Mercurial > repos > mingchen0919 > aurora_deseq2

annotate rmarkdown_report_render.R @ 0:55d2db17c67c draft

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author mingchen0919
date Fri, 14 Dec 2018 00:21:26 -0500
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1 ##============ Sink warnings and errors to a file ==============
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2 ## use the sink() function to wrap all code within it.
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3 ##==============================================================
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4 zz = file(paste0(Sys.getenv('REPORT_FILES_PATH'), '/r_rendering.log.txt'))
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5 sink(zz)
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6 sink(zz, type = 'message')
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7
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8 #============== preparation ====================================
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9 # import libraries
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10 #------------------------------------------------------------------
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11 # ADD MORE LIBRARIES HERE IF YOUR TOOL DEPENDS ON OTHER R LIBRARIES
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12 #------------------------------------------------------------------
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13 library('getopt')
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14 library('rmarkdown')
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15 library('htmltools')
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16 library('ggplot2')
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17 library('plotly')
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18 library('DESeq2')
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19 library('pheatmap')
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20 #------------------------------------------------------------------
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21 options(stringsAsFactors = FALSE)
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22
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23
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24 # define two helper functions
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25 #-----: helper function 1
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26 #' \code{getopt_specification_matrix} returns a getopt specification matrix.
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27 #'
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28 #' @param specification_file a cvs file within the \code{galaxy_tool_directory} which stores getopt specification matrix data.
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29 #' The first column are short flags, the second column are argument masks, the third column
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30 #' is data types. The fourth column are variable names used in the tool XML. These three columns are required.
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31 #' @param gtg_name the name of a running GTG.
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32 getopt_specification_matrix = function(specification_file,
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33 gtg_name = 'gtg',
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34 tool_dir = Sys.getenv('TOOL_INSTALL_DIR')) {
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35 df = read.csv(
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36 paste0(tool_dir, '/', specification_file),
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37 header = TRUE,
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38 stringsAsFactors = FALSE
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39 )
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40 # check if there are duplicated short flags
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41 short_flags = df[, 1]
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42 if (length(unique(short_flags)) < length(short_flags)) {
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43 cat('----Duplicated short flags found ----\n')
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44 cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n')
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45 stop('Duplicated short flags are not allowed.')
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46 }
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47
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48 # use short flags to generate long flags
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49 long_flags = paste0('X_', df[, 1])
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50
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51 # specification matrix
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52 df2 = data.frame(
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53 long_flags = long_flags,
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54 short_flags = df[, 1],
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55 argument_mask = df[, 2],
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56 data_type = df[, 3]
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57 )
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58
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59 as.matrix(df2)
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60 }
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61
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62 #-----: helper function 2
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63 #' \code{file_tree} generate file tree of a directory in the format of HTML lists.
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64 #'
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65 #' @param dir the path to the directory for generating the file tree.
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66 #' @param output_dir the REPORT_FILES_PATH folder name, which has the name style: dataset_NUMBER_files.
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67 # define a recursive function to build html string of the file tree
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68 file_tree = function(dir = '.') {
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69 # get the OUTPUT_DIR folder data: dataset_NUMBER_files
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70 report_files_path = Sys.getenv('REPORT_FILES_PATH')
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71 output_dir = tail(strsplit(report_files_path, '/')[[1]], 1)
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72
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73 files = list.files(path = dir,
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74 recursive = FALSE,
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75 full.names = TRUE)
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76 # files also include directorys, need to remove directorys
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77 files = files[!dir.exists(files)]
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78 dirs = list.dirs(path = dir,
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79 recursive = FALSE,
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80 full.names = TRUE)
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81 tags$ul({
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82 if (length(files) > 0) {
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83 lapply(files, function(x) {
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84 path_end = tail(strsplit(x, '/')[[1]], 1)
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85 href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
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86 li_item = tags$li(tags$a(path_end, href = href_path))
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87 li_item$attribs = list('data-jstree' = '{"icon":"jstree-file"}')
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88 li_item
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89 })
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90 }
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91 },
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92 {
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93 if (length(dirs) > 0) {
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94 lapply(dirs, function(x) {
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95 path_end = tail(strsplit(x, '/')[[1]], 1)
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96 # hide vakata-jstree-3.3.5 folder
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97 if (!(path_end %in% c('vakata-jstree-3.3.5', 'rmarkdown_report_files', 'site_libs'))) {
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98 # x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
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99 li_item = tags$li(path_end, file_tree(x))
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100 li_item$attribs = list('data-jstree' = '{"icon":"jstree-folder"}')
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101 li_item
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102 }
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103 })
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104 }
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105 })
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106 }
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107 #----------------- end of help functions -------------------------
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108
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109
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110 # import getopt specification matrix from a csv file
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111 opt = getopt(getopt_specification_matrix('command-line-arguments.csv',
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112 tool_dir = Sys.getenv('TOOL_INSTALL_DIR')))
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113 # define environment variables for all input values. this is useful when we
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114 # want to use input values by other programming language in r markdown
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115 do.call(Sys.setenv, opt[-1])
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116 #===============================================================
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117
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118
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119 #======================== render Rmd files =========================
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120 # copy jstree javascript library to tool output directory
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121 file.copy(
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122 from = paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/vakata-jstree-3.3.5'),
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123 to = Sys.getenv('REPORT_FILES_PATH'),
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124 recursive = TRUE
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125 )
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126
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127 # if '_site.yml' file exists, this tool is assumed to render a website.
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128 # otherwise, it renders a single html.
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129 if (file.exists(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/_site.yml'))) {
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130 # render a website
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131 system(command = 'cp -r ${TOOL_INSTALL_DIR}/*.Rmd ${REPORT_FILES_PATH}')
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132 system(command = 'cp -r ${TOOL_INSTALL_DIR}/_site.yml ${REPORT_FILES_PATH}')
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133 render_site(input = Sys.getenv('REPORT_FILES_PATH'))
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134 } else {
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135 # render a single html
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136 system(command = 'cp -r ${TOOL_INSTALL_DIR}/rmarkdown_report.Rmd ${REPORT_FILES_PATH}')
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137 # add a few lines to 'rmarkdown_report.Rmd' to generate file tree outputs
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138 jstree_lines = '
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139 ## Outputs
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140
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141 ```{r, echo=FALSE}
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142 tags$div(id="jstree", file_tree(Sys.getenv(\'REPORT_FILES_PATH\')))
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143 ```'
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144 write(
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145 x = jstree_lines,
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146 append = TRUE,
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147 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd')
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148 )
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149 render(input = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd'))
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150 }
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151 #===============================================================
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152
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153
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154 #============== expose outputs to galaxy history ===============
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155 system(command = 'sh ${TOOL_INSTALL_DIR}/expose-outputs-to-galaxy-history.sh')
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156 #===============================================================
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157
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158
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159 ##--------end of code rendering .Rmd templates----------------
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160 sink()
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161 ##=========== End of sinking output=============================