added first line to all func to run from

scripts/functions/aa_prop_bp.R

@@ -1,3 +1,4 @@
+#!/usr/bin/env Rscript             
 library(ggplot2)
 library(tidyverse)
 library(data.table)
@@ -18,5 +19,3 @@ aa_prop_bp <- function(plotdf
                       , name = leg_name)
   return(mp)
 }
-
-

scripts/functions/myaf_or_calcs.R

@@ -1,3 +1,7 @@
+#!/usr/bin/env Rscript             
+########################################################################
+# TASK:calculate af and or for gwas data
+########################################################################
 my_afor <- function (  drug
                      , gene
                      , infile_master

scripts/functions/mychisq_or.R

@@ -9,5 +9,4 @@ mychisq_or = function(dst_numeric, mut_numeric){
   d = tab[1,1]
   if (d==0){ d<-0.5}
   (a/b)/(c/d)
-  
+}
-}

scripts/functions/plotting_data.R

@@ -117,7 +117,6 @@ all_df = list(my_df, my_df_u, my_df_u_lig, dup_muts)
 
 return(all_df)
 }
-
 ########################################################################
 #               end of data extraction and cleaning for plots          #
 ########################################################################

scripts/functions/test_aa_prop_bp.R

@@ -1,3 +1,4 @@
+#!/usr/bin/env Rscript             
 library(ggplot2)
 library(tidyverse)
 library(data.table)

scripts/functions/test_bp.R

@@ -1,3 +1,4 @@
+#!/usr/bin/env Rscript             
 setwd("~/git/LSHTM_analysis/scripts/functions/")
 getwd()
 #############################################################

scripts/functions/test_plotting_data.R

@@ -1,3 +1,4 @@
+#!/usr/bin/env Rscript             
 getwd()
 setwd("~/git/LSHTM_analysis/scripts/functions/")
 getwd()
@@ -26,4 +27,4 @@ my_df       = pd_df[[1]]
 my_df_u     = pd_df[[2]]
 my_df_u_lig = pd_df[[3]]
 dup_muts    = pd_df[[4]]
-#===============================================================
+#===============================================================

scripts/plotting/logo_multiple_muts.R

@@ -102,8 +102,9 @@ plot_logo_multiple_muts = paste0(plotdir,"/", logo_multiple_muts)
 
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 # REASSIGNMENT
-my_df = merged_df3 
+my_df = merged_df3
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
 colnames(my_df)
 str(my_df)
 
@@ -113,7 +114,7 @@ c1 = unique(my_df$position)
 nrow(my_df) 
 
 # get freq count of positions so you can subset freq<1
-require(data.table)
+#require(data.table)
 setDT(my_df)[, mut_pos_occurrence := .N, by = .(position)] #189, 36
 
 table(my_df$position)