Methods for GXL manipulations in package graph
GXL http://www.gupro.de/GXL is "an XML sublanguage designed to be a standard exchange format for graphs". This document describes tools in the graph package for importing GXL data to R and for writing graph data out as GXL.
- currently returns a graphNEL when possible. This
function is based on
xmlEventParsewith handlers defined in the function NELhandler. The dump() element of this handler should emit information on all children of nodes and edges; the asGraphNEL() element will return a
graphNELobject with weights if child
with name attribute "weights" is present for each edge element.
- for an input of class "graphNEL", returns an object of class c("XMLInternalDOM", "XMLOutputStream"); see the example for how to convert this to a text stream encoding XML
- returns an R list with all the node, edge, and named attribute information specified in the GXL stream
- returns silently (invisibly returns the parsed tree) for a DTD-compliant stream, or is otherwise very noisy
At present, toGXL does not return a validating GXL stream
because XML package does not properly handle the dtd and namespaces
arguments to xmlTree. This is being repaired. To fix
the stream, add
Some structures in a graphNEL and some tags in GXL may not be handled at this time.
- con = connection: returns a graphNEL based on a parsing of the GXL stream on the connection
- con = connection: returns an R list based on a parsing of the GXL stream on the connection
- con = connection: checks the GXL stream against its DTD
- object = graphNEL: creates an XMLInternalDOM representing the graph in GXL
sf <- file(system.file("GXL/simpleExample.gxl", package="graph")) show(fromGXL(sf)) print(dumpGXL(sf)) close(sf) #validateGXL(sf) # bad <- file(system.file("GXL/c2.gxl", package="graph")) # here's how you can check if the GXL is well-formed, if # you have a libxml2-based version of R XML package # # try( validateGXL(bad) ) # gR <- graphNEL(nodes=letters[1:4], edgeL=list( a=list(edges=4), b=list(edges=3), c=list(edges=c(2,1)), d=list(edges=1)), edgemode="directed") # # following requires that you are using XML bound with recent libxml2 # #an <- as.numeric #if (an(libxmlVersion()$major)>=2 && an(libxmlVersion()$minor)>=4) ## since toGXL returns an XML object, we need to attach the XML ## package. library("XML") cat(saveXML(toGXL(gR)$value())) wtd <- file(system.file("GXL/kmstEx.gxl", package="graph")) wtdg <- fromGXL(wtd) close(wtd) print(edgeWeights(wtdg))