sourced plotting script in mean_stability calcs

scripts/plotting/mcsm_mean_stability.R

@@ -9,12 +9,16 @@ getwd()
 source("Header_TT.R")
 require(data.table)
 require(dplyr)
+source("plotting_data.R")
+# should return
+#my_df
+#my_df_u
+#dup_muts
+
 #========================================================
 #	Read file: call script for combining df for PS
 #source("../combining_two_df.R")
 
-#???????????
-
 #========================================================
 #%% variable assignment: input and output paths & filenames
 drug = "pyrazinamide"
@@ -45,47 +49,7 @@ outfile_mean_stability = paste0(outdir, "/", out_filename_mean_stability)
 print(paste0("Output file:", outfile_mean_stability))
 
 #%%===============================================================
-###########################
-# Read file: struct params
-###########################
-cat("Reading struct params including mcsm:", in_filename_params)
 
-my_df = read.csv(infile_params
-                 #, stringsAsFactors = F
-                 , header = T)
-
-cat("Input dimensions:", dim(my_df)) 
-
-# clear variables
-rm(in_filename_params, infile_params)
-
-# quick checks
-colnames(my_df)
-str(my_df)
-
-# check for duplicate mutations
-if ( length(unique(my_df$mutationinformation)) != length(my_df$mutationinformation)){
-  cat(paste0("CAUTION:", " Duplicate mutations identified"
-             , "\nExtracting these..."))
-  dup_muts = my_df[duplicated(my_df$mutationinformation),]
-  dup_muts_nu = length(unique(dup_muts$mutationinformation))
-  cat(paste0("\nDim of duplicate mutation df:", nrow(dup_muts)
-             , "\nNo. of unique duplicate mutations:", dup_muts_nu
-             , "\n\nExtracting df with unique mutations only"))
-  my_df_u = my_df[!duplicated(my_df$mutationinformation),]
-}else{
-  cat(paste0("No duplicate mutations detected"))
-  my_df_u = my_df
-}
-
-upos = unique(my_df_u$position)
-cat("Dim of clean df:")
-cat(dim(my_df_u))
-cat("\nNo. of unique mutational positions:"); cat(length(upos))
-
-########################################################################
-#               end of data extraction and cleaning for plots          #
-########################################################################
 #================
 # Data for plots
 #================