如何使用具有 NA 值的顶点属性对 igraph object（图）进行子图化 - R

Question

I'm trying to subgraph a graph using igraph in by filtering vertices based on the value of an attribute of the vertices. the attribute values can be NA and I want those with NA values to be excluded.

here is my graph

> require(igraph)
> 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)
> subgraph <- make_ego_graph(graph, order=1, c("A", "D", "F"))  # this works because i'm using the names of vertices but it's not what I want

all i'm trying to do here is to get the names of the vertices that have att1==1, and use that instead of to subgraph. But this doesn't work and gives me the following error

 > V(graph)[att1 == 1, na_ok = TRUE]$name  

    Error in if (is.numeric(v) && any(v < 0)) { :    missing value where
        TRUE/FALSE needed

how do I get the vector of the names for vertices that have att1 == 1 to pass it to the subgraph function? or is there another way to subgraph using an attribute value? I want the subgraph to include all the vertices selected (att1 == 1) AND the vertices that connect to those vertices.

Answer 1

Is this what you are looking for?

require(igraph)
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)

V(graph)$name[which(V(graph)$att1 == 1)] 
#> [1] "A" "D"

Lately I became a fan of the tidygraph package which is a wrapper around igraph , so graphs can be manipulated using dplyr and other tidyverse packages. In this case:

library(tidygraph)
library(dplyr)

as_tbl_graph(graph) %>% 
  activate(nodes) %>% 
  filter(att1 == 1) %>% 
  pull(name)
#> [1] "A" "D"

Or directly subset the graph (afaik)

graph_tidy <- as_tbl_graph(graph) %>% 
  activate(nodes) %>% 
  filter(att1 == 1)

graph_tidy
#> # A tbl_graph: 2 nodes and 0 edges
#> #
#> # An undirected simple graph with 2 components
#> #
#> # Node Data: 2 x 2 (active)
#>   name   att1
#>   <chr> <dbl>
#> 1 A         1
#> 2 D         1
#> #
#> # Edge Data: 0 x 2
#> # ... with 2 variables: from <int>, to <int>