# # # R代码从装饰图案的seqTools_qual_report来源。Rnw的utf - 8编码:# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:seqTools_qual_report。Rnw: 88 - 95 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(seqTools) fqdir <系统。文件(“extdata”,包=“seqTools”) fqq < -fastqq(文件。路径(fqdir c (“g4_l101_n100.fq。广州”、“g5_l101_n100.fq.gz”), k = 4, probeLabel = c(“四国集团”、“g5)) #设置到其他位置basedir < -getwd() # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:seqTools_qual_report。Rnw: 99 - 100 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # fqq # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:seqTools_qual_report。Rnw: 105 - 109 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # dfr < -data.frame(文件= basename(文件名(fqq)),样品= probeLabel (fqq),读取=格式(nReads (fqq) big.mark = Sys.localeconv()[7]))打印(dfr) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:seqTools_qual_report。Rnw: 117 - 118 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # plotNucCount (fqq) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:seqTools_qual_report。Rnw: 123 - 124 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # plotGCcontent (fqq) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:seqTools_qual_report。Rnw: 130 - 142 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #,(我在1:nfile (fqq)){文件< - file。路径(basedir,粘贴(“nucFreq_”,我,”。pdf”, 9 = " ")) pdf(文件、宽= 6,高= 6)plotNucFreq (fqq,我)不可见(dev.off())猫(“\ \{图}[H] \ n”)猫(“\ \{中心}\ n”)猫(“\ \ includegraphics{”文件,“}\ n”, 9 = " ")猫(“\ \{中心}\ n”)猫(“\ \{图}\ n \ n”)} # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:seqTools_qual_report。Rnw: 152 - 164 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #,(我在1:nfile (fqq)){文件< - file。路径(basedir粘贴(“phredQuant_”,我“. pdf”, 9 = " ")) pdf(文件)plotPhredQuant (fqq, i) dev.off()猫(“\ \{图}[H] \ n”)猫(“\ \{中心}\ n”)猫(“\ \ includegraphics{”文件,“}\ n”, 9 = " ")猫(“\ \{中心}\ n”)猫(“\ \{图}\ n \ n”)} # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:seqTools_qual_report。Rnw: 172 - 198 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # fqi < -fqq probeLabel (fqi) <粘贴(1:nfile (fqi) probeLabel (fqi), 9 =“_”) lbl < -probeLabel (fqi) #可以设置另一个调色板关口< -terrain.colors (4) col_label <函数(n){如果(is.leaf (n)){<属性(n)我<——(美元标签= = lbl)猫(美元的标签,“\ t”,我“\ n”) attr (n, nodePar) < - c (nodePar美元,列表(实验室。坳=关口[% % 4 + 1],pch = " ", lab.cex = 1.2))}返回(n)} cbm < -cbDistMatrix (fqi) hc < -as.dendrogram (hclust (as.dist (cbm))) hcd < -dendrapply (hc, col_label) # op < - par (oma = c (1, 1, 1, 1), 3 = c(1, 1, 1, 12) + 0.1)情节(hcd,水平的= TRUE, edgePar =列表(lwd = 2, lty = 1)票面(凤凰社)