R: Error in xy.coords(x, y, xlabel, ylabel, log) : 'x' is a list, but does not have components 'x' and 'y'

Question

I am using the R programming language. I am trying to follow the instructions here to make a "k nearest neighbor graph" of my data: https://igraph.org/r/doc/knn.html

Using the "igraph" library, I created some fake data and made a graph:

library(igraph)
file <-data.frame(
    
    "source" = c(
        "John",
        "John",
        "Tim",
        "Tim",
        "Alex",
        "Andrew",
        "Andrew",
        "Andrew",
        "Oliver",
        "Oliver",
        "Oliver",
        "Matt",
        "Steven",
        "Steven",
        "Steven",
        "Matt",
        "Charles",
        "Charles",
        "Charles",
        "Sean",
        "Ted",
        "Ryan",
        "Ryan",
        "Ryan",
        "Ted",
        "Phil",
        "Phil",
        "Phil",
        "Sam",
        "Toby",
        "Toby",
        "Donald",
        "Donald",
        "Donald",
        "Mitch",
        "Mitch",
        "Mitch"),
    
    "target" = c("Sam",
                 "Tim",
                 "Alex",
                 "Matt",
                 "Andrew",
                 "Sean",
                 "Peter",
                 "Ben",
                 "Kevin",
                 "Thomas",
                 "Dave",
                 "Steven",
                 "Kenny",
                 "Derek",
                 "CJ",
                 "Charles",
                 "Ivan",
                 "Kyle",
                 "Andrew",
                 "Ted",
                 "Ryan",
                 "Daniel",
                 "Chris",
                 "Scott",
                 "Phil",
                 "Henry",
                 "George",
                 "Paul",
                 "Toby",
                 "Donald",
                 "Mitch",
                 "Jack",
                 "Luke",
                 "Myles",
                 "Elliot",
                 "Harvey",
                 "Owen")
    
)

graph <- graph.data.frame(file, directed=F)
graph <- simplify(graph)
plot(graph)

From here, I was able to successfully convert this graph into a "k nearest neighbor graph" (note: I am not sure how to specify the "number of neighbors"):

 knn(graph)

$knn
    John      Tim     Alex   Andrew   Oliver     Matt   Steven  Charles     Sean      Ted     Ryan     Phil      Sam 
2.500000 2.333333 4.000000 2.000000 1.000000 3.666667 1.500000 2.500000 4.000000 3.333333 1.500000 1.500000 2.500000 
    Toby   Donald    Mitch    Peter      Ben    Kevin   Thomas     Dave    Kenny    Derek       CJ     Ivan     Kyle 
3.333333 1.500000 1.500000 5.000000 5.000000 3.000000 3.000000 3.000000 4.000000 4.000000 4.000000 4.000000 4.000000 
  Daniel    Chris    Scott    Henry   George     Paul     Jack     Luke    Myles   Elliot   Harvey     Owen 
4.000000 4.000000 4.000000 4.000000 4.000000 4.000000 4.000000 4.000000 4.000000 4.000000 4.000000 4.000000 

$knnk
[1] 3.954545 3.250000 2.733333 1.666667 2.000000

But for some reason, I am not able to plot this graph:

plot(knn(graph))

Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'

Does anyone know why this error is appearing? Can someone please show me what I am doing wrong?

Thanks

Answer 1

You should know that knn(graph) is a list, ie,

> class(knn(graph))
[1] "list"

that why you cannot use plot over knn(graph)

---

I guess what you want to plot is knn(graph)$knn , eg,

plot(rev(stack(knn(graph)$knn)))

or

plot(knn(graph)$knn)