R/ProteinNetwork.R

In emilyso-99/MicroMetaGraph: MicroMetaGraph: Construction Interaction Networks using Metatranscriptomic Data

#' The Protein Network Function 
#' 
#' from beginning to end, using the query functions that were done before, this function constructs a protein interaction network 
#' that is protein-specific-each node is a protein, with information on the functional annotation and the ortholog group. there 
#' are lines connecting interactoin scores 
#' @param proteins A list that contains a sequence of NCBI/Genbank protein ids
#' @param benchmark Minimum benchmark for associaton score
#' @return graph of interaction network 
#' @keywords interaction network 
#' @importFrom igraph make_empty_graph
#' @importFrom igraph vcount
#' @importFrom igraph set_vertex_attr
#' @importFrom igraph add_edges
#' @importFrom igraph set_edge_attr
#' @importFrom igraph plot.igraph
#' @importFrom igraph vertex_attr
#' @importFrom utils data
#' @export
ProteinNetwork <- function(proteins,benchmark=0){
# get orthology data 
ProteinGraph = igraph::make_empty_graph(n=length(proteins))
orthologs <- GetOrthology(proteins)
annotations <- FunctionalAnnotation(orthologs$COGID)
CogLinks <- CogLinker(orthologs$COGID,benchmark)
vercount <- igraph::vcount(ProteinGraph)
for(x in 1:vercount) {
ProteinGraph <- igraph::set_vertex_attr(ProteinGraph,"protein",index=x,value=proteins[x])
ProteinGraph <- igraph::set_vertex_attr(ProteinGraph,"ortholog", index=x,value = orthologs$OG[x])
ProteinGraph <- igraph::set_vertex_attr(ProteinGraph,"description",index=x,value= annotations$description[x])
}
# add edges
if (length(CogLinks$association_score > 0)){
for(j in 1:nrow(CogLinks)) {
  row <- CogLinks[j,]
  if (!is.na(row$group1)) {
  firstgroup_index <- which(vertex_attr(ProteinGraph,"ortholog") %in% row$group1)
  SecondGroupIndex <- which(vertex_attr(ProteinGraph,"ortholog") %in% row$group2)
  for (item in firstgroup_index) {
    for (NextItem in SecondGroupIndex) {
      ProteinGraph <- igraph::add_edges(ProteinGraph, c(item,NextItem))
      ProteinGraph <- igraph::set_edge_attr(ProteinGraph,"link", value=row$association_score)
    }
  }
  }
}
}
igraph::plot.igraph(ProteinGraph,vertex.label=proteins,vertex.size=50,vertex.colour="red",edge.arrow.mode="-")
return(ProteinGraph)
}