How to create an edge list from a matrix in R?

Question

The relationship is expressed as a matrix x like this:

      A    B    C     D
A     0    2    1     1
B     2    0    1     0
C     1    1    0     1
D     1    0    1     0

The entries refer to the number of connections they have.

Could anyone show me how to write it as an edge list?

I would prefer to write it as an edge list:

A B
A B
A C
A D
B C

But would this edge list allow me to create a network plot?

Answer 1

Using the igraph package:

x <- matrix(c(0,2,1,1,2,0,1,0,1,1,0,1,1,0,1,0), 4, 4)
rownames(x) <- colnames(x) <- LETTERS[1:4]

library(igraph)
g <- graph.adjacency(x)
get.edgelist(g)

#      [,1] [,2]
#  [1,] "A"  "B" 
#  [2,] "A"  "B" 
#  [3,] "A"  "C" 
#  [4,] "A"  "D" 
#  [5,] "B"  "A" 
#  [6,] "B"  "A" 
#  [7,] "B"  "C" 
#  [8,] "C"  "A" 
#  [9,] "C"  "B" 
# [10,] "C"  "D" 
# [11,] "D"  "A" 
# [12,] "D"  "C"

I would also recommend you spend some time reading the igraph documentation at http://igraph.sourceforge.net/index.html since a lot of your recent questions are all simple case usages.

(As a bonus, plot(g) will answer your other question How to plot relationships in R?)

Answer 2

using melt in reshape2, and then delete the weight==0. if no need to print the weight. just delete it.

x
    sample1 sample2 sample3 sample4
feature1       0       2       1       1
feature2       2       0       1       0
feature3       1       1       0       1
feature4       1       0       1       0

melt(x)
   Var1    Var2 value
1  feature1 sample1     0
2  feature2 sample1     2
3  feature3 sample1     1
4  feature4 sample1     1
5  feature1 sample2     2