## ----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")

