From 67e8f12e103f48329d8b3e38125c0e84b9dc089d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 17 May 2018 16:32:44 +0000
Subject: Added script to quantile normalize a data set and enter its
 normalized sample data into ElasticSearch

Added option to replace trait page sample/strain values with normalized ones

Began editing Lei's scatterplot code

Changed elasticsearch_tools' get_elasticsearch_connection so that it can also be used for purposes other than user authentication (by adding a "for_user" parameter)
---
 wqflask/base/anon_collection.py                    |  22 -
 wqflask/base/trait_collection.py                   |  53 ---
 wqflask/maintenance/quantile_normalize.py          | 129 ++++++
 wqflask/utility/elasticsearch_tools.py             |   5 +-
 wqflask/wqflask/correlation/corr_scatter_plot.py   |  53 +--
 wqflask/wqflask/show_trait/SampleList.py           |  77 ++--
 wqflask/wqflask/show_trait/show_trait.py           |   4 -
 .../wqflask/static/new/css/corr_scatter_plot.css   |  40 +-
 .../static/new/javascript/draw_corr_scatterplot.js |  71 ++-
 .../wqflask/static/new/javascript/show_trait.js    |  13 +
 .../new/javascript/show_trait_mapping_tools.js     |   2 +-
 wqflask/wqflask/templates/corr_scatterplot.html    | 476 +++++++++++----------
 .../wqflask/templates/show_trait_edit_data.html    |   6 +-
 13 files changed, 567 insertions(+), 384 deletions(-)
 delete mode 100644 wqflask/base/anon_collection.py
 delete mode 100644 wqflask/base/trait_collection.py
 create mode 100644 wqflask/maintenance/quantile_normalize.py

(limited to 'wqflask')

diff --git a/wqflask/base/anon_collection.py b/wqflask/base/anon_collection.py
deleted file mode 100644
index dd1aa27f..00000000
--- a/wqflask/base/anon_collection.py
+++ /dev/null
@@ -1,22 +0,0 @@
-class AnonCollection(TraitCollection):
-    
-    def __init__(self, anon_id):
-        self.anon_id = anon_id
-        self.collection_members = Redis.smembers(self.anon_id)
-        print("self.collection_members is:", self.collection_members)
-        self.num_members = len(self.collection_members)
-        
-
-    @app.route("/collections/remove", methods=('POST',))
-    def remove_traits(traits_to_remove):
-        print("traits_to_remove:", traits_to_remove)
-        for trait in traits_to_remove:
-            Redis.srem(self.anon_id, trait)
-
-        members_now = self.collection_members - traits_to_remove
-        print("members_now:", members_now)
-        print("Went from {} to {} members in set.".format(len(self.collection_members), len(members_now)))
-
-        # We need to return something so we'll return this...maybe in the future
-        # we can use it to check the results
-        return str(len(members_now))
diff --git a/wqflask/base/trait_collection.py b/wqflask/base/trait_collection.py
deleted file mode 100644
index d388a3af..00000000
--- a/wqflask/base/trait_collection.py
+++ /dev/null
@@ -1,53 +0,0 @@
-class TraitCollection(object):
-    
-    def __init__(self, is_anon=False):
-        self.is_anon = is_anon
-        
-        
-    @app.route("/collections/remove", methods=('POST',))
-    def remove_traits():
-        if is_anon:
-            AnonCollection.remove_traits()
-        else:
-            UserCollection.remove_traits()
-            
-        params = request.form
-        print("params are:", params)
-        uc_id = params['uc_id']
-        uc = model.UserCollection.query.get(uc_id)
-        traits_to_remove = params.getlist('traits[]')
-        print("traits_to_remove are:", traits_to_remove)
-        traits_to_remove = process_traits(traits_to_remove)
-        print("\n\n  after processing, traits_to_remove:", traits_to_remove)
-        all_traits = uc.members_as_set()
-        print("  all_traits:", all_traits)
-        members_now = all_traits - traits_to_remove
-        print("  members_now:", members_now)
-        print("Went from {} to {} members in set.".format(len(all_traits), len(members_now)))
-        uc.members = json.dumps(list(members_now))
-        uc.changed_timestamp = datetime.datetime.utcnow()
-        db_session.commit()
-    
-        # We need to return something so we'll return this...maybe in the future
-        # we can use it to check the results
-        return str(len(members_now))
-
-    def __init__(self, anon_id)
-        self.anon_key = anon_key
-        self.collection_members = Redis.smembers(self.anon_id)
-        print("self.collection_members is:", self.collection_members)
-        self.num_members = len(self.collection_members)
-        
-
-    @app.route("/collections/remove", methods=('POST',))
-    def remove_traits(traits_to_remove):
-        print("traits_to_remove:", traits_to_remove)
-        for trait in traits_to_remove:
-            Redis.srem(self.anon_id, trait)
-        members_now = self.collection_members - traits_to_remove
-        print("members_now:", members_now)
-        print("Went from {} to {} members in set.".format(len(self.collection_members), len(members_now)))
-
-        # We need to return something so we'll return this...maybe in the future
-        # we can use it to check the results
-        return str(len(members_now))
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
new file mode 100644
index 00000000..c11073fb
--- /dev/null
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -0,0 +1,129 @@
+from __future__ import absolute_import, print_function, division
+
+import sys
+sys.path.insert(0,'./')
+
+from itertools import izip
+
+import MySQLdb
+import urlparse
+
+import numpy as np
+import pandas as pd
+from elasticsearch import Elasticsearch, TransportError
+from elasticsearch.helpers import bulk
+
+from flask import Flask, g, request
+
+from wqflask import app
+from utility.elasticsearch_tools import get_elasticsearch_connection
+from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT, SQL_URI
+
+def parse_db_uri():
+    """Converts a database URI to the db name, host name, user name, and password"""
+
+    parsed_uri = urlparse.urlparse(SQL_URI)
+
+    db_conn_info = dict(
+                        db = parsed_uri.path[1:],
+                        host = parsed_uri.hostname,
+                        user = parsed_uri.username,
+                        passwd = parsed_uri.password)
+
+    print(db_conn_info)
+    return db_conn_info
+
+def create_dataframe(input_file):
+    with open(input_file) as f:
+        ncols = len(f.readline().split("\t"))
+
+    input_array = np.loadtxt(open(input_file, "rb"), delimiter="\t", skiprows=1, usecols=range(1, ncols))
+    return pd.DataFrame(input_array)
+
+#This function taken from https://github.com/ShawnLYU/Quantile_Normalize
+def quantileNormalize(df_input):
+    df = df_input.copy()
+    #compute rank
+    dic = {}
+    for col in df:
+        dic.update({col : sorted(df[col])})
+    sorted_df = pd.DataFrame(dic)
+    rank = sorted_df.mean(axis = 1).tolist()
+    #sort
+    for col in df:
+        t = np.searchsorted(np.sort(df[col]), df[col])
+        df[col] = [rank[i] for i in t]
+    return df
+
+def set_data(dataset_name):
+    orig_file = "/home/zas1024/cfw_data/" + dataset_name + ".txt"
+
+    sample_list = []
+    with open(orig_file, 'r') as orig_fh, open('quant_norm.csv', 'r') as quant_fh:
+        for i, (line1, line2) in enumerate(izip(orig_fh, quant_fh)):
+            trait_dict = {}
+            sample_list = []
+            if i == 0:
+                sample_names = line1.split('\t')[1:]
+            else:
+                trait_name = line1.split('\t')[0]
+                for i, sample in enumerate(sample_names):
+                    this_sample = {
+                                    "name": sample,
+                                    "value": line1.split('\t')[i+1],
+                                    "qnorm": line2.split('\t')[i+1]
+                                  }
+                    sample_list.append(this_sample)
+                query = """SELECT Species.SpeciesName, InbredSet.InbredSetName, ProbeSetFreeze.FullName
+                           FROM Species, InbredSet, ProbeSetFreeze, ProbeFreeze, ProbeSetXRef, ProbeSet
+                           WHERE Species.Id = InbredSet.SpeciesId and
+                                 InbredSet.Id = ProbeFreeze.InbredSetId and
+                                 ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId and
+                                 ProbeSetFreeze.Name = '%s' and
+                                 ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId and
+                                 ProbeSetXRef.ProbeSetId = ProbeSet.Id and
+                                 ProbeSet.Name = '%s'""" % (dataset_name, line1.split('\t')[0])
+                Cursor.execute(query)
+                result_info = Cursor.fetchone()
+
+                yield {
+                    "_index": "traits",
+                    "_type": "trait",
+                    "_source": {
+                        "name": trait_name,
+                        "species": result_info[0],
+                        "group": result_info[1],
+                        "dataset": dataset_name,
+                        "dataset_fullname": result_info[2],
+                        "samples": sample_list,
+                        "transform_types": "qnorm"
+                    }
+                }
+
+if __name__ == '__main__':
+    Conn = MySQLdb.Connect(**parse_db_uri())
+    Cursor = Conn.cursor()
+
+    #es = Elasticsearch([{
+    #    "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
+    #}], timeout=60) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
+
+    es = get_elasticsearch_connection(for_user=False)
+
+    #input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt"
+    #input_df = create_dataframe(input_filename)
+    #output_df = quantileNormalize(input_df)
+
+    #output_df.to_csv('quant_norm.csv', sep='\t')
+
+    #out_filename = sys.argv[1][:-4] + '_quantnorm.txt'
+
+    #success, _ = bulk(es, set_data(sys.argv[1]))
+
+    response = es.search(
+        index = "traits", doc_type = "trait", body = {
+            "query": { "match": { "name": "ENSMUSG00000028982" } }
+        }
+    )
+
+    print(response)
\ No newline at end of file
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index cce210c3..293a9ae6 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -52,7 +52,7 @@ def test_elasticsearch_connection():
     if not es.ping():
         logger.warning("Elasticsearch is DOWN")
 
-def get_elasticsearch_connection():
+def get_elasticsearch_connection(for_user=True):
     """Return a connection to ES. Returns None on failure"""
     logger.info("get_elasticsearch_connection")
     es = None
@@ -65,7 +65,8 @@ def get_elasticsearch_connection():
             "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
         }]) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
 
-        setup_users_index(es)
+        if for_user:
+            setup_users_index(es)
 
         es_logger = logging.getLogger("elasticsearch")
         es_logger.setLevel(logging.INFO)
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 94711c67..831baf7e 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -6,44 +6,19 @@ from utility import corr_result_helpers
 from scipy import stats
 import numpy as np
 
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
 class CorrScatterPlot(object):
     """Page that displays a correlation scatterplot with a line fitted to it"""
 
     def __init__(self, params):
         self.data_set_1 = data_set.create_dataset(params['dataset_1'])
         self.data_set_2 = data_set.create_dataset(params['dataset_2'])
+        #self.data_set_3 = data_set.create_dataset(params['dataset_3'])
         self.trait_1 = GeneralTrait(name=params['trait_1'], dataset=self.data_set_1)
         self.trait_2 = GeneralTrait(name=params['trait_2'], dataset=self.data_set_2)
-
-        try:
-            width = int(params['width'])
-        except:
-            width = 800
-
-        try:
-            height = int(params['height'])
-        except:
-            height = 600
-
-        try:
-            circle_color = params['circle_color']
-        except:
-            circle_color = '#3D85C6'
-
-        try:
-            circle_radius = int(params['circle_radius'])
-        except:
-            circle_radius = 5
-
-        try:
-            line_color = params['line_color']
-        except:
-            line_color = '#FF0000'
-
-        try:
-            line_width = int(params['line_width'])
-        except:
-            line_width = 1
+        #self.trait_3 = GeneralTrait(name=params['trait_3'], dataset=self.data_set_3)
 
         samples_1, samples_2, num_overlap = corr_result_helpers.normalize_values_with_samples(self.trait_1.data, self.trait_2.data)
 
@@ -60,14 +35,18 @@ class CorrScatterPlot(object):
 
         x = np.array(vals_1)
         y = np.array(vals_2)
-        slope, intercept, r_value, p_value, _std_err = stats.linregress(x, y)
+        slope, intercept, r_value, p_value, std_err = stats.linregress(x, y)
         
         rx = stats.rankdata(x)
         ry = stats.rankdata(y)        
         self.rdata = []
         self.rdata.append(rx.tolist())
         self.rdata.append(ry.tolist())        
-        srslope, srintercept, srr_value, srp_value, _srstd_err = stats.linregress(rx, ry)
+        srslope, srintercept, srr_value, srp_value, srstd_err = stats.linregress(rx, ry)
+
+        #vals_3 = []
+        #for sample in self.trait_3.data:
+        #    vals_3.append(self.trait_3.data[sample].value)
 
         self.js_data = dict(
             data = self.data,
@@ -89,13 +68,9 @@ class CorrScatterPlot(object):
             srslope = srslope,
             srintercept = srintercept,
             srr_value = srr_value,
-            srp_value = srp_value,
+            srp_value = srp_value
 
-            width = width,
-            height = height,
-            circle_color = circle_color,
-            circle_radius = circle_radius,
-            line_color = line_color,
-            line_width = line_width
+            #trait3 = self.trait_3.data,
+            #vals_3 = vals_3
         )
         self.jsdata = self.js_data
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 6d84a960..78bb3b42 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -10,8 +10,12 @@ import numpy as np
 from scipy import stats
 from pprint import pformat as pf
 
+import simplejson as json
+
 import itertools
 
+from utility.elasticsearch_tools import get_elasticsearch_connection
+
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
 
@@ -33,6 +37,8 @@ class SampleList(object):
 
         self.get_attributes()
 
+        self.sample_qnorm = get_transform_vals(self.dataset, this_trait)
+
         if self.this_trait and self.dataset and self.dataset.type == 'ProbeSet':
             self.get_extra_attribute_values()
 
@@ -152,36 +158,47 @@ class SampleList(object):
 
         return any(sample.variance for sample in self.sample_list)
 
-#def z_score(vals):
-#    vals_array = np.array(vals)
-#    mean = np.mean(vals_array)
-#    stdv = np.std(vals_array)
-#
-#    z_scores = []
-#    for val in vals_array:
-#        z_score = (val - mean)/stdv
-#        z_scores.append(z_score)
-#
-#
-#
-#    return z_scores
-
-
-#def z_score(row):
-#    L = [n for n in row if not np.isnan(n)]
-#    m = np.mean(L)
-#    s = np.std(L)
-#    zL = [1.0 * (n - m) / s for n in L]
-#    if len(L) == len(row):  return zL
-#    # deal with nan
-#    retL = list()
-#    for n in row:
-#        if np.isnan(n):
-#            retL.append(nan)
-#        else:
-#            retL.append(zL.pop(0))
-#    assert len(zL) == 0
-#    return retL
+def get_transform_vals(dataset, trait):
+    es = get_elasticsearch_connection(for_user=False)
+
+    logger.info("DATASET NAME:", dataset.name)
+
+    query = '{"bool": {"must": [{"match": {"name": "%s"}}, {"match": {"dataset": "%s"}}]}}' % (trait.name, dataset.name)
+
+    es_body = {
+          "query": {
+            "bool": {
+              "must": [
+                {
+                  "match": {
+                    "name": "%s" % (trait.name)
+                  }
+                },
+                {
+                  "match": {
+                    "dataset": "%s" % (dataset.name)
+                  }
+                }
+              ]
+            }
+          }
+    }
+
+    response = es.search( index = "traits", doc_type = "trait", body = es_body )
+    logger.info("THE RESPONSE:", response)
+    results = response['hits']['hits']
+
+    if len(results) > 0:
+        samples = results[0]['_source']['samples']
+
+        sample_dict = {}
+        for sample in samples:
+            sample_dict[sample['name']] = sample['qnorm']
+
+        logger.info("SAMPLE DICT:", sample_dict)
+        return sample_dict
+    else:
+        return None
 
 def natural_sort_key(x):
     """Get expected results when using as a key for sort - ints or strings are sorted properly"""
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 8b801396..d6d83c02 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -26,9 +26,6 @@ from db import webqtlDatabaseFunction
 
 from pprint import pformat as pf
 
-from utility.tools import flat_files, flat_file_exists
-from utility.tools import get_setting
-
 from utility.logger import getLogger
 logger = getLogger(__name__ )
 
@@ -306,7 +303,6 @@ def get_nearest_marker(this_trait, this_db):
         #return "", ""
     else:
         return result[0][0]
-        #return result[0][0], result[1][0]
 
 def get_genofiles(this_dataset):
     jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, this_dataset.group.name)
diff --git a/wqflask/wqflask/static/new/css/corr_scatter_plot.css b/wqflask/wqflask/static/new/css/corr_scatter_plot.css
index c62d4c9a..a2ebb252 100644
--- a/wqflask/wqflask/static/new/css/corr_scatter_plot.css
+++ b/wqflask/wqflask/static/new/css/corr_scatter_plot.css
@@ -1,13 +1,41 @@
-.chart {
+.nvd3 .nv-axis.nv-x text {
+  font-size: 16px;
+  font-weight: normal;
+  fill: black;
+}
 
+.nvd3 .nv-axis.nv-y text {
+  font-size: 16px;
+  font-weight: normal;
+  fill: black;
 }
 
-.main text {
-    font: 10px sans-serif;	
+.nv-x .nv-axis g path.domain {
+    stroke: black;
+    stroke-width: 2;
 }
 
-.axis line, .axis path {
-    shape-rendering: crispEdges;
+.nv-y .nv-axis g path.domain {
     stroke: black;
-    fill: none;
+    stroke-width: 2;
+}
+
+.nvd3 .nv-axis.nv-x path.domain {
+    stroke-opacity: 1;
+}
+
+.nvd3 .nv-axis.nv-y path.domain {
+    stroke-opacity: 1;
+}
+
+line.nv-regLine {
+    stroke: red;
+    stroke-width: 1;
+}
+
+.nv-axisMin-x,
+.nv-axisMax-x,
+.nv-axisMin-y,
+.nv-axisMax-y {
+    display: none;
 }
diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
index cfde6f09..c290cdfe 100644
--- a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
@@ -1,3 +1,5 @@
+// http://gn2-lei.genenetwork.org/corr_scatter_plot2?dataset_1=HC_M2_0606_P&dataset_2=HC_M2_0606_P&dataset_3=HC_M2_0606_P&trait_1=1427571_at&trait_2=1457022_at&trait_3=1427571_at
+
 var chart;
 var srchart;
 
@@ -7,7 +9,7 @@ function drawg() {
     //
     chart.showLegend(false);
     chart.duration(300);
-    chart.color(d3.scale.category10().range());
+    //chart.color(d3.scale.category10().range());
     chart.pointRange([0, 400]);
     chart.pointDomain([0, 10]);
     //
@@ -74,18 +76,47 @@ function getdata(size, shape) {
             slope: js_data.slope,
             intercept: js_data.intercept
         });
+
+    sizemin = 1;
+    sizemax = 50;
+    if ('vals_3' in js_data) {
+        datamin = d3.min(js_data.vals_3);
+        datamax = d3.max(js_data.vals_3);
+        colormin = $("#cocolorfrom").val();
+        colormax = $("#cocolorto").val();
+        compute = d3.interpolate(colormin, colormax);
+        linear = d3.scale.linear().domain([datamin, datamax]).range([0,1]);
+    }
+
     for (j = 0; j < js_data.data[0].length; j++) {
+        if ('trait3' in js_data) {
+          if (js_data.indIDs[j] in js_data.trait3) {
+            datav = js_data.trait3[js_data.indIDs[j]].value;
+            // size = (sizemax - sizemin) * (datav - datamin) / (datamax - datamin) + sizemin;
+            sizev = map1to2(datamin, datamax, sizemin, sizemax, datav);
+          }
+        } else {
+            datav = 0;
+            sizev = sizemin;
+        }
         data[0].values.push({
             x: js_data.data[0][j],
             y: js_data.data[1][j],
             name: js_data.indIDs[j],
-            size: size,
-            shape: shape
+            size: sizev,
+            shape: shape,
+            v3: datav
         });
     }
+    console.log(data);
     return data;
 }
 
+function map1to2 (min1, max1, min2, max2, v1) {
+    v2 = (v1 - min1) * (max2 - min2) / (max1 - min1) + min2;
+    return v2;
+}
+
 function srgetdata(size, shape) {
     var data = [];
     data.push({
@@ -94,6 +125,12 @@ function srgetdata(size, shape) {
             intercept: js_data.srintercept
         });
     for (j = 0; j < js_data.rdata[0].length; j++) {
+        if (js_data.indIDs[j] in js_data.trait3) {
+            size = js_data.trait3[js_data.indIDs[j]].value;
+            //console.log("yes "+js_data.indIDs[j]+", "+size);
+        } else {
+            //console.log("no "+js_data.indIDs[j]);
+        }
         data[0].values.push({
             x: js_data.rdata[0][j],
             y: js_data.rdata[1][j],
@@ -163,13 +200,39 @@ function chartupdatewh() {
     window.dispatchEvent(new Event('resize'));
 }
 
+ function colorer(d) {
+    datamin = d3.min(js_data.vals_3);
+    datamax = d3.max(js_data.vals_3);
+    //colormin = d3.rgb(255,0,0);
+    //colormax = d3.rgb(0,255,0);
+    colormin = $("#cocolorfrom").val();
+    colormax = $("#cocolorto").val();
+
+    console.log("colormin: "+colormin);
+    console.log("colormax: "+colormax);
+
+    compute = d3.interpolate(colormin, colormax);
+    linear = d3.scale.linear().domain([datamin, datamax]).range([0,1]);
+    //console.log(d[0].x);
+          c= compute(linear(d[0].x));
+          //console.log(c);
+          return c;
+  }
+
 function chartupdatedata() {
     //
     var size = $("#marksize").val();
     var shape = $("#markshape").val();
     //
-    d3.select('#scatterplot2 svg').datum(nv.log(getdata(size, shape))).call(chart);
+    d3.select('#scatterplot2 svg').datum(getdata(size, shape)).call(chart);
     d3.select('#srscatterplot2 svg').datum(nv.log(srgetdata(size, shape))).call(srchart);
+    //
+    d3.selectAll('.nv-point')
+      .attr({
+          'stroke': colorer,
+          'fill':   colorer
+      });
+    //
     nv.utils.windowResize(chart.update);
     nv.utils.windowResize(srchart.update);
 }
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index dfdafaf0..17afc814 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -559,6 +559,18 @@
       })(this));
     };
     $('#reset').click(reset_samples_table);
+    switch_qnorm_data = function() {
+      return $('.trait_value_input').each((function(_this) {
+        return function(_index, element) {
+          transform_val = $(element).data('transform')
+          if (transform_val != "") {
+              $(element).val(transform_val.toFixed(3));
+          }
+          return transform_val
+        };
+      })(this));
+    };
+    $('#qnorm').click(switch_qnorm_data);
     get_sample_table_data = function(table_name) {
       var samples;
       samples = [];
@@ -871,6 +883,7 @@
     $('#exclude_group').click(edit_data_change);
     $('#block_outliers').click(edit_data_change);
     $('#reset').click(edit_data_change);
+    $('#qnorm').click(edit_data_change);
     return console.log("end");
   });
 
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 81123de7..daa5b3f2 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -213,7 +213,7 @@
       var form_data, url;
       console.log("RUNNING GEMMA");
       url = "/loading";
-      $('input[name=method]').val("gemma_bimbam");
+      $('input[name=method]').val("gemma");
       $('input[name=num_perm]').val(0);
       $('input[name=genofile]').val($('#genofile_gemma').val());
       $('input[name=maf]').val($('input[name=maf_gemma]').val());
diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html
index 87588534..e0f017c2 100644
--- a/wqflask/wqflask/templates/corr_scatterplot.html
+++ b/wqflask/wqflask/templates/corr_scatterplot.html
@@ -1,222 +1,254 @@
-{% extends "base.html" %}
-
-{% block css %}
-    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
-    <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
-    <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
-	<link rel="stylesheet" type="text/css" href="//cdnjs.cloudflare.com/ajax/libs/nvd3/1.8.5/nv.d3.min.css">
-	<link rel="stylesheet" type="text/css" href="/static/new/css/corr_scatter_plot2.css" />
-{% endblock %}
-
-{% block content %}
-
-<div class="container-fluid">
-
-<h2>Correlation Scatterplot</h2>
-
-<div style="margin-left: 0px;">
-
-    {% if trait_1.dataset.type == "ProbeSet" %}
-		<div>
-			X axis:
-			<a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
-				{{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.tissue + " "  + trait_1.dataset.name + ": " + trait_1.name|string}}
-			</a>
-		</div>
-		<div>
-			[{{trait_1.symbol}} on {{trait_1.location_repr}} Mb]
-			{{trait_1.description_display}}
-		</div>
-    {% elif trait_1.dataset.type == "Publish" %}
-		<div>
-			X axis:
-            <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
-                {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.name + ": " + trait_1.name|string}}
-            </a>
-		</div>
-		<div>
-			<a href="{{trait_1.pubmed_link}}">PubMed: {{trait_1.pubmed_text}}</a>
-			{{trait_1.description_display}}	
-		</div>
-    {% endif %}
-
-	<br/>
-
-    {% if trait_2.dataset.type == "ProbeSet" %}
-		<div>
-			Y axis:
-            <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
-                {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.tissue + " "  + trait_2.dataset.name + ": " + trait_2.name|string}}
-            </a>
-        </div>
-        <div>
-			[{{trait_2.symbol}} on {{trait_2.location_repr}} Mb]
-			{{trait_2.description_display}}
-		</div>
-    {% elif trait_2.dataset.type == "Publish" %}
-        <div>
-			Y axis:
-            <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
-                {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.name + ": " + trait_2.name|string}}
-            </a>
-        </div>
-        <div>
-			<a href="{{trait_2.pubmed_link}}">PubMed: {{trait_2.pubmed_text}}</a>
-			{{trait_2.description_display}}
-		</div>
-    {% endif %}
-	
-</div>
-
-<br>
-
-<table class="table">
-	<tr>
-        <td style="vertical-align: middle;">Width <input class="chartupdatewh" id="width" type="text" value="1000" style="width: 44px; height: 22px;"> px</td>
-        <td style="vertical-align: middle;">Height <input class="chartupdatewh" id="height" type="text" value="800" style="width: 44px; height: 22px;"> px</td>
-    </tr>
-</table>
-
-<table class="table">
-    <tr>
-		<td style="vertical-align: middle;">Mark
-            <input class="chartupdate" id="markcolor" type="color" value="#8fbbda">
-            <select class="chartupdatedata" id="marksize" style="width: 44px; height: 22px;">
-                <option value="0">0</option>
-                <option value="1">1</option>
-                <option value="2">2</option>
-                <option value="3">3</option>
-                <option value="4">4</option>
-                <option value="5" selected>5</option>
-                <option value="6">6</option>
-                <option value="7">7</option>
-                <option value="8">8</option>
-                <option value="9">9</option>
-                <option value="10">10</option>
-                <option value="15">15</option>
-                <option value="20">20</option>
-                <option value="25">25</option>
-                <option value="30">30</option>
-            </select>
-            <select class="chartupdatedata" id="markshape" style="width: 100px; height: 22px;">
-                <option value="circle" selected>Circle</option>
-                <option value="cross">Cross</option>
-                <option value="triangle-up">Triangle-up</option>
-                <option value="triangle-down">Triangle-down</option>
-                <option value="diamond">Diamond</option>
-                <option value="square">Square</option>
-            </select>
-        </td>
-    </tr>
-</table>
-
-<table class="table">    
-    <tr>
-        <td style="vertical-align: middle;">Label
-            <input class="chartupdate" id="labelcolor" type="color" value="#000000">
-            <input class="chartupdate" id="labelfont" type="text" value="16" style="width: 44px; height: 22px;"> px
-        </td>
-        <td style="vertical-align: middle;">Number
-            <input class="chartupdate" id="numbercolor" type="color" value="#000000">
-            <input class="chartupdate" id="numberfont" type="text" value="16" style="width: 44px; height: 22px;"> px
-        </td>
-        <td style="vertical-align: middle;">Axis
-            <input class="chartupdate" id="axiscolor" type="color" value="#000000">
-            <input class="chartupdate" id="axiswidth" type="text" value="2" style="width: 44px; height: 22px;"> px
-        </td>
-        <td style="vertical-align: middle;">Line
-            <input class="chartupdate" id="linecolor" type="color" value="#8fbbda">
-            <input class="chartupdate" id="linewidth" type="text" value="1" style="width: 44px; height: 22px;"> px
-        </td>
-    </tr>
-</table>
-
-<br>
-
-<ul class="nav nav-tabs">
-    <li class="active"><a href="#tp1" data-toggle="tab">Pearson</a></li>
-    <li>               <a href="#tp2" data-toggle="tab">Spearman Rank</a></li>
-</ul>
-
-<div class="tab-content">
-    <div class="tab-pane active" id="tp1">
-
-<br>
-
-<div><a id="a_svg_pcs" href="#" onclick="javascript:saveassvg_pcs();" class="btn btn-primary">Save as SVG</a></div>
-
-<div style="width: 1000px; text-align: center;"><h2>Pearson Correlation Scatterplot</h2></div>
-
-<div id="scatterplot2"><svg id="svg_pcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg></div>
-
-<br>
-
-<table class="table table-hover table-striped table-bordered" style="width: 200px; margin-left: 80px; text-align: right;">
-    <thead>
-        <tr><th style="text-align: right;">Statistic</th><th style="text-align: right;">Value</th></tr>
-    </thead>
-	<tbody>
-		<tr><td>Number</td>		<td>{{jsdata.num_overlap}}</td></tr>
-		<tr><td>Slope</td>		<td>{{'%0.3f' % jsdata.slope}}</td></tr>
-		<tr><td>Intercept</td>	<td>{{'%0.3f' % jsdata.intercept}}</td></tr>
-		<tr><td>r value</td>	<td>{{'%0.3f' % jsdata.r_value}}</td></tr>
-   		<tr><td>P value</td>	<td>{% if jsdata.p_value < 0.001 %}{{'%0.3e' % jsdata.p_value}}{% else %}{{'%0.3f' % jsdata.p_value}}{% endif %}</td></tr>
-        <tr>
-            <td style="text-align: left;" colspan="2">
-                Regression Line
-                <br>
-                y = {{'%0.3f' % jsdata.slope}} * x + {{'%0.3f' % jsdata.intercept}}
-            </td>
-        </tr>
-	</tbody>
-</table>
-
-    </div>
-    
-    <div class="tab-pane" id="tp2">
-    
-<br>
-
-<div><a id="a_svg_srcs" href="#" onclick="javascript:saveassvg_srcs();" class="btn btn-primary">Save as SVG</a></div>
-
-<div style="width: 1000px; text-align: center;"><h2>Spearman Rank Correlation Scatterplot</h2></div>
-
-<div id="srscatterplot2"><svg id="svg_srcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg></div>
-
-<br>
-
-<table class="table table-hover table-striped table-bordered" style="width: 200px; margin-left: 80px; text-align: right;">
-    <thead>
-        <tr><th style="text-align: right;">Statistic</th><th style="text-align: right;">Value</th></tr>
-    </thead>
-	<tbody>
-		<tr><td>Number</td>		<td>{{jsdata.num_overlap}}</td></tr>
-		<tr><td>Slope</td>		<td>{{'%0.3f' % jsdata.srslope}}</td></tr>
-		<tr><td>Intercept</td>	<td>{{'%0.3f' % jsdata.srintercept}}</td></tr>
-		<tr><td>r value</td>	<td>{{'%0.3f' % jsdata.srr_value}}</td></tr>
-		<tr><td>P value</td>	<td>{% if jsdata.srp_value < 0.001 %}{{'%0.3e' % jsdata.srp_value}}{% else %}{{'%0.3f' % jsdata.srp_value}}{% endif %}</td></tr>
-	</tbody>
-</table>
-
-    </div>
-    
-</div>
-
-</div>
-
-{% endblock %}
-
-{% block js %}
-    <script>
-       js_data = {{ js_data | safe }};
-    </script>
-    <script language="javascript" type="text/javascript" src="//cdnjs.cloudflare.com/ajax/libs/d3/3.5.17/d3.min.js"></script>
-	<script language="javascript" type="text/javascript" src="//cdnjs.cloudflare.com/ajax/libs/nvd3/1.8.5/nv.d3.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/draw_corr_scatterplot-2.js"></script>
-{% endblock %}
+{% extends "base.html" %}
+
+{% block css %}
+    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+    <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
+    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+    <link rel="stylesheet" type="text/css" href="//cdnjs.cloudflare.com/ajax/libs/nvd3/1.8.5/nv.d3.min.css">
+    <link rel="stylesheet" type="text/css" href="/static/new/css/corr_scatter_plot.css" />
+{% endblock %}
+
+{% block content %}
+
+<div class="container-fluid">
+
+  <h2>Correlation Scatterplot</h2>
+
+  <div style="margin-left: 0px;">
+    {% if trait_1.dataset.type == "ProbeSet" %}
+    <div>
+      X axis:
+      <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
+        {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.tissue + " "  + trait_1.dataset.name + ": " + trait_1.name|string}}
+      </a>
+    </div>
+    <div>
+      [{{trait_1.symbol}} on {{trait_1.location_repr}} Mb]
+      {{trait_1.description_display}}
+    </div>
+    {% elif trait_1.dataset.type == "Publish" %}
+    <div>
+      X axis:
+      <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
+        {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.name + ": " + trait_1.name|string}}
+      </a>
+    </div>
+    <div>
+      <a href="{{trait_1.pubmed_link}}">PubMed: {{trait_1.pubmed_text}}</a>
+        {{trait_1.description_display}}
+    </div>
+    {% endif %}
+
+    <br/>
+
+    {% if trait_2.dataset.type == "ProbeSet" %}
+    <div>
+      Y axis:
+      <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
+        {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.tissue + " "  + trait_2.dataset.name + ": " + trait_2.name|string}}
+      </a>
+    </div>
+    <div>
+      [{{trait_2.symbol}} on {{trait_2.location_repr}} Mb]
+      {{trait_2.description_display}}
+    </div>
+    {% elif trait_2.dataset.type == "Publish" %}
+    <div>
+      Y axis:
+      <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
+        {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.name + ": " + trait_2.name|string}}
+      </a>
+    </div>
+    <div>
+      <a href="{{trait_2.pubmed_link}}">PubMed: {{trait_2.pubmed_text}}</a>
+        {{trait_2.description_display}}
+    </div>
+    {% endif %}
+
+    <br/>
+
+    {% if trait_3 %}
+    {% if trait_3.dataset.type == "ProbeSet" %}
+    <div>
+      Cofactor:
+      <a href="{{url_for('show_trait_page', trait_id = trait_3.name, dataset = trait_3.dataset.name)}}">
+        {{trait_3.dataset.group.species + " " + trait_3.dataset.group.name + " " + trait_3.dataset.tissue + " "  + trait_3.dataset.name + ": " + trait_3.name|string}}
+      </a>
+    </div>
+    <div>
+      [{{trait_3.symbol}} on {{trait_3.location_repr}} Mb]
+      {{trait_3.description_display}}
+    </div>
+    {% elif trait_3.dataset.type == "Publish" %}
+    <div>
+      Cofactor:
+      <a href="{{url_for('show_trait_page', trait_id = trait_3.name, dataset = trait_3.dataset.name)}}">
+        {{trait_3.dataset.group.species + " " + trait_3.dataset.group.name + " " + trait_3.dataset.name + ": " + trait_3.name|string}}
+      </a>
+    </div>
+    <div>
+      <a href="{{trait_3.pubmed_link}}">PubMed: {{trait_3.pubmed_text}}</a>
+        {{trait_3.description_display}}
+    </div>
+    {% endif %}
+    {% endif %}
+
+    <input class="chartupdatedata" id="cocolorfrom" type="color" value="#000000">
+    <input class="chartupdatedata" id="cocolorto" type="color" value="#000000">
+
+  </div>
+
+  <br>
+
+  <table class="table">
+    <tr>
+      <td style="vertical-align: middle;">Width <input class="chartupdatewh" id="width" type="text" value="1000" style="width: 44px; height: 22px;"> px</td>
+      <td style="vertical-align: middle;">Height <input class="chartupdatewh" id="height" type="text" value="800" style="width: 44px; height: 22px;"> px</td>
+    </tr>
+  </table>
+
+  <table class="table">
+    <tr>
+      <td style="vertical-align: middle;">Label
+        <input class="chartupdate" id="labelcolor" type="color" value="#000000">
+        <input class="chartupdate" id="labelfont" type="text" value="16" style="width: 44px; height: 22px;"> px
+      </td>
+      <td style="vertical-align: middle;">Number
+        <input class="chartupdate" id="numbercolor" type="color" value="#000000">
+        <input class="chartupdate" id="numberfont" type="text" value="16" style="width: 44px; height: 22px;"> px
+      </td>
+      <td style="vertical-align: middle;">Axis
+        <input class="chartupdate" id="axiscolor" type="color" value="#000000">
+        <input class="chartupdate" id="axiswidth" type="text" value="2" style="width: 44px; height: 22px;"> px
+      </td>
+      <td style="vertical-align: middle;">Line
+        <input class="chartupdate" id="linecolor" type="color" value="#8fbbda">
+        <input class="chartupdate" id="linewidth" type="text" value="1" style="width: 44px; height: 22px;"> px
+      </td>
+    </tr>
+  </table>
+
+  <br>
+
+  <ul class="nav nav-tabs">
+    <li class="active">
+      <a href="#tp1" data-toggle="tab">Pearson</a>
+    </li>
+    <li>
+      <a href="#tp2" data-toggle="tab">Spearman Rank</a>
+    </li>
+  </ul>
+
+  <div class="tab-content">
+
+    <div class="tab-pane active" id="tp1">
+      <br>
+      <div>
+        <a id="a_svg_pcs" href="#" onclick="javascript:saveassvg_pcs();" class="btn btn-primary">Save as SVG</a>
+      </div>
+      <div style="width: 1000px; text-align: center;">
+        <h2>Pearson Correlation Scatterplot</h2>
+      </div>
+      <div id="scatterplot2">
+        <svg id="svg_pcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg>
+      </div>
+      <br>
+      <table class="table table-hover table-striped table-bordered" style="width: 200px; margin-left: 80px; text-align: right;">
+        <thead>
+          <tr><th style="text-align: right;">Statistic</th><th style="text-align: right;">Value</th></tr>
+        </thead>
+        <tbody>
+          <tr>
+            <td>Number</td>
+            <td>{{jsdata.num_overlap}}</td>
+          </tr>
+          <tr>
+            <td>Slope</td>
+            <td>{{'%0.3f' % jsdata.slope}}</td>
+          </tr>
+          <tr>
+            <td>Intercept</td>
+            <td>{{'%0.3f' % jsdata.intercept}}</td>
+          </tr>
+          <tr>
+            <td>r value</td>
+            <td>{{'%0.3f' % jsdata.r_value}}</td>
+          </tr>
+          <tr>
+            <td>P value</td>
+            <td>{% if jsdata.p_value < 0.001 %}{{'%0.3e' % jsdata.p_value}}{% else %}{{'%0.3f' % jsdata.p_value}}{% endif %}</td>
+          </tr>
+          <tr>
+            <td style="text-align: left;" colspan="2">
+              Regression Line
+              <br>
+              y = {{'%0.3f' % jsdata.slope}} * x + {{'%0.3f' % jsdata.intercept}}
+            </td>
+          </tr>
+        </tbody>
+      </table>
+    </div>
+
+    <div class="tab-pane" id="tp2">
+
+      <br>
+
+      <div>
+        <a id="a_svg_srcs" href="#" onclick="javascript:saveassvg_srcs();" class="btn btn-primary">Save as SVG</a>
+      </div>
+      <div style="width: 1000px; text-align: center;">
+        <h2>Spearman Rank Correlation Scatterplot</h2>
+      </div>
+      <div id="srscatterplot2">
+        <svg id="svg_srcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg>
+      </div>
+
+      <br>
+
+      <table class="table table-hover table-striped table-bordered" style="width: 200px; margin-left: 80px; text-align: right;">
+        <thead>
+          <tr><th style="text-align: right;">Statistic</th><th style="text-align: right;">Value</th></tr>
+        </thead>
+        <tbody>
+          <tr>
+            <td>Number</td>
+            <td>{{jsdata.num_overlap}}</td>
+          </tr>
+          <tr>
+            <td>Slope</td>
+            <td>{{'%0.3f' % jsdata.srslope}}</td>
+          </tr>
+          <tr>
+            <td>Intercept</td>
+            <td>{{'%0.3f' % jsdata.srintercept}}</td>
+          </tr>
+          <tr>
+            <td>r value</td>
+            <td>{{'%0.3f' % jsdata.srr_value}}</td>
+          </tr>
+	  <tr>
+            <td>P value</td>
+            <td>{% if jsdata.srp_value < 0.001 %}{{'%0.3e' % jsdata.srp_value}}{% else %}{{'%0.3f' % jsdata.srp_value}}{% endif %}</td>
+          </tr>
+        </tbody>
+      </table>
+    </div>
+
+  </div>
+
+</div>
+
+{% endblock %}
+
+{% block js %}
+    <script>
+       js_data = {{ js_data | safe }};
+    </script>
+    <script language="javascript" type="text/javascript" src="//cdnjs.cloudflare.com/ajax/libs/d3/3.5.17/d3.min.js"></script>
+	<script language="javascript" type="text/javascript" src="//cdnjs.cloudflare.com/ajax/libs/nvd3/1.8.5/nv.d3.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/draw_corr_scatterplot.js"></script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index a431821e..1402db47 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -54,6 +54,10 @@
                   <option value="csv">CSV</option>
                 </select>
               </span>
+              <br>
+              {% if sample_groups[0].sample_qnorm is not none %}
+              <input type="button" id="qnorm" class="btn btn-default" value="Quantile Normalize">
+              {% endif %}
             </div>
         </fieldset>
         <br>
@@ -111,7 +115,7 @@
         
                         {# Todo: Add IDs #}
                         <td class="column_name-Value" align="right">
-                          <input type="text" data-value="{{ sample.display_value }}" name="{{ 'value:' + sample.name }}"
+                          <input type="text" data-value="{{ sample.display_value }}" data-transform="{{ sample_type.sample_qnorm[sample.name] }}" name="{{ 'value:' + sample.name }}"
                                  style="text-align:right;"
                                  class="trait_value_input edit_sample_value"
                                  value="{{ sample.display_value }}"
-- 
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