clean up

mpc-bioinformatics · Mar 25, 2024 · b1c014f · b1c014f
1 parent f592a8a
commit b1c014f
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Showing 3 changed files with 8 additions and 8 deletions.
diff --git a/R/helpers-isomorphisms.R b/R/helpers-isomorphisms.R
@@ -21,8 +21,8 @@ isomorphic_bipartite <- function(graph1, graph2, ...) {
   #iso <- igraph::isomorphic(graph1, graph2)
 
   ## direct graphs if they are not directed yet
-  if (!is.directed(graph1))   graph1 <- bppg::direct_bipartite_graph(graph1)
-  if (!is.directed(graph2))   graph2 <- bppg::direct_bipartite_graph(graph2)
+  if (!igraph::is_directed(graph1))   graph1 <- bppg::direct_bipartite_graph(graph1)
+  if (!igraph::is_directed(graph2))   graph2 <- bppg::direct_bipartite_graph(graph2)
   #graph2 <- bppg::direct_bipartite_graph(graph2)
 
 

diff --git a/tests/testthat/test_isomorphism.R b/tests/testthat/test_isomorphism.R
@@ -5,11 +5,11 @@ test_that("isomorphic_bipartite works as intended", {
 
   # N shape graph
   M <- matrix(c(1,1,0,1), nrow = 2, byrow = TRUE)
-  G <- igraph::graph_from_incidence_matrix(M)
+  G <- igraph::graph_from_biadjacency_matrix(M)
 
   # W shape graph
   M2 <- matrix(c(1,1,0,0,1,1), nrow = 2, byrow = TRUE)
-  G2 <- igraph::graph_from_incidence_matrix(M2)
+  G2 <- igraph::graph_from_biadjacency_matrix(M2)
 
   # M shape graph
   G3 <- G2
@@ -22,7 +22,7 @@ test_that("isomorphic_bipartite works as intended", {
 
   # M + 1 graph
   M4 <- matrix(c(1,1,0,0, 1, 0,0,1,1), nrow = 3, byrow = TRUE)
-  G4 <- igraph::graph_from_incidence_matrix(M4)
+  G4 <- igraph::graph_from_biadjacency_matrix(M4)
 
   G5 <- G4
   igraph::V(G5)$type <- !igraph::V(G4)$type
@@ -38,11 +38,11 @@ test_that("generation of a prototype list", {
 
   # N shape graph
   M <- matrix(c(1,1,0,1), nrow = 2, byrow = TRUE)
-  G <- igraph::graph_from_incidence_matrix(M)
+  G <- igraph::graph_from_biadjacency_matrix(M)
 
   # W shape graph
   M2 <- matrix(c(1,1,0,0,1,1), nrow = 2, byrow = TRUE)
-  G2 <- igraph::graph_from_incidence_matrix(M2)
+  G2 <- igraph::graph_from_biadjacency_matrix(M2)
 
   # M shape graph
   G3 <- G2

diff --git a/tests/testthat/tests-attributes.R b/tests/testthat/tests-attributes.R
@@ -6,7 +6,7 @@ test_that("test add_uniqueness_attributes", {
 
   # W shaped graph
   M <- matrix(c(1,1,0,0,1,1), nrow = 2, byrow = TRUE)
-  G <- igraph::graph_from_incidence_matrix(M)
+  G <- igraph::graph_from_biadjacency_matrix(M)
   G_new <- bppg::add_uniqueness_attributes(G)
 
   expect_equal(igraph::V(G_new)$nr_unique_peptides, c(NA, NA, 0, 0, 0))