＃＃ - - 设置 - - - - - - - - - - - - - - - - - - - - - ---------------------------------- knitr::opts_chunk$set(tidy=FALSE, cache=TRUE, dev="png", message=FALSE, error=FALSE, warning=TRUE) ## ----install, eval=TRUE------------------------------------------------------- if(!"MAGeCKFlute" %in% installed.packages()) BiocManager::install("MAGeCKFlute") if(!"ggplot2" %in% installed.packages()) BiocManager::install("ggplot2") library(MAGeCKFlute) library(ggplot2) ## ----load--------------------------------------------------------------------- file1 = file.path(system.file("extdata", package = "MAGeCKFlute"), "testdata/rra.gene_summary.txt") gdata = ReadRRA(file1) genelist = gdata$Score names(genelist) = gdata$id genelist = sort(genelist, decreasing = TRUE) head(genelist) ## ----HGT---------------------------------------------------------------------- # Alternative functions EnrichAnalyzer and enrich.HGT. hgtRes1 = EnrichAnalyzer(genelist[1:200], method = "HGT", type = "Pathway", organism = "mmu") head(hgtRes1@result) # hgtRes2 = enrich.HGT(genelist[1:200]) # head(hgtRes2@result) ## ----ORT---------------------------------------------------------------------- if(!"clusterProfiler" %in% installed.packages()){ BiocManager::install("clusterProfiler") } library(clusterProfiler) # Alternative functions EnrichAnalyzer and enrich.ORT. ortRes1 = EnrichAnalyzer(genelist[1:200], method = "ORT", type = "KEGG", organism = "mmu") head(ortRes1@result) # ortRes2 = enrich.ORT(genelist[genelist< -1]) # head(ortRes2@result) ## ----GSE---------------------------------------------------------------------- library(clusterProfiler) # Alternative functions EnrichAnalyzer and enrich.GSE. gseRes1 = EnrichAnalyzer(genelist, method = "GSEA", type = "Pathway", organism = "mmu") ## ----barview, fig.height=3.5, fig.width=7, dpi=150---------------------------- require(ggplot2) df = hgtRes1@result df$logFDR = -log10(df$p.adjust) p = BarView(df[1:5,], "Description", 'logFDR') p = p + labs(x = NULL) + coord_flip() p # Or use function barplot from enrichplot package barplot(hgtRes1, showCategory = 5) ## ---- fig.height=3.5, fig.width=7, dpi=150------------------------------------ ## top: up-regulated pathways; ## bottom: down-regulated pathways EnrichedView(hgtRes1, top = 5, bottom = 0, mode = 1) EnrichedView(hgtRes1, top = 5, bottom = 0, mode = 2) dotplot(hgtRes1, showCategory = 5) ## ----enrichplot, fig.height=3.5, fig.width=7, dpi=150------------------------- library(enrichplot) hgtRes1@result$geneID = hgtRes1@result$geneName cnetplot(hgtRes1, 5) heatplot(hgtRes1, showCategory = 5, foldChange = genelist) tmp <- pairwise_termsim(hgtRes1) emapplot(tmp, showCategory = 5, layout = "kk") ## ----gseaplot2, fig.height=5, fig.width=7, dpi=150---------------------------- # show GSEA results of one pathway idx = which(gseRes1$NES>0)[1] gseaplot(gseRes1, geneSetID = idx, title = gseRes1$Description[idx]) # show GSEA results of multiple pathways gseaplot2(gseRes1, geneSetID = which(gseRes1$NES>0)[1:3]) ## ----pathway, eval=FALSE------------------------------------------------------ # ## combination of the gene sets # enrichComb = EnrichAnalyzer(genelist[1:200], type = "KEGG+REACTOME", organism = "mmu") # EnrichedView(enrichComb, top = 5) # ## All pathways # enrich = EnrichAnalyzer(geneList = genelist[1:200], type = "REACTOME", organism = "mmu") # EnrichedView(enrich, top = 5) # ## All gene ontology # enrichGo = EnrichAnalyzer(genelist[1:200], type = "GOBP", organism = "mmu") ## ---- fig.height=3.5, fig.width=7, dpi=150------------------------------------ enrichPro = EnrichAnalyzer(genelist[1:200], type = "Complex", organism = "mmu") EnrichedView(enrichPro, top = 5) ## ----limit, fig.height=3.5, fig.width=7, dpi=150------------------------------ enrich = EnrichAnalyzer(genelist[1:200], type = "GOBP", limit = c(2, 80), organism = "mmu") EnrichedView(enrich, top = 5) ## ----filter1, fig.height=3.5, fig.width=7, dpi=150---------------------------- enrich1 = EnrichAnalyzer(genelist[1:200], type = "Pathway", organism = "mmu") enrich2 = EnrichedFilter(enrich1) EnrichedView(enrich1, top = 15) EnrichedView(enrich2, top = 15) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()