tests/testthat/test-graph.adjacency.R

In igraph: Network Analysis and Visualization

test_that("graph_from_adjacency_matrix works", {
  M1 <- rbind(
    c(0, 0, 1, 1),
    c(1, 0, 0, 0),
    c(0, 1, 0, 1),
    c(1, 0, 0, 1)
  )
  g1 <- graph_from_adjacency_matrix(M1)
  el1 <- as_edgelist(g1)
  expect_that(
    el1[order(el1[, 1], el1[, 2]), ],
    equals(
      structure(
        c(
          1, 1, 2, 3, 3, 4, 4, 3, 4, 1, 2, 4,
          1, 4
        ),
        .Dim = c(7L, 2L)
      )
    )
  )

  M2 <- rbind(
    c(0, 1, 1, 1),
    c(1, 0, 0, 0),
    c(1, 0, 0, 1),
    c(1, 0, 1, 0)
  )
  g2 <- graph_from_adjacency_matrix(M2, mode = "undirected")
  el2 <- as_edgelist(g2)
  expect_that(
    el2[order(el2[, 1], el2[, 2]), ],
    equals(structure(c(1, 1, 1, 3, 2, 3, 4, 4),
      .Dim = c(4L, 2L)
    ))
  )

  M3 <- rbind(
    c(0, 1, 1, 2),
    c(1, 0, 0, 0),
    c(1, 0, 0, 0),
    c(1, 0, 1, 0)
  )
  g3 <- graph_from_adjacency_matrix(M3, mode = "min")
  el3 <- as_edgelist(g3)
  expect_that(
    el3[order(el3[, 1], el3[, 2]), ],
    equals(structure(c(1, 1, 1, 2, 3, 4), .Dim = c(3L, 2L)))
  )

  M4 <- rbind(
    c(0, 1, 1, 2),
    c(1, 0, 0, 0),
    c(1, 0, 0, 0),
    c(1, 0, 1, 0)
  )
  g4 <- graph_from_adjacency_matrix(M4, mode = "max")
  el4 <- as_edgelist(g4)
  expect_that(
    el4[order(el4[, 1], el4[, 2]), ],
    equals(
      structure(
        c(
          1, 1, 1, 1, 3,
          2, 3, 4, 4, 4
        ),
        .Dim = c(5L, 2L)
      )
    )
  )

  M5 <- rbind(
    c(0, 1, 1, 2),
    c(1, 0, 0, 0),
    c(1, 0, 0, 0),
    c(1, 0, 1, 0)
  )
  g5 <- graph_from_adjacency_matrix(M5, mode = "upper")
  el5 <- as_edgelist(g5)
  expect_that(
    el5[order(el5[, 1], el5[, 2]), ],
    equals(structure(c(1, 1, 1, 1, 2, 3, 4, 4), .Dim = c(4L, 2L)))
  )

  M6 <- rbind(
    c(0, 1, 1, 2),
    c(1, 0, 0, 0),
    c(1, 0, 0, 0),
    c(1, 0, 1, 0)
  )
  g6 <- graph_from_adjacency_matrix(M6, mode = "lower")
  el6 <- as_edgelist(g6)
  expect_that(
    el6[order(el6[, 1], el6[, 2]), ],
    equals(structure(c(1, 1, 1, 3, 2, 3, 4, 4), .Dim = c(4L, 2L)))
  )

  M7 <- rbind(
    c(0, 1, 1, 2),
    c(1, 0, 0, 0),
    c(1, 0, 0, 0),
    c(1, 0, 1, 0)
  )
  g7 <- graph_from_adjacency_matrix(M7, mode = "plus")
  el7 <- as_edgelist(g7)
  expect_that(
    el7[order(el7[, 1], el7[, 2]), ],
    equals(
      structure(
        c(
          1, 1, 1, 1, 1, 1, 1, 3, 2, 2, 3, 3,
          4, 4, 4, 4
        ),
        .Dim = c(8L, 2L)
      )
    )
  )

  M8 <- rbind(
    c(0, 1, 1, 0.5),
    c(1, 0, 0, 0),
    c(1, 0, 0, 0),
    c(1, 0, 2, 0)
  )
  g8 <- graph_from_adjacency_matrix(M8, mode = "directed", weighted = TRUE)
  el8 <- cbind(as_edgelist(g8), E(g8)$weight)
  expect_that(
    el8[order(el8[, 1], el8[, 2]), ],
    equals(structure(
      c(
        1, 1, 1, 2, 3, 4, 4, 2, 3, 4, 1, 1,
        1, 3, 1, 1, 0.5, 1, 1, 1, 2
      ),
      .Dim =
        c(7L, 3L)
    ))
  )

  M9 <- rbind(
    c(0, 1, 1, 3),
    c(1, 0, 0, 0),
    c(1, 0, 0, 2),
    c(3, 0, 2, 0)
  )
  g9 <- graph_from_adjacency_matrix(M9, mode = "undirected", weighted = TRUE)
  el9 <- cbind(as_edgelist(g9), E(g9)$weight)
  expect_that(
    el9[order(el9[, 1], el9[, 2]), ],
    equals(structure(c(1, 1, 1, 3, 2, 3, 4, 4, 1, 1, 3, 2),
      .Dim = c(4L, 3L)
    ))
  )

  M10 <- rbind(
    c(0, 1, 1, 0.5),
    c(1, 0, 0, 0),
    c(1, 0, 0, 0),
    c(1, 0, 2, 0)
  )
  g10 <- graph_from_adjacency_matrix(M10, mode = "max", weighted = TRUE)
  el10 <- cbind(as_edgelist(g10), E(g10)$weight)
  expect_that(
    el10[order(el10[, 1], el10[, 2]), ],
    equals(structure(c(1, 1, 1, 3, 2, 3, 4, 4, 1, 1, 1, 2),
      .Dim = c(4L, 3L)
    ))
  )

  M11 <- rbind(
    c(0, 1, 1, 0.5),
    c(1, 0, 0, 0),
    c(1, 0, 0, 0),
    c(1, 0, 2, 0)
  )
  g11 <- graph_from_adjacency_matrix(M11, mode = "min", weighted = TRUE)
  el11 <- cbind(as_edgelist(g11), E(g11)$weight)
  expect_that(
    el11[order(el11[, 1], el11[, 2]), ],
    equals(structure(c(1, 1, 1, 2, 3, 4, 1, 1, 0.5),
      .Dim =
        c(3L, 3L)
    ))
  )

  M12 <- rbind(
    c(0, 1, 1, 0.5),
    c(1, 0, 0, 0),
    c(1, 0, 0, 0),
    c(1, 0, 2, 0)
  )
  g12 <- graph_from_adjacency_matrix(M12, mode = "lower", weighted = TRUE)
  el12 <- cbind(as_edgelist(g12), E(g12)$weight)
  expect_that(
    el12[order(el12[, 1], el12[, 2]), ],
    equals(structure(c(1, 1, 1, 3, 2, 3, 4, 4, 1, 1, 1, 2),
      .Dim = c(4L, 3L)
    ))
  )

  M13 <- rbind(
    c(0, 1, 1, 0.5),
    c(1, 0, 0, 0),
    c(1, 0, 0, 0),
    c(1, 0, 2, 0)
  )
  g13 <- graph_from_adjacency_matrix(M13, mode = "upper", weighted = TRUE)
  el13 <- cbind(as_edgelist(g13), E(g13)$weight)
  expect_that(
    el13[order(el13[, 1], el13[, 2]), ],
    equals(structure(c(1, 1, 1, 2, 3, 4, 1, 1, 0.5),
      .Dim =
        c(3L, 3L)
    ))
  )

  M14 <- rbind(
    c(0, 1, 1, 0.5),
    c(1, 0, 0, 0),
    c(1, 0, 0, 0),
    c(1, 0, 2, 0)
  )
  g14 <- graph_from_adjacency_matrix(M14, mode = "plus", weighted = TRUE)
  el14 <- cbind(as_edgelist(g14), E(g14)$weight)
  expect_that(
    el14[order(el14[, 1], el14[, 2]), ],
    equals(
      structure(
        c(
          1, 1, 1, 3, 2, 3, 4, 4, 2, 2, 1.5,
          2
        ),
        .Dim = c(4L, 3L)
      )
    )
  )
})

test_that("graph_from_adjacency_matrix 2 edge bug is fixed", {
  A <- Matrix::Matrix(0, 10, 10, sparse = TRUE, doDiag = FALSE)
  A[3, 5] <- A[5, 3] <- 1
  g <- graph_from_adjacency_matrix(A, mode = "undirected")
  expect_that(g[], equals(A))
})

test_that("graph_from_adjacency_matrix empty graph bug is fixed", {
  A <- Matrix::Matrix(0, 10, 10, sparse = TRUE, doDiag = FALSE)
  g <- graph_from_adjacency_matrix(A, mode = "undirected")
  expect_equal(ignore_attr = TRUE, as.matrix(g[]), as.matrix(A))
})

test_that("bug #554 is fixed", {
  M <- Matrix::Matrix(0, 5, 5, doDiag = FALSE)
  M[1, 2] <- M[2, 1] <- M[3, 4] <- M[4, 3] <- 1
  g <- graph_from_adjacency_matrix(M, mode = "undirected", weighted = TRUE)
  expect_that(g[], equals(M))
})

test_that("graph_from_adjacency_matrix works for sparse matrices without values", {
  # https://github.com/igraph/rigraph/issues/269
  M <- Matrix::sparseMatrix(i = c(1, 3), j = c(3, 4), dims = c(5, 5))
  g <- graph_from_adjacency_matrix(M)
  M <- Matrix::sparseMatrix(i = c(1, 3), j = c(3, 4), dims = c(5, 5), x = 1)
  expect_that(g[], equals(M))
})