tidied plotting_data.R as a function returning a lits of dfs

scripts/plotting/basic_barplots_PS.R

@@ -3,40 +3,27 @@
 # TASK: producing barplots
 # basic barplots with count of mutations
 # basic barplots with frequency of count of mutations
+
+# Depends on
+ ## plotting_globals.R (previously dir.R)
+ ## plotting_data.R 
 #########################################################
-#=======================================================================
-# working dir and loading libraries
+# working dir 
 getwd()
 setwd("~/git/LSHTM_analysis/scripts/plotting")
 getwd()
 
+# load libraries
 #source("Header_TT.R")
 library(ggplot2)
 library(data.table)
 library(dplyr)
+require("getopt", quietly = TRUE) # cmd parse arguments
 
-# Set globals: 
+# load functions
 source("plotting_globals.R")
-# pretent cli
-drug = "streptomycin"
-gene = "gid"
-infile = "merged_df3_short.csv"
-
-import_dirs(drug, gene)
-
 source("plotting_data.R")
-plotting_data("merged_df3_short.csv")
-
-if (!exists("infile") && exists("gene")){
-  #in_filename_params = paste0(tolower(gene), "_all_params.csv") 
-  in_filename_params = paste0(tolower(gene), "_comb_stab_struc_params.csv") # part combined for gid
-  infile = paste0(outdir, "/", in_filename_params)
-}
-
-plotting_data(infile)
-
-
-#=======================================================================
+#########################################################
 # command line args
 spec = matrix(c(
   "drug"   , "d", 1, "character",
@@ -56,9 +43,29 @@ gene = opt$gene
 if(is.null(drug)|is.null(gene)) {
   stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
 }
-#=======================================================================
+#########################################################
+# call functions with relevant args
+drug = "streptomycin"
+gene = "gid"
+import_dirs(drug, gene)
 
-# should return the following dfs, directories and variables
+if (!exists("infile") && exists("gene")){
+  #in_filename_params = paste0(tolower(gene), "_all_params.csv") 
+  in_filename_params = paste0(tolower(gene), "_comb_stab_struc_params.csv") # part combined for gid
+  infile = paste0(outdir, "/", in_filename_params)
+}
+
+#infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
+#infile = ""
+
+# Get the DFs out of plotting_data()
+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]]
+#########################################################
+# This script: should return the following dfs, directories and variables
 # my_df
 # my_df_u
 # my_df_u_lig
@@ -85,11 +92,11 @@ rm(my_df, upos, dup_muts, my_df_u_lig)
 # output
 #=======
 # plot 1
-basic_bp_duet = "basic_barplot_PS.svg"
+basic_bp_duet =  paste0(tolower(gene), "_basic_barplot_PS.svg")
 plot_basic_bp_duet  =  paste0(plotdir,"/", basic_bp_duet)
 
 # plot 2
-pos_count_duet = "position_count_PS.svg"
+pos_count_duet =  paste0(tolower(gene), "_position_count_PS.svg")
 plot_pos_count_duet = paste0(plotdir, "/", pos_count_duet)
 
 #=======================================================================
@@ -194,12 +201,38 @@ foo = select(df, mutationinformation
 #--------------
 # start plot 2
 #--------------
-
 svg(plot_pos_count_duet)
 print(paste0("plot filename:", plot_pos_count_duet))
+my_ats = 25 # axis text size
+my_als = 22 # axis label size
+
+# to make x axis display all positions
+# not sure if to use with sort or directly
+my_x = sort(unique(snpsBYpos_df$snpsBYpos)) 
+
+g = ggplot(snpsBYpos_df, aes(x = snpsBYpos))
+OutPlot_pos_count = g + geom_bar(aes (alpha = 0.5)
+                                 , show.legend = FALSE) +
+  scale_x_continuous(breaks = unique(snpsBYpos_df$snpsBYpos)) +
+  #scale_x_continuous(breaks = my_x) +
+  geom_label(stat = "count", aes(label = ..count..)
+             , color = "black"
+             , size = 10) +
+  theme(axis.text.x = element_text(size = my_ats
+                                   , angle = 0)
+        , axis.text.y = element_text(size = my_ats
+                                     , angle = 0
+                                     , hjust = 1)
+        , axis.title.x = element_text(size = my_als)
+        , axis.title.y = element_text(size = my_als)
+        , plot.title = element_blank()) +
+  
+  labs(x = "Number of nsSNPs"
+       , y = "Number of Sites")
+
+print(OutPlot_pos_count)
 
-source("dirs.R")
 dev.off()
 ########################################################################
 #               			end of PS barplots         			   
-########################################################################
+########################################################################