## Example R code

setwd("/Users/chaocheng/WorSpa/Transition/HirNet/code/Web/")	## set your working directory here
mynet = read.table("Sample_Data_Yeast_Regulome.txt", sep="\t", colClasses=rep("character", 2))

source(file="HirNet_functions.R")

## plot HS vs. anneal.coeff (determine the anneal.coeff)
Opt_anneal.coeff3(mynet, kmax=10000, anneal.coeff=(1:100)*1e-6, lev=3, myoutf = "result.txt")

## plot HS vs. Kmax (determine kmax) 
Opt_kmax3(mynet, kmax=10000, anneal.coeff= 1e-6, lev=3, myoutf = "result.txt")


## calculate the hierarchical structure with Lev =2,3,4,5,6
myres = cal_hier_score26(mynet, kmax=10000, ptim=100, anneal.coeff=1e-6,  myoutf = "Hierarchical_Structure_Regulome.txt")