Create a Graph from a matrix by using Graphs.jl

[Charles Novaes de Santana]

Dear all,

I am starting to use Graphs.jl and some simple questions arrived. It is not clear for me how to create a Graph from my data if my data is in a matrix format, for example.

The documentation is plenty of information about how the classes, types, and algorithms are defined, and they also provide some good examples to use these functions once you have a graph object. But I couldn't find a clear example about how to create a graph from my data. Let's suppose my data is the matrix 'mat' (representing the distances between each pair of nodes in my graph), as defined below:

julia> mat=rand(4,4);

julia> for i in 1:4
        mat[i,i]=0;
        end

julia> mat
4x4 Array{Float64,2}:
 0.0       0.310287  0.497059  0.0472071
 0.624904  0.0       0.256988  0.675347
 0.305605  0.504063  0.0       0.915409
 0.85426   0.145528  0.055314  0.0     

Please forgive me if this information has been asked before and I didn't find the correct reference. I would much appreciate any help.

Best wishes,

Charles

--

Um axé! :)

--
Charles Novaes de Santana, PhD
http://www.imedea.uib-csic.es/~charles

[Charles Novaes de Santana]

Just to complete the information. I am using Julia Version 0.3.0-prerelease+3841 (2014-06-22 11:24 UTC)

Charles

[Benjamin Lind]

There are a few ways to do it. I prefer to make arrays of the vertices and then the edges and enter them into the graph function. For example:

mat=rand(4,4)

nnodes = size(mat, 1)

nedges = nnodes * (nnodes - 1)

vlist = Array(KeyVertex{Int64}, nnodes)

for i = 1:nnodes

    vlist[i] = KeyVertex(i, i)

end

ecounter = 1

elist = Array(ExEdge{typeof(vlist[1])}, nedges)

for i = 1:nnodes

    for j = 1:nnodes

        if i != j

            elist[ecounter] = ExEdge(ecounter, vlist[i], vlist[j])

            elist[ecounter].attributes["distance"] = mat[i, j]

            ecounter += 1

        end

    end

end

g = graph(vlist, elist, is_directed = true)

[Charles Novaes de Santana]

Thank you, Benjamin!

I was wondering if Graphs had something like function "graph.adjacency" in Igraph library (http://www.inside-r.org/packages/cran/igraph/docs/graph.adjacency). But your suggestion is very good for what I am doing. Thank you, indeed!!

Best regards,

Charles

[Kevin Squire]

Graphs.jl does implement some Matrix representations for graphs: http://graphsjl-docs.readthedocs.org/en/latest/matrix.html.  However, I haven't used them, and it's a little unclear from the docs how to do so.

There is an issue (https://github.com/JuliaLang/Graphs.jl/issues/111) to add examples to the documentation, but it hasn't been followed up on yet.

Cheers,

   Kevin