going through functions and script for interactive plots

scripts/functions/combining_dfs_plotting.R

@@ -21,7 +21,7 @@
 # 1) large combined df including NAs for AF, OR,etc
 # 		Dim: same no. of rows as gene associated meta_data_with_AFandOR
 # 2) small combined df including NAs for AF, OR, etc.
-# 		Dim: same as mcsm data
+# 		Dim: same as mcsm data or foldX
 # 3) large combined df excluding NAs 
 # 		Dim: dim(#1) - na_count_df2
 # 4) small combined df excluding NAs
@@ -31,10 +31,13 @@
 # 6) LIGAND small combined df excluding NAs
 # 		Dim: dim()
 #==========================================================
+#lig_dist_colname = 'ligand_distance' or global var LigDist_colname
+#lig_dist_cutoff  =  10 or global var LigDist_cutoff
+
 combining_dfs_plotting <- function(  my_df_u
                                    , gene_metadata
-                                   , lig_dist_colname = 'ligand_distance'
-                                   , lig_dist_cutoff = 10){
+                                   , lig_dist_colname = ''
+                                   , lig_dist_cutoff = ''){
 
   # counting NAs in AF, OR cols
   # or_mychisq

scripts/functions/plotting_data.R

@@ -16,9 +16,12 @@ library(dplyr)
   ## my_df_u_lig
   ## dup_muts
 #========================================================
+#lig_dist_colname = 'ligand_distance' or global var LigDist_colname
+#lig_dist_cutoff  =  10 or global var LigDist_cutoff
+
 plotting_data <- function(df
-                          , lig_dist_colname = 'ligand_distance'
-                          , lig_dist_cutoff = 10) {
+                          , lig_dist_colname = '' 
+                          , lig_dist_cutoff = '') {
 my_df       = data.frame()
 my_df_u     = data.frame()
 my_df_u_lig = data.frame()

scripts/functions/plotting_globals.R

@@ -23,12 +23,16 @@ import_dirs <- function(drug_name, gene_name) {
   
   dr_muts_col    <<- paste0('dr_mutations_', drug_name)
   other_muts_col <<- paste0('other_mutations_', drug_name)
-  resistance_col <<- "drtype"
   gene_match     <<- paste0(gene_name,"_p.")
   
 }
 
-# other globals
+# Other globals
+#=====================
+# Resistance colname
+#=====================
+resistance_col <<- "drtype"
+
 #===============================
 # mcsm ligand distance cut off
 #===============================
@@ -39,7 +43,6 @@ LigDist_cutoff <<- 10
 # Angstroms symbol
 #==================
 angstroms_symbol <<- "\u212b"
-#cat(paste0("There are ", nrow(my_df_u_lig), " sites lying within 10", angstroms_symbol, " of the ligand\n"))
 
 #===============
 # Delta symbol