R/interactions.R

In CEMiTool: Co-expression Modules identification Tool

#' @importFrom igraph graph_from_data_frame
NULL

#' Retrieve and set interaction data to CEMiTool object
#'
#' @param cem Object of class \code{CEMiTool}.
#' @param value a data.frame or matrix containing two columns
#' @param ... parameters for igraph::graph_from_data_frame
#'
#' @return Object of class \code{CEMiTool} 
#'
#' @examples
#' # Get example CEMiTool object
#' data(cem)
#' # Read example interactions data
#' int_df <- read.delim(system.file("extdata", "interactions.tsv", 
#'     package = "CEMiTool"))
#' # Insert interactions data
#' interactions_data(cem) <- int_df
#' # Check interactions data
#' interactions_data(cem)
#' 
#' @rdname interactions_data
#' @export
setGeneric('interactions_data', function(cem, ...) {
    standardGeneric('interactions_data')
})

#' @rdname interactions_data
#' @export
setMethod('interactions_data', signature('CEMiTool'), 
    function(cem) {
        return(cem@interactions)
    })
#' @rdname interactions_data
#' @export
setGeneric("interactions_data<-", function(cem, value) {
    standardGeneric("interactions_data<-")
})

#' @rdname interactions_data
setReplaceMethod("interactions_data", signature("CEMiTool"),
    function(cem, value){
        if(nrow(cem@module) == 0){
            stop("No genes in modules! Did you run find_modules?")
        }
        #cem <- get_args(cem, vars=mget(ls()))
        genes_by_module <- split(cem@module$genes, cem@module$modules)
        cem@interactions <- lapply(genes_by_module, function(x) {
            rows <- which(value[,1] %in% x | value[, 2] %in% x)
            ig <- igraph::simplify(igraph::graph_from_data_frame(value[rows,], directed=FALSE))
            return(ig)
        })
        return(cem)
    })