added corr data to get_plotting_dfs.R and generate corr plots

scripts/plotting/corr_data.R

@@ -61,12 +61,6 @@ all_plot_dfs = combining_dfs_plotting(my_df_u
                                       , lig_dist_colname = 'ligand_distance'
                                       , lig_dist_cutoff = 10)
 
-
-
-
-
-
-
 cat(paste0("Directories imported:"
            , "\ndatadir:", datadir
            , "\nindir:", indir
@@ -110,7 +104,6 @@ df_lig = merged_df2_lig
 #======================
 # adding log cols 
 #======================
-
 df_ps$log10_or_mychisq = log10(df_ps$or_mychisq)
 df_ps$neglog_pval_fisher = -log10(df_ps$pval_fisher)
 
@@ -119,9 +112,9 @@ df_ps$neglog_pwald_kin = -log10(df_ps$pwald_kin)
 
 #df_ps$mutation_info_labels = ifelse(df_ps$mutation_info == dr_muts_col, 1, 0)
 
-#===========================
+#===============================
 # Data for Correlation plots:PS
-#===========================
+#===============================
 # subset data to generate pairwise correlations
 cols_to_select =  c("mutationinformation"
                     , "duet_scaled"
@@ -136,7 +129,7 @@ cols_to_select =  c("mutationinformation"
                     , "or_kin"
                     , "neglog_pwald_kin"
                     , "af"
-                    , "af_kin"
+                    #, "af_kin"
                     , "duet_outcome"
                     , drug)
 
@@ -176,9 +169,9 @@ offset = 1
 corr_ps_df2 = corr_data_ps[start:end]
 head(corr_ps_df2)
 
-#-----------------
+#--------------------------
 # short_df ps:  merged_df3
-#-----------------
+#--------------------------
 corr_ps_df3 = corr_ps_df2[!duplicated(corr_ps_df2$Mutation),]
 
 na_or = sum(is.na(corr_ps_df3$`Log (OR)`))
@@ -194,9 +187,9 @@ check2 = nrow(corr_ps_df3) - na_adj_or
 #}
 
 ################################################################################################
-#===========================
+#=================================
 # Data for Correlation plots: LIG
-#===========================
+#=================================
 table(df_lig$ligand_outcome)
 
 df_lig$log10_or_mychisq = log10(df_lig$or_mychisq)
@@ -258,7 +251,6 @@ offset = 1
 corr_lig_df2 = corr_data_lig[start:end]
 head(corr_lig_df2)
 
-
 #-----------------
 # short_df lig:  merged_df3_lig
 #-----------------