R/igraph-compatibility.R

In sparsebnUtils: Utilities for Learning Sparse Bayesian Networks

#
#  igraph-compatibility.R
#  sparsebnUtils
#
#  Created by Bryon Aragam (local) on 1/30/16.
#  Copyright (c) 2014-2017 Bryon Aragam. All rights reserved.
#

#
# Various utility functions for enforcing compatibility with the 'igraph' package.
#

### Conversion to igraph object
#' @rdname sparsebn-compat
#' @export
to_igraph <- function(x){
    ### This function requires the 'igraph' package to be installed
    if (!requireNamespace("igraph", quietly = TRUE)) {
        stop("igraph package required to coerce data to 'igraph' type!", call. = FALSE)
    }

    UseMethod("to_igraph", x)
}

#' @export
to_igraph.igraph <- function(x){
    x
}

#' @export
to_igraph.edgeList <- function(x){
    # if(num.edges(x) > 0){
    #     el.igraph <- edgeList_to_igraph_edgelist(x)
    #     #
    #     # !!! This igraph method ignores isolated edges! See ?igraph::graph
    #     #     for a possible fix. Also affects to_igraph.network.
    #     #
    #     igraph::graph_from_edgelist(el.igraph, directed = TRUE)
    # } else{
    #     ### Special case to create empty graph
    #     igraph::graph.empty(n = num.nodes(x), directed = TRUE)
    # }

    ### to_graphNEL loses node names
    # to_igraph(to_graphNEL(x))

    ### Slow, but keeps node names
    igraph::graph.adjacency(as.matrix(x))
}

#' @export
to_igraph.graphNEL <- function(x){
    # to_igraph(to_edgeList(x))
    # igraph::graph_from_graphnel(x) ### This function is deprecated as of igraph v1.1.2
    igraph::igraph.from.graphNEL(x)
}

#' @export
to_igraph.network <- function(x){
    to_igraph(to_edgeList(x))
}

#' @export
to_igraph.bn <- function(x){
    to_igraph(to_edgeList(x))
}

#' @export
to_igraph.sparsebnFit <- function(x){
    x$edges <- to_igraph(x$edges)

    x
}

#' @export
to_igraph.sparsebnPath <- function(x){
    sparsebnPath(lapply(x, to_igraph))
}

#
# Helper function to convert an edge list to a igraph compatible edge list matrix
#  The output is a 2 column matrix where each row represents one edge:
#       [i j] = (i, j)
#
edgeList_to_igraph_edgelist <- function(el){
    #----------- EXAMPLE -----------
    # Default:
    # [[1]]
    # integer(0)
    #
    # [[2]]
    # [1] 1
    #
    # [[3]]
    # [1] 1
    #
    # igraph:
    # 1 2
    # 1 3
    #
    #-------------------------------

    ### Slick version
    el.igraph <- matrix(NA, nrow=0, ncol=2) # base case for null graph
    if(num.edges(el) > 0){
        #
        # Bugfix: By default, SIMPLIFY is set to TRUE, which causes problem when
        #         do.call is called below ('Error in do.call("rbind", el.igraph) : second argument must be a list')
        #         Need to set SIMPLIFY = FALSE to prevent pre-mature matrixification.
        #
        el.igraph <- mapply(function(x, y){
            if(length(x) > 0) cbind(x, y)
        }, el, 1:num.nodes(el), SIMPLIFY = FALSE)

        el.igraph <- do.call("rbind", el.igraph)
    }

    ### Equivalent code: What the slick version does under the hood
#         numnode <- num.nodes(el) # number of nodes in edgeList
#         numedge <- num.edges(el) # number of edges in edgeList
#
#         el.igraph <- matrix(NA, ncol = 2, nrow = numedge)
#         start <- 1
#         for(j in 1:numnode){
#             this.size <- length(el[[j]])
#             end <- start + this.size - 1
#             if(this.size > 0){
#                 el.igraph[start:end, ] <- cbind(el[[j]], j) # el[[j]] are the parents
#                 start <- end + 1
#             }
#         }

    el.igraph
}

#' @export
to_edgeList.igraph <- function(x){
    edgeList(igraph_to_edgeList_list(x))
}

#
# Helper function to convert a igraph object to an edgeList compatible list
#
igraph_to_edgeList_list <- function(igr){
    ### NOTE: Consider using igraph::as_edgelist here instead
    igr.edgeL <- igraph::as_adj_list(igr, mode = "in")
    igr.edgeL <- lapply(igr.edgeL, as.integer)

    igr.edgeL
}