## ----setup, include=TRUE------------------------------------------------------ library(EWCE) set.seed(1234) #### Package name #### pkg <- tolower("EWCE") #### Username of DockerHub account #### docker_user <- "neurogenomicslab" ## ----------------------------------------------------------------------------- ctd <- ewceData::ctd() ## ----fig.width=7, fig.height=5, error=TRUE------------------------------------ plt_exp <- EWCE::plot_ctd(ctd = ctd, level = 1, genes = c("Apoe","Gfap","Gapdh"), metric = "mean_exp") ## ----fig.width=9, fig.height=5, error=TRUE------------------------------------ plt_spec <- EWCE::plot_ctd(ctd = ctd, level = 2, genes = c("Apoe","Gfap","Gapdh"), metric = "specificity") ## ----------------------------------------------------------------------------- hits <- ewceData::example_genelist() print(hits) ## ----------------------------------------------------------------------------- reps <- 100 annotLevel <- 1 ## ----------------------------------------------------------------------------- full_results <- EWCE::bootstrap_enrichment_test(sct_data = ctd, sctSpecies = "mouse", genelistSpecies = "human", hits = hits, reps = reps, annotLevel = annotLevel) ## ----------------------------------------------------------------------------- knitr::kable(full_results$results) ## ----error=TRUE--------------------------------------------------------------- plot_list <- EWCE::ewce_plot(total_res = full_results$results, mtc_method = "BH", ctd = ctd) print(plot_list$withDendro) ## ----Session Info------------------------------------------------------------- utils::sessionInfo()