Mercurial > repos > mingchen0919 > rmarkdown_deseq2

annotate DESeq_render.R @ 8:5f7665898fd9 draft

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fix citation error
author mingchen0919
date Tue, 07 Nov 2017 14:27:38 -0500
parents 2f8ddef8d545
children
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6
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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(stringi)
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6 library(DESeq2)
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7 library(pheatmap)
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8 library(RColorBrewer)
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9 library(DT)
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10
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11 ##============ Sink warnings and errors to a file ==============
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12 ## use the sink() function to wrap all code within it.
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13 ##==============================================================
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14 zz = file('warnings_and_errors.txt')
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15 sink(zz)
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16 sink(zz, type = 'message')
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17 ##---------below is the code for rendering .Rmd templates-----
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18
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19 ##=============STEP 1: handle command line arguments==========
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20 ##
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21 ##============================================================
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22 # column 1: the long flag name
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23 # column 2: the short flag alias. A SINGLE character string
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24 # column 3: argument mask
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25 # 0: no argument
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26 # 1: argument required
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27 # 2: argument is optional
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28 # column 4: date type to which the flag's argument shall be cast.
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29 # possible values: logical, integer, double, complex, character.
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30 #-------------------------------------------------------------
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31 #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
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32 # 1. short flag alias should match the flag in the command section in the XML file.
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33 # 2. long flag name can be any legal R variable names
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34 # 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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35 # for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
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36 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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37 args_list=list()
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38 ##------- 1. input data ---------------------
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39 args_list$ECHO = c('echo', 'e', '1', 'character')
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40 args_list$COUNT_FILE_PATHS = c('count_file_paths', 'P', '1', 'character')
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41 args_list$COUNT_FILE_NAMES = c('count_file_names', 'N', '1', 'character')
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42 args_list$SAMPLE_TABLE = c('sample_table', 'S', '1', 'character')
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43 args_list$DESIGN_FORMULA = c('design_formula', 'p', '1', 'character')
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44 ##--------2. output report and outputs --------------
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45 args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
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46 args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
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47 args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character')
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48 args_list$WORKSPACE = c('deseq_workspace', 'w', '1', 'character')
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49 ##--------3. .Rmd templates in the tool directory ----------
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50 args_list$deseq_RMD = c('deseq_rmd', 't', '1', 'character')
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51 ##-----------------------------------------------------------
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52 opt = getopt(t(as.data.frame(args_list)))
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54
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55
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56 ##=======STEP 2: create report directory (optional)==========
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57 ##
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58 ##===========================================================
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59 dir.create(opt$report_dir)
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60
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61 ##=STEP 3: replace placeholders in .Rmd with argument values=
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62 ##
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63 ##===========================================================
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64 #++ need to replace placeholders with args values one by one+
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65 readLines(opt$deseq_rmd) %>%
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66 (function(x) {
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67 gsub('ECHO', opt$echo, x)
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68 }) %>%
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69 (function(x) {
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70 gsub('DESEQ_WORKSPACE', opt$deseq_workspace, x)
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71 }) %>%
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72 (function(x) {
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73 gsub('DESIGN_FORMULA', opt$design_formula, x)
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74 }) %>%
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75 (function(x) {
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76 gsub('REPORT_DIR', opt$report_dir, x)
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77 }) %>%
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78 (function(x) {
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79 fileConn = file('deseq.Rmd')
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80 writeLines(x, con=fileConn)
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81 close(fileConn)
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82 })
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83
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84
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85 ##=============STEP 4: render .Rmd templates=================
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86 ##
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87 ##===========================================================
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88 render('deseq.Rmd', output_file = opt$report_html)
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89
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90
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91 ##--------end of code rendering .Rmd templates----------------
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92 sink()
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93 ##=========== End of sinking output=============================