Merge branch 'master' of github.com:genenetwork/genenetwork2

author: Lei Yan 2017-04-06 18:20:51 +0000
committer: Lei Yan 2017-04-06 18:20:51 +0000
commit: 67218be3a181de7aad617237c11ee33436b8d762 (patch)
tree: d999c5a59bda8d82f04cfb151fb4bba57f2f19be
parent: 0b25ab1565faf3824d591c545dfe71dbd28c38ee (diff)
parent: f419b8bc824303009817ad9d52e1452b870b0039 (diff)
download: genenetwork2-67218be3a181de7aad617237c11ee33436b8d762.tar.gz
29 files changed, 1081 insertions, 888 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 54dd3c4b..7f08135f 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -61,14 +61,17 @@ logger = getLogger(__name__ )
 # Each subclass will add to this
 DS_NAME_MAP = {}
 
-def create_dataset(dataset_name, dataset_type = None, get_samplelist = True):
+def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, group_name = None):
     if not dataset_type:
         dataset_type = Dataset_Getter(dataset_name)
         logger.debug("dataset_type", dataset_type)
 
     dataset_ob = DS_NAME_MAP[dataset_type]
     dataset_class = globals()[dataset_ob]
-    return dataset_class(dataset_name, get_samplelist)
+    if dataset_type == "Temp":
+        return dataset_class(dataset_name, get_samplelist, group_name)
+    else:
+        return dataset_class(dataset_name, get_samplelist)
 
 class Dataset_Types(object):
 
@@ -261,10 +264,13 @@ class DatasetGroup(object):
     has multiple datasets associated with it.
 
     """
-    def __init__(self, dataset):
+    def __init__(self, dataset, name=None):
         """This sets self.group and self.group_id"""
         #logger.debug("DATASET NAME2:", dataset.name)
-        self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group)
+        if name == None:
+            self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group)
+        else:
+            self.name, self.id, self.genetic_type = fetchone("SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM InbredSet where Name='%s'" % name)
         if self.name == 'BXD300':
             self.name = "BXD"
 
@@ -304,7 +310,7 @@ class DatasetGroup(object):
         elif mapping_id == "2":
             mapping_names = ["GEMMA"]
         elif mapping_id == "4":
-            mapping_names = ["PLINK"]
+            mapping_names = ["GEMMA", "PLINK"]
         else:
             mapping_names = []
 
@@ -319,9 +325,7 @@ class DatasetGroup(object):
         def check_plink_gemma():
             if flat_file_exists("mapping"):
                 MAPPING_PATH = flat_files("mapping")+"/"
-                if (os.path.isfile(MAPPING_PATH+self.name+".bed") and
-                    (os.path.isfile(MAPPING_PATH+self.name+".map") or
-                     os.path.isfile(MAPPING_PATH+self.name+".bim"))):
+                if os.path.isfile(MAPPING_PATH+self.name+".bed"):
                     return True
             return False
 
@@ -481,7 +485,7 @@ class DataSet(object):
 
     """
 
-    def __init__(self, name, get_samplelist = True):
+    def __init__(self, name, get_samplelist = True, group_name = None):
 
         assert name, "Need a name"
         self.name = name
@@ -493,11 +497,12 @@ class DataSet(object):
 
         self.setup()
 
-        self.check_confidentiality()
-
-        self.retrieve_other_names()
-
-        self.group = DatasetGroup(self)   # sets self.group and self.group_id and gets genotype
+        if self.type == "Temp": #Need to supply group name as input if temp trait
+            self.group = DatasetGroup(self, group_name)   # sets self.group and self.group_id and gets genotype
+        else:
+            self.check_confidentiality()
+            self.retrieve_other_names()
+            self.group = DatasetGroup(self)   # sets self.group and self.group_id and gets genotype
         if get_samplelist == True:
              self.group.get_samplelist()
         self.species = species.TheSpecies(self)
@@ -1156,6 +1161,8 @@ class MrnaAssayDataSet(DataSet):
 class TempDataSet(DataSet):
     '''Temporary user-generated data set'''
 
+    DS_NAME_MAP['Temp'] = 'TempDataSet'
+
     def setup(self):
         self.search_fields = ['name',
                               'description']
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index bf87e879..e22a51e4 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -62,6 +62,11 @@ class GeneralTrait(object):
         self.strand_probe = None
         self.symbol = None
 
+        self.LRS_score_repr = "N/A"
+        self.LRS_score_value = 0
+        self.LRS_location_repr = "N/A"
+        self.LRS_location_value = 1000000
+
         if kw.get('fullname'):
             name2 = value.split("::")
             if len(name2) == 2:
@@ -72,9 +77,10 @@ class GeneralTrait(object):
 
         # Todo: These two lines are necessary most of the time, but perhaps not all of the time
         # So we could add a simple if statement to short-circuit this if necessary
-        self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info)
-        if get_sample_info != False:
-            self = retrieve_sample_data(self, self.dataset)
+        if self.dataset.type != "Temp":
+            self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info)
+            if get_sample_info != False:
+                self = retrieve_sample_data(self, self.dataset)
 
 
     def get_name(self):
@@ -315,12 +321,12 @@ def get_sample_data():
     #
     #return jsonable_sample_data
     
-def jsonable(trait, dataset_name):
+def jsonable(trait):
     """Return a dict suitable for using as json
 
     Actual turning into json doesn't happen here though"""
 
-    dataset = create_dataset(dataset_name)
+    dataset = create_dataset(dataset_name = trait.dataset.name, dataset_type = trait.dataset.type, group_name = trait.dataset.group.name)
     
     if dataset.type == "ProbeSet":
         return dict(name=trait.name,
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index e5f10edf..1e47e183 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -65,7 +65,7 @@ ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?sp
 # want to reach this base dir
 assert_writable_dir(TEMPDIR)
 
-TMPDIR               = mk_dir(TEMPDIR+'/gn2/')
+TMPDIR               = mk_dir(TEMPDIR+'gn2')
 assert_writable_dir(TMPDIR)
 
 CACHEDIR             = mk_dir(TMPDIR+'/cache/')
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index 0342b7ad..a6ae28af 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -50,5 +50,5 @@ else: # staging/production modes
             debug=False,
             use_debugger=False,
             threaded=True,
-            processes=8,
+            processes=0,
             use_reloader=True)
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index ba555094..478dbcaa 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -203,7 +203,8 @@ def process_traits(unprocessed_traits):
         data, _separator, hmac = trait.rpartition(':')
         data = data.strip()
         assert hmac==user_manager.actual_hmac_creation(data), "Data tampering?"
-        traits.add                                                                                               (str(data))
+        traits.add(str(data))
+
     return traits
 
 def report_change(len_before, len_now):
@@ -244,7 +245,6 @@ def collections_new():
 
     if "sign_in" in params:
         return redirect(url_for('login'))
-
     if "create_new" in params:
         print("in create_new")
         collection_name = params['new_collection']
@@ -376,13 +376,17 @@ def view_collection():
 
     for atrait in traits:
         name, dataset_name = atrait.split(':')
-        dataset = create_dataset(dataset_name)
-        
-        trait_ob = trait.GeneralTrait(name=name, dataset=dataset)
-        trait_ob = trait.retrieve_trait_info(trait_ob, dataset, get_qtl_info=True)
+        if dataset_name == "Temp":
+            group = name.split("_")[2]
+            dataset = create_dataset(dataset_name, dataset_type = "Temp", group_name = group)
+            trait_ob = trait.GeneralTrait(name=name, dataset=dataset)
+        else:
+            dataset = create_dataset(dataset_name)
+            trait_ob = trait.GeneralTrait(name=name, dataset=dataset)
+            trait_ob = trait.retrieve_trait_info(trait_ob, dataset, get_qtl_info=True)
         trait_obs.append(trait_ob)
 
-        json_version.append(trait.jsonable(trait_ob, dataset_name))
+        json_version.append(trait.jsonable(trait_ob))
 
     if "uc_id" in params:
         collection_info = dict(trait_obs=trait_obs,
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index cc21d1bf..7957e643 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -96,7 +96,14 @@ class CorrelationResults(object):
         print("TESTING...")
 
         with Bench("Doing correlations"):
-            helper_functions.get_species_dataset_trait(self, start_vars)
+            if start_vars['dataset'] == "Temp":
+                self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = start_vars['group'])
+                self.trait_id = "Temp"
+                self.this_trait = GeneralTrait(dataset=self.dataset,
+                                           name=self.trait_id,
+                                           cellid=None)
+            else:
+                helper_functions.get_species_dataset_trait(self, start_vars)
 
             self.dataset.group.read_genotype_file()
 
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 630980c7..95a5f6a6 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -33,6 +33,9 @@ import math
 import collections
 import resource
 
+import numarray
+import numarray.linear_algebra as la
+import numpy as np
 import scipy
 
 from rpy2.robjects.packages import importr
@@ -91,31 +94,40 @@ class CorrelationMatrix(object):
                     this_trait_vals.append('')
             self.sample_data.append(this_trait_vals)
 
+        if len(this_trait_vals) < len(self.trait_list): #Shouldn't do PCA if there are more traits than observations/samples
+            return False
+
         self.lowest_overlap = 8 #ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning)
 
         self.corr_results = []
         self.pca_corr_results = []
+        self.trait_data_array = []
         for trait_db in self.trait_list:
             this_trait = trait_db[0]
             this_db = trait_db[1]
 
-            this_db_samples = this_db.group.samplelist
+            this_db_samples = this_db.group.all_samples_ordered()
             this_sample_data = this_trait.data
 
+            this_trait_vals = []
+            for index, sample in enumerate(this_db_samples):
+                if (sample in this_sample_data):
+                    sample_value = this_sample_data[sample].value
+                    this_trait_vals.append(sample_value)
+            self.trait_data_array.append(this_trait_vals)
+
             corr_result_row = []
             pca_corr_result_row = []
             is_spearman = False #ZS: To determine if it's above or below the diagonal
             for target in self.trait_list:
                 target_trait = target[0]
                 target_db = target[1]
-                target_samples = target_db.group.samplelist
-
+                target_samples = target_db.group.all_samples_ordered()
                 target_sample_data = target_trait.data
 
                 this_trait_vals = []
                 target_vals = []
                 for index, sample in enumerate(target_samples):
-
                     if (sample in this_sample_data) and (sample in target_sample_data):
                         sample_value = this_sample_data[sample].value
                         target_sample_value = target_sample_data[sample].value
@@ -144,13 +156,14 @@ class CorrelationMatrix(object):
             self.corr_results.append(corr_result_row)
             self.pca_corr_results.append(pca_corr_result_row)
 
-        print("corr_results:", pf(self.corr_results))
+        corr_result_eigen = la.eigenvectors(numarray.array(self.pca_corr_results))
+        corr_eigen_value, corr_eigen_vectors = sortEigenVectors(corr_result_eigen)
 
         groups = []
         for sample in self.all_sample_list:
             groups.append(1)
 
-        pca = self.calculate_pca(self.pca_corr_results, range(len(self.traits)))
+        pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors)
 
         self.loadings_array = self.process_loadings()
 
@@ -180,31 +193,34 @@ class CorrelationMatrix(object):
         #print("trait_list:", self.trait_list)
 
 
-    def calculate_pca(self, corr_results, cols):
+    def calculate_pca(self, cols, corr_eigen_value, corr_eigen_vectors):
         base = importr('base')
         stats = importr('stats')
-        print("checking:", pf(stats.rnorm(100)))
 
-        corr_results_to_list = robjects.FloatVector([item for sublist in corr_results for item in sublist])
-        print("corr_results:",  pf(corr_results_to_list))
+        corr_results_to_list = robjects.FloatVector([item for sublist in self.pca_corr_results for item in sublist])
 
         m = robjects.r.matrix(corr_results_to_list, nrow=len(cols))
         eigen = base.eigen(m)
-        print("eigen:", eigen)
         pca = stats.princomp(m, cor = "TRUE")
-        print("pca:", pca)
         self.loadings = pca.rx('loadings')
         self.scores = pca.rx('scores')
         self.scale = pca.rx('scale')
-        print("scores:", pca.rx('scores'))
-        print("scale:", pca.rx('scale'))
 
+        trait_array = zScore(self.trait_data_array)
+        trait_array = np.array(trait_array)
+        trait_array_vectors = np.dot(corr_eigen_vectors, trait_array)
+
+        pca_traits = []
+        for i, vector in enumerate(trait_array_vectors):
+            if corr_eigen_value[i-1] < 100.0/len(self.trait_list):
+                pca_traits.append(vector*-1.0)
+
+        print("pca_traits:", pca_traits)
         return pca
 
     def process_loadings(self):
         loadings_array = []
         loadings_row = []
-        print("before loop:", self.loadings[0])
         for i in range(len(self.trait_list)):
             loadings_row = []
             if len(self.trait_list) > 2:
@@ -215,6 +231,45 @@ class CorrelationMatrix(object):
                 position = i + len(self.trait_list)*j
                 loadings_row.append(self.loadings[0][position])
             loadings_array.append(loadings_row)
-        print("loadings:", loadings_array)
         return loadings_array
 
+def zScore(trait_data_array):
+    NN = len(trait_data_array[0])
+    if NN < 10:
+        return trait_data_array
+    else:
+        i = 0
+        for data in trait_data_array:
+            N = len(data)
+            S = reduce(lambda x,y: x+y, data, 0.)
+            SS = reduce(lambda x,y: x+y*y, data, 0.)
+            mean = S/N
+            var = SS - S*S/N
+            stdev = math.sqrt(var/(N-1))
+            if stdev == 0:
+                stdev = 1e-100
+            data2 = map(lambda x:(x-mean)/stdev,data)
+            trait_data_array[i] = data2
+            i += 1
+        return trait_data_array
+
+def sortEigenVectors(vector):
+    try:
+        eigenValues = vector[0].tolist()
+        eigenVectors = vector[1].tolist()
+        combines = []
+        i = 0
+        for item in eigenValues:
+            combines.append([eigenValues[i],eigenVectors[i]])
+            i += 1
+        combines.sort(webqtlUtil.cmpEigenValue)
+        A = []
+        B = []
+        for item in combines:
+            A.append(item[0])
+            B.append(item[1])
+        sum = reduce(lambda x,y: x+y, A, 0.0)
+        A = map(lambda x:x*100.0/sum, A) 
+        return [A,B]
+    except:
+        return []
+\ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 3bde61cd..6e2cb972 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -1,22 +1,22 @@
 import os, math
 
 from base import webqtlConfig
-from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_RESULTS_PATH
+from utility.tools import flat_files, GEMMA_COMMAND
 
 def run_gemma(this_dataset, samples, vals):
     """Generates p-values for each marker using GEMMA"""
 
     print("INSIDE GEMMA_MAPPING")
 
-    gen_pheno_txt_file(this_dataset, samples, vals)
+    gen_pheno_txt_file(this_dataset, vals)
 
     # use GEMMA_RUN in the next one, create a unique temp file
 
-    gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 1 -outdir %s/output -o %s_output' % (flat_files('mapping'),
+    gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 1 -maf 0.1 -outdir %s -o %s_output' % (flat_files('mapping'),
                                                                                     this_dataset.group.name,
                                                                                     flat_files('mapping'),
                                                                                     this_dataset.group.name,
-                                                                                    GEMMA_RESULTS_PATH,
+                                                                                    webqtlConfig.GENERATED_IMAGE_DIR,
                                                                                     this_dataset.group.name)
     print("gemma_command:" + gemma_command)
 
@@ -26,7 +26,7 @@ def run_gemma(this_dataset, samples, vals):
 
     return marker_obs
 
-def gen_pheno_txt_file(this_dataset, samples, vals):
+def gen_pheno_txt_file(this_dataset, vals):
     """Generates phenotype file for GEMMA"""
 
     current_file_data = []
@@ -47,7 +47,7 @@ def parse_gemma_output(this_dataset):
     included_markers = []
     p_values = []
     marker_obs = []
-    with open("{}/output/{}_output.assoc.txt".format(GEMMA_RESULTS_PATH, this_dataset.group.name)) as output_file:
+    with open("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, this_dataset.group.name)) as output_file:
         for line in output_file:
             if line.startswith("chr"):
                 continue
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index b1d2f811..87532445 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -211,6 +211,8 @@ class MarkerRegression(object):
                                                                                                                                                         self.control_marker,
                                                                                                                                                         self.manhattan_plot)
         elif self.mapping_method == "plink":
+            self.score_type = "-log(p)"
+            self.manhattan_plot = True
             results = plink_mapping.run_plink(self.this_trait, self.dataset, self.species, self.vals, self.maf)
             #results = self.run_plink()
         elif self.mapping_method == "pylmm":
@@ -263,52 +265,53 @@ class MarkerRegression(object):
 
             self.trimmed_markers = trim_markers_for_table(results)
 
-            self.json_data['chr'] = []
-            self.json_data['pos'] = []
-            self.json_data['lod.hk'] = []
-            self.json_data['markernames'] = []
-
-            self.json_data['suggestive'] = self.suggestive
-            self.json_data['significant'] = self.significant
-
-            #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
-            for index, qtl in enumerate(self.qtl_results):
-                #if index<40:
-                #    logger.debug("lod score is:", qtl['lod_score'])
-                if qtl['chr'] == highest_chr and highest_chr != "X" and highest_chr != "X/Y":
-                    #logger.debug("changing to X")
-                    self.json_data['chr'].append("X")
-                else:
-                    self.json_data['chr'].append(str(qtl['chr']))
-                self.json_data['pos'].append(qtl['Mb'])
-                if 'lrs_value' in qtl.keys():
-                    self.json_data['lod.hk'].append(str(qtl['lrs_value']))
-                else:
-                    self.json_data['lod.hk'].append(str(qtl['lod_score']))
-                self.json_data['markernames'].append(qtl['name'])
-
-            #Get chromosome lengths for drawing the interval map plot
-            chromosome_mb_lengths = {}
-            self.json_data['chrnames'] = []
-            for key in self.species.chromosomes.chromosomes.keys():
-                self.json_data['chrnames'].append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length])
-                chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length
-
-            # logger.debug("json_data:", self.json_data)
-
-            self.js_data = dict(
-                result_score_type = self.score_type,
-                json_data = self.json_data,
-                this_trait = self.this_trait.name,
-                data_set = self.dataset.name,
-                maf = self.maf,
-                manhattan_plot = self.manhattan_plot,
-                mapping_scale = self.mapping_scale,
-                chromosomes = chromosome_mb_lengths,
-                qtl_results = self.qtl_results,
-                num_perm = self.num_perm,
-                perm_results = self.perm_output,
-            )
+            if self.mapping_method != "gemma":
+                self.json_data['chr'] = []
+                self.json_data['pos'] = []
+                self.json_data['lod.hk'] = []
+                self.json_data['markernames'] = []
+
+                self.json_data['suggestive'] = self.suggestive
+                self.json_data['significant'] = self.significant
+
+                #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
+                for index, qtl in enumerate(self.qtl_results):
+                    #if index<40:
+                    #    logger.debug("lod score is:", qtl['lod_score'])
+                    if qtl['chr'] == highest_chr and highest_chr != "X" and highest_chr != "X/Y":
+                        #logger.debug("changing to X")
+                        self.json_data['chr'].append("X")
+                    else:
+                        self.json_data['chr'].append(str(qtl['chr']))
+                    self.json_data['pos'].append(qtl['Mb'])
+                    if 'lrs_value' in qtl.keys():
+                        self.json_data['lod.hk'].append(str(qtl['lrs_value']))
+                    else:
+                        self.json_data['lod.hk'].append(str(qtl['lod_score']))
+                    self.json_data['markernames'].append(qtl['name'])
+
+                #Get chromosome lengths for drawing the interval map plot
+                chromosome_mb_lengths = {}
+                self.json_data['chrnames'] = []
+                for key in self.species.chromosomes.chromosomes.keys():
+                    self.json_data['chrnames'].append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length])
+                    chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length
+
+                # logger.debug("json_data:", self.json_data)
+
+                self.js_data = dict(
+                    result_score_type = self.score_type,
+                    json_data = self.json_data,
+                    this_trait = self.this_trait.name,
+                    data_set = self.dataset.name,
+                    maf = self.maf,
+                    manhattan_plot = self.manhattan_plot,
+                    mapping_scale = self.mapping_scale,
+                    chromosomes = chromosome_mb_lengths,
+                    qtl_results = self.qtl_results,
+                    num_perm = self.num_perm,
+                    perm_results = self.perm_output,
+                )
 
     def run_rqtl_plink(self):
         # os.chdir("") never do this inside a webserver!!
@@ -599,8 +602,7 @@ def trim_markers_for_table(markers):
 
     #ZS: So we end up with a list of just 200 markers
     if len(sorted_markers) >= 200:
-        trimming_factor = 200 / len(sorted_markers)
-        trimmed_sorted_markers = sorted_markers[:int(len(sorted_markers) * trimming_factor)]
+        trimmed_sorted_markers = sorted_markers[:200]
         return trimmed_sorted_markers
     else:
         return sorted_markers
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 392ad745..49959a74 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -181,7 +181,8 @@ class MarkerRegression(object):
             self.mapmodel_rqtl_geno = start_vars['model']
             self.pair_scan = start_vars['pair_scan']
 
-        self.js_data = start_vars['js_data']
+        if self.mapping_method != "gemma" and self.mapping_method != "plink":
+            self.js_data = start_vars['js_data']
         self.trimmed_markers = start_vars['trimmed_markers'] #Top markers to display in table
 
         #ZS: Think I can just get all this from dataset object now
@@ -564,7 +565,6 @@ class MarkerRegression(object):
         gifmap = self.plotIntMapping(intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm)
 
         self.gifmap = gifmap.__str__()
-        #print("GIFMAP:", gifmap.__str__())
 
         self.filename= webqtlUtil.genRandStr("Itvl_")
         intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename), format='jpeg')
@@ -847,8 +847,7 @@ class MarkerRegression(object):
             pass
 
         #draw position, no need to use a separate function
-        if self.genotype.Mbmap:
-            self.drawProbeSetPosition(canvas, plotXScale, offset=newoffset, zoom = zoom)
+        self.drawProbeSetPosition(canvas, plotXScale, offset=newoffset, zoom = zoom)
 
         return gifmap
 
@@ -1010,35 +1009,34 @@ class MarkerRegression(object):
                     locPixel = xLeftOffset + (Mb-self.startMb)*plotXScale
             else:
                 locPixel = xLeftOffset
-                for i, _chr in enumerate(self.genotype):
-                    if _chr.name != Chr:
-                        locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
+                for i, _chr in enumerate(self.ChrList[1:]):
+                    if _chr[0] != Chr:
+                        locPixel += (self.ChrLengthDistList[i-1] + self.GraphInterval)*plotXScale
                     else:
                         locPixel += Mb*plotXScale
                         break
         else:
             if self.selectedChr > -1:
-                if self.genotype[0].name != Chr:
-                    return
-                else:
-                    for i, _locus in enumerate(self.genotype[0]):
-                        #the trait's position is on the left of the first genotype
-                        if i==0 and _locus.Mb >= Mb:
-                            locPixel=-1
-                            break
+                for i, qtlresult in enumerate(self.qtlresults):
+                    if qtlresult['Chr'] != self.selectedChr:
+                        continue
 
-                        #the trait's position is between two traits
-                        if i > 0 and self.genotype[0][i-1].Mb < Mb and _locus.Mb >= Mb:
-                            locPixel = xLeftOffset + plotXScale*(self.genotype[0][i-1].cM+(_locus.cM-self.genotype[0][i-1].cM)*(Mb -self.genotype[0][i-1].Mb)/(_locus.Mb-self.genotype[0][i-1].Mb))
-                            break
+                    if i==0 and qtlresult['Mb'] >= Mb:
+                        locPixel=-1
+                        break
+
+                    #the trait's position is between two traits
+                    if i > 0 and self.qtlresults[i-1]['Mb'] < Mb and qtlresult['Mb'] >= Mb:
+                        locPixel = xLeftOffset + plotXScale*(self.qtlresults[i-1]['cM']+(qtlresult['cM']-self.qtlresults[i-1]['cM'])*(Mb - self.qtlresults[i-1]['Mb'])/(qtlresult['Mb']-self.qtlresults[i-1]['Mb']))
+                        break
 
-                        #the trait's position is on the right of the last genotype
-                        if i==len(self.genotype[0]) and Mb>=_locus.Mb:
-                            locPixel = -1
+                    #the trait's position is on the right of the last genotype
+                    if i==len(self.qtlresults) and Mb>=qtlresult['Mb']:
+                        locPixel = -1
             else:
                 locPixel = xLeftOffset
-                for i, _chr in enumerate(self.genotype):
-                    if _chr.name != Chr:
+                for i, _chr in enumerate(self.ChrList):
+                    if _chr != Chr:
                         locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
                     else:
                         locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale
@@ -1190,13 +1188,16 @@ class MarkerRegression(object):
         else:
             if self.mapping_method == "gemma":
                 string2 = 'Using GEMMA mapping method with no control for other QTLs.'
+            elif self.mapping_method == "plink":
+                string2 = 'Using PLINK mapping method with no control for other QTLs.'
             else:
                 string2 = 'Using Haldane mapping function with no control for other QTLs'
-        d = 4+ max(canvas.stringWidth(string1,font=labelFont),canvas.stringWidth(string2,font=labelFont))
         if self.this_trait.name:
             identification = "Trait ID: %s : %s" % (self.dataset.fullname, self.this_trait.name)
+            d = 4+ max(canvas.stringWidth(identification, font=labelFont), canvas.stringWidth(string1, font=labelFont), canvas.stringWidth(string2, font=labelFont))
             canvas.drawString(identification,canvas.size[0] - xRightOffset-d,20*fontZoom,font=labelFont,color=labelColor)
-
+        else:
+            d = 4+ max(canvas.stringWidth(string1, font=labelFont), canvas.stringWidth(string2, font=labelFont))
         canvas.drawString(string1,canvas.size[0] - xRightOffset-d,35*fontZoom,font=labelFont,color=labelColor)
         canvas.drawString(string2,canvas.size[0] - xRightOffset-d,50*fontZoom,font=labelFont,color=labelColor)
 
@@ -1915,7 +1916,7 @@ class MarkerRegression(object):
         if self.lrsMax <= 0:  #sliding scale
             if "lrs_value" in self.qtlresults[0]:
                 LRS_LOD_Max = max([result['lrs_value'] for result in self.qtlresults])
-                if self.LRS_LOD == "LOD":
+                if self.LRS_LOD == "LOD" or self.LRS_LOD == "-log(p)":
                     LRS_LOD_Max = LRS_LOD_Max / self.LODFACTOR
                     if self.permChecked and self.nperm > 0 and not self.multipleInterval:
                         self.significant = min(self.significant / self.LODFACTOR, webqtlConfig.MAXLRS)
@@ -2118,7 +2119,7 @@ class MarkerRegression(object):
                 # fix the over limit LRS graph issue since genotype trait may give infinite LRS;
                 # for any lrs is over than 460(LRS max in this system), it will be reset to 460
                 if 'lrs_value' in qtlresult:
-                    if self.LRS_LOD == "LOD":
+                    if self.LRS_LOD == "LOD" or self.LRS_LOD == "-log(p)":
                         if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf':
                             Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRS_LOD_Max*self.LODFACTOR)
                         else:
@@ -2143,7 +2144,11 @@ class MarkerRegression(object):
                 #    Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max
 
                 if self.manhattan_plot == True:
-                    canvas.drawString("5", Xc-canvas.stringWidth("5",font=symbolFont)/2+1,Yc+2,color=pid.black, font=symbolFont)
+                    if previous_chr_as_int % 2 == 1:
+                        point_color = pid.grey
+                    else:
+                        point_color = pid.black
+                    canvas.drawString("5", Xc-canvas.stringWidth("5",font=symbolFont)/2+1,Yc+2,color=point_color, font=symbolFont)
                 else:
                     LRSCoordXY.append((Xc, Yc))
 
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index b457b9a0..3d31da1a 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -3,7 +3,7 @@ import os
 
 from base.webqtlConfig import TMPDIR
 from utility import webqtlUtil
-from utility.tools import PLINK_COMMAND
+from utility.tools import flat_files, PLINK_COMMAND
 
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
@@ -11,12 +11,11 @@ logger = utility.logger.getLogger(__name__ )
 def run_plink(this_trait, dataset, species, vals, maf):
     plink_output_filename = webqtlUtil.genRandStr("%s_%s_"%(dataset.group.name, this_trait.name))
 
-    gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = plink_output_filename)
+    gen_pheno_txt_file(dataset, vals)
+    #gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = plink_output_filename)
 
-    plink_command = PLINK_COMMAND + ' --noweb --ped %s/%s.ped --no-fid --no-parents --no-sex --no-pheno --map %s/%s.map --pheno %s%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (
-        PLINK_PATH, dataset.group.name, PLINK_PATH, dataset.group.name,
-        TMPDIR, plink_output_filename, this_trait.name, maf, TMPDIR,
-        plink_output_filename)
+    plink_command = PLINK_COMMAND + ' --noweb --bfile %s/%s --no-fid --no-parents --no-sex --maf %s --missing-phenotype -9 --out %s/%s --assoc ' % (
+        flat_files('mapping'), dataset.group.name, maf, TMPDIR, plink_output_filename)
     logger.debug("plink_command:", plink_command)
 
     os.system(plink_command)
@@ -29,11 +28,27 @@ def run_plink(this_trait, dataset, species, vals, maf):
     #        self.dataset.group.markers.markers.remove(marker)
     #        #del self.dataset.group.markers.markers[marker]
 
-    logger.debug("p_values:", pf(p_values))
+    logger.debug("p_values:", p_values)
     dataset.group.markers.add_pvalues(p_values)
 
     return dataset.group.markers.markers
 
+def gen_pheno_txt_file(this_dataset, vals):
+    """Generates phenotype file for GEMMA/PLINK"""
+
+    current_file_data = []
+    with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "r") as outfile:
+        for i, line in enumerate(outfile):
+            split_line = line.split()
+            current_file_data.append(split_line)
+
+    with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "w") as outfile:
+        for i, line in enumerate(current_file_data):
+            if vals[i] == "x":
+                this_val = -9
+            else:
+                this_val = vals[i]
+            outfile.write(line[1] + " " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n")
 
 def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''):
     ped_sample_list = get_samples_from_ped_file(dataset)
@@ -71,7 +86,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''):
 
 # get strain name from ped file in order
 def get_samples_from_ped_file(dataset):
-    ped_file= open("{}/{}.ped".format(PLINK_PATH, dataset.group.name),"r")
+    ped_file= open("{}{}.ped".format(flat_files('mapping'), dataset.group.name),"r")
     line = ped_file.readline()
     sample_list=[]
 
@@ -89,9 +104,9 @@ def get_samples_from_ped_file(dataset):
 def parse_plink_output(output_filename, species):
     plink_results={}
 
-    threshold_p_value = 0.01
+    threshold_p_value = 1
 
-    result_fp = open("%s%s.qassoc"% (TMPDIR, output_filename), "rb")
+    result_fp = open("%s/%s.qassoc"% (TMPDIR, output_filename), "rb")
 
     header_line = result_fp.readline()# read header line
     line = result_fp.readline()
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 7e7503d4..6d84a960 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -32,7 +32,6 @@ class SampleList(object):
         self.sample_attribute_values = {}
 
         self.get_attributes()
-        # logger.debug("camera: attributes are:", pf(self.attributes))
 
         if self.this_trait and self.dataset and self.dataset.type == 'ProbeSet':
             self.get_extra_attribute_values()
@@ -40,12 +39,18 @@ class SampleList(object):
         for counter, sample_name in enumerate(sample_names, 1):
             sample_name = sample_name.replace("_2nd_", "")
 
-            #ZS - If there's no value for the sample/strain, create the sample object (so samples with no value are still displayed in the table)
-            try:
-                sample = self.this_trait.data[sample_name]
-            except KeyError:
-                logger.debug("No sample %s, let's create it now" % sample_name)
-                sample = webqtlCaseData.webqtlCaseData(sample_name)
+            if type(self.this_trait) is list: #ZS: self.this_trait will be a list if it is a Temp trait
+                if counter <= len(self.this_trait) and self.this_trait[counter-1] != 'X':
+                    sample = webqtlCaseData.webqtlCaseData(name=sample_name, value=float(self.this_trait[counter-1]))
+                else:
+                    sample = webqtlCaseData.webqtlCaseData(name=sample_name)
+            else:
+                #ZS - If there's no value for the sample/strain, create the sample object (so samples with no value are still displayed in the table)
+                try:
+                    sample = self.this_trait.data[sample_name]
+                except KeyError:
+                    logger.debug("No sample %s, let's create it now" % sample_name)
+                    sample = webqtlCaseData.webqtlCaseData(name=sample_name)
 
             #sampleNameAdd = ''
             #if fd.RISet == 'AXBXA' and sampleName in ('AXB18/19/20','AXB13/14','BXA8/17'):
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 5d55ebe1..b2dfc4ac 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -2,6 +2,7 @@ from __future__ import absolute_import, print_function, division
 
 import string
 import os
+import datetime
 import cPickle
 import uuid
 import json as json
@@ -9,6 +10,9 @@ import json as json
 
 from collections import OrderedDict
 
+import redis
+Redis = redis.StrictRedis()
+
 from flask import Flask, g
 
 from htmlgen import HTMLgen2 as HT
@@ -42,16 +46,33 @@ class ShowTrait(object):
     def __init__(self, kw):
         logger.debug("in ShowTrait, kw are:", kw)
 
-        if kw['trait_id'] != None:
+        if 'trait_id' in kw and kw['dataset'] != "Temp":
             self.temp_trait = False
             self.trait_id = kw['trait_id']
             helper_functions.get_species_dataset_trait(self, kw)
-        else:
+        elif 'group' in kw:
             self.temp_trait = True
-            self.trait_vals = kw['trait_paste'].split()
-            self.temp_group = kw['group']
+            self.trait_id = "Temp_"+kw['species']+ "_" + kw['group'] + "_" + datetime.datetime.now().strftime("%m%d%H%M%S")
             self.temp_species = kw['species']
-            #self.create_temp_trait()
+            self.temp_group = kw['group']
+            self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = self.temp_group)
+            self.this_trait = GeneralTrait(dataset=self.dataset,
+                                           name=self.trait_id,
+                                           cellid=None)
+            self.trait_vals = kw['trait_paste'].split()
+
+            # Put values in Redis so they can be looked up later if added to a collection
+            Redis.set(self.trait_id, kw['trait_paste'])
+        else:
+            self.temp_trait = True
+            self.trait_id = kw['trait_id']
+            self.temp_species = self.trait_id.split("_")[1]
+            self.temp_group = self.trait_id.split("_")[2]
+            self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = self.temp_group)
+            self.this_trait = GeneralTrait(dataset=self.dataset,
+                                           name=self.trait_id,
+                                           cellid=None)
+            self.trait_vals = Redis.get(self.trait_id).split()
 
         #self.dataset.group.read_genotype_file()
 
@@ -64,17 +85,17 @@ class ShowTrait(object):
         self.build_correlation_tools()
 
         #Get nearest marker for composite mapping
+        if not self.temp_trait:
+            if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish":
+                self.nearest_marker = get_nearest_marker(self.this_trait, self.dataset)
+                #self.nearest_marker1 = get_nearest_marker(self.this_trait, self.dataset)[0]
+                #self.nearest_marker2 = get_nearest_marker(self.this_trait, self.dataset)[1]
+            else:
+                self.nearest_marker = ""
+                #self.nearest_marker1 = ""
+                #self.nearest_marker2 = ""
 
-        if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish":
-            self.nearest_marker = get_nearest_marker(self.this_trait, self.dataset)
-            #self.nearest_marker1 = get_nearest_marker(self.this_trait, self.dataset)[0]
-            #self.nearest_marker2 = get_nearest_marker(self.this_trait, self.dataset)[1]
-        else:
-            self.nearest_marker = ""
-            #self.nearest_marker1 = ""
-            #self.nearest_marker2 = ""
-
-        self.make_sample_lists(self.this_trait)
+        self.make_sample_lists()
 
         # Todo: Add back in the ones we actually need from below, as we discover we need them
         hddn = OrderedDict()
@@ -84,17 +105,22 @@ class ShowTrait(object):
 
         hddn['trait_id'] = self.trait_id
         hddn['dataset'] = self.dataset.name
+        hddn['temp_trait'] = False
+        if self.temp_trait:
+           hddn['temp_trait'] = True
+           hddn['group'] = self.temp_group
+           hddn['species'] = self.temp_species
         hddn['use_outliers'] = False
         hddn['method'] = "pylmm"
         hddn['mapping_display_all'] = True
         hddn['suggestive'] = 0
         hddn['num_perm'] = 0
         hddn['manhattan_plot'] = ""
-        if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish":
-            hddn['control_marker'] = self.nearest_marker
-            #hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2
-        else:
-            hddn['control_marker'] = ""
+        hddn['control_marker'] = ""
+        if not self.temp_trait:
+            if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish":
+                hddn['control_marker'] = self.nearest_marker
+                #hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2
         hddn['do_control'] = False
         hddn['maf'] = 0.01
         hddn['compare_traits'] = []
@@ -118,11 +144,12 @@ class ShowTrait(object):
 
         self.trait_table_width = get_trait_table_width(self.sample_groups)
 
-        if self.this_trait.symbol:
-            trait_symbol = self.this_trait.symbol
-        else:
-            trait_symbol = None
-        js_data = dict(trait_id = self.this_trait.name,
+        trait_symbol = None
+        if not self.temp_trait:
+            if self.this_trait.symbol:
+                trait_symbol = self.this_trait.symbol
+
+        js_data = dict(trait_id = self.trait_id,
                        trait_symbol = trait_symbol,
                        dataset_type = self.dataset.type,
                        data_scale = self.dataset.data_scale,
@@ -149,7 +176,7 @@ class ShowTrait(object):
             else:
                 return False
 
-        self.genofiles = get_genofiles(self.this_trait)
+        self.genofiles = get_genofiles(self.dataset)
         self.use_plink_gemma = check_plink_gemma()
         self.use_pylmm_rqtl = check_pylmm_rqtl()
 
@@ -173,8 +200,8 @@ class ShowTrait(object):
                 dataset_menu = data_set.datasets(this_group, self.dataset.group)
             dataset_menu_selected = None
             if len(dataset_menu):
-                if self.this_trait and self.this_trait.dataset:
-                    dataset_menu_selected = self.this_trait.dataset.name
+                if self.dataset:
+                    dataset_menu_selected = self.dataset.name
 
                 return_results_menu = (100, 200, 500, 1000, 2000, 5000, 10000, 15000, 20000)
                 return_results_menu_selected = 500
@@ -185,52 +212,57 @@ class ShowTrait(object):
                                           return_results_menu_selected = return_results_menu_selected,)
 
 
-    def make_sample_lists(self, this_trait):
+    def make_sample_lists(self):
         all_samples_ordered = self.dataset.group.all_samples_ordered()
         
         primary_sample_names = list(all_samples_ordered)
 
-        other_sample_names = []
-        for sample in this_trait.data.keys():
-            if (this_trait.data[sample].name2 in primary_sample_names) and (this_trait.data[sample].name not in primary_sample_names):
-                primary_sample_names.append(this_trait.data[sample].name)
-                primary_sample_names.remove(this_trait.data[sample].name2)
-            elif sample not in all_samples_ordered:
-                all_samples_ordered.append(sample)
-                other_sample_names.append(sample)
-
-        if self.dataset.group.species == "human":
-            primary_sample_names += other_sample_names
-
-        primary_samples = SampleList(dataset = self.dataset,
-                                        sample_names=primary_sample_names,
-                                        this_trait=this_trait,
-                                        sample_group_type='primary',
-                                        header="%s Only" % (self.dataset.group.name))
-        logger.debug("primary_samples is: ", pf(primary_samples))
-
-        logger.debug("other_sample_names2:", other_sample_names)
-        if other_sample_names and self.dataset.group.species != "human" and self.dataset.group.name != "CFW":
-            parent_f1_samples = None
-            if self.dataset.group.parlist and self.dataset.group.f1list:
-                parent_f1_samples = self.dataset.group.parlist + self.dataset.group.f1list
-
-            other_sample_names.sort() #Sort other samples
-            if parent_f1_samples:
-                other_sample_names = parent_f1_samples + other_sample_names
-
-            logger.debug("other_sample_names:", other_sample_names)
-
-            other_samples = SampleList(dataset=self.dataset,
-                                        sample_names=other_sample_names,
-                                        this_trait=this_trait,
-                                        sample_group_type='other',
-                                        header="Non-%s" % (self.dataset.group.name))
-
-            self.sample_groups = (primary_samples, other_samples)
+        if not self.temp_trait:
+            other_sample_names = []
+            for sample in self.this_trait.data.keys():
+                if (self.this_trait.data[sample].name2 in primary_sample_names) and (self.this_trait.data[sample].name not in primary_sample_names):
+                    primary_sample_names.append(self.this_trait.data[sample].name)
+                    primary_sample_names.remove(self.this_trait.data[sample].name2)
+                elif sample not in all_samples_ordered:
+                    all_samples_ordered.append(sample)
+                    other_sample_names.append(sample)
+
+            if self.dataset.group.species == "human":
+                primary_sample_names += other_sample_names
+
+            primary_samples = SampleList(dataset = self.dataset,
+                                            sample_names=primary_sample_names,
+                                            this_trait=self.this_trait,
+                                            sample_group_type='primary',
+                                            header="%s Only" % (self.dataset.group.name))
+
+            if other_sample_names and self.dataset.group.species != "human" and self.dataset.group.name != "CFW":
+                parent_f1_samples = None
+                if self.dataset.group.parlist and self.dataset.group.f1list:
+                    parent_f1_samples = self.dataset.group.parlist + self.dataset.group.f1list
+
+                other_sample_names.sort() #Sort other samples
+                if parent_f1_samples:
+                    other_sample_names = parent_f1_samples + other_sample_names
+
+                logger.debug("other_sample_names:", other_sample_names)
+
+                other_samples = SampleList(dataset=self.dataset,
+                                            sample_names=other_sample_names,
+                                            this_trait=self.this_trait,
+                                            sample_group_type='other',
+                                            header="Non-%s" % (self.dataset.group.name))
+
+                self.sample_groups = (primary_samples, other_samples)
+            else:
+                self.sample_groups = (primary_samples,)
         else:
+            primary_samples = SampleList(dataset = self.dataset,
+                                            sample_names=primary_sample_names,
+                                            this_trait=self.trait_vals,
+                                            sample_group_type='primary',
+                                            header="%s Only" % (self.dataset.group.name))
             self.sample_groups = (primary_samples,)
-
         #TODO: Figure out why this if statement is written this way - Zach
         #if (other_sample_names or (fd.f1list and this_trait.data.has_key(fd.f1list[0]))
         #        or (fd.f1list and this_trait.data.has_key(fd.f1list[1]))):
@@ -261,8 +293,8 @@ def get_nearest_marker(this_trait, this_db):
         return result[0][0]
         #return result[0][0], result[1][0]
 
-def get_genofiles(this_trait):
-    jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, this_trait.dataset.group.name)
+def get_genofiles(this_dataset):
+    jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, this_dataset.group.name)
     try:
         f = open(jsonfile)
     except:
@@ -271,7 +303,7 @@ def get_genofiles(this_trait):
     return jsondata['genofile']
 
 def get_trait_table_width(sample_groups):
-    table_width = 20
+    table_width = 25
     if sample_groups[0].se_exists():
         table_width += 15
     if (table_width + len(sample_groups[0].attributes)*10) > 100:
diff --git a/wqflask/wqflask/static/new/images/a1.gif b/wqflask/wqflask/static/new/images/a1.gif
new file mode 100644
index 00000000..283921a0
--- /dev/null
+++ b/wqflask/wqflask/static/new/images/a1.gif
diff --git a/wqflask/wqflask/static/new/images/arrowdown.gif b/wqflask/wqflask/static/new/images/arrowdown.gif
new file mode 100644
index 00000000..577e5476
--- /dev/null
+++ b/wqflask/wqflask/static/new/images/arrowdown.gif
diff --git a/wqflask/wqflask/static/new/images/step1.gif b/wqflask/wqflask/static/new/images/step1.gif
new file mode 100644
index 00000000..42d2bc7d
--- /dev/null
+++ b/wqflask/wqflask/static/new/images/step1.gif
diff --git a/wqflask/wqflask/static/new/images/step2.gif b/wqflask/wqflask/static/new/images/step2.gif
new file mode 100644
index 00000000..b3dca656
--- /dev/null
+++ b/wqflask/wqflask/static/new/images/step2.gif
diff --git a/wqflask/wqflask/static/new/images/step3.gif b/wqflask/wqflask/static/new/images/step3.gif
new file mode 100644
index 00000000..0e0c7ea2
--- /dev/null
+++ b/wqflask/wqflask/static/new/images/step3.gif
diff --git a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
index e5787564..f23dad0c 100644
--- a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
@@ -45,7 +45,7 @@
         chart = nv.models.scatterChart().width(w).height(h).showLegend(true).color(d3.scale.category10().range());
         chart.pointRange([50, 50]);
         chart.legend.updateState(false);
-        chart.xAxis.axisLabel("Expected Z score").tickFormat(d3.format('.02f'));
+        chart.xAxis.axisLabel("Expected Z score").axisLabelDistance(20).tickFormat(d3.format('.02f'));
         chart.tooltipContent(function(obj) {
           return '<b style="font-size: 20px">' + obj.point.name + '</b>';
         });
@@ -78,13 +78,19 @@
           }
           return results;
         })();
-        chart.yAxis.axisLabel("Trait value").tickFormat(d3.format('.0'+max_decimals.toString()+'f'));
+        //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]
+        chart.yDomain(y_domain)
+        chart.yAxis.axisLabel("Trait value").axisLabelDistance(10).tickFormat(d3.format('.0'+max_decimals.toString()+'f'));
         sw_result = ShapiroWilkW(sorted_values);
         W = sw_result.w.toFixed(3);
         pvalue = sw_result.p.toFixed(3);
         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]
+        chart.xDomain(x_domain)
         slope = jStat.stdev(sorted_values);
         intercept = jStat.mean(sorted_values);
         make_data = function(group_name) {
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 8223a38c..bb1af326 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -195,7 +195,7 @@
         }
         row_line = "<tr>";
         if (row.url != null) {
-          row_line += "<td id=\"" + row.vn + "\"><a href=\"" + row.url + "\">" + row.pretty + "</a></td>";
+          row_line += "<td id=\"" + row.vn + "\"><a href=\"" + row.url + "\" style=\"color: #000000;\">" + row.pretty + "</a></td>";
         } else {
           row_line += "<td id=\"" + row.vn + "\">" + row.pretty + "</td>";
         }
diff --git a/wqflask/wqflask/static/new/packages/nvd3/nv.d3.css b/wqflask/wqflask/static/new/packages/nvd3/nv.d3.css
index 694b9218..593d3889 100644
--- a/wqflask/wqflask/static/new/packages/nvd3/nv.d3.css
+++ b/wqflask/wqflask/static/new/packages/nvd3/nv.d3.css
@@ -1,96 +1,96 @@
 /* nvd3 version 1.8.1 (https://github.com/novus/nvd3) 2015-05-25 */
-.nvd3 .nv-axis {
-    pointer-events:none;
-    opacity: 1;
-}
-
-.nvd3 .nv-axis path {
-    fill: none;
-    stroke: #000;
-    stroke-opacity: .75;
-    shape-rendering: crispEdges;
-}
-
-.nvd3 .nv-axis path.domain {
-    stroke-opacity: .75;
-}
-
-.nvd3 .nv-axis.nv-x path.domain {
-    stroke-opacity: 1;
-}
-
-.nvd3 .nv-axis line {
-    fill: none;
-    stroke: #e5e5e5;
-    shape-rendering: crispEdges;
-}
-
-.nvd3 .nv-axis .zero line,
-    /*this selector may not be necessary*/ .nvd3 .nv-axis line.zero {
-    stroke-opacity: .75;
-}
-
-.nvd3 .nv-axis .nv-axisMaxMin text {
-    font-weight: bold;
-}
-
-.nvd3 .x  .nv-axis .nv-axisMaxMin text,
-.nvd3 .x2 .nv-axis .nv-axisMaxMin text,
-.nvd3 .x3 .nv-axis .nv-axisMaxMin text {
-    text-anchor: middle
-}
-
-.nvd3 .nv-axis.nv-disabled {
-    opacity: 0;
-}
-
-.nvd3 .nv-bars rect {
-    fill-opacity: .75;
-
-    transition: fill-opacity 250ms linear;
-    -moz-transition: fill-opacity 250ms linear;
-    -webkit-transition: fill-opacity 250ms linear;
-}
-
-.nvd3 .nv-bars rect.hover {
-    fill-opacity: 1;
-}
-
-.nvd3 .nv-bars .hover rect {
-    fill: lightblue;
-}
-
-.nvd3 .nv-bars text {
-    fill: rgba(0,0,0,0);
-}
-
-.nvd3 .nv-bars .hover text {
-    fill: rgba(0,0,0,1);
-}
-
-.nvd3 .nv-multibar .nv-groups rect,
-.nvd3 .nv-multibarHorizontal .nv-groups rect,
-.nvd3 .nv-discretebar .nv-groups rect {
-    stroke-opacity: 0;
-
-    transition: fill-opacity 250ms linear;
-    -moz-transition: fill-opacity 250ms linear;
-    -webkit-transition: fill-opacity 250ms linear;
-}
-
-.nvd3 .nv-multibar .nv-groups rect:hover,
-.nvd3 .nv-multibarHorizontal .nv-groups rect:hover,
-.nvd3 .nv-candlestickBar .nv-ticks rect:hover,
-.nvd3 .nv-discretebar .nv-groups rect:hover {
-    fill-opacity: 1;
-}
-
-.nvd3 .nv-discretebar .nv-groups text,
-.nvd3 .nv-multibarHorizontal .nv-groups text {
-    font-weight: bold;
-    fill: rgba(0,0,0,1);
-    stroke: rgba(0,0,0,0);
-}
+.nvd3 .nv-axis {
+    pointer-events:none;
+    opacity: 1;
+}
+
+.nvd3 .nv-axis path {
+    fill: none;
+    stroke: #000;
+    stroke-opacity: .75;
+    shape-rendering: crispEdges;
+}
+
+.nvd3 .nv-axis path.domain {
+    stroke-opacity: .75;
+}
+
+.nvd3 .nv-axis.nv-x path.domain {
+    stroke-opacity: 1;
+}
+
+.nvd3 .nv-axis line {
+    fill: none;
+    stroke: #e5e5e5;
+    shape-rendering: crispEdges;
+}
+
+.nvd3 .nv-axis .zero line,
+    /*this selector may not be necessary*/ .nvd3 .nv-axis line.zero {
+    stroke-opacity: .75;
+}
+
+.nvd3 .nv-axis .nv-axisMaxMin text {
+    font-weight: bold;
+}
+
+.nvd3 .x  .nv-axis .nv-axisMaxMin text,
+.nvd3 .x2 .nv-axis .nv-axisMaxMin text,
+.nvd3 .x3 .nv-axis .nv-axisMaxMin text {
+    text-anchor: middle
+}
+
+.nvd3 .nv-axis.nv-disabled {
+    opacity: 0;
+}
+
+.nvd3 .nv-bars rect {
+    fill-opacity: .75;
+
+    transition: fill-opacity 250ms linear;
+    -moz-transition: fill-opacity 250ms linear;
+    -webkit-transition: fill-opacity 250ms linear;
+}
+
+.nvd3 .nv-bars rect.hover {
+    fill-opacity: 1;
+}
+
+.nvd3 .nv-bars .hover rect {
+    fill: lightblue;
+}
+
+.nvd3 .nv-bars text {
+    fill: rgba(0,0,0,0);
+}
+
+.nvd3 .nv-bars .hover text {
+    fill: rgba(0,0,0,1);
+}
+
+.nvd3 .nv-multibar .nv-groups rect,
+.nvd3 .nv-multibarHorizontal .nv-groups rect,
+.nvd3 .nv-discretebar .nv-groups rect {
+    stroke-opacity: 0;
+
+    transition: fill-opacity 250ms linear;
+    -moz-transition: fill-opacity 250ms linear;
+    -webkit-transition: fill-opacity 250ms linear;
+}
+
+.nvd3 .nv-multibar .nv-groups rect:hover,
+.nvd3 .nv-multibarHorizontal .nv-groups rect:hover,
+.nvd3 .nv-candlestickBar .nv-ticks rect:hover,
+.nvd3 .nv-discretebar .nv-groups rect:hover {
+    fill-opacity: 1;
+}
+
+.nvd3 .nv-discretebar .nv-groups text,
+.nvd3 .nv-multibarHorizontal .nv-groups text {
+    font-weight: bold;
+    fill: rgba(0,0,0,1);
+    stroke: rgba(0,0,0,0);
+}
 
 /* boxplot CSS */
 .nvd3 .nv-boxplot circle {
@@ -112,57 +112,57 @@
 .nv-boxplot-tick:hover {
   stroke-width: 2.5px;
 }
-/* bullet */
-.nvd3.nv-bullet { font: 10px sans-serif; }
-.nvd3.nv-bullet .nv-measure { fill-opacity: .8; }
-.nvd3.nv-bullet .nv-measure:hover { fill-opacity: 1; }
-.nvd3.nv-bullet .nv-marker { stroke: #000; stroke-width: 2px; }
-.nvd3.nv-bullet .nv-markerTriangle { stroke: #000; fill: #fff; stroke-width: 1.5px; }
-.nvd3.nv-bullet .nv-tick line { stroke: #666; stroke-width: .5px; }
-.nvd3.nv-bullet .nv-range.nv-s0 { fill: #eee; }
-.nvd3.nv-bullet .nv-range.nv-s1 { fill: #ddd; }
-.nvd3.nv-bullet .nv-range.nv-s2 { fill: #ccc; }
-.nvd3.nv-bullet .nv-title { font-size: 14px; font-weight: bold; }
-.nvd3.nv-bullet .nv-subtitle { fill: #999; }
-
-
-.nvd3.nv-bullet .nv-range {
-    fill: #bababa;
-    fill-opacity: .4;
-}
-.nvd3.nv-bullet .nv-range:hover {
-    fill-opacity: .7;
-}
-
-.nvd3.nv-candlestickBar .nv-ticks .nv-tick {
-    stroke-width: 1px;
-}
-
-.nvd3.nv-candlestickBar .nv-ticks .nv-tick.hover {
-    stroke-width: 2px;
-}
-
-.nvd3.nv-candlestickBar .nv-ticks .nv-tick.positive rect {
-    stroke: #2ca02c;
-    fill: #2ca02c;
-}
-
-.nvd3.nv-candlestickBar .nv-ticks .nv-tick.negative rect {
-    stroke: #d62728;
-    fill: #d62728;
-}
-
-.with-transitions .nv-candlestickBar .nv-ticks .nv-tick {
-    transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
-    -moz-transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
-    -webkit-transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
-
-}
-
-.nvd3.nv-candlestickBar .nv-ticks line {
-    stroke: #333;
-}
-
+/* bullet */
+.nvd3.nv-bullet { font: 10px sans-serif; }
+.nvd3.nv-bullet .nv-measure { fill-opacity: .8; }
+.nvd3.nv-bullet .nv-measure:hover { fill-opacity: 1; }
+.nvd3.nv-bullet .nv-marker { stroke: #000; stroke-width: 2px; }
+.nvd3.nv-bullet .nv-markerTriangle { stroke: #000; fill: #fff; stroke-width: 1.5px; }
+.nvd3.nv-bullet .nv-tick line { stroke: #666; stroke-width: .5px; }
+.nvd3.nv-bullet .nv-range.nv-s0 { fill: #eee; }
+.nvd3.nv-bullet .nv-range.nv-s1 { fill: #ddd; }
+.nvd3.nv-bullet .nv-range.nv-s2 { fill: #ccc; }
+.nvd3.nv-bullet .nv-title { font-size: 14px; font-weight: bold; }
+.nvd3.nv-bullet .nv-subtitle { fill: #999; }
+
+
+.nvd3.nv-bullet .nv-range {
+    fill: #bababa;
+    fill-opacity: .4;
+}
+.nvd3.nv-bullet .nv-range:hover {
+    fill-opacity: .7;
+}
+
+.nvd3.nv-candlestickBar .nv-ticks .nv-tick {
+    stroke-width: 1px;
+}
+
+.nvd3.nv-candlestickBar .nv-ticks .nv-tick.hover {
+    stroke-width: 2px;
+}
+
+.nvd3.nv-candlestickBar .nv-ticks .nv-tick.positive rect {
+    stroke: #2ca02c;
+    fill: #2ca02c;
+}
+
+.nvd3.nv-candlestickBar .nv-ticks .nv-tick.negative rect {
+    stroke: #d62728;
+    fill: #d62728;
+}
+
+.with-transitions .nv-candlestickBar .nv-ticks .nv-tick {
+    transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
+    -moz-transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
+    -webkit-transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
+
+}
+
+.nvd3.nv-candlestickBar .nv-ticks line {
+    stroke: #333;
+}
+
 
 .nvd3 .nv-legend .nv-disabled rect {
     /*fill-opacity: 0;*/
@@ -187,455 +187,455 @@
     opacity: 0;
 }
 
-/* line plus bar */
-.nvd3.nv-linePlusBar .nv-bar rect {
-    fill-opacity: .75;
-}
-
-.nvd3.nv-linePlusBar .nv-bar rect:hover {
-    fill-opacity: 1;
-}
-.nvd3 .nv-groups path.nv-line {
-    fill: none;
-}
-
-.nvd3 .nv-groups path.nv-area {
-    stroke: none;
-}
-
-.nvd3.nv-line .nvd3.nv-scatter .nv-groups .nv-point {
-    fill-opacity: 0;
-    stroke-opacity: 0;
-}
-
-.nvd3.nv-scatter.nv-single-point .nv-groups .nv-point {
-    fill-opacity: .5 !important;
-    stroke-opacity: .5 !important;
-}
-
-
-.with-transitions .nvd3 .nv-groups .nv-point {
-    transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
-    -moz-transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
-    -webkit-transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
-
-}
-
-.nvd3.nv-scatter .nv-groups .nv-point.hover,
-.nvd3 .nv-groups .nv-point.hover {
-    stroke-width: 7px;
-    fill-opacity: .95 !important;
-    stroke-opacity: .95 !important;
-}
-
-
-.nvd3 .nv-point-paths path {
-    stroke: #aaa;
-    stroke-opacity: 0;
-    fill: #eee;
-    fill-opacity: 0;
-}
-
-
-
-.nvd3 .nv-indexLine {
-    cursor: ew-resize;
-}
-
-/********************
- * SVG CSS
- */
-
-/********************
-  Default CSS for an svg element nvd3 used
-*/
-svg.nvd3-svg {
-    -webkit-touch-callout: none;
-    -webkit-user-select: none;
-    -khtml-user-select: none;
-    -ms-user-select: none;
-    -moz-user-select: none;
-    user-select: none;
-    display: block;
-    width:100%;
-    height:100%;
-}
-
-/********************
-  Box shadow and border radius styling
-*/
-.nvtooltip.with-3d-shadow, .with-3d-shadow .nvtooltip {
-    -moz-box-shadow: 0 5px 10px rgba(0,0,0,.2);
-    -webkit-box-shadow: 0 5px 10px rgba(0,0,0,.2);
-    box-shadow: 0 5px 10px rgba(0,0,0,.2);
-
-    -webkit-border-radius: 5px;
-    -moz-border-radius: 5px;
-    border-radius: 5px;
-}
-
-
-.nvd3 text {
-    font: normal 12px Arial;
-}
-
-.nvd3 .title {
-    font: bold 14px Arial;
-}
-
-.nvd3 .nv-background {
-    fill: white;
-    fill-opacity: 0;
-}
-
-.nvd3.nv-noData {
-    font-size: 18px;
-    font-weight: bold;
-}
-
-
-/**********
-*  Brush
-*/
-
-.nv-brush .extent {
-    fill-opacity: .125;
-    shape-rendering: crispEdges;
-}
-
-.nv-brush .resize path {
-    fill: #eee;
-    stroke: #666;
-}
-
-
-/**********
-*  Legend
-*/
-
-.nvd3 .nv-legend .nv-series {
-    cursor: pointer;
-}
-
-.nvd3 .nv-legend .nv-disabled circle {
-    fill-opacity: 0;
-}
-
-/* focus */
-.nvd3 .nv-brush .extent {
-    fill-opacity: 0 !important;
-}
-
-.nvd3 .nv-brushBackground rect {
-    stroke: #000;
-    stroke-width: .4;
-    fill: #fff;
-    fill-opacity: .7;
-}
-
-
-.nvd3.nv-ohlcBar .nv-ticks .nv-tick {
-    stroke-width: 1px;
-}
-
-.nvd3.nv-ohlcBar .nv-ticks .nv-tick.hover {
-    stroke-width: 2px;
-}
-
-.nvd3.nv-ohlcBar .nv-ticks .nv-tick.positive {
-    stroke: #2ca02c;
-}
-
-.nvd3.nv-ohlcBar .nv-ticks .nv-tick.negative {
-    stroke: #d62728;
-}
-
-
-.nvd3 .background path {
-    fill: none;
-    stroke: #EEE;
-    stroke-opacity: .4;
-    shape-rendering: crispEdges;
-}
-
-.nvd3 .foreground path {
-    fill: none;
-    stroke-opacity: .7;
-}
-
-.nvd3 .nv-parallelCoordinates-brush .extent 
-{
-    fill: #fff;
-    fill-opacity: .6;
-    stroke: gray;
-    shape-rendering: crispEdges;
-}
-
-.nvd3 .nv-parallelCoordinates .hover  {
-    fill-opacity: 1;
-	stroke-width: 3px;
-}
-
-
-.nvd3 .missingValuesline line {
-  fill: none;
-  stroke: black;
-  stroke-width: 1;
-  stroke-opacity: 1;
-  stroke-dasharray: 5, 5; 
-}
-.nvd3.nv-pie path {
-    stroke-opacity: 0;
-    transition: fill-opacity 250ms linear, stroke-width 250ms linear, stroke-opacity 250ms linear;
-    -moz-transition: fill-opacity 250ms linear, stroke-width 250ms linear, stroke-opacity 250ms linear;
-    -webkit-transition: fill-opacity 250ms linear, stroke-width 250ms linear, stroke-opacity 250ms linear;
-
-}
-
-.nvd3.nv-pie .nv-pie-title {
-    font-size: 24px;
-    fill: rgba(19, 196, 249, 0.59);
-}
-
-.nvd3.nv-pie .nv-slice text {
-    stroke: #000;
-    stroke-width: 0;
-}
-
-.nvd3.nv-pie path {
-    stroke: #fff;
-    stroke-width: 1px;
-    stroke-opacity: 1;
-}
-
-.nvd3.nv-pie .hover path {
-    fill-opacity: .7;
-}
-.nvd3.nv-pie .nv-label {
-    pointer-events: none;
-}
-.nvd3.nv-pie .nv-label rect {
-    fill-opacity: 0;
-    stroke-opacity: 0;
-}
-
-/* scatter */
-.nvd3 .nv-groups .nv-point.hover {
-    stroke-width: 20px;
-    stroke-opacity: .5;
-}
-
-.nvd3 .nv-scatter .nv-point.hover {
-    fill-opacity: 1;
-}
-.nv-noninteractive {
-    pointer-events: none;
-}
-
-.nv-distx, .nv-disty {
-    pointer-events: none;
-}
-
-/* sparkline */
-.nvd3.nv-sparkline path {
-    fill: none;
-}
-
-.nvd3.nv-sparklineplus g.nv-hoverValue {
-    pointer-events: none;
-}
-
-.nvd3.nv-sparklineplus .nv-hoverValue line {
-    stroke: #333;
-    stroke-width: 1.5px;
-}
-
-.nvd3.nv-sparklineplus,
-.nvd3.nv-sparklineplus g {
-    pointer-events: all;
-}
-
-.nvd3 .nv-hoverArea {
-    fill-opacity: 0;
-    stroke-opacity: 0;
-}
-
-.nvd3.nv-sparklineplus .nv-xValue,
-.nvd3.nv-sparklineplus .nv-yValue {
-    stroke-width: 0;
-    font-size: .9em;
-    font-weight: normal;
-}
-
-.nvd3.nv-sparklineplus .nv-yValue {
-    stroke: #f66;
-}
-
-.nvd3.nv-sparklineplus .nv-maxValue {
-    stroke: #2ca02c;
-    fill: #2ca02c;
-}
-
-.nvd3.nv-sparklineplus .nv-minValue {
-    stroke: #d62728;
-    fill: #d62728;
-}
-
-.nvd3.nv-sparklineplus .nv-currentValue {
-    font-weight: bold;
-    font-size: 1.1em;
-}
-/* stacked area */
-.nvd3.nv-stackedarea path.nv-area {
-    fill-opacity: .7;
-    stroke-opacity: 0;
-    transition: fill-opacity 250ms linear, stroke-opacity 250ms linear;
-    -moz-transition: fill-opacity 250ms linear, stroke-opacity 250ms linear;
-    -webkit-transition: fill-opacity 250ms linear, stroke-opacity 250ms linear;
-}
-
-.nvd3.nv-stackedarea path.nv-area.hover {
-    fill-opacity: .9;
-}
-
-
-.nvd3.nv-stackedarea .nv-groups .nv-point {
-    stroke-opacity: 0;
-    fill-opacity: 0;
-}
-
-
-.nvtooltip {
-    position: absolute;
-    background-color: rgba(255,255,255,1.0);
-    color: rgba(0,0,0,1.0);
-    padding: 1px;
-    border: 1px solid rgba(0,0,0,.2);
-    z-index: 10000;
-    display: block;
-
-    font-family: Arial;
-    font-size: 13px;
-    text-align: left;
-    pointer-events: none;
-
-    white-space: nowrap;
-
-    -webkit-touch-callout: none;
-    -webkit-user-select: none;
-    -khtml-user-select: none;
-    -moz-user-select: none;
-    -ms-user-select: none;
-    user-select: none;
-}
-
-.nvtooltip {
-    background: rgba(255,255,255, 0.8);
-    border: 1px solid rgba(0,0,0,0.5);
-    border-radius: 4px;
-}
-
-/*Give tooltips that old fade in transition by
-    putting a "with-transitions" class on the container div.
-*/
-.nvtooltip.with-transitions, .with-transitions .nvtooltip {
-    transition: opacity 50ms linear;
-    -moz-transition: opacity 50ms linear;
-    -webkit-transition: opacity 50ms linear;
-
-    transition-delay: 200ms;
-    -moz-transition-delay: 200ms;
-    -webkit-transition-delay: 200ms;
-}
-
-.nvtooltip.x-nvtooltip,
-.nvtooltip.y-nvtooltip {
-    padding: 8px;
-}
-
-.nvtooltip h3 {
-    margin: 0;
-    padding: 4px 14px;
-    line-height: 18px;
-    font-weight: normal;
-    background-color: rgba(247,247,247,0.75);
-    color: rgba(0,0,0,1.0);
-    text-align: center;
-
-    border-bottom: 1px solid #ebebeb;
-
-    -webkit-border-radius: 5px 5px 0 0;
-    -moz-border-radius: 5px 5px 0 0;
-    border-radius: 5px 5px 0 0;
-}
-
-.nvtooltip p {
-    margin: 0;
-    padding: 5px 14px;
-    text-align: center;
-}
-
-.nvtooltip span {
-    display: inline-block;
-    margin: 2px 0;
-}
-
-.nvtooltip table {
-    margin: 6px;
-    border-spacing:0;
-}
-
-
-.nvtooltip table td {
-    padding: 2px 9px 2px 0;
-    vertical-align: middle;
-}
-
-.nvtooltip table td.key {
-    font-weight:normal;
-}
-.nvtooltip table td.value {
-    text-align: right;
-    font-weight: bold;
-}
-
-.nvtooltip table tr.highlight td {
-    padding: 1px 9px 1px 0;
-    border-bottom-style: solid;
-    border-bottom-width: 1px;
-    border-top-style: solid;
-    border-top-width: 1px;
-}
-
-.nvtooltip table td.legend-color-guide div {
-    width: 8px;
-    height: 8px;
-    vertical-align: middle;
-}
-
-.nvtooltip table td.legend-color-guide div {
-    width: 12px;
-    height: 12px;
-    border: 1px solid #999;
-}
-
-.nvtooltip .footer {
-    padding: 3px;
-    text-align: center;
-}
-
-.nvtooltip-pending-removal {
-    pointer-events: none;
-    display: none;
-}
-
-
-/****
-Interactive Layer
-*/
-.nvd3 .nv-interactiveGuideLine {
-    pointer-events:none;
-}
-.nvd3 line.nv-guideline {
-    stroke: #ccc;
+/* line plus bar */
+.nvd3.nv-linePlusBar .nv-bar rect {
+    fill-opacity: .75;
+}
+
+.nvd3.nv-linePlusBar .nv-bar rect:hover {
+    fill-opacity: 1;
+}
+.nvd3 .nv-groups path.nv-line {
+    fill: none;
+}
+
+.nvd3 .nv-groups path.nv-area {
+    stroke: none;
+}
+
+.nvd3.nv-line .nvd3.nv-scatter .nv-groups .nv-point {
+    fill-opacity: 0;
+    stroke-opacity: 0;
+}
+
+.nvd3.nv-scatter.nv-single-point .nv-groups .nv-point {
+    fill-opacity: .5 !important;
+    stroke-opacity: .5 !important;
+}
+
+
+.with-transitions .nvd3 .nv-groups .nv-point {
+    transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
+    -moz-transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
+    -webkit-transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
+
+}
+
+.nvd3.nv-scatter .nv-groups .nv-point.hover,
+.nvd3 .nv-groups .nv-point.hover {
+    stroke-width: 7px;
+    fill-opacity: .95 !important;
+    stroke-opacity: .95 !important;
+}
+
+
+.nvd3 .nv-point-paths path {
+    stroke: #aaa;
+    stroke-opacity: 0;
+    fill: #eee;
+    fill-opacity: 0;
+}
+
+
+
+.nvd3 .nv-indexLine {
+    cursor: ew-resize;
+}
+
+/********************
+ * SVG CSS
+ */
+
+/********************
+  Default CSS for an svg element nvd3 used
+*/
+svg.nvd3-svg {
+    -webkit-touch-callout: none;
+    -webkit-user-select: none;
+    -khtml-user-select: none;
+    -ms-user-select: none;
+    -moz-user-select: none;
+    user-select: none;
+    display: block;
+    width:100%;
+    height:100%;
+}
+
+/********************
+  Box shadow and border radius styling
+*/
+.nvtooltip.with-3d-shadow, .with-3d-shadow .nvtooltip {
+    -moz-box-shadow: 0 5px 10px rgba(0,0,0,.2);
+    -webkit-box-shadow: 0 5px 10px rgba(0,0,0,.2);
+    box-shadow: 0 5px 10px rgba(0,0,0,.2);
+
+    -webkit-border-radius: 5px;
+    -moz-border-radius: 5px;
+    border-radius: 5px;
+}
+
+
+.nvd3 text {
+    font: normal 14px Arial;
+}
+
+.nvd3 .title {
+    font: bold 14px Arial;
+}
+
+.nvd3 .nv-background {
+    fill: white;
+    fill-opacity: 0;
+}
+
+.nvd3.nv-noData {
+    font-size: 18px;
+    font-weight: bold;
+}
+
+
+/**********
+*  Brush
+*/
+
+.nv-brush .extent {
+    fill-opacity: .125;
+    shape-rendering: crispEdges;
+}
+
+.nv-brush .resize path {
+    fill: #eee;
+    stroke: #666;
+}
+
+
+/**********
+*  Legend
+*/
+
+.nvd3 .nv-legend .nv-series {
+    cursor: pointer;
+}
+
+.nvd3 .nv-legend .nv-disabled circle {
+    fill-opacity: 0;
+}
+
+/* focus */
+.nvd3 .nv-brush .extent {
+    fill-opacity: 0 !important;
+}
+
+.nvd3 .nv-brushBackground rect {
+    stroke: #000;
+    stroke-width: .4;
+    fill: #fff;
+    fill-opacity: .7;
+}
+
+
+.nvd3.nv-ohlcBar .nv-ticks .nv-tick {
+    stroke-width: 1px;
+}
+
+.nvd3.nv-ohlcBar .nv-ticks .nv-tick.hover {
+    stroke-width: 2px;
+}
+
+.nvd3.nv-ohlcBar .nv-ticks .nv-tick.positive {
+    stroke: #2ca02c;
+}
+
+.nvd3.nv-ohlcBar .nv-ticks .nv-tick.negative {
+    stroke: #d62728;
+}
+
+
+.nvd3 .background path {
+    fill: none;
+    stroke: #EEE;
+    stroke-opacity: .4;
+    shape-rendering: crispEdges;
+}
+
+.nvd3 .foreground path {
+    fill: none;
+    stroke-opacity: .7;
+}
+
+.nvd3 .nv-parallelCoordinates-brush .extent 
+{
+    fill: #fff;
+    fill-opacity: .6;
+    stroke: gray;
+    shape-rendering: crispEdges;
+}
+
+.nvd3 .nv-parallelCoordinates .hover  {
+    fill-opacity: 1;
+	stroke-width: 3px;
+}
+
+
+.nvd3 .missingValuesline line {
+  fill: none;
+  stroke: black;
+  stroke-width: 1;
+  stroke-opacity: 1;
+  stroke-dasharray: 5, 5; 
+}
+.nvd3.nv-pie path {
+    stroke-opacity: 0;
+    transition: fill-opacity 250ms linear, stroke-width 250ms linear, stroke-opacity 250ms linear;
+    -moz-transition: fill-opacity 250ms linear, stroke-width 250ms linear, stroke-opacity 250ms linear;
+    -webkit-transition: fill-opacity 250ms linear, stroke-width 250ms linear, stroke-opacity 250ms linear;
+
+}
+
+.nvd3.nv-pie .nv-pie-title {
+    font-size: 24px;
+    fill: rgba(19, 196, 249, 0.59);
+}
+
+.nvd3.nv-pie .nv-slice text {
+    stroke: #000;
+    stroke-width: 0;
+}
+
+.nvd3.nv-pie path {
+    stroke: #fff;
+    stroke-width: 1px;
+    stroke-opacity: 1;
+}
+
+.nvd3.nv-pie .hover path {
+    fill-opacity: .7;
+}
+.nvd3.nv-pie .nv-label {
+    pointer-events: none;
+}
+.nvd3.nv-pie .nv-label rect {
+    fill-opacity: 0;
+    stroke-opacity: 0;
+}
+
+/* scatter */
+.nvd3 .nv-groups .nv-point.hover {
+    stroke-width: 20px;
+    stroke-opacity: .5;
+}
+
+.nvd3 .nv-scatter .nv-point.hover {
+    fill-opacity: 1;
+}
+.nv-noninteractive {
+    pointer-events: none;
+}
+
+.nv-distx, .nv-disty {
+    pointer-events: none;
+}
+
+/* sparkline */
+.nvd3.nv-sparkline path {
+    fill: none;
+}
+
+.nvd3.nv-sparklineplus g.nv-hoverValue {
+    pointer-events: none;
+}
+
+.nvd3.nv-sparklineplus .nv-hoverValue line {
+    stroke: #333;
+    stroke-width: 1.5px;
+}
+
+.nvd3.nv-sparklineplus,
+.nvd3.nv-sparklineplus g {
+    pointer-events: all;
+}
+
+.nvd3 .nv-hoverArea {
+    fill-opacity: 0;
+    stroke-opacity: 0;
+}
+
+.nvd3.nv-sparklineplus .nv-xValue,
+.nvd3.nv-sparklineplus .nv-yValue {
+    stroke-width: 0;
+    font-size: .9em;
+    font-weight: normal;
+}
+
+.nvd3.nv-sparklineplus .nv-yValue {
+    stroke: #f66;
+}
+
+.nvd3.nv-sparklineplus .nv-maxValue {
+    stroke: #2ca02c;
+    fill: #2ca02c;
+}
+
+.nvd3.nv-sparklineplus .nv-minValue {
+    stroke: #d62728;
+    fill: #d62728;
+}
+
+.nvd3.nv-sparklineplus .nv-currentValue {
+    font-weight: bold;
+    font-size: 1.1em;
+}
+/* stacked area */
+.nvd3.nv-stackedarea path.nv-area {
+    fill-opacity: .7;
+    stroke-opacity: 0;
+    transition: fill-opacity 250ms linear, stroke-opacity 250ms linear;
+    -moz-transition: fill-opacity 250ms linear, stroke-opacity 250ms linear;
+    -webkit-transition: fill-opacity 250ms linear, stroke-opacity 250ms linear;
+}
+
+.nvd3.nv-stackedarea path.nv-area.hover {
+    fill-opacity: .9;
+}
+
+
+.nvd3.nv-stackedarea .nv-groups .nv-point {
+    stroke-opacity: 0;
+    fill-opacity: 0;
+}
+
+
+.nvtooltip {
+    position: absolute;
+    background-color: rgba(255,255,255,1.0);
+    color: rgba(0,0,0,1.0);
+    padding: 1px;
+    border: 1px solid rgba(0,0,0,.2);
+    z-index: 10000;
+    display: block;
+
+    font-family: Arial;
+    font-size: 13px;
+    text-align: left;
+    pointer-events: none;
+
+    white-space: nowrap;
+
+    -webkit-touch-callout: none;
+    -webkit-user-select: none;
+    -khtml-user-select: none;
+    -moz-user-select: none;
+    -ms-user-select: none;
+    user-select: none;
+}
+
+.nvtooltip {
+    background: rgba(255,255,255, 0.8);
+    border: 1px solid rgba(0,0,0,0.5);
+    border-radius: 4px;
+}
+
+/*Give tooltips that old fade in transition by
+    putting a "with-transitions" class on the container div.
+*/
+.nvtooltip.with-transitions, .with-transitions .nvtooltip {
+    transition: opacity 50ms linear;
+    -moz-transition: opacity 50ms linear;
+    -webkit-transition: opacity 50ms linear;
+
+    transition-delay: 200ms;
+    -moz-transition-delay: 200ms;
+    -webkit-transition-delay: 200ms;
+}
+
+.nvtooltip.x-nvtooltip,
+.nvtooltip.y-nvtooltip {
+    padding: 8px;
+}
+
+.nvtooltip h3 {
+    margin: 0;
+    padding: 4px 14px;
+    line-height: 18px;
+    font-weight: normal;
+    background-color: rgba(247,247,247,0.75);
+    color: rgba(0,0,0,1.0);
+    text-align: center;
+
+    border-bottom: 1px solid #ebebeb;
+
+    -webkit-border-radius: 5px 5px 0 0;
+    -moz-border-radius: 5px 5px 0 0;
+    border-radius: 5px 5px 0 0;
+}
+
+.nvtooltip p {
+    margin: 0;
+    padding: 5px 14px;
+    text-align: center;
+}
+
+.nvtooltip span {
+    display: inline-block;
+    margin: 2px 0;
+}
+
+.nvtooltip table {
+    margin: 6px;
+    border-spacing:0;
+}
+
+
+.nvtooltip table td {
+    padding: 2px 9px 2px 0;
+    vertical-align: middle;
+}
+
+.nvtooltip table td.key {
+    font-weight:normal;
+}
+.nvtooltip table td.value {
+    text-align: right;
+    font-weight: bold;
+}
+
+.nvtooltip table tr.highlight td {
+    padding: 1px 9px 1px 0;
+    border-bottom-style: solid;
+    border-bottom-width: 1px;
+    border-top-style: solid;
+    border-top-width: 1px;
+}
+
+.nvtooltip table td.legend-color-guide div {
+    width: 8px;
+    height: 8px;
+    vertical-align: middle;
+}
+
+.nvtooltip table td.legend-color-guide div {
+    width: 12px;
+    height: 12px;
+    border: 1px solid #999;
+}
+
+.nvtooltip .footer {
+    padding: 3px;
+    text-align: center;
+}
+
+.nvtooltip-pending-removal {
+    pointer-events: none;
+    display: none;
+}
+
+
+/****
+Interactive Layer
+*/
+.nvd3 .nv-interactiveGuideLine {
+    pointer-events:none;
+}
+.nvd3 line.nv-guideline {
+    stroke: #ccc;
 }
 \ No newline at end of file
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index cedb65a1..3bde7dc7 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -32,65 +32,65 @@
         <br />
         <br />
 
-        <div style="width: {% if target_dataset.type == "ProbeSet" %}1600px{% elif target_dataset.type == "Publish" %}1200px{% else %}800px{% endif %}; background-color: #eeeeee; border: 1px solid black;">
+        <div style="width: {% if target_dataset.type == "ProbeSet" %}1600px{% elif target_dataset.type == "Publish" %}1400px{% else %}800px{% endif %};">
             <table width="1600px" id="trait_table" class="table table-hover table-striped">
                 <thead>
                     <tr>
-                        <th style="width: 30px; background-color: #eeeeee;"></th>
+                        <th style="width: 30px;"></th>
                     {% for header in target_dataset.header_fields %}
                         {% if header == 'Year' %}
-                        <th style="text-align: right; background-color: #eeeeee;">{{header}}</th>
+                        <th>{{header}}</th>
                         {% elif header == 'Max LRS' %}
-                        <th style="text-align: right; background-color: #eeeeee;">Max&nbsp;&nbsp;<br>LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+                        <th>Max LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
                         {% elif header == 'Max LRS Location' %}
-                        <th style="text-align: right; background-color: #eeeeee;">{{header}}</th>
+                        <th>{{header}}</th>
                         {% elif header == 'Location' %}
-                        <th style="text-align: right; background-color: #eeeeee;">{{header}}</th>
+                        <th>{{header}}</th>
                         {% elif header == 'Mean' %}
-                        <th style="text-align: right; background-color: #eeeeee;">{{header}}</th>
+                        <th>{{header}}</th>
                         {% elif header == 'Additive Effect' %}
-                        <th style="text-align: right; background-color: #eeeeee;">Add&nbsp;&nbsp;<br>Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+                        <th>Additive Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
                         {% elif header == 'Index' %}
-                        <th style="text-align: right; background-color: #eeeeee; padding-left: 0px; margin-left: 0px;">{{header}}</th>
+                        <th>{{header}}</th>
                         {% elif header == 'N' %}
-                        <th style="text-align: right; background-color: #eeeeee;">{{header}}</th>
+                        <th>{{header}}</th>
                         {% else %}
-                        <th style="background-color: #eeeeee;">{{header}}</th>
+                        <th>{{header}}</th>
                         {% endif %}
                     {% endfor %}
                     {% if target_dataset.type == "ProbeSet" %}
                         {% if corr_method == 'pearson' %}
-                        <th style="text-align: right; background-color: #eeeeee;">Sample r</th>
-                        <th style="text-align: right; background-color: #eeeeee;">&nbsp;&nbsp;N</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Sample p(r)</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Lit r</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Tissue r</th>
+                        <th>Sample r</th>
+                        <th>&nbsp;&nbsp;N</th>
+                        <th>Sample p(r)</th>
+                        <th>Lit r</th>
+                        <th>Tissue r</th>
                         {% else %}
-                        <th style="text-align: right; background-color: #eeeeee;">Sample rho</th>
-                        <th style="text-align: right; background-color: #eeeeee;">N</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Sample p(rho)</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Lit r</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Tissue rho</th>
+                        <th>Sample rho</th>
+                        <th>N</th>
+                        <th>Sample p(rho)</th>
+                        <th>Lit r</th>
+                        <th>Tissue rho</th>
                         {% endif %}
                     {% elif target_dataset.type == "Publish" %}
                         {% if corr_method == 'pearson' %}
-                        <th style="text-align: right; background-color: #eeeeee;">Sample r</th>
-                        <th style="text-align: right; background-color: #eeeeee;">&nbsp;&nbsp;N</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Sample p(r)</th>
+                        <th>Sample r</th>
+                        <th>&nbsp;&nbsp;N</th>
+                        <th>Sample p(r)</th>
                         {% else %}
-                        <th style="text-align: right; background-color: #eeeeee;">Sample rho</th>
-                        <th style="text-align: right; background-color: #eeeeee;">&nbsp;&nbsp;N</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Sample p(rho)</th>
+                        <th>Sample rho</th>
+                        <th>&nbsp;&nbsp;N</th>
+                        <th>Sample p(rho)</th>
                         {% endif %}
                     {% elif target_dataset.type == "Geno" %}
                         {% if corr_method == 'pearson' %}
-                        <th style="text-align: right; background-color: #eeeeee;">Sample r</th>
-                        <th style="text-align: right; background-color: #eeeeee;">N</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Sample p(r)</th>
+                        <th>Sample r</th>
+                        <th>N</th>
+                        <th>Sample p(r)</th>
                         {% else %}
-                        <th style="text-align: right; background-color: #eeeeee;">Sample rho</th>
-                        <th style="text-align: right; background-color: #eeeeee;">N</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Sample p(rho)</th>
+                        <th>Sample rho</th>
+                        <th>N</th>
+                        <th>Sample p(rho)</th>
                         {% endif %}
                     {% endif %}
                     </tr>
@@ -99,7 +99,7 @@
                 <tbody>
                 {% for trait in correlation_results %}
                     <tr>
-                        <td>&nbsp;<INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" VALUE="{{ data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) }}"></td>
+                        <td align="center" style="padding-right: 0px;">&nbsp;<INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="padding-right: 0px;" VALUE="{{ data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) }}"></td>
                         <td align="right">{{ loop.index }}</td>
                         <td>
                             <a href="{{ url_for('show_trait_page',
@@ -114,21 +114,21 @@
                         <td>{{ trait.description_display }}</TD>
                         <td align="right"style="white-space: nowrap;">{{ trait.location_repr }}</td>
                         <td align="right">{{ '%0.3f' % trait.mean|float }}</td>
-                        <td align="right" style="padding-right: 15px;">{% if trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % trait.LRS_score_repr|float }}{% else %}N/A{% endif %}</td>
-                        <td align="right" style="padding-right: 15px;">{{ trait.LRS_location_repr }}</td>
-                        <td align="right" style="padding-right: 15px;">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
-                        <td align="right" style="padding-right: 15px;"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td>
-                        <td align="right" style="padding-right: 15px;">{{ trait.num_overlap }}</td>
-                        <td align="right" style="padding-right: 15px;">{{'%0.3e'|format(trait.sample_p)}}</td>
+                        <td align="right">{% if trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % trait.LRS_score_repr|float }}{% else %}N/A{% endif %}</td>
+                        <td align="right">{{ trait.LRS_location_repr }}</td>
+                        <td align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
+                        <td align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td>
+                        <td align="right">{{ trait.num_overlap }}</td>
+                        <td align="right">{{'%0.3e'|format(trait.sample_p)}}</td>
                         {% if trait.lit_corr == "" or trait.lit_corr == 0.000 %}
-                        <td align="right" style="padding-right: 15px;">--</td>
+                        <td align="right">--</td>
                         {% else %}
-                        <td align="right" style="padding-right: 15px;">{{'%0.3f'|format(trait.lit_corr)}}</td>
+                        <td align="right">{{'%0.3f'|format(trait.lit_corr)}}</td>
                         {% endif %}
                         {% if trait.tissue_corr == "" or trait.tissue_corr == 0.000 %}
-                        <td align="right" style="padding-right: 15px;">--</td>
+                        <td align="right">--</td>
                         {% else %}
-                        <td align="right" style="padding-right: 15px;">{{'%0.3f'|format(trait.tissue_corr)}}</td>
+                        <td align="right">{{'%0.3f'|format(trait.tissue_corr)}}</td>
                         {% endif %}
                       {% elif target_dataset.type == "Publish" %}
                         <td>{{ trait.description_display }}</td>
@@ -138,17 +138,17 @@
                                 {{ trait.pubmed_text }}
                             </a>
                         </td>
-                        <td align="right" style="padding-right: 15px;">{{ trait.LRS_score_repr }}</td>
-                        <td align="right" style="padding-right: 15px;">{{ trait.LRS_location_repr }}</td>
-                        <td align="right" style="padding-right: 15px;">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
-                        <td align="right" style="padding-right: 15px;"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td>
-                        <td align="right" style="padding-right: 15px;">{{ trait.num_overlap }}</td>
-                        <td align="right" style="padding-right: 15px;">{{'%0.3e'|format(trait.sample_p)}}</td>
+                        <td align="right">{{ trait.LRS_score_repr }}</td>
+                        <td align="right">{{ trait.LRS_location_repr }}</td>
+                        <td align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
+                        <td align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td>
+                        <td align="right">{{ trait.num_overlap }}</td>
+                        <td align="right">{{'%0.3e'|format(trait.sample_p)}}</td>
                       {% elif target_dataset.type == "Geno" %}
-                        <td align="right" style="padding-right: 15px;">{{ trait.location_repr }}</TD>
-                        <td align="right" style="padding-right: 15px;"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td>
-                        <td align="right" style="padding-right: 15px;">{{ trait.num_overlap }}</td>
-                        <td align="right" style="padding-right: 15px;">{{'%0.3e'|format(trait.sample_p)}}</td>
+                        <td align="right">{{ trait.location_repr }}</TD>
+                        <td align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td>
+                        <td align="right">{{ trait.num_overlap }}</td>
+                        <td align="right">{{'%0.3e'|format(trait.sample_p)}}</td>
                       {% endif %}
                     </tr>
                 {% endfor %}
@@ -278,6 +278,13 @@
                     { "type": "natural" },
                     { "type": "natural" }
                 ],
+                "createdRow": function ( row, data, index ) {
+                    $('td', row).eq(4).attr('title', $('td', row).eq(4).text());
+                    if ($('td', row).eq(4).text().length > 60) {
+                        $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 60));
+                        $('td', row).eq(4).text($('td', row).eq(4).text() + '...')
+                    }
+                },
                 "order": [[12, "asc" ]],
                 "sDom": "Btir",
                 "autoWidth": false,
@@ -287,7 +294,6 @@
             } );
 
             var table = $('#trait_table').DataTable();
-            new $.fn.dataTable.FixedHeader( table );
 
             {% elif target_dataset.type == "Publish" %}
             $('#trait_table').dataTable( {
@@ -311,7 +317,7 @@
                     { "type": "natural" },
                     { "type": "natural" },
                     { "type": "natural", "width": "25%" },
-                    { "type": "natural", "width": "10%" },
+                    { "type": "natural", "width": "15%" },
                     { "type": "natural" },
                     { "type": "natural" },
                     { "type": "natural" },
@@ -320,6 +326,13 @@
                     { "type": "natural" },
                     { "type": "scientific" }
                 ],
+                "createdRow": function ( row, data, index ) {
+                    $('td', row).eq(4).attr('title', $('td', row).eq(4).text());
+                    if ($('td', row).eq(4).text().length > 60) {
+                        $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 60));
+                        $('td', row).eq(4).text($('td', row).eq(4).text() + '...')
+                    }
+                },
                 "order": [[11, "asc" ]],
                 "sDom": "Btir",
                 "autoWidth": false,
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 1694eae5..72ced084 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -173,6 +173,16 @@
             </div>
 
             <div style="padding-left:120px" class="col-xs-4" style="width: 600px !important;">
+                <section id="websites">
+                    <div class="page-header">
+                        <h1>Github</h1>
+                    </div>
+                    <ul>
+                      <li><a href="https://github.com/genenetwork/genenetwork2">GN2 Source Code</a></li>
+                      <li><a href="https://github.com/genenetwork/sysmaintenance">System Maintenance Code</a></li>
+                      <li><a href="https://github.com/genenetwork/genenetwork">GN1 Source Code</a></li>
+                    </ul>
+               </section>
                 <section id="news-section">
                     <div class="page-header">
                         <h1>News</h1>
@@ -212,7 +222,7 @@
 
                 <section id="websites">
                     <div class="page-header">
-                        <h2>Links</h2>
+                        <h1>Links</h1>
                     </div>
                     <h3>GeneNetwork v2:</h3>
                       <ul>
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 6d3f9326..4cea51b2 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -137,9 +137,9 @@
             <li id="gn1_map_tab">
               <a href="#gn1_map" data-toggle="tab" aria-expanded="true">GN1 Map</a>
             </li>
-            {% if mapping_method != "gemma" %}
+            {% if mapping_method != "gemma" and mapping_method != "plink" %}
             <li id="vector_map_tab">
-              <a href="#vector_map" data-toggle="tab" {% if mapping_method != "gemma" %}aria-expanded="false"{% else %}aria-expanded="true"{% endif %}>Vector Map</a>
+              <a href="#vector_map" data-toggle="tab" {% if mapping_method != "gemma" and mapping_method != "plink" %}aria-expanded="false"{% else %}aria-expanded="true"{% endif %}>Vector Map</a>
             </li>
             {% endif %}
           </ul>
@@ -161,7 +161,7 @@
                   {% endif %}
               </div>
             </div>
-            {% if mapping_method != "gemma" %}
+            {% if mapping_method != "gemma" and mapping_method != "plink" %}
             <div class="tab-pane {% if mapping_method == "gemma" %}active{% endif %}" id="vector_map">
               <div id="chart_container">
                 <div class="qtlcharts" id="topchart"></div>
@@ -277,11 +277,13 @@
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
 
+    {% if mapping_method != "gemma" and mapping_method != "plink" %}
     <script>
         js_data = {{ js_data | safe }}
     </script>
+    {% endif %}
 
-    {% if mapping_method != "gemma" %}
+    {% if mapping_method != "gemma" and mapping_method != "plink" %}
     <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script> 
     <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
@@ -385,6 +387,7 @@
             return $('#marker_regression_form').submit(); 
         };
 
+        {% if mapping_method != "gemma" and mapping_method != "plink" %}
         export_perm_data = function() {
             var num_perm, perm_data;
             num_perm = js_data.num_perm
@@ -393,7 +396,8 @@
             $('input[name=perm_results]').val(json_perm_data);
             $('#marker_regression_form').attr('action', '/export_perm_data');
             return $('#marker_regression_form').submit();
-    };
+        }
+        {% endif %}
 
     </script>
 
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 772c4314..56b6cc62 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -17,7 +17,9 @@
 {% block content %} <!-- Start of body -->
 
 <!--
-    {% if this_trait.dataset.type != 'Geno' %}
+    {% if dataset.type == 'Temp' %}
+	{{ header("{}".format("Temporary Trait")) }}
+    {% elif dataset.type != 'Geno' %}
 	{{ header("{}".format(this_trait.name_header_fmt),
 	    '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
     {% else %}
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 547c3c27..a0c40c7f 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -3,10 +3,12 @@
         <td>Species and Group</td>
         <td>{{ this_trait.dataset.group.species }}, {{ this_trait.dataset.group.name }}</td>
     </tr>
+    {% if this_trait.dataset.type == 'Publish' %}
     <tr>
         <td>Tissue</td>
         <td>{{ this_trait.dataset.tissue }}</td>
     </tr>
+    {% endif %}
     {% if this_trait.dataset.type == 'ProbeSet' %}
     {% if this_trait.symbol != None %}
     <tr>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 12ba80b9..23c09d05 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -17,16 +17,17 @@
                 </li>
                 {% endif %}
                 {# if use_plink_gemma #}
-                {% if dataset.group.mapping_id == "2" or dataset.group.mapping_id == "4" %}
+                {% for mapping_method in dataset.group.mapping_names %}
+                {% if mapping_method == "GEMMA" %}
                 <li class="active">
                     <a href="#gemma" data-toggle="tab">GEMMA</a>
                 </li>
-                {% if dataset.group.mapping_id == "4" %}
+                {% elif mapping_method == "PLINK" %}
                 <li>
                     <a href="#plink" data-toggle="tab">PLINK</a>
                 </li>
                 {% endif %}
-                {% endif %}
+                {% endfor %}
                 <!--<li>
                     <a href="#pair_scan" data-toggle="tab">Pair Scan</a>
                 </li>-->
diff --git a/wqflask/wqflask/templates/submit_trait.html b/wqflask/wqflask/templates/submit_trait.html
index 2529a4f4..8d624ffd 100644
--- a/wqflask/wqflask/templates/submit_trait.html
+++ b/wqflask/wqflask/templates/submit_trait.html
@@ -2,7 +2,7 @@
 {% block title %}Trait Submission{% endblock %}
 {% block content %}
 <!-- Start of body -->
-  <form method="post" action="/show_trait">
+  <form method="post" action="/show_temp_trait">
     <div class="container-fluid">
 
         {{ flash_me() }}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index ab6c433d..39f4a686 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -389,6 +389,20 @@ def export_perm_data():
                     mimetype='text/csv',
                     headers={"Content-Disposition":"attachment;filename=perm_data.csv"})
 
+@app.route("/show_temp_trait", methods=('POST',))
+def show_temp_trait_page():
+    template_vars = show_trait.ShowTrait(request.form)
+    #logger.info("js_data before dump:", template_vars.js_data)
+    template_vars.js_data = json.dumps(template_vars.js_data,
+                                       default=json_default_handler,
+                                       indent="   ")
+    # Sorting the keys messes up the ordered dictionary, so don't do that
+                                       #sort_keys=True)
+
+    #logger.info("js_data after dump:", template_vars.js_data)
+    #logger.info("show_trait template_vars:", pf(template_vars.__dict__))
+    return render_template("show_trait.html", **template_vars.__dict__)
+
 @app.route("/show_trait")
 def show_trait_page():
     template_vars = show_trait.ShowTrait(request.args)
@@ -575,9 +589,10 @@ def marker_regression_page():
         with Bench("Total time in MarkerRegression"):
             template_vars = marker_regression.MarkerRegression(start_vars, temp_uuid)
 
-        template_vars.js_data = json.dumps(template_vars.js_data,
-                                           default=json_default_handler,
-                                           indent="   ")
+        if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink":
+            template_vars.js_data = json.dumps(template_vars.js_data,
+                                               default=json_default_handler,
+                                               indent="   ")
 
         result = template_vars.__dict__
 
@@ -598,13 +613,15 @@ def marker_regression_page():
             #    logger.info("  ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
 
             gn1_template_vars = marker_regression_gn1.MarkerRegression(result).__dict__
-
-            pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
-            logger.info("pickled result length:", len(pickled_result))
-            Redis.set(key, pickled_result)
-            Redis.expire(key, 1*60)
+            #pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
+            #logger.info("pickled result length:", len(pickled_result))
+            #Redis.set(key, pickled_result)
+            #Redis.expire(key, 1*60)
 
             with Bench("Rendering template"):
+                if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"):
+                    gn1_template_vars.pop('qtlresults', None)
+                print("TEMPLATE KEYS:", list(gn1_template_vars.keys()))
                 rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars)
 
     # with Bench("Rendering template"):
author	Lei Yan	2017-04-06 18:20:51 +0000
committer	Lei Yan	2017-04-06 18:20:51 +0000
commit	67218be3a181de7aad617237c11ee33436b8d762 (patch)
tree	d999c5a59bda8d82f04cfb151fb4bba57f2f19be
parent	0b25ab1565faf3824d591c545dfe71dbd28c38ee (diff)
parent	f419b8bc824303009817ad9d52e1452b870b0039 (diff)
download	genenetwork2-67218be3a181de7aad617237c11ee33436b8d762.tar.gz