added replace b factor scripts for lig affinity and ppi2
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2 changed files with 558 additions and 0 deletions
281
scripts/plotting/replaceBfactor_pdb_affinity.R
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281
scripts/plotting/replaceBfactor_pdb_affinity.R
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#!/usr/bin/env Rscript
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#########################################################
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# TASK: Replace B-factors in the pdb file with the mean
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# normalised stability values.
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# read pdb file
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# read mcsm mean stability value files
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# extract the respective mean values and assign to the
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# b-factor column within their respective pdbs
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# generate some distribution plots for inspection
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#########################################################
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# working dir and loading libraries
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getwd()
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setwd("~/git/LSHTM_analysis/scripts/plotting")
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cat(c(getwd(),"\n"))
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#source("~/git/LSHTM_analysis/scripts/Header_TT.R")
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library(bio3d)
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require("getopt", quietly = TRUE) # cmd parse arguments
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#========================================================
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#drug = "pyrazinamide"
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#gene = "pncA"
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# command line args
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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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), byrow = TRUE, ncol = 4)
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opt = getopt(spec)
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drug = opt$drug
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gene = opt$gene
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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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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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#outdir_plots = paste0("~/git/Data", "/", drug, "/output/plots")
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outdir_plots = paste0("~/git/Writing/thesis/images/results/", tolower(gene))
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#======
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# input
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#======
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in_filename_pdb = paste0(tolower(gene), "_complex.pdb")
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infile_pdb = paste0(indir, "/", in_filename_pdb)
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cat(paste0("Input file:", infile_pdb) )
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#in_filename_mean_stability = paste0(tolower(gene), "_mean_stability.csv")
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#infile_mean_stability = paste0(outdir, "/", in_filename_mean_stability)
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in_filename_mean_affinity = paste0(tolower(gene), "_mean_ligand.csv")
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infile_mean_affinity = paste0(outdir_plots, "/", in_filename_mean_affinity)
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cat(paste0("Input file:", infile_mean_affinity) )
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#=======
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# output
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#=======
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#out_filename_duet_mspdb = paste0(tolower(gene), "_complex_bduet_ms.pdb")
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out_filename_lig_mspdb = paste0(tolower(gene), "_complex_b_lig_ms.pdb")
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outfile_lig_mspdb = paste0(outdir_plots, "/", out_filename_lig_mspdb)
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print(paste0("Output file:", outfile_lig_mspdb))
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#%%===============================================================
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#NOTE: duet here refers to the ensemble stability values
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###########################
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# Read file: average stability values
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# or mcsm_normalised file
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###########################
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my_df <- read.csv(infile_mean_stability, header = T)
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str(my_df)
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#############
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# Read pdb
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#############
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# list of 8
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my_pdb = read.pdb(infile_pdb
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, maxlines = -1
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, multi = FALSE
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, rm.insert = FALSE
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, rm.alt = TRUE
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, ATOM.only = FALSE
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, hex = FALSE
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, verbose = TRUE)
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rm(in_filename_mean_affinity, in_filename_pdb)
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# assign separately for duet and ligand
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my_pdb_duet = my_pdb
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#=========================================================
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# Replacing B factor with mean stability scores
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# within the respective dfs
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#==========================================================
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# extract atom list into a variable
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# since in the list this corresponds to data frame, variable will be a df
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#df_duet = my_pdb_duet[[1]]
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df_duet= my_pdb_duet[['atom']]
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# make a copy: required for downstream sanity checks
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d2_duet = df_duet
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# sanity checks: B factor
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max(df_duet$b); min(df_duet$b)
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#==================================================
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# histograms and density plots for inspection
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# 1: original B-factors
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# 2: original mean stability values
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# 3: replaced B-factors with mean stability values
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#==================================================
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# Set the margin on all sides
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par(oma = c(3,2,3,0)
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, mar = c(1,3,5,2)
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#, mfrow = c(3,2)
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#, mfrow = c(3,4))
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, mfrow = c(3,2))
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#=============
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# Row 1 plots: original B-factors
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# duet and affinity
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#=============
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hist(df_duet$b
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, xlab = ""
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, main = "Bfactor affinity")
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plot(density(df_duet$b)
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, xlab = ""
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, main = "Bfactor affinity")
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#=============
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# Row 2 plots: original mean stability values
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# duet and affinity
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#=============
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#hist(my_df$averaged_duet
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hist(my_df$avg_lig_scaled
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, xlab = ""
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, main = "mean affinity values")
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#plot(density(my_df$averaged_duet)
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plot(density(my_df$avg_lig_scaled)
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, xlab = ""
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, main = "mean affinity values")
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#==============
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# Row 3 plots: replaced B-factors with mean stability values
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# After actual replacement in the b factor column
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#===============
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################################################################
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#=========
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# step 0_P1: DONT RUN once you have double checked the matched output
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#=========
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# sanity check: match and assign to a separate column to double check
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# colnames(my_df)
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# df_duet$duet_scaled = my_df$averge_duet_scaled[match(df_duet$resno, my_df$position)]
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#=========
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# step 1_P1
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#=========
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# Be brave and replace in place now (don"t run sanity check)
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# this makes all the B-factor values in the non-matched positions as NA
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#df_duet$b = my_df$averaged_duet_scaled[match(df_duet$resno, my_df$position)]
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df_duet$b = my_df$avg_lig_scaled[match(df_duet$resno, my_df$position)]
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#=========
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# step 2_P1
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#=========
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# count NA in Bfactor
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b_na_duet = sum(is.na(df_duet$b)) ; b_na_duet
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# count number of 0"s in Bactor
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sum(df_duet$b == 0)
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# replace all NA in b factor with 0
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na_rep = 2
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df_duet$b[is.na(df_duet$b)] = na_rep
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# # sanity check: should be 0 and True
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# # duet and lig
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# if ( (sum(df_duet$b == na_rep) == b_na_duet) && (sum(df_lig$b == na_rep) == b_na_lig) ) {
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# print ("PASS: NA's replaced with 0s successfully in df_duet and df_lig")
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# } else {
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# print("FAIL: NA replacement in df_duet NOT successful")
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# quit()
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# }
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#
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# max(df_duet$b); min(df_duet$b)
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#
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# # sanity checks: should be True
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# if( (max(df_duet$b) == max(my_df$avg_ens_stability_scaled)) & (min(df_duet$b) == min(my_df$avg_ens_stability_scaled)) ){
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# print("PASS: B-factors replaced correctly in df_duet")
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# } else {
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# print ("FAIL: To replace B-factors in df_duet")
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# quit()
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# }
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# if( (max(df_lig$b) == max(my_df$avg_ens_affinity_scaled)) & (min(df_lig$b) == min(my_df$avg_ens_affinity_scaled)) ){
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# print("PASS: B-factors replaced correctly in df_lig")
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# } else {
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# print ("FAIL: To replace B-factors in df_lig")
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# quit()
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# }
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#=========
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# step 3_P1
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#=========
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# sanity check: dim should be same before reassignment
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if ( (dim(df_duet)[1] == dim(d2_duet)[1]) &
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(dim(df_duet)[2] == dim(d2_duet)[2])
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){
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print("PASS: Dims of both dfs as expected")
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} else {
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print ("FAIL: Dims mismatch")
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quit()}
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#=========
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# step 4_P1:
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# VERY important
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#=========
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# assign it back to the pdb file
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my_pdb_duet[['atom']] = df_duet
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max(df_duet$b); min(df_duet$b)
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table(df_duet$b)
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sum(is.na(df_duet$b))
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#=========
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# step 5_P1
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#=========
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cat(paste0("output file duet mean stability pdb:"
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, outfile_lig_mspdb))
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write.pdb(my_pdb_duet, outfile_lig_mspdb)
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#============================
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# Add the 3rd histogram and density plots for comparisons
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#============================
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# Plots continued...
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# Row 3 plots: hist and density of replaced B-factors with stability values
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hist(df_duet$b
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, xlab = ""
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, main = "repalcedB duet")
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plot(density(df_duet$b)
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, xlab = ""
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, main = "replacedB duet")
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# graph titles
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mtext(text = "Frequency"
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, side = 2
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, line = 0
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, outer = TRUE)
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mtext(text = paste0(tolower(gene), ": afinity distribution")
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, side = 3
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, line = 0
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, outer = TRUE)
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#============================================
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#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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# NOTE: This replaced B-factor distribution has the same
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# x-axis as the PredAff normalised values, but the distribution
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# is affected since 0 is overinflated/or hs an additional blip because
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# of the positions not associated with resistance. This is because all the positions
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# where there are no SNPs have been assigned 0???
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#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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277
scripts/plotting/replaceBfactor_pdb_ppi2.R
Normal file
277
scripts/plotting/replaceBfactor_pdb_ppi2.R
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@ -0,0 +1,277 @@
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#!/usr/bin/env Rscript
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#########################################################
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# TASK: Replace B-factors in the pdb file with the mean
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# normalised stability values.
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# read pdb file
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# read mcsm mean stability value files
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# extract the respective mean values and assign to the
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# b-factor column within their respective pdbs
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# generate some distribution plots for inspection
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#########################################################
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# working dir and loading libraries
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getwd()
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setwd("~/git/LSHTM_analysis/scripts/plotting")
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cat(c(getwd(),"\n"))
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#source("~/git/LSHTM_analysis/scripts/Header_TT.R")
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library(bio3d)
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require("getopt", quietly = TRUE) # cmd parse arguments
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#========================================================
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#drug = "pyrazinamide"
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#gene = "pncA"
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# command line args
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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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), byrow = TRUE, ncol = 4)
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opt = getopt(spec)
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drug = opt$drug
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gene = opt$gene
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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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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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#outdir_plots = paste0("~/git/Data", "/", drug, "/output/plots")
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outdir_plots = paste0("~/git/Writing/thesis/images/results/", tolower(gene))
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#======
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# input
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#======
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in_filename_pdb = paste0(tolower(gene), "_complex.pdb")
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infile_pdb = paste0(indir, "/", in_filename_pdb)
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cat(paste0("Input file:", infile_pdb) )
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# mean ppi2
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in_filename_mean_ppi2 = paste0(tolower(gene), "_mean_ppi2.csv")
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infile_mean_ppi2 = paste0(outdir_plots, "/", in_filename_mean_ppi2)
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cat(paste0("Input file:", infile_mean_ppi2) )
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#=======
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# output
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#=======
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#out_filename_duet_mspdb = paste0(tolower(gene), "_complex_bduet_ms.pdb")
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out_filename_ppi2_mspdb = paste0(tolower(gene), "_complex_b_ppi2_ms.pdb")
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outfile_ppi2_mspdb = paste0(outdir_plots, "/", out_filename_ppi2_mspdb)
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print(paste0("Output file:", outfile_ppi2_mspdb))
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#%%===============================================================
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#NOTE: duet here refers to the ensemble stability values
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###########################
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# Read file: average stability values
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# or mcsm_normalised file
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###########################
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my_df <- read.csv(infile_mean_ppi2, header = T)
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str(my_df)
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#############
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# Read pdb
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#############
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# list of 8
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my_pdb = read.pdb(infile_pdb
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, maxlines = -1
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, multi = FALSE
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, rm.insert = FALSE
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, rm.alt = TRUE
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, ATOM.only = FALSE
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, hex = FALSE
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, verbose = TRUE)
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# assign separately for duet and ligand
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||||||
|
my_pdb_duet = my_pdb
|
||||||
|
|
||||||
|
#=========================================================
|
||||||
|
# Replacing B factor with mean stability scores
|
||||||
|
# within the respective dfs
|
||||||
|
#==========================================================
|
||||||
|
# extract atom list into a variable
|
||||||
|
# since in the list this corresponds to data frame, variable will be a df
|
||||||
|
#df_duet = my_pdb_duet[[1]]
|
||||||
|
df_duet= my_pdb_duet[['atom']]
|
||||||
|
|
||||||
|
# make a copy: required for downstream sanity checks
|
||||||
|
d2_duet = df_duet
|
||||||
|
|
||||||
|
# sanity checks: B factor
|
||||||
|
max(df_duet$b); min(df_duet$b)
|
||||||
|
|
||||||
|
#==================================================
|
||||||
|
# histograms and density plots for inspection
|
||||||
|
# 1: original B-factors
|
||||||
|
# 2: original mean stability values
|
||||||
|
# 3: replaced B-factors with mean stability values
|
||||||
|
#==================================================
|
||||||
|
# Set the margin on all sides
|
||||||
|
par(oma = c(3,2,3,0)
|
||||||
|
, mar = c(1,3,5,2)
|
||||||
|
#, mfrow = c(3,2)
|
||||||
|
#, mfrow = c(3,4))
|
||||||
|
, mfrow = c(3,2))
|
||||||
|
|
||||||
|
#=============
|
||||||
|
# Row 1 plots: original B-factors
|
||||||
|
# duet and affinity
|
||||||
|
#=============
|
||||||
|
hist(df_duet$b
|
||||||
|
, xlab = ""
|
||||||
|
, main = "Bfactor ppi2")
|
||||||
|
|
||||||
|
plot(density(df_duet$b)
|
||||||
|
, xlab = ""
|
||||||
|
, main = "Bfactor ppi2")
|
||||||
|
|
||||||
|
#=============
|
||||||
|
# Row 2 plots: original mean stability values
|
||||||
|
# duet and affinity
|
||||||
|
#=============
|
||||||
|
|
||||||
|
#hist(my_df$averaged_duet
|
||||||
|
hist(my_df$avg_ppi2_scaled
|
||||||
|
, xlab = ""
|
||||||
|
, main = "mean ppi2 values")
|
||||||
|
|
||||||
|
#plot(density(my_df$averaged_duet)
|
||||||
|
plot(density(my_df$avg_ppi2_scaled)
|
||||||
|
, xlab = ""
|
||||||
|
, main = "mean ppi2 values")
|
||||||
|
|
||||||
|
#==============
|
||||||
|
# Row 3 plots: replaced B-factors with mean stability values
|
||||||
|
# After actual replacement in the b factor column
|
||||||
|
#===============
|
||||||
|
################################################################
|
||||||
|
#=========
|
||||||
|
# step 0_P1: DONT RUN once you have double checked the matched output
|
||||||
|
#=========
|
||||||
|
# sanity check: match and assign to a separate column to double check
|
||||||
|
# colnames(my_df)
|
||||||
|
# df_duet$duet_scaled = my_df$averge_duet_scaled[match(df_duet$resno, my_df$position)]
|
||||||
|
|
||||||
|
#=========
|
||||||
|
# step 1_P1
|
||||||
|
#=========
|
||||||
|
# Be brave and replace in place now (don"t run sanity check)
|
||||||
|
# this makes all the B-factor values in the non-matched positions as NA
|
||||||
|
|
||||||
|
#df_duet$b = my_df$averaged_duet_scaled[match(df_duet$resno, my_df$position)]
|
||||||
|
df_duet$b = my_df$avg_ppi2_scaled[match(df_duet$resno, my_df$position)]
|
||||||
|
|
||||||
|
#=========
|
||||||
|
# step 2_P1
|
||||||
|
#=========
|
||||||
|
# count NA in Bfactor
|
||||||
|
b_na_duet = sum(is.na(df_duet$b)) ; b_na_duet
|
||||||
|
|
||||||
|
# count number of 0"s in Bactor
|
||||||
|
sum(df_duet$b == 0)
|
||||||
|
|
||||||
|
# replace all NA in b factor with 0
|
||||||
|
na_rep = 2
|
||||||
|
df_duet$b[is.na(df_duet$b)] = na_rep
|
||||||
|
|
||||||
|
# # sanity check: should be 0 and True
|
||||||
|
# # duet and lig
|
||||||
|
# if ( (sum(df_duet$b == na_rep) == b_na_duet) && (sum(df_lig$b == na_rep) == b_na_lig) ) {
|
||||||
|
# print ("PASS: NA's replaced with 0s successfully in df_duet and df_lig")
|
||||||
|
# } else {
|
||||||
|
# print("FAIL: NA replacement in df_duet NOT successful")
|
||||||
|
# quit()
|
||||||
|
# }
|
||||||
|
#
|
||||||
|
# max(df_duet$b); min(df_duet$b)
|
||||||
|
#
|
||||||
|
# # sanity checks: should be True
|
||||||
|
# if( (max(df_duet$b) == max(my_df$avg_ens_stability_scaled)) & (min(df_duet$b) == min(my_df$avg_ens_stability_scaled)) ){
|
||||||
|
# print("PASS: B-factors replaced correctly in df_duet")
|
||||||
|
# } else {
|
||||||
|
# print ("FAIL: To replace B-factors in df_duet")
|
||||||
|
# quit()
|
||||||
|
# }
|
||||||
|
|
||||||
|
# if( (max(df_lig$b) == max(my_df$avg_ens_affinity_scaled)) & (min(df_lig$b) == min(my_df$avg_ens_affinity_scaled)) ){
|
||||||
|
# print("PASS: B-factors replaced correctly in df_lig")
|
||||||
|
# } else {
|
||||||
|
# print ("FAIL: To replace B-factors in df_lig")
|
||||||
|
# quit()
|
||||||
|
# }
|
||||||
|
|
||||||
|
#=========
|
||||||
|
# step 3_P1
|
||||||
|
#=========
|
||||||
|
# sanity check: dim should be same before reassignment
|
||||||
|
if ( (dim(df_duet)[1] == dim(d2_duet)[1]) &
|
||||||
|
(dim(df_duet)[2] == dim(d2_duet)[2])
|
||||||
|
){
|
||||||
|
print("PASS: Dims of both dfs as expected")
|
||||||
|
} else {
|
||||||
|
print ("FAIL: Dims mismatch")
|
||||||
|
quit()}
|
||||||
|
|
||||||
|
#=========
|
||||||
|
# step 4_P1:
|
||||||
|
# VERY important
|
||||||
|
#=========
|
||||||
|
# assign it back to the pdb file
|
||||||
|
my_pdb_duet[['atom']] = df_duet
|
||||||
|
max(df_duet$b); min(df_duet$b)
|
||||||
|
table(df_duet$b)
|
||||||
|
sum(is.na(df_duet$b))
|
||||||
|
|
||||||
|
#=========
|
||||||
|
# step 5_P1
|
||||||
|
#=========
|
||||||
|
cat(paste0("output file mean ppi2 pdb:"
|
||||||
|
, outfile_ppi2_mspdb))
|
||||||
|
write.pdb(my_pdb_duet, outfile_ppi2_mspdb)
|
||||||
|
|
||||||
|
#============================
|
||||||
|
# Add the 3rd histogram and density plots for comparisons
|
||||||
|
#============================
|
||||||
|
# Plots continued...
|
||||||
|
# Row 3 plots: hist and density of replaced B-factors with stability values
|
||||||
|
hist(df_duet$b
|
||||||
|
, xlab = ""
|
||||||
|
, main = "repalcedB duet")
|
||||||
|
|
||||||
|
plot(density(df_duet$b)
|
||||||
|
, xlab = ""
|
||||||
|
, main = "replacedB duet")
|
||||||
|
|
||||||
|
# graph titles
|
||||||
|
mtext(text = "Frequency"
|
||||||
|
, side = 2
|
||||||
|
, line = 0
|
||||||
|
, outer = TRUE)
|
||||||
|
|
||||||
|
mtext(text = paste0(tolower(gene), ": ppi2 distribution")
|
||||||
|
, side = 3
|
||||||
|
, line = 0
|
||||||
|
, outer = TRUE)
|
||||||
|
#============================================
|
||||||
|
|
||||||
|
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
||||||
|
# NOTE: This replaced B-factor distribution has the same
|
||||||
|
# x-axis as the PredAff normalised values, but the distribution
|
||||||
|
# is affected since 0 is overinflated/or hs an additional blip because
|
||||||
|
# of the positions not associated with resistance. This is because all the positions
|
||||||
|
# where there are no SNPs have been assigned 0???
|
||||||
|
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
||||||
Loading…
Add table
Add a link
Reference in a new issue