moved combining_dfs_plotting.R to function and added test script for this as well

scripts/functions/test_aa_prop_bp.R

@@ -2,14 +2,14 @@ library(ggplot2)
 library(tidyverse)
 library(data.table)
 
-setwd("~/git/LSHTM_analysis/scripts/plotting/functions")
+setwd("~/git/LSHTM_analysis/scripts/functions/")
 getwd()
 #############################################################
 #===========================================
 # load functions, data, dirs, hardocded vars
 # that will be used in testing the functions
 #===========================================
-source("../plotting_data.R")
+source("plotting_data.R")
 infile = "/home/tanu/git/Data/streptomycin/output/"
 pd_df = plotting_data(infile)
 my_df       = pd_df[[1]]

scripts/functions/test_af_or_calcs.R

@@ -7,11 +7,15 @@
 #source("Header_TT.R")
 require("getopt", quietly = TRUE) # cmd parse arguments
 
+# working dir and loading libraries
+getwd()
+setwd("~/git/LSHTM_analysis/scripts/functions/")
+getwd()
 
 # load functions
-source("functions/plotting_globals.R")
-source("functions/mychisq_or.R")
-source("functions/myaf_or_calcs.R")
+source("plotting_globals.R")
+source("mychisq_or.R")
+source("myaf_or_calcs.R")
 
 # cmd options + sensible defaults
 drug = "streptomycin"

scripts/functions/test_bp.R

@@ -1,11 +1,11 @@
-setwd("~/git/LSHTM_analysis/scripts/plotting/functions")
+setwd("~/git/LSHTM_analysis/scripts/functions/")
 getwd()
 #############################################################
 #===========================================
 # load functions, data, dirs, hardocded vars
 # that will be used in testing the functions
 #===========================================
-source("../plotting_data.R")
+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]]
@@ -13,7 +13,7 @@ my_df_u     = pd_df[[2]]
 my_df_u_lig = pd_df[[3]]
 dup_muts    = pd_df[[4]]
 
-source("../plotting_globals.R")
+source("plotting_globals.R")
 drug = "streptomycin"
 gene = "gid"
 
@@ -100,4 +100,4 @@ site_snp_count_bp(plotdf = my_df_u_lig
                   , df_colname = "position")
 
 dev.off()
-#===============================================================
+#===============================================================

scripts/functions/test_combining_dfs_plotting.R

@@ -0,0 +1,87 @@
+# #!/usr/bin/env Rscript
+
+# working dir and loading libraries
+getwd()
+setwd("~/git/LSHTM_analysis/scripts/functions/")
+getwd()
+
+# infile_params = paste0(outdir, "/" , tolower(gene), "_comb_afor.csv")
+# infile_metadata = paste0(outdir, "/", tolower(gene), "_metadata")
+# 
+# 
+# source("combining_dfs_plotting_func.R")
+# 
+####################################################################
+# in_file_params = "~/git/Data/streptomycin/output/gid_comb_afor.csv"
+# in_file_metadata = "~/git/Data/streptomycin/output/gid_metadata.csv"
+# 
+# all_plot_dfs = combining_dfs_plotting(df1_mcsm_comb = infile_params
+#                        , df2_gene_metadata = infile_metadata
+#                        , lig_dist_colname = 'ligand_distance'
+#                        , lig_dist_cutoff = 10)
+# 
+# merged_df2        = all_plot_dfs[[1]]
+# merged_df3        = all_plot_dfs[[2]]
+# merged_df2_comp   = all_plot_dfs[[3]]
+# merged_df3_comp   = all_plot_dfs[[4]]
+# merged_df2_lig    = all_plot_dfs[[5]]
+# merged_df3_lig    = all_plot_dfs[[6]]
+# 
+# bar_colnames = data.frame(colnames(merged_df2))
+###########################################################
+source("plotting_globals.R")
+source("plotting_data.R")
+source("combining_dfs_plotting.R")
+
+gene = 'gid'
+drug = 'streptomycin'
+
+#---------------------
+# call: import_dirs()
+#---------------------
+import_dirs(drug, gene)
+
+if (!exists("infile_params") && exists("gene")){
+#if (!is.character(infile_params) && exists("gene")){
+  #in_filename_params = paste0(tolower(gene), "_all_params.csv") 
+  in_filename_params = paste0(tolower(gene), "_comb_afor.csv") # part combined for gid
+  infile_params = paste0(outdir, "/", in_filename_params)
+  cat("\nInput file for mcsm comb data not specified, assuming filename: ", infile_params, "\n")
+}
+
+if (!exists("infile_metadata") && exists("gene")){
+#if (!is.character(infile_params) && exists("gene")){{
+  in_filename_metadata = paste0(tolower(gene), "_metadata.csv") # part combined for gid
+  infile_metadata = paste0(outdir, "/", in_filename_metadata)
+  cat("\nInput file for gene metadata not specified, assuming filename: ", infile_metadata, "\n")
+}
+
+#============================
+# Input 1: plotting_data()
+#============================
+#---------------------
+# call: plotting_data()
+#---------------------
+pd_df = plotting_data(infile_params)
+my_df       = pd_df[[1]] # this forms one of the input for combining_dfs_plotting()
+
+#======================================
+# Input 2: read <gene>_meta data.csv
+#======================================
+cat("\nReading meta data file:", infile_metadata)
+
+gene_metadata <- read.csv(infile_metadata
+                          , stringsAsFactors = F
+                          , header = T)
+
+all_plot_dfs = combining_dfs_plotting(my_df_u
+                       , gene_metadata
+                       , lig_dist_colname = 'ligand_distance'
+                       , lig_dist_cutoff = 10)
+
+merged_df2        = all_plot_dfs[[1]]
+merged_df3        = all_plot_dfs[[2]]
+merged_df2_comp   = all_plot_dfs[[3]]
+merged_df3_comp   = all_plot_dfs[[4]]
+merged_df2_lig    = all_plot_dfs[[5]]
+merged_df3_lig    = all_plot_dfs[[6]]