## ----- echo = false -----------------------------------------------------------------------------------------------------------------库（Knitr）knitr :: opts_chunk $ set（错误= false，tidy = false，message = false，warning，parnning = false，frice，fig.width = width =6，图。Height= 6，图。Align=“ Center”）库（GetOptlong）选项（Digits = 4）## --------------------------------------------------------------------------------------------------------------------------------------------------库（SC3）库（goexpress）## ------------------------------------------------------------------------------------------------------------------------------------------------------------------- # ComplexHeatmap::pheatmap(...) # htShiny() ## ---- eval = FALSE----------------------------------------------------------------------------------------------＃library（singlecellexperiment）＃library（sc3）＃library（scater）＃＃＃sce <-singlecellexperiment（＃assays = list = list = as.matrix（yan），＃logcounts，＃logcounts = log2（as。矩阵（yan） + 1）＃），＃coldata = ann＃）＃＃＃rowdata（sce）$ feature_symbol <-Rownames（sce）＃sce <-sce <-sce [！deplicated（rowdata（sce）$ features_symbol），]＃sce＃sce在k = 3）## -------------------------------------------------------------------------------------------------------------- # assignInNamespace("pheatmap", ComplexHeatmap::pheatmap, ns = "pheatmap") # library(InteractiveComplexHeatmap) # sc3_plot_expression(sce，k = 3）＃htshiny（）## ---------------------------------------------------------------------------------------------------------------------------------- selectMethod（“ sc3_plot_expression”，signature =“ singlecellexperiment”） ## ---- eval = FALSE------------------------------------------------------------ # library(GOexpress) # data(AlvMac) # set.seed(4543) # AlvMac_results <- GO_analyse( # eSet = AlvMac, f = "Treatment", # 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.main=1, main.Lsplit=30) ## ----------------------------------------------------------------------------- heatmap_GO ## ---- eval = FALSE------------------------------------------------------------ # detach("package:GOexpress", unload = TRUE) # assignInNamespace("heatmap.2", ComplexHeatmap:::heatmap.2, ns = "gplots") # library(GOexpress) # # library(InteractiveComplexHeatmap) # heatmap_GO( # go_id = "GO:0034142", result = BP.5, eSet=AlvMac, cexRow=0.4, # cexCol=1, cex.main=1, main.Lsplit=30) # htShiny() ## ---- eval = FALSE------------------------------------------------------------ # library(pheatmap) # library(gplots) # assignInNamespace("heatmap", ComplexHeatmap:::heatmap, ns = "stats") # assignInNamespace("heatmap.2", ComplexHeatmap:::heatmap.2, ns = "gplots") # assignInNamespace("pheatmap", ComplexHeatmap::pheatmap, ns = "pheatmap")