moved functions/ in the scripts dir

scripts/functions/test_functions.R

@@ -0,0 +1,103 @@
+setwd("~/git/LSHTM_analysis/scripts/plotting/functions")
+getwd()
+#############################################################
+#===========================================
+# 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)
+my_df       = pd_df[[1]]
+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")
+
+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()
+#===============================================================