Just did some more work on the heatmap

4 files changed, 112 insertions, 63 deletions

diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 4069b07f..85bc7fd5 100755
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -64,66 +64,7 @@ class CorrelationMatrix(object):
     def __init__(self, start_vars):

         trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]

         

-        self.get_trait_db_obs(trait_db_list)

-        

-        #self.corr_results = {}

-        #for trait_db in self.trait_list:

-        #    this_trait = trait_db[0]

-        #    this_db = trait_db[1]

-        #    

-        #    this_db_samples = this_db.group.samplelist

-        #    this_sample_data = this_trait.data

-        #    print("this_sample_data", len(this_sample_data))

-        #    

-        #    corr_result_row = {}

-        #

-        #    for target in self.trait_list:

-        #        target_trait = target[0]

-        #        target_db = target[1]

-        #        target_samples = target_db.group.samplelist

-        #        

-        #        if this_trait == target_trait and this_db == target_db:

-        #            corr_result_row[this_trait.name] = {'sample_r': 1,

-        #                                                'sample_p': 0,

-        #                                                'num_overlap': len(target_samples),

-        #                                                'this_trait': this_trait.name,

-        #                                                'this_db': this_trait.dataset.name,

-        #                                                'target_trait': this_trait.name,

-        #                                                'target_db': this_trait.dataset.name}

-        #            continue

-        #

-        #        target_sample_data = target_trait.data

-        #        print("target_samples", len(target_samples))

-        #        

-        #        this_trait_vals = []

-        #        target_vals = []

-        #        for index, sample in enumerate(target_samples):

-        #            

-        #            if (sample in this_sample_data) and (sample in target_sample_data):

-        #                sample_value = this_sample_data[sample].value

-        #                target_sample_value = target_sample_data[sample].value

-        #                this_trait_vals.append(sample_value)

-        #                target_vals.append(target_sample_value)

-        #

-        #        #print("this_trait_vals:", this_trait_vals)

-        #        #print("target_vals:", target_vals)

-        #

-        #        this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(

-        #        this_trait_vals, target_vals)

-        #        

-        #        sample_r, sample_p = scipy.stats.pearsonr(this_trait_vals, target_vals)

-        #

-        #        corr_matrix_cell = {"sample_r": sample_r,

-        #                            "sample_p": sample_p,

-        #                            "num_overlap": num_overlap,

-        #                            "this_trait": this_trait.name,

-        #                            "this_db": this_trait.dataset.name,

-        #                            "target_trait": target_trait.name,

-        #                            "target_db": target_trait.dataset.name}

-        #        

-        #        corr_result_row[target_trait.name] = corr_matrix_cell

-        #        

-        #    self.corr_results[this_trait.name] = corr_result_row

+        helper_functions.get_trait_db_obs(trait_db_list)

 

         self.all_sample_list = []

         self.traits = []

diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 3ee33184..d9c02381 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -1,9 +1,94 @@
 from __future__ import absolute_import, print_function, division

 

-class HeatMapobject):

+import sys

+sys.path.append(".")

+

+import gc

+import string

+import cPickle

+import os

+import time

+import pp

+import math

+import collections

+import resource

+

+import scipy

+

+from pprint import pformat as pf

+

+from htmlgen import HTMLgen2 as HT

+import reaper

+

+from base import webqtlConfig

+from utility.THCell import THCell

+from utility.TDCell import TDCell

+from base.trait import GeneralTrait

+from base import data_set

+from base.templatePage import templatePage

+from utility import webqtlUtil, helper_functions, corr_result_helpers

+from dbFunction import webqtlDatabaseFunction

+import utility.webqtlUtil #this is for parallel computing only.

+from wqflask.correlation import correlation_functions

+from utility.benchmark import Bench

+

+from MySQLdb import escape_string as escape

+

+from pprint import pformat as pf

+

+from flask import Flask, g

+

+class Heatmap(object):

 

     def __init__(self, start_vars):

     

         trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]

-        helper_functions.get_trait_db_obs(trait_db_list)

-        
\ No newline at end of file
+        

+        helper_functions.get_trait_db_obs(self, trait_db_list)

+        

+        self.all_sample_list = []

+        self.traits = []

+        for trait_db in self.trait_list:

+            this_trait = trait_db[0]

+            self.traits.append(this_trait.name)

+            this_sample_data = this_trait.data

+            

+            for sample in this_sample_data:

+                if sample not in self.all_sample_list:

+                    self.all_sample_list.append(sample)

+                    

+        self.sample_data = []

+        for trait_db in self.trait_list:

+            this_trait = trait_db[0]

+            this_sample_data = this_trait.data

+            

+            #self.sample_data[this_trait.name] = []

+            this_trait_vals = []

+            for sample in self.all_sample_list:

+                if sample in this_sample_data:

+                    this_trait_vals.append(this_sample_data[sample].value)

+                    #self.sample_data[this_trait.name].append(this_sample_data[sample].value)

+                else:

+                    this_trait_vals.append('')

+                    #self.sample_data[this_trait.name].append('')

+            self.sample_data.append(this_trait_vals)

+

+        self.trait_results = {}

+        for trait_db in self.trait_list:

+            this_trait = trait_db[0]

+            this_db = trait_db[1]

+            

+            this_db_samples = this_db.group.samplelist

+            this_sample_data = this_trait.data

+            print("this_sample_data", this_sample_data)

+                this_trait_vals = []

+                for index, sample in enumerate(target_samples):

+                    

+                    if (sample in this_sample_data) and (sample in target_sample_data):

+                        sample_value = this_sample_data[sample].value

+                        target_sample_value = target_sample_data[sample].value

+                        this_trait_vals.append(sample_value)

+                        target_vals.append(target_sample_value)

+            

+            

+            
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 2f6c5188..eee22afe 100755
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -36,6 +36,18 @@
                        class="btn btn-small"
                        value="Correlation Matrix" />
             </form>
+            <form action="/heatmap" method="post">
+                {% if uc %}
+                <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
+                {% endif %}
+                <input type="hidden" name="trait_list" id="trait_list" value= "
+                {% for this_trait in trait_obs %}
+                    {{ this_trait.name }}:{{ this_trait.dataset.name }},
+                {% endfor %}" >
+                <input type="submit"
+                       class="btn btn-small"
+                       value="Heatmap" />
+            </form>
         </div>
 
 
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 47a18149..e65da914 100755
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -32,6 +32,7 @@ from base.data_set import DataSet    # Used by YAML in marker_regression
 from base.data_set import create_datasets_list
 from wqflask.show_trait import show_trait
 from wqflask.show_trait import export_trait_data
+from wqflask.heatmap import heatmap
 from wqflask.marker_regression import marker_regression
 from wqflask.interval_mapping import interval_mapping
 from wqflask.correlation import show_corr_results
@@ -352,6 +353,16 @@ def corr_matrix_page():
     
     return render_template("correlation_matrix.html", **template_vars.__dict__)
 
+@app.route("/heatmap", methods=('POST',))
+def heatmap_page():
+    print("In heatmap, request.form is:", pf(request.form))
+    template_vars = heatmap.Heatmap(request.form)
+    template_vars.js_data = json.dumps(template_vars.js_data,
+                                       default=json_default_handler,
+                                       indent="   ")
+    
+    return render_template("heatmap.html", **template_vars.__dict__)
+
 @app.route("/corr_scatter_plot")
 def corr_scatter_plot_page():
     template_vars = corr_scatter_plot.CorrScatterPlot(request.args)