starting corr plots

scripts/functions/corr_plot_data.R

@@ -1,28 +1,7 @@
 #!/usr/bin/env Rscript  
 #########################################################
 # TASK: Script to format data for Correlation plots: 
-
 # corr_data_extract()
-# INPUT:
-    # df: data with all parameters (my_use case)
-        # merged_df3 or merged_df2!?
-    # gene: [sanity check]
-    # drug: relates to a column name that will need to extracted
-    # ligand_dist_colname = LigDist_colname (variable from plotting_globals()
-   
-# colnames_to_extract = c("mutationinformation", "duet_affinity_change")
-# display_colnames_key = c(mutationinformation = "MUT" , duet_affinity_change = "DUET")
-# extract_scaled_cols = T or F, so that parameters with the _scaled suffix can be extracted.
-    # NOTE*: No formatting applied to these cols i.e display name
-
-# RETURNS: DF
-    # containing all the columns required for generating downstream correlation plots
-
-# TODO: ADD
-#lineage_count_all
-#lineage_count_unique
-#my_df['lineage_proportion']      = my_df['lineage_count_unique']/my_df['lineage_count_all']
-#my_df['dist_lineage_proportion'] = my_df['lineage_count_unique']/total_mtblineage_uc
 
 ##################################################################
 # LigDist_colname   #from globals: plotting_globals.R
@@ -31,14 +10,11 @@
 corr_data_extract <- function(df
                               , gene
                               , drug
-                              #, ligand_dist_colname = LigDist_colname
                               , colnames_to_extract
                               , colnames_display_key
                               , extract_scaled_cols = F){
   
   if ( missing(colnames_to_extract) || missing(colnames_display_key) ){
-  #if ( missing(colnames_to_extract) ){
-      
     cat("\n=========================================="
         , "\nCORR PLOTS data: ALL params"
         , "\n=========================================")

scripts/plotting/plotting_thesis/corr_plots_thesis.R

@@ -127,6 +127,7 @@ dev.off()
 #================
 # ppi2 affinity
 #================
+if (tolower(gene)%in%geneL_ppi2){
   corr_ppi2_colnames = c("mCSM-PPI2"
                          , "MAF"             
                          , "Log(OR)"       
@@ -169,6 +170,7 @@ my_corr_pairs(corr_data_all = corr_df_ppi2
                 , corr_value_size = 1)
   
   dev.off()
+}
 
 # FIXME: ADD distance
 #==================
@@ -177,6 +179,8 @@ dev.off()
 #================
 # NA affinity
 #================
+if (tolower(gene)%in%geneL_na){
+    
   corr_na_colnames = c("mCSM-NA"
                        , "MAF"             
                        , "Log(OR)"       
@@ -219,6 +223,8 @@ my_corr_pairs(corr_data_all = corr_df_na
                 , corr_value_size = 1)
   
   dev.off()
+}
+
 
 ####################################################
 # CONSERVATION
@@ -265,3 +271,6 @@ my_corr_pairs(corr_data_all = corr_df_cons
               , corr_value_size = 1)
 
 dev.off()
+
+
+#