# #——风格,回声= FALSE,结果= '飞机 '-------------------------------------------------------- BiocStyle:减价()选项(宽度= 100,max.print = 1000) knitr:: opts_chunk设置(eval = as.logical (Sys美元。采用“KNITR_EVAL”,“真正的”)),缓存= as.logical (Sys。采用“KNITR_CACHE”,“真正的”)),错误= FALSE) # #——加载数据 ------------------------------------------------------------------------------------ 图书馆(“气道”)的数据(气管)# #——玩 ----------------------------------------------------------------------------------------- 库(“气道”)数据(气管)se < -气道se # #——revise-se ------------------------------------------------------------------------------------ (试验(se) colSums(化验(se)) colData (se) rowRanges (se) # #——make-dds ------------------------------------------------------------------------------------- 图书馆(DESeq2) dds < - DESeqDataSet (,设计= ~细胞+敏捷)# #——do-rlog -------------------------------------------------------------------------------------- 行< - rlog (dds)头(化验(行 )) ## ---- 经销 ----------------------------------------------------------------------------------------- sampleDists < -区域(t(化验(行)))sampleDists # #——消息= FALSE -------------------------------------------------------------------------------- 库(gplots)库(RColorBrewer) sampleDistMatrix < -。<- paste(rld$dex, rld$cell, sep="-") color <- colorRampPalette(rev(brewer. txt);pal(9，“蓝调”))(255)hc <- hclust(样本)热图。2 (sampleDistMatrix Rowv = as.dendrogram (hc)、symm = TRUE,跟踪=“没有”,上校=颜色,利润率= c (2, 10), labCol = FALSE ) ## ---- 主成分分析 ------------------------------------------------------------------------------------------ plotPCA(行,intgroup = c(“敏捷”,“细胞 ")) ## ---- mds ------------------------------------------------------------------------------------------ 库(ggplot2) mds < - data.frame (cmdscale (sampleDistMatrix)) mds < cbind (mds,colData(行))qplot (X1, X2,颜色=敏捷,形状=细胞,data = as.data.frame (mds )) ## ---- sessionInfo ---------------------------------------------------------------------------------- sessionInfo ()