## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "vignettes/figures/", out.width = "100%" ) ## ----eval = FALSE, message = FALSE-------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("fedup") ## ----message = FALSE---------------------------------------------------------- devtools::install_github("rosscm/fedup", quiet = TRUE) ## ----message = FALSE---------------------------------------------------------- library(fedup) library(dplyr) library(tidyr) library(ggplot2) ## ----------------------------------------------------------------------------- data(geneDouble) data(pathwaysGMT) ## ----------------------------------------------------------------------------- str(geneDouble) str(head(pathwaysGMT)) ## ----------------------------------------------------------------------------- fedupRes <- runFedup(geneDouble, pathwaysGMT) ## ----------------------------------------------------------------------------- set <- "FASN_negative" print(head(fedupRes[[set]][which(fedupRes[[set]]$status == "enriched"),])) print(head(fedupRes[[set]][which(fedupRes[[set]]$status == "depleted"),])) ## ----------------------------------------------------------------------------- set <- "FASN_positive" print(head(fedupRes[[set]][which(fedupRes[[set]]$status == "enriched"),])) print(head(fedupRes[[set]][which(fedupRes[[set]]$status == "depleted"),])) ## ----------------------------------------------------------------------------- fedupPlot <- fedupRes %>% bind_rows(.id = "set") %>% separate(col = "set", into = c("set", "sign"), sep = "_") %>% subset(qvalue < 0.05) %>% mutate(log10qvalue = -log10(qvalue)) %>% mutate(pathway = gsub("\\%.*", "", pathway)) %>% as.data.frame() ## ----fedupDotPlot, fig.width = 11, fig.height = 15.5-------------------------- p <- plotDotPlot( df = fedupPlot, xVar = "log10qvalue", yVar = "pathway", xLab = "-log10(qvalue)", fillVar = "sign", fillLab = "Genetic interaction", fillCol = c("#6D90CA", "#F6EB13"), sizeVar = "fold_enrichment", sizeLab = "Fold enrichment") + facet_grid("sign", scales = "free", space = "free") + theme(strip.text.y = element_blank()) print(p) ## ----------------------------------------------------------------------------- resultsFolder <- tempdir() writeFemap(fedupRes, resultsFolder) ## ----------------------------------------------------------------------------- gmtFile <- tempfile("pathwaysGMT", fileext = ".gmt") writePathways(pathwaysGMT, gmtFile) ## ----fedupEM_geneDouble, eval = FALSE----------------------------------------- # netFile <- tempfile("fedupEM_geneDouble", fileext = ".png") # plotFemap( # gmtFile = gmtFile, # resultsFolder = resultsFolder, # qvalue = 0.05, # chartData = "DATA_SET", # hideNodeLabels = TRUE, # netName = "fedupEM_geneDouble", # netFile = netFile # ) ## ----------------------------------------------------------------------------- sessionInfo()