Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing

33 files changed, 1189 insertions, 521 deletions

diff --git a/doc/README.org b/doc/README.org
index 937a9549..cc141098 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -257,6 +257,12 @@ if that works run genenetwork after setting SQL_URI to something like
 
 : export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s
 
+* Running ElasticSearch
+
+In order to start up elasticsearch, change user to "elasticsearch" and use the following command:
+
+: env JAVA_HOME=/opt/jdk-9.0.4 /opt/elasticsearch-6.2.1/bin/elasticsearch
+
 * Read more
 
 If you want to understand the architecture of GN2 read
diff --git a/etc/default_settings.py b/etc/default_settings.py
index da8cbb7c..3e54ad1f 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -77,7 +77,7 @@ USE_GN_SERVER   = 'False'   # Use GN_SERVER SQL calls
 HOME            = os.environ['HOME']
 
 # ---- Default locations
-GENENETWORK_FILES   = HOME+"/gn2_data"  # base dir for all static data files
+GENENETWORK_FILES   = HOME+"/genotype_files"  # base dir for all static data files
 
 # ---- Path overrides for Genenetwork - the defaults are normally
 #      picked up from Guix or in the HOME directory
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index b71dacf6..3daf9ea9 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -18,7 +18,7 @@ import simplejson as json
 from MySQLdb import escape_string as escape
 from pprint import pformat as pf
 
-from flask import Flask, g, request
+from flask import Flask, g, request, url_for
 
 from utility.logger import getLogger
 logger = getLogger(__name__ )
@@ -176,13 +176,23 @@ def get_sample_data():
 
     trait_ob = GeneralTrait(name=trait, dataset_name=dataset)
 
-    return json.dumps([trait, {key: value.value for key, value in trait_ob.data.iteritems() }])
-
-    #jsonable_sample_data = {}
-    #for sample in trait_ob.data.iteritems():
-    #    jsonable_sample_data[sample] = trait_ob.data[sample].value
-    #
-    #return jsonable_sample_data
+    trait_dict = {}
+    trait_dict['name'] = trait
+    trait_dict['db'] = dataset
+    trait_dict['type'] = trait_ob.dataset.type
+    trait_dict['group'] = trait_ob.dataset.group.name
+    trait_dict['tissue'] = trait_ob.dataset.tissue
+    trait_dict['species'] = trait_ob.dataset.group.species
+    trait_dict['url'] = url_for('show_trait_page', trait_id = trait, dataset = dataset)
+    trait_dict['description'] = trait_ob.description_display
+    if trait_ob.dataset.type == "ProbeSet":
+        trait_dict['symbol'] = trait_ob.symbol
+        trait_dict['location'] = trait_ob.location_repr
+    elif trait_ob.dataset.type == "Publish":
+        trait_dict['pubmed_link'] = trait_ob.pubmed_link
+        trait_dict['pubmed_text'] = trait_ob.pubmed_text
+
+    return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }])
     
 def jsonable(trait):
     """Return a dict suitable for using as json
diff --git a/wqflask/utility/corr_result_helpers.py b/wqflask/utility/corr_result_helpers.py
index ef644d85..b543c589 100644
--- a/wqflask/utility/corr_result_helpers.py
+++ b/wqflask/utility/corr_result_helpers.py
@@ -15,7 +15,7 @@ def normalize_values(a_values, b_values):
     a_new = []
     b_new = []
     for counter in range(min_length):
-        if a_values[counter] and b_values[counter]:
+        if (a_values[counter] or a_values[counter] == 0) and (b_values[counter] or b_values[counter] == 0):
             a_new.append(a_values[counter])
             b_new.append(b_values[counter])
 
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index 293a9ae6..15cdd0bc 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -63,7 +63,7 @@ def get_elasticsearch_connection(for_user=True):
 
         es = Elasticsearch([{
             "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
-        }]) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
+        }], timeout=30, retry_on_timeout=True) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
 
         if for_user:
             setup_users_index(es)
diff --git a/wqflask/wqflask/comparison_bar_chart/__init__.py b/wqflask/wqflask/comparison_bar_chart/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/wqflask/comparison_bar_chart/__init__.py
diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
new file mode 100644
index 00000000..b9e6f450
--- /dev/null
+++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
@@ -0,0 +1,118 @@
+## Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Dr. Robert W. Williams at rwilliams@uthsc.edu
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+
+from __future__ import absolute_import, print_function, division
+
+import sys
+# sys.path.append(".")   Never do this in a webserver!
+
+import string
+import cPickle
+import os
+import time
+import pp
+import math
+import collections
+import resource
+
+
+from pprint import pformat as pf
+
+from htmlgen import HTMLgen2 as HT
+import reaper
+
+from base.trait import GeneralTrait
+from base import data_set
+from utility import webqtlUtil, helper_functions, corr_result_helpers
+from db import webqtlDatabaseFunction
+import utility.webqtlUtil #this is for parallel computing only.
+from wqflask.correlation import correlation_functions
+from utility.benchmark import Bench
+
+from MySQLdb import escape_string as escape
+
+from pprint import pformat as pf
+
+from flask import Flask, g
+
+
+class ComparisonBarChart(object):
+
+    def __init__(self, start_vars):
+        trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
+
+        helper_functions.get_trait_db_obs(self, trait_db_list)
+
+        self.all_sample_list = []
+        self.traits = []
+        self.insufficient_shared_samples = False
+        this_group = self.trait_list[0][1].group.name #ZS: Getting initial group name before verifying all traits are in the same group in the following loop
+        for trait_db in self.trait_list:
+            
+            if trait_db[1].group.name != this_group:
+                self.insufficient_shared_samples = True
+                break
+            else:
+                this_group = trait_db[1].group.name
+            this_trait = trait_db[0]
+            self.traits.append(this_trait)
+            
+            this_sample_data = this_trait.data
+
+            for sample in this_sample_data:
+                if sample not in self.all_sample_list:
+                    self.all_sample_list.append(sample)
+
+        if self.insufficient_shared_samples:
+            pass
+        else:
+            self.sample_data = []
+            for trait_db in self.trait_list:
+                this_trait = trait_db[0]
+                this_sample_data = this_trait.data
+
+                this_trait_vals = []
+                for sample in self.all_sample_list:
+                    if sample in this_sample_data:
+                        this_trait_vals.append(this_sample_data[sample].value)
+                    else:
+                        this_trait_vals.append('')
+                self.sample_data.append(this_trait_vals)
+
+            self.js_data = dict(traits = [trait.name for trait in self.traits],
+                                samples = self.all_sample_list,
+                                sample_data = self.sample_data,)
+        
+    def get_trait_db_obs(self, trait_db_list):
+
+        self.trait_list = []
+        for i, trait_db in enumerate(trait_db_list):
+            if i == (len(trait_db_list) - 1):
+                break
+            trait_name, dataset_name = trait_db.split(":")
+            #print("dataset_name:", dataset_name)
+            dataset_ob = data_set.create_dataset(dataset_name)
+            trait_ob = GeneralTrait(dataset=dataset_ob,
+                                   name=trait_name,
+                                   cellid=None)
+            self.trait_list.append((trait_ob, dataset_ob))
+
+        #print("trait_list:", self.trait_list)
+
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index fe1e17d2..37eb46cb 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -5,6 +5,8 @@ from base.data_set import create_dataset
 from base.trait import GeneralTrait
 from db import webqtlDatabaseFunction
 
+from base import webqtlConfig
+
 from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
 from utility.benchmark import Bench
 
@@ -57,10 +59,29 @@ class GSearch(object):
             self.trait_list = []
             with Bench("Creating trait objects"):
                 for line in re:
-                    dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
-                    trait_id = line[4]
+                    this_trait = {}
+                    this_trait['name'] = line[4]
+                    this_trait['dataset'] = line[3]
+                    this_trait['species'] = line[0]
+                    this_trait['group'] = line[1]
+                    this_trait['tissue'] = line[2]
+                    this_trait['symbol'] = line[5]
+                    this_trait['description'] = line[6]
+                    this_trait['location_repr'] = 'N/A'
+                    if (line[7] != "NULL" and line[7] != "") and (line[8] != 0):
+                        this_trait['location_repr'] = 'Chr%s: %.6f' % (line[7], float(line[8]))
+                    this_trait['mean'] = line[9]
+                    this_trait['LRS_score_repr'] = "N/A"
+                    if line[10] != "" and line[10] != None:
+                        this_trait['LRS_score_repr'] = '%3.1f' % line[10]
+                    this_trait['additive'] = "N/A"
+                    if line[13] != "":
+                        this_trait['additive'] = line[13]
+
+                    #dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
+                    #trait_id = line[4]
                     #with Bench("Building trait object"):
-                    this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
+                    #this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=False, get_sample_info=False)
                     self.trait_list.append(this_trait)
 
         elif self.type == "phenotype":
@@ -73,8 +94,8 @@ class GSearch(object):
                 Phenotype.`Post_publication_description`,
                 Publication.`Authors`,
                 Publication.`Year`,
+                Publication.`PubMed_ID`,
                 PublishXRef.`LRS`,
-                PublishXRef.`Locus`,
                 PublishXRef.`additive`
                 FROM Species,InbredSet,PublishFreeze,PublishXRef,Phenotype,Publication
                 WHERE PublishXRef.`InbredSetId`=InbredSet.`Id`
@@ -100,7 +121,30 @@ class GSearch(object):
             self.trait_list = []
             with Bench("Creating trait objects"):
                 for line in re:
-                    dataset = create_dataset(line[2], "Publish")
-                    trait_id = line[3]
-                    this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
+                    this_trait = {}
+                    this_trait['name'] = line[3]
+                    this_trait['dataset'] = line[2]
+                    this_trait['species'] = line[0]
+                    this_trait['group'] = line[1]
+                    this_trait['description'] = line[4]
+                    this_trait['authors'] = line[5]
+                    this_trait['year'] = line[6]
+                    if this_trait['year'].isdigit():
+                        this_trait['pubmed_text'] = this_trait['year']
+                    else:
+                        this_trait['pubmed_text'] = "N/A"
+                    if line[7] != "" and line[7] != None:
+                        this_trait['pubmed_link'] = webqtlConfig.PUBMEDLINK_URL % line[7]
+                    else:
+                        this_trait['pubmed_link'] = "N/A"
+                    this_trait['LRS_score_repr'] = "N/A"
+                    if line[8] != "" and line[8] != None:
+                        this_trait['LRS_score_repr'] = '%3.1f' % line[8]
+                    this_trait['additive'] = "N/A"
+                    if line[9] != "":
+                        this_trait['additive'] = line[9]
+
+                    #dataset = create_dataset(line[2], "Publish")
+                    #trait_id = line[3]
+                    #this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
                     self.trait_list.append(this_trait)
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 9423aabf..cbd0bae5 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -148,13 +148,16 @@ def parse_gemma_output(genofile_name):
 
     with open("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, genofile_name)) as output_file:
         for line in output_file:
-            if line.startswith("chr"):
+            if line.startswith("chr\t"):
                 continue
             else:
                 marker = {}
                 marker['name'] = line.split("\t")[1]
                 if line.split("\t")[0] != "X" and line.split("\t")[0] != "X/Y":
-                    marker['chr'] = int(line.split("\t")[0])
+                    if "chr" in line.split("\t")[0]:
+                        marker['chr'] = int(line.split("\t")[0][3:])
+                    else:
+                        marker['chr'] = int(line.split("\t")[0])
                 else:
                     marker['chr'] = line.split("\t")[0]
                 marker['Mb'] = float(line.split("\t")[2]) / 1000000
@@ -190,13 +193,16 @@ def parse_loco_output(this_dataset, gwa_output_filename):
     for this_file in output_filelist:
         with open(this_file) as output_file:
             for line in output_file:
-                if line.startswith("chr"):
+                if line.startswith("chr\t"):
                     continue
                 else:
                     marker = {}
                     marker['name'] = line.split("\t")[1]
                     if line.split("\t")[0] != "X" and line.split("\t")[0] != "X/Y":
-                        marker['chr'] = int(line.split("\t")[0])
+                        if "chr" in line.split("\t")[0]:
+                            marker['chr'] = int(line.split("\t")[0][3:])
+                        else:
+                            marker['chr'] = int(line.split("\t")[0])
                         if marker['chr'] > previous_chr:
                             previous_chr = marker['chr']
                         elif marker['chr'] < previous_chr:
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 40402597..94145bb3 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -68,12 +68,10 @@ class MarkerRegression(object):
     # ** GENES **********
     BAND_SPACING = 4
 
-    #ENSEMBL_BAND_Y      = UCSC_BAND_Y + UCSC_BAND_HEIGHT + BAND_SPACING
-    UCSC_BAND_HEIGHT = 10
-    ENSEMBL_BAND_HEIGHT = 10
-    WEBQTL_BAND_HEIGHT = 10
+    BAND_HEIGHT = 10
+    BAND_HEIGHT = 10
+    BAND_HEIGHT = 10
 
-    #GENE_START_Y        = ENSEMBL_BAND_Y + ENSEMBL_BAND_HEIGHT + BAND_SPACING
     NUM_GENE_ROWS       = 10
     EACH_GENE_HEIGHT    = 6  # number of pixels tall, for each gene to display
     EACH_GENE_ARROW_WIDTH = 5
@@ -124,6 +122,10 @@ class MarkerRegression(object):
     CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR = pid.HexColor(0xFCE9E9)
     CLICKABLE_WEBQTL_TEXT_COLOR       = pid.HexColor(0x912828)
 
+    CLICKABLE_PHENOGEN_REGION_COLOR   = pid.HexColor(0xA2FB94)
+    CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR = pid.HexColor(0xCEFEC7)
+    CLICKABLE_PHENOGEN_TEXT_COLOR     = pid.HexColor(0x1FD504)
+
     CLICKABLE_UCSC_REGION_COLOR     = pid.HexColor(0xDDDDEE)
     CLICKABLE_UCSC_REGION_OUTLINE_COLOR = pid.HexColor(0xEDEDFF)
     CLICKABLE_UCSC_TEXT_COLOR       = pid.HexColor(0x333366)
@@ -498,7 +500,10 @@ class MarkerRegression(object):
         #Drawing Area Height
         drawAreaHeight = plotHeight
         if self.plotScale == 'physic' and self.selectedChr > -1:
-            drawAreaHeight -= self.ENSEMBL_BAND_HEIGHT + self.UCSC_BAND_HEIGHT+ self.WEBQTL_BAND_HEIGHT + 3*self.BAND_SPACING+ 10*zoom
+            if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
+                drawAreaHeight -= 4*self.BAND_HEIGHT + 4*self.BAND_SPACING+ 10*zoom
+            else:
+                drawAreaHeight -= 3*self.BAND_HEIGHT + 3*self.BAND_SPACING+ 10*zoom
             if self.geneChecked:
                 drawAreaHeight -= self.NUM_GENE_ROWS*self.EACH_GENE_HEIGHT + 3*self.BAND_SPACING + 10*zoom
         else:
@@ -1023,7 +1028,10 @@ class MarkerRegression(object):
 
             #Draw Genes
             geneYLocation = yPaddingTop + (gIndex % self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT*zoom
-            geneYLocation += self.UCSC_BAND_HEIGHT + self.BAND_SPACING + self.ENSEMBL_BAND_HEIGHT + self.BAND_SPACING + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
+            if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
+                geneYLocation += 4*self.BAND_HEIGHT + 4*self.BAND_SPACING
+            else:
+                geneYLocation += 3*self.BAND_HEIGHT + 3*self.BAND_SPACING
 
             #draw the detail view
             if self.endMb - self.startMb <= self.DRAW_DETAIL_MB and geneEndPix - geneStartPix > self.EACH_GENE_ARROW_SPACING * 3:
@@ -1217,7 +1225,10 @@ class MarkerRegression(object):
                 #Draw Genes
 
                 geneYLocation = yPaddingTop + self.NUM_GENE_ROWS * (self.EACH_GENE_HEIGHT)*zoom
-                geneYLocation += self.UCSC_BAND_HEIGHT + self.BAND_SPACING + self.ENSEMBL_BAND_HEIGHT + self.BAND_SPACING + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
+                if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
+                    geneYLocation += 4*self.BAND_HEIGHT + 4*self.BAND_SPACING
+                else:
+                    geneYLocation += 3*self.BAND_HEIGHT + 3*self.BAND_SPACING
 
                 if self.genotype[0][i].name != " - " :
 
@@ -1335,49 +1346,70 @@ class MarkerRegression(object):
         i = 0
 
         paddingTop = yTopOffset
-        ucscPaddingTop = paddingTop + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
-        ensemblPaddingTop = ucscPaddingTop + self.UCSC_BAND_HEIGHT + self.BAND_SPACING
+        if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
+            phenogenPaddingTop = paddingTop + (self.BAND_HEIGHT + self.BAND_SPACING)
+            ucscPaddingTop = paddingTop + 2*(self.BAND_HEIGHT + self.BAND_SPACING)
+            ensemblPaddingTop = paddingTop + 3*(self.BAND_HEIGHT + self.BAND_SPACING)
+        else:
+            ucscPaddingTop = paddingTop + (self.BAND_HEIGHT + self.BAND_SPACING)
+            ensemblPaddingTop = paddingTop + 2*(self.BAND_HEIGHT + self.BAND_SPACING)
 
         if zoom == 1:
             for pixel in range(xLeftOffset, xLeftOffset + plotWidth, pixelStep):
 
                 calBase = self.kONE_MILLION*(startMb + (endMb-startMb)*(pixel-xLeftOffset-0.0)/plotWidth)
+                if pixel == (xLeftOffset + pixelStep*2):
+                  logger.debug("CALBASE:", calBase)
+                  logger.debug("FLANKING:", flankingWidthInBases)
 
                 xBrowse1 = pixel
                 xBrowse2 = min(xLeftOffset + plotWidth, (pixel + pixelStep - 1))
 
-                WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop+self.WEBQTL_BAND_HEIGHT))
+                WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop+self.BAND_HEIGHT))
                 WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0)
 
                 WEBQTL_TITLE = "Click to view this section of the genome in WebQTL"
                 gifmap.areas.append(HT.Area(shape='rect',coords=WEBQTL_COORDS,href=WEBQTL_HREF, title=WEBQTL_TITLE))
-                canvas.drawRect(xBrowse1, paddingTop, xBrowse2, (paddingTop + self.WEBQTL_BAND_HEIGHT), edgeColor=self.CLICKABLE_WEBQTL_REGION_COLOR, fillColor=self.CLICKABLE_WEBQTL_REGION_COLOR)
-                canvas.drawLine(xBrowse1, paddingTop, xBrowse1, (paddingTop + self.WEBQTL_BAND_HEIGHT), color=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR)
+                canvas.drawRect(xBrowse1, paddingTop, xBrowse2, (paddingTop + self.BAND_HEIGHT), edgeColor=self.CLICKABLE_WEBQTL_REGION_COLOR, fillColor=self.CLICKABLE_WEBQTL_REGION_COLOR)
+                canvas.drawLine(xBrowse1, paddingTop, xBrowse1, (paddingTop + self.BAND_HEIGHT), color=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR)
+
+                if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
+                    PHENOGEN_COORDS = "%d, %d, %d, %d" % (xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT))
+                    if self.dataset.group.species == "mouse":
+                        PHENOGEN_HREF = "https://phenogen.ucdenver.edu/PhenoGen/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
+                    else:
+                        PHENOGEN_HREF = "https://phenogen.ucdenver.edu/PhenoGen/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
+                    PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen"
+                    gifmap.areas.append(HT.Area(shape='rect',coords=PHENOGEN_COORDS,href=PHENOGEN_HREF, title=PHENOGEN_TITLE))
+                    canvas.drawRect(xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT), edgeColor=self.CLICKABLE_PHENOGEN_REGION_COLOR, fillColor=self.CLICKABLE_PHENOGEN_REGION_COLOR)
+                    canvas.drawLine(xBrowse1, phenogenPaddingTop, xBrowse1, (phenogenPaddingTop+self.BAND_HEIGHT), color=self.CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR)
 
-                UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.UCSC_BAND_HEIGHT))
+                UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT))
                 if self.dataset.group.species == "mouse":
                     UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases, webqtlConfig.PORTADDR, self.selectedChr)
                 else:
                     UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                 UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser"
                 gifmap.areas.append(HT.Area(shape='rect',coords=UCSC_COORDS,href=UCSC_HREF, title=UCSC_TITLE))
-                canvas.drawRect(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.UCSC_BAND_HEIGHT), edgeColor=self.CLICKABLE_UCSC_REGION_COLOR, fillColor=self.CLICKABLE_UCSC_REGION_COLOR)
-                canvas.drawLine(xBrowse1, ucscPaddingTop, xBrowse1, (ucscPaddingTop+self.UCSC_BAND_HEIGHT), color=self.CLICKABLE_UCSC_REGION_OUTLINE_COLOR)
+                canvas.drawRect(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT), edgeColor=self.CLICKABLE_UCSC_REGION_COLOR, fillColor=self.CLICKABLE_UCSC_REGION_COLOR)
+                canvas.drawLine(xBrowse1, ucscPaddingTop, xBrowse1, (ucscPaddingTop+self.BAND_HEIGHT), color=self.CLICKABLE_UCSC_REGION_OUTLINE_COLOR)
 
-                ENSEMBL_COORDS = "%d, %d, %d, %d" %(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT))
+                ENSEMBL_COORDS = "%d, %d, %d, %d" %(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.BAND_HEIGHT))
                 if self.dataset.group.species == "mouse":
                     ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                 else:
                     ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                 ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser"
                 gifmap.areas.append(HT.Area(shape='rect',coords=ENSEMBL_COORDS,href=ENSEMBL_HREF, title=ENSEMBL_TITLE))
-                canvas.drawRect(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT), edgeColor=self.CLICKABLE_ENSEMBL_REGION_COLOR, fillColor=self.CLICKABLE_ENSEMBL_REGION_COLOR)
-                canvas.drawLine(xBrowse1, ensemblPaddingTop, xBrowse1, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT), color=self.CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR)
+                canvas.drawRect(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.BAND_HEIGHT), edgeColor=self.CLICKABLE_ENSEMBL_REGION_COLOR, fillColor=self.CLICKABLE_ENSEMBL_REGION_COLOR)
+                canvas.drawLine(xBrowse1, ensemblPaddingTop, xBrowse1, (ensemblPaddingTop+self.BAND_HEIGHT), color=self.CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR)
             # end for
 
-            canvas.drawString("Click to view the corresponding section of the genome in an 8x expanded WebQTL map", (xLeftOffset + 10), paddingTop + self.WEBQTL_BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_WEBQTL_TEXT_COLOR)
-            canvas.drawString("Click to view the corresponding section of the genome in the UCSC Genome Browser", (xLeftOffset + 10), ucscPaddingTop + self.UCSC_BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_UCSC_TEXT_COLOR)
-            canvas.drawString("Click to view the corresponding section of the genome in the Ensembl Genome Browser", (xLeftOffset+10), ensemblPaddingTop + self.ENSEMBL_BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_ENSEMBL_TEXT_COLOR)
+            canvas.drawString("Click to view the corresponding section of the genome in an 8x expanded WebQTL map", (xLeftOffset + 10), paddingTop + self.BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_WEBQTL_TEXT_COLOR)
+            if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
+                canvas.drawString("Click to view the corresponding section of the genome in PhenoGen", (xLeftOffset + 10), phenogenPaddingTop + self.BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_PHENOGEN_TEXT_COLOR)
+            canvas.drawString("Click to view the corresponding section of the genome in the UCSC Genome Browser", (xLeftOffset + 10), ucscPaddingTop + self.BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_UCSC_TEXT_COLOR)
+            canvas.drawString("Click to view the corresponding section of the genome in the Ensembl Genome Browser", (xLeftOffset+10), ensemblPaddingTop + self.BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_ENSEMBL_TEXT_COLOR)
 
             #draw the gray text
             chrFont = pid.Font(ttf="verdana", size=26*zoom, bold=1)
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 78bb3b42..8dbba530 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -37,7 +37,7 @@ class SampleList(object):
 
         self.get_attributes()
 
-        self.sample_qnorm = get_transform_vals(self.dataset, this_trait)
+        #self.sample_qnorm = get_transform_vals(self.dataset, this_trait)
 
         if self.this_trait and self.dataset and self.dataset.type == 'ProbeSet':
             self.get_extra_attribute_values()
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index d6d83c02..7b952af4 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -12,6 +12,8 @@ from collections import OrderedDict
 import redis
 Redis = redis.StrictRedis()
 
+import scipy.stats as ss
+
 from flask import Flask, g
 
 from htmlgen import HTMLgen2 as HT
@@ -137,6 +139,8 @@ class ShowTrait(object):
 
         self.make_sample_lists()
 
+        self.qnorm_vals = quantile_normalize_vals(self.sample_groups)
+
         # Todo: Add back in the ones we actually need from below, as we discover we need them
         hddn = OrderedDict()
 
@@ -281,6 +285,44 @@ class ShowTrait(object):
             self.sample_groups = (primary_samples,)
         self.dataset.group.allsamples = all_samples_ordered
 
+def quantile_normalize_vals(sample_groups):
+    def normf(trait_vals):
+        ranked_vals = ss.rankdata(trait_vals)
+        p_list = []
+        for i, val in enumerate(trait_vals):
+            p_list.append(((i+1) - 0.5)/len(trait_vals))
+
+        z = ss.norm.ppf(p_list)
+        normed_vals = []
+        for rank in ranked_vals:
+            normed_vals.append("%0.3f" % z[int(rank)-1])
+
+        return normed_vals
+
+    qnorm_by_group = []
+    for sample_type in sample_groups:
+        trait_vals = []
+        for sample in sample_type.sample_list:
+            try:
+                trait_vals.append(float(sample.value))
+            except:
+                continue
+
+        qnorm_vals = normf(trait_vals)
+
+        qnorm_vals_with_x = []
+        counter = 0
+        for sample in sample_type.sample_list:
+            if sample.display_value == "x":
+                qnorm_vals_with_x.append("x")
+            else:
+                qnorm_vals_with_x.append(qnorm_vals[counter])
+                counter += 1
+
+        qnorm_by_group.append(qnorm_vals_with_x)
+
+    return qnorm_by_group
+
 def get_nearest_marker(this_trait, this_db):
     this_chr = this_trait.locus_chr
     logger.debug("this_chr:", this_chr)
diff --git a/wqflask/wqflask/static/new/javascript/comparison_bar_chart.js b/wqflask/wqflask/static/new/javascript/comparison_bar_chart.js
new file mode 100644
index 00000000..5e73807c
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/comparison_bar_chart.js
@@ -0,0 +1,25 @@
+generate_traces = function() {
+  traces = [];
+  for (i = 0, _len = js_data.traits.length; i < _len; i++) {
+    this_trace = {
+      x: js_data.samples,
+      y: js_data.sample_data[i],
+      name: js_data.traits[i],
+      type: 'bar',
+      bargap: 20
+    }
+
+    traces.push(this_trace)   
+  }
+
+  return traces
+}
+
+create_bar_chart = function() {
+  var data = generate_traces()
+  var layout = {barmode: 'group', bargap: 5};
+
+  Plotly.newPlot('comp_bar_chart', data, layout);
+}
+
+create_bar_chart();
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index c605329b..81185136 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -1751,7 +1751,7 @@
             ],
             "Phenotypes": [
                [
-                  "None",
+                  "651",
                   "B6D2RIPublish",
                   "B6D2RI Published Phenotypes"
                ]
@@ -2616,6 +2616,16 @@
                   "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
                ],
                [
+                  "849",
+                  "EPFLMouseLiverCDEx0413",
+                  "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
+               ],
+               [
+                  "848",
+                  "EPFLMouseLiverHFCEx0413",
+                  "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
+               ],
+               [
                   "700",
                   "UTHSC-VGX_MmBXDHepatocytesRMA1014",
                   "UT-VGX Hepatocytes Affy Mouse Gene 1.0 ST Gene Level (Oct14) RMA"
@@ -2783,7 +2793,7 @@
             ],
             "Phenotypes": [
                [
-                  "None",
+                  "602",
                   "BXDPublish",
                   "BXD Published Phenotypes"
                ]
@@ -3030,6 +3040,18 @@
                   "842",
                   "UTHSC-BXD-Liv-0917",
                   "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) RMA **"
+               ],
+               [
+                  "850",
+                  "UTHSC-BXD-Liv-0818",
+                  "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Aug18) RMA **"
+               ]
+            ],
+            "Phenotypes": [
+               [
+                  "None",
+                  "BXD-HarvestedPublish",
+                  "BXD-Harvested Published Phenotypes"
                ]
             ]
          },
@@ -3638,7 +3660,7 @@
          "HSNIH-Palmer": {
             "Phenotypes": [
                [
-                  "None",
+                  "652",
                   "HSNIH-PalmerPublish",
                   "HSNIH-Palmer Published Phenotypes"
                ]
@@ -3892,11 +3914,11 @@
          ],
          [
             "AKXD",
-            "AKXD"
+            "AKXD RI Family"
          ],
          [
             "AXBXA",
-            "AXB/BXA"
+            "AXB/BXA RI Family"
          ],
          [
             "B6BTBRF2",
@@ -3931,10 +3953,6 @@
             "BHF2 (Apoe Null) UCLA"
          ],
          [
-            "BXD",
-            "BXD"
-         ],
-         [
             "B6D2RI",
             "BXD Aged"
          ],
@@ -3947,12 +3965,16 @@
             "BXD NIA Longevity Study"
          ],
          [
+            "BXD",
+            "BXD RI Family"
+         ],
+         [
             "BXD300",
             "BXD300"
          ],
          [
             "BXH",
-            "BXH"
+            "BXH RI Family"
          ],
          [
             "CTB6F2",
@@ -3976,7 +3998,7 @@
          ],
          [
             "CXB",
-            "CXB"
+            "CXB RI Family (strain means)"
          ],
          [
             "D2GM",
@@ -4000,11 +4022,11 @@
          ],
          [
             "LXS",
-            "LXS"
+            "ILSXISS (LXS) RI Family (strain means)"
          ],
          [
             "MDP",
-            "Mouse Diversity Panel"
+            "Mouse Diversity Panel (strain means)"
          ],
          [
             "NZBXFVB-N2",
@@ -5114,6 +5136,10 @@
          ],
          "BXD-Harvested": [
             [
+               "Phenotypes",
+               "Phenotypes"
+            ],
+            [
                "Liver mRNA",
                "Liver mRNA"
             ]
diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
index c290cdfe..57dae378 100644
--- a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
@@ -1,75 +1,80 @@
-// http://gn2-lei.genenetwork.org/corr_scatter_plot2?dataset_1=HC_M2_0606_P&dataset_2=HC_M2_0606_P&dataset_3=HC_M2_0606_P&trait_1=1427571_at&trait_2=1457022_at&trait_3=1427571_at
-
 var chart;
 var srchart;
 
+var layout = {
+    height: 700,
+    width: 800,
+    margin: {
+        l: 60,
+        r: 30,
+        t: 80,
+        b: 50
+    },
+    xaxis: {
+        title: js_data.trait_1,
+        zeroline: false,
+        visible: true,
+        linecolor: 'black',
+        linewidth: 1,
+    },
+    yaxis: {
+        title: js_data.trait_2,
+        zeroline: false,
+        visible: true,
+        linecolor: 'black',
+        linewidth: 1,
+    }
+}
+
+cofactor1_dict = {}
+ranked_cofactor1_dict = {}
+cofactor1_values = []
+ranked_cofactor1_values = []
+cofactor2_dict = {}
+ranked_cofactor2_dict = {}
+
 function drawg() {
-    //
-    chart = nv.models.scatterChart();
-    //
-    chart.showLegend(false);
-    chart.duration(300);
-    //chart.color(d3.scale.category10().range());
-    chart.pointRange([0, 400]);
-    chart.pointDomain([0, 10]);
-    //
-    chart.xAxis.axisLabel(js_data.trait_1);
-    chart.xAxis.axisLabelDistance(11);
-    chart.yAxis.axisLabel(js_data.trait_2);
-    chart.yAxis.axisLabelDistance(11);
-    //
-    xmin = d3.min(js_data.data[0]);
-    xmax = d3.max(js_data.data[0]);
-    xrange = xmax - xmin;
-    ymin = d3.min(js_data.data[1]);
-    ymax = d3.max(js_data.data[1]);
-    yrange = ymax - ymin;
-    chart.xDomain([xmin - xrange/10, xmax + xrange/10]);
-    chart.yDomain([ymin - yrange/10, ymax + yrange/10]);
-    chart.xAxis.tickFormat(d3.format(checkformat(xrange)));
-    chart.yAxis.tickFormat(d3.format(checkformat(yrange)));
-    //
-    chart.tooltip.contentGenerator(function (obj) {
-        return tiptext(obj);
-    });
+    x_values = []
+    y_values = []
+    sample_names = []
+    for (j = 0; j < js_data.data[0].length; j++) {
+      x_values.push(js_data.data[0][j])
+      y_values.push(js_data.data[1][j])
+      sample_names.push(js_data.indIDs[j])
+    }
+
+    var trace = {
+        x: x_values,
+        y: y_values,
+        mode: 'markers',
+        text: sample_names
+    }
+
+    Plotly.newPlot('scatterplot2', [trace], layout)
+
 }
 
 function srdrawg() {
-    //
-    srchart = nv.models.scatterChart();
-    //
-    srchart.showLegend(false);
-    srchart.duration(300);
-    srchart.color(d3.scale.category10().range());
-    srchart.pointRange([0, 400]);
-    srchart.pointDomain([0, 10]);
-    //
-    srchart.xAxis.axisLabel(js_data.trait_1);
-    srchart.xAxis.axisLabelDistance(11);
-    srchart.yAxis.axisLabel(js_data.trait_2);
-    srchart.yAxis.axisLabelDistance(11);
-    //
-    xmin = d3.min(js_data.rdata[0]);
-    xmax = d3.max(js_data.rdata[0]);
-    xrange = xmax - xmin;
-    ymin = d3.min(js_data.rdata[1]);
-    ymax = d3.max(js_data.rdata[1]);
-    yrange = ymax - ymin;
-    srchart.xDomain([0, xmax + xrange/10]);
-    srchart.yDomain([0, ymax + yrange/10]);
-    srchart.xAxis.tickFormat(d3.format(checkformat(xrange)));
-    srchart.yAxis.tickFormat(d3.format(checkformat(yrange)));
-    //
-    srchart.tooltip.contentGenerator(function (obj) {
-        return tiptext(obj);
-    });
-}
+    x_values = []
+    y_values = []
+    sample_names = []
+    for (j = 0; j < js_data.rdata[0].length; j++) {
+      x_values.push(js_data.rdata[0][j])
+      y_values.push(js_data.rdata[1][j])
+      sample_names.push(js_data.indIDs[j])
+    }
 
-function tiptext(obj) {
-    return '<b style="font-size: 18px">' + obj.point.name + " (" + obj.point.x + ', ' + obj.point.y + ')</b>';
+    var trace = {
+        x: x_values,
+        y: y_values,
+        mode: 'markers',
+        text: sample_names
+    }
+
+    Plotly.newPlot('srscatterplot2', [trace], layout)
 }
 
-function getdata(size, shape) {
+function getdata() {
     var data = [];
     data.push({
             values: [],
@@ -79,37 +84,91 @@ function getdata(size, shape) {
 
     sizemin = 1;
     sizemax = 50;
-    if ('vals_3' in js_data) {
-        datamin = d3.min(js_data.vals_3);
-        datamax = d3.max(js_data.vals_3);
-        colormin = $("#cocolorfrom").val();
-        colormax = $("#cocolorto").val();
-        compute = d3.interpolate(colormin, colormax);
-        linear = d3.scale.linear().domain([datamin, datamax]).range([0,1]);
+
+    if ($('input[name=cofactor1_vals]').val()){
+        just_vals = []
+        val_sample_dict = {}
+        val_sample_pairs = $('input[name=cofactor1_vals]').val().split(",")
+        for (i=0; i < val_sample_pairs.length; i++) {
+          just_vals.push(parseFloat(val_sample_pairs[i].split(":")[1]))
+          val_sample_dict[val_sample_pairs[i].split(":")[0]] = parseFloat(val_sample_pairs[i].split(":")[1])
+        }
+
+        cofactor1_dict = val_sample_dict
+        cofactor1_values = just_vals
+    }
+
+    if ($('input[name=cofactor2_vals]').val()){
+        vals_3 = [];
+        samples_3 = [];
+        val_sample_dict = {}
+        val_sample_pairs = $('input[name=cofactor2_vals]').val().split(",")
+        for (i=0; i < val_sample_pairs.length; i++) {
+          samples_3.push(val_sample_pairs[i].split(":")[0])
+          vals_3.push(parseFloat(val_sample_pairs[i].split(":")[1]))
+          val_sample_dict[val_sample_pairs[i].split(":")[0]] = val_sample_pairs[i].split(":")[1]
+        }
+        datamin = d3.min(vals_3);
+        datamax = d3.max(vals_3);
+
+        cofactor2_dict = val_sample_dict
     }
 
+    x_values = []
+    y_values = []
+    sample_names = []
+    sizes = []
+
     for (j = 0; j < js_data.data[0].length; j++) {
-        if ('trait3' in js_data) {
-          if (js_data.indIDs[j] in js_data.trait3) {
-            datav = js_data.trait3[js_data.indIDs[j]].value;
-            // size = (sizemax - sizemin) * (datav - datamin) / (datamax - datamin) + sizemin;
+        if ($('input[name=cofactor2_vals]').val()){
+          if (samples_3.indexOf(js_data.indIDs[j])) {
+            datav = vals_3[j]
             sizev = map1to2(datamin, datamax, sizemin, sizemax, datav);
           }
         } else {
             datav = 0;
-            sizev = sizemin;
+            sizev = 10;
         }
+
+        x_values.push(js_data.data[0][j])
+        y_values.push(js_data.data[1][j])
+        sample_names.push(js_data.indIDs[j])
+        sizes.push(sizev)
+
         data[0].values.push({
+            type: "normal",
             x: js_data.data[0][j],
             y: js_data.data[1][j],
             name: js_data.indIDs[j],
             size: sizev,
-            shape: shape,
             v3: datav
         });
     }
-    console.log(data);
-    return data;
+
+    point_text = []
+    for (j = 0; j < sample_names.length; j++) {
+      this_text = ""
+      this_text += sample_names[j]
+      if (sample_names[j] in cofactor1_dict){
+        this_text += "<br>Cofactor 1: " + cofactor1_dict[sample_names[j]]
+      }
+      if (sample_names[j] in cofactor2_dict){
+        this_text += "<br>Cofactor 2: " + cofactor2_dict[sample_names[j]]
+      }
+      point_text.push(this_text)
+    }
+
+    var trace = {
+        x: x_values,
+        y: y_values,
+        mode: 'markers',
+        text: point_text,
+        marker: {
+          size: sizes
+        }
+    }
+
+    return [trace];
 }
 
 function map1to2 (min1, max1, min2, max2, v1) {
@@ -117,167 +176,223 @@ function map1to2 (min1, max1, min2, max2, v1) {
     return v2;
 }
 
-function srgetdata(size, shape) {
+function srgetdata() {
     var data = [];
     data.push({
             values: [],
             slope: js_data.srslope,
             intercept: js_data.srintercept
         });
+
+    sizemin = 1;
+    sizemax = 50;
+
+    x_values = []
+    y_values = []
+    sample_names = []
+    sizes = []
+
+    if ($('input[name=ranked_cofactor1_vals]').val()){
+        just_vals = []
+        val_sample_dict = {}
+        val_sample_pairs = $('input[name=ranked_cofactor1_vals]').val().split(",")
+        for (i=0; i < val_sample_pairs.length; i++) {
+          just_vals.push(parseFloat(val_sample_pairs[i].split(":")[1]))
+          val_sample_dict[val_sample_pairs[i].split(":")[0]] = parseFloat(val_sample_pairs[i].split(":")[1])
+        }
+
+        ranked_cofactor1_dict = val_sample_dict
+        ranked_cofactor1_values = just_vals
+    }
+
+    if ($('input[name=ranked_cofactor2_vals]').val()){
+        vals_3 = []
+        samples_3 = [];
+        val_sample_dict = {}
+        val_sample_pairs = $('input[name=ranked_cofactor2_vals]').val().split(",")
+        for (i=0; i<val_sample_pairs.length; i++){
+          samples_3.push(val_sample_pairs[i].split(":")[0])
+          vals_3.push(val_sample_pairs[i].split(":")[1])
+          val_sample_dict[val_sample_pairs[i].split(":")[0]] = val_sample_pairs[i].split(":")[1]
+        }
+        datamin = d3.min(vals_3);
+        datamax = d3.max(vals_3);
+
+        ranked_cofactor2_dict = val_sample_dict
+    }
+
     for (j = 0; j < js_data.rdata[0].length; j++) {
-        if (js_data.indIDs[j] in js_data.trait3) {
-            size = js_data.trait3[js_data.indIDs[j]].value;
-            //console.log("yes "+js_data.indIDs[j]+", "+size);
+        if ($('input[name=ranked_cofactor2_vals]').val()){
+          if (samples_3.indexOf(js_data.indIDs[j])) {
+            datav = vals_3[j]
+            sizev = map1to2(datamin, datamax, sizemin, sizemax, datav);
+          }
         } else {
-            //console.log("no "+js_data.indIDs[j]);
+            sizev = 10;
         }
+
+        x_values.push(js_data.rdata[0][j])
+        y_values.push(js_data.rdata[1][j])
+        sample_names.push(js_data.indIDs[j])
+        sizes.push(sizev)
+
         data[0].values.push({
+            type: "ranked",
             x: js_data.rdata[0][j],
             y: js_data.rdata[1][j],
             name: js_data.indIDs[j],
-            size: size,
-            shape: shape
+            size: sizev,
         });
     }
-    return data;
-}
-    
-function checkformat(range) {
-    cell = range / 10.0;
-    if (cell >= 1) {
-        return ",r";
-    } else {
-        cell = -Math.log(cell);
-        n = cell.toString().split(".")[0].length;
-        return ",.0" + n + "f";
+
+    point_text = []
+    for (j = 0; j < sample_names.length; j++) {
+      this_text = ""
+      this_text += sample_names[j]
+      if (sample_names[j] in ranked_cofactor1_dict){
+        this_text += "<br>Cofactor 1: " + ranked_cofactor1_dict[sample_names[j]]
+      }
+      if (sample_names[j] in ranked_cofactor2_dict){
+        this_text += "<br>Cofactor 2: " + ranked_cofactor2_dict[sample_names[j]]
+      }
+      point_text.push(this_text)
+    }
+
+    var trace = {
+        x: x_values,
+        y: y_values,
+        mode: 'markers',
+        text: point_text,
+        marker: {
+          size: sizes
+        }
     }
-}
 
-function chartupdate() {
-    //
-    var labelcolor = $("#labelcolor").val();
-    $(".nvd3 .nv-axis.nv-x text").css("fill", labelcolor);
-    $(".nvd3 .nv-axis.nv-y text").css("fill", labelcolor);
-    //
-    var labelfont = $("#labelfont").val();
-    $(".nvd3 .nv-axis.nv-x text").css("font-size", labelfont);
-    $(".nvd3 .nv-axis.nv-y text").css("font-size", labelfont);
-    //
-    var numbercolor = $("#numbercolor").val();
-    $("g.tick text").css("fill", numbercolor);
-    //
-    var numberfont = $("#numberfont").val();
-    $("g.tick text").css("font-size", numberfont);
-    //
-    var axiscolor = $("#axiscolor").val();
-    $(".nv-x .nv-axis g path.domain").css("stroke", axiscolor);
-    $(".nv-y .nv-axis g path.domain").css("stroke", axiscolor);
-    //
-    var axiswidth = $("#axiswidth").val();
-    $(".nv-x .nv-axis g path.domain").css("stroke-width", axiswidth);
-    $(".nv-y .nv-axis g path.domain").css("stroke-width", axiswidth);
-    //
-    var linecolor = $("#linecolor").val();
-    $("line.nv-regLine").css("stroke", linecolor);
-    //
-    var linewidth = $("#linewidth").val();
-    $("line.nv-regLine").css("stroke-width", linewidth);
-    //
-    var markcolor = $("#markcolor").val();
-    $(".nvd3 g path").css("fill", markcolor);
+    return [trace];
 }
 
 function chartupdatewh() {
-    //
     var width = $("#width").val();
-    $("#scatterplot2 svg").css("width", width);
-    $("#srscatterplot2 svg").css("width", width);
-    //
     var height = $("#height").val();
-    $("#scatterplot2 svg").css("height", height);
-    $("#srscatterplot2 svg").css("height", height);
-    //
-    window.dispatchEvent(new Event('resize'));
+
+    width_height_update = {
+      height: height,
+      width: width
+    }
+
+    Plotly.newPlot('scatterplot2', getdata(), layout)
+    Plotly.relayout('scatterplot2', width_height_update)
+    Plotly.newPlot('srscatterplot2', srgetdata(), layout)
+    Plotly.relayout('srscatterplot2', width_height_update)
 }
 
- function colorer(d) {
-    datamin = d3.min(js_data.vals_3);
-    datamax = d3.max(js_data.vals_3);
-    //colormin = d3.rgb(255,0,0);
-    //colormax = d3.rgb(0,255,0);
+function colorer(d) {
+    datamin = d3.min(cofactor1_values);
+    datamax = d3.max(cofactor1_values);
     colormin = $("#cocolorfrom").val();
     colormax = $("#cocolorto").val();
 
-    console.log("colormin: "+colormin);
-    console.log("colormax: "+colormax);
+    compute = d3.interpolate(colormin, colormax);
+    linear = d3.scale.linear().domain([datamin, datamax]).range([0,1]);
+
+    this_sample = d.tx.split("<br>")[0]
+
+    c = compute(linear(cofactor1_dict[this_sample]));
+
+    return c;
+}
+
+function ranked_colorer(d) {
+    datamin = d3.min(ranked_cofactor1_values);
+    datamax = d3.max(ranked_cofactor1_values);
+    colormin = $("#cocolorfrom").val();
+    colormax = $("#cocolorto").val();
 
     compute = d3.interpolate(colormin, colormax);
     linear = d3.scale.linear().domain([datamin, datamax]).range([0,1]);
-    //console.log(d[0].x);
-          c= compute(linear(d[0].x));
-          //console.log(c);
-          return c;
-  }
+
+    this_sample = d.tx.split("<br>")[0]
+
+    c= compute(linear(ranked_cofactor1_dict[this_sample]));
+
+    return c;
+}
 
 function chartupdatedata() {
-    //
     var size = $("#marksize").val();
     var shape = $("#markshape").val();
-    //
-    d3.select('#scatterplot2 svg').datum(getdata(size, shape)).call(chart);
-    d3.select('#srscatterplot2 svg').datum(nv.log(srgetdata(size, shape))).call(srchart);
-    //
-    d3.selectAll('.nv-point')
-      .attr({
-          'stroke': colorer,
-          'fill':   colorer
-      });
-    //
-    nv.utils.windowResize(chart.update);
-    nv.utils.windowResize(srchart.update);
-}
 
-function savesvg(svgEl, name) {
-    svgEl.setAttribute("xmlns", "http://www.w3.org/2000/svg");
-    var svgData = svgEl.outerHTML;
-    var preface = '<?xml version="1.0" standalone="no"?>\r\n';
-    preface += '<?xml-stylesheet type="text/css" href="http://cdnjs.cloudflare.com/ajax/libs/nvd3/1.8.5/nv.d3.min.css"?>\r\n';
-    var svgBlob = new Blob([preface, svgData], {type:"image/svg+xml;charset=utf-8"});
-    var svgUrl = URL.createObjectURL(svgBlob);
-    var downloadLink = document.createElement("a");
-    downloadLink.href = svgUrl;
-    downloadLink.download = name;
-    document.body.appendChild(downloadLink);
-    downloadLink.click();
-    document.body.removeChild(downloadLink);
-}
+    var pearson_title_update = {
+      title: "Pearson Correlation Scatterplot"
+    }
+    var spearman_title_update = {
+      title: "Spearman Rank Correlation Scatterplot"
+    }
 
-function saveassvg_pcs() {
-    savesvg($("#svg_pcs")[0], "Pearson Correlation Scatterplot.svg");
-}
+    Plotly.newPlot('scatterplot2', getdata(), layout)
+    Plotly.relayout('scatterplot2', pearson_title_update)
+    Plotly.newPlot('srscatterplot2', srgetdata(), layout)
+    Plotly.relayout('srscatterplot2', spearman_title_update)
 
-function saveassvg_srcs() {
-    savesvg($("#svg_srcs")[0], "Spearman Rank Correlation Scatterplot.svg");
+    if ($('input[name=cofactor1_vals]').val()){
+      d3.select('#scatterplot2 svg').selectAll('.point')
+        .style({
+            'stroke': colorer,
+            'fill':   colorer
+      });
+      d3.select('#srscatterplot2 svg').selectAll('.point')
+        .style({
+            'stroke': ranked_colorer,
+            'fill':   ranked_colorer
+      });
+    }
 }
 
 drawg();
 srdrawg();
 
-$(".chartupdate").change(function () {
-    chartupdate();
-});
-
 $(".chartupdatewh").change(function () {
     chartupdatewh();
-    chartupdate();
 });
 
 $(".chartupdatedata").change(function () {
     chartupdatedata();
-    chartupdate();
 });
 
+$(".cofactor1_type").change(function () {
+    console.log("cofactor1 type:", $(".cofactor1_type").val())
+    if ($(".cofactor1_type").val() == "color"){
+      $(".cofactor2_type").val("size")
+    } else {
+      $(".cofactor2_type").val("color")
+    }
+});
+
+open_covariate_selection = function() {
+  return $('#collections_holder').load('/collections/list #collections_list', (function(_this) {
+    return function() {
+      $.colorbox({
+        inline: true,
+        href: "#collections_holder",
+        onComplete: function(){
+            $.getScript("/static/new/javascript/get_traits_from_collection.js");
+        }
+      });
+      return $('a.collection_name').attr('onClick', 'return false');
+    };
+  })(this));
+};
+
 $(document).ready(function(){
     chartupdatedata();
-    chartupdate();
+
+    $('#select_cofactor1').click(function () {
+        $('input[name=selecting_which_cofactor]').val("1");
+        open_covariate_selection();
+    });
+
+    $('#select_cofactor2').click(function () {
+        $('input[name=selecting_which_cofactor]').val("2");
+        open_covariate_selection();
+    });
 });
diff --git a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
index f23dad0c..3d756303 100644
--- a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
@@ -26,7 +26,7 @@
   redraw_prob_plot = function(samples, sample_group) {
     var container, h, margin, totalh, totalw, w;
     h = 600;
-    w = 600;
+    w = 500;
     margin = {
       left: 60,
       top: 40,
diff --git a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
index 4abb0735..8a79627a 100644
--- a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
+++ b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
@@ -4,7 +4,7 @@ var add_trait_data, assemble_into_json, back_to_collections, collection_click, c
 
 console.log("before get_traits_from_collection");
 
-collection_list = null;
+//collection_list = null;
 
 this_trait_data = null;
 
@@ -15,7 +15,6 @@ collection_click = function() {
   console.log("Clicking on:", $(this));
   this_collection_url = $(this).find('.collection_name').prop("href");
   this_collection_url += "&json";
-  console.log("this_collection_url", this_collection_url);
   collection_list = $("#collections_holder").html();
   return $.ajax({
     dataType: "json",
@@ -42,7 +41,6 @@ submit_click = function() {
       success: add_trait_data
     });
   });
-  console.log("SELECTED_TRAITS IS:", selected_traits);
   trait_names = [];
   samples = $('input[name=allsamples]').val().split(" ");
   all_vals = [];
@@ -117,7 +115,6 @@ trait_click = function() {
   trait = $(this).parent().find('.trait').text();
   dataset = $(this).parent().find('.dataset').text();
   this_trait_url = "/trait/get_sample_data?trait=" + trait + "&dataset=" + dataset;
-  console.log("this_trait_url", this_trait_url);
   $.ajax({
     dataType: "json",
     url: this_trait_url,
@@ -134,28 +131,84 @@ add_trait_data = function(trait_data, textStatus, jqXHR) {
   return console.log("selected_traits:", selected_traits);
 };
 
+populate_cofactor_info = function(trait_info) {
+  if ($('input[name=selecting_which_cofactor]').val() == "1"){
+    $('#cofactor1_trait_link').attr("href", trait_info['url'])
+    if (trait_info['type'] == "ProbeSet"){
+      $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name'])
+      $('#cofactor1_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description'])
+    } else {
+      $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
+      $('#cofactor1_description').html('<a href=\"' + trait_info['pubmed_link'] + '\">PubMed: ' + trait_info['pubmed_text'] + '</a><br>' + trait_info['description'])
+    }
+    $('#select_cofactor1').text("Change Cofactor 1");
+    $('#cofactor1_info_container').css("display", "inline");
+    $('#cofactor2_button').css("display", "inline");
+  } else {
+    $('#cofactor2_trait_link').attr("href", trait_info['url'])
+    if (trait_info['type'] == "ProbeSet"){
+      $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name'])
+      $('#cofactor2_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description'])
+    } else {
+      $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
+      $('#cofactor2_description').html('<a href=\"' + trait_info['pubmed_link'] + '\">PubMed: ' + trait_info['pubmed_text'] + '</a><br>' + trait_info['description'])
+    }
+    $('#select_cofactor2').text("Change Cofactor 2");
+    $('#cofactor2_info_container').css("display", "inline");
+  }
+}
+
 get_trait_data = function(trait_data, textStatus, jqXHR) {
   var sample, samples, this_trait_vals, trait_sample_data, vals, _i, _len;
-  console.log("trait:", trait_data[0]);
   trait_sample_data = trait_data[1];
-  console.log("trait_sample_data:", trait_sample_data);
-  samples = $('input[name=allsamples]').val().split(" ");
+  if ( $('input[name=allsamples]').length ) {
+    samples = $('input[name=allsamples]').val().split(" ");
+  } else {
+    samples = js_data.indIDs
+  }
+  sample_vals = [];
   vals = [];
   for (_i = 0, _len = samples.length; _i < _len; _i++) {
     sample = samples[_i];
-    if (__indexOf.call(Object.keys(trait_sample_data), sample) >= 0) {
-      vals.push(parseFloat(trait_sample_data[sample]));
+    if (sample in trait_sample_data) {
+      sample_vals.push(sample + ":" + parseFloat(trait_sample_data[sample]))
+      vals.push(parseFloat(trait_sample_data[sample]))
     } else {
-      vals.push(null);
+      sample_vals.push(null)
+      vals.push(null)
     }
   }
-  if ($('input[name=samples]').length < 1) {
-    $('#hidden_inputs').append('<input type="hidden" name="samples" value="[' + samples.toString() + ']" />');
+  if ( $('input[name=allsamples]').length ) {
+    if ($('input[name=samples]').length < 1) {
+      $('#hidden_inputs').append('<input type="hidden" name="samples" value="[' + samples.toString() + ']" />');
+    }
+    $('#hidden_inputs').append('<input type="hidden" name="vals" value="[' + vals.toString() + ']" />');
+    this_trait_vals = get_this_trait_vals(samples);
+    return color_by_trait(trait_sample_data);
+  } else{
+    populate_cofactor_info(trait_data[0])
+    sorted = vals.slice().sort(function(a,b){return a-b})
+    ranks = vals.slice().map(function(v){ return sorted.indexOf(v)+1 });
+    sample_ranks = []
+    for (_i = 0; _i < samples.length; _i++){
+      if (samples[_i] in trait_sample_data){
+        sample_ranks.push(samples[_i] + ":" + ranks[_i])
+      } else {
+        sample_ranks.push(null)
+      }
+    }
+
+    if ($('input[name=selecting_which_cofactor]').val() == "1"){
+      $('input[name=cofactor1_vals]').val(sample_vals)
+      $('input[name=ranked_cofactor1_vals]').val(sample_ranks)
+    } else {
+      $('input[name=cofactor2_vals]').val(sample_vals)
+      $('input[name=ranked_cofactor2_vals]').val(sample_ranks)
+    }
+    chartupdatedata();
+    chartupdate();
+    return false
   }
-  $('#hidden_inputs').append('<input type="hidden" name="vals" value="[' + vals.toString() + ']" />');
-  this_trait_vals = get_this_trait_vals(samples);
-  console.log("THE LENGTH IS:", $('input[name=vals]').length);
-  return color_by_trait(trait_sample_data);
 };
 
 get_this_trait_vals = function(samples) {
@@ -215,14 +268,17 @@ process_traits = function(trait_data, textStatus, jqXHR) {
   }
   the_html += "</tbody>";
   the_html += "</table>";
+  the_html += "<div id=\"collection_list_html\" style=\"display: none;\">"
+  the_html += collection_list
+  the_html += "</div>"
   the_html += "<script type='text/javascript' src='/static/new/javascript/get_traits_from_collection.js'></script>"
   $("#collections_holder").html(the_html);
   return $('#collections_holder').colorbox.resize();
 };
 
 back_to_collections = function() {
-  console.log("collection_list:", collection_list);
-  $("#collections_holder").html(collection_list);
+  collection_list_html = $('#collection_list_html').html()
+  $("#collections_holder").html(collection_list_html);
   $(document).on("click", ".collection_line", collection_click);
   return $('#collections_holder').colorbox.resize();
 };
diff --git a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
index 49fd53b1..97d768c8 100644
--- a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
@@ -25,7 +25,7 @@
 
   redraw_prob_plot = function(samples, sample_group) {
     var container, h, margin, totalh, totalw, w;
-    h = 600;
+    h = 370;
     w = 600;
     margin = {
       left: 60,
@@ -71,11 +71,11 @@
     })();
     //ZS: 0.1 indicates buffer, increase to increase buffer
     y_domain = [sorted_values[0] - (sorted_values.slice(-1)[0] - sorted_values[0])*0.1, sorted_values.slice(-1)[0] + (sorted_values.slice(-1)[0] - sorted_values[0])*0.1]
-    sw_result = ShapiroWilkW(sorted_values);
-    W = sw_result.w.toFixed(3);
-    pvalue = sw_result.p.toFixed(3);
-    pvalue_str = pvalue > 0.05 ? pvalue.toString() : "<span style='color:red'>" + pvalue + "</span>";
-    test_str = "Shapiro-Wilk test statistic is " + W + " (p = " + pvalue_str + ")";
+    //sw_result = ShapiroWilkW(sorted_values);
+    //W = sw_result.w.toFixed(3);
+    //pvalue = sw_result.p.toFixed(3);
+    //pvalue_str = pvalue > 0.05 ? pvalue.toString() : "<span style='color:red'>" + pvalue + "</span>";
+    //test_str = "Shapiro-Wilk test statistic is " + W + " (p = " + pvalue_str + ")";
     z_scores = get_z_scores(sorted_values.length);
     //ZS: 0.1 indicates buffer, increase to increase buffer
     x_domain = [z_scores[0] - (z_scores.slice(-1)[0] - z_scores[0])*0.1, z_scores.slice(-1)[0] + (z_scores.slice(-1)[0] - z_scores[0])*0.1]
@@ -106,7 +106,6 @@
       };
     };
     data = [make_data('samples_primary'), make_data('samples_other'), make_data('samples_all')];
-    console.log("THE DATA IS:", data);
     x_values = {}
     y_values = {}
     point_names = {}
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 17afc814..e9dd3c9d 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -247,6 +247,9 @@
       }
       root.bar_data[0]['x'] = trait_samples
       Plotly.newPlot('bar_chart', root.bar_data, root.bar_layout);
+      Plotly.relayout('bar_chart', {
+          'yaxis.autorange': true
+      });
     };
 
     redraw_box_plot = function() {
@@ -549,6 +552,7 @@
     };
     $('#block_outliers').click(block_outliers);
     reset_samples_table = function() {
+      $('input[name="transform"]').val("");
       return $('.trait_value_input').each((function(_this) {
         return function(_index, element) {
           console.log("value is:", $(element).val());
@@ -559,6 +563,72 @@
       })(this));
     };
     $('#reset').click(reset_samples_table);
+
+    log_normalize_data = function() {
+      return $('.trait_value_input').each((function(_this) {
+        return function(_index, element) {
+          current_value = parseFloat($(element).data("value")) + 1;
+          if(isNaN(current_value)) {
+            return current_value
+          } else {
+            $(element).val(Math.log2(current_value).toFixed(3));
+            return Math.log2(current_value).toFixed(3)
+          }
+        };
+      })(this));
+    };
+
+    sqrt_normalize_data = function() {
+      return $('.trait_value_input').each((function(_this) {
+        return function(_index, element) {
+          current_value = parseFloat($(element).data("value")) + 1;
+          if(isNaN(current_value)) {
+            return current_value
+          } else {
+            $(element).val(Math.sqrt(current_value).toFixed(3));
+            return Math.sqrt(current_value).toFixed(3)
+          }
+        };
+      })(this));
+    };
+
+    qnorm_data = function() {
+      return $('.trait_value_input').each((function(_this) {
+        return function(_index, element) {
+          current_value = $(element).data("value");
+          if(isNaN(current_value)) {
+            return current_value
+          } else {
+            $(element).val($(element).data("qnorm"));
+            return $(element).data("qnorm");
+          }
+        };
+      })(this));
+    };
+
+    normalize_data = function() {
+      if ($('#norm_method option:selected').val() == 'log2'){
+        if ($('input[name="transform"]').val() != "log2") {
+          log_normalize_data()
+          $('input[name="transform"]').val("log2")
+        }
+      }
+      else if ($('#norm_method option:selected').val() == 'sqrt'){
+        if ($('input[name="transform"]').val() != "sqrt") {
+          sqrt_normalize_data()
+          $('input[name="transform"]').val("sqrt")
+        }
+      }
+      else if ($('#norm_method option:selected').val() == 'qnorm'){
+        if ($('input[name="transform"]').val() != "qnorm") {
+          qnorm_data()
+          $('input[name="transform"]').val("qnorm")
+        }
+      }
+    }
+
+    $('#normalize').click(normalize_data);
+
     switch_qnorm_data = function() {
       return $('.trait_value_input').each((function(_this) {
         return function(_index, element) {
@@ -734,7 +804,7 @@
         box_data = [trace1, trace2, trace3]
     } else {
         var box_layout = {
-            width: 500,
+            width: 300,
             height: 500,
             margin: {
                 l: 50,
@@ -819,6 +889,7 @@
     max_y_val = Math.max(...positive_error_vals)
 
     if (min_y_val == 0) {
+        range_top = max_y_val + Math.abs(max_y_val)*0.1
         range_bottom = 0;
     } else {
         range_top = max_y_val + Math.abs(max_y_val)*0.1
@@ -834,7 +905,7 @@
 
     var layout = {
         yaxis: {
-            range: [range_bottom, range_top]
+            range: [range_bottom, range_top],
         },
         width: 1200,
         height: 500,
@@ -884,6 +955,7 @@
     $('#block_outliers').click(edit_data_change);
     $('#reset').click(edit_data_change);
     $('#qnorm').click(edit_data_change);
+    $('#normalize').click(edit_data_change);
     return console.log("end");
   });
 
diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html
index d45aa015..603947f4 100644
--- a/wqflask/wqflask/templates/collections/add.html
+++ b/wqflask/wqflask/templates/collections/add.html
@@ -1,36 +1,38 @@
 <div id="myModal">
     <div class="modal-header">
-        <h3>Add to collection</h3>
-        <p>You have two choices: Create and name a collection,
-        or add the traits to an existing collection.</p>
+        <h2>Define or Add to Collection</h2>
+        <p>You have two choices: Name a new collection
+        or add to an existing collection.</p>
     </div>
-    <div class="modal-body">
+    <div class="modal-body" style="margin-left: 20px;">
         <form action="/collections/new" data-validate="parsley" id="add_form">
             <input type="hidden" name="traits" value="{{ traits }}" />
             <fieldset>
-                <legend>Create a new named collection</legend>
-                <label>New collection name</label>
-                <input type="text" name="new_collection" placeholder="Name of new collection..."
-                    data-trigger="change" data-minlength="5" data-maxlength="50">
-                <span class="help-block">Type the name of the new collection.</span>
+              <legend>1. Create a new collection</legend>
+              <div style="margin-left: 20px;">
+                <!--<label>Collection name:</label>-->
+                <input type="text" name="new_collection" placeholder=" Name of new collection..."
+                    data-trigger="change" data-minlength="5" data-maxlength="50" style="width: 100%">
+                <button type="submit" name="create_new" class="btn btn-primary" style="margin-top: 20px;">Create collection</button>
                 {% if uc is not defined %}
                 <span class="help-block" style="color:red;">This collection will be saved to this computer for 5 days.</span>
                 {% endif %}
-                <button type="submit" name="create_new" class="btn">Create and add traits</button>
+              </div>
             </fieldset>
             <hr />
             <fieldset>
-                <legend>Or add to an existing collection</legend>
-                <label>Existing collection name</label>
-
+              <legend>2. Add to an existing collection</legend>
+              <div style="margin-left: 20px;">  
+                <!--<label>Existing collection name:</label>-->
                 <select name="existing_collection" class="form-control">
+                    <option selected disabled>Select Collection</option>
                 {% for col in collections %}
                     <option value="{{ col.id }}:{{ col.name }}">{{ col.name }}</option>
                 {% endfor %}
                 </select>
                 <br />
-
-                <button type="submit" name="add_to_existing" class="btn">Add to existing collection</button>
+                <button type="submit" name="add_to_existing" class="btn btn-primary">Add to existing collection</button>
+              </div>
             </fieldset>
         </form>
     </div>
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index 11c33673..64d5a676 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -3,7 +3,6 @@
 {% block css %}
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
-    <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
 {% endblock %}
 {% block content %}
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index cae03b4a..864299a2 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -29,10 +29,6 @@
                 {{ this_trait.name }}:{{ this_trait.dataset.name }},
             {% endfor %}" >
 
-                <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" title="Delete this collection" >
-                Delete this collection
-                </button>
-
 
                 <button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" >
                     Correlation Matrix
@@ -58,6 +54,15 @@
                     Heatmap
                 </button>
 
+                <button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" >
+                    Comparison Bar Chart
+                </button>
+
+
+                <button id="delete" class="btn btn-danger submit_special" style="margin-left: 15px;" data-url="/collections/delete" title="Delete this collection" >
+                    Delete Collection
+                </button>
+
           </form>
         </div>
 
@@ -66,8 +71,8 @@
             <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button>
             <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button>
             <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button>
-            <button class="btn" id="add" disabled="disabled"><i class="icon-plus-sign"></i> Add Record to Other Collection</button>
-            <button class="btn" id="remove" disabled="disabled"><i class="icon-minus-sign"></i> Remove Record</button>
+            <button class="btn btn-danger" id="remove" disabled="disabled"><i class="icon-minus-sign"></i> Delete From Collection</button>
+            <button class="btn" id="add" disabled="disabled"><i class="icon-plus-sign"></i> Copy Record to Other Collection</button>
             <br />
             <br />
             <form id="export_form" method="POST" action="/export_traits_csv">
@@ -246,6 +251,14 @@
                 url = $(this).data("url")
                 return submit_special(url)
             });
+            $("#comp_bar_chart").on("click", function() {
+                traits = $("#trait_table input:checked").map(function() {
+                    return $(this).val();
+                }).get();
+                $("#trait_list").val(traits)
+                url = $(this).data("url")
+                return submit_special(url)
+            });
         });
         
     </script>
diff --git a/wqflask/wqflask/templates/comparison_bar_chart.html b/wqflask/wqflask/templates/comparison_bar_chart.html
new file mode 100644
index 00000000..033ff0a4
--- /dev/null
+++ b/wqflask/wqflask/templates/comparison_bar_chart.html
@@ -0,0 +1,39 @@
+{% extends "base.html" %}
+{% block title %}Comparison Bar Chart{% endblock %}
+{% block css %}
+    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+    <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
+{% endblock %}
+{% block content %} <!-- Start of body -->
+
+    {{ header("Comparison Bar Chart") }}
+
+    <div class="container">
+        <div>
+            <h3>
+                The following is a grouped bar chart with the sample values for each selected trait. 
+            </h3>
+        </div>
+        <div id="chart_container">
+            <div id="comp_bar_chart"></div>
+        </div>
+    
+    </div>
+
+    <!-- End of body -->
+
+{% endblock %}
+
+{% block js %}  
+    <script>
+        js_data = {{ js_data | safe }}
+    </script>
+
+    <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+    <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/comparison_bar_chart.js"></script>
+
+{% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html
index e0f017c2..6451fda5 100644
--- a/wqflask/wqflask/templates/corr_scatterplot.html
+++ b/wqflask/wqflask/templates/corr_scatterplot.html
@@ -12,124 +12,74 @@
 
 <div class="container-fluid">
 
-  <h2>Correlation Scatterplot</h2>
+  <input type="hidden" name="cofactor1_vals"></input>
+  <input type="hidden" name="ranked_cofactor1_vals"></input>
+  <input type="hidden" name="cofactor2_vals"></input>
+  <input type="hidden" name="ranked_cofactor2_vals"></input>
+  <input type="hidden" name="selecting_which_cofactor"></input>
 
-  <div style="margin-left: 0px;">
-    {% if trait_1.dataset.type == "ProbeSet" %}
-    <div>
-      X axis:
-      <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
-        {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.tissue + " "  + trait_1.dataset.name + ": " + trait_1.name|string}}
-      </a>
-    </div>
-    <div>
-      [{{trait_1.symbol}} on {{trait_1.location_repr}} Mb]
-      {{trait_1.description_display}}
-    </div>
-    {% elif trait_1.dataset.type == "Publish" %}
-    <div>
-      X axis:
-      <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
-        {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.name + ": " + trait_1.name|string}}
-      </a>
-    </div>
-    <div>
-      <a href="{{trait_1.pubmed_link}}">PubMed: {{trait_1.pubmed_text}}</a>
-        {{trait_1.description_display}}
-    </div>
-    {% endif %}
+  <h2>Correlation Scatterplot</h2>
 
-    <br/>
+  <table class="table">
+    <tr>
+      <td style="vertical-align: middle;">Width <input class="chartupdatewh" id="width" type="text" value="800" style="width: 44px; height: 22px;"> px</td>
+      <td style="vertical-align: middle;">Height <input class="chartupdatewh" id="height" type="text" value="700" style="width: 44px; height: 22px;"> px</td>
+    </tr>
+  </table>
 
-    {% if trait_2.dataset.type == "ProbeSet" %}
-    <div>
-      Y axis:
-      <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
-        {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.tissue + " "  + trait_2.dataset.name + ": " + trait_2.name|string}}
-      </a>
-    </div>
-    <div>
-      [{{trait_2.symbol}} on {{trait_2.location_repr}} Mb]
-      {{trait_2.description_display}}
-    </div>
-    {% elif trait_2.dataset.type == "Publish" %}
-    <div>
-      Y axis:
-      <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
-        {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.name + ": " + trait_2.name|string}}
-      </a>
-    </div>
-    <div>
-      <a href="{{trait_2.pubmed_link}}">PubMed: {{trait_2.pubmed_text}}</a>
-        {{trait_2.description_display}}
+  <div>
+    <button type="button" class="btn btn-default" id="select_cofactor1">
+      Select Cofactor 1
+    </button>
+<!--
+    <select class="cofactor1_type">
+      <option value="color">Color</option>
+      <option value="size">Size</option>
+    </select>
+-->
+    <div id="cofactor2_button" style="margin-left: 10px; display: none;">
+      <button type="button" class="btn btn-default" id="select_cofactor2">
+        Add a Second Cofactor?
+      </button>
+<!--
+      <select class="cofactor2_type">
+        <option value="color">Color</option>
+        <option value="size" selected="selected">Size</option>
+      </select>
+-->
     </div>
-    {% endif %}
-
-    <br/>
+  </div>
+  <div id="collections_holder_wrapper" style="display:none;">
+      <div id="collections_holder"></div>
+  </div>
+  <br/>
 
-    {% if trait_3 %}
-    {% if trait_3.dataset.type == "ProbeSet" %}
+  <div id="cofactor1_info_container" style="margin-left: 0px; display: none;">
     <div>
-      Cofactor:
-      <a href="{{url_for('show_trait_page', trait_id = trait_3.name, dataset = trait_3.dataset.name)}}">
-        {{trait_3.dataset.group.species + " " + trait_3.dataset.group.name + " " + trait_3.dataset.tissue + " "  + trait_3.dataset.name + ": " + trait_3.name|string}}
-      </a>
+      <b>Cofactor 1</b>: <a id="cofactor1_trait_link" href="#"></a>
     </div>
-    <div>
-      [{{trait_3.symbol}} on {{trait_3.location_repr}} Mb]
-      {{trait_3.description_display}}
+    <div id="cofactor1_description"></div>
+    <br>
+    <div style="margin-bottom: 10px;">
+    <b>Cofactor 1 Color Range:</b> 
+    <input class="chartupdatedata" id="cocolorfrom" type="color" value="#D9D9D9">
+    <input class="chartupdatedata" id="cocolorto" type="color" value="#000000">
     </div>
-    {% elif trait_3.dataset.type == "Publish" %}
+  </div>
+
+  <div id="cofactor2_info_container" style="margin-left: 0px; display: none;">
+    <hr>
     <div>
-      Cofactor:
-      <a href="{{url_for('show_trait_page', trait_id = trait_3.name, dataset = trait_3.dataset.name)}}">
-        {{trait_3.dataset.group.species + " " + trait_3.dataset.group.name + " " + trait_3.dataset.name + ": " + trait_3.name|string}}
-      </a>
+      <b>Cofactor 2</b>: <a id="cofactor2_trait_link" href="#"></a>
     </div>
-    <div>
-      <a href="{{trait_3.pubmed_link}}">PubMed: {{trait_3.pubmed_text}}</a>
-        {{trait_3.description_display}}
+    <div id="cofactor2_description"></div>
+    <br>
+    <div style="margin-bottom: 20px;">
+    <b>Cofactor 2 corresponds to point radius</b> 
     </div>
-    {% endif %}
-    {% endif %}
-
-    <input class="chartupdatedata" id="cocolorfrom" type="color" value="#000000">
-    <input class="chartupdatedata" id="cocolorto" type="color" value="#000000">
-
+    <br>
   </div>
 
-  <br>
-
-  <table class="table">
-    <tr>
-      <td style="vertical-align: middle;">Width <input class="chartupdatewh" id="width" type="text" value="1000" style="width: 44px; height: 22px;"> px</td>
-      <td style="vertical-align: middle;">Height <input class="chartupdatewh" id="height" type="text" value="800" style="width: 44px; height: 22px;"> px</td>
-    </tr>
-  </table>
-
-  <table class="table">
-    <tr>
-      <td style="vertical-align: middle;">Label
-        <input class="chartupdate" id="labelcolor" type="color" value="#000000">
-        <input class="chartupdate" id="labelfont" type="text" value="16" style="width: 44px; height: 22px;"> px
-      </td>
-      <td style="vertical-align: middle;">Number
-        <input class="chartupdate" id="numbercolor" type="color" value="#000000">
-        <input class="chartupdate" id="numberfont" type="text" value="16" style="width: 44px; height: 22px;"> px
-      </td>
-      <td style="vertical-align: middle;">Axis
-        <input class="chartupdate" id="axiscolor" type="color" value="#000000">
-        <input class="chartupdate" id="axiswidth" type="text" value="2" style="width: 44px; height: 22px;"> px
-      </td>
-      <td style="vertical-align: middle;">Line
-        <input class="chartupdate" id="linecolor" type="color" value="#8fbbda">
-        <input class="chartupdate" id="linewidth" type="text" value="1" style="width: 44px; height: 22px;"> px
-      </td>
-    </tr>
-  </table>
-
-  <br>
-
   <ul class="nav nav-tabs">
     <li class="active">
       <a href="#tp1" data-toggle="tab">Pearson</a>
@@ -143,17 +93,11 @@
 
     <div class="tab-pane active" id="tp1">
       <br>
-      <div>
-        <a id="a_svg_pcs" href="#" onclick="javascript:saveassvg_pcs();" class="btn btn-primary">Save as SVG</a>
-      </div>
-      <div style="width: 1000px; text-align: center;">
-        <h2>Pearson Correlation Scatterplot</h2>
-      </div>
-      <div id="scatterplot2">
-        <svg id="svg_pcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg>
-      </div>
+      <div id="scatterplot2"></div>
       <br>
-      <table class="table table-hover table-striped table-bordered" style="width: 200px; margin-left: 80px; text-align: right;">
+      <div class="row" style="width: 70%;">
+      <div class="col-xs-3">
+      <table class="table table-hover table-striped table-bordered" style="width: 80%; margin-left: 60px; text-align: right;">
         <thead>
           <tr><th style="text-align: right;">Statistic</th><th style="text-align: right;">Value</th></tr>
         </thead>
@@ -187,53 +131,147 @@
           </tr>
         </tbody>
       </table>
-    </div>
-
-    <div class="tab-pane" id="tp2">
+      </div>
+      <div class="col-xs-9">
+        {% if trait_1.dataset.type == "ProbeSet" %}
+        <div>
+          X axis:
+          <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
+            {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.tissue + " "  + trait_1.dataset.name + ": " + trait_1.name|string}}
+          </a>
+        </div>
+        <div>
+          [{{trait_1.symbol}} on {{trait_1.location_repr}} Mb]
+          {{trait_1.description_display}}
+        </div>
+        {% elif trait_1.dataset.type == "Publish" %}
+        <div>
+          X axis:
+          <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
+            {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.name + ": " + trait_1.name|string}}
+          </a>
+        </div>
+        <div>
+          <a href="{{trait_1.pubmed_link}}">PubMed: {{trait_1.pubmed_text}}</a>
+            {{trait_1.description_display}}
+        </div>
+        {% endif %}
 
-      <br>
+        <br/>
 
-      <div>
-        <a id="a_svg_srcs" href="#" onclick="javascript:saveassvg_srcs();" class="btn btn-primary">Save as SVG</a>
-      </div>
-      <div style="width: 1000px; text-align: center;">
-        <h2>Spearman Rank Correlation Scatterplot</h2>
+        {% if trait_2.dataset.type == "ProbeSet" %}
+        <div>
+          Y axis:
+          <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
+            {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.tissue + " "  + trait_2.dataset.name + ": " + trait_2.name|string}}
+          </a>
+        </div>
+        <div>
+          [{{trait_2.symbol}} on {{trait_2.location_repr}} Mb]
+          {{trait_2.description_display}}
+        </div>
+        {% elif trait_2.dataset.type == "Publish" %}
+        <div>
+          Y axis:
+          <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
+            {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.name + ": " + trait_2.name|string}}
+          </a>
+        </div>
+        <div>
+          <a href="{{trait_2.pubmed_link}}">PubMed: {{trait_2.pubmed_text}}</a>
+            {{trait_2.description_display}}
+        </div>
+        {% endif %}
       </div>
-      <div id="srscatterplot2">
-        <svg id="svg_srcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg>
       </div>
+    </div>
 
+    <div class="tab-pane" id="tp2">
+      <br>
+      <div id="srscatterplot2"></div>
       <br>
+      <div class="row" style="width: 70%;">
+      <div class="col-xs-3">
+        <table class="table table-hover table-striped table-bordered" style="width: 80%; margin-left: 60px; text-align: right;">
+          <thead>
+            <tr><th style="text-align: right;">Statistic</th><th style="text-align: right;">Value</th></tr>
+          </thead>
+          <tbody>
+            <tr>
+              <td>Number</td>
+              <td>{{jsdata.num_overlap}}</td>
+            </tr>
+            <tr>
+              <td>Slope</td>
+              <td>{{'%0.3f' % jsdata.srslope}}</td>
+            </tr>
+            <tr>
+              <td>Intercept</td>
+              <td>{{'%0.3f' % jsdata.srintercept}}</td>
+            </tr>
+            <tr>
+              <td>r value</td>
+              <td>{{'%0.3f' % jsdata.srr_value}}</td>
+            </tr>
+	    <tr>
+              <td>P value</td>
+              <td>{% if jsdata.srp_value < 0.001 %}{{'%0.3e' % jsdata.srp_value}}{% else %}{{'%0.3f' % jsdata.srp_value}}{% endif %}</td>
+            </tr>
+          </tbody>
+        </table>
+      </div>
+      <div class="col-xs-9">
+        {% if trait_1.dataset.type == "ProbeSet" %}
+        <div>
+          X axis:
+          <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
+            {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.tissue + " "  + trait_1.dataset.name + ": " + trait_1.name|string}}
+          </a>
+        </div>
+        <div>
+          [{{trait_1.symbol}} on {{trait_1.location_repr}} Mb]
+          {{trait_1.description_display}}
+        </div>
+        {% elif trait_1.dataset.type == "Publish" %}
+        <div>
+          X axis:
+          <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
+            {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.name + ": " + trait_1.name|string}}
+          </a>
+        </div>
+        <div>
+          <a href="{{trait_1.pubmed_link}}">PubMed: {{trait_1.pubmed_text}}</a>
+            {{trait_1.description_display}}
+        </div>
+        {% endif %}
 
-      <table class="table table-hover table-striped table-bordered" style="width: 200px; margin-left: 80px; text-align: right;">
-        <thead>
-          <tr><th style="text-align: right;">Statistic</th><th style="text-align: right;">Value</th></tr>
-        </thead>
-        <tbody>
-          <tr>
-            <td>Number</td>
-            <td>{{jsdata.num_overlap}}</td>
-          </tr>
-          <tr>
-            <td>Slope</td>
-            <td>{{'%0.3f' % jsdata.srslope}}</td>
-          </tr>
-          <tr>
-            <td>Intercept</td>
-            <td>{{'%0.3f' % jsdata.srintercept}}</td>
-          </tr>
-          <tr>
-            <td>r value</td>
-            <td>{{'%0.3f' % jsdata.srr_value}}</td>
-          </tr>
-	  <tr>
-            <td>P value</td>
-            <td>{% if jsdata.srp_value < 0.001 %}{{'%0.3e' % jsdata.srp_value}}{% else %}{{'%0.3f' % jsdata.srp_value}}{% endif %}</td>
-          </tr>
-        </tbody>
-      </table>
-    </div>
+        <br/>
 
+        {% if trait_2.dataset.type == "ProbeSet" %}
+        <div>
+          Y axis:
+          <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
+            {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.tissue + " "  + trait_2.dataset.name + ": " + trait_2.name|string}}
+          </a>
+        </div>
+        <div>
+          [{{trait_2.symbol}} on {{trait_2.location_repr}} Mb]
+          {{trait_2.description_display}}
+        </div>
+        {% elif trait_2.dataset.type == "Publish" %}
+        <div>
+          Y axis:
+          <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
+            {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.name + ": " + trait_2.name|string}}
+          </a>
+        </div>
+        <div>
+          <a href="{{trait_2.pubmed_link}}">PubMed: {{trait_2.pubmed_text}}</a>
+            {{trait_2.description_display}}
+        </div>
+        {% endif %}
+      </div>
+      </div>
   </div>
 
 </div>
@@ -250,5 +288,7 @@
     <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script>
+    <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/draw_corr_scatterplot.js"></script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index c4668e05..e4fd3136 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -1,8 +1,6 @@
 {% extends "base.html" %}
 {% block css %}
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
-    <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
-    <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/corr_matrix.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
@@ -107,8 +105,6 @@
     <script type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
     <script type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/js_external/chroma.js"></script>
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 6f2ad0b8..0612bfcc 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -43,26 +43,24 @@
                     <th data-export="Location">Location</th>
                     <th data-export="Mean">Mean</th>
                     <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
-                    <th data-export="Max LRS Location">Max LRS Location</th>
                     <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
                   </tr>
                 </thead> 
                 <tbody>
                   {% for this_trait in trait_list %}
-                  <tr id="trait:{{ this_trait.name }}:{{ this_trait.dataset.name }}">
-                    <td align="center" style="padding-right: 0px; padding-left: 5px;"><input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}"></td>
+                  <tr id="trait:{{ this_trait.name }}:{{ this_trait.dataset }}">
+                    <td align="center" style="padding-right: 0px; padding-left: 5px;"><input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset)) }}"></td>
                     <td align="right" data-export="{{ loop.index }}">{{ loop.index }}</td>
-                    <td data-export="{{ this_trait.name }}"><a href="{{ url_for('show_trait_page', trait_id = this_trait.name, dataset = this_trait.dataset.name)}}">{{ this_trait.name }}</a></td>
-                    <td data-export="{{ this_trait.dataset.group.species }}">{{ this_trait.dataset.group.species }}</td>
-                    <td data-export="{{ this_trait.dataset.group.name }}">{{ this_trait.dataset.group.name }}</td>
-                    <td data-export="{{ this_trait.dataset.tissue }}">{{ this_trait.dataset.tissue }}</td>
-                    <td data-export="{{ this_trait.dataset.name }}">{{ this_trait.dataset.name }}</td>
+                    <td data-export="{{ this_trait.name }}"><a href="{{ url_for('show_trait_page', trait_id = this_trait.name, dataset = this_trait.dataset)}}">{{ this_trait.name }}</a></td>
+                    <td data-export="{{ this_trait.species }}">{{ this_trait.species }}</td>
+                    <td data-export="{{ this_trait.group }}">{{ this_trait.group }}</td>
+                    <td data-export="{{ this_trait.tissue }}">{{ this_trait.tissue }}</td>
+                    <td data-export="{{ this_trait.dataset }}">{{ this_trait.dataset }}</td>
                     <td data-export="{{ this_trait.symbol }}">{{ this_trait.symbol }}</td>
-                    <td data-export="{{ this_trait.description_display }}">{{ this_trait.description_display }}</td>
+                    <td data-export="{{ this_trait.description }}">{{ this_trait.description }}</td>
                     <td data-export="{{ this_trait.location_repr }}" align="right">{{ this_trait.location_repr }}</td>
                     <td data-export="{{ '%0.3f' % this_trait.mean|float }}" align="right">{{ '%0.3f' % this_trait.mean|float }}</td>
                     <td data-export="{% if this_trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % this_trait.LRS_score_repr|float }}{% else %}N/A{% endif %}" align="right">{% if this_trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % this_trait.LRS_score_repr|float }}{% else %}N/A{% endif %}</td>
-                    <td data-export="{{ this_trait.LRS_location_repr }}" align="right">{{ this_trait.LRS_location_repr }}</td>
                     <td data-export="{% if this_trait.additive != "" %}{{ '%0.3f' % this_trait.additive|float }}{% else %}N/A{% endif %}" align="right">{% if this_trait.additive != "" %}{{ '%0.3f' % this_trait.additive|float }}{% else %}N/A{% endif %}</td>
                   </tr>
                   {% endfor %}
@@ -81,7 +79,6 @@
                     <th>Location</th>
                     <th>Mean</th>
                     <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
-                    <th data-export="LRS Location">Max LRS Location</th>
                     <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
                   </tr>
                 </tfoot> 
@@ -142,7 +139,6 @@
                     { "type": "natural", "width": "7%" },
                     { "type": "natural", "width": "4%" },
                     { "type": "natural", "width": "5%" },
-                    { "type": "natural", "width": "7%" },
                     { "type": "natural", "width": "5%" }
                 ],
                 "columnDefs": [
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index 7a8ca07b..c2cbdadd 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -40,23 +40,21 @@
                         <th data-export="Authors">Authors</th>
                         <th data-export="Year">Year</th>
                         <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
-                        <th data-export="LRS Location">Max LRS Location</th>
                         <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
                     </tr>
                 </thead>
                 <tbody>
                  {% for this_trait in trait_list %}
-                    <tr id="trait:{{ this_trait.name }}:{{ this_trait.dataset.name }}">
-                        <td align="center" style="padding-right: 0px; padding-left: 5px;"><input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}"></td>
+                    <tr id="trait:{{ this_trait.name }}:{{ this_trait.dataset }}">
+                        <td align="center" style="padding-right: 0px; padding-left: 5px;"><input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset)) }}"></td>
                         <td align="right" data-export="{{ loop.index }}">{{ loop.index }}</td>
-                        <td data-export="{{ this_trait.dataset.group.species }}">{{ this_trait.dataset.group.species }}</td>
-                        <td data-export="{{ this_trait.dataset.group.name }}">{{ this_trait.dataset.group.name }}</td>
-                        <td data-export="{{ this_trait.name }}"><a href="{{ url_for('show_trait_page', trait_id = this_trait.name, dataset = this_trait.dataset.name)}}">{{ this_trait.name }}</a></td>
-                        <td data-export="{{ this_trait.description_display }}">{{ this_trait.description_display }}</td>
+                        <td data-export="{{ this_trait.species }}">{{ this_trait.species }}</td>
+                        <td data-export="{{ this_trait.group }}">{{ this_trait.group }}</td>
+                        <td data-export="{{ this_trait.name }}"><a href="{{ url_for('show_trait_page', trait_id = this_trait.name, dataset = this_trait.dataset)}}">{{ this_trait.name }}</a></td>
+                        <td data-export="{{ this_trait.description }}">{{ this_trait.description }}</td>
                         <td data-export="{{ this_trait.authors }}">{{ this_trait.authors }}</td>
                         <td data-export="{{ this_trait.pubmed_text }}" data-order="{{ this_trait.pubmed_text }}"><a href="{{ this_trait.pubmed_link }}">{{ this_trait.pubmed_text }}</a></td>
                         <td data-export="{% if this_trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % this_trait.LRS_score_repr|float }}{% else %}N/A{% endif %}" align="right">{% if this_trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % this_trait.LRS_score_repr|float }}{% else %}N/A{% endif %}</td>
-                        <td data-export="{{ this_trait.LRS_location_repr }}" align="right">{{ this_trait.LRS_location_repr }}</td>
                         <td data-export="{% if this_trait.additive != "" %}{{ this_trait.additive }}{% else %}N/A{% endif %}" align="right">{% if this_trait.additive != "" %}{{ this_trait.additive }}{% else %}N/A{% endif %}</td>
                     </tr>
                 {% endfor %}
@@ -72,7 +70,6 @@
                         <th>Authors</th>
                         <th>Year</th>
                         <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
-                        <th data-export="LRS Location">Max LRS Location</th>
                         <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
                     </tr>
                 </tfoot>
@@ -135,7 +132,6 @@
                     { "type": "natural", "width": "25%"},
                     { "type": "natural" },
                     { "type": "natural", "width": "8%"},
-                    { "type": "natural", "width": "12%"},
                     { "type": "natural" }
                 ],
                 "columnDefs": [
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 2a5556ea..dba3e266 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -34,11 +34,11 @@
 
                                 <div class="form-group">
                                     <label for="species" class="col-xs-1 control-label" style="width: 65px !important;">Species:</label>
-                                    <div class="col-xs-10 controls input-append" style="padding-right: 0px;">
-                                        <div class="col-xs-8">
-                                          <select name="species" id="species" class="form-control span3" style="width: 280px !important;"></select>
+                                    <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;">
+                                        <div class="col-8">
+                                          <select name="species" id="species" class="form-control" style="width: 280px !important;"></select>
                                         </div>
-                                        <div class="col-xs-4">
+                                        <div class="col-4" style="margin-left: 10px;">
                                           <button type="button" id="make_default" class="btn btn-primary form-control">Make Default</button>
                                         </div>
                                     </div>
@@ -46,9 +46,9 @@
 
                                 <div class="form-group">
                                     <label for="group" class="col-xs-1 control-label" style="width: 65px !important;">Group:</label>
-                                    <div class="col-xs-10 controls input-append">
-                                        <div class="col-xs-8">
-                                          <select name="group" id="group" class="form-control span3" style="width: 280px !important;"></select>
+                                    <div class="col-xs-10 controls input-append" style="padding-left: 20px;">
+                                        <div class="col-8">
+                                          <select name="group" id="group" class="form-control" style="width: 280px !important;"></select>
                                           <i class="icon-question-sign"></i>
                                         </div>
                                     </div>
@@ -56,21 +56,21 @@
 
                                 <div class="form-group">
                                     <label for="tissue" class="col-xs-1 control-label" style="width: 65px !important;">Type:</label>
-                                    <div class="col-xs-10 controls">
-                                        <div class="col-xs-8">
-                                          <select name="type" id="type" class="form-control span3" style="width: 280px !important;"></select>
+                                    <div class="col-xs-10 controls" style="padding-left: 20px;">
+                                        <div class="col-8">
+                                          <select name="type" id="type" class="form-control" style="width: 280px !important;"></select>
                                         </div>
                                     </div>
                                 </div>
 
                                 <div class="form-group">
                                     <label for="dataset" class="col-xs-1 control-label" style="width: 65px !important;">Dataset:</label>
-                                    <div class="col-xs-10 controls input-append">
-                                        <div class="col-xs-10">
-                                          <select name="dataset" id="dataset" class="form-control span5" style="width: 340px !important;"></select>
+                                    <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;">
+                                        <div class="col-9">
+                                          <select name="dataset" id="dataset" class="form-control" style="width: 340px !important;"></select>
                                           <i class="icon-question-sign"></i>
                                         </div>
-                                        <div class="col-xs-2">
+                                        <div class="col-3" style="margin-left: 10px;">
                                           <button type="button" id="dataset_info" class="btn btn-primary form-control" style="width: 75px !important;">Info</button>
                                         </div>
                                     </div>
@@ -85,8 +85,8 @@
 
                                 <div class="form-group">
                                     <label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label>
-                                    <div class="col-xs-10 controls">
-                                        <div class="col-xs-8">
+                                    <div class="col-xs-10 controls" style="padding-left: 20px;">
+                                        <div class="col-8">
                                           <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="or_search"></textarea>
                                         </div>
                                     </div>
@@ -95,8 +95,8 @@
                                 <!--  GET ANY HELP   -->
                                 <div class="form-group">
                                     <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label>
-                                    <div class="col-xs-10 controls">
-                                        <div class="col-xs-12 controls">
+                                    <div class="col-xs-10 controls" style="padding-left: 20px;">
+                                        <div class="col-12 controls">
                                             Enter terms, genes, ID numbers in the <b>Search</b> field.<br>
                                             Use <b>*</b> or <b>?</b> wildcards (Cyp*a?, synap*).<br>
                                             Use <b>quotes</b> for terms such as <i>"tyrosine kinase"</i>.
@@ -106,8 +106,8 @@
 
                                 <div class="form-group">
                                     <label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label>
-                                    <div class="col-xs-10 controls">
-                                        <div class="col-xs-8">
+                                    <div class="col-xs-10 controls" style="padding-left: 20px;">
+                                        <div class="col-8">
                                           <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="and_search"></textarea>
                                         </div>
                                     </div>
@@ -115,8 +115,8 @@
 
                                 <div class="form-group">
                                     <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label>
-                                    <div class="col-xs-10 controls">
-                                        <div class="col-xs-2 controls" style="width: 100px !important;">
+                                    <div class="col-xs-10 controls" style="padding-left: 20px;">
+                                        <div class="col-2 controls" style="width: 100px !important;">
                                             <input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search">
                                         </div>
                                     </div>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 4aad4242..f67fff90 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -35,6 +35,7 @@
         <input type="hidden" name="temp_uuid" id="temp_uuid" value="{{ temp_uuid }}">
         <input type="hidden" name="genofile" value="">
         <input type="hidden" name="covariates" value="">
+        <input type="hidden" name="transform" value="">
 
         <div class="container">
             <div class="panel-group" id="accordion">
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 1402db47..ac2f1078 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -9,7 +9,7 @@
                 needed.
             </p>
 
-            <div id="blockMenuSpan" class="input-append">
+            <div id="blockMenuSpan" class="input-append" style="margin-bottom: 10px;">
                 <label for="remove_samples_field">Block samples by index:</label>
                 <input type="text" id="remove_samples_field">
                 <select id="block_group" size="1">
@@ -25,11 +25,8 @@
             <div id="remove_samples_invalid" class="alert alert-error" style="display:none;">
                   Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong>
             </div>
-
-            <br>
-
             {% if sample_groups[0].attributes %}
-            <div class="input-append">
+            <div class="input-append" style="margin-top:10px; margin-bottom:10px;">
                 <label for="exclude_menu">Block samples by group:</label>
                 <select id="exclude_menu" size=1>
                   {% for attribute in sample_groups[0].attributes %}
@@ -42,7 +39,6 @@
                 <input type="button" id="exclude_group" class="btn" value="Block">
             </div>
             {% endif %}
-            <br>
             <div>
               <input type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value">
               <input type="button" id="block_outliers" class="btn btn-default" value="Block Outliers">
@@ -55,9 +51,19 @@
                 </select>
               </span>
               <br>
+              <div style="margin-top:10px;">
+              <input type="button" id="normalize" class="btn btn-default" value="Normalize">
+              <select id="norm_method" class="select optional span2">
+                <option value="log2">Log2</option>
+                <option value="qnorm">Quantile</option>
+                <option value="sqrt">Square Root</option>
+              </select>
+              </div>
+              <!--
               {% if sample_groups[0].sample_qnorm is not none %}
               <input type="button" id="qnorm" class="btn btn-default" value="Quantile Normalize">
               {% endif %}
+              -->
             </div>
         </fieldset>
         <br>
@@ -79,6 +85,7 @@
 
     <!--<div id="edit_sample_lists">-->
     {% for sample_type in sample_groups %}
+        {% set outer_loop = loop %}
         <div class="sample_group" style="width:{{ trait_table_width }}%;">
             <h3>{{ sample_type.header }}</h3>
             <hr>
@@ -115,7 +122,7 @@
         
                         {# Todo: Add IDs #}
                         <td class="column_name-Value" align="right">
-                          <input type="text" data-value="{{ sample.display_value }}" data-transform="{{ sample_type.sample_qnorm[sample.name] }}" name="{{ 'value:' + sample.name }}"
+                          <input type="text" data-value="{{ sample.display_value }}" data-qnorm="{{ qnorm_vals[outer_loop.index - 1][loop.index - 1] }}" name="{{ 'value:' + sample.name }}"
                                  style="text-align:right;"
                                  class="trait_value_input edit_sample_value"
                                  value="{{ sample.display_value }}"
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 9c19028c..495a266e 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -14,9 +14,11 @@
                 <li>
                     <a href="#rqtl_geno" data-toggle="tab">R/qtl</a>
                 </li>
+<!--
                 <li>
                     <a href="#pylmm" data-toggle="tab">pyLMM</a>
                 </li>
+-->
                 {% endif %}
                 {% for mapping_method in dataset.group.mapping_names %}
                 {% if mapping_method == "GEMMA" %}
@@ -71,8 +73,16 @@
                         <div class="mapping_method_fields form-group">
                             <label style="text-align: right;" class="col-xs-3 control-label">Covariates</label>
                             <div style="margin-left:20px;" class="col-xs-7">
-                              {% if g.user_session.logged_in and (g.user_session.num_collections > 0) %}
+                              {% if g.user_session.logged_in %}
+                              {% if g.user_session.num_collections < 1 %}
                               No collections available. Please add traits to a collection to use them as covariates.
+                              {% else %}
+                              <div style="margin-bottom: 10px;" class="btn-group" role="group">
+                                <button type="button" id="select_covariates" class="btn btn-default">Select</button>
+                                <button type="button" id="remove_covariates" class="btn btn-default">Remove</button>
+                              </div>
+                              <textarea rows="3" cols="20" readonly placeholder="No covariates selected" style="overflow-y: scroll; resize: none;" class="selected_covariates"></textarea>
+                              {% endif %}
                               {% elif g.cookie_session.display_num_collections() == "" %}
                               No collections available. Please add traits to a collection to use them as covariates.
                               {% else %}
@@ -328,8 +338,10 @@
              <dd>Interval mapping is a process in which the statistical significance of a hypothetical QTL is evaluated at regular points across a chromosome, even in the absence of explicit genotype data at those points.</dd>
              <dt>R/qtl</dt>
              <dd>R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.</dd>
+<!--
              <dt>pyLMM</dt>
              <dd>pyLMM is a fast and lightweight linear mixed-model (LMM) solver for use in genome-wide association studies (GWAS).</dd>
+-->
              {% endif %}
         </dl>
     </div>
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 5d388d66..87149cdb 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -49,30 +49,18 @@ def timestamp():
 
 class AnonUser(object):
     """Anonymous user handling"""
-    cookie_name = 'anon_user_v8'
+    cookie_name = 'anon_user_v1'
 
     def __init__(self):
         self.cookie = request.cookies.get(self.cookie_name)
         if self.cookie:
             logger.debug("ANON COOKIE ALREADY EXISTS")
             self.anon_id = verify_cookie(self.cookie)
-
         else:
             logger.debug("CREATING NEW ANON COOKIE")
             self.anon_id, self.cookie = create_signed_cookie()
-        self.key = "anon_collection:v1:{}".format(self.anon_id)
 
-        #ZS: This was originally the commented out function below
-        #    For some reason I don't yet understand the commented out code works on production, 
-        #    but wouldn't set cookies for staging and my branch. The new code (using @app.after_request) seems to work.
-        @app.after_request
-        def set_cookie(response):
-            response.set_cookie(self.cookie_name, self.cookie)
-            return response
-
-        #@after.after_this_request
-        #def set_cookie(response):
-        #    response.set_cookie(self.cookie_name, self.cookie)
+        self.key = "anon_collection:v1:{}".format(self.anon_id)
 
     def add_collection(self, new_collection):
         collection_dict = dict(name = new_collection.name,
@@ -142,6 +130,7 @@ class AnonUser(object):
             print("Couldn't display_num_collections:", why)
             return ""
 
+
 def verify_cookie(cookie):
     the_uuid, separator, the_signature = cookie.partition(':')
     assert len(the_uuid) == 36, "Is session_id a uuid?"
@@ -422,12 +411,17 @@ def before_request():
     g.user_session = UserSession()
     g.cookie_session = AnonUser()
 
+@app.after_request
+def set_cookie(response):
+    if not request.cookies.get(g.cookie_session.cookie_name):
+        response.set_cookie(g.cookie_session.cookie_name, g.cookie_session.cookie)
+    return response
+
 class UsersManager(object):
     def __init__(self):
         self.users = model.User.query.all()
         logger.debug("Users are:", self.users)
 
-
 class UserManager(object):
     def __init__(self, kw):
         self.user_id = kw['user_id']
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 2089f9de..ae333e73 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -43,6 +43,7 @@ from base.data_set import DataSet    # Used by YAML in marker_regression
 from wqflask.show_trait import show_trait
 from wqflask.show_trait import export_trait_data
 from wqflask.heatmap import heatmap
+from wqflask.comparison_bar_chart import comparison_bar_chart
 from wqflask.marker_regression import marker_regression
 from wqflask.marker_regression import marker_regression_gn1
 from wqflask.network_graph import network_graph
@@ -464,6 +465,27 @@ def heatmap_page():
 
     return rendered_template
 
+@app.route("/comparison_bar_chart", methods=('POST',))
+def comp_bar_chart_page():
+    logger.info("In comp bar chart, request.form is:", pf(request.form))
+    logger.info(request.url)
+
+    start_vars = request.form
+
+    traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
+    if traits[0] != "":
+        template_vars = comparison_bar_chart.ComparisonBarChart(request.form)
+        template_vars.js_data = json.dumps(template_vars.js_data,
+                                               default=json_default_handler,
+                                               indent="   ")
+
+        result = template_vars.__dict__
+        rendered_template = render_template("comparison_bar_chart.html", **result)
+    else:
+        rendered_template = render_template("empty_collection.html", **{'tool':'Comparison Bar Chart'})
+
+    return rendered_template
+
 @app.route("/mapping_results_container")
 def mapping_results_container_page():
     return render_template("mapping_results_container.html")