Update file plots.py

jass/models/plots.py

@@ -252,6 +252,9 @@ def create_qq_plot(work_file_path: str, qq_plot_path: str):
     df[['JASS_PVAL', 'UNIVARIATE_MIN_PVAL', "UNIVARIATE_MIN_QVAL"]] = replaceZeroes(
         df[['JASS_PVAL', 'UNIVARIATE_MIN_PVAL','UNIVARIATE_MIN_QVAL']])
 
+
+    dfr = read_hdf(work_file_path, "SumStatTab", where="Region==1"))
+    k= len([c for c in  dfr.columns if c[:2]=="z_"])
     pvalue = -np.log10(df.JASS_PVAL)
     pvalue_univ = -np.log10(df.UNIVARIATE_MIN_PVAL)
     qvalue_univ = -np.log10(df.UNIVARIATE_MIN_QVAL)
@@ -273,9 +276,9 @@ def create_qq_plot(work_file_path: str, qq_plot_path: str):
     pval_median_quniv = df.UNIVARIATE_MIN_QVAL.median()
 
     print("median pval")
-    print(pval_median)
-    lambda_value_jass = chi2.sf(pval_median, df=1) / chi2.sf(0.5, df=1)
-    lambda_value_jass
+
+    lambda_value_jass = chi2.sf(pval_median, df=k) / chi2.sf(0.5, df=k)
+    
     lambda_value_univ = chi2.sf(pval_median_univ, df=1) / chi2.sf(0.5, df=1)
     lambda_value_quniv = chi2.sf(pval_median_quniv, df=1) / chi2.sf(0.5, df=1)