Mercurial > repos > mingchen0919 > rmarkdown_deseq2_count_matrix
view rmarkdown_deseq2_count_matrix_render.R @ 1:629323b5fc0c draft
update tool
author | mingchen0919 |
---|---|
date | Sat, 30 Dec 2017 16:39:39 -0500 |
parents | c1f718dd6c7a |
children |
line wrap: on
line source
library(getopt) library(rmarkdown) library(htmltools) library(dplyr) library(DT) library(DESeq2) ##============ 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$ECHO = c('echo', 'e', '1', 'logical') args_list$c = c('count_data', 'c', '1', 'character') args_list$n = c('count_matrix_column_names', 'n', '1', 'character') args_list$n = c('count_matrix_column_names', 'n', '1', 'character') args_list$C = c('col_data', 'C', '1', 'character') args_list$D = c('design_formula', 'D', '1', 'character') args_list$k = c('contrast_condition', 'k', '1', 'character') args_list$T = c('treatment', 'T', '1', 'character') args_list$K = c('control', 'K', '1', 'character') ##--------2. output report and outputs -------------- args_list$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') ##--------3. .Rmd templates in the tool directory ---------- args_list$TOOL_TEMPLATE_RMD = c('tool_template_rmd', 't', '1', 'character') ##----------------------------------------------------------- opt = getopt(t(as.data.frame(args_list))) ##=======STEP 2: create report directory (optional)========== ## ##=========================================================== dir.create(opt$report_dir) ##=STEP 3: replace placeholders in .Rmd with argument values= ## ##=========================================================== #++ need to replace placeholders with args values one by one+ readLines(opt$tool_template_rmd) %>% # (function(x) { # gsub('ECHO', opt$echo, x) # }) %>% # (function(x) { # gsub('REPORT_DIR', opt$report_dir, x) # }) %>% (function(x) { fileConn = file('tool_template.Rmd') writeLines(x, con=fileConn) close(fileConn) }) ##=============STEP 4: render .Rmd templates================= ## ##=========================================================== render('tool_template.Rmd', output_file = opt$report_html) ##--------end of code rendering .Rmd templates---------------- sink() ##=========== End of sinking output=============================