rBiopaxParser: igraph vs. graphNEL

라벨: Informatics
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library(rBiopaxParser)

## from layoutRegulatoryGraph()
f2= function (mygraph, label = "", node.fixedsize = FALSE, edge.weights = c("green", 
    "black", "red"), edge.arrowheads = c("normal", "tee"), subgraphs = list(), 
    subgraphs.colors = c("#B3E2CD", "#FDCDAC", "#F4CAE4", "#E6F5C9", "#FFF2AE")) 
{

    if (is.null(mygraph)) 
        stop("Error: layoutRegulatoryGraph: supplied graph parameter was NULL.")
    if (!("graphNEL" %in% class(mygraph))) 
        stop("Error: layoutRegulatoryGraph: supplied graph has to be of class graphNEL.")
    if (length(nodes(mygraph)) == 0) {
        warning("warning: layoutRegulatoryGraph: supplied graph has no nodes. No layout was done.")
        return(mygraph)
    }
    if (!require(graph)) {
        message("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!")
        return(NULL)
    }
    if (!require(Rgraphviz)) {
        message("This functions needs the Rgraphviz library installed, albeit it cannot be found. Check out the installation instructions!")
        return(NULL)
    }
#    if (label != "") 
    graph::graphRenderInfo(mygraph) = list(label = label, labelJust = "l", labelLoc = "t")
    graph::nodeRenderInfo(mygraph) = list(shape = "circle", fill = "#e0e0e0", fixedsize = node.fixedsize)
    mygraph = Rgraphviz::layoutGraph(mygraph)

#    if (label != "") 
    graph::graphRenderInfo(mygraph) = list(label = label, labelJust = "l", labelLoc = "t")

    x = unlist(graph::edgeData(mygraph))
    names(x) = gsub(".weight", "", names(x))
    names(x) = gsub("|", "~", names(x), fixed = TRUE)
    arrowhead = x
    arrowhead[TRUE] = rep(edge.arrowheads[1], length(x))
    arrowhead[x == 1] = edge.arrowheads[1]
    arrowhead[x == -1] = edge.arrowheads[2]
    graph::edgeRenderInfo(mygraph) = list(arrowhead = arrowhead)
    color = x
    color[TRUE] = rep(edge.weights[2], length(x))
    color[x == 1] = edge.weights[1]
    color[x == -1] = edge.weights[3]
    graph::edgeRenderInfo(mygraph) = list(col = color)
    graph::nodeRenderInfo(mygraph) = list(shape = "circle", fill = "#e0e0e0", fixedsize = node.fixedsize)

    if (length(subgraphs) > 0) {
        for (i in 1:length(subgraphs)) {
            for (n in subgraphs[[i]]) {
                graph::nodeRenderInfo(mygraph)$fill[n] = subgraphs.colors[i]
            }
        }
    }
    return(mygraph)
}

library(igraph)
p = igraph.from.graphNEL( graphNEL.object, name = TRUE, weight = TRUE, unlist.attrs = TRUE)  # see weight E(p)$weight

pp = igraph.to.graphNEL( p )
unlist( graph::edgeData(pp) )  # P40|P11 --- P40~P11

Rgraphviz::renderGraph( f2(pp) )  

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라벨: Informatics