added log10 OR and P values to myaf_or_calcs.R

scripts/combining_dfs.py

@@ -297,14 +297,14 @@ print('Output filename:', outfile_stab_struc
       , '\n===================================================================')
 
 # write csv
-print('Writing file: combined stability and structural parameters')
+print('\nWriting file: combined stability and structural parameters')
 combined_df_clean.to_csv(outfile_stab_struc, index = False)
 print('\nFinished writing file:'
       , '\nNo. of rows:', combined_df_clean.shape[0]
       , '\nNo. of cols:', combined_df_clean.shape[1])
 #%%=====================================================================
-print('======================================='
-      , '\nFifth merge:
+print('\n======================================='
+      , '\nFifth merge:'
       , '\ncombined_df_clean + afor_df '
       , '\n=======================================')
 
@@ -372,4 +372,4 @@ combined_stab_afor.to_csv(outfile_comb_afor, index = False)
 print('\nFinished writing file:'
       , '\nNo. of rows:', combined_stab_afor.shape[0]
       , '\nNo. of cols:', combined_stab_afor.shape[1])
-#%% end of script
+#%% end of script

scripts/functions/myaf_or_calcs.R

@@ -180,6 +180,12 @@ my_afor <- function (  drug
     ci_lower_fisher = fisher.test(table(dst, mut))$conf.int[1]
     ci_upper_fisher = fisher.test(table(dst, mut))$conf.int[2]
     
+    #--------------------
+    # adding log cols : NEW
+    #--------------------
+    log10_or_mychisq = log10(or_mychisq)
+    neglog_pval_fisher = -log10(pval_fisher)
+    
     #-------------------
     # chi sq estimates 
     #-------------------
@@ -198,9 +204,11 @@ my_afor <- function (  drug
                      , zval_logistic = zval_logistic
                      , ci_low_logistic = ci_lower_logistic
                      , ci_hi_logistic = ci_upper_logistic
-                     , or_mychisq = or_mychisq 
+                     , or_mychisq = or_mychisq
+                     , log10_or_mychisq = log10_or_mychisq # NEW
                      , or_fisher = or_fisher
                      , pval_fisher = pval_fisher
+                     , neglog_pval_fisher = neglog_pval_fisher # NEW
                      , ci_low_fisher= ci_lower_fisher
                      , ci_hi_fisher = ci_upper_fisher
                      , est_chisq = est_chisq

scripts/functions/plotting_data.R

@@ -76,6 +76,14 @@ if ( all(c1 == c2) ){
   exit()
 }
 
+#------------------------------
+# renaming foldx column from 
+# "ddg" --> "ddg_foldx"
+#------------------------------
+
+# change name to foldx
+colnames(df)[n] <- "ddg_foldx"
+
 #==================================
 # extract unique mutation entries
 #==================================

scripts/plotting/get_plotting_dfs.R

@@ -101,7 +101,7 @@ cols_to_select = c("mutationinformation", "drtype"
                    , "chain", "ligand_id", "ligand_distance"
                    , "duet_stability_change", "duet_outcome", "duet_scaled"
                    , "ligand_affinity_change", "ligand_outcome", "affinity_scaled"
-                   , "ddg", "foldx_scaled", "foldx_outcome"
+                   , "ddg_foldx", "foldx_scaled", "foldx_outcome"
                    , "deepddg", "deepddg_outcome" # comment out as not available for pnca
                    , "asa", "rsa", "rd_values", "kd_values"
                    , "af", "or_mychisq", "pval_fisher" 
@@ -375,10 +375,10 @@ cat("\n=========================================="
 df_ps = merged_df2
 
 #--------------------
-# adding log cols 
+# adding log cols : NEW UNCOMMENT
 #--------------------
-df_ps$log10_or_mychisq = log10(df_ps$or_mychisq)
-df_ps$neglog_pval_fisher = -log10(df_ps$pval_fisher)
+#df_ps$log10_or_mychisq = log10(df_ps$or_mychisq)
+#df_ps$neglog_pval_fisher = -log10(df_ps$pval_fisher)
 
 ##df_ps$log10_or_kin = log10(df_ps$or_kin)
 ##df_ps$neglog_pwald_kin = -log10(df_ps$pwald_kin)
@@ -484,10 +484,10 @@ df_lig = merged_df2_lig
 table(df_lig$ligand_outcome)
 
 #--------------------
-# adding log cols 
+# adding log cols : NEW UNCOMMENT
 #--------------------
-df_lig$log10_or_mychisq = log10(df_lig$or_mychisq)
-df_lig$neglog_pval_fisher = -log10(df_lig$pval_fisher)
+#df_lig$log10_or_mychisq = log10(df_lig$or_mychisq)
+#df_lig$neglog_pval_fisher = -log10(df_lig$pval_fisher)
 
 ##df_lig$log10_or_kin = log10(df_lig$or_kin)
 ##df_lig$neglog_pwald_kin = -log10(df_lig$pwald_kin)
@@ -583,3 +583,7 @@ identical(corr_data_ps, corr_ps_df2)
 #                           End of script
 ########################################################################
 rm(foo)
+
+cat("\n===================================================\n"
+      , "\nSuccessful: get_plotting_dfs.R worked!"
+      , "\n====================================================")