# #——回声= FALSE ------------------------------------------------------------ 库(knitr) knitr: opts_chunk美元集(错误= FALSE,整洁= FALSE,消息= FALSE,警告= FALSE, fig.width = 6, fig.height = 6,fig.align = "中心")库(GetoptLong)选项(数字= 4 ) ## ---- 回声= FALSE ------------------------------------------------------------ 库(SC3)库(GOexpress) # # - eval = FALSE ------------------------------------------------------------- # # htShiny ComplexHeatmap: pheatmap(…) () ## ---- eval = FALSE ------------------------------------------------------------ # 库(SingleCellExperiment) #库(SC3) #库(嘘)# # sce < - SingleCellExperiment(#(#化验=列表数量= as.matrix(严),# logcounts = log2 (as.matrix (yan) + 1) #), # colData =安#)构成了rowData (sce) $ # # feature_symbol < - rownames南加州爱迪生公司(sce) # < - sce[!重复构成了rowData (sce) feature_symbol美元)(,)# sce < - runPCA南加州爱迪生公司(sce) # < - sc3 (sce、ks = 2:4,生物学= TRUE) # # sc3_plot_expression (sce k = 3 ) ## ---- eval = FALSE ------------------------------------------------------------ # assignInNamespace(“pheatmap”,ComplexHeatmap:: pheatmap,ns = " pheatmap”)#库(InteractiveComplexHeatmap) # sc3_plot_expression (sce、k = 3) # htShiny () ## ----------------------------------------------------------------------------- selectMethod(“sc3_plot_expression”,签名= " SingleCellExperiment ") ## ---- eval = FALSE ------------------------------------------------------------ # 数据(AlvMac)库(GOexpress) # # set.seed (4543) # AlvMac_results < - GO_analyse (# eSet = AlvMac, f =“治疗”,# GO_genes = AlvMac_GOgenes,all_GO=AlvMac_allGO, all_genes=AlvMac_allgenes) # BP.5 <- subset_scores(# result = AlvMac_results. #pVal， # namespace = "biological_process"， # total = 5， # p.val=0.05) # heatmap_GO(# go_id = "GO:0034142"， result = BP.5, eSet=AlvMac, cexRow=0.4， # cexCol=1, cex. 0)主要= 1,main.Lsplit = 30 ) ## ----------------------------------------------------------------------------- heatmap_GO # # - eval = FALSE ------------------------------------------------------------ # 分离(“包:GOexpress”,卸载= TRUE) # assignInNamespace(“热图。2”,ComplexHeatmap:::热图。2, ns = "gplots") # library(GOexpress) # # library(InteractiveComplexHeatmap) # heatmap_GO(# go_id = "GO:0034142"， result = BP.5, eSet=AlvMac, cexRow=0.4， # cexCol=1, cex. 5， # cexCol= # #主要= 1,# htShiny main.Lsplit = 30) () ## ---- eval = FALSE ------------------------------------------------------------ # 库(pheatmap) #库(gplots) # assignInNamespace(“热图”,ComplexHeatmap:::的热图,ns =“统计数据”)# assignInNamespace(“热图。2”,ComplexHeatmap:::热图。2、ns = "gplots") # assignInNamespace("pheatmap"， ComplexHeatmap::pheatmap, ns = "pheatmap")