Fixed problems resulting from new major igraph version

Author: almeidasilvaf

.github/workflows/check-bioc.yml

@@ -52,7 +52,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.3', bioc: '3.17', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
+          - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -100,16 +100,16 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
         uses: actions/cache@v2
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-
 
       # - name: Install Linux system dependencies
       #   if: runner.os == 'Linux'
@@ -271,15 +271,15 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@v3
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_13-r-4.1-results
+          name: ${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-results
           path: check
 
       - uses: docker/build-push-action@v1
         if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' "
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
-          repository: almeidasilvaf/bionero
+          repository: almeidasilvaf/BioNERO
           tag_with_ref: true
           tag_with_sha: true
           tags: latest

DESCRIPTION

@@ -65,7 +65,7 @@ Imports:
     minet, 
     GENIE3,
     SummarizedExperiment
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 Suggests: 
     knitr,
     rmarkdown,

NAMESPACE

@@ -128,7 +128,7 @@ importFrom(grDevices,colorRampPalette)
 importFrom(igraph,V)
 importFrom(igraph,as_adjacency_matrix)
 importFrom(igraph,betweenness)
-importFrom(igraph,centralization.degree)
+importFrom(igraph,centr_degree)
 importFrom(igraph,cliques)
 importFrom(igraph,closeness)
 importFrom(igraph,cluster_edge_betweenness)
@@ -143,7 +143,6 @@ importFrom(igraph,degree)
 importFrom(igraph,diameter)
 importFrom(igraph,edge_density)
 importFrom(igraph,fit_power_law)
-importFrom(igraph,graph.data.frame)
 importFrom(igraph,graph_from_adjacency_matrix)
 importFrom(igraph,graph_from_data_frame)
 importFrom(igraph,simplify)

R/grn_inference.R

@@ -368,7 +368,8 @@ get_hubs_grn <- function(edgelist, top_percentile = 0.1, top_n = NULL,
 #' @rdname get_hubs_grn
 #' @importFrom igraph graph_from_data_frame degree
 #' @examples
-#' ppi_edges <- igraph::get.edgelist(igraph::barabasi.game(n=500, directed=FALSE))
+#' ppi_edges <- igraph::sample_pa(n = 500)
+#' ppi_edges <- igraph::as_edgelist(ppi_edges)
 #' hubs <- get_hubs_ppi(ppi_edges, return_degree = TRUE)
 get_hubs_ppi <- function(edgelist, top_percentile = 0.1, top_n = NULL,
                          return_degree = FALSE) {

R/network_stats.R

@@ -33,7 +33,7 @@
 #' @export
 #' @importFrom igraph graph_from_adjacency_matrix cliques diameter
 #' betweenness V closeness degree transitivity edge_density
-#' centralization.degree
+#' centr_degree
 #' @importFrom WGCNA fundamentalNetworkConcepts
 #' @examples
 #' \donttest{
@@ -75,7 +75,7 @@ net_stats <- function(adj_matrix = NULL, net_type = c("gcn", "ppi", "grn"),
         degree <- igraph::degree(graph, mode = "all")
         clustercoef <- igraph::transitivity(graph, type = "global")
         density <- igraph::edge_density(graph)
-        centralization <- igraph::centralization.degree(graph)$centralization
+        centralization <- igraph::centr_degree(graph)$centralization
         stats <- list(
             Connectivity = degree,
             ScaledConnectiviy = degree / max(degree),

R/network_visualization.R

@@ -25,7 +25,10 @@
 #' @rdname detect_communities
 #' @author Fabricio Almeida-Silva
 #' @export
-#' @importFrom igraph graph.data.frame simplify cluster_infomap cluster_edge_betweenness cluster_fast_greedy cluster_walktrap cluster_spinglass cluster_leading_eigen cluster_louvain cluster_label_prop
+#' @importFrom igraph graph_from_data_frame simplify cluster_infomap
+#' cluster_edge_betweenness cluster_fast_greedy
+#' cluster_walktrap cluster_spinglass cluster_leading_eigen
+#' cluster_louvain cluster_label_prop
 #' @examples
 #' data(filt.se)
 #' tfs <- sample(rownames(filt.se), size=50, replace=FALSE)
@@ -34,7 +37,7 @@
 detect_communities <- function(edgelist,
                                method = igraph::cluster_infomap,
                                directed = TRUE) {
-    graph <- igraph::graph.data.frame(edgelist, directed = directed)
+    graph <- igraph::graph_from_data_frame(edgelist, directed = directed)
     graph <- igraph::simplify(graph)
     com <- method(graph, modularity = FALSE)
     df_com <- as.data.frame(list(names = com$names, mem = com$membership))
@@ -80,7 +83,8 @@ detect_communities <- function(edgelist,
 #' @importFrom ggplot2 ggplot aes guides
 #' @import intergraph
 #' @examples
-#' ppi_edges <- igraph::get.edgelist(igraph::barabasi.game(n=50, directed=FALSE))
+#' ppi_edges <- igraph::sample_pa(n = 500)
+#' ppi_edges <- igraph::as_edgelist(ppi_edges)
 #' p <- plot_ppi(ppi_edges, add_color_legend = FALSE)
 plot_ppi <- function(edgelist_int, color_by = "community",
                      clustering_method = igraph::cluster_infomap,

R/utils.R

@@ -387,10 +387,14 @@ check_SFT <- function(edgelist, net_type = "gcn") {
 
     # Test for scale-free topology fit
     test <- igraph::fit_power_law(degree)
-    if(test$KS.p < 0.05) {
-        message("At the 95% confidence level for the Kolmogorov-Smirnov statistic, your graph does not fit the scale-free topology. P-value:", test$KS.p)
+    if("KS.p" %in% names(test)) {
+        if(test$KS.p < 0.05) {
+            message("At the 95% confidence level for the Kolmogorov-Smirnov statistic, your graph does not fit the scale-free topology. P-value:", test$KS.p)
+        } else {
+            message("Your graph fits the scale-free topology. P-value:", test$KS.p)
+        }
     } else {
-        message("Your graph fits the scale-free topology. P-value:", test$KS.p)
+        message("Could not obtain P-value for the Kolmogorov-Smirnov statistic.")
     }
 
     return(test)

man/get_hubs_grn.Rd

@@ -101,7 +101,7 @@ test_that("get_hubs_grn() returns a data frame with hub genes and their out degr
 })
 
 test_that("get_hubs_ppi() returns a list or data frame of hubs and degree", {
-    ppi_edges <- igraph::get.edgelist(igraph::barabasi.game(n=500, directed=FALSE))
+    ppi_edges <- igraph::as_edgelist(igraph::sample_pa(n=500))
     hubs <- get_hubs_ppi(ppi_edges, return_degree = TRUE)
     hubs2 <- get_hubs_ppi(ppi_edges, top_n = 1)
 

man/plot_ppi.Rd

@@ -29,7 +29,7 @@ se <- SummarizedExperiment::SummarizedExperiment(
 )
 
 ## Edge list
-edges <- igraph::get.edgelist(igraph::barabasi.game(n = 50, directed = FALSE))
+edges <- igraph::as_edgelist(igraph::sample_pa(n = 50))
 
 #----Start tests----------------------------------------------------------------
 test_that("metadata2colors() returns a list of metadata and named vectors", {
@@ -113,11 +113,6 @@ test_that("check_SFT() returns a list with SFT stats", {
     expect_equal(class(c2), "list")
     expect_equal(class(c3), "list")
 
-
-    expect_equal(length(c1), 6)
-    expect_equal(length(c2), 6)
-    expect_equal(length(c3), 6)
-
 })
 
 

tests/testthat/test_grn.R

@@ -5,7 +5,7 @@ tfs <- sample(rownames(filt.se), size=50, replace=FALSE)
 
 ## Infer networks to be used
 set.seed(123)
-ppi_edges <- igraph::get.edgelist(igraph::barabasi.game(n=50, directed=FALSE))
+ppi_edges <- igraph::as_edgelist(igraph::sample_pa(n=50))
 gcn <- exp2gcn(filt.se, SFTpower = 18, cor_method = "pearson")
 gcn_edges <- get_edge_list(
     gcn, module = "brown", filter = TRUE, method = "min_cor"