## ----setup,echo = FALSE, include = TRUE--------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----load_packages, message=FALSE, warning=FALSE, include=FALSE--------------- library(GNET2) ## ----echo = TRUE-------------------------------------------------------------- set.seed(2) init_group_num = 8 init_method = 'boosting' exp_data <- matrix(rnorm(300*12),300,12) reg_names <- paste0('TF',1:20) rownames(exp_data) <- c(reg_names,paste0('gene',1:(nrow(exp_data)-length(reg_names)))) colnames(exp_data) <- paste0('condition_',1:ncol(exp_data)) ## ---- echo=TRUE--------------------------------------------------------------- gnet_result <- gnet(exp_data,reg_names,init_method,init_group_num,heuristic = TRUE) ## ---- echo=TRUE,fig.width=10, fig.height=12----------------------------------- plot_gene_group(gnet_result,group_idx = 1,plot_leaf_labels = T) ## ---- echo=TRUE,fig.width=10, fig.height=12----------------------------------- exp_labels = rep(paste0('Exp_',1:4),each = 3) plot_gene_group(gnet_result,group_idx = 1,group_labels = exp_labels) ## ---- echo=TRUE,fig.width=10, fig.height=12----------------------------------- exp_labels_factor = as.numeric(factor(exp_labels)) print('Similarity to categorical experimental conditions of each module:') print(similarity_score(gnet_result,exp_labels_factor)) print('Similarity to ordinal experimental conditions of each module:') print(similarity_score(gnet_result,exp_labels_factor),ranked=TRUE) ## ---- echo=TRUE,fig.width=8, fig.height=8------------------------------------- plot_tree(gnet_result,group_idx = 1) ## ---- echo=TRUE,fig.width=8, fig.height=8------------------------------------- group_above_kn <- plot_group_correlation(gnet_result) print(group_above_kn) ## ---- echo=TRUE,fig.width=8, fig.height=8------------------------------------- print('Total number of modules:') print(gnet_result$modules_count) ## ---- echo=TRUE,fig.width=8, fig.height=8------------------------------------- group_index = 1 print('Regulators in module 1:') print(gnet_result$regulators[[group_index]]) print('Targets in module 1:') print(gnet_result$target_genes[[group_index]]) ## ---- echo=TRUE,fig.width=8, fig.height=8------------------------------------- mat <- extract_edges(gnet_result) print(dim(mat)) ## ---- echo=TRUE--------------------------------------------------------------- sessionInfo()