Fix issue 121 122

jass/models/plots.py

@@ -262,6 +262,7 @@ def create_quadrant_plot(work_file_path: str,
 
 def create_qq_plot(work_file_path: str, qq_plot_path: str):
     df = read_hdf(work_file_path, "SumStatTab")
+
     df[['JASS_PVAL', 'UNIVARIATE_MIN_PVAL']] = replaceZeroes(
         df[['JASS_PVAL', 'UNIVARIATE_MIN_PVAL']])
 
@@ -270,8 +271,10 @@ def create_qq_plot(work_file_path: str, qq_plot_path: str):
     x = -np.log10(np.arange(1, pvalue.shape[0] + 1) / (pvalue.shape[0] + 2))
     y = pvalue.sort_values()
     plt.scatter(x[::-1], y, s=5)
-    pval_median = np.nanmedian(y)
-    lambda_value = pval_median / np.median(x)
+    pval_median = df.JASS_PVAL.median()
+    print("median pval")
+    print(pval_median)
+    lambda_value = pval_median / 0.5
     x_1 = np.linspace(0, 6)
     y_1 = lambda_value * x_1
     x_2 = np.linspace(0, 6)

jass/models/worktable.py

@@ -865,11 +865,18 @@ def get_worktable_gencov(project_hdf_path: str):
 
     for i in range(gencov.shape[0]):
         for j in range(i, gencov.shape[0]):
-            lines.append({
-                "phenotypeID_A": sorted_trait.iloc[i],
-                "phenotypeID_B": sorted_trait.iloc[j],
-                "gencov":gencov.loc[sorted_trait.index[i], sorted_trait.index[j]]
-                })
+            if np.isnan(gencov.loc[sorted_trait.index[i], sorted_trait.index[j]]):
+                lines.append({
+                    "phenotypeID_A": sorted_trait.iloc[i],
+                    "phenotypeID_B": sorted_trait.iloc[j],
+                    "gencov":"null"
+                    })
+            else:
+                lines.append({
+                    "phenotypeID_A": sorted_trait.iloc[i],
+                    "phenotypeID_B": sorted_trait.iloc[j],
+                    "gencov":gencov.loc[sorted_trait.index[i], sorted_trait.index[j]]
+                    })
 
     print(lines)
     return lines
@@ -1062,4 +1069,4 @@ def create_genome_full_csv_lock_file(project_hdf_path):
     the_lock = "The lock is set on : workTable.csv is not yet available"
     file_lock = open(the_lock_path, "w")
     file_lock.write(the_lock)
-    file_lock.close()
\ No newline at end of file
+    file_lock.close()