created prominent effect calcualtions

scripts/functions/combining_dfs_plotting.R

@@ -684,6 +684,9 @@ combining_dfs_plotting <- function(  my_df_u
   #TODO
   # Choose few columns to return as plot_df
   
+  
+  
+  
   ####################################################################
   return(list(  merged_df2
                 , merged_df3

scripts/plotting/plotting_thesis/preformatting.R

@@ -15,9 +15,14 @@ source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
 outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
 ###################################################################
 # FIXME: ADD distance to NA when SP replies
-# DONE: plotting_globals.R
-dist_columns = c("ligand_distance", "interface_dist")
-DistCutOff = 10
+
+geneL_normal  = c("pnca")
+geneL_na      = c("gid", "rpob")
+geneL_ppi2    = c("alr", "embb", "katg", "rpob")
+
+# LigDist_colname # from globals used
+# ppi2Dist_colname #from globals used 
+# naDist_colname #from globals used
 
 common_cols  = c("mutationinformation"
                  , "X5uhc_position"