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comparison QDNAseq.R @ 66:823791a3d7e1 draft

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Uploaded
author stef
date Wed, 20 Aug 2014 11:22:43 -0400
parents 2f0af8970aea
children 2d939f4c23fe
comparison
equal deleted inserted replaced
65:46161d4fb9cb 66:823791a3d7e1
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
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