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authorLei Yan2013-05-30 23:14:50 +0000
committerLei Yan2013-05-30 23:14:50 +0000
commit466be48f92d4943995c7a3e7bcb9fd1efd775bf6 (patch)
tree3afd09770d889176cf96b9be4425daddda00626d /wqflask
parentcb639316fe007c8bcad731976e8b095dee59115e (diff)
downloadgenenetwork2-466be48f92d4943995c7a3e7bcb9fd1efd775bf6.tar.gz
Rewrote some code in get_trait_info in dataset.py
Added spearman correlation to show_corr_results and template
Diffstat (limited to 'wqflask')
-rwxr-xr-xwqflask/base/data_set.py123
-rwxr-xr-xwqflask/base/trait.py4
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py36
-rw-r--r--wqflask/wqflask/templates/correlation_page.html52
4 files changed, 126 insertions, 89 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index c2380f8c..4c5c46a5 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -672,12 +672,13 @@ class MrnaAssayDataSet(DataSet):
query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(self.type,
self.type,
self.type))
- #XZ, 03/04/2009: Xiaodong changed Data to %sData and changed parameters from %(item,item, db.type,item,item) to %(db.type, item,item, db.type,item,item)
+
for item in sample_ids_step:
query += """
left join {}Data as T{} on T{}.Id = {}XRef.DataId
and T{}.StrainId={}\n
""".format(*mescape(self.type, item, item, self.type, item, item))
+
query += """
WHERE {}XRef.{}FreezeId = {}Freeze.Id
and {}Freeze.Name = '{}'
@@ -690,17 +691,19 @@ class MrnaAssayDataSet(DataSet):
trait_count = len(trait_sample_data[0])
self.trait_data = collections.defaultdict(list)
+
# put all of the separate data together into a dictionary where the keys are
# trait names and values are lists of sample values
- for j in range(trait_count):
- trait_name = trait_sample_data[0][j][0]
- for i in range(int(number_chunks)):
- self.trait_data[trait_name] += trait_sample_data[i][j][data_start_pos:]
-
+ for trait_counter in range(trait_count):
+ trait_name = trait_sample_data[0][trait_counter][0]
+ for chunk_counter in range(int(number_chunks)):
+ self.trait_data[trait_name] += (
+ trait_sample_data[chunk_counter][trait_counter][data_start_pos:])
+
def get_trait_info(self, trait_list=None, species=''):
- # Note: setting trait_list to [] is probably not a great idea.
+ # Note: setting trait_list to [] is probably not a great idea.
if not trait_list:
trait_list = []
@@ -709,9 +712,7 @@ class MrnaAssayDataSet(DataSet):
if not this_trait.haveinfo:
this_trait.retrieveInfo(QTL=1)
- if this_trait.symbol:
- pass
- else:
+ if not this_trait.symbol:
this_trait.symbol = "N/A"
#XZ, 12/08/2008: description
@@ -719,60 +720,56 @@ class MrnaAssayDataSet(DataSet):
description_string = str(this_trait.description).strip()
target_string = str(this_trait.probe_target_description).strip()
- description_display = ''
-
if len(description_string) > 1 and description_string != 'None':
description_display = description_string
else:
description_display = this_trait.symbol
- if len(description_display) > 1 and description_display != 'N/A' and len(target_string) > 1 and target_string != 'None':
+ if (len(description_display) > 1 and description_display != 'N/A' and
+ len(target_string) > 1 and target_string != 'None'):
description_display = description_display + '; ' + target_string.strip()
# Save it for the jinja2 template
this_trait.description_display = description_display
- #print(" xxxxdd [%s]: %s" % (type(this_trait.description_display), description_display))
#XZ: trait_location_value is used for sorting
trait_location_repr = 'N/A'
trait_location_value = 1000000
if this_trait.chr and this_trait.mb:
- try:
- trait_location_value = int(this_trait.chr)*1000 + this_trait.mb
- except:
- if this_trait.chr.upper() == 'X':
- trait_location_value = 20*1000 + this_trait.mb
- else:
- trait_location_value = ord(str(this_trait.chr).upper()[0])*1000 + this_trait.mb
-
- this_trait.location_repr = 'Chr %s: %.4f Mb' % (this_trait.chr, float(this_trait.mb) )
+ #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
+ #This is so we can convert the location to a number used for sorting
+ trait_location_value = self.convert_location_to_value(this_trait.chr, this_trait.mb)
+ #try:
+ # trait_location_value = int(this_trait.chr)*1000 + this_trait.mb
+ #except ValueError:
+ # if this_trait.chr.upper() == 'X':
+ # trait_location_value = 20*1000 + this_trait.mb
+ # else:
+ # trait_location_value = (ord(str(this_trait.chr).upper()[0])*1000 +
+ # this_trait.mb)
+
+ #ZS: Put this in function currently called "convert_location_to_value"
+ this_trait.location_repr = 'Chr %s: %.4f Mb' % (this_trait.chr,
+ float(this_trait.mb))
this_trait.location_value = trait_location_value
- #this_trait.trait_location_value = trait_location_value
- #XZ, 01/12/08: This SQL query is much faster.
+ #Get mean expression value
query = (
-"""select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
- where ProbeSetXRef.ProbeSetFreezeId = %s and
- ProbeSet.Id = ProbeSetXRef.ProbeSetId and
- ProbeSet.Name = '%s'
+ """select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
+ where ProbeSetXRef.ProbeSetFreezeId = %s and
+ ProbeSet.Id = ProbeSetXRef.ProbeSetId and
+ ProbeSet.Name = '%s'
""" % (escape(str(this_trait.dataset.id)),
escape(this_trait.name)))
print("query is:", pf(query))
result = g.db.execute(query).fetchone()
+
+ mean = result[0] if result else 0
- if result:
- if result[0]:
- mean = result[0]
- else:
- mean=0
- else:
- mean = 0
-
- #XZ, 06/05/2009: It is neccessary to turn on nowrap
- this_trait.mean = repr = "%2.3f" % mean
+ this_trait.mean = "%2.3f" % mean
#LRS and its location
this_trait.LRS_score_repr = 'N/A'
@@ -791,23 +788,39 @@ class MrnaAssayDataSet(DataSet):
result = self.cursor.fetchone()
if result:
- if result[0] and result[1]:
- LRS_Chr = result[0]
- LRS_Mb = result[1]
-
- #XZ: LRS_location_value is used for sorting
- try:
- LRS_location_value = int(LRS_Chr)*1000 + float(LRS_Mb)
- except:
- if LRS_Chr.upper() == 'X':
- LRS_location_value = 20*1000 + float(LRS_Mb)
- else:
- LRS_location_value = ord(str(LRS_chr).upper()[0])*1000 + float(LRS_Mb)
+ #if result[0] and result[1]:
+ # lrs_chr = result[0]
+ # lrs_mb = result[1]
+ lrs_chr, lrs_mb = result
+ #XZ: LRS_location_value is used for sorting
+ lrs_location_value = self.convert_location_to_value(lrs_chr, lrs_mb)
+
+ #try:
+ # lrs_location_value = int(lrs_chr)*1000 + float(lrs_mb)
+ #except:
+ # if lrs_chr.upper() == 'X':
+ # lrs_location_value = 20*1000 + float(lrs_mb)
+ # else:
+ # lrs_location_value = (ord(str(LRS_chr).upper()[0])*1000 +
+ # float(lrs_mb))
+
+ this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs
+ this_trait.LRS_score_value = this_trait.lrs
+ this_trait.LRS_location_repr = 'Chr %s: %.4f Mb' % (lrs_chr, float(lrs_mb))
+
+
+ def convert_location_to_value(chromosome, mb):
+ try:
+ location_value = int(chromosome)*1000 + float(mb)
+ except ValueError:
+ if chromosome.upper() == 'X':
+ location_value = 20*1000 + float(mb)
+ else:
+ location_value = (ord(str(chromosome).upper()[0])*1000 +
+ float(mb))
+
+ return location_value
- this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
- this_trait.LRS_score_value = LRS_score_value = this_trait.lrs
- this_trait.LRS_location_repr = LRS_location_repr = 'Chr %s: %.4f Mb' % (LRS_Chr, float(LRS_Mb) )
-
def get_sequence(self):
query = """
SELECT
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 7c1c035c..5fde114f 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -15,7 +15,7 @@ from pprint import pformat as pf
from flask import Flask, g
-class GeneralTrait:
+class GeneralTrait(object):
"""
Trait class defines a trait in webqtl, can be either Microarray,
Published phenotype, genotype, or user input trait
@@ -78,7 +78,7 @@ class GeneralTrait:
#desc = self.handle_pca(desc)
stringy = desc
return stringy
-
+
def display_name(self):
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index aa20eba1..5d40c835 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -30,7 +30,6 @@
from __future__ import absolute_import, print_function, division
import string
-from math import *
import cPickle
import os
import time
@@ -106,6 +105,7 @@ class CorrelationResults(object):
corr_samples_group = start_vars['corr_samples_group']
self.sample_data = {}
+ self.corr_method = start_vars['corr_sample_method']
#The two if statements below append samples to the sample list based upon whether the user
#rselected Primary Samples Only, Other Samples Only, or All Samples
@@ -123,27 +123,31 @@ class CorrelationResults(object):
#if statement if the user selected All Samples)
if corr_samples_group != 'samples_primary':
self.process_samples(start_vars, self.this_trait.data.keys(), primary_samples)
+
self.target_dataset = data_set.create_dataset(start_vars['corr_dataset'])
self.target_dataset.get_trait_data()
+
self.correlation_data = {}
for trait, values in self.target_dataset.trait_data.iteritems():
- trait_values = []
+ this_trait_values = []
target_values = []
for index, sample in enumerate(self.target_dataset.samplelist):
- target_value = values[index]
- if sample in self.sample_data.keys():
- this_value = self.sample_data[sample]
- trait_values.append(this_value)
- target_values.append(target_value)
- (trait_values, target_values) = normalize_values(trait_values, target_values)
- correlation = scipy.stats.pearsonr(trait_values, target_values)
- #correlation = cal_correlation(trait_values, target_values)
- self.correlation_data[trait] = correlation[0]
- #print ('correlation result: %s %s' % (trait, correlation))
-
- for trait in self.correlation_data:
- print("correlation: ", self.correlation_data[trait])
-
+ if sample in self.sample_data:
+ sample_value = self.sample_data[sample]
+ target_sample_value = values[index]
+ this_trait_values.append(sample_value)
+ target_values.append(target_sample_value)
+
+ this_trait_values, target_values = normalize_values(this_trait_values, target_values)
+ if self.corr_method == 'pearson':
+ sample_r, sample_p = scipy.stats.pearsonr(this_trait_values, target_values)
+ else:
+ sample_r, sample_p = scipy.stats.spearmanr(this_trait_values, target_values)
+ self.correlation_data[trait] = [sample_r, sample_p]
+ self.correlation_data = collections.OrderedDict(
+ sorted(self.correlation_data.items(),
+ key=lambda t: -abs(t[1][0])))
+
#XZ, 09/18/2008: get all information about the user selected database.
#target_db_name = fd.corr_dataset
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index be750a0c..68fe81ed 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -1,21 +1,42 @@
{% extends "base.html" %}
-{% block content %}
-<table id="corr_results" class="table table-hover table-striped table-bordered">
- <thead>
- <tr>
- <td>Correlation</td>
- </tr>
- </thead>
- <tbody>
- {% for trait in correlation_data %}
- <tr>
- <td>{{ correlation_data[trait] }}</td>
- </tr>
- {% endfor %}
- </tbody>
-</table>
+{% block css %}
+ <link rel="stylesheet" type="text/css" href="/static/packages/jqplot/jquery.jqplot.min.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" />
{% endblock %}
+{% block content %}
+ <header class="jumbotron subhead" id="overview">
+ <div class="container">
+ <h1>Correlation</h1>
+ </div>
+ </header>
+
+ <table id="corr_results" class="table table-hover table-striped table-bordered">
+ <thead>
+ <tr>
+ <th>Trait</th>
+ {% if corr_method == 'pearson' %}
+ <th>Sample r</th>
+ <th>Sample p(r)</th>
+ {% else %}
+ <th>Sample rho</th>
+ <th>Sample p(rho)</th>
+ {% endif %}
+ </tr>
+ </thead>
+ <tbody>
+ {% for trait in correlation_data %}
+ <tr>
+ <td>{{ trait }}</td>
+ <td>{{ correlation_data[trait][0] }}</td>
+ <td>{{ correlation_data[trait][1] }}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+{% endblock %}
{% block js %}
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
@@ -23,7 +44,6 @@
<script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
<script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
-
<script type="text/javascript" charset="utf-8">
$(document).ready( function () {
console.time("Creating table");