view QDNAseq-plot.R @ 78:81ba2f857fe2 draft

Uploaded

#!/usr/bin/Rscript

## --------------------
## prints all arguments as msg
## --------------------
catMsg <- function( msg=c() ){	
	cat( MAIN_NAME, paste( msg, collapse="" ), "\n", sep='')
}


## ==================================================
## Start of analysis
## ==================================================
MAIN_NAME <- '[INFO] '
catMsg( "Starting QDNAseq-plot wrapper" )
catMsg( "Loading R libraries" )

## supress msg to allow R to finish with non-error msg
suppressWarnings( suppressMessages( library( QDNAseq, quietly = TRUE ) ) )

## only one param: the tmp config file
cmdLineArgs <- commandArgs(TRUE)
config      <- cmdLineArgs[1]

## sourcing the config file will load all input params
## many variables are imported via sourced "config"
source( config ) # outputPngPath, outputPdfPath, allOrOne, rdsFilePath
#cat( "ALL? ", allOrOne, sep='' )

## desparate tries to make png text scale well, damn you R...!
PLOT_RES  <- min( PLOT_WIDTH, PLOT_HEIGHT ) / 6.3 
PAR_SET   <- list( pch=22 )
systemUser <- system("whoami",T)
qdnaseqVersion <- packageDescription( "QDNAseq" )$Version
rVersion <- R.version.string
catMsg( c("QDNAseq version: ", qdnaseqVersion) )
catMsg( c( rVersion ) )

qdnaseqObject <- readRDS( rdsFilePath )
## COPYNUMBER PLOT
sample <- SAMPLE_INDEX
png( outputPngPath, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES )
	par( PAR_SET )
	plot( qdnaseqObject[ ,sample ] ) 
	#mtext( "plotted in galaxy", 3 )
	abline( h=c(-2,-1,1,2,3,4), lty=1, lwd=0.5, col="grey" )
dev.off()


## all ok
q(status=0)