Count edges using the adjacency matrix-CodePudding

Based on the adjacency matrix, I would like to count the number of unique edges in a network. In the below example I coloured the unique edges between the different nodes. But I don't know how to proceed.

Desired output:

Sample data

structure(list(...1 = c("m1", "m2", "m3", "m4"), m1 = c(0.2, 
0.2, 0.2, 0.3), m2 = c(0.1, 0.2, 0.2, 0.6), m3 = c(0.5, 0.2, 
1, 0), m4 = c(0.3, 0, 0, 0.1)), row.names = c(NA, -4L), spec = structure(list(
    cols = list(...1 = structure(list(), class = c("collector_character", 
    "collector")), m1 = structure(list(), class = c("collector_double", 
    "collector")), m2 = structure(list(), class = c("collector_double", 
    "collector")), m3 = structure(list(), class = c("collector_double", 
    "collector")), m4 = structure(list(), class = c("collector_double", 
    "collector"))), default = structure(list(), class = c("collector_guess", 
    "collector")), delim = ","), class = "col_spec"),  class = c("spec_tbl_df", 
"tbl_df", "tbl", "data.frame"))

CodePudding user response：

Assuming that this is an undirected graph such that 0 indicates no edge and a positive number indicates an edge, convert the input DF to a logical matrix and from that to an igraph object. Then get its edges and the names of those edges. (Another possible output is by using as_edgelist(g) to get a 2 column matrix such that each row defines an edge.)

library(igraph)

m <- as.matrix(DF[-1])
rownames(m) <- colnames(m)

g <- graph_from_adjacency_matrix(m > 0)
e <- E(g)

attr(e, "vnames")
## [1] "m1|m1" "m1|m2" "m1|m3" "m1|m4" "m2|m1" "m2|m2" "m2|m3" "m3|m1" "m3|m2"
## [10] "m3|m3" "m4|m1" "m4|m2" "m4|m4"

Alternately as a pipeline

library(igraph)
library(tibble)

DF %>%
  column_to_rownames("...1") %>%
  as.matrix %>%
  sign %>%
  graph_from_adjacency_matrix %>%
  E %>%
  attr("vnames")
## [1] "m1|m1" "m1|m2" "m1|m3" "m1|m4" "m2|m1" "m2|m2" "m2|m3" "m3|m1" "m3|m2"
## [10] "m3|m3" "m4|m1" "m4|m2" "m4|m4"

The graph of g looks like this:

set.seed(123)
plot(g)

Note

DF <-
structure(list(...1 = c("m1", "m2", "m3", "m4"), m1 = c(0.2, 
0.2, 0.2, 0.3), m2 = c(0.1, 0.2, 0.2, 0.6), m3 = c(0.5, 0.2, 
1, 0), m4 = c(0.3, 0, 0, 0.1)), row.names = c(NA, -4L), spec = structure(list(
    cols = list(...1 = structure(list(), class = c("collector_character", 
    "collector")), m1 = structure(list(), class = c("collector_double", 
    "collector")), m2 = structure(list(), class = c("collector_double", 
    "collector")), m3 = structure(list(), class = c("collector_double", 
    "collector")), m4 = structure(list(), class = c("collector_double", 
    "collector"))), default = structure(list(), class = c("collector_guess", 
    "collector")), delim = ","), class = "col_spec"),  class = c("spec_tbl_df", 
"tbl_df", "tbl", "data.frame"))