Merge pull request #599 from zsloan/bug/fix_mapping_recompute_issue

Bug/fix mapping recompute issue

5 files changed, 15 insertions, 11 deletions

diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 9b2c6735..d4256a46 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -139,7 +139,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
     max_D = max(data)
     min_D = min(data)
     # add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong
-    if max_D == float('inf') or max_D > webqtlConfig.MAXLRS:
+    if (max_D == float('inf') or max_D > webqtlConfig.MAXLRS) and min_D < webqtlConfig.MAXLRS:
         max_D = webqtlConfig.MAXLRS  # maximum LRS value
 
     xLow, xTop, stepX = detScale(min_D, max_D)
@@ -156,7 +156,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
         j += step
 
     for i, item in enumerate(data):
-        if item == float('inf') or item > webqtlConfig.MAXLRS:
+        if (item == float('inf') or item > webqtlConfig.MAXLRS) and min_D < webqtlConfig.MAXLRS:
             item = webqtlConfig.MAXLRS  # maximum LRS value
         j = int((item - xLow) / step)
         Count[j] += 1
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index f601201b..ebad7d36 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -220,7 +220,7 @@ class RunMapping:
         elif self.mapping_method == "rqtl_plink":
             results = self.run_rqtl_plink()
         elif self.mapping_method == "rqtl_geno":
-            perm_strata = []
+            self.perm_strata = []
             if "perm_strata" in start_vars and "categorical_vars" in start_vars:
                 self.categorical_vars = start_vars["categorical_vars"].split(
                     ",")
@@ -229,7 +229,7 @@ class RunMapping:
                                                  sample_names=self.samples,
                                                  this_trait=self.this_trait)
 
-                    perm_strata = get_perm_strata(
+                    self.perm_strata = get_perm_strata(
                         self.this_trait, primary_samples, self.categorical_vars, self.samples)
             self.score_type = "LOD"
             self.control_marker = start_vars['control_marker']
@@ -243,10 +243,10 @@ class RunMapping:
             #    self.pair_scan = True
             if self.permCheck and self.num_perm > 0:
                 self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl(
-                    self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates)
+                    self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method, self.num_perm, self.perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates)
             else:
                 results = rqtl_mapping.run_rqtl(self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method,
-                                                     self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates)
+                                                     self.num_perm, self.perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates)
         elif self.mapping_method == "reaper":
             if "startMb" in start_vars:  # ZS: Check if first time page loaded, so it can default to ON
                 if "additiveCheck" in start_vars:
@@ -765,9 +765,9 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples):
         if sample in list(sample_list.sample_attribute_values.keys()):
             combined_string = ""
             for var in categorical_vars:
-                if var.lower() in sample_list.sample_attribute_values[sample]:
+                if var in sample_list.sample_attribute_values[sample]:
                     combined_string += str(
-                        sample_list.sample_attribute_values[sample][var.lower()])
+                        sample_list.sample_attribute_values[sample][var])
                 else:
                     combined_string += "NA"
         else:
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 96f6901a..36e69fa3 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -701,7 +701,7 @@ def get_categorical_variables(this_trait, sample_list) -> list:
     if len(sample_list.attributes) > 0:
         for attribute in sample_list.attributes:
             if len(sample_list.attributes[attribute].distinct_values) < 10:
-                categorical_var_list.append(sample_list.attributes[attribute].name)
+                categorical_var_list.append(str(sample_list.attributes[attribute].id))
 
     return categorical_var_list
 
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 35d8a157..81eb1ba1 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -44,7 +44,12 @@
         {% endif %}
         <input type="hidden" name="num_perm" value="{{ nperm }}">
         <input type="hidden" name="perm_info" value="">
-        <input type="hidden" name="perm_strata" value="{{ perm_strata }}">
+        {% if categorical_vars is defined %}
+        <input type="hidden" name="categorical_vars" value="{{ categorical_vars|join(',') }}">
+        {% endif %}
+        {% if perm_strata is defined %}
+        <input type="hidden" name="perm_strata" value="True">
+        {% endif %}
         <input type="hidden" name="num_bootstrap" value="{{ nboot }}">
         <input type="hidden" name="do_control" value="{{ doControl }}">
         <input type="hidden" name="control_marker" value="{{ controlLocus }}">
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 957c34be..11a9380c 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1067,7 +1067,6 @@ def mapping_results_page():
         'num_perm',
         'permCheck',
         'perm_strata',
-        'strat_var',
         'categorical_vars',
         'perm_output',
         'num_bootstrap',