Re: Re: FromAdjacencyMatrix /

*To*: mathgroup at smc.vnet.net*Subject*: [mg104346] Re: [mg104220] Re: [mg104192] FromAdjacencyMatrix /*From*: Thomas Dowling <thomasgdowling at gmail.com>*Date*: Wed, 28 Oct 2009 04:09:09 -0500 (EST)*References*: <200910230233.WAA27768@smc.vnet.net>

Hello, Syd and Andrew, Just to confirm, I have evaluated your notebook (confirmation for andrew.nb) on my Mac (non-intel PowerBook G4 running Mathematica 7.0, with Mac OS X ver 10.5.7) and I have (still) not been able to reproduce the problem on this system. The arrows run from 3 -> 1 on both G2 graphs afer evaluation on my Mac, but point from 1 -> 3 on the downloaded notebook. Also, the final command Edges[g] == Edges[g2] evaluates to True (It has evaluated to False in the downloaded notebook). This must be a bug, which is a bit worrying. We are soon to update to M. 7.1 (in the next few days), and it will be interesting to see what happens. Tom Dowling "7.0 for Mac OS X PowerPC (32-bit) " Tom Dowling On Sat, Oct 24, 2009 at 6:38 AM, Thomas Dowling <thomasgdowling at gmail.com>wrote: > Hello, > > I have not been able to reproduce your problem on a Mac (Non-Intel) running > Mathematica v 7.0.0. All the code you posted works fine, but there is no > edge-order reversal, > and the final graph is the same as the one you started out with. Perhaps I > am missing something? > > > Edges[g2] == Edges[g] > > Out[53] = True > > (Loading Graphics Utilities Package) > > EdgeList[g2] == EdgeList[g] > > Out[54]= True > > VertexList[g2] == VertexList[g] > > Out[56]= True > > EdgeList[ToCombinatoricaGraph[mg]] == EdgeList[g] > > Out[57]= True. > > mgalt = Normal@AdjacencyMatrix[g] > > mgalt == mg > > Out[63] = True > > Is this a particular problem with your system, or is it peculiar to > Mathematica 7.0.1? > > Tom Dowling. > > > > On Fri, Oct 23, 2009 at 3:33 AM, Andrew <dr.a.graham at googlemail.com> > wrote: > > > Hello group, > > > > This question seems to have been touched on in the past but I'm not > > sure if it has ever been definitively answered. I would be grateful > > for some advice! > > > > I have some data that I would like to explore. It concerns a set of > > directed graphs, without edge weights. The data comes to me as the > > corresponding asymmetric adjacency matrices. > > > > I can visualise the graphs directly using the native function > > GraphPlot. > > However, I would prefer to visualise them using ShowGraph from the > > Combinatorica package - but this requires that the adjacency matrix is > > converted to the Combinatorica graph format first. > > > > The trouble is that (for directed graphs at least), > > FromAdjacencyMatrix appears to be broken. > > > > Example: > > g = Cycle[3, Type -> Directed] (*construct a simple directed graph in > > Combinatorica graph format*) > > > > Edges[g] (*List of edges*) > > > > Vertices[g] (*List of vertices*) > > > > GraphOptions[g] (*Shows the graph options*) > > > > ShowGraph[g, VertexNumber -> True] /. > > x : Arrow[__] -> {Arrowheads[{{Automatic, 0.6}}], x} (*Visualises the > > graph with ShowGraph, using a workaround to place the arrowheads mid- > > edge, as suggested Apr 2 2008 by dh*) > > GraphPlot[g, VertexLabeling -> True, DirectedEdges -> True] > > (*Visualises the graph with GraphPlot - the same outcome*) > > > > mg = ToAdjacencyMatrix[g, Type -> Directed] (*Convert to adjacency > > matrix*) > > > > mg // TableForm (*Inspect - seems appropriate*) > > > > mg // MatrixForm (*Ditto*) > > > > GraphPlot[mg, VertexLabeling -> True, DirectedEdges -> True] (*Cannot > > plot directly with ShowGraph, but with GraphPlot the graph is still > > preserved at this stage*) > > > > g2 = FromAdjacencyMatrix[mg, Type -> Directed] (*Convert back to a > > graph*) > > > > Edges[g2] (*Oh dear. The direction of edge #3 has been reversed*) > > > > Vertices[g2] (*Vertices are preserved*) > > > > GraphOptions[g2] (*Graph options are preserved*) > > > > ShowGraph[g2, VertexNumber -> True] /. > > x : Arrow[__] -> {Arrowheads[{{Automatic, 0.6}}], x} > > GraphPlot[g2, VertexLabeling -> True, DirectedEdges -> True] (*And > > visualising the graph with both ShowGraph & GraphPlot it is no longer > > the same as the graph we started out with*) > > > > The problem seems to be with FromAdjacencyMatrix > > FromAdjacencyLists shows the same problem > > > > Is there something wrong with the code above, or are these functions > > truly broken? If they are broken, can anyone help with writing a > > function that will correctly turn a directed adjacency matrix into > > Combinatorica lists of edges & vertices? > > > > Finally, if these functions are broken, can they be fixed? I have > > otherwise found Combinatorica very easy to work with & would prefer to > > stick with it rather than native functions if possible. The > > Combinatorica book has recently been republished in paperback & I have > > found it very helpful. > > > > Many thanks > > > > Andrew Graham > > Dept of Neurology > > Addenbrooke's Hospital > > > > > > >

**References**:**FromAdjacencyMatrix / FromAdjacencyLists - broken? Workaround?***From:*Andrew <dr.a.graham@googlemail.com>