Compare two graphs
# Load query graphs
source_dir <- system.file(file.path("extdata", "VRPINS"), package = "netdist")
graph_1 <- read_simple_graph(file.path(source_dir, "EBV.txt"),
format = "ncol")
graph_2 <- read_simple_graph(file.path(source_dir, "ECL.txt"),
format = "ncol")
# Calculate netdis statistics
netdis_one_to_one(graph_1, graph_2,
ref_graph,
max_graphlet_size = max_graphlet_size,
neighbourhood_size = neighbourhood_size,
min_ego_nodes = min_ego_nodes,
min_ego_edges = min_ego_edges)
## netdis3 netdis4
## 0.1846655 0.1749835
Compare one graph to many other graphs
# Load query graphs
graphs <- read_simple_graphs(source_dir, format = "ncol", pattern = "*")
graph_1 <- graphs$EBV
graphs_compare <- graphs[c("ECL", "HSV-1", "KSHV", "VZV")]
# Calculate netdis statistics
netdis_one_to_many(graph_1, graphs_compare,
ref_graph,
max_graphlet_size = max_graphlet_size,
neighbourhood_size = neighbourhood_size,
min_ego_nodes = min_ego_nodes,
min_ego_edges = min_ego_edges)
## ECL HSV-1 KSHV VZV
## netdis3 0.1846655 0.008264222 0.01005385 0.006777578
## netdis4 0.1749835 0.165264120 0.01969246 0.159711160
Do pairwise netdis calculations for many graphs
# Load query graphs
source_dir <- system.file(file.path("extdata", "VRPINS"), package = "netdist")
graphs <- read_simple_graphs(source_dir, format = "ncol", pattern = "*")
# Calculate netdis statistics
results <- netdis_many_to_many(graphs,
ref_graph,
max_graphlet_size = max_graphlet_size,
neighbourhood_size = neighbourhood_size,
min_ego_nodes = min_ego_nodes,
min_ego_edges = min_ego_edges)
print(results$netdis)
## [,1] [,2] [,3] [,4] [,5] [,6]
## netdis3 0.1846655 0.008264222 0.01005385 0.006777578 0.2065762 0.2091241
## netdis4 0.1749835 0.165264120 0.01969246 0.159711160 0.2917612 0.2215579
## [,7] [,8] [,9] [,10]
## netdis3 0.2075471 0.0001335756 0.0001748254 0.0005964448
## netdis4 0.4171614 0.0760242643 0.0343418653 0.1311552411
## name_a name_b index_a index_b
## 1 EBV ECL 1 2
## 2 EBV HSV-1 1 3
## 3 EBV KSHV 1 4
## 4 EBV VZV 1 5
## 5 ECL HSV-1 2 3
## 6 ECL KSHV 2 4
## 7 ECL VZV 2 5
## 8 HSV-1 KSHV 3 4
## 9 HSV-1 VZV 3 5
## 10 KSHV VZV 4 5