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-rw-r--r--wqflask/wqflask/static/new/javascript/biodalliance.js1
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html68
-rw-r--r--wqflask/wqflask/views.py3
3 files changed, 64 insertions, 8 deletions
diff --git a/wqflask/wqflask/static/new/javascript/biodalliance.js b/wqflask/wqflask/static/new/javascript/biodalliance.js
index b6808d8a..3cfc26eb 100644
--- a/wqflask/wqflask/static/new/javascript/biodalliance.js
+++ b/wqflask/wqflask/static/new/javascript/biodalliance.js
@@ -23,6 +23,7 @@ BD.createBrowser = function(chr, start, end, speciesName, sources) {
 
         sources: sources,
 
+        maxHeight: 1000,
         setDocumentTitle: false,
         prefix: '/dalliance/',
         workerPrefix: 'build/',
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 47e282cf..aba903c7 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -266,8 +266,9 @@
          checking the headers */
       list = [
       "/static/new/javascript/biodalliance.js",
-      "http://d3js.org/d3.v3.min.js",
+      "/dalliance/build/dalliance-all.js",
       "/static/new/js_external/underscore-min.js",
+      "http://d3js.org/d3.v3.min.js",
       "https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"
       ];
       for (var i = 0; i < list.length; i++) {
@@ -280,8 +281,8 @@
           },
           error: function() {
             // page does not exist
-            console.log("Failed to load "+url);
-            alert("Failed to load Javascript for "+url);
+            console.log("Failed to load "+this.url);
+            alert("Failed to load Javascript for "+this.url);
           }
       })};
     </script>
@@ -369,6 +370,55 @@
                    tier_type: 'sequence',
                    provides_entrypoints: true
      });
+     BD.putSource({name: 'Genotype',
+                   controlURI: "http://test-gn2.genenetwork.org/api_pre1/genotype/mouse/BXD.json",
+                   URIBase: "http://test-gn2.genenetwork.org/api_pre1/genotype/mouse/",
+                   tier_type:            'rqtl-genotype',
+                   pinned: true,
+                   transposed: true,
+                   style: [
+                       { type: "default",
+                         method: "U",
+                         style: { glyph: "BOX",
+                                  LINE: "0.5",
+                                  FGCOLOR: "black",
+                                  BGCOLOR: "white",
+                                  BGITEM: "true",
+                                  HEIGHT: "2",
+                                  BUMP: "true",
+                         }},
+                       { type: "default",
+                         method: "B",
+                         style: { glyph: "BOX",
+                                  LINE: "0.5",
+                                  FGCOLOR: "blue",
+                                  BGCOLOR: "blue",
+                                  BGITEM: "true",
+                                  HEIGHT: "2",
+                                  BUMP: "true",
+                         }},
+                       { type: "default",
+                         method: "H",
+                         style: { glyph: "BOX",
+                                  LINE: "0.5",
+                                  FGCOLOR: "green",
+                                  BGCOLOR: "green",
+                                  BGITEM: "true",
+                                  HEIGHT: "2",
+                                  BUMP: "true",
+                         }},
+                       { type: "default",
+                         method: "D",
+                         style: { glyph: "BOX",
+                                  LINE: "0.5",
+                                  FGCOLOR: "red",
+                                  BGCOLOR: "red",
+                                  BGITEM: "true",
+                                  HEIGHT: "2",
+                                  BUMP: "true",
+                         }},
+                   ]
+     });
      BD.putSource({name: 'QTL',
                    tier_type: 'qtl',
                    uri: 'http://localhost:5003/generated_text/{{csv_filename}}',
@@ -377,16 +427,20 @@
                        style: {
                            glyph: "LINEPLOT",
                            MIN: 0,
-                           MAX: 2.5,
-                           HEIGHT: 120,
+                           MAX: 3,
+                           HEIGHT: 200,
                            STEPS: 500,
                            COLOR1: "blue",
                        }
-                   }]
+                   }],
+     });
+     BD.putSource({name: 'SNP density',
+                   jbURI: "http://test-gn2.genenetwork.org/api_pre1/snp",
+                   jbQuery: "",
+                   stylesheet_uri: "http://test-gn2.genenetwork.org/api_pre1/stylesheets/snp-stylesheet.xml",
      });
     </script>
 
-
     <script type="text/javascript" charset="utf-8">
         $(document).ready( function () {
             BD.putData({species: "{{ dataset.group.species }}" });
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 5cc22cc4..14e019d2 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -481,7 +481,8 @@ def marker_regression_page():
             writer = csv.writer(csv_file)
             writer.writerow(("Locus", "Chr", "Mb", "LOD"))
             for (row) in qtl_results:
-                writer.writerow((row["name"], row["chr"], row["Mb"], row["lod_score"]))
+                score = row["lod_score"] if "lod_score" in row else row["lrs_value"]
+                writer.writerow((row["name"], row["chr"], row["Mb"], score))
 
 
         result = template_vars.__dict__