CODEWITHSUNDEEP
rdistanceigraphminimum-spanning-treeadjacency-matrix
Andrea Ianni
Andrea Ianni

Reputation: 839

From a matrix of distances to a matrix of adjacency

I have a matrix of distances 1024x1024 with all the couple of distances between all the terms. I want to define a graph starting from that. So I defined a minimum spanning tree and I computed the matrix of adjacency on that.

My matrix of distances is distMat.

matrix_of_distances <- as.matrix(distMat)
myGraph <- graph.adjacency(matrix_of_distances, weighted=TRUE)

My graph is a graph with all the possible arcs (because the distances between all the couple of terms are a finite value). I need another graph, sparser:

mst <- as.undirected(minimum.spanning.tree(myGraph))

From that sparse graph I can compute the matrix of adjacency with:

adjacency <- as_adjacency_matrix(mst, type = c("both", "upper", "lower"), attr = NULL, edges = FALSE, names = TRUE, sparse =igraph_opt("sparsematrices"))

Now I want to create the matrix adjacency differently, passing another minimum spanning tree object. Suppose I have created another spanning tree:

spt <- spantree(matrix_of_distances)

If I do:

adjacency <- as_adjacency_matrix(spt, type = c("both", "upper", "lower"), attr = NULL, edges = FALSE, names = TRUE, sparse =igraph_opt("sparsematrices"))

I get the error:

Error in as_adjacency_matrix(spt, type = c("both", "upper", "lower"), : Not a graph object

Again, I'm trying to generate a matrix of adjacency from a minimum spanning tree. How can I solve that?

Upvotes: 2

Views: 4357

Answers (1)

Vincent Guillemot
Vincent Guillemot

Reputation: 3429

The error comes from your using function as_adjacency_matrix on an object of class spantree when it expects an igraph.

Since you are using igraph, one simple solution would be to compute the minimum spanning tree from your original "distance graph" with igraph's function mst.

Here is how spantree computes the minimum spanning tree:

require(vegan)
data(dune)
dis <- vegdist(dune)
tr <- spantree(dis)

The result is the following tree (plot(tr, type="t"))

enter image description here:

You could get the same result only with igraph functions:

library(igraph)
g  <- graph.adjacency(as.matrix(dis), weighted=TRUE)
g_mst <- mst(g)

And the resulting tree looks like this (plot(g_mst, vertex.color=NA, vertex.size=10, edge.arrow.size=0.5)):

enter image description here

Once you have your igraph tree, you already know that you can transform it into an adjacency matrix with function as_adjacency_matrix:

A <- as_adjacency_matrix(mst)

Upvotes: 1

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