Merge pull request #246 from zsloan/master

Added genetic_type to DatasetGroup object to differentiate between wh…

7 files changed, 137 insertions, 115 deletions

diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index ad3eab79..e1df1e63 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -826,7 +826,8 @@ class PositionSearch(DoSearch):
 
     def get_where_clause(self):
         self.search_term = [float(value) if is_number(value) else value for value in self.search_term]
-        self.chr, self.mb_min, self.mb_max = self.search_term[:3]
+        chr, self.mb_min, self.mb_max = self.search_term[:3]
+        self.chr = str(chr).lower()
         self.get_chr()
 
         where_clause = """ %s.Chr = %s and
@@ -846,9 +847,9 @@ class PositionSearch(DoSearch):
             self.chr = int(self.chr)
         except:
             if 'chr' in self.chr:
-                self.chr = int(self.chr.replace('chr', ''))
+                self.chr = self.chr.replace('chr', '')
             else:
-                self.chr = int(self.chr.replace('CHR', ''))
+                self.chr = self.chr.replace('CHR', '')
 
     def run(self):
 
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 3e145e40..5d55ebe1 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -118,7 +118,13 @@ class ShowTrait(object):
 
         self.trait_table_width = get_trait_table_width(self.sample_groups)
 
-        js_data = dict(dataset_type = self.dataset.type,
+        if self.this_trait.symbol:
+            trait_symbol = self.this_trait.symbol
+        else:
+            trait_symbol = None
+        js_data = dict(trait_id = self.this_trait.name,
+                       trait_symbol = trait_symbol,
+                       dataset_type = self.dataset.type,
                        data_scale = self.dataset.data_scale,
                        sample_group_types = self.sample_group_types,
                        sample_lists = sample_lists,
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index ad4d9419..861af3d6 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -117,14 +117,14 @@
                   "Barley1 Leaf MAS 5.0 SCRI (Dec06)"
                ],
                [
-                  "125",
-                  "B30_K_1206_R",
-                  "Barley1 Leaf gcRMA SCRI (Dec06)"
-               ],
-               [
                   "126",
                   "B30_K_1206_Rn",
                   "Barley1 Leaf gcRMAn SCRI (Dec06)"
+               ],
+               [
+                  "125",
+                  "B30_K_1206_R",
+                  "Barley1 Leaf gcRMA SCRI (Dec06)"
                ]
             ],
             "Phenotypes": [
@@ -1526,14 +1526,14 @@
                   "NCI Mammary LMT miRNA v2 (Apr09) RMA"
                ],
                [
-                  "36",
-                  "MA_M_0704_M",
-                  "NCI Mammary mRNA M430 (July04) MAS5"
-               ],
-               [
                   "37",
                   "MA_M_0704_R",
                   "NCI Mammary mRNA M430 (July04) RMA"
+               ],
+               [
+                  "36",
+                  "MA_M_0704_M",
+                  "NCI Mammary mRNA M430 (July04) MAS5"
                ]
             ]
          },
@@ -1591,14 +1591,14 @@
             ],
             "Liver mRNA": [
                [
-                  "38",
-                  "LVF2_M_0704_M",
-                  "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5"
-               ],
-               [
                   "39",
                   "LVF2_M_0704_R",
                   "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA"
+               ],
+               [
+                  "38",
+                  "LVF2_M_0704_M",
+                  "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5"
                ]
             ],
             "Phenotypes": [
@@ -1621,11 +1621,6 @@
          "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"
@@ -1636,19 +1631,24 @@
                   "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"
                ],
                [
-                  "31",
-                  "BRF2_M_0304_M",
-                  "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5"
-               ],
-               [
                   "32",
                   "BRF2_M_0304_R",
                   "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA"
+               ],
+               [
+                  "31",
+                  "BRF2_M_0304_M",
+                  "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5"
                ]
             ],
             "Genotypes": [
@@ -1727,11 +1727,6 @@
             ],
             "Striatum mRNA": [
                [
-                  "83",
-                  "SA_M2_0905_M",
-                  "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5"
-               ],
-               [
                   "85",
                   "SA_M2_0905_P",
                   "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN"
@@ -1740,6 +1735,11 @@
                   "84",
                   "SA_M2_0905_R",
                   "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
+               ],
+               [
+                  "83",
+                  "SA_M2_0905_M",
+                  "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5"
                ]
             ]
          },
@@ -2081,11 +2081,6 @@
                   "Eye M430v2 WT Gpnmb (Sep08) RMA"
                ],
                [
-                  "382",
-                  "Eye_M2_0908_WTWT",
-                  "Eye M430v2 WT WT (Sep08) RMA"
-               ],
-               [
                   "279",
                   "Eye_M2_0908_R_WT",
                   "Eye M430v2 WT Tyrp1 (Sep08) RMA"
@@ -2096,6 +2091,11 @@
                   "Eye M430v2 Mutant Tyrp1 (Sep08) RMA"
                ],
                [
+                  "382",
+                  "Eye_M2_0908_WTWT",
+                  "Eye M430v2 WT WT (Sep08) RMA"
+               ],
+               [
                   "400",
                   "DBA2J-ONH-1212",
                   "Howell et al. 2011, DBA/2J Glaucoma Optic Nerve Head M430 2.0 (Dec12) RMA"
@@ -2332,16 +2332,16 @@
             ],
             "Kidney mRNA": [
                [
-                  "240",
-                  "MA_M2M_0706_R",
-                  "Mouse kidney M430v2 Male (Aug06) RMA"
-               ],
-               [
                   "239",
                   "MA_M2F_0706_R",
                   "Mouse kidney M430v2 Female (Aug06) RMA"
                ],
                [
+                  "240",
+                  "MA_M2M_0706_R",
+                  "Mouse kidney M430v2 Male (Aug06) RMA"
+               ],
+               [
                   "118",
                   "MA_M2_0806_R",
                   "Mouse kidney M430v2 Sex Balanced (Aug06) RMA"
@@ -2352,14 +2352,14 @@
                   "Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN"
                ],
                [
-                  "115",
-                  "MA_M2_0706_R",
-                  "Mouse Kidney M430v2 (Jul06) RMA"
-               ],
-               [
                   "116",
                   "MA_M2_0706_P",
                   "Mouse Kidney M430v2 (Jul06) PDNN"
+               ],
+               [
+                  "115",
+                  "MA_M2_0706_R",
+                  "Mouse Kidney M430v2 (Jul06) RMA"
                ]
             ],
             "Liver Metabolome": [
@@ -2521,16 +2521,16 @@
             ],
             "Neocortex mRNA": [
                [
-                  "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"
                ],
                [
+                  "374",
+                  "DevNeocortex_ILM6.2P3RInv_1111",
+                  "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv"
+               ],
+               [
                   "284",
                   "HQFNeoc_1210v2_RankInv",
                   "HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv"
@@ -2761,11 +2761,6 @@
             ],
             "Ventral Tegmental Area mRNA": [
                [
-                  "228",
-                  "VCUSal_0609_R",
-                  "VCU BXD VTA Sal M430 2.0 (Jun09) RMA"
-               ],
-               [
                   "230",
                   "VCUEtvsSal_0609_R",
                   "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) RMA"
@@ -2774,6 +2769,11 @@
                   "229",
                   "VCUEtOH_0609_R",
                   "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA"
+               ],
+               [
+                  "228",
+                  "VCUSal_0609_R",
+                  "VCU BXD VTA Sal M430 2.0 (Jun09) RMA"
                ]
             ]
          },
@@ -3023,14 +3023,14 @@
             ],
             "Hippocampus mRNA": [
                [
-                  "99",
-                  "HC_M2CB_1205_P",
-                  "Hippocampus Consortium M430v2 CXB (Dec05) PDNN"
-               ],
-               [
                   "100",
                   "HC_M2CB_1205_R",
                   "Hippocampus Consortium M430v2 CXB (Dec05) RMA"
+               ],
+               [
+                  "99",
+                  "HC_M2CB_1205_P",
+                  "Hippocampus Consortium M430v2 CXB (Dec05) PDNN"
                ]
             ],
             "Phenotypes": [
@@ -3097,16 +3097,6 @@
             ],
             "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"
-               ],
-               [
                   "213",
                   "Illum_LXS_Hipp_NOS_1008",
                   "Hippocampus Illumina NOS (Oct08) RankInv beta"
@@ -3122,6 +3112,16 @@
                   "Hippocampus Illumina RSE (Oct08) RankInv beta"
                ],
                [
+                  "214",
+                  "Illum_LXS_Hipp_NOE_1008",
+                  "Hippocampus Illumina NOE (Oct08) RankInv beta"
+               ],
+               [
+                  "211",
+                  "Illum_LXS_Hipp_RSS_1008",
+                  "Hippocampus Illumina RSS (Oct08) RankInv beta"
+               ],
+               [
                   "143",
                   "Illum_LXS_Hipp_loess0807",
                   "Hippocampus Illumina (Aug07) LOESS"
@@ -3212,14 +3212,14 @@
             ],
             "Hippocampus mRNA": [
                [
-                  "272",
-                  "HC_M2_0606_MDP",
-                  "Hippocampus Consortium M430v2 (Jun06) RMA MDP"
-               ],
-               [
                   "273",
                   "UMUTAffyExon_0209_RMA_MDP",
                   "UMUTAffy Hippocampus Exon (Feb09) RMA MDP"
+               ],
+               [
+                  "272",
+                  "HC_M2_0606_MDP",
+                  "Hippocampus Consortium M430v2 (Jun06) RMA MDP"
                ]
             ],
             "Liver mRNA": [
diff --git a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
index 1eeb6e73..e5787564 100644
--- a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
@@ -45,8 +45,7 @@
         chart = nv.models.scatterChart().width(w).height(h).showLegend(true).color(d3.scale.category10().range());
         chart.pointRange([50, 50]);
         chart.legend.updateState(false);
-        chart.xAxis.axisLabel("Theoretical quantiles").tickFormat(d3.format('.02f'));
-        //chart.yAxis.axisLabel("Sample quantiles").tickFormat(d3.format('.02f'));
+        chart.xAxis.axisLabel("Expected Z score").tickFormat(d3.format('.02f'));
         chart.tooltipContent(function(obj) {
           return '<b style="font-size: 20px">' + obj.point.name + '</b>';
         });
@@ -79,7 +78,7 @@
           }
           return results;
         })();
-        chart.yAxis.axisLabel("Sample quantiles").tickFormat(d3.format('.0'+max_decimals.toString()+'f'));
+        chart.yAxis.axisLabel("Trait value").tickFormat(d3.format('.0'+max_decimals.toString()+'f'));
         sw_result = ShapiroWilkW(sorted_values);
         W = sw_result.w.toFixed(3);
         pvalue = sw_result.p.toFixed(3);
@@ -115,7 +114,12 @@
         data = [make_data('samples_primary'), make_data('samples_other')];
         console.log("THE DATA IS:", data);
         d3.select("#prob_plot_container svg").datum(data).call(chart);
-        $("#prob_plot_title").html("<h3>Normal probability plot</h3>" + test_str);
+        if (js_data.trait_symbol != null) {
+            $("#prob_plot_title").html("<h3>" + js_data.trait_symbol + ": " + js_data.trait_id + "</h3>");
+        } else {
+            $("#prob_plot_title").html("<h3>" + js_data.trait_id + "</h3>");
+        }
+        $("#shapiro_wilk_text").html(test_str)
         $("#prob_plot_container .nv-legendWrap").toggle(sample_group === "samples_all");
         return chart;
       };
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index de901ff5..6d3f9326 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -192,7 +192,7 @@
                 {% if 'additive' in trimmed_markers[0] %}
                 <th>Add Eff</th>
                 {% endif %}
-                {% if 'dominance' in trimmed_markers[0] %}
+                {% if 'dominance' in trimmed_markers[0] and dataset.group.genetic_type != "riset" %}
                 <th>Dom Eff</th>
                 {% endif %}
               </tr>
@@ -225,7 +225,7 @@
                 {% if 'additive' in marker %}
                 <td align="right">{{ '%0.3f' | format(marker.additive|float) }}</td>
                 {% endif %}
-                {% if 'dominance' in marker %}
+                {% if 'dominance' in marker and dataset.group.genetic_type != "riset" %}
                 <td align="right">{{ '%0.2f' | format(marker.dominance|float) }}</td>
                 {% endif %}
               </tr>
@@ -292,6 +292,7 @@
         $(document).ready( function () {
             console.time("Creating table");
             $('#qtl_results').DataTable( {
+                {% if mapping_method != "reaper" %}
                 "columns": [
                     { "type": "natural", "width": "5%" },
                     { "type": "natural", "width": "8%" },
@@ -299,7 +300,29 @@
                     { "type": "natural", "width": "8%" },
                     { "type": "natural", "width": "8%" },
                     { "type": "natural", "width": "15%" }
-                    ],
+                ],
+                {% elif dataset.group.genetic_type == "riset" %}
+                "columns": [
+                    { "type": "natural", "width": "5%" },
+                    { "type": "natural", "width": "8%" },
+                    { "type": "natural", "width": "20%" },
+                    { "type": "natural", "width": "8%" },
+                    { "type": "natural", "width": "8%" },
+                    { "type": "natural", "width": "15%" },
+                    { "type": "natural", "width": "8%" }
+                ],
+                {% else %}
+                "columns": [
+                    { "type": "natural", "width": "5%" },
+                    { "type": "natural", "width": "8%" },
+                    { "type": "natural", "width": "20%" },
+                    { "type": "natural", "width": "8%" },
+                    { "type": "natural", "width": "8%" },
+                    { "type": "natural", "width": "15%" },
+                    { "type": "natural", "width": "8%" },
+                    { "type": "natural", "width": "8%" }
+                ],
+                {% endif %}
                 "columnDefs": [ {
                     "targets": 0,
                     "orderable": false
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index d4b70a02..547c3c27 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -1,17 +1,19 @@
 <table class="table">
     <tr>
-        <td>Species</td>
-        <td>{{ this_trait.dataset.group.species }}</td>
-    </tr>
-    <tr>
-        <td>Group</td>
-        <td>{{ this_trait.dataset.group.name }}</td>
+        <td>Species and Group</td>
+        <td>{{ this_trait.dataset.group.species }}, {{ this_trait.dataset.group.name }}</td>
     </tr>
     <tr>
         <td>Tissue</td>
         <td>{{ this_trait.dataset.tissue }}</td>
     </tr>
     {% if this_trait.dataset.type == 'ProbeSet' %}
+    {% if this_trait.symbol != None %}
+    <tr>
+        <td>Gene Symbol</td>
+        <td>{{ this_trait.symbol }}</td>
+    </tr>
+    {% endif %}
     <tr>
         <td>Aliases</td>
         <td>{{ this_trait.alias_fmt|replace(",",";") }}</td>
@@ -74,49 +76,35 @@
 <div style="margin-bottom:15px;" class="btn-toolbar">
     <div class="btn-group">
         <a href="#redirect">
-        <button type="button" id="add_to_collection" class="btn btn-primary" title="Add to collection">
-            <i class="icon-plus-sign icon-white"></i> Add
-        </button>
+        <button type="button" id="add_to_collection" class="btn btn-primary" title="Add to collection">Add</button>
         </a>
         {% if this_trait.dataset.type == 'ProbeSet' %}
         {% if this_trait.symbol != None %}
         <a href="http://www.genenetwork.org/webqtl/main.py?cmd=sch&amp;gene={{ this_trait.symbol }}&amp;alias=1&amp;species={{ dataset.group.species }}">
-        <button type="button" class="btn btn-default" title="Find similar expression data">
-            <i class="icon-search"></i> Find
-        </button>
+        <button type="button" class="btn btn-default" title="Find similar expression data">Find</button>
         </a>
         {% endif %}
         {% if UCSC_BLAT_URL != "" %}
         <a href="{{ UCSC_BLAT_URL }}">
-        <button type="button" class="btn btn-default" title="Check probe locations at UCSC">
-            <i class="icon-ok"></i> Verify
-        </button>
+        <button type="button" class="btn btn-default" title="Check probe locations at UCSC">Verify</button>
         </a>
         {% endif %}
         {% if this_trait.symbol != None %}
         <a href="http://genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}">
-        <button type="button" class="btn btn-default" title="Write or review comments about this gene">
-            <i class="icon-edit"></i> GeneWiki
-        </button>
+        <button type="button" class="btn btn-default" title="Write or review comments about this gene">GeneWiki</button>
         </a>
         <a href="http://genenetwork.org/webqtl/main.py?FormID=SnpBrowserResultPage&submitStatus=1&diffAlleles=True&customStrain=True&geneName={{ this_trait.symbol }}">
-        <button type="button" class="btn btn-default" title="View SNPs and Indels">
-            <i class="icon-road"></i> SNPs
-        </button>
+        <button type="button" class="btn btn-default" title="View SNPs and Indels">SNPs</button>
         </a>
         {% endif %}
         {% if UTHSC_BLAT_URL != "" %}
         <a href="{{ UTHSC_BLAT_URL }}">
-        <button type="button" class="btn btn-default" title="View probes, SNPs, and RNA-seq at UTHSC">
-            <i class="icon-eye-close"></i> RNA-seq
-        </button>
+        <button type="button" class="btn btn-default" title="View probes, SNPs, and RNA-seq at UTHSC">RNA-seq</button>
         </a>
         {% endif %}
         {% if show_probes == "True" %}
         <a href="http://genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON">
-        <button type="button" class="btn btn-default" title="Check sequence of probes">
-            <i class="icon-list"></i> Probes
-        </button>
+        <button type="button" class="btn btn-default" title="Check sequence of probes">Probes</button>
         </a>
         {% endif %}
         {% endif %}
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 8e237868..0a0e9990 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -106,11 +106,11 @@
                             <div id="prob_plot_title"></div>
                             <svg></svg>
                         </div>
-
+                        <div id="shapiro_wilk_text"></div>
                         <div>
                             More about <a href="http://en.wikipedia.org/wiki/Normal_probability_plot">Normal Probability Plots</a> and more
                             about interpreting these plots from the <a href="http://genenetwork.org/glossary.html#normal_probability">glossary</a>
-                            </div>
+                        </div>
 
                     </div>