Mercurial > repos > mingchen0919 > rmarkdown_wgcna
view wgcna_eigengene_visualization_render.R @ 3:240af4b07b92 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit a23e23222252167ef7c3338a4872e84706df8f83-dirty
author | mingchen0919 |
---|---|
date | Tue, 08 Aug 2017 15:06:26 -0400 |
parents | 4275479ada3a |
children |
line wrap: on
line source
##======= Handle arguments from command line ======== # setup R error handline to go to stderr options(show.error.messages=FALSE, error=function(){ cat(geterrmessage(), file=stderr()) quit("no", 1, F) }) # we need that to not crash galaxy with an UTF8 error on German LC settings. loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") # suppress warning options(warn = -1) options(stringsAsFactors=FALSE, useFancyQuotes=FALSE) args = commandArgs(trailingOnly=TRUE) suppressPackageStartupMessages({ library(getopt) library(tools) }) # 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. spec_list=list() ##------- 1. input data --------------------- spec_list$ECHO = c('echo', 'e', '1', 'character') spec_list$CONSTRUCT_NETWORK_WORKSPACE = c('construct_network_workspace', 'w', '1', 'character') spec_list$SOFT_THRESHOLD_POWER = c('soft_threshold_power', 'p', '2', 'double') spec_list$PLOT_GENES = c('plot_genes', 'n', '1', 'integer') ##--------2. output report and report site directory -------------- spec_list$OUTPUT_HTML = c('wgcna_eigengene_visualization_html', 'o', '1', 'character') spec_list$OUTPUT_DIR = c('wgcna_eigengene_visualization_dir', 'd', '1', 'character') ##--------3. Rmd templates in the tool directory ---------- spec_list$WGCNA_EIGENGENE_VISUALIZATION_RMD = c('wgcna_eigengene_visualization_rmd', 'M', '1', 'character') ##------------------------------------------------------------------ spec = t(as.data.frame(spec_list)) opt = getopt(spec) # arguments are accessed by long flag name (the first column in the spec matrix) # NOT by element name in the spec_list # example: opt$help, opt$expression_file ##====== End of arguments handling ========== #------ Load libraries --------- library(rmarkdown) library(WGCNA) library(DT) library(htmltools) library(ggplot2) #----- 1. create the report directory ------------------------ system(paste0('mkdir -p ', opt$wgcna_eigengene_visualization_dir)) #----- 2. generate Rmd files with Rmd templates -------------- # a. templates without placeholder variables: # copy templates from tool directory to the working directory. # b. templates with placeholder variables: # substitute variables with user input values and place them in the working directory. #----- 01 wgcna_eigengene_visualization.Rmd ----------------------- readLines(opt$wgcna_eigengene_visualization_rmd) %>% (function(x) { gsub('ECHO', opt$echo, x) }) %>% (function(x) { gsub('CONSTRUCT_NETWORK_WORKSPACE', opt$construct_network_workspace, x) }) %>% (function(x) { gsub('SOFT_THRESHOLD_POWER', opt$soft_threshold_power, x) }) %>% (function(x) { gsub('PLOT_GENES', opt$plot_genes, x) }) %>% (function(x) { gsub('OUTPUT_DIR', opt$wgcna_eigengene_visualization_dir, x) }) %>% (function(x) { fileConn = file('wgcna_eigengene_visualization.Rmd') writeLines(x, con=fileConn) close(fileConn) }) #------ 3. render all Rmd files -------- render('wgcna_eigengene_visualization.Rmd', output_file = opt$wgcna_eigengene_visualization_html) #-------4. manipulate outputs -----------------------------