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1 #!/usr/bin/Rscript
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2
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3 ## --------------------
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4 ## prints all arguments as msg
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5 ## --------------------
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6 catMsg <- function( msg=c() ){
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7 cat( MAIN_NAME, paste( msg, collapse="" ), "\n", sep='')
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8 }
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9
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10
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11 ## ==================================================
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12 ## Start of analysis
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13 ## ==================================================
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14 MAIN_NAME <- '[INFO] '
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15 catMsg( "Starting QDNAseq-plot wrapper" )
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16 catMsg( "Loading R libraries" )
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17
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18 ## supress msg to allow R to finish with non-error msg
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19 suppressWarnings( suppressMessages( library( QDNAseq, quietly = TRUE ) ) )
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20
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21 ## only one param: the tmp config file
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22 cmdLineArgs <- commandArgs(TRUE)
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23 config <- cmdLineArgs[1]
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24
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25 ## sourcing the config file will load all input params
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26 ## many variables are imported via sourced "config"
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27 source( config ) # outputPngPath, outputPdfPath, allOrOne, rdsFilePath
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28 #cat( "ALL? ", allOrOne, sep='' )
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29
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30 ## desparate tries to make png text scale well, damn you R...!
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31 PLOT_RES <- min( PLOT_WIDTH, PLOT_HEIGHT ) / 6.3
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32 PAR_SET <- list( pch=22 )
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33 systemUser <- system("whoami",T)
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34 qdnaseqVersion <- packageDescription( "QDNAseq" )$Version
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35 rVersion <- R.version.string
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36 catMsg( c("QDNAseq version: ", qdnaseqVersion) )
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37 catMsg( c( rVersion ) )
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38
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39 qdnaseqObject <- readRDS( rdsFilePath )
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40 ## COPYNUMBER PLOT
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41 sample <- SAMPLE_INDEX
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42 png( outputPngPath, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES )
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43 par( PAR_SET )
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44 plot( qdnaseqObject[ ,sample ] )
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45 #mtext( "plotted in galaxy", 3 )
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46 abline( h=c(-2,-1,1,2,3,4), lty=1, lwd=0.5, col="grey" )
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47 dev.off()
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48
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49
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50 ## all ok
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51 q(status=0)
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