## ---- echo = FALSE------------------------------------------------------------ library(knitr) knitr::opts_chunk$set( error = FALSE, tidy = FALSE, message = FALSE, warning = FALSE, fig.width = 6, fig.height = 6, fig.align = "center" ) library(GetoptLong) options(digits = 4) ## ---- echo = FALSE------------------------------------------------------------ library(SC3) library(GOexpress) ## ----eval = FALSE------------------------------------------------------------- # ComplexHeatmap::pheatmap(...) # htShiny() ## ---- eval = FALSE------------------------------------------------------------ # library(SingleCellExperiment) # library(SC3) # library(scater) # # sce <- SingleCellExperiment( # assays = list( # counts = as.matrix(yan), # logcounts = log2(as.matrix(yan) + 1) # ), # colData = ann # ) # # rowData(sce)$feature_symbol <- rownames(sce) # sce <- sce[!duplicated(rowData(sce)$feature_symbol), ] # sce <- runPCA(sce) # sce <- sc3(sce, ks = 2:4, biology = TRUE) # # sc3_plot_expression(sce, k = 3) ## ---- eval = FALSE------------------------------------------------------------ # 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")