## ----style, echo=FALSE, results="asis", message=FALSE------------------------- knitr::opts_chunk$set(tidy = FALSE, warning = FALSE, message = FALSE, cache=TRUE) ## ----------------------------------------------------------------------------- BiocManager::install("CEMiTool") library("CEMiTool") # load expression data data(expr0) head(expr0[,1:4]) ## ----results='hide'----------------------------------------------------------- cem <- cemitool(expr0) ## ----------------------------------------------------------------------------- cem ## ----------------------------------------------------------------------------- # inspect modules nmodules(cem) head(module_genes(cem)) ## ----eval=FALSE--------------------------------------------------------------- # generate_report(cem) ## ----------------------------------------------------------------------------- write_files(cem) ## ----------------------------------------------------------------------------- save_plots(cem, "all") ## ----------------------------------------------------------------------------- # load your sample annotation data data(sample_annot) head(sample_annot) ## ----results='hide'----------------------------------------------------------- # run cemitool with sample annotation cem <- cemitool(expr0, sample_annot) ## ----------------------------------------------------------------------------- sample_annotation(cem, sample_name_column="SampleName", class_column="Class") <- sample_annot ## ----------------------------------------------------------------------------- # generate heatmap of gene set enrichment analysis cem <- mod_gsea(cem) cem <- plot_gsea(cem) show_plot(cem, "gsea") ## ----------------------------------------------------------------------------- # plot gene expression within each module cem <- plot_profile(cem) plots <- show_plot(cem, "profile") plots[1] ## ----------------------------------------------------------------------------- # read GMT file gmt_fname <- system.file("extdata", "pathways.gmt", package = "CEMiTool") gmt_in <- read_gmt(gmt_fname) ## ----------------------------------------------------------------------------- # perform over representation analysis cem <- mod_ora(cem, gmt_in) ## ----------------------------------------------------------------------------- # plot ora results cem <- plot_ora(cem) plots <- show_plot(cem, "ora") plots[1] ## ----------------------------------------------------------------------------- # read interactions int_fname <- system.file("extdata", "interactions.tsv", package = "CEMiTool") int_df <- read.delim(int_fname) head(int_df) ## ----------------------------------------------------------------------------- # plot interactions library(ggplot2) interactions_data(cem) <- int_df # add interactions cem <- plot_interactions(cem) # generate plot plots <- show_plot(cem, "interaction") # view the plot for the first module plots[1] ## ----eval=FALSE--------------------------------------------------------------- # # run cemitool # library(ggplot2) # cem <- cemitool(expr0, sample_annot, gmt_in, interactions=int_df, # filter=TRUE, plot=TRUE, verbose=TRUE) # # create report as html document # generate_report(cem, directory="./Report") # # # write analysis results into files # write_files(cem, directory="./Tables") # # # save all plots # save_plots(cem, "all", directory="./Plots") ## ----eval=FALSE--------------------------------------------------------------- # diagnostic_report(cem)