Moved a bunch of functions out of the GeneralTrait class that didn't need to be there and changed the code that calls them accordingly

Improved loadings plot on the correlation matrix page to look like GN1's figure (though it's vector and GN1's was static)

Removed some unused code from show_trait.py

changed appearance of table headers some, though needs a little more work

Updated dataset_menu_structure.json

2 files changed, 190 insertions, 150 deletions

diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index d3db1853..dc0af7d0 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": [
@@ -1340,14 +1340,14 @@
                   "GSE9588 Human Liver Normal (Mar11) Both Sexes"
                ],
                [
-                  "384",
-                  "HLCF_0311",
-                  "GSE9588 Human Liver Normal (Mar11) Females"
-               ],
-               [
                   "383",
                   "HLCM_0311",
                   "GSE9588 Human Liver Normal (Mar11) Males"
+               ],
+               [
+                  "384",
+                  "HLCF_0311",
+                  "GSE9588 Human Liver Normal (Mar11) Females"
                ]
             ],
             "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": [
@@ -1616,23 +1616,11 @@
                   "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"
@@ -1643,19 +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": [
@@ -1683,6 +1676,23 @@
             ]
          },
          "B6D2RI": {
+            "Hippocampus mRNA": [
+               [
+                  "712",
+                  "UTHSC_BXDAged_0615",
+                  "UTHSC BXD Aged Hippocampus Affy Mouse Gene 1.0 ST (Jun15) RMA"
+               ],
+               [
+                  "805",
+                  "UTHSC_BXDAgedEx_1116",
+                  "UTHSC BXD Aged Hippocampus Affy Mouse Gene 1.0 ST (Jun15) Exon Level RMA"
+               ],
+               [
+                  "391",
+                  "UTHSC_B6D2RI_H_0912",
+                  "UTHSC B6D2RI Aged Hippocampus Affy Mouse Gene 1.0 ST (Sep12) RMA"
+               ]
+            ],
             "Phenotypes": [
                [
                   "None",
@@ -1717,6 +1727,11 @@
             ],
             "Striatum mRNA": [
                [
+                  "84",
+                  "SA_M2_0905_R",
+                  "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
+               ],
+               [
                   "83",
                   "SA_M2_0905_M",
                   "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5"
@@ -1725,27 +1740,22 @@
                   "85",
                   "SA_M2_0905_P",
                   "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN"
-               ],
-               [
-                  "84",
-                  "SA_M2_0905_R",
-                  "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
                ]
             ]
          },
          "BHF2": {
             "Adipose mRNA": [
                [
-                  "197",
-                  "UCLA_BHF2_ADIPOSE_FEMALE",
-                  "UCLA BHF2 Adipose Female mlratio"
-               ],
-               [
                   "196",
                   "UCLA_BHF2_ADIPOSE_MALE",
                   "UCLA BHF2 Adipose Male mlratio"
                ],
                [
+                  "197",
+                  "UCLA_BHF2_ADIPOSE_FEMALE",
+                  "UCLA BHF2 Adipose Female mlratio"
+               ],
+               [
                   "165",
                   "UCLA_BHF2_ADIPOSE_0605",
                   "UCLA BHF2 Adipose (June05) mlratio"
@@ -1753,16 +1763,16 @@
             ],
             "Brain mRNA": [
                [
-                  "199",
-                  "UCLA_BHF2_BRAIN_FEMALE",
-                  "UCLA BHF2 Brain Female mlratio"
-               ],
-               [
                   "198",
                   "UCLA_BHF2_BRAIN_MALE",
                   "UCLA BHF2 Brain Male mlratio"
                ],
                [
+                  "199",
+                  "UCLA_BHF2_BRAIN_FEMALE",
+                  "UCLA BHF2 Brain Female mlratio"
+               ],
+               [
                   "166",
                   "UCLA_BHF2_BRAIN_0605",
                   "UCLA BHF2 Brain (June05) mlratio"
@@ -1777,16 +1787,16 @@
             ],
             "Liver mRNA": [
                [
-                  "201",
-                  "UCLA_BHF2_LIVER_FEMALE",
-                  "UCLA BHF2 Liver Female mlratio"
-               ],
-               [
                   "200",
                   "UCLA_BHF2_LIVER_MALE",
                   "UCLA BHF2 Liver Male mlratio"
                ],
                [
+                  "201",
+                  "UCLA_BHF2_LIVER_FEMALE",
+                  "UCLA BHF2 Liver Female mlratio"
+               ],
+               [
                   "167",
                   "UCLA_BHF2_LIVER_0605",
                   "UCLA BHF2 Liver (June05) mlratio"
@@ -1990,11 +2000,6 @@
                   "UTHSC Brain mRNA U74Av2 (Nov05) PDNN"
                ],
                [
-                  "81",
-                  "BR_U_0805_P",
-                  "UTHSC Brain mRNA U74Av2 (Aug05) PDNN"
-               ],
-               [
                   "80",
                   "BR_U_0805_M",
                   "UTHSC Brain mRNA U74Av2 (Aug05) MAS5"
@@ -2005,6 +2010,11 @@
                   "UTHSC Brain mRNA U74Av2 (Aug05) RMA"
                ],
                [
+                  "81",
+                  "BR_U_0805_P",
+                  "UTHSC Brain mRNA U74Av2 (Aug05) PDNN"
+               ],
+               [
                   "42",
                   "CB_M_0204_P",
                   "INIA Brain mRNA M430 (Feb04) PDNN"
@@ -2071,11 +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"
@@ -2086,6 +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"
@@ -2322,16 +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"
@@ -2342,14 +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": [
@@ -2418,8 +2428,23 @@
             ],
             "Liver mRNA": [
                [
+                  "430",
+                  "EPFLMouseLiverRMA0413",
+                  "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
+               ],
+               [
+                  "431",
+                  "EPFLMouseLiverHFDRMA0413",
+                  "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
+               ],
+               [
+                  "432",
+                  "EPFLMouseLiverCDRMA0413",
+                  "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
+               ],
+               [
                   "700",
-                  "UT-VGX_HGL1014",
+                  "UTHSC-VGX_MmBXDHepatocytesRMA1014",
                   "UT-VGX Hepatocytes Affy Mouse Gene 1.0 ST Gene Level (Oct14) RMA"
                ],
                [
@@ -2441,21 +2466,6 @@
                   "702",
                   "SUH_Liv_RMAEx_0611",
                   "SUH BXD Liver CCl4-treated Affy Mouse Gene 1.0 ST Exon Level (Jun11) RMA"
-               ],
-               [
-                  "430",
-                  "EPFLMouseLiverRMA0413",
-                  "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
-               ],
-               [
-                  "431",
-                  "EPFLMouseLiverHFDRMA0413",
-                  "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
-               ],
-               [
-                  "432",
-                  "EPFLMouseLiverCDRMA0413",
-                  "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
                ]
             ],
             "Lung mRNA": [
@@ -2479,21 +2489,6 @@
             ],
             "Muscle mRNA": [
                [
-                  "395",
-                  "EPFLMouseMuscleRMA_Ex1112",
-                  "EPFL/LISP BXD CD+HFD Muscle Affy Mouse Gene 1.0 ST (Nov12) RMA Exon Level"
-               ],
-               [
-                  "396",
-                  "EPFLMouseMuscleHFDRMAEx1112",
-                  "EPFL/LISP BXD HFD Muscle Affy Mouse Gene 1.0 ST (Nov12) RMA Exon Level"
-               ],
-               [
-                  "397",
-                  "EPFLMouseMuscleCDRMAEx1112",
-                  "EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Nov12) RMA Exon Level"
-               ],
-               [
                   "378",
                   "EPFLMouseMuscleRMA1211",
                   "EPFL/LISP BXD CD+HFD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA"
@@ -2507,20 +2502,35 @@
                   "379",
                   "EPFLMouseMuscleCDRMA1211",
                   "EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA"
+               ],
+               [
+                  "395",
+                  "EPFLMouseMuscleRMA_Ex1112",
+                  "EPFL/LISP BXD CD+HFD Muscle Affy Mouse Gene 1.0 ST (Nov12) RMA Exon Level"
+               ],
+               [
+                  "396",
+                  "EPFLMouseMuscleHFDRMAEx1112",
+                  "EPFL/LISP BXD HFD Muscle Affy Mouse Gene 1.0 ST (Nov12) RMA Exon Level"
+               ],
+               [
+                  "397",
+                  "EPFLMouseMuscleCDRMAEx1112",
+                  "EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Nov12) RMA Exon Level"
                ]
             ],
             "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"
@@ -2536,14 +2546,14 @@
                   "HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv"
                ],
                [
-                  "275",
-                  "DevNeocortex_ILM6.2P14RInv_1110",
-                  "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv"
-               ],
-               [
                   "274",
                   "DevNeocortex_ILM6.2P3RInv_1110",
                   "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv"
+               ],
+               [
+                  "275",
+                  "DevNeocortex_ILM6.2P14RInv_1110",
+                  "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv"
                ]
             ],
             "Nucleus Accumbens mRNA": [
@@ -2751,6 +2761,11 @@
             ],
             "Ventral Tegmental Area mRNA": [
                [
+                  "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"
@@ -2759,11 +2774,15 @@
                   "230",
                   "VCUEtvsSal_0609_R",
                   "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) RMA"
-               ],
+               ]
+            ]
+         },
+         "BXD-Bone": {
+            "Phenotypes": [
                [
-                  "229",
-                  "VCUEtOH_0609_R",
-                  "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA"
+                  "None",
+                  "BXD-BonePublish",
+                  "BXD-Bone Published Phenotypes"
                ]
             ]
          },
@@ -2959,14 +2978,14 @@
             ],
             "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": [
@@ -3033,6 +3052,16 @@
             ],
             "Hippocampus mRNA": [
                [
+                  "219",
+                  "Illum_LXS_Hipp_NON_1008",
+                  "Hippocampus Illumina NON (Oct08) RankInv beta"
+               ],
+               [
+                  "212",
+                  "Illum_LXS_Hipp_RSE_1008",
+                  "Hippocampus Illumina RSE (Oct08) RankInv beta"
+               ],
+               [
                   "214",
                   "Illum_LXS_Hipp_NOE_1008",
                   "Hippocampus Illumina NOE (Oct08) RankInv beta"
@@ -3048,16 +3077,6 @@
                   "Hippocampus Illumina NOS (Oct08) RankInv beta"
                ],
                [
-                  "219",
-                  "Illum_LXS_Hipp_NON_1008",
-                  "Hippocampus Illumina NON (Oct08) RankInv beta"
-               ],
-               [
-                  "212",
-                  "Illum_LXS_Hipp_RSE_1008",
-                  "Hippocampus Illumina RSE (Oct08) RankInv beta"
-               ],
-               [
                   "143",
                   "Illum_LXS_Hipp_loess0807",
                   "Hippocampus Illumina (Aug07) LOESS"
@@ -3148,14 +3167,14 @@
             ],
             "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": [
@@ -3524,6 +3543,10 @@
             "BXD"
          ],
          [
+            "BXD-Bone",
+            "BXD Bone"
+         ],
+         [
             "BXH",
             "BXH"
          ],
@@ -4387,10 +4410,6 @@
             [
                "Phenotypes",
                "Phenotypes"
-            ],
-            [
-               "Retina mRNA",
-               "Retina mRNA"
             ]
          ],
          "B6D2F2": [
@@ -4417,6 +4436,10 @@
             [
                "Phenotypes",
                "Phenotypes"
+            ],
+            [
+               "Hippocampus mRNA",
+               "Hippocampus mRNA"
             ]
          ],
          "BDF2-1999": [
@@ -4621,6 +4644,12 @@
                "Ventral Tegmental Area mRNA"
             ]
          ],
+         "BXD-Bone": [
+            [
+               "Phenotypes",
+               "Phenotypes"
+            ]
+         ],
          "BXH": [
             [
                "Phenotypes",
diff --git a/wqflask/wqflask/static/new/javascript/loadings_plot.js b/wqflask/wqflask/static/new/javascript/loadings_plot.js
index 5bc901ec..c44288c0 100644
--- a/wqflask/wqflask/static/new/javascript/loadings_plot.js
+++ b/wqflask/wqflask/static/new/javascript/loadings_plot.js
@@ -1,4 +1,4 @@
-var margin = {top: 20, right: 60, bottom: 60, left: 60}
+var margin = {top: 20, right: 70, bottom: 60, left: 60}
   , width = 960 - margin.left - margin.right
   , height = 500 - margin.top - margin.bottom;
     
@@ -29,7 +29,7 @@ var xAxis = d3.svg.axis()
 
 main.append('g')
     .attr('transform', 'translate(0,' + height + ')')
-    .attr('class', 'main axis date')
+    .attr('class', 'x axis')
     .call(xAxis);
     
 chart.append("text")
@@ -38,6 +38,7 @@ chart.append("text")
     .attr("x", 550)
     .attr("y", 480)
     .style("font-size", 14)
+    .style("fill", "blue")
     .text("Factor (1)");
     
 chart.append("text")
@@ -48,6 +49,7 @@ chart.append("text")
     .attr("dy", ".75em")
     .attr("transform", "rotate(-90)")
     .style("font-size", 14)
+    .style("fill", "blue")
     .text("Factor (2)");
 
 // draw the y axis
@@ -57,9 +59,17 @@ var yAxis = d3.svg.axis()
 
 main.append('g')
     .attr('transform', 'translate(0,0)')
-    .attr('class', 'main axis date')
+    .attr('class', 'y axis')
     .call(yAxis);
 
+chart.select('.x.axis')
+    .selectAll("text")
+        .style("font-size","14px");
+        
+chart.select('.y.axis')
+    .selectAll("text")
+        .style("font-size","14px");
+    
 var g = main.append("svg:g"); 
     
 g.selectAll("scatter-dots")
@@ -84,7 +94,8 @@ g.selectAll("scatter-dots")
             .attr("x", function(d, i) { return x(d[1][0]); })
             .attr("y", function(d) { return y(d[1][1]); })
             .text(function(d) { return d[0]; })
-            .style("fill", "blue");
+                .style("font-size", 12)
+                .style("fill", "blue");
             
 g.selectAll("scatter-lines")
   .data(loadings)