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-rw-r--r--wqflask/base/anon_collection.py22
-rw-r--r--wqflask/base/trait_collection.py53
-rw-r--r--wqflask/maintenance/quantile_normalize.py129
-rw-r--r--wqflask/utility/elasticsearch_tools.py5
-rw-r--r--wqflask/wqflask/correlation/corr_scatter_plot.py53
-rw-r--r--wqflask/wqflask/show_trait/SampleList.py77
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py4
-rw-r--r--wqflask/wqflask/static/new/css/corr_scatter_plot.css40
-rw-r--r--wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js71
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js13
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js2
-rw-r--r--wqflask/wqflask/templates/corr_scatterplot.html476
-rw-r--r--wqflask/wqflask/templates/show_trait_edit_data.html6
13 files changed, 567 insertions, 384 deletions
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 }}"
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 10:32:56 +0000