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-rw-r--r--wqflask/base/data_set.py3
-rw-r--r--wqflask/base/trait.py40
-rw-r--r--wqflask/utility/helper_functions.py5
-rw-r--r--wqflask/wqflask/collect.py5
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py2
-rw-r--r--wqflask/wqflask/correlation_matrix/show_corr_matrix.py37
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py11
-rw-r--r--wqflask/wqflask/templates/correlation_matrix.html7
-rw-r--r--wqflask/wqflask/templates/network_graph.html15
9 files changed, 95 insertions, 30 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index ca6621e9..beb2a8a2 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -277,7 +277,6 @@ class DatasetGroup(object):
"""
def __init__(self, dataset, name=None):
"""This sets self.group and self.group_id"""
- #logger.debug("DATASET NAME2:", dataset.name)
if name == None:
self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group)
else:
@@ -500,7 +499,7 @@ class DataSet(object):
self.setup()
if self.type == "Temp": #Need to supply group name as input if temp trait
- self.group = DatasetGroup(self, group_name) # sets self.group and self.group_id and gets genotype
+ self.group = DatasetGroup(self, name=group_name) # sets self.group and self.group_id and gets genotype
else:
self.check_confidentiality()
self.retrieve_other_names()
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 79aa196f..0689e950 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -6,6 +6,9 @@ import codecs
from htmlgen import HTMLgen2 as HT
+import redis
+Redis = redis.StrictRedis()
+
from base import webqtlConfig
from base.webqtlCaseData import webqtlCaseData
from base.data_set import create_dataset
@@ -35,13 +38,15 @@ class GeneralTrait(object):
def __init__(self, get_qtl_info=False, get_sample_info=True, **kw):
# xor assertion
assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name";
+ self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc.
if kw.get('dataset_name'):
- self.dataset = create_dataset(kw.get('dataset_name'))
- #print(" in GeneralTrait created dataset:", self.dataset)
+ if kw.get('dataset_name') == "Temp":
+ temp_group = self.name.split("_")[2]
+ self.dataset = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group)
+ else:
+ self.dataset = create_dataset(kw.get('dataset_name'))
else:
self.dataset = kw.get('dataset')
- self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc.
- #print("THE NAME IS:", self.name)
self.cellid = kw.get('cellid')
self.identification = kw.get('identification', 'un-named trait')
self.haveinfo = kw.get('haveinfo', False)
@@ -73,8 +78,8 @@ class GeneralTrait(object):
# So we could add a simple if statement to short-circuit this if necessary
if self.dataset.type != "Temp":
self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info)
- if get_sample_info != False:
- self = retrieve_sample_data(self, self.dataset)
+ if get_sample_info != False:
+ self = retrieve_sample_data(self, self.dataset)
def export_informative(self, include_variance=0):
"""
@@ -154,18 +159,27 @@ def retrieve_sample_data(trait, dataset, samplelist=None):
if samplelist == None:
samplelist = []
- results = dataset.retrieve_sample_data(trait.name)
+ if dataset.type == "Temp":
+ results = Redis.get(trait.name).split()
+ else:
+ results = dataset.retrieve_sample_data(trait.name)
# Todo: is this necessary? If not remove
trait.data.clear()
- all_samples_ordered = dataset.group.all_samples_ordered()
-
if results:
- for item in results:
- name, value, variance, num_cases, name2 = item
- if not samplelist or (samplelist and name in samplelist):
- trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases)
+ if dataset.type == "Temp":
+ all_samples_ordered = dataset.group.all_samples_ordered()
+ for i, item in enumerate(results):
+ try:
+ trait.data[all_samples_ordered[i]] = webqtlCaseData(all_samples_ordered[i], float(item))
+ except:
+ pass
+ else:
+ for item in results:
+ name, value, variance, num_cases, name2 = item
+ if not samplelist or (samplelist and name in samplelist):
+ trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases)
return trait
@app.route("/trait/get_sample_data")
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 1c8dad10..6980af4e 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -45,7 +45,10 @@ def get_trait_db_obs(self, trait_db_list):
data = data.strip()
assert hmac==user_manager.actual_hmac_creation(data), "Data tampering?"
trait_name, dataset_name = data.split(":")
- dataset_ob = data_set.create_dataset(dataset_name)
+ if dataset_name == "Temp":
+ dataset_ob = data_set.create_dataset(dataset_name=dataset_name, dataset_type="Temp", group_name=trait_name.split("_")[2])
+ else:
+ dataset_ob = data_set.create_dataset(dataset_name)
trait_ob = GeneralTrait(dataset=dataset_ob,
name=trait_name,
cellid=None)
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index eb0e2726..6e1ac592 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -233,7 +233,10 @@ def collections_new():
collection_id = params['existing_collection'].split(":")[0]
collection_name = params['existing_collection'].split(":")[1]
if g.user_session.logged_in:
- unprocessed_traits = Redis.get(params['hash'])
+ if "hash" in params:
+ unprocessed_traits = Redis.get(params['hash'])
+ else:
+ unprocessed_traits = params['traits']
traits = list(process_traits(unprocessed_traits))
g.user_session.add_traits_to_collection(collection_id, traits)
return redirect(url_for('view_collection', uc_id=collection_id))
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index c15c3579..0c6b8a2b 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -93,7 +93,7 @@ class CorrelationResults(object):
with Bench("Doing correlations"):
if start_vars['dataset'] == "Temp":
self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = start_vars['group'])
- self.trait_id = "Temp"
+ self.trait_id = start_vars['trait_id']
self.this_trait = GeneralTrait(dataset=self.dataset,
name=self.trait_id,
cellid=None)
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 4bb4d65d..007e8e47 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -26,6 +26,7 @@ import sys
import string
import cPickle
import os
+import datetime
import time
import pp
import math
@@ -45,6 +46,9 @@ from pprint import pformat as pf
from htmlgen import HTMLgen2 as HT
import reaper
+import redis
+Redis = redis.StrictRedis()
+
from utility.THCell import THCell
from utility.TDCell import TDCell
from base.trait import GeneralTrait
@@ -59,8 +63,10 @@ from MySQLdb import escape_string as escape
from pprint import pformat as pf
-from flask import Flask, g
+from flask import Flask, g, url_for
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
class CorrelationMatrix(object):
@@ -111,6 +117,7 @@ class CorrelationMatrix(object):
self.corr_results = []
self.pca_corr_results = []
self.trait_data_array = []
+ self.shared_samples_list = self.all_sample_list
for trait_db in self.trait_list:
this_trait = trait_db[0]
this_db = trait_db[1]
@@ -138,6 +145,8 @@ class CorrelationMatrix(object):
target_vals = []
for index, sample in enumerate(target_samples):
if (sample in this_sample_data) and (sample in target_sample_data):
+ if sample not in self.shared_samples_list:
+ self.shared_samples_list.remove(sample)
sample_value = this_sample_data[sample].value
target_sample_value = target_sample_data[sample].value
this_trait_vals.append(sample_value)
@@ -174,6 +183,7 @@ class CorrelationMatrix(object):
try:
self.pca_works = "True"
+ self.pca_trait_ids = []
pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors)
self.loadings_array = self.process_loadings()
except:
@@ -201,9 +211,6 @@ class CorrelationMatrix(object):
cellid=None)
self.trait_list.append((trait_ob, dataset_ob))
- #print("trait_list:", self.trait_list)
-
-
def calculate_pca(self, cols, corr_eigen_value, corr_eigen_vectors):
base = importr('base')
stats = importr('stats')
@@ -224,9 +231,27 @@ class CorrelationMatrix(object):
pca_traits = []
for i, vector in enumerate(trait_array_vectors):
if corr_eigen_value[i-1] < 100.0/len(self.trait_list):
- pca_traits.append(vector*-1.0)
+ pca_traits.append((vector*-1.0).tolist())
+
+ this_group_name = self.trait_list[0][1].group.name
+ temp_dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = this_group_name)
+ temp_dataset.group.get_samplelist()
+ for i, pca_trait in enumerate(pca_traits):
+ trait_id = "PCA" + str(i+1) + "_" + temp_dataset.group.species + "_" + this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S")
+ this_vals_string = ""
+ position = 0
+ for sample in temp_dataset.group.all_samples_ordered():
+ if sample in self.shared_samples_list:
+ this_vals_string += str(pca_trait[position])
+ this_vals_string += " "
+ position += 1
+ else:
+ this_vals_string += "x "
+ this_vals_string = this_vals_string[:-1]
+
+ Redis.set(trait_id, this_vals_string)
+ self.pca_trait_ids.append(trait_id)
- print("pca_traits:", pca_traits)
return pca
def process_loadings(self):
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 41d5c9d0..39e0d712 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -932,10 +932,13 @@ class DisplayMappingResults(object):
if self.this_trait.symbol:
identification += "Trait: %s - %s" % (self.this_trait.name, self.this_trait.symbol)
- elif self.this_trait.post_publication_abbreviation:
- identification += "Trait: %s - %s" % (self.this_trait.name, self.this_trait.post_publication_abbreviation)
- elif self.this_trait.pre_publication_abbreviation:
- identification += "Trait: %s - %s" % (self.this_trait.name, self.this_trait.pre_publication_abbreviation)
+ elif self.dataset.type == "Publish":
+ if self.this_trait.post_publication_abbreviation:
+ identification += "Trait: %s - %s" % (self.this_trait.name, self.this_trait.post_publication_abbreviation)
+ elif self.this_trait.pre_publication_abbreviation:
+ identification += "Trait: %s - %s" % (self.this_trait.name, self.this_trait.pre_publication_abbreviation)
+ else:
+ identification += "Trait: %s" % (self.this_trait.name)
else:
identification += "Trait: %s" % (self.this_trait.name)
identification += " with %s samples" % (self.n_samples)
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 8698b710..9c790780 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -60,6 +60,13 @@
{% if pca_works == "True" %}
<br>
<br>
+<h2>PCA Traits</h2>
+<ul>
+ {% for this_trait_id in pca_trait_ids %}
+ <li><a href="{{ url_for('show_trait_page', trait_id = pca_trait_ids[loop.index - 1], dataset = "Temp") }}">{{ pca_trait_ids[loop.index - 1] }}</a></li>
+ {% endfor %}
+</ul>
+<br>
<h2>Factor Loadings Plot</h2>
<div id="loadings_plot" style="margin-top: 20px; margin-bottom: 20px; width: 980px; border-style: solid; border-width: 1px;"></div>
<h2>Factor Loadings Table</h2>
diff --git a/wqflask/wqflask/templates/network_graph.html b/wqflask/wqflask/templates/network_graph.html
index 6bee11e7..4492dd3f 100644
--- a/wqflask/wqflask/templates/network_graph.html
+++ b/wqflask/wqflask/templates/network_graph.html
@@ -34,7 +34,11 @@
<select name="focus_select">
<option disabled selected value>Select Trait</option>
{% for trait in traits %}
+ {% if trait.symbol == None %}
+ <option value="{{ trait.name }}:{{ trait.dataset.name }}">{{ trait.name }}</option>
+ {% else %}
<option value="{{ trait.name }}:{{ trait.dataset.name }}">{{ trait.symbol }} ({{ trait.name }})</option>
+ {% endif %}
{% endfor %}
</select>
</td>
@@ -46,11 +50,18 @@
</tr>
<tr>
<td colspan="1">
+ <div style="text-align: center;">
+ <div style="float: left;"><font size="2"><b>-1</b></font></div>
+ <font size="2"><b>0</b></font>
+ <div style="float: right;"><font size="2"><b>1</b></font></div>
+ </div>
+ <!--
<font size="2"><b>-1 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1</b></font><br>
- <input type="range" id="neg_slide" min="-1" max="0" value="0" step="0.001" list="corr_range" style="display: inline; width: 45%">
- <input type="range" id="pos_slide" min="0" max="1" value="0" step="0.001" list="corr_range" style="display: inline; width: 45%">
+ -->
+ <input type="range" id="neg_slide" min="-1" max="0" value="0" step="0.001" list="corr_range" style="display: inline; width: 49%">
+ <input type="range" id="pos_slide" min="0" max="1" value="0" step="0.001" list="corr_range" style="display: inline; width: 49%">
</td>
</tr>
<tr>