From d94aa10c9b80d224a15671c9d3fa9f24e7917356 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Mon, 1 Aug 2022 21:44:11 +0100 Subject: [PATCH] saving work --- .../replaceBfactor_pdb_stability_5uhc_rpob.R | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) diff --git a/scripts/plotting/replaceBfactor_pdb_stability_5uhc_rpob.R b/scripts/plotting/replaceBfactor_pdb_stability_5uhc_rpob.R index 25cb705..d263820 100644 --- a/scripts/plotting/replaceBfactor_pdb_stability_5uhc_rpob.R +++ b/scripts/plotting/replaceBfactor_pdb_stability_5uhc_rpob.R @@ -50,31 +50,29 @@ datadir = paste0("~/git/Data") indir = paste0(datadir, "/", drug, "/input") outdir = paste0("~/git/Data", "/", drug, "/output") #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 #====== #in_filename_pdb = paste0(tolower(gene), "_complex.pdb") in_filename_pdb = "5uhc.pdb" - infile_pdb = paste0(indir, "/", in_filename_pdb) cat(paste0("Input file:", infile_pdb) ) #in_filename_mean_stability = paste0(tolower(gene), "_mean_stability.csv") #infile_mean_stability = paste0(outdir, "/", in_filename_mean_stability) -in_filename_mean_stability = paste0(tolower(gene), "_mean_ens_stability.csv") -infile_mean_stability = paste0(outdir_plots, "/", in_filename_mean_stability) - +in_filename_mean_stability = paste0("/5uhc_", tolower(gene), "_mean_ens_stability.csv") +infile_mean_stability = paste0(outdir_plots, in_filename_mean_stability) cat(paste0("Input file:", infile_mean_stability) ) #======= # output #======= #out_filename_duet_mspdb = paste0(tolower(gene), "_complex_bduet_ms.pdb") -out_filename_duet_mspdb = paste0(tolower(gene), "_complex_b_stab_ms.pdb") -outfile_duet_mspdb = paste0(outdir_plots, "/", out_filename_duet_mspdb) +out_filename_duet_mspdb = paste0("/5uhc_", tolower(gene), "_complex_b_stab_ms.pdb") +outfile_duet_mspdb = paste0(outdir_plots, out_filename_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) str(my_df) +my_df = na.omit(my_df) ############# # Read pdb @@ -132,8 +131,6 @@ par(oma = c(3,2,3,0) #, mfrow = c(3,2) #, mfrow = c(3,4)) , mfrow = c(3,2)) - - #============= # Row 1 plots: original B-factors # duet and affinity @@ -180,7 +177,7 @@ plot(density(my_df$avg_ens_stability_scaled) # this makes all the B-factor values in the non-matched positions as NA #df_duet$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