Merge branch 'igraph' into dev

* igraph:
  Increment version number to 1.2.3.9000
  🐞 Fix: rename deprecated igraph functions

Author: wleoncio

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: DIscBIO
 Date: 2026-01-08
 Title: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics
-Version: 1.2.3
+Version: 1.2.3.9000
 Authors@R:
   c(
     person(

NAMESPACE

@@ -91,14 +91,14 @@ importFrom(httr,status_code)
 importFrom(igraph,E)
 importFrom(igraph,V)
 importFrom(igraph,as_adjacency_matrix)
-importFrom(igraph,average.path.length)
+importFrom(igraph,mean_distance)
 importFrom(igraph,betweenness)
 importFrom(igraph,degree)
 importFrom(igraph,distance_table)
-importFrom(igraph,get.adjacency)
+importFrom(igraph,as_adjacency_matrix)
 importFrom(igraph,get.edgelist)
 importFrom(igraph,get.shortest.paths)
-importFrom(igraph,graph.data.frame)
+importFrom(igraph,graph_from_data_frame)
 importFrom(igraph,graph_from_adjacency_matrix)
 importFrom(igraph,mean_distance)
 importFrom(igraph,mst)

NEWS.md

@@ -1,3 +1,7 @@
+# DIscBIO (development version)
+
+* Replaced deprecated functions from `igraph`
+
 # DIscBIO 1.2.3
 
 * Delinted package

R/NetAnalysis.R

@@ -7,8 +7,8 @@
 #'   PPI function.
 #' @param export if `TRUE`, exports the analysis table as a csv file
 #' @param FileName suffix for the file name (if export = TRUE)
-#' @importFrom igraph graph.data.frame as_adjacency_matrix distance_table
-#'   average.path.length get.adjacency V E mean_distance betweenness
+#' @importFrom igraph graph_from_data_frame as_adjacency_matrix distance_table
+#'   mean_distance as_adjacency_matrix V E mean_distance betweenness
 #' @importFrom NetIndices GenInd
 #' @return A network analysis table
 NetAnalysis <- function(
@@ -17,7 +17,7 @@ NetAnalysis <- function(
     stop("No Protein-Protein Interactions")
   }
   df <- data[, -c(1, 2)]
-  gg <- graph.data.frame(df)
+  gg <- graph_from_data_frame(df)
   betweenness <- betweenness(gg)
   betweenness.table <- data.frame(betweenness)
   names <- rownames(betweenness.table)
@@ -38,14 +38,14 @@ NetAnalysis <- function(
     write.csv(AnalysisTable, file = paste0(FileName, ".csv"))
   }
 
-  test.graph.adj <- get.adjacency(gg, sparse = FALSE)
+  test.graph.adj <- as_adjacency_matrix(gg, sparse = FALSE)
   test.graph.properties <- GenInd(test.graph.adj)
   message("Number of nodes: ", test.graph.properties$N)
   message("Number of links: ", test.graph.properties$Ltot)
   message("Link Density: ", test.graph.properties$LD)
   message("The connectance of the graph: ", test.graph.properties$C)
   message("Mean Distences", mean_distance(gg))
-  message("Average Path Length", average.path.length(gg), "\n")
+  message("Average Path Length", mean_distance(gg), "\n")
   AnalysisTable <-
     AnalysisTable[order(AnalysisTable[, 2], decreasing = TRUE), ]
   return(AnalysisTable)