4

First of all I want to say that I already read answers for the question: "issues with R “igraph” package neighbor function" and I tried to solve my problem but I couldn't. I tried to ask my question as follow up comment but because of low level of reputation I couldn't, therefore I open this new question. Now here is my question: I have the same problem with neighbors function as it has been explained in: "igraph” package neighbor function but when I try the solution which is given by Gabor Csardi I just received null as result. I attached that part of my code here as well. I would be really thankful for any help and answer. my table:

edgelist <- read.table(text = "
1 2
2 3
3 4
4 5
3 6
6 7")
library(igraph)
graph <- graph.data.frame(edgelist)

str(graph)
## IGRAPH DN-- 7 6 -- 
## + attr: name (v/c)
## + edges (vertex names):
## [1] 1->2 2->3 3->4 4->5 3->6 6->7

now if I want the neighbors of the node 3 it should be 

2, 4, 6

but the result I got is:

2, 4, 5

I noticed it changed the order of my nodes. As I explained before I try the solution that I found in stack overflow but I got null as result:

graph$name[neighbors(graph, 3)]
   NULL

I don't know what else I can do, I would appreciate any help.

Community
  • 1
  • 1
tolou
  • 53
  • 2
  • 6

2 Answers2

9

Before we begin, you should be careful to not confused the label/name and the index/number of a given vertex. When you use both numbers for labels and indicies things quickly become confusing. To avoid all confusion, I've here used letters

edgelist <- read.table(text = "
A B
B C
C D
D E
C F
F G")  

library(igraph)
graph <- graph.data.frame(edgelist)
str(graph)
#IGRAPH DN-- 7 6 -- 
# + attr: name (v/c)
# + edges (vertex names):
# [1] A->B B->C C->D D->E C->F F->G

To see what were dealing with, we plot it:

plot(graph)

Imgur

To get the index of the neighbors do something like: (remember there is a mode argument)

neighbors(graph, 3, mode = "total")  # Index of neighbours by index
## [1] 2 4 5
neighbors(graph, "C", mode = "total")  # Index of neighbours by label
## [1] 2 4 5

To do what Gabor suggests you need to do the following. (I think he missed V( ) and wrote graph$name when he meant V(graph)$name in his post)

# Label of neighbours by label
V(graph)$name[neighbors(graph, "C", mode = "total")]
## [1] "B" "D" "F"

This gives the labels of the corresponding "neighbors". Which does agree with the image.

EDIT Oops. I messed up. Used E() instead of V(). It seems to work as intended. Sorry.

EDIT 2 To see a plot of the neighbors (induced subgraph) you can do something like:

n <- neighbors(graph, "C", mode = "total")

subgraph <- induced.subgraph(graph, n)
plot(subgraph)

subgraph

In this case, a rather boring subgraph. You might want to include the vertex in question as well:

subgraph2 <- induced.subgraph(graph, c(n, V(graph)["C"]))
plot(subgraph2)

subgraph 2

Anders Ellern Bilgrau
  • 9,928
  • 1
  • 30
  • 37
  • @ Anders: great answer! how do you convert "file = neighbors(graph, 3, mode = "total")" into an igraph object? – stats_noob Mar 03 '23 at 08:33
  • suppose I want to plot : plot(neighbors(graph, 3, mode = "total")) .... is this possible? – stats_noob Mar 03 '23 at 08:33
  • @stats_noob What would you expect in that case? I assume you either want the subgraph of 1) only the neighbors or 2) the neighbors *and* the vertex in question. I've edited the answer to show both. – Anders Ellern Bilgrau Mar 05 '23 at 20:18
0

Or, you can use which to give you the index you want:

neighbors(g,which(V(g)$name %in% 'A'),mode='in')
katie lu
  • 489
  • 1
  • 5
  • 23