fromGXL-methods {graph} | R Documentation |
GXL 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.
fromGXL |
currently returns a graphNEL when possible. This function is based on xmlEventParse with 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 graphNEL object with weights if child <attr> with name attribute "weights" is present for each edge element. |
toGXL |
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 |
dumpGXL |
returns an R list with all the node, edge, and named attribute information specified in the GXL stream |
validateGXL |
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
<!DOCTYPE gxl SYSTEM "http://www.gupro.de/GXL/gxl-1.0.1.dtd">
as second record in the output.
Some structures in a graphNEL and some tags in GXL may not be handled at this time.
Note added 18 Jul 2003: It has been observed that graphviz dot2gxl generates GXL with graph attribute edgeids=FALSE. fromGXL will fail to process the edges correctly. You can manually add arbitrary edgeids to the dot2gxl output edges and fromGXL will succeed. Perhaps fromGXL can be made less dependent on edge id attributes.
Note added 15 August 2003: dot2gxl is supposed to introduce edgeids now.
Note added 15 August 2003: all GXL to be handled should possess an edgemode attribute.
Vince Carey <stvjc@channing.harvard.edu>
sf <- file(system.file("GXL/simpleExample.gxl", package="graph")) show(fromGXL(sf)) print(dumpGXL(sf)) #validateGXL(sf) #bad <- file(system.file("GXL/c2.gxl", package="graph")) # here's how you can check if the GXL is well-formed # # try( validateGXL(bad) ) # gR <- new("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) cat(saveXML(toGXL(gR)$value())) wtd <- file(system.file("GXL/kmstEx.gxl", package="graph")) wtdg <- fromGXL(wtd) print(edgeWeights(wtdg))