moved plotting_func to functions and replaced 3 basic_barplots scripts with 1

scripts/plotting/functions/test_functions.R

@@ -1,9 +1,10 @@
 setwd("~/git/LSHTM_analysis/scripts/plotting/functions")
 getwd()
-
-# =================
-# Test function
-# ==================
+#############################################################
+#===========================================
+# load functions, data, dirs, hardocded vars
+# that will be used in testing the functions
+#===========================================
 source("../plotting_data.R")
 infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
 pd_df = plotting_data(infile)
@@ -12,30 +13,91 @@ my_df_u     = pd_df[[2]]
 my_df_u_lig = pd_df[[3]]
 dup_muts    = pd_df[[4]]
 
+source("../plotting_globals.R")
+drug = "streptomycin"
+gene = "gid"
+
+import_dirs(drug, gene)
+
+#=====================
+# functions to test 
+#=====================
+source("stability_count_bp.R")
+source("position_count_bp.R")
+
+##################################################################
 # ------------------------------
 # barplot for mscm stability
 # ------------------------------
+basic_bp_duet =  paste0(tolower(gene), "_basic_barplot_PS.svg")
+plot_basic_bp_duet  =  paste0(plotdir,"/", basic_bp_duet)
+
+svg(plot_basic_bp_duet)
+print(paste0("plot filename:", basic_bp_duet))
+
+# function only
 stability_count_bp(plotdf = my_df_u
                , df_colname = "duet_outcome"
                , leg_title = "DUET outcome")
 
+dev.off()
+
 # ------------------------------
 # barplot for ligand affinity
 # ------------------------------
+basic_bp_ligand =  paste0(tolower(gene), "_basic_barplot_LIG.svg")
+plot_basic_bp_ligand  =  paste0(plotdir, "/", basic_bp_ligand)
+
+svg(plot_basic_bp_ligand)
+print(paste0("plot filename:", basic_bp_ligand))
+
+# function only
 stability_count_bp(plotdf = my_df_u_lig
                , df_colname = "ligand_outcome"
                , leg_title = "Ligand outcome"
-               , bp_plot_title = "Sites < 10 Ang of ligand"
-)
+               , bp_plot_title = "Sites < 10 Ang of ligand")
 
+dev.off()
+# ------------------------------
+# barplot for foldX
+# ------------------------------
+basic_bp_foldx = paste0(tolower(gene), "_basic_barplot_foldx.svg")
+plot_basic_bp_foldx  =  paste0(plotdir,"/", basic_bp_foldx)
+
+svg(plot_basic_bp_foldx)
+print(paste0("plot filename:", plot_basic_bp_foldx))
+
+stability_count_bp(plotdf = my_df_u
+                   , df_colname = "foldx_outcome"
+                   , leg_title = "FoldX outcome")
+dev.off()
+#===============================================================
 # ------------------------------
 # barplot for nssnp site count: all
 # ------------------------------
+pos_count_duet =  paste0(tolower(gene), "_position_count_PS.svg")
+plot_pos_count_duet = paste0(plotdir, "/", pos_count_duet)
+
+svg(plot_pos_count_duet)
+print(paste0("plot filename:", plot_pos_count_duet))
+
+# function only
 site_snp_count_bp(plotdf = my_df_u
                   , df_colname = "position")
 
+dev.off()
 # ------------------------------
 # barplot for nssnp site count: within 10 Ang
 # ------------------------------
+pos_count_ligand =  paste0(tolower(gene), "_position_count_LIG.svg")
+plot_pos_count_ligand = paste0(plotdir, "/", pos_count_ligand)
+
+svg(plot_pos_count_ligand)
+print(paste0("plot filename:", plot_pos_count_ligand))
+
+# function only
 site_snp_count_bp(plotdf = my_df_u_lig
                   , df_colname = "position")
+
+dev.off()
+#===============================================================