generated subcolour bps for PS
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ed739aeb71
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3 changed files with 121 additions and 96 deletions
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@ -3,105 +3,71 @@ setwd("~/git/LSHTM_analysis/scripts/plotting")
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getwd()
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#########################################################
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# TASK:
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# TASK: output barplot by position with each bar coloured by
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# its stability value and NO coloured positions indicated
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#########################################################
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#=======================================================================
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########################################################################
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# Installing and loading required packages and functions #
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########################################################################
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############################################################
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# 1: Installing and loading required packages and functions
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#############################################################
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source("Header_TT.R")
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#source("Header_TT.R")
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library(ggplot2)
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library(data.table)
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source("barplot_colour_function.R")
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source("plotting_data.R")
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########################################################################
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# Read file: call script for combining df for PS #
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########################################################################
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#?????????????
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#
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# should return the following dfs, directories and variables
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# mut_pos_cols
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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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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("Variables imported:"
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, "\ndrug:", drug
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, "\ngene:", gene
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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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# clear excess variable
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rm(my_df, upos, dup_muts, my_df_u_lig)
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########################################################
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#%% variable assignment: input and output paths & filenames
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drug = "pyrazinamide"
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gene = "pncA"
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gene_match = paste0(gene,"_p.")
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cat(gene_match)
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#=============
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# directories
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#=============
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datadir = paste0("~/git/Data")
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indir = paste0(datadir, "/", drug, "/input")
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outdir = paste0("~/git/Data", "/", drug, "/output")
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#======
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# input
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#======
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#in_filename = "mcsm_complex1_normalised.csv"
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in_filename_params = paste0(tolower(gene), "_all_params.csv")
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infile_params = paste0(outdir, "/", in_filename_params)
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cat(paste0("Input file:", infile_params) )
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#=======
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# output
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#=======
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subcols_bp_duet = "barplot_subcols_DUET.svg"
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outPlot_subcols_bp_duet = paste0(outdir, "/plots/", subcols_bp_duet)
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print(paste0("plot will be in:", plotdir))
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bp_subcols_duet = "barplot_coloured_PS.svg"
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plot_bp_subcols_duet = paste0(plotdir, "/", bp_subcols_duet)
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#%%===============================================================
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###########################
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# Read file: struct params
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###########################
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cat("Reading struct params including mcsm:", in_filename_params)
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my_df = read.csv(infile_params
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#, stringsAsFactors = F
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, header = T)
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cat("Input dimensions:", dim(my_df))
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# clear variables
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rm(in_filename_params, infile_params)
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# quick checks
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colnames(my_df)
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str(my_df)
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# check for duplicate mutations
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if ( length(unique(my_df$mutationinformation)) != length(my_df$mutationinformation)){
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cat(paste0("CAUTION:", " Duplicate mutations identified"
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, "\nExtracting these..."))
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dup_muts = my_df[duplicated(my_df$mutationinformation),]
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dup_muts_nu = length(unique(dup_muts$mutationinformation))
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cat(paste0("\nDim of duplicate mutation df:", nrow(dup_muts)
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, "\nNo. of unique duplicate mutations:", dup_muts_nu
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, "\n\nExtracting df with unique mutations only"))
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my_df_u = my_df[!duplicated(my_df$mutationinformation),]
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}else{
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cat(paste0("No duplicate mutations detected"))
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my_df_u = my_df
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}
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upos = unique(my_df_u$position)
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cat("Dim of clean df:"); cat(dim(my_df_u))
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cat("\nNo. of unique mutational positions:"); cat(length(upos))
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########################################################################
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# end of data extraction and cleaning for plots #
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########################################################################
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#===================
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# Data for plots
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#===================
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# REASSIGNMENT as necessary
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df = my_df_u
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rm(my_df)
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# sanity checks
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str(df)
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upos = unique(df$position)
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# should be a factor
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is.factor(my_df$duet_outcome)
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#[1] TRUE
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if (is.factor(df$duet_outcome)){
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print("duet_outcome is factor")
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}else{
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print("convert duet_outcome to factor")
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df$duet_outcome = as.factor(df$duet_outcome)
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}
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is.factor(df$duet_outcome)
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table(df$duet_outcome)
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@ -167,12 +133,7 @@ my_yaxts = 15
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#******************
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# generate plot: NO axis colours
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# no ordering of x-axis
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#******************
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# plot name and location
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print(paste0("plot will be in:", outdir))
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bp_subcols_duet = "barplot_coloured_PS.svg"
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plot_bp_subcols_duet = paste0(outdir, "/plots/", bp_subcols_duet)
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print(paste0("plot name:", plot_bp_subcols_duet))
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svg(plot_bp_subcols_duet, width = 26, height = 4)
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@ -192,7 +153,8 @@ outPlot = g +
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, vjust = 0)
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, axis.title.x = element_text(size = my_xaxts)
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, axis.title.y = element_text(size = my_yaxts ) ) +
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labs(title = my_title
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labs(title = ""
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#title = my_title
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, x = "position"
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, y = "Frequency")
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@ -75,6 +75,15 @@ my_axis_colours = mut_pos_cols$lab_fg
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# now clear mut_pos_cols
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rm(mut_pos_cols)
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#=======
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# output
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#=======
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# plot name and location
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print(paste0("plot will be in:", plotdir))
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bp_aa_subcols_duet = "barplot_acoloured_PS.svg"
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plot_bp_aa_subcols_duet = paste0(plotdir, "/", bp_aa_subcols_duet)
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#=======================================================================
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#================
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# Data for plots
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@ -125,7 +134,13 @@ snp_count = sort(unique(snpsBYpos_df$snpsBYpos))
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# sanity checks
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# should be a factor
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df$duet_outcome = as.factor(df$duet_outcome)
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if (is.factor(df$duet_outcome)){
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print("duet_outcome is factor")
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}else{
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print("convert duet_outcome to factor")
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df$duet_outcome = as.factor(df$duet_outcome)
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}
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is.factor(df$duet_outcome)
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table(df$duet_outcome)
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@ -189,14 +204,6 @@ my_yats = 18
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#******************
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# generate plot: with axis colours
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#******************
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# plot name and location
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# outdir/ (should be imported from reading file)
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plotdir = paste0(outdir, "/", "plots") #should be imported from reading file
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print(paste0("plot will be in:", plotdir))
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bp_aa_subcols_duet = "barplot_acoloured_PS.svg"
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plot_bp_aa_subcols_duet = paste0(outdir, "/plots/", bp_aa_subcols_duet)
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print(paste0("plot name:", plot_bp_aa_subcols_duet))
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svg(plot_bp_aa_subcols_duet, width = 26, height = 4)
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@ -230,6 +237,7 @@ outPlot = g +
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, axis.title.y = element_text(size = my_yals )
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, axis.ticks.x = element_blank()) +
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labs(title = ""
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#title = my_title
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, x = "position"
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, y = "Frequency")
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@ -3,20 +3,75 @@
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#========
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#=======================
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#1) plotting_data.R
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plotting_data.R
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#=======================
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??? update how to run
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#=======================
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# mcsm_mean_stability.R
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mcsm_mean_stability.R
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#=======================
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??? update how to run
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# input: calls the "plotting_data.R"
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# output: <gene>_mean_stability.csv
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#======================
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# replaceBfactor_pdb.R
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replaceBfactor_pdb.R
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#=======================
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# input: 2 files; pdb file and <gene>_mean_stability.csv (output from "mcsm_mean_stability.R")
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# output: 2 pdb files with bfactors replaced with 1) mean_duet and 2) mean_affinity values
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#=======================
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basic_barplots_PS.R
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#=======================
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# input: calls the "plotting_data.R"
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output plots: 2 svgs
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1) basic_barplot_PS.svg
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2) position_count_PS.svg
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#=======================
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barplot_colour_function.R"
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#=======================
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function that generates stability coloures (red to blue) based on the
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corresponding value. It is sourced by other scripts.
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#=======================
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subcols_axis_PS.R
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# assigns colours to position numebers with bg and fg colours
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# sourced by other scripts.
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#=======================
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# input: calls the "plotting_data.R"
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# sourced by other scripts, no output perse!
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#=======================
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barplots_subcolours_aa_PS.R
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# barplot coloured by stability and position numbers coloured by active site colours
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#=======================
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# input: calls the "subcols_axis.R" and "barplot_colour_function.R"
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# output plots: 1 svg
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1) barplot_acoloured_PS.svg
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#=======================
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barplots_subcolours_PS.R
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# same as the above script expcet no positional colouring
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#=======================
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# input: calls the "plotting_data.R" and "barplot_colour_function.R"
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# output plots: 1 svg
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1) barplot_coloured_PS.svg
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########################################################################
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# ligand plots
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########################################################################
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#=======================
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basic_barplots_LIG.R
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# generates two basic barplots
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# No. of stabilsing and destabilising mutations for ligand_distance<10A
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# No. of SNPs per site
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#=======================
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# input: calls the "plotting_data.R"
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# output plots: 2 svgs
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1) basic_barplot_LIG.svg
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2) position_count_LIg.svg
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