sourcing plotting_data for subcols_axis_PS

scripts/plotting/subcols_axis_PS.R

@@ -1,52 +1,21 @@
+#########################################################
+# TASK: Adding colours to positions labels according to 
+# active site residues. This is so these can be seen promptly
+# when visualising the barplot.
+#########################################################
+#=======================================================================
 getwd()
 setwd("~/git/LSHTM_analysis/scripts/plotting")
 getwd()
 
-#########################################################
-# TASK:
+source("plotting_data.R")
+   # should return the following dfs and directories
+   # my_df
+   # my_df_u
+   # my_df_u_lig
+   # dup_muts
 
-#########################################################
-
-########################################################################
-# 		Installing and loading required packages and functions		   #	
-########################################################################
-
-#source("Header_TT.R")
-#source("barplot_colour_function.R")
-
-########################################################################
-#		 Read file: call script for combining df for PS			   	   #
-########################################################################
-#?????????????
-#
-########################################################
-#%% variable assignment: input and output paths & filenames
-drug = "pyrazinamide"
-gene = "pncA"
-gene_match = paste0(gene,"_p.")
-cat(gene_match)
-
-#=============
-# directories
-#=============
-datadir = paste0("~/git/Data")
-indir = paste0(datadir, "/", drug, "/input")
-outdir = paste0("~/git/Data", "/", drug, "/output")
-
-#======
-# input
-#======
-#in_filename = "mcsm_complex1_normalised.csv"
-in_filename_params = paste0(tolower(gene), "_all_params.csv") 
-infile_params = paste0(outdir, "/", in_filename_params)
-cat(paste0("Input file:", infile_params) )
-
-#=======
-# output
-#=======
-
-
-#%%===============================================================
+#=======================================================================
 ###########################
 # Read file: struct params
 ###########################
@@ -83,7 +52,7 @@ if ( length(unique(my_df$mutationinformation)) != length(my_df$mutationinformati
 upos = unique(my_df_u$position)
 cat("Dim of clean df:"); cat(dim(my_df_u))
 cat("\nNo. of unique mutational positions:"); cat(length(upos))
-#======================================================
+#=======================================================================
 # create a new df with unique position numbers and cols
 position = unique(my_df$position) #130
 position_cols = as.data.frame(position)
@@ -235,6 +204,5 @@ rm(aa_cols_ref
    , lab_bg
    , lab_bg2
    , lab_fg
-   , position
-   , dup_muts)
+   , position)