From f9b9524367c45a1b362a9e074985b58d6e8e1419 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 1 Mar 2019 16:14:08 -0600
Subject: Added alternating point colors for manhattan plots

---
 wqflask/wqflask/marker_regression/display_mapping_results.py  | 11 +++++++++--
 .../wqflask/static/new/javascript/show_trait_mapping_tools.js |  4 +++-
 2 files changed, 12 insertions(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 2d0ed1d7..bc8f8fd9 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -148,6 +148,7 @@ class DisplayMappingResults(object):
         self.this_trait = start_vars['this_trait']
         self.n_samples = len(start_vars['vals'])
         self.species = start_vars['species']
+        self.genofile_string = ""
         if 'genofile_string' in start_vars:
             self.genofile_string = start_vars['genofile_string']
 
@@ -887,7 +888,10 @@ class DisplayMappingResults(object):
 
         string1 = 'Dataset: %s' % (dataset_label)
 
-        string2 = 'Using Genotype File: %s' % self.genofile_string
+        if self.genofile_string == "":
+            string2 = 'Genotype File: %s.geno' % self.dataset.group.name
+        else:
+            string2 = 'Genotype File: %s' % self.genofile_string
 
         string4 = ''
         if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam":
@@ -1852,7 +1856,10 @@ class DisplayMappingResults(object):
                             Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRS_LOD_Max
 
                 if self.manhattan_plot == True:
-                    point_color = pid.black
+                    if self.selectedChr == -1 and (previous_chr_as_int % 2 == 1):
+                        point_color = pid.grey
+                    else:
+                        point_color = pid.black
                     canvas.drawString("5", Xc-canvas.stringWidth("5",font=symbolFont)/2+1,Yc+2,color=point_color, font=symbolFont)
                 else:
                     LRSCoordXY.append((Xc, Yc))
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 d9cf50e2..3eb34d03 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -152,7 +152,7 @@
   })(this));
 
   //ZS: This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping
-  var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
+  var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
                             'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
                             'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile', 
                             'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', 
@@ -198,6 +198,7 @@
       $('input[name=genofile]').val($('#genofile_gemma').val());
       $('input[name=maf]').val($('input[name=maf_gemma]').val());
       $('input[name=tool_used]').val("Mapping");
+      $('input[name=form_url]').val("/run_mapping");
       $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
       return submit_special(url);
     };
@@ -218,6 +219,7 @@
       $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]'));
       $('input[name=suggestive]').val($('input[name=suggestive_reaper]'));
       $('input[name=tool_used]').val("Mapping");
+      $('input[name=form_url]').val("/run_mapping");
       $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
       return submit_special(url);
     };
-- 
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