--- a/DESeq_results_render.R	Tue Aug 08 15:06:40 2017 -0400
+++ b/DESeq_results_render.R	Tue Nov 07 13:50:32 2017 -0500
@@ -1,120 +1,108 @@
-##======= Handle arguments from command line ========
-# setup R error handline to go to stderr
-options(show.error.messages=FALSE,
-        error=function(){
-          cat(geterrmessage(), file=stderr())
-          quit("no", 1, F)
-        })
-
-# we need that to not crash galaxy with an UTF8 error on German LC settings.
-loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
-
-# suppress warning
-options(warn = -1)
-
-options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
-args = commandArgs(trailingOnly=TRUE)
-
-suppressPackageStartupMessages({
-  library(getopt)
-  library(tools)
-})
+library(getopt)
+library(rmarkdown)
+library(htmltools)
+library(dplyr)
+library(DESeq2)
+library(pheatmap)
+library(genefilter)
+library(DT)
+library(stringi)
+library(RColorBrewer)
+library(ggplot2)
 
-# column 1: the long flag name
-# column 2: the short flag alias. A SINGLE character string
-# column 3: argument mask
-#           0: no argument
-#           1: argument required
-#           2: argument is optional
-# column 4: date type to which the flag's argument shall be cast.
-#           possible values: logical, integer, double, complex, character.
-spec_list=list()
-
-##------- 1. input data ---------------------
-spec_list$ECHO = c('echo', 'e', '1', 'character')
-spec_list$DESEQ_WORKSPACE = c('deseq_workspace', 'w', '1', 'character')
-spec_list$SAMPLE_TABLE = c('sample_table', 's', '1', 'character')
-spec_list$CONTRAST_GROUP = c('contrast_group', 'c', '1', 'character')
-spec_list$TREATMENT_LEVEL = c('treatment_level', 't', '1', 'character')
-spec_list$CONDITION_LEVEL = c('condition_level', 'k', '1', 'character')
-spec_list$CLUSTERING_GROUPS = c('clustering_groups', 'm', '1', 'character')
-
-##--------2. output report and report site directory --------------
-spec_list$OUTPUT_HTML = c('deseq_results_html', 'o', '1', 'character')
-spec_list$OUTPUT_DIR = c('deseq_results_dir', 'd', '1', 'character')
-
-##--------3. Rmd templates sitting in the tool directory ----------
-
-spec_list$DESEQ_VISUALIZATION_RMD = c('deseq_results_rmd', 'D', '1', 'character')
-
+##============ Sink warnings and errors to a file ==============
+## use the sink() function to wrap all code within it.
+##==============================================================
+zz = file('warnings_and_errors.txt')
+sink(zz)
+sink(zz, type = 'message')
+  ##---------below is the code for rendering .Rmd templates-----
+  
+  ##=============STEP 1: handle command line arguments==========
+  ##
+  ##============================================================
+  # column 1: the long flag name
+  # column 2: the short flag alias. A SINGLE character string
+  # column 3: argument mask
+  #           0: no argument
+  #           1: argument required
+  #           2: argument is optional
+  # column 4: date type to which the flag's argument shall be cast.
+  #           possible values: logical, integer, double, complex, character.
+  #-------------------------------------------------------------
+  #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
+  # 1. short flag alias should match the flag in the command section in the XML file.
+  # 2. long flag name can be any legal R variable names
+  # 3. two names in args_list can have common string but one name should not be a part of another name.
+  #    for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
+  #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+  args_list=list()
+  ##------- 1. input data ---------------------
+  args_list$ECHO = c('echo', 'e', '1', 'character')
+  args_list$DESEQ_WORKSPACE = c('deseq_workspace', 'W', '1', 'character')
+  args_list$CONTRAST_FACTOR = c('contrast_factor', 'C', '1', 'character')
+  args_list$TREATMENT_LEVEL = c('treatment_level', 'T', '1', 'character')
+  args_list$CONDITION_LEVEL = c('condition_level', 'K', '1', 'character')
+  args_list$CLUSTERING_FACTORS = c('clustering_factors', 'M', '1', 'character')
+  ##--------2. output report and outputs --------------
+  args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
+  args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
+  args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character')
+  args_list$DESEQ_RESULTS = c('deseq_results', 'R', '1', 'character')
+  ##--------3. .Rmd templates in the tool directory ----------
+  args_list$deseq_results_RMD = c('deseq_results_rmd', 't', '1', 'character')
+  ##-----------------------------------------------------------
+  opt = getopt(t(as.data.frame(args_list)))
 
 
-##------------------------------------------------------------------
-
-spec = t(as.data.frame(spec_list))
-opt = getopt(spec)
-# arguments are accessed by long flag name (the first column in the spec matrix)
-#                        NOT by element name in the spec_list
-# example: opt$help, opt$expression_file
-##====== End of arguments handling ==========
+  
+  ##=======STEP 2: create report directory (optional)==========
+  ##
+  ##===========================================================
+  dir.create(opt$report_dir)
+  
+  ##=STEP 3: replace placeholders in .Rmd with argument values=
+  ##
+  ##===========================================================
+  #++ need to replace placeholders with args values one by one+
+  readLines(opt$deseq_results_rmd) %>%
+    (function(x) {
+      gsub('ECHO', opt$echo, x)
+    }) %>%
+    (function(x) {
+      gsub('DESEQ_WORKSPACE', opt$deseq_workspace, x)
+    }) %>%
+    (function(x) {
+      gsub('CONTRAST_FACTOR', opt$contrast_factor, x)
+    }) %>%
+    (function(x) {
+      gsub('TREATMENT_LEVEL', opt$treatment_level, x)
+    }) %>%
+    (function(x) {
+      gsub('CONDITION_LEVEL', opt$condition_level, x)
+    }) %>%
+    (function(x) {
+      gsub('CLUSTERING_FACTORS', opt$clustering_factors, x)
+    }) %>%
+    (function(x) {
+      gsub('REPORT_DIR', opt$report_dir, x)
+    }) %>%
+    (function(x) {
+      gsub('DESEQ_RESULTS', opt$deseq_results, x)
+    }) %>%
+    (function(x) {
+      fileConn = file('deseq_results.Rmd')
+      writeLines(x, con=fileConn)
+      close(fileConn)
+    })
+  
 
-#------ Load libraries ---------
-library(rmarkdown)
-library(plyr)
-library(stringr)
-library(dplyr)
-library(highcharter)
-library(DT)
-library(reshape2)
-# library(Kmisc)
-library(plotly)
-library(formattable)
-library(htmltools)
-
-
-#----- 1. create the report directory ------------------------
-system(paste0('mkdir -p ', opt$deseq_results_dir))
-
-
-#----- 2. generate Rmd files with Rmd templates --------------
-#   a. templates without placeholder variables:
-#         copy templates from tool directory to the working directory.
-#   b. templates with placeholder variables:
-#         substitute variables with user input values and place them in the working directory.
+  ##=============STEP 4: render .Rmd templates=================
+  ##
+  ##===========================================================
+  render('deseq_results.Rmd', output_file = opt$report_html)
 
 
-#----- 01 DESeq_results.Rmd -----------------------
-readLines(opt$deseq_results_rmd) %>%
-  (function(x) {
-    gsub('ECHO', opt$echo, x)
-  }) %>%
-  (function(x) {
-    gsub('DESEQ_WORKSPACE', opt$deseq_workspace, x)
-  }) %>%
-  (function(x) {
-    gsub('CONTRAST_GROUP', opt$contrast_group, x)
-  }) %>%
-  (function(x) {
-    gsub('TREATMENT_LEVEL', opt$treatment_level, x)
-  }) %>%
-  (function(x) {
-    gsub('CONDITION_LEVEL', opt$condition_level, x)
-  }) %>%
-  (function(x) {
-    gsub('CLUSTERING_GROUPS', opt$clustering_groups, x)
-  }) %>%
-  (function(x) {
-    gsub('OUTPUT_DIR', opt$deseq_results_dir, x)
-  }) %>%
-  (function(x) {
-    fileConn = file('DESeq_results.Rmd')
-    writeLines(x, con=fileConn)
-    close(fileConn)
-  })
-
-
-#------ 3. render all Rmd files --------
-render('DESeq_results.Rmd', output_file = opt$deseq_results_html)
-
-
-#-------4. manipulate outputs -----------------------------
+  ##--------end of code rendering .Rmd templates----------------
+sink()
+##=========== End of sinking output=============================
\ No newline at end of file