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("Header_TT.R")
-source('barplot_colour_function.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'
+drug = "pyrazinamide"
-gene = 'pncA'
+gene = "pncA"
-gene_match = paste0(gene,'_p.')
+gene_match = paste0(gene,"_p.")
 cat(gene_match)
 
 #=============
 # directories
 #=============
-datadir = paste0('~/git/Data')
+datadir = paste0("~/git/Data")
-indir = paste0(datadir, '/', drug, '/input')
+indir = paste0(datadir, "/", drug, "/input")
-outdir = paste0('~/git/Data', '/', drug, '/output')
+outdir = paste0("~/git/Data", "/", drug, "/output")
 
 #======
 # input
 #======
-#in_filename = 'mcsm_complex1_normalised.csv'
+#in_filename = "mcsm_complex1_normalised.csv"
-in_filename_params = paste0(tolower(gene), '_all_params.csv') 
+in_filename_params = paste0(tolower(gene), "_all_params.csv") 
-infile_params = paste0(outdir, '/', in_filename_params)
+infile_params = paste0(outdir, "/", in_filename_params)
-cat(paste0('Input file:', infile_params) )
+cat(paste0("Input file:", infile_params) )
 
 #=======
 # output
 #=======
-subcols_bp_duet = 'barplot_subcols_DUET.svg'
+subcols_bp_duet = "barplot_subcols_DUET.svg"
-outPlot_subcols_bp_duet  =  paste0(outdir, '/plots/', subcols_bp_duet)
+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'
+  cat(paste0("CAUTION:", " Duplicate mutations identified"
-             , '\nExtracting these...'))
+             , "\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)
+  cat(paste0("\nDim of duplicate mutation df:", nrow(dup_muts)
-             , '\nNo. of unique duplicate mutations:', dup_muts_nu
+             , "\nNo. of unique duplicate mutations:", dup_muts_nu
-             , '\n\nExtracting df with unique mutations only'))
+             , "\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("Dim of clean df:"); cat(dim(my_df_u))
-cat('\nNo. of unique mutational positions:'); cat(length(upos))
+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

scripts/plotting/barplots_subcolours_aa_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()
 # 1: Installing and loading required packages and functions
 ############################################################
 
-#source('Header_TT.R')
+#source("Header_TT.R")
-source('barplot_colour_function.R')
+source("barplot_colour_function.R")
 
 ############################################################
 # 2: Read file: struct params data with columns containing
@@ -134,7 +134,7 @@ 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)"
 
 #========================
@@ -158,12 +158,12 @@ my_yats = 18
 #******************
 # plot name and location
 # outdir/ (should be imported from reading file)
-print(paste0('plot will be in:', outdir))
+print(paste0("plot will be in:", outdir))
 
 bp_aa_subcols_duet = "barplot_acoloured_PS.svg"
 plot_bp_aa_subcols_duet = paste0(outdir, "/plots/", bp_aa_subcols_duet)
 
-print(paste0('plot name:', plot_bp_aa_subcols_duet))
+print(paste0("plot name:", plot_bp_aa_subcols_duet))
 
 svg(plot_bp_aa_subcols_duet, width = 26, height = 4)
 
@@ -176,13 +176,13 @@ outPlot = g +
                   , clip = "off") +
   geom_bar(aes(fill = group), colour = "grey") +
   scale_fill_manual(values = colours
-                     , guide = 'none') +
+                     , guide = "none") +
   geom_tile(aes(,-0.8, width = 0.95, height = 0.85)
             , fill = df$lab_bg) +
   geom_tile(aes(,-1.2, width = 0.95, height = -0.2)
             , fill = df$lab_bg2) +
   
-# Here it's important to specify that your axis goes from 1 to max number of levels
+# Here it"s important to specify that your axis goes from 1 to max number of levels
   theme(axis.text.x = element_text(size = my_xats
                                     , angle = 90
                                     , hjust = 1

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'
+drug = "pyrazinamide"
-gene = 'pncA'
+gene = "pncA"
-gene_match = paste0(gene,'_p.')
+gene_match = paste0(gene,"_p.")
 cat(gene_match)
 
 #=============
 # directories
 #=============
-datadir = paste0('~/git/Data')
+datadir = paste0("~/git/Data")
-indir = paste0(datadir, '/', drug, '/input')
+indir = paste0(datadir, "/", drug, "/input")
-outdir = paste0('~/git/Data', '/', drug, '/output')
+outdir = paste0("~/git/Data", "/", drug, "/output")
 
 #======
 # input
 #======
-#in_filename = 'mcsm_complex1_normalised.csv'
+#in_filename = "mcsm_complex1_normalised.csv"
-in_filename_params = paste0(tolower(gene), '_all_params.csv') 
+in_filename_params = paste0(tolower(gene), "_all_params.csv") 
-infile_params = paste0(outdir, '/', in_filename_params)
+infile_params = paste0(outdir, "/", in_filename_params)
-cat(paste0('Input file 1:', infile_params) )
+cat(paste0("Input file 1:", infile_params) )
 
 #=======
 # output
 #=======
 # plot 1
-basic_bp_duet = 'basic_barplot_PS.svg'
+basic_bp_duet = "basic_barplot_PS.svg"
-plot_basic_bp_duet  =  paste0(outdir, '/plots/', basic_bp_duet)
+plot_basic_bp_duet  =  paste0(outdir, "/plots/", basic_bp_duet)
 
 # plot 2
-pos_count_duet = 'position_count_PS.svg'
+pos_count_duet = "position_count_PS.svg"
-plot_pos_count_duet = paste0(outdir, '/plots/', pos_count_duet)
+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'
+  cat(paste0("CAUTION:", " Duplicate mutations identified"
-             , '\nExtracting these...'))
+             , "\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)
+  cat(paste0("\nDim of duplicate mutation df:", nrow(dup_muts)
-             , '\nNo. of unique duplicate mutations:', dup_muts_nu
+             , "\nNo. of unique duplicate mutations:", dup_muts_nu
-             , '\n\nExtracting df with unique mutations only'))
+             , "\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("Dim of clean df:"); cat(dim(my_df_u))
-cat('\nNo. of unique mutational positions:'); cat(length(upos))
+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

scripts/plotting/mcsm_mean_stability.R

@@ -1,5 +1,5 @@
 getwd()
-setwd('~/git/LSHTM_analysis/scripts/plotting')
+setwd("~/git/LSHTM_analysis/scripts/plotting")
 getwd()
 
 #########################################################
@@ -17,25 +17,25 @@ require(dplyr)
 
 #========================================================
 #%% variable assignment: input and output paths & filenames
-drug = 'pyrazinamide'
+drug = "pyrazinamide"
-gene = 'pncA'
+gene = "pncA"
-gene_match = paste0(gene,'_p.')
+gene_match = paste0(gene,"_p.")
 cat(gene_match)
 
 #=============
 # directories
 #=============
-datadir = paste0('~/git/Data')
+datadir = paste0("~/git/Data")
-indir = paste0(datadir, '/', drug, '/input')
+indir = paste0(datadir, "/", drug, "/input")
-outdir = paste0('~/git/Data', '/', drug, '/output')
+outdir = paste0("~/git/Data", "/", drug, "/output")
 
 #======
 # input
 #======
-#in_filename = 'mcsm_complex1_normalised.csv'
+#in_filename = "mcsm_complex1_normalised.csv"
-in_filename_params = paste0(tolower(gene), '_all_params.csv') 
+in_filename_params = paste0(tolower(gene), "_all_params.csv") 
-infile_params = paste0(outdir, '/', in_filename_params)
+infile_params = paste0(outdir, "/", in_filename_params)
-cat(paste0('Input file 1:', infile_params) )
+cat(paste0("Input file 1:", infile_params) )
 
 #=======
 # output
@@ -48,13 +48,13 @@ print(paste0("Output file:", outfile_mean_stability))
 ###########################
 # 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)
@@ -65,23 +65,23 @@ str(my_df)
 
 # check for duplicate mutations
 if ( length(unique(my_df$mutationinformation)) != length(my_df$mutationinformation)){
-  cat(paste0('CAUTION:', ' Duplicate mutations identified'
+  cat(paste0("CAUTION:", " Duplicate mutations identified"
-             , '\nExtracting these...'))
+             , "\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)
+  cat(paste0("\nDim of duplicate mutation df:", nrow(dup_muts)
-             , '\nNo. of unique duplicate mutations:', dup_muts_nu
+             , "\nNo. of unique duplicate mutations:", dup_muts_nu
-             , '\n\nExtracting df with unique mutations only'))
+             , "\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 of clean df:")
 cat(dim(my_df_u))
-cat('\nNo. of unique mutational positions:'); cat(length(upos))
+cat("\nNo. of unique mutational positions:"); cat(length(upos))
 
 ########################################################################
 #               end of data extraction and cleaning for plots          #
@@ -160,4 +160,4 @@ cat("Finished writing file:\n"
     , "\nNo. of cols:", ncol(combined_df))
 
 # end of script
-#===============================================================
+#===============================================================

scripts/plotting/subcols_axis_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("Header_TT.R")
-#source('barplot_colour_function.R')
+#source("barplot_colour_function.R")
 
 ########################################################################
 #		 Read file: call script for combining df for PS			   	   #
@@ -21,25 +21,25 @@ getwd()
 #
 ########################################################
 #%% variable assignment: input and output paths & filenames
-drug = 'pyrazinamide'
+drug = "pyrazinamide"
-gene = 'pncA'
+gene = "pncA"
-gene_match = paste0(gene,'_p.')
+gene_match = paste0(gene,"_p.")
 cat(gene_match)
 
 #=============
 # directories
 #=============
-datadir = paste0('~/git/Data')
+datadir = paste0("~/git/Data")
-indir = paste0(datadir, '/', drug, '/input')
+indir = paste0(datadir, "/", drug, "/input")
-outdir = paste0('~/git/Data', '/', drug, '/output')
+outdir = paste0("~/git/Data", "/", drug, "/output")
 
 #======
 # input
 #======
-#in_filename = 'mcsm_complex1_normalised.csv'
+#in_filename = "mcsm_complex1_normalised.csv"
-in_filename_params = paste0(tolower(gene), '_all_params.csv') 
+in_filename_params = paste0(tolower(gene), "_all_params.csv") 
-infile_params = paste0(outdir, '/', in_filename_params)
+infile_params = paste0(outdir, "/", in_filename_params)
-cat(paste0('Input file:', infile_params) )
+cat(paste0("Input file:", infile_params) )
 
 #=======
 # output
@@ -50,13 +50,13 @@ cat(paste0('Input file:', infile_params) )
 ###########################
 # 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)
@@ -67,22 +67,22 @@ str(my_df)
 
 # check for duplicate mutations
 if ( length(unique(my_df$mutationinformation)) != length(my_df$mutationinformation)){
-  cat(paste0('CAUTION:', ' Duplicate mutations identified'
+  cat(paste0("CAUTION:", " Duplicate mutations identified"
-             , '\nExtracting these...'))
+             , "\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)
+  cat(paste0("\nDim of duplicate mutation df:", nrow(dup_muts)
-             , '\nNo. of unique duplicate mutations:', dup_muts_nu
+             , "\nNo. of unique duplicate mutations:", dup_muts_nu
-             , '\n\nExtracting df with unique mutations only'))
+             , "\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$position)
-cat('Dim of clean df:'); cat(dim(my_df_u))
+cat("Dim of clean df:"); cat(dim(my_df_u))
-cat('\nNo. of unique mutational positions:'); cat(length(upos))
+cat("\nNo. of unique mutational positions:"); cat(length(upos))
 #======================================================
 # create a new df with unique position numbers and cols
 position = unique(my_df$position) #130
@@ -174,7 +174,7 @@ mut_pos_cols = merge(position_cols, aa_cols_ref
             , all.x = TRUE) 
 
 head(mut_pos_cols)
-# replace NA's 
+# replace NA"s 
 # :column "lab_bg" with "white"
 # : column "lab_fg" with "black"
 mut_pos_cols$lab_bg[is.na(mut_pos_cols$lab_bg)] <- "white"