150 lines
4.5 KiB
R
Executable file
150 lines
4.5 KiB
R
Executable file
#!/usr/bin/env Rscript
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#########################################################
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# TASK: producing barplots
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# basic barplots with count of mutations
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# basic barplots with frequency of count of mutations
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# Depends on
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## plotting_globals.R (previously dir.R)
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## plotting_data.R
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#########################################################
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# working dir
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getwd()
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setwd("~/git/LSHTM_analysis/scripts/plotting")
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getwd()
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# load libraries
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#source("~/git/LSHTM_analysis/scripts/Header_TT.R")
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library(ggplot2)
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library(data.table)
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library(dplyr)
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require("getopt", quietly = TRUE) # cmd parse arguments
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# load functions
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source("functions/plotting_globals.R")
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source("functions/plotting_data.R")
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source("functions/stability_count_bp.R")
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source("functions/position_count_bp.R")
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#########################################################
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# command line args
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#********************
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# !!!FUTURE TODO!!!
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# Can pass additional params of output/plot dir by user.
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# Not strictly required for my workflow since it is optimised
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# to have a streamlined input/output flow without filename worries.
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#********************
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spec = matrix(c(
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"drug" ,"d", 1, "character",
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"gene" ,"g", 1, "character",
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"data" ,"f", 2, "character"
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), byrow = TRUE, ncol = 4)
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opt = getopt(spec)
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#FIXME: detect if script running from cmd, then set these
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drug = opt$drug
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gene = opt$gene
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infile = opt$data
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# hardcoding when not using cmd
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#drug = "streptomycin"
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#gene = "gid"
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if(is.null(drug)|is.null(gene)) {
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stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
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}
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#########################################################
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# call functions with relevant args
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#------------------------------------------
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# import_dirs()
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# should return the follwoing variables:
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# datadir
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# indir
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# outdir
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# plotdir
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# dr_muts_col
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# other_muts_col
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# resistance_col
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#--------------------------------------------
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import_dirs(drug, gene)
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#---------------------------------------------
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# plotting_data()
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# should return the following dfs:
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# my_df
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# my_df_u
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# my_df_u_lig
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# dup_muts
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#----------------------------------------------
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#infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
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#infile = ""
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#if (!exists("infile") && exists("gene")){
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if (!is.character(infile) && exists("gene")){
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#in_filename_params = paste0(tolower(gene), "_all_params.csv")
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in_filename_params = paste0(tolower(gene), "_comb_stab_struc_params.csv") # part combined for gid
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infile = paste0(outdir, "/", in_filename_params)
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cat("\nInput file not specified, assuming filename: ", infile, "\n")
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}
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# Get the DFs out of plotting_data()
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pd_df = plotting_data(infile)
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my_df = pd_df[[1]]
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my_df_u = pd_df[[2]]
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my_df_u_lig = pd_df[[3]]
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dup_muts = pd_df[[4]]
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#########################################################
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cat(paste0("Directories imported:"
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, "\ndatadir:", datadir
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, "\nindir:", indir
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, "\noutdir:", outdir
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, "\nplotdir:", plotdir))
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cat(paste0("\nVariables imported:"
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, "\ndrug:", drug
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, "\ngene:", gene
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, "\n"))
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#, "\ngene_match:", gene_match
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#, "\nLength of upos:", length(upos)
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#, "\nAngstrom symbol:", angstroms_symbol))
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#=======================================================================
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#=======
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# output
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#=======
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# plot 1
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basic_bp_duet = paste0(tolower(gene), "_basic_barplot_PS.svg")
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plot_basic_bp_duet = paste0(plotdir,"/", basic_bp_duet)
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# plot 2
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pos_count_duet = paste0(tolower(gene), "_position_count_PS.svg")
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plot_pos_count_duet = paste0(plotdir, "/", pos_count_duet)
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#=======================================================================
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#****************
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# Plot 1: Count of stabilising and destabilsing muts
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#****************
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svg(plot_basic_bp_duet)
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print(paste0("plot1 filename:", basic_bp_duet))
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stability_count_bp(plotdf = my_df_u
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, df_colname = "duet_outcome"
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, leg_title = "DUET outcome")
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dev.off()
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table(my_df_u$duet_outcome)
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#=======================================================================
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#****************
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# Plot 2: frequency of positions
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#****************
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svg(plot_pos_count_duet)
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print(paste0("plot filename:", plot_pos_count_duet))
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# function only
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site_snp_count_bp(plotdf = my_df_u
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, df_colname = "position")
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dev.off()
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########################################################################
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# end of PS barplots
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########################################################################
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