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Tanushree Tunstall 2022-08-01 21:44:11 +01:00
parent 66337c289c
commit d94aa10c9b
1 changed files with 7 additions and 10 deletions
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17
scripts/plotting/replaceBfactor_pdb_stability_5uhc_rpob.R
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@ -50,31 +50,29 @@ 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")
#outdir_plots = paste0("~/git/Data", "/", drug, "/output/plots") #outdir_plots = paste0("~/git/Data", "/", drug, "/output/plots")
outdir_plots = paste0("~/git/Writing/thesis/images/results/5uhc_rpob_", tolower(gene)) outdir_plots = paste0("~/git/Writing/thesis/images/results/", tolower(gene))
#====== #======
# input # input
#====== #======
#in_filename_pdb = paste0(tolower(gene), "_complex.pdb") #in_filename_pdb = paste0(tolower(gene), "_complex.pdb")
in_filename_pdb = "5uhc.pdb" in_filename_pdb = "5uhc.pdb"
infile_pdb = paste0(indir, "/", in_filename_pdb) infile_pdb = paste0(indir, "/", in_filename_pdb)
cat(paste0("Input file:", infile_pdb) ) cat(paste0("Input file:", infile_pdb) )
#in_filename_mean_stability = paste0(tolower(gene), "_mean_stability.csv") #in_filename_mean_stability = paste0(tolower(gene), "_mean_stability.csv")
#infile_mean_stability = paste0(outdir, "/", in_filename_mean_stability) #infile_mean_stability = paste0(outdir, "/", in_filename_mean_stability)
in_filename_mean_stability = paste0(tolower(gene), "_mean_ens_stability.csv") in_filename_mean_stability = paste0("/5uhc_", tolower(gene), "_mean_ens_stability.csv")
infile_mean_stability = paste0(outdir_plots, "/", in_filename_mean_stability) infile_mean_stability = paste0(outdir_plots, in_filename_mean_stability)
cat(paste0("Input file:", infile_mean_stability) ) cat(paste0("Input file:", infile_mean_stability) )
#======= #=======
# output # output
#======= #=======
#out_filename_duet_mspdb = paste0(tolower(gene), "_complex_bduet_ms.pdb") #out_filename_duet_mspdb = paste0(tolower(gene), "_complex_bduet_ms.pdb")
out_filename_duet_mspdb = paste0(tolower(gene), "_complex_b_stab_ms.pdb") out_filename_duet_mspdb = paste0("/5uhc_", tolower(gene), "_complex_b_stab_ms.pdb")
outfile_duet_mspdb = paste0(outdir_plots, "/", out_filename_duet_mspdb) outfile_duet_mspdb = paste0(outdir_plots, out_filename_duet_mspdb)
print(paste0("Output file:", outfile_duet_mspdb)) print(paste0("Output file:", outfile_duet_mspdb))
#%%=============================================================== #%%===============================================================
@ -86,6 +84,7 @@ print(paste0("Output file:", outfile_duet_mspdb))
########################### ###########################
my_df <- read.csv(infile_mean_stability, header = T) my_df <- read.csv(infile_mean_stability, header = T)
str(my_df) str(my_df)
my_df = na.omit(my_df)
############# #############
# Read pdb # Read pdb
@ -132,8 +131,6 @@ par(oma = c(3,2,3,0)
#, mfrow = c(3,2) #, mfrow = c(3,2)
#, mfrow = c(3,4)) #, mfrow = c(3,4))
, mfrow = c(3,2)) , mfrow = c(3,2))
#============= #=============
# Row 1 plots: original B-factors # Row 1 plots: original B-factors
# duet and affinity # duet and affinity
@ -180,7 +177,7 @@ plot(density(my_df$avg_ens_stability_scaled)
# this makes all the B-factor values in the non-matched positions as NA # this makes all the B-factor values in the non-matched positions as NA
#df_duet$b = my_df$averaged_duet_scaled[match(df_duet$resno, my_df$position)] #df_duet$b = my_df$averaged_duet_scaled[match(df_duet$resno, my_df$position)]
df_duet$b = my_df$avg_ens_stability_scaled[match(df_duet$resno, my_df$position)] df_duet$b = my_df$avg_ens_stability_scaled[match(df_duet$resno, my_df$X5uhc_position)]
#========= #=========
# step 2_P1 # step 2_P1