## ----setup, echo=FALSE, fig.height=4, fig.width=20, dpi=150------------------- knitr::opts_chunk$set(tidy=FALSE, cache=TRUE, dev="png", message=FALSE, error=FALSE, warning=TRUE) ## ----load--------------------------------------------------------------------- library(MAGeCKFlute) file1 = file.path(system.file("extdata", package = "MAGeCKFlute"), "testdata/rra.gene_summary.txt") gdata = ReadRRA(file1) genelist = gdata$Score names(genelist) = gdata$id genelist[1:5] ## ----HGT---------------------------------------------------------------------- # Alternative functions EnrichAnalyzer and enrich.HGT. hgtRes1 = EnrichAnalyzer(genelist[genelist< -1], method = "HGT") head(hgtRes1@result) # hgtRes2 = enrich.HGT(genelist[genelist< -1]) # head(hgtRes2@result) ## ----ORT---------------------------------------------------------------------- # Alternative functions EnrichAnalyzer and enrich.ORT. ortRes1 = EnrichAnalyzer(genelist[genelist< -1], method = "ORT") head(ortRes1@result) # ortRes2 = enrich.ORT(genelist[genelist< -1]) # head(ortRes2@result) ## ----GSE---------------------------------------------------------------------- # Alternative functions EnrichAnalyzer and enrich.GSE. gseRes1 = EnrichAnalyzer(genelist, method = "GSEA") head(gseRes1@result) # gseRes2 = enrich.GSE(genelist) # head(gseRes2@result) ## ----barview, fig.height=4, fig.width=9, dpi=150------------------------------ require(ggplot2) df = hgtRes1@result df$logFDR = -log10(df$p.adjust) p = BarView(df[1:5,], "Description", 'logFDR') p = p + labs(x = NULL) + coord_flip() p # Or use function barplot from enrichplot package barplot(hgtRes1, showCategory = 5) ## ---- fig.height=4, fig.width=9, dpi=150-------------------------------------- EnrichedView(hgtRes1, bottom = 5, mode = 1) EnrichedView(hgtRes1, bottom = 5, mode = 2) dotplot(hgtRes1, showCategory = 5) ## ---- fig.height=7, fig.width=9, dpi=150-------------------------------------- hgtRes1@result$geneID = hgtRes1@result$geneName #cnetplot cnetplot(hgtRes1, 2) ## ---- fig.height=7, fig.width=15, dpi=150------------------------------------- heatplot(hgtRes1, showCategory = 3, foldChange=genelist) emapplot(hgtRes1, layout="kk") ## ---- fig.height=4, fig.width=7, dpi=150-------------------------------------- #gseaplot gseaplot(gseRes1, geneSetID = 1, title = gseRes1$Description[1]) gseaplot(gseRes1, geneSetID = 1, by = "runningScore", title = gseRes1$Description[1]) gseaplot(gseRes1, geneSetID = 1, by = "preranked", title = gseRes1$Description[1]) #or gseaplot2(gseRes1, geneSetID = 1:3) ## ----pathway, fig.height=4, fig.width=7, dpi=150------------------------------ ## KEGG and REACTOME pathways enrich = EnrichAnalyzer(geneList = genelist[genelist< -1], type = "KEGG+REACTOME") EnrichedView(enrich, bottom = 5) ## Only KEGG pathways enrich = EnrichAnalyzer(geneList = genelist[genelist< -1], type = "KEGG") EnrichedView(enrich, bottom = 5) ## Gene ontology enrichGo = EnrichAnalyzer(genelist[genelist< -1], type = "GOBP+GOMF") EnrichedView(enrichGo, bottom = 5) ## ---- fig.height=4, fig.width=7, dpi=150-------------------------------------- enrichPro = EnrichAnalyzer(genelist[genelist< -1], type = "CORUM") EnrichedView(enrichPro, bottom = 5) ## ---- fig.height=4, fig.width=7, dpi=150-------------------------------------- enrichComb = EnrichAnalyzer(genelist[genelist< -1], type = "GOBP+KEGG") EnrichedView(enrichComb, bottom = 5) ## ----limit, fig.height=4, fig.width=7, dpi=150-------------------------------- enrich = EnrichAnalyzer(genelist[genelist< -1], type = "GOBP", limit = c(1, 80)) EnrichedView(enrich, bottom = 5) ## ----filter1, fig.height=4, fig.width=7, dpi=150------------------------------ enrich1 = EnrichAnalyzer(genelist[genelist< -1], type = "GOMF+GOBP") enrich2 = EnrichAnalyzer(genelist[genelist< -1], type = "GOMF+GOBP", filter = TRUE) enrich3 = EnrichedFilter(enrich1) EnrichedView(enrich1, bottom = 15) EnrichedView(enrich2, bottom = 15) EnrichedView(enrich3, bottom = 15) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()