# # # R代码从装饰图案来源的策划。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:策划。Rnw: 5 - 6 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #选项(宽度= 80)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:策划。Rnw: 47 - 64 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #要求(Genominator)选项(verbose = FALSE) N < - 100000 #观测的数量。K < - 100 #注释区域,数量不少于10 df < - data.frame(对应=样本(1:16,大小= N,取代= TRUE),位置=样本(1:1000大小= N,取代= TRUE),链=样本(c (1 l, 1升),大小= N,取代= TRUE)) eData < - aggregateExpData (importToExpData (df, dbFilename = " pmy。db”,覆盖= TRUE,表名= " ex_tbl”)) annoData < data.frame(对应=样本(1:16,大小= K,取代= TRUE),链=样本(c(1, 1),大小= K,取代= TRUE),开始=(圣<——样本(大小= K, 1:1000取代= TRUE)),结束=圣+ rpois (K, 75),功能= c(“基因”,“基因间”)(样本(1:2,大小= K,取代= TRUE)]) rownames (annoData) < - - - - - -粘贴(“英语教学”,1:K, 9 =“。”) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:策划。Rnw: 67 - 69 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # rp < - Genominator::: makeRegionPlotter(列表(“跟踪。1”=列表(expData = eData =“计数”)))args (rp) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:策划。Rnw: 74 - 75 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # rp(1, 1000) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:策划。Rnw: 82 - 85 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # rp < - Genominator::: makeRegionPlotter(列表(“跟踪。1”=列表(expData = eData, =“计数”,dp = DisplayPars (lwd =。45,颜色= "灰色"))))rp(400、500) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:策划。Rnw: 93 - 103 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # annoFactory < - Genominator::: makeAnnoFactory (annoData featureColumnName =“特性”,groupColumnName = NULL, idColumnName = NULL, dp = DisplayPars(“基因”=“蓝色”、“基因间”=“绿色”))rp < - Genominator::: makeRegionPlotter(列表(“跟踪。1”=列表(expData = eData, =“计数”,dp = DisplayPars (lwd =。2,颜色=“灰色”))”。2”=列表(expData = eData, =“计数”,fx = log2 DisplayPars (lwd =。3, color = "black"))), annoFactory = annoFactory) rp(annoData[1,"chr"], annoData[1, "start"] - 100, annoData[1, "end"] + 100) ################################################### ### code chunk number 7: plotting.Rnw:113-127 ################################################### require("biomaRt") mart <- useMart("ensembl", dataset = "scerevisiae_gene_ensembl") annoFactory <- Genominator:::makeAnnoFactory(mart, chrFunction = function(chr) as.roman(chr)) load(system.file("data", "chr1_yeast.rda", package = "Genominator")) head(chr1_yeast) yData <- importToExpData(chr1_yeast, dbFilename = "my.db", tablename = "yeast", overwrite = TRUE) rp <- Genominator:::makeRegionPlotter(list("track.-" = list(expData = yData, what = c("mRNA_1", "mRNA_2"), fx = rowMeans, strand = -1, dp = DisplayPars(lwd=.3, color = "grey"))), annoFactory = annoFactory) rp(1, 20000, 50000) ################################################### ### code chunk number 8: sessionInfo ################################################### toLatex(sessionInfo())