Adjacency matrix in R

7
votes

I want to find the adjacency matrix from a csv file that includes the information as follows:

A B 
1 2
1 3
1 4
2 5
3 7

and so on. There are 100 nodes but everytime I try to create a matrix and subsequently plot the graph, the error is that it is a non-square matrix. Can somebody help me with the correct code in R?

2
radjacency-matrix
What code are you using to "create the matrix" and "plot the graph"? To me it seems that your CSV has two columns and many rows, which when read into a table/matrix of course is not square? - mathematical.coffee
That's right...it does have 2 columns and many rows...is there a way that i can create an adjacency matrix using this data? I am trying to use the functions as.matrix and graph.adjacency. - user2203793

2 Answers

18
votes

What you have is an edge list. You can build a graph from that and then covert it to an adjacency matrix:

library(igraph)

dat <- read.table(text="A B 
1 2
1 3
1 4
2 5
3 7", header=TRUE)

get.adjacency(graph.edgelist(as.matrix(dat), directed=FALSE))

That gives

7 x 7 sparse Matrix of class "dgCMatrix"

[1,] . 1 1 1 . . .
[2,] 1 . . . 1 . .
[3,] 1 . . . . . 1
[4,] 1 . . . . . .
[5,] . 1 . . . . .
[6,] . . . . . . .
[7,] . . 1 . . . .
7
votes

Maybe something like:

dat <- read.table(text="A B 
1 2
1 3
1 4
2 5
3 7", header=TRUE)

x <- table(dat)
x %*% t(x)

But maybe you actually want: igraph::graph.data.frame