# # # R代码从装饰图案来源qrqc。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:qrqc。Rnw:百分比较# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(qrqc)。fastq < readSeqFile(系统。文件(“extdata”、“测试。fastq’,包= ' qrqc ')) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:qrqc。Rnw: 54-55 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #。fastq@filename < -”测试。fastq’#否则长临时dir将这里# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 3号代码块:qrqc。Rnw: 69 - 70 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #。fastq # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:figQualPlot # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # qualPlot (s.fastq) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:figQualPlot-list # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # s.trimmed。fastq < readSeqFile(系统。文件(“extdata”、“test-trimmed。fastq’,包= ' qrqc ')) qualPlot(列表(“修剪”= s.trimmed。fastq,“修剪”= s.fastq)) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:figBasePlot-freqs # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # basePlot (s.fastq) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:figBasePlot-prop # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # basePlot (s。fastq基地= c (“G”、“c”),几何学=“酒吧”,类型=“比例”)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:figSeqlenPlot # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # seqlenPlot (s.trimmed.fastq) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块9号:figGcPlot # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # gcPlot (s.fastq) + geom_hline (yintercept = 0.5,颜色=“紫色”)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块10号:figEntropy # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #。兰德< - readSeqFile(系统。文件(“extdata”、“随机的。fasta’,包= ' qrqc '),类型=“fasta”) kmerEntropyPlot(列表(“污染”=。fastq“随机”=。rand)) ################################################### ### code chunk number 11: figKmerKL ################################################### kmerKLPlot(s.fastq) ################################################### ### code chunk number 12: figKmerKLRand ################################################### contam.file <- system.file('extdata', 'test-contam.fastq', package='qrqc') s.contam <- readSeqFile(contam.file, kmer=TRUE, k=5) kmerKLPlot(list("contaminated"=s.fastq, "random"=s.rand, "highly contaminated"=s.contam)) ################################################### ### code chunk number 13: figCoord ################################################### basePlot(s.fastq, geom="bar") + coord_flip() ################################################### ### code chunk number 14: figZoom ################################################### qualPlot(s.fastq) + scale_x_continuous(limits=c(60, 85)) + theme_bw() ################################################### ### code chunk number 15: figAltqual ################################################### ggplot(getQual(s.fastq)) + geom_linerange(aes(x=position, ymin=lower, ymax=upper, color=mean)) + scale_color_gradient("mean quality", low="red", high="green") + scale_y_continuous("quality") ################################################### ### code chunk number 16: qrqc.Rnw:404-405 ################################################### sessionInfo()