Permutations now work with rqtl

9 files changed, 49 insertions, 14 deletions

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 1524143e..539bc995 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -61,6 +61,8 @@ class MarkerRegression(object):
  

         self.mapping_method = start_vars['method']

         self.maf = start_vars['maf'] # Minor allele frequency

+        self.suggestive = ""

+        self.significant = ""

         #print("self.maf:", self.maf)

  

         self.dataset.group.get_markers()

@@ -103,6 +105,9 @@ class MarkerRegression(object):
         self.json_data['lod.hk'] = []

         self.json_data['markernames'] = []

 

+        self.json_data['suggestive'] = self.suggestive

+        self.json_data['significant'] = self.significant

+

         #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary

         self.qtl_results = []

         for qtl in self.filtered_markers:

@@ -293,24 +298,42 @@ class MarkerRegression(object):
             r_string = 'scanone(the_cross, pheno.col="the_pheno", n.perm='+self.num_perm+', addcovar=covariates, intcovar=covariates[,'+ str(len(control_markers)) +'])'

             print("r_string:", r_string)

             

-            if self.num_perm > 0:

+            if int(self.num_perm) > 0:

                 thresholds = robjects.r(r_string)

-                print("thresholds:", thresholds)

-            

+                self.suggestive, self.significant = self.process_rqtl_perm_results(results)

+                r_string = 'scanone(the_cross, pheno.col="the_pheno", addcovar=covariates, intcovar=covariates[,'+ str(len(control_markers)) +'])'

+                

             #r_string = 'scanone(the_cross, pheno.col='+pheno_as_string+', addcovar='+control_as_string+')'

             

         else:

         #r_string = 'scanone(the_cross, pheno.col='+pheno_as_string+', n.perm='+self.num_perm+')'

             r_string = 'scanone(the_cross, pheno.col="the_pheno", n.perm='+self.num_perm+')'

+            if int(self.num_perm) > 0:

+                results = robjects.r(r_string)

+                self.suggestive, self.significant = self.process_rqtl_perm_results(results)

+                r_string = 'scanone(the_cross, pheno.col="the_pheno")'

             

         print("r_string:", r_string)

         result_data_frame = robjects.r(r_string)

         #print("results:", result_data_frame)

 

         qtl_results = self.process_rqtl_results(result_data_frame)

-        

+

         return qtl_results

     

+    def process_rqtl_perm_results(self, results):

+

+        perm_vals = []

+        for line in str(results).split("\n")[1:(int(self.num_perm)+1)]:

+            print("line:", line.split())

+            perm_vals.append(float(line.split()[1]))

+        

+        self.suggestive = np.percentile(np.array(perm_vals), 67)

+        self.significant = np.percentile(np.array(perm_vals), 95)

+        

+        return self.suggestive, self.significant

+            

+    

     def process_rqtl_results(self, result):

         qtl_results = []

         

diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 51cf337c..833c3b06 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -92,7 +92,7 @@ class ShowTrait(object):
 
         #Get nearest marker for composite mapping
 
-        if self.dataset.type != "Geno":
+        if self.dataset.type != "Geno" and self.dataset.type != "Publish":
             self.nearest_marker1 = get_nearest_marker(self.this_trait, self.dataset)[0]
             self.nearest_marker2 = get_nearest_marker(self.this_trait, self.dataset)[1]
 
@@ -109,8 +109,10 @@ class ShowTrait(object):
         hddn['suggestive'] = 0
         hddn['num_perm'] = 0
         hddn['manhattan_plot'] = False
-        if self.dataset.type != "Geno":
+        if self.dataset.type != "Geno" and self.dataset.type != "Publish":
             hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2
+        else:
+            hddn['control_marker'] = ""
         hddn['maf'] = 0.01
         hddn['compare_traits'] = []
     
@@ -489,10 +491,14 @@ class ShowTrait(object):
 
                     #self.cursor.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = '%s'" % this_trait.symbol)
                     #try:
-                    this_chr, txst, txen = g.db.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = %s", (this_trait.symbol)).fetchone()
-                    if this_chr and txst and txen and this_trait.refseq_transcriptid :
-                        txst = int(txst*1000000)
-                        txen = int(txen*1000000)
+                    print("this_trait.symbol:", this_trait.symbol)
+                    result = g.db.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = %s", (this_trait.symbol)).fetchone()
+                    if result != None:
+                        this_chr, txst, txen = result[0], result[1], result[2]
+                    #this_chr, txst, txen = g.db.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = %s", (this_trait.symbol)).fetchone()
+                        if this_chr and txst and txen and this_trait.refseq_transcriptid :
+                            txst = int(txst*1000000)
+                            txen = int(txen*1000000)
                         #tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\
                         #        title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('mm9',
                         #                                                                                  this_trait.refseq_transcriptid,
diff --git a/wqflask/wqflask/static/new/javascript/create_interval_map.coffee b/wqflask/wqflask/static/new/javascript/create_interval_map.coffee
index c8e1b318..b01e2651 100644
--- a/wqflask/wqflask/static/new/javascript/create_interval_map.coffee
+++ b/wqflask/wqflask/static/new/javascript/create_interval_map.coffee
@@ -12,7 +12,7 @@ create_interval_map = () ->
                         .height(h)

                         .width(w)

                         .margin(margin)

-    

+                            

     data = js_data.json_data

     

     d3.select("div#topchart")

diff --git a/wqflask/wqflask/static/new/javascript/create_manhattan_plot.coffee b/wqflask/wqflask/static/new/javascript/create_manhattan_plot.coffee
index 0cd9e124..a4c41227 100644
--- a/wqflask/wqflask/static/new/javascript/create_manhattan_plot.coffee
+++ b/wqflask/wqflask/static/new/javascript/create_manhattan_plot.coffee
@@ -14,6 +14,7 @@ create_manhattan_plot = ->
                         .height(h)

                         .width(w)

                         .margin(margin)

+                        .ylab("LOD score")

                         .manhattanPlot(js_data.manhattan_plot)

                         

     data = js_data.json_data

diff --git a/wqflask/wqflask/static/new/javascript/create_manhattan_plot.js b/wqflask/wqflask/static/new/javascript/create_manhattan_plot.js
index d30e8e6a..c577fb93 100644
--- a/wqflask/wqflask/static/new/javascript/create_manhattan_plot.js
+++ b/wqflask/wqflask/static/new/javascript/create_manhattan_plot.js
@@ -16,7 +16,7 @@ create_manhattan_plot = function() {
   totalh = halfh * 2;
   totalw = w + margin.left + margin.right;
   console.log("js_data:", js_data);
-  mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).manhattanPlot(js_data.manhattan_plot);
+  mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).ylab("LOD score").manhattanPlot(js_data.manhattan_plot);
   data = js_data.json_data;
   d3.select("div#topchart").datum(data).call(mychart);
   chrrect = mychart.chrSelect();
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index 959f2366..d522b667 100755
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -16,6 +16,9 @@ class Lod_Chart
         @this_trait = js_data.this_trait

         @data_set = js_data.data_set

         @maf = js_data.maf #Minor allele frequency

+        

+        @suggestive = js_data.suggestive

+        @significant = js_data.significant

         
         @total_length = 0
 
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js
index 1bdc784f..a033cf0c 100755
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -24,6 +24,8 @@ Lod_Chart = (function() {
     this.this_trait = js_data.this_trait;
     this.data_set = js_data.data_set;
     this.maf = js_data.maf;
+    this.suggestive = js_data.suggestive;
+    this.significant = js_data.significant;
     this.total_length = 0;
     this.max_chr = this.get_max_chr();
     this.x_coords = [];
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
index 72d2bbe4..d25c1d3a 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -213,7 +213,7 @@ $ ->
     $("#plink_compute").click(() =>
         $("#static_progress_bar_container").modal()
         url = "/marker_regression"
-        $('input[name=method]').val("plink")
+        $('input[nsssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssegbame=method]').val("plink")
         $('input[name=mapping_display_all]').val($('input[name=display_all_plink]').val())
         $('input[name=suggestive]').val($('input[name=suggestive_plink]').val())
         $('input[name=maf]').val($('input[name=maf_plink]').val())
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 4eaceffe..d178879c 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -149,7 +149,7 @@ $(function() {
       var form_data, url;
       $("#static_progress_bar_container").modal();
       url = "/marker_regression";
-      $('input[name=method]').val("plink");
+      $('input[nsssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssegbame=method]').val("plink");
       $('input[name=mapping_display_all]').val($('input[name=display_all_plink]').val());
       $('input[name=suggestive]').val($('input[name=suggestive_plink]').val());
       $('input[name=maf]').val($('input[name=maf_plink]').val());