% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/moduleVisual.R
 \name{moduleVisual}
 \alias{moduleVisual}
 \title{Modules visualization and network topology}

 \usage{

 moduleVisual(TOM, value.matrix, moduleColors, mymodule, cutoff = 0.02,

   prefix = NULL, sve = FALSE)
 }
 \arguments{
 \item{TOM}{the topological overlap matrix in WGCNA generated from

 the epiNetwork() function}

 \item{value.matrix}{A data frame generated from the epiNetwork() function.

 the row name is patients in one subtype. the column name is the DEH loci
 the value in the matrix is epigenetic heterogeneity on one DEH loci
 for one patient}
 

 \item{moduleColors}{the module assignment generated from the epiNetwork()

 function}
 
 \item{mymodule}{a character vector containing the module colors
 you want to visulaize}
 

 \item{cutoff}{adjacency threshold for including edges in the output (default:0.02)}

 \item{prefix}{a character for output filename}

 
 \item{sve}{A boolean to save the plot (default: FALSE)}
 }
 \value{
 a list containing all module edge and node information for mymodule
 }
 \description{

 Visualize the modules identified by epiNetwork() function, and calculate
 network topology

 }
 \examples{
 correlation.m<-matrix(0,12,12)

 correlation.m[1,c(2:10)]<-c(0.006,0.054,0.079,0.078, 0.011,0.033,0.014,

 0.023,0.034)

 correlation.m[2,c(3:10)]<-c(0.026,0.014,0.045,0.037, 0.026,0.011,0.034,

 0.012)

 correlation.m[3,c(4:10)]<-c(0.016,0.024,0.039,0.045, 0.009,0.003,0.028)
 correlation.m[4,c(5:10)]<-c(0.039,0.002,0.053,0.066, 0.012,0.039)
 correlation.m[5,c(6:10)]<-c(0.019,0.016,0.047,0.046, 0.013)
 correlation.m[6,c(7:10)]<-c(0.017,0.057,0.029,0.056)
 correlation.m[7,c(8:10)]<-c(0.071,0.018,0.001)
 correlation.m[8,c(9:10)]<-c(0.046,0.014)
 correlation.m[9,10]<-0.054
 correlation.m[lower.tri(correlation.m)] <-

 t(correlation.m)[lower.tri(correlation.m)]
 
 matrix.v<-matrix(0.5,5,12)

 matrix.v<-as.data.frame(matrix.v)

 colnames(matrix.v)<-c("NM_052960","NR_138250","NM_015074","NM_183416",

 "NM_017891","NM_001330306","NM_014917","NM_001312688","NM_001330665",
 "NM_017766","NM_001079843","NM_001040709")
 modulecolor<-c(rep(c("yellow","cyan"),c(10,2)))

 module.topology<-epihet::moduleVisual(correlation.m,

                                      value.matrix=matrix.v,
                                      moduleColors=modulecolor,
                                      mymodule="yellow",cutoff=0.02,
                                      prefix='CEBPA_sil_epipoly',sve = TRUE)
 }