R/edgelist_from_matrices.R

In ILSM: Analyze Interconnection Structure of Tripartite Interaction Networks

#' Convert interaction matrices into a list of vector of edges.
#'
#' @param mat1 A matrix.
#' @param mat2 A matrix.
#' @param isDirected1 Logical; Default TRUE.
#' @param isDirected2 Logical; Default TRUE.
#'
#' @encoding UTF-8
#'
#' @return
#' An extended link list (ELL). This is a table with five columns (but can
#' contain more if link attributes exist). Link lists can also be called edge
#' lists (these are interchangeable terms)
#'
#' @noRd

edgelist_from_matrices<-function(mat1,mat2,isDirected1=TRUE,isDirected2=TRUE){
   if(is.null(rownames(mat1)) | is.null(rownames(mat2))){
      rownames(mat1)<-paste0("mid_spe",seq=1:nrow(mat1))
      rownames(mat2)<-paste0("mid_spe",seq=1:nrow(mat2))
      matrow<-unique(c(rownames(mat1),rownames(mat2)))
   }
   if(!is.null(rownames(mat1)) & !is.null(rownames(mat2)) & sum(is.na(rownames(mat1)))==0 & sum(is.na(rownames(mat2)))==0)
      matrow<-unique(c(rownames(mat1),rownames(mat2)))
   else
      stop("Make sure matrices either have no row names or have full row names. No NA!!!")
   mat_1<-matrix(0,length(matrow),ncol(mat1))
   rownames(mat_1)<-matrow
   colnames(mat_1)<-colnames(mat1)
   mat_1[rownames(mat1),]<-mat1
   mat_1[mat_1>0]<-1
   mat_2<-matrix(0,length(matrow),ncol(mat2))
   rownames(mat_2)<-matrow
   colnames(mat_2)<-colnames(mat2)
   mat_2[rownames(mat2),]<-mat2
   mat_2[mat_2>0]<-1
   mat1<-mat_1
   mat2<-mat_2



   if(is.null(colnames(mat1)))
      colnames(mat1)<-paste0("up_spe",seq=1:ncol(mat1))
   if(is.null(colnames(mat2)))
      colnames(mat2)<-paste0("down_spe",seq=1:ncol(mat2))
   spe<-unique(c(colnames(mat1),rownames(mat1),rownames(mat2),colnames(mat2)))
   me_interlayer<-function(mat,U,V,isDirected=FALSE){
      spe_v<-NULL
      mat[mat[]>0]<-1
      mat[is.na(mat)]<-0
      for (i in 1:ncol(mat)) {
         spe_v<-c(spe_v,mat[,i])
      }
      spe_mat<-data.frame(spe1=rep(rownames(mat),ncol(mat)),layer=rep(U,ncol(mat)*nrow(mat)),spe2=(rep(colnames(mat),each=nrow(mat))),layer1=rep(V,nrow(mat)*ncol(mat)),value=spe_v)
      colnames(spe_mat)<-NULL
      spe_mat<-as.matrix(spe_mat)
      spe_mat<-spe_mat[spe_mat[,5]==1,]
      if(isDirected==FALSE){
         spe_m<-spe_mat
         spe_m[,1:2]<-spe_mat[,3:4]
         spe_m[,3:4]<-spe_mat[,1:2]
         spe_m<-as.matrix(spe_m)
         spe_mat<-as.matrix(spe_mat)
         spe_mat<-rbind(spe_mat,spe_m)
      }
      rownames(spe_mat)<-NULL
      return(spe_mat)
   }
   matt<-rbind(me_interlayer(t(mat1),1,2,isDirected1),me_interlayer(mat2,2,3,isDirected2))
   for (i in 1:sum(!(is.na(spe)))) {
      matt[matt[,1]%in%spe[i],1]<-i
      matt[matt[,3]%in%spe[i],3]<-i
   }
   matt<-as.data.frame(matt)
   matt<-apply(matt, 2,function(x){as.numeric(x)})
   degree<-c(colSums(mat1),rowSums(mat1)+rowSums(mat2),colSums(mat2))
   return(list(matt,spe=spe,degree=degree))
}