separting data processing from plotting, started with basic_barplots_PS script

scripts/plotting/basic_barplots_PS.R

@@ -1,46 +1,29 @@
+#!/usr/bin/env Rscript  
+#########################################################
+# TASK: producing barplots
+# basic barplots with count of mutations
+# basic barplots with frequency of count of mutations
+#########################################################
+# working dir and loading libraries
 getwd()
 setwd("~/git/LSHTM_analysis/scripts/plotting")
 getwd()
 
-#########################################################
-# TASK:
-
-#########################################################
-
-
-########################################################################
-# 		Installing and loading required packages and functions		   #	
-########################################################################
 #source("Header_TT.R")
-#https://stackoverflow.com/questions/38851592/r-append-column-in-a-dataframe-with-frequency-count-based-on-two-columns
+library(ggplot2)
+library(data.table)
+library(dplyr)
+source("plotting_data.R")
+    # should return
+    #my_df
+    #my_df_u
+    #dup_muts
 
-########################################################################
+#========================================================
-#		 Read file: call script for combining df for PS			   	   #
+cat(paste0("Directories imported:"
-########################################################################
+           , "\ndatadir:", datadir
-#source("../combining_two_df.R")
+           , "\nindir:", indir
-#?????????????
+           , "\noutdir:", outdir))
-
-#########################################################
-#%% variable assignment: input and output paths & filenames
-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")
-
-#======
-# 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) )
 
 #=======
 # output
@@ -54,74 +37,34 @@ 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)
-    
-my_df = read.csv(infile_params
-                 #, stringsAsFactors = F
-                 , header = T)
-
-cat("Input dimensions:", dim(my_df)) 
-
-# clear variables
-rm(in_filename_params, infile_params)
-
-# quick checks
-colnames(my_df)
-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..."))
-  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"))
-  my_df_u = my_df[!duplicated(my_df$mutationinformation),]
-}else{
-  cat(paste0("No duplicate mutations detected"))
-  my_df_u = my_df
-}
-
-upos = unique(my_df_u$position)
-cat("Dim of clean df:"); cat(dim(my_df_u))
-cat("\nNo. of unique mutational positions:"); cat(length(upos))
-  
-########################################################################
-#               end of data extraction and cleaning for plots          #
-########################################################################
-
 #================
 # Data for plots
 #================
 # REASSIGNMENT as necessary
 df  = my_df_u
-rm(my_df)
+rm(my_df, upos, dup_muts)
 
 # sanity checks
 str(df)
-library(ggplot2)
 #%%=======================================================================
 #****************
 # Plot 1:Count of stabilising and destabilsing muts
 #****************
+
 #svg("basic_barplots_PS.svg")
 svg(plot_basic_bp_duet)
-print(paste0("plot filename:", basic_bp_duet))
+print(paste0("plot1 filename:", basic_bp_duet))
 
 my_ats = 25 # axis text size
 my_als = 22 # axis label size
 
 theme_set(theme_grey())
 
-# uncomment as necessary for either directly outputting results or 
+#--------------
-# printing on the screen
+# start plot 1
+#--------------
 g = ggplot(df, aes(x = duet_outcome))
-prinfFile = g + geom_bar(aes(fill = duet_outcome)
+outPlot = g + geom_bar(aes(fill = duet_outcome)
                          , show.legend = TRUE) + 
   geom_label(stat = "count"
              , aes(label = ..count..)
@@ -143,22 +86,36 @@ prinfFile = g + geom_bar(aes(fill = duet_outcome)
   scale_fill_discrete(name = "DUET Outcome"
                       , labels = c("Destabilising", "Stabilising"))
 
-print(prinfFile)
+print(outPlot)
 dev.off()
 #%%=======================================================================
 #****************
 # Plot 2: frequency of positions
 #****************
-library(data.table)
+df_ncols = ncol(df)
+df_nrows = nrow(df)
+
+cat(paste0("original df dimensions:"
+    , "\nNo. of rows:", df_nrows
+    , "\nNo. of cols:", df_ncols
+    , "\nNow adding column: frequency of mutational positions"))
+
 #setDT(df)[, .(pos_count := .N), by = .(position)] 
 setDT(df)[, pos_count := .N, by = .(position)]
 
+rm(df_nrows, df_ncols) 
+
+df_nrows = nrow(df)
+df_ncols = ncol(df)
+
+cat(paste0("revised df dimensions:"
+           , "\nNo. of rows:", df_nrows
+           , "\nNo. of cols:", df_ncols))
+
 # this is cummulative
 table(df$pos_count)
 
 # use group by on this
-library(dplyr)
-
 snpsBYpos_df <- df %>%
   group_by(position) %>%
   summarize(snpsBYpos = mean(pos_count))
@@ -178,6 +135,9 @@ foo = select(df, mutationinformation
 #write.csv(foo, "/pos_count_freq.csv")
 #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
+#--------------
+# start plot 2
+#--------------
 #svg("position_count_PS.svg")
 svg(plot_pos_count_duet)
 print(paste0("plot filename:", plot_pos_count_duet))
@@ -185,11 +145,12 @@ print(paste0("plot filename:", plot_pos_count_duet))
 my_ats = 25 # axis text size
 my_als = 22 # axis label size
 
-my_x = sort(unique(snpsBYpos_df$snpsBYpos))
+# to make x axis display all positions
-
+# not sure if to use with sort or directly
+my_x = sort(unique(snpsBYpos_df$snpsBYpos)) 
 
 g = ggplot(snpsBYpos_df, aes(x = snpsBYpos))
-prinfFile = g + geom_bar(aes (alpha = 0.5)
+outPlot_pos = g + geom_bar(aes (alpha = 0.5)
                          , show.legend = FALSE) +
   scale_x_continuous(breaks = unique(snpsBYpos_df$snpsBYpos)) +
   #scale_x_continuous(breaks = my_x) +
@@ -208,7 +169,7 @@ prinfFile = g + geom_bar(aes (alpha = 0.5)
   labs(x = "Number of SNPs"
        , y = "Number of Sites")
 
-print(prinfFile)
+print(outPlot_pos)
 dev.off()
 ########################################################################
 #               			end of DUET barplots         			   

scripts/plotting/plotting_data.R

@@ -0,0 +1,90 @@
+#!/usr/bin/env Rscript             
+#########################################################
+# TASK: formatting data that will be used for various plots
+
+# useful links
+#https://stackoverflow.com/questions/38851592/r-append-column-in-a-dataframe-with-frequency-count-based-on-two-columns
+#########################################################
+# working dir and loading libraries
+getwd()
+setwd("~/git/LSHTM_analysis/scripts/plotting")
+getwd()
+
+#source("Header_TT.R")
+require("getopt", quietly = TRUE) #cmd parse arguments
+#========================================================
+# command line args
+#spec = matrix(c(
+#  "drug"   , "d", 1, "character",
+#  "gene"   , "g", 1, "character"
+#), byrow = TRUE, ncol = 4)
+
+#opt = getopt(spec)
+
+#drug = opt$druggene = opt$gene
+
+#if(is.null(drug)|is.null(gene)) {
+#  stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
+#}
+#========================================================
+#%% variable assignment: input and output paths & filenames
+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")
+
+#======
+# 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) )
+
+#%%===============================================================
+###########################
+# Read file: struct params
+###########################
+cat("Reading struct params including mcsm:", in_filename_params)
+    
+my_df = read.csv(infile_params, header = T)
+
+cat("Input dimensions:", dim(my_df)) 
+
+# quick checks
+#colnames(my_df)
+#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..."))
+  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"))
+  my_df_u = my_df[!duplicated(my_df$mutationinformation),]
+}else{
+  cat(paste0("No duplicate mutations detected"))
+  my_df_u = my_df
+}
+
+upos = unique(my_df_u$position)
+cat("Dim of clean df:"); cat(dim(my_df_u))
+cat("\nNo. of unique mutational positions:"); cat(length(upos))
+  
+########################################################################
+#               end of data extraction and cleaning for plots          #
+########################################################################
+# clear variables
+rm(opt, spec)
+
+