## ----setup,echo = FALSE, include = TRUE--------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----load_packages, message=FALSE, warning=FALSE, include=FALSE--------------- library(GNET2) ## ----echo = TRUE-------------------------------------------------------------- set.seed(2) init_group_num = 8 init_method = 'boosting' exp_data <- matrix(rnorm(600*12),600,12) reg_names <- paste0('TF',1:20) rownames(exp_data) <- c(reg_names,paste0('gene',1:(nrow(exp_data)-length(reg_names)))) colnames(exp_data) <- paste0('condition_',1:ncol(exp_data)) se <- SummarizedExperiment::SummarizedExperiment(assays=list(counts=exp_data)) ## ---- echo=TRUE--------------------------------------------------------------- gnet_result <- gnet(se,reg_names,init_method,init_group_num,heuristic = TRUE) ## ---- echo=TRUE,fig.width=10, fig.height=12----------------------------------- plot_gene_group(gnet_result,group_idx = 1) ## ---- echo=TRUE,fig.width=8, fig.height=8------------------------------------- plot_tree(gnet_result,group_idx = 1) ## ---- echo=TRUE,fig.width=8, fig.height=8------------------------------------- group_above_kn <- plot_group_correlation(gnet_result) print(group_above_kn) ## ---- echo=TRUE--------------------------------------------------------------- sessionInfo()