Mercurial > repos > xuebing > sharplabtool
diff Start_GenometriCorr.R @ 14:76e1b1b21cce default tip
Deleted selected files
author | xuebing |
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date | Tue, 13 Mar 2012 19:05:10 -0400 |
parents | 292186c14b08 |
children |
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--- a/Start_GenometriCorr.R Sat Mar 10 08:17:36 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,105 +0,0 @@ -# Start_GenometriCorr.R - -################################################### -# # -# command-line interface to GenometriCorr # -# functions, for use with Galaxy. # -# # -################################################### - -capture.output <- function (result, pdffile, output_options) -{ - if(output_options != "stats") - { - pdf(file=pdffile, width=10, height=19, paper="special") - - if (output_options != "vis") #need to do a plot - { - mymat <- matrix(ncol=3, nrow=4) - mymat[1,1] <- 1 - mymat[1,2] <- 2 - mymat[1,3] <- 3 - mymat[2,1] <- 4 - mymat[2,2] <- 5 - mymat[2,3] <- 6 - mymat[3,1] <- 7 - mymat[3,2] <- 8 - mymat[3,3] <- 9 - mymat[4,1] <- 10 - mymat[4,2] <- 11 - mymat[4,3] <- 12 - - layout(mymat, heights=c(0.2,0.2,0.2,0.2)) - plot(result, pdffile, make.new=FALSE) - } - if (output_options != "plot") #need to do the bigger graphic - { - mymat <- matrix(ncol=2, nrow=8) - mymat[1,1] <- 2 - mymat[1,2] <- 3 - mymat[2,1] <- 4 - mymat[2,2] <- 4 - mymat[3,1] <- 1 - mymat[3,2] <- 1 - mymat[4,1] <- 5 - mymat[4,2] <- 6 - mymat[5,1] <- 7 - mymat[5,2] <- 7 - mymat[6,1] <- 8 - mymat[6,2] <- 9 - mymat[7,1] <- 10 - mymat[7,2] <- 10 - mymat[8,1] <- 11 - mymat[8,2] <- 12 - layoutresults <- 3 - - layout(mymat, heights=c(0.05,0.05,0.15,0.15,0.15,0.15,0.15,0.15)) - visualize(result, pdffile, make.new=FALSE) - } - dev.off() - } - - if (output_options == "stats") - { - show(result) - } -} - - - -# Reads the command line arguments -args <- commandArgs(trailingOnly=T) - -suppressPackageStartupMessages(library('GenometriCorr', warn.conflicts=F, verbose=F)) -suppressPackageStartupMessages(library('graphics', warn.conflicts=F, verbose=F)) -suppressPackageStartupMessages(library('gdata', warn.conflicts=F, verbose=F)) -suppressPackageStartupMessages(library('gplots', warn.conflicts=F, verbose=F)) -suppressPackageStartupMessages(library('gtools', warn.conflicts=F, verbose=F)) -suppressPackageStartupMessages(library('caTools', warn.conflicts=F, verbose=F)) -suppressPackageStartupMessages(library('grid', warn.conflicts=F, verbose=F)) - - - -# Variables -query_file <- "" -reference_file <- "" -config_file <- "" -output_options <- "" - -# Parse the command line arguments - -config_file <- args[1] -query_file <- as.character(args[2]) -reference_file <- as.character(args[3]) -output_options <- args[4] -pdffile <- args[5] - -conf<-new("GenometriCorrConfig",config_file) - -print('OK') - -result<-suppressWarnings(suppressPackageStartupMessages(GenometriCorr:::run.config(conf,query=query_file,reference=reference_file))) -print('OK2') - -hideoutput <- capture.output(result, pdffile=args[5], output_options) -