Question: Best practices for converting adj matrix -> graphNEL
gravatar for bryon
2.8 years ago by
bryon10 wrote:

What is the preferred way to convert a weighted adjacency matrix into a graphNEL object? I typically try to use

as(adj, "graphNEL")

but this tends to fail on edge cases. For example, it does not allow negative edge weights (not sure why this is a problem). Also, since edgemode cannot be directly set (I think?), I cannot specify if it is directed or undirected. Both of these issues can be hacked around in various ways, but I am curious what the maintainers / developers intend for this.

Long story short, what is the intended method to take a weighted adjacency matrix and coerce it to a graphNEL object?


graph adjacency matrix • 661 views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by bryon10
Answer: Best practices for converting adj matrix -> graphNEL
gravatar for Wolfgang Huber
2.8 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:

Dear Bryon

I am not sure there is "the intended method". Most of the code in this package is >10 years old, and it was contributed by several authors at the time. So, contributions and patches from you will also be welcome.

Some observations that might be useful:

  • as(adj, "graphNEL") with adj a matrix proceeds via matrix -> graphAM -> graphNEL (look for setAs("matrix", "graphNEL") in mat2graph.R), and for setAs(from="graphAM", to="graphNEL") in methods-graphAM.R. None of that code is set in stone, nor is it very complicated, and patches are welcome.
  • There is also the function ftM2graphNEL (which internally invokes .ftM2other), and this might be closer to what you need. (ftM stands for 'from-to-matrix', and the design idea at the time was to implement the core functionality as normal R functions and only in a second layer wrap them into S4 methods.) The transformation from adjacency matrix to from-to-matrix is simple (essentially, which(aM!=0, arr.ind=TRUE)). In any case, also that function is simple and you could modify it to your needs.
  • And then there is aM2bpG, which is intended for bipartite graphs (i.e. the matrix can be non-square and is expected to have different sets of row and column names) - but there I noted a line that assumes positive edge weights, for no obvious reason, and simply replacing a > operator with an != should generalize that.

Another question is whether you have to use the graph package. There are more actively maintained packages with overlapping aims (e.g. the igraph package on CRAN) - which is part of the reasons why graph authors have decided to maintain, but not further develop the latter.

Hope this helps



ADD COMMENTlink written 2.8 years ago by Wolfgang Huber13k


Thanks for the detailed response -- this is enormously helpful for my purposes. I was not aware that `graph` was not under active development, which is good to know.



ADD REPLYlink written 2.8 years ago by bryon10
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