replaced single quotes with double in R scripts

scripts/plotting/basic_barplots_PS.R

@@ -1,5 +1,5 @@
 getwd()
-setwd('~/git/LSHTM_analysis/scripts/plotting')
+setwd("~/git/LSHTM_analysis/scripts/plotting")
 getwd()
 
 #########################################################
@@ -22,48 +22,48 @@ getwd()
 
 #########################################################
 #%% variable assignment: input and output paths & filenames
-drug = 'pyrazinamide'
-gene = 'pncA'
-gene_match = paste0(gene,'_p.')
+drug = "pyrazinamide"
+gene = "pncA"
+gene_match = paste0(gene,"_p.")
 cat(gene_match)
 
 #=============
 # directories
 #=============
-datadir = paste0('~/git/Data')
-indir = paste0(datadir, '/', drug, '/input')
-outdir = paste0('~/git/Data', '/', drug, '/output')
+datadir = paste0("~/git/Data")
+indir = paste0(datadir, "/", drug, "/input")
+outdir = paste0("~/git/Data", "/", drug, "/output")
 
 #======
 # input
 #======
-#in_filename = 'mcsm_complex1_normalised.csv'
-in_filename_params = paste0(tolower(gene), '_all_params.csv') 
-infile_params = paste0(outdir, '/', in_filename_params)
-cat(paste0('Input file 1:', infile_params) )
+#in_filename = "mcsm_complex1_normalised.csv"
+in_filename_params = paste0(tolower(gene), "_all_params.csv") 
+infile_params = paste0(outdir, "/", in_filename_params)
+cat(paste0("Input file 1:", infile_params) )
 
 #=======
 # output
 #=======
 # plot 1
-basic_bp_duet = 'basic_barplot_PS.svg'
-plot_basic_bp_duet  =  paste0(outdir, '/plots/', basic_bp_duet)
+basic_bp_duet = "basic_barplot_PS.svg"
+plot_basic_bp_duet  =  paste0(outdir, "/plots/", basic_bp_duet)
 
 # plot 2
-pos_count_duet = 'position_count_PS.svg'
-plot_pos_count_duet = paste0(outdir, '/plots/', pos_count_duet)
+pos_count_duet = "position_count_PS.svg"
+plot_pos_count_duet = paste0(outdir, "/plots/", pos_count_duet)
 
 #%%===============================================================
 ###########################
 # Read file: struct params
 ###########################
-cat('Reading struct params including mcsm:', in_filename_params)
+cat("Reading struct params including mcsm:", in_filename_params)
     
 my_df = read.csv(infile_params
                  #, stringsAsFactors = F
                  , header = T)
 
-cat('Input dimensions:', dim(my_df)) 
+cat("Input dimensions:", dim(my_df)) 
 
 # clear variables
 rm(in_filename_params, infile_params)
@@ -74,22 +74,22 @@ str(my_df)
 
 # check for duplicate mutations
 if ( length(unique(my_df$mutationinformation)) != length(my_df$mutationinformation)){
-  cat(paste0('CAUTION:', ' Duplicate mutations identified'
-             , '\nExtracting these...'))
+  cat(paste0("CAUTION:", " Duplicate mutations identified"
+             , "\nExtracting these..."))
   dup_muts = my_df[duplicated(my_df$mutationinformation),]
   dup_muts_nu = length(unique(dup_muts$mutationinformation))
-  cat(paste0('\nDim of duplicate mutation df:', nrow(dup_muts)
-             , '\nNo. of unique duplicate mutations:', dup_muts_nu
-             , '\n\nExtracting df with unique mutations only'))
+  cat(paste0("\nDim of duplicate mutation df:", nrow(dup_muts)
+             , "\nNo. of unique duplicate mutations:", dup_muts_nu
+             , "\n\nExtracting df with unique mutations only"))
   my_df_u = my_df[!duplicated(my_df$mutationinformation),]
 }else{
-  cat(paste0('No duplicate mutations detected'))
+  cat(paste0("No duplicate mutations detected"))
   my_df_u = my_df
 }
 
 upos = unique(my_df_u$position)
-cat('Dim of clean df:'); cat(dim(my_df_u))
-cat('\nNo. of unique mutational positions:'); cat(length(upos))
+cat("Dim of clean df:"); cat(dim(my_df_u))
+cat("\nNo. of unique mutational positions:"); cat(length(upos))
   
 ########################################################################
 #               end of data extraction and cleaning for plots          #
@@ -109,9 +109,9 @@ library(ggplot2)
 #****************
 # Plot 1:Count of stabilising and destabilsing muts
 #****************
-#svg('basic_barplots_PS.svg')
+#svg("basic_barplots_PS.svg")
 svg(plot_basic_bp_duet)
-print(paste0('plot filename:', basic_bp_duet))
+print(paste0("plot filename:", basic_bp_duet))
 
 my_ats = 25 # axis text size
 my_als = 22 # axis label size
@@ -138,7 +138,7 @@ prinfFile = g + geom_bar(aes(fill = duet_outcome)
         , plot.title = element_blank()) + 
   labs(title = ""
        , y = "Number of SNPs"
-      #, fill='DUET Outcome'
+      #, fill="DUET Outcome"
       ) + 
   scale_fill_discrete(name = "DUET Outcome"
                       , labels = c("Destabilising", "Stabilising"))
@@ -178,9 +178,9 @@ foo = select(df, mutationinformation
 #write.csv(foo, "/pos_count_freq.csv")
 #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-#svg('position_count_PS.svg')
+#svg("position_count_PS.svg")
 svg(plot_pos_count_duet)
-print(paste0('plot filename:', plot_pos_count_duet))
+print(paste0("plot filename:", plot_pos_count_duet))
 
 my_ats = 25 # axis text size
 my_als = 22 # axis label size