
+               "Adipose tissue, visceral mRNA"
+            ],
+            [
                "Adrenal Gland mRNA",
                "Adrenal Gland mRNA"
             ],
@@ -4159,10 +4187,6 @@
                "Stomach mRNA"
             ],
             [
-               "Subcutaneous mRNA",
-               "Subcutaneous mRNA"
-            ],
-            [
                "Substantia Nigra mRNA",
                "Substantia Nigra mRNA"
             ],
@@ -4187,10 +4211,6 @@
                "Vagina mRNA"
             ],
             [
-               "Visceral mRNA",
-               "Visceral mRNA"
-            ],
-            [
                "Whole Blood mRNA",
                "Whole Blood mRNA"
             ]
@@ -4363,6 +4383,16 @@
                "Liver mRNA"
             ]
          ],
+         "B6D2": [
+            [
+               "Phenotypes",
+               "Phenotypes"
+            ],
+            [
+               "Retina mRNA",
+               "Retina mRNA"
+            ]
+         ],
          "B6D2F2": [
             [
                "Genotypes",
diff --git a/wqflask/wqflask/static/new/javascript/network_graph.js b/wqflask/wqflask/static/new/javascript/network_graph.js
index da90ae26..e8ca6be0 100644
--- a/wqflask/wqflask/static/new/javascript/network_graph.js
+++ b/wqflask/wqflask/static/new/javascript/network_graph.js
@@ -12,7 +12,7 @@ window.onload=function() {
             selector: 'node',
             style: {
               'background-color': '#666',
-              'label': 'data(id)',
+              'label': 'data(symbol)',
               'font-size': 10
             }
           },
@@ -154,6 +154,15 @@ window.onload=function() {
         
     });
     
+    $('#reset_graph').click(function() {
+        eles.restore() 
+        $('#slide').val(0)
+        cy.layout({ name: $('select[name=layout_select]').val(),
+                    fit: true, // whether to fit the viewport to the graph
+                    padding: 25 // the padding on fit              
+                  });
+    });
+    
     $('select[name=focus_select]').change(function() {
         focus_trait = $(this).val()
 
diff --git a/wqflask/wqflask/templates/network_graph.html b/wqflask/wqflask/templates/network_graph.html
index ec3a7971..57426af7 100644
--- a/wqflask/wqflask/templates/network_graph.html
+++ b/wqflask/wqflask/templates/network_graph.html
@@ -22,6 +22,11 @@
                   <tbody>
                     <tr>
                       <td>
+                        <button id="reset_graph">Reset Graph</button>
+                      </td>
+                    </tr>
+                    <tr>
+                      <td>
                         Focus Trait
                       </td>
                     </tr>
@@ -29,7 +34,7 @@
                       <td>
                         <select name="focus_select">
                           {% for trait in traits %}
-                          <option value="{{ trait.name }}:{{ trait.dataset.name }}">{{ trait.name }}</option>
+                          <option value="{{ trait.name }}:{{ trait.dataset.name }}">{{ trait.symbol }} ({{ trait.name }})</option>
                           {% endfor %}
                         </select>
                       </td>