Subgraphing an IGraph Object Using Vertices Attribute with NA Values in R

Introduction

The igraph package is a powerful tool for graph manipulation and analysis in R. While it provides an extensive set of functions for creating, manipulating, and analyzing graphs, it can be challenging to subgraph a graph using vertices attribute values that contain missing values (NA). In this article, we will explore how to achieve this goal.

Background

The igraph package uses a variety of data structures to represent graphs, including the igraph object, which is a graph with vertices and edges. The vertices can have attributes attached to them, such as labels or numerical values. When subgraphing an igraph object, we need to specify the vertices that should be included in the subgraph.

Problem Statement

The question you posed on Stack Overflow is quite common among users of the igraph package. You are trying to subgraph a graph using an attribute value that has NA values and want those with NA values to be excluded from the subgraph. However, when you use the which function to filter vertices based on this attribute value, it throws an error because the NA value cannot be directly compared.

Solution Using tidygraph

The tidygraph package is a wrapper around igraph that provides a more convenient and consistent interface for graph manipulation using the tidyverse packages. In particular, we can use the dplyr package to filter vertices based on an attribute value.

Here’s how you can achieve this:

library(igraph)
library(tidygraph)
library(dplyr)

# Create a sample graph with vertices and an attribute
graph <- make_ring(7)
V(graph)$name <- c("A", "B", "C", "D", "E", "F", "G")
V(graph)$att1 <- c(1, 2, NA, 1, 2, 3, NA)

# Filter vertices based on the 'att1' attribute value
subgraph_vertices <- V(graph)[which(V(graph)$att1 == 1)]

# Extract the names of these vertices
names <- subgraph_vertices$name

print(names)

In this code snippet:

• We create a sample graph using make_ring(7).
• We add an attribute att1 to each vertex with values ranging from 1 to 3.
• We use the which function in combination with the $att1 == 1 condition to select vertices that have an att1 value equal to 1, ignoring the NA values.
• The selected vertex names are extracted and printed.

Subgraphing Using tidygraph

Alternatively, you can directly use the tidygraph package to create a subgraph with the desired vertices. Here’s how:

library(igraph)
library(tidygraph)
library(dplyr)

# Create a sample graph with vertices and an attribute
graph <- make_ring(7)
V(graph)$name <- c("A", "B", "C", "D", "E", "F", "G")
V(graph)$att1 <- c(1, 2, NA, 1, 2, 3, NA)

# Convert the graph to a tbl_graph
graph_tidy <- as_tbl_graph(graph) %>%
    activate(nodes) %>%
    filter(att1 == 1) %>%
    pull(name)

print(graph_tidy)

In this code snippet:

• We create a sample graph using make_ring(7).
• We add an attribute att1 to each vertex with values ranging from 1 to 3.
• We convert the graph to a tbl_graph, which is a data frame-like object that can be easily filtered.
• We use the filter function to select vertices that have an att1 value equal to 1 and extract their names.

Subgraphing Using igraph Directly

If you prefer not to use tidygraph or dplyr, you can achieve this result using igraph directly. However, it might be more challenging and less efficient than the methods above.

Here’s a basic example:

library(igraph)

# Create a sample graph with vertices and an attribute
graph <- make_ring(7)
V(graph)$name <- c("A", "B", "C", "D", "E", "F", "G")
V(graph)$att1 <- c(1, 2, NA, 1, 2, 3, NA)

# Initialize an empty graph
subgraph <- new('igraph', directed = FALSE)

# Add edges to the subgraph from selected vertices
for (v in V(graph)[which(V(graph)$att1 == 1)]) {
    for (w in neighbors(V(graph), v)) {
        if (!exists("e")) {
            add_edge(subgraph, v, w)
        }
    }
}

# Print the subgraph
print(subgraph)

In this code snippet:

• We create a sample graph using make_ring(7).
• We add an attribute att1 to each vertex with values ranging from 1 to 3.
• We initialize an empty graph, subgraph, and add edges to it from the selected vertices.

Conclusion

Subgraphing an igraph object using vertices attribute with NA values can be challenging. However, by utilizing packages like tidygraph or dplyr, you can achieve this goal efficiently. The code snippets above demonstrate how to use these approaches to subgraph a graph based on vertex attributes.

Last modified on 2025-03-09