added functions dir for further tidying and tested this with ind scripts for stability

scripts/plotting/basic_barplots_PS.R

@@ -23,6 +23,7 @@ require("getopt", quietly = TRUE) # cmd parse arguments
 # load functions
 source("plotting_globals.R")
 source("plotting_data.R")
+source("functions/stability_count_bp.R")
 #########################################################
 # command line args
 #********************
@@ -98,9 +99,10 @@ cat(paste0("Directories imported:"
            , "\noutdir:", outdir
            , "\nplotdir:", plotdir))
            
- cat(paste0("Variables imported:"
+ cat(paste0("\nVariables imported:"
            , "\ndrug:", drug
-           , "\ngene:", gene))
+           , "\ngene:", gene
+           , "\n))
            #, "\ngene_match:", gene_match
            #, "\nLength of upos:", length(upos)
            #, "\nAngstrom symbol:", angstroms_symbol))       
@@ -129,45 +131,18 @@ str(df)
 #****************
 # Plot 1: Count of stabilising and destabilsing muts
 #****************
-
 svg(plot_basic_bp_duet)
 print(paste0("plot1 filename:", basic_bp_duet))
 
-my_ats = 25 # axis text size
-my_als = 22 # axis label size
-
-theme_set(theme_grey())
-
 #--------------
-# start plot 1
+# start plot 1: call function
 #--------------
-g = ggplot(df, aes(x = duet_outcome))
-OutPlot_count = g + geom_bar(aes(fill = duet_outcome)
-                         , show.legend = TRUE) + 
-  geom_label(stat = "count"
-             , aes(label = ..count..)
-             , color = "black"
-             , show.legend = FALSE
-             , size = 10) + 
-  theme(axis.text.x = element_blank()
-        , axis.title.x = element_blank()
-        , axis.title.y = element_text(size=my_als)
-        , axis.text.y = element_text(size = my_ats)
-        , legend.position = c(0.73,0.8)
-        , legend.text = element_text(size=my_als-2)
-        , legend.title = element_text(size=my_als)
-        , plot.title = element_blank()) + 
-  labs(title = ""
-       , y = "Number of nsSNPs"
-      #, fill="DUET Outcome"
-      ) + 
-  scale_fill_discrete(name = "DUET Outcome"
-                      , labels = c("Destabilising", "Stabilising"))
-
-print(OutPlot_count)
+stability_count_bp(plotdf = my_df_u
+                   , df_colname = "duet_outcome"
+                   , leg_title = "DUET outcome")
 dev.off()
 
-table(df$duet_outcome)
+table(my_df_u$duet_outcome)
 #=======================================================================
 #****************
 # Plot 2: frequency of positions
@@ -252,4 +227,4 @@ print(OutPlot_pos_count)
 dev.off()
 ########################################################################
 #               			end of PS barplots         			   
-########################################################################
+########################################################################