Made pearson/spearman options disappear if lit correlation is chosen, began to address how to deal with Trait object in CorrelationPage

6 files changed, 68 insertions, 21 deletions

diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py
index 337493ef..8240eafc 100755
--- a/wqflask/base/webqtlTrait.py
+++ b/wqflask/base/webqtlTrait.py
@@ -660,3 +660,37 @@ class webqtlTrait:
         else:
             return dict(name = self.db.fullname,
                         url = webqtlConfig.INFOPAGEHREF % self.db.name)
+        
+    def calculate_correlation(self, values, method):
+        """Calculate the correlation value and p value according to the method specified"""
+
+        #ZS: This takes the list of values of the trait our selected trait is being correlated against and removes the values of the samples our trait has no value for
+        #There's probably a better way of dealing with this, but I'll have to ask Christian
+        updated_raw_values = []
+        updated_values = []
+        for i in range(len(values)):
+            if values[i] != "None":
+                updated_raw_values.append(self.raw_values[i])
+                updated_values.append(values[i])
+
+        self.raw_values = updated_raw_values
+        values = updated_values
+
+        if method == METHOD_SAMPLE_PEARSON or method == METHOD_LIT or method == METHOD_TISSUE_PEARSON:
+            corr, nOverlap = webqtlUtil.calCorrelation(self.raw_values, values, len(values))
+        else:
+            corr, nOverlap = webqtlUtil.calCorrelationRank(self.raw_values, values, len(values))
+
+        self.correlation = corr
+        self.overlap = nOverlap
+
+        if self.overlap < 3:
+            self.p_value = 1.0
+        else:
+            #ZS - This is probably the wrong way to deal with this. Correlation values of 1.0 definitely exist (the trait correlated against itself), so zero division needs to br prevented.
+            if abs(self.correlation) >= 1.0:
+                self.p_value = 0.0
+            else:
+                ZValue = 0.5*log((1.0+self.correlation)/(1.0-self.correlation))
+                ZValue = ZValue*sqrt(self.overlap-3)
+                self.p_value = 2.0*(1.0 - reaper.normp(abs(ZValue)))        
diff --git a/wqflask/wqflask/correlation/CorrelationPage.py b/wqflask/wqflask/correlation/CorrelationPage.py
index 1f7f2553..a9db493b 100644
--- a/wqflask/wqflask/correlation/CorrelationPage.py
+++ b/wqflask/wqflask/correlation/CorrelationPage.py
@@ -72,7 +72,9 @@ class AuthException(Exception): pass
 
 
 class Trait(object):
-    def __init__(self, name, raw_values = None, lit_corr = None, tissue_corr = None, p_tissue = None):
+    
+    
+    def __init__(self, name, raw_values = None, lit_corr = None, tissue_corr = None, p_tissue = None):    
         self.name = name
         self.raw_values = raw_values
         self.lit_corr = lit_corr
@@ -260,16 +262,16 @@ def auth_user_for_db(db, cursor, target_db_name, privilege, username):
 
 class CorrelationPage(templatePage):
 
-    corrMinInformative = 4
+    corr_min_informative = 4
 
     PAGE_HEADING = "Correlation Table"
-    CORRELATION_METHODS = {"1" : "Genetic Correlation (Pearson's r)",
-                           "2" : "Genetic Correlation (Spearman's rho)",
-                           "3" : "SGO Literature Correlation",
-                           "4" : "Tissue Correlation (Pearson's r)",
-                           "5" : "Tissue Correlation (Spearman's rho)"}
-
-    RANK_ORDERS = {"1": 0, "2": 1, "3": 0, "4": 0, "5": 1}
+    #CORRELATION_METHODS = {"1" : "Genetic Correlation (Pearson's r)",
+    #                       "2" : "Genetic Correlation (Spearman's rho)",
+    #                       "3" : "SGO Literature Correlation",
+    #                       "4" : "Tissue Correlation (Pearson's r)",
+    #                       "5" : "Tissue Correlation (Spearman's rho)"}
+    #
+    #RANK_ORDERS = {"1": 0, "2": 1, "3": 0, "4": 0, "5": 1}
 
 
     def error(self, message, *args, **kw):
@@ -288,7 +290,7 @@ class CorrelationPage(templatePage):
         #print("in CorrelationPage __init__ now fd is:", pf(fd.__dict__))
         # Connect to the database
         if not self.openMysql():
-            returnt
+            return
 
         # Read the genotype from a file
         if not fd.genotype:
@@ -329,19 +331,20 @@ class CorrelationPage(templatePage):
 
         print("samplenames is:", pf(self.sample_names))
         #CF - If less than a minimum number of strains/cases in common, don't calculate anything
-        if len(self.sample_names) < self.corrMinInformative:
-            detail = ['Fewer than %d strain data were entered for %s data set. No calculation of correlation has been attempted.' % (self.corrMinInformative, fd.RISet)]
+        if len(self.sample_names) < self.corr_min_informative:
+            detail = ['Fewer than %d strain data were entered for %s data set. No calculation of correlation has been attempted.' % (self.corr_min_informative, fd.RISet)]
             self.error(heading=None, detail=detail)
         
         for key, value in self.__dict__.items():
             if key.startswith("corr"):
                 print("[red] %s - %s" % (key, value))
         
-        correlation_method = self.CORRELATION_METHODS[self.method]
-        rankOrder = self.RANK_ORDERS[self.method]
+        #correlation_method = self.CORRELATION_METHODS[self.method]
+        #rankOrder = self.RANK_ORDERS[self.method]
 
         # CF - Number of results returned
-        self.returnNumber = int(fd.criteria)
+        # Todo: Get rid of self.returnNumber
+        self.returnNumber = self.corr_return_results
 
         self.record_count = 0
 
diff --git a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee
index 5aef18e5..2952bef5 100644
--- a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee
+++ b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee
@@ -196,6 +196,10 @@ $ ->
         console.log("corr_method is:", corr_method)
         $('.correlation_desc').hide()
         $('#' + corr_method + "_r_desc").show().effect("highlight")
+        if corr_method == "lit"
+            $("#corr_sample_method_options").hide()
+        else
+            $("#corr_sample_method_options").show()
 
     $('select[name=corr_method]').change(on_corr_method_change)
     
diff --git a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js
index 05b25197..04f43822 100644
--- a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js
+++ b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js
@@ -218,7 +218,12 @@
       corr_method = $('select[name=corr_method]').val();
       console.log("corr_method is:", corr_method);
       $('.correlation_desc').hide();
-      return $('#' + corr_method + "_r_desc").show().effect("highlight");
+      $('#' + corr_method + "_r_desc").show().effect("highlight");
+      if (corr_method === "lit") {
+        return $("#corr_sample_method_options").hide();
+      } else {
+        return $("#corr_sample_method_options").show();
+      }
     };
     $('select[name=corr_method]').change(on_corr_method_change);
     console.log("before registering show_hide_outliers");
diff --git a/wqflask/wqflask/templates/trait_data_and_analysis.html b/wqflask/wqflask/templates/trait_data_and_analysis.html
index 05fd457a..16f2e2be 100644
--- a/wqflask/wqflask/templates/trait_data_and_analysis.html
+++ b/wqflask/wqflask/templates/trait_data_and_analysis.html
@@ -762,10 +762,11 @@
                                   
                                 </table>
                                 <br>
-                                Pearson <input type="radio" name="corr_sample_method" value="pearson" checked>
-                                &nbsp;&nbsp;&nbsp;
-                                Spearman Rank <input type="radio" name="corr_sample_method" value="spearman">
-                                <br>
+                                <div id="corr_sample_method_options">
+                                    Pearson <input type="radio" name="corr_sample_method" value="pearson" checked>
+                                    &nbsp;&nbsp;&nbsp;
+                                    Spearman Rank <input type="radio" name="corr_sample_method" value="spearman">
+                                </div>
                                 <br>
                                     
                                 <input type="submit" name="corr_compute" id="corr_compute" class="button" value="Compute"><br><br>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 1b60f255..0befb74a 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -90,7 +90,7 @@ def corr_compute():
     print("Have fd")
     template_vars = CorrelationPage.CorrelationPage(fd)
     print("Made it to  rendering")
-    return render_template("corr_compute.html", **template_vars.__dict__)
+    return render_template("correlation_page.html", **template_vars.__dict__)
 
 
 # Todo: Can we simplify this? -Sam