Mapping works for rqtl and centimorgan scale

3 files changed, 38 insertions, 22 deletions

diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index a0033bd2..23d5a631 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -517,10 +517,10 @@ class MarkerRegression(object):
         ################################################################
         # Plots goes here
         ################################################################
-        if self.plotScale != 'physic' or self.multipleInterval:
-            showLocusForm =  webqtlUtil.genRandStr("fm_")
-        else:
-            showLocusForm = ""
+        #if self.plotScale != 'physic' or self.multipleInterval:
+        #    showLocusForm =  webqtlUtil.genRandStr("fm_")
+        #else:
+        showLocusForm = ""
         intCanvas = pid.PILCanvas(size=(self.graphWidth,self.graphHeight))
         gifmap = self.plotIntMapping(intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm)    
 
@@ -1789,7 +1789,8 @@ class MarkerRegression(object):
                             edgeColor=rectColor,fillColor=rectColor,edgeWidth = 0)
                     COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\
                             xLeftOffset+offsetA,yZero+40+Zorder*(LRectWidth+3)+LRectWidth)
-                    HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname)
+                    HREF="/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name+"Geno")
+                    #HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname)
                     Areas=HT.Area(shape='rect',coords=COORDS,href=HREF, title="Locus : " + Lname)
                     gifmap.areas.append(Areas)
                 ##piddle bug
@@ -1947,21 +1948,32 @@ class MarkerRegression(object):
                 #DominanceCoordXY = []
                 #for k, _locus in enumerate(_chr):
                 if 1 == 1:
-                    if self.plotScale == 'physic':
+                    Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
+                    #if self.plotScale == 'physic':
                         #Xc = startPosX + (_locus.Mb-startMb)*plotXScale
-                        Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
-                    else:
+                        #Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
+                    #else:
                         #Xc = startPosX + (_locus.cM-_chr[0].cM)*plotXScale
-                        Xc = startPosX + (qtlresult['cM']-qtlresult[0]['cM'])*plotXScale
+                        #Xc = startPosX + (qtlresult['cM']-qtlresult[0]['cM'])*plotXScale
 
                     # updated by NL 06-18-2011:
                     # fix the over limit LRS graph issue since genotype trait may give infinite LRS;
                     # for any lrs is over than 460(LRS max in this system), it will be reset to 460
-                    if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf':
-                    #if self.qtlresults[j]['lrs_value'] > 460 or self.qtlresults[j]['lrs_value']=='inf':
-                        Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSMax
+                    if self.LRS_LOD == "LRS":
+                        if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf':
+                            Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSMax
+                        else:
+                            Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSMax
                     else:
-                        Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSMax
+                        if qtlresult['lod_score'] > 100 or qtlresult['lod_score']=='inf':
+                            Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSMax
+                        else:
+                            Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRSMax
+                    #if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf':
+                    #if self.qtlresults[j]['lrs_value'] > 460 or self.qtlresults[j]['lrs_value']=='inf':
+                    #    Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSMax
+                    #else:
+                    #    Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSMax
 
                     LRSCoordXY.append((Xc, Yc))
                     #if not self.multipleInterval and self.additiveChecked:
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 721752dd..16eeb8df 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -180,7 +180,7 @@
   $("#rqtl_geno_compute").on("click", (function(_this) {
     return function() {
       var form_data, url;
-      $("#progress_bar_container").modal();
+      //$("#progress_bar_container").modal();
       url = "/marker_regression";
       $('input[name=method]').val("rqtl_geno");
       $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
@@ -189,20 +189,22 @@
       $('input[name=do_control]').val($('input[name=do_control_rqtl]:checked').val());
       form_data = $('#trait_data_form').serialize();
       console.log("form_data is:", form_data);
-      return do_ajax_post(url, form_data);
+      return submit_special(url);
+      //return do_ajax_post(url, form_data);
     };
   })(this));
 
   $("#plink_compute").on("click", (function(_this) {
     return function() {
       var form_data, url;
-      $("#static_progress_bar_container").modal();
+      //$("#static_progress_bar_container").modal();
       url = "/marker_regression";
       $('input[name=method]').val("plink");
       $('input[name=maf]').val($('input[name=maf_plink]').val());
       form_data = $('#trait_data_form').serialize();
       console.log("form_data is:", form_data);
-      return do_ajax_post(url, form_data);
+      return submit_special(url);
+      //return do_ajax_post(url, form_data);
     };
   })(this));
 
@@ -210,13 +212,14 @@
     return function() {
       var form_data, url;
       console.log("RUNNING GEMMA");
-      $("#static_progress_bar_container").modal();
+      //$("#static_progress_bar_container").modal();
       url = "/marker_regression";
       $('input[name=method]').val("gemma");
       $('input[name=maf]').val($('input[name=maf_gemma]').val());
       form_data = $('#trait_data_form').serialize();
       console.log("form_data is:", form_data);
-      return do_ajax_post(url, form_data);
+      return submit_special(url);
+      //return do_ajax_post(url, form_data);
     };
   })(this));
 
@@ -232,7 +235,7 @@
     return function() {
       var form_data, url;
       console.log("In interval mapping");
-      $("#progress_bar_container").modal();
+      //$("#progress_bar_container").modal();
       url = "/interval_mapping";
       $('input[name=method]').val("reaper");
       $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val());
@@ -240,7 +243,8 @@
       $('input[name=suggestive]').val($('input[name=suggestive_reaper]'));
       form_data = $('#trait_data_form').serialize();
       console.log("form_data is:", form_data);
-      return do_ajax_post(url, form_data);
+      return submit_special(url);
+      //return do_ajax_post(url, form_data);
     };
   })(this));
 
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index f5bec6ea..05623462 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -59,7 +59,7 @@
                                        value="{{ marker.name }}" checked="checked">
                             </td>
                             <Td align="right">{{ loop.index }}</Td>
-                            {% if score_type == "LOD" %}
+                            {% if LRS_LOD == "LOD" %}
                             <td>{{ '%0.2f' | format(marker.lod_score|float) }}</td>
                             {% else %}
                             <td>{{ '%0.2f' | format(marker.lrs_value|float) }}</td>