Mercurial > repos > vmarcon > summary_statistics
comparison summary_statistics_galaxy.R @ 0:46ddb0591d8b draft default tip
planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
| author | vmarcon |
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| date | Thu, 18 Jan 2018 07:44:37 -0500 |
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| -1:000000000000 | 0:46ddb0591d8b |
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| 1 ########################################################################### | |
| 2 # Quality controls and descriptive analysis plots # | |
| 3 ########################################################################### | |
| 4 # Authors: Melanie Petera # | |
| 5 ########################################################################### | |
| 6 # Description : This script allows various displays of data for quality # | |
| 7 # control and descriptive analysis. The input data is a matrix of # | |
| 8 # quantitative variables, and it returns chosen plots in png format # | |
| 9 # and a table with chosen statistics. # | |
| 10 ########################################################################### | |
| 11 # Specific R packages: # | |
| 12 # - edgeR (needed for MA plots) # | |
| 13 ########################################################################### | |
| 14 # Version 1 (06-06-2014): display boxplot, histogram, density plot, # | |
| 15 # MA plot, pairs plot, and return a table of chosen statistics # | |
| 16 # (quantiles, mean, variance, standard error of the mean) # | |
| 17 ########################################################################### | |
| 18 | |
| 19 | |
| 20 ##------------------------------ | |
| 21 ## Libraries laoding | |
| 22 ##------------------------------ | |
| 23 # For parseCommandArgs function | |
| 24 library(batch) | |
| 25 | |
| 26 # R script call | |
| 27 source_local <- function(fname) | |
| 28 { | |
| 29 argv <- commandArgs(trailingOnly = FALSE) | |
| 30 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) | |
| 31 source(paste(base_dir, fname, sep="/")) | |
| 32 } | |
| 33 | |
| 34 #Import the different functions used for Summary_Statistics | |
| 35 source_local("summary_statistics.R") | |
| 36 | |
| 37 ##------------------------------ | |
| 38 ## Lecture parametres | |
| 39 ##------------------------------ | |
| 40 argLs <- parseCommandArgs(evaluate=FALSE) | |
| 41 | |
| 42 desc_fct(file.in=argLs[["file_in"]], | |
| 43 nacode=argLs[["NA_code"]], | |
| 44 table_file=argLs[["table_file"]], | |
| 45 graph_file=argLs[["graph_file"]], | |
| 46 stat=argLs[["stat"]], | |
| 47 chosen.stat=argLs[["stat_chosen"]], | |
| 48 ploting=argLs[["ploting"]], | |
| 49 chosen.plot=argLs[["plot_chosen"]], | |
| 50 log_file=argLs[["log_file"]]) | |
| 51 | |
| 52 |