replaced single quotes with double in R scripts

scripts/plotting/barplots_subcolours_PS.R

@@ -1,5 +1,5 @@
 getwd()
-setwd('~/git/LSHTM_analysis/scripts/plotting')
+setwd("~/git/LSHTM_analysis/scripts/plotting")
 getwd()
 
 #########################################################
@@ -11,8 +11,8 @@ getwd()
 # 		Installing and loading required packages and functions		   #	
 ########################################################################
 
-source('Header_TT.R')
-source('barplot_colour_function.R')
+source("Header_TT.R")
+source("barplot_colour_function.R")
 
 ########################################################################
 #		 Read file: call script for combining df for PS			   	   #
@@ -21,43 +21,43 @@ source('barplot_colour_function.R')
 #
 ########################################################
 #%% 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:', 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:", infile_params) )
 
 #=======
 # output
 #=======
-subcols_bp_duet = 'barplot_subcols_DUET.svg'
-outPlot_subcols_bp_duet  =  paste0(outdir, '/plots/', subcols_bp_duet)
+subcols_bp_duet = "barplot_subcols_DUET.svg"
+outPlot_subcols_bp_duet  =  paste0(outdir, "/plots/", subcols_bp_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)
@@ -68,22 +68,22 @@ 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          #
@@ -154,7 +154,7 @@ df$group <- paste0(df$duet_outcome, "_", my_grp, sep = "")
 
 # Call the function to create the palette based on the group defined above
 colours <- ColourPalleteMulti(df, "duet_outcome", "my_grp")
-print(paste0('Colour palette generated for: ', length(colours), ' colours'))
+print(paste0("Colour palette generated for: ", length(colours), " colours"))
 my_title = "Protein stability (DUET)"
 
 # axis label size
@@ -170,10 +170,10 @@ my_yaxts = 15
 # no ordering of x-axis
 #******************
 # plot name and location
-print(paste0('plot will be in:', outdir))
+print(paste0("plot will be in:", outdir))
 bp_subcols_duet = "barplot_coloured_PS.svg"
 plot_bp_subcols_duet = paste0(outdir, "/plots/", bp_subcols_duet) 
-print(paste0('plot name:', plot_bp_subcols_duet))
+print(paste0("plot name:", plot_bp_subcols_duet))
 
 svg(plot_bp_subcols_duet, width = 26, height = 4)
 
@@ -181,7 +181,7 @@ g = ggplot(df, aes(factor(position, ordered = T)))
 outPlot = g + 
   geom_bar(aes(fill = group), colour = "grey") +
   scale_fill_manual( values = colours
-                     , guide = 'none') +
+                     , guide = "none") +
   theme( axis.text.x = element_text(size = my_xaxls
                                     , angle = 90
                                     , hjust = 1