minor tweak to plotting_globals.R to make gene_match a global var

scripts/functions/plotting_globals.R

@@ -11,8 +11,6 @@
 # output: dir names for input and output files
 
 import_dirs <- function(drug, gene) {
-  gene_match = paste0(gene,"_p.")
-  cat(gene_match)
   
   #============================
   # directories and variables
@@ -26,6 +24,7 @@ import_dirs <- function(drug, gene) {
   dr_muts_col    <<- paste0('dr_mutations_', drug)
   other_muts_col <<- paste0('other_mutations_', drug)
   resistance_col <<- "drtype"
+  gene_match     <<- paste0(gene,"_p.")
   
 }
 
@@ -58,4 +57,4 @@ mcsm_red1 <<-  "#f8766d"
 mcsm_mid <<- "white" # middle
 
 mcsm_blue1 <<- "#00bfc4"
-mcsm_blue2 <<- "#007d85" # most positive
+mcsm_blue2 <<- "#007d85" # most positive

scripts/plotting/basic_barplots.R

@@ -8,7 +8,6 @@
 setwd("~/git/LSHTM_analysis/scripts/plotting")
 getwd()
 
-
 # load libraries
 #source("Header_TT.R")
 library(ggplot2)
@@ -88,14 +87,15 @@ my_df_u_lig = pd_df[[3]]
 dup_muts    = pd_df[[4]]
 
 cat(paste0("Directories imported:"
-           , "\ndatadir:", datadir
+           , "\ndatadir:" , datadir
-           , "\nindir:", indir
+           , "\nindir:"   , indir
-           , "\noutdir:", outdir
+           , "\noutdir:"  , outdir
-           , "\nplotdir:", plotdir))
+           , "\nplotdir:" , plotdir))
 
 cat(paste0("\nVariables imported:"
-           , "\ndrug:", drug
+           , "\ndrug:"       , drug
-           , "\ngene:", gene
+           , "\ngene:"       , gene
+           , "\ngene match:" , gene_match
            , "\n"))
 #=======================================================================
 #=======