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comparison QDNAseq.R @ 69:b4477584bb03 draft

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Uploaded
author stef
date Tue, 26 Aug 2014 08:40:24 -0400
parents 68a090cffb6f
children fb2dfd8ba417
comparison
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68:68a090cffb6f 69:b4477584bb03
297 297
298 ## COPYNUMBER PLOT 298 ## COPYNUMBER PLOT
299 png( img_file_path, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES ); 299 png( img_file_path, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES );
300 par( PAR_SET ) 300 par( PAR_SET )
301 plot( copyNumbersSmooth[ ,sample ], main=paste(sample, ": CopyNumbers", sep="") ) 301 plot( copyNumbersSmooth[ ,sample ], main=paste(sample, ": CopyNumbers", sep="") )
302 mtext( paste( binSizeString, " bins" sep=""), 3 ) 302 mtext( paste( binSizeString, " bins", sep=""), 3 )
303 abline( h=c(-2,-1,1,2,3,4), lty=1, lwd=0.5, col="grey" ) 303 abline( h=c(-2,-1,1,2,3,4), lty=1, lwd=0.5, col="grey" )
304 dev.off() 304 dev.off()
305 305
306 plotted_images[[ paste(binSize, sample, type, sep="_" ) ]] <- img_file 306 plotted_images[[ paste(binSize, sample, type, sep="_" ) ]] <- img_file
307 307
311 img_file_path <- paste( outputPath, '/', img_file, sep='' ) 311 img_file_path <- paste( outputPath, '/', img_file, sep='' )
312 312
313 ## COPYNUMBER PLOT 313 ## COPYNUMBER PLOT
314 png( img_file_path, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES ); 314 png( img_file_path, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES );
315 par( PAR_SET ) 315 par( PAR_SET )
316 plot( copyNumbersSegmented[ ,sample ], main=paste(sample, ": CopyNumbers and Segments", sep="") ); 316 plot( copyNumbersSegmented[ ,sample ], main=paste(sample, ": CopyNumbers and Segments", sep="") )
317 mtext( paste( "(", binSizeString, " bins)" sep=""), 3 ) 317 mtext( paste( "(", binSizeString, " bins)", sep=""), 3 )
318 abline( h=c(-2,-1,1,2,3,4), lty=1, lwd=0.5, col="grey" ) 318 abline( h=c(-2,-1,1,2,3,4), lty=1, lwd=0.5, col="grey" )
319 dev.off() 319 dev.off()
320 320
321 plotted_images[[ paste(binSize, sample, type, sep="_" ) ]] <- img_file 321 plotted_images[[ paste(binSize, sample, type, sep="_" ) ]] <- img_file
322 322