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#' @import parmigene
#' @importFrom infotheo discretize mutinformation
#' @importFrom igraph graph.adjacency simplify igraph_opt layout.circle
NULL
#' Plots mutual information network (mrnet algorithm) connection using the parmigene package. Mutual information calculated with infotheo package.
#' @param dataMatrix data matrix
#' @param threshold the maximum number of edges to draw for each subpopulation mutual information network
#'
#' @export
#'
MINetworkPlot_topEdges<-function(dataMatrix, threshold){
dat<-discretize(dataMatrix)
dataMatrix_mi<-mutinformation(dat, method="emp")
dataMatrix_net<-mrnet(dataMatrix_mi)
filterLevel<-dataMatrix_net[order(dataMatrix_net, decreasing=TRUE)][threshold]
dataMatrix_net[dataMatrix_net<filterLevel]<-0
g_dataMatrix_net <- graph.adjacency(dataMatrix_net, weighted=TRUE, mode="undirected")
g_dataMatrix_net<-simplify(g_dataMatrix_net, remove.multiple=TRUE, remove.loops=TRUE, edge.attr.comb=igraph_opt("edge.attr.comb"))
networkPlot<-plot(g_dataMatrix_net, vertex.color=rainbow(ncol(dataMatrix)), edge.width=3,layout=layout.circle(g_dataMatrix_net))
}
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