import igraph >= 2.0.0

DESCRIPTION

@@ -12,7 +12,7 @@ Maintainer: Chi Liu <[email protected]>
 Description: A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.
 URL: https://github.com/ChiLiubio/microeco
 Depends: R (>= 3.5.0)
-Imports: R6, stats, ape, vegan, rlang, data.table, magrittr, dplyr, tibble, scales, grid, ggplot2 (>= 3.5.0), RColorBrewer, reshape2, igraph
+Imports: R6, stats, ape, vegan, rlang, data.table, magrittr, dplyr, tibble, scales, grid, ggplot2 (>= 3.5.0), RColorBrewer, reshape2, igraph (>= 2.0.0)
 Suggests: GUniFrac, MASS, ggpubr, randomForest, ggdendro, ggrepel, agricolae, gridExtra, picante, pheatmap, rgexf, mice, GGally
 License: GPL-3
 LazyData: true

R/trans_network.R

@@ -309,7 +309,7 @@ trans_network <- R6Class(classname = "trans_network",
 						stop("All the correlation coefficients larger than COR_cut parameter are not significant under current COR_p_thres parameter!")
 					}
 					cor_matrix[cor_matrix != 1] <- 0
-					network <- graph.adjacency(cor_matrix, mode = "undirected") # graph_from_adjacency_matrix
+					network <- graph_from_adjacency_matrix(cor_matrix, mode = "undirected")
 					edges <- t(sapply(1:ecount(network), function(x) ends(network, x)))
 					E(network)$label <- unlist(lapply(seq_len(nrow(edges)), function(x) ifelse(cortable[edges[x, 1], edges[x, 2]] > 0, "+", "-")))
 					if(COR_weight == T){
@@ -414,7 +414,7 @@ trans_network <- R6Class(classname = "trans_network",
 						b[t(beem.out$resample$b.stab < beemStatic_t_stab)] <- 0
 					}
 					b[abs(b) < beemStatic_t_strength] <- 0
-					network <- graph.adjacency(b, mode = 'directed', weighted = 'weight')
+					network <- graph_from_adjacency_matrix(b, mode = 'directed', weighted = 'weight')
 					V(network)$name <- rownames(use_abund)
 				}
 				if(ecount(network) == 0){