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1 library(getopt)
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2 library(rmarkdown)
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3 library(htmltools)
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4 library(dplyr)
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5 library(DESeq2)
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6 library(pheatmap)
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7 library(genefilter)
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8 library(DT)
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9 library(stringi)
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10 library(RColorBrewer)
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11 library(ggplot2)
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12
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13 ##============ Sink warnings and errors to a file ==============
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14 ## use the sink() function to wrap all code within it.
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15 ##==============================================================
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16 zz = file('warnings_and_errors.txt')
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17 sink(zz)
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18 sink(zz, type = 'message')
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19 ##---------below is the code for rendering .Rmd templates-----
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20
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21 ##=============STEP 1: handle command line arguments==========
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22 ##
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23 ##============================================================
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24 # column 1: the long flag name
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25 # column 2: the short flag alias. A SINGLE character string
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26 # column 3: argument mask
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27 # 0: no argument
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28 # 1: argument required
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29 # 2: argument is optional
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30 # column 4: date type to which the flag's argument shall be cast.
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31 # possible values: logical, integer, double, complex, character.
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32 #-------------------------------------------------------------
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33 #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
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34 # 1. short flag alias should match the flag in the command section in the XML file.
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35 # 2. long flag name can be any legal R variable names
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36 # 3. two names in args_list can have common string but one name should not be a part of another name.
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37 # for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
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38 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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39 args_list=list()
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40 ##------- 1. input data ---------------------
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41 args_list$ECHO = c('echo', 'e', '1', 'character')
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42 args_list$DESEQ_WORKSPACE = c('deseq_workspace', 'W', '1', 'character')
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43 args_list$CONTRAST_FACTOR = c('contrast_factor', 'C', '1', 'character')
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44 args_list$TREATMENT_LEVEL = c('treatment_level', 'T', '1', 'character')
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45 args_list$CONDITION_LEVEL = c('condition_level', 'K', '1', 'character')
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46 args_list$CLUSTERING_FACTORS = c('clustering_factors', 'M', '1', 'character')
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47 ##--------2. output report and outputs --------------
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48 args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
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49 args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
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50 args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character')
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51 args_list$DESEQ_RESULTS = c('deseq_results', 'R', '1', 'character')
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52 ##--------3. .Rmd templates in the tool directory ----------
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53 args_list$deseq_results_RMD = c('deseq_results_rmd', 't', '1', 'character')
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54 ##-----------------------------------------------------------
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55 opt = getopt(t(as.data.frame(args_list)))
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56
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57
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58
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59 ##=======STEP 2: create report directory (optional)==========
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60 ##
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61 ##===========================================================
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62 dir.create(opt$report_dir)
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63
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64 ##=STEP 3: replace placeholders in .Rmd with argument values=
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65 ##
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66 ##===========================================================
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67 #++ need to replace placeholders with args values one by one+
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68 readLines(opt$deseq_results_rmd) %>%
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69 (function(x) {
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70 gsub('ECHO', opt$echo, x)
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71 }) %>%
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72 (function(x) {
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73 gsub('DESEQ_WORKSPACE', opt$deseq_workspace, x)
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74 }) %>%
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75 (function(x) {
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76 gsub('CONTRAST_FACTOR', opt$contrast_factor, x)
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77 }) %>%
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78 (function(x) {
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79 gsub('TREATMENT_LEVEL', opt$treatment_level, x)
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80 }) %>%
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81 (function(x) {
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82 gsub('CONDITION_LEVEL', opt$condition_level, x)
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83 }) %>%
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84 (function(x) {
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85 gsub('CLUSTERING_FACTORS', opt$clustering_factors, x)
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86 }) %>%
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87 (function(x) {
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88 gsub('REPORT_DIR', opt$report_dir, x)
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89 }) %>%
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90 (function(x) {
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91 gsub('DESEQ_RESULTS', opt$deseq_results, x)
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92 }) %>%
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93 (function(x) {
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94 fileConn = file('deseq_results.Rmd')
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95 writeLines(x, con=fileConn)
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96 close(fileConn)
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97 })
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98
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99
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100 ##=============STEP 4: render .Rmd templates=================
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101 ##
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102 ##===========================================================
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103 render('deseq_results.Rmd', output_file = opt$report_html)
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104
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105
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106 ##--------end of code rendering .Rmd templates----------------
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107 sink()
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108 ##=========== End of sinking output============================= |
