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rgraphigraphneighbours

neighbors function in igraph package in R

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.

Solution

  • 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