# #设置,呼应= FALSE,包括= TRUE --------------------------------------- knitr: opts_chunk美元集(崩溃= TRUE,发表评论 = "#>" ) ## ---- = FALSE load_packages,消息= FALSE,警告,包括= FALSE --------------- 库(GNET2) # #——回声= TRUE -------------------------------------------------------------- set.seed (2) init_group_num = 8 init_method = '增加' exp_data < -矩阵(rnorm(300 * 12), 300年,12)reg_names < - paste0 (TF, 1:20) rownames (exp_data) < - c (reg_names, paste0(“基因”,1:(nrow (exp_data)长度(reg_names)))) colnames (exp_data) < - paste0 (condition_, 1: ncol (exp_data )) ## ---- 回声= TRUE --------------------------------------------------------------- gnet_result < -gnet(exp_data,reg_names,init_method,init_group_num,heuristic =TRUE) ## ---- echo=TRUE，图。宽度= 10,fig.height = 12 ----------------------------------- plot_gene_group (gnet_result group_idx = 1, plot_leaf_labels = T ) ## ---- 回声= TRUE,无花果。宽度= 10,fig.height = 12 ----------------------------------- exp_labels =代表(paste0 (Exp_, 1:4),每个= 3)plot_gene_group (gnet_result group_idx = 1, group_labels = exp_labels ) ## ---- 回声= TRUE,无花果。width=10, fig.height=12----------------------------------- exp_labels_factor = as.numeric(factor(exp_labels)) print('与每个模块的分类实验条件相似度:')print(similarity_score(gnet_result,exp_labels_factor)) print('与每个模块的顺序实验条件相似度:')print(similarity_score(gnet_result,exp_labels_factor)， sorted =TRUE) ## ---- echo=TRUE，图。宽度= 8,fig.height = 8 ------------------------------------- plot_tree (gnet_result group_idx = 1 ) ## ---- 回声= TRUE,无花果。宽度= 8,fig.height = 8 ------------------------------------- group_above_kn < - plot_group_correlation (gnet_result)打印(group_above_kn ) ## ---- 回声= TRUE,无花果。宽度= 8,fig.height = 8 ------------------------------------- print(模块:总数)打印(gnet_result modules_count美元 ) ## ---- 回声= TRUE,无花果。宽度= 8,fig.height = 8 ------------------------------------- group_index = 1打印(模块1:监管部门)打印(gnet_result监管者美元[[group_index]])打印(“目标模块1:”)打印(gnet_result target_genes美元[[group_index ]]) ## ---- 回声= TRUE,无花果。宽度= 8,fig.height = 8 ------------------------------------- 垫< - extract_edges (gnet_result)打印(暗(垫 )) ## ---- 回声= TRUE --------------------------------------------------------------- sessionInfo ()