sourcing plotting_data for subcols_axis_PS

scripts/plotting/basic_barplots_PS.R

@@ -4,6 +4,7 @@
 # basic barplots with count of mutations
 # basic barplots with frequency of count of mutations
 #########################################################
+#=======================================================================
 # working dir and loading libraries
 getwd()
 setwd("~/git/LSHTM_analysis/scripts/plotting")
@@ -14,18 +15,30 @@ library(ggplot2)
 library(data.table)
 library(dplyr)
 source("plotting_data.R")
-    # should return
-    #my_df
-    #my_df_u
-    #dup_muts
 
-#========================================================
+# should return the following dfs, directories and variables
+# my_df
+# my_df_u
+# my_df_u_lig
+# dup_muts
+
 cat(paste0("Directories imported:"
            , "\ndatadir:", datadir
            , "\nindir:", indir
            , "\noutdir:", outdir
            , "\nplotdir:", plotdir))
+           
+ cat(paste0("Variables imported:"
+           , "\ndrug:", drug
+           , "\ngene:", gene
+           , "\ngene_match:", gene_match
+           , "\nLength of upos:", length(upos))
+           , "\nAngstrom symbol:", angstroms_symbol))       
+           
+# clear excess variable
+rm(my_df, upos, dup_muts, my_df_u_lig)
 
+#=======================================================================
 #=======
 # output
 #=======
@@ -37,17 +50,16 @@ plot_basic_bp_duet  =  paste0(plotdir,"/", basic_bp_duet)
 pos_count_duet = "position_count_PS.svg"
 plot_pos_count_duet = paste0(plotdir, "/", pos_count_duet)
 
-#%%===============================================================
+#=======================================================================
 #================
 # Data for plots
 #================
 # REASSIGNMENT as necessary
 df  = my_df_u
-rm(my_df, upos, dup_muts)
 
 # sanity checks
 str(df)
-#%%=======================================================================
+#=======================================================================
 #****************
 # Plot 1:Count of stabilising and destabilsing muts
 #****************
@@ -89,7 +101,9 @@ outPlot = g + geom_bar(aes(fill = duet_outcome)
 
 print(outPlot)
 dev.off()
-#%%=======================================================================
+
+table(df$duet_outcome)
+#=======================================================================
 #****************
 # Plot 2: frequency of positions
 #****************
@@ -173,6 +187,6 @@ outPlot_pos = g + geom_bar(aes (alpha = 0.5)
 print(outPlot_pos)
 dev.off()
 ########################################################################
-#               			end of DUET barplots         			   
+#               			end of Ligand barplots         			   
 ########################################################################