Mercurial > repos > mingchen0919 > rmarkdown_deseq2_test

annotate DESeq_render.R @ 0:61c184384d02 draft default tip

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author mingchen0919
date Tue, 07 Nov 2017 10:02:57 -0500
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61c184384d02 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2
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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
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10 ##============ Sink warnings and errors to a file ==============
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11 ## use the sink() function to wrap all code within it.
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12 ##==============================================================
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13 zz = file('warnings_and_errors.txt')
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14 sink(zz)
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15 sink(zz, type = 'message')
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16 ##---------below is the code for rendering .Rmd templates-----
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17
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18 ##=============STEP 1: handle command line arguments==========
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19 ##
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20 ##============================================================
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21 # column 1: the long flag name
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22 # column 2: the short flag alias. A SINGLE character string
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23 # column 3: argument mask
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24 # 0: no argument
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25 # 1: argument required
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26 # 2: argument is optional
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27 # column 4: date type to which the flag's argument shall be cast.
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28 # possible values: logical, integer, double, complex, character.
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29 #-------------------------------------------------------------
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30 #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
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31 # 1. short flag alias should match the flag in the command section in the XML file.
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32 # 2. long flag name can be any legal R variable names
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33 # 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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34 # for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
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35 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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36 args_list=list()
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37 ##------- 1. input data ---------------------
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38 args_list$ECHO = c('echo', 'e', '1', 'character')
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39 args_list$COUNT_FILES = c('count_files', 'c', '1', 'character')
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40 args_list$SAMPLE_TABLE = c('sample_table', 'S', '1', 'character')
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41 args_list$DESIGN_FORMULA = c('design_formula', 'p', '1', 'character')
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42 ##--------2. output report and outputs --------------
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43 args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
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44 args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
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45 args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character')
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46 args_list$WORKSPACE = c('deseq_workspace', 'w', '1', 'character')
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47 ##--------3. .Rmd templates in the tool directory ----------
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48 args_list$deseq_RMD = c('deseq_rmd', 't', '1', 'character')
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49 ##-----------------------------------------------------------
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50 opt = getopt(t(as.data.frame(args_list)))
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51
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52
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53
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54 ##=======STEP 2: create report directory (optional)==========
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55 ##
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56 ##===========================================================
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57 dir.create(opt$report_dir)
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58
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59 ##=STEP 3: replace placeholders in .Rmd with argument values=
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60 ##
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61 ##===========================================================
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62 #++ need to replace placeholders with args values one by one+
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63 readLines(opt$deseq_rmd) %>%
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64 (function(x) {
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65 gsub('ECHO', opt$echo, x)
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66 }) %>%
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67 (function(x) {
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68 gsub('DESEQ_WORKSPACE', opt$deseq_workspace, x)
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69 }) %>%
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70 (function(x) {
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71 gsub('DESIGN_FORMULA', opt$design_formula, x)
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72 }) %>%
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73 (function(x) {
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74 gsub('REPORT_DIR', opt$output_dir, x)
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75 }) %>%
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76 (function(x) {
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77 fileConn = file('deseq.Rmd')
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78 writeLines(x, con=fileConn)
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79 close(fileConn)
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80 })
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81
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83 ##=============STEP 4: render .Rmd templates=================
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84 ##
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85 ##===========================================================
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86 render('deseq.Rmd', output_file = opt$report_html)
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87
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89 ##--------end of code rendering .Rmd templates----------------
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90 sink()
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91 ##=========== End of sinking output=============================