graph_from_edgelist automatically infers the existance of unnamed vertices.

[TheLaughingDuck]

The function graph_from_edgelist automatically infers the existance of unmentioned vertices
I found no clarification of this in the function doc. I think it's an unintuitive programming practice.

Example
This code describes a graph with three vertices, and two edges. However, because the vertices just happen to be named 100,101,102, the generated plot is massive and contains vertices named 1-99, not connected to the actual graph described.

edges <- data.frame(V1 = c(100,101), V2 = c(101,102))
edges <- as.matrix(edges)
plot(igraph::graph_from_edgelist(edges))

[maelle]

Thank you! Posting your reproducible example as reprex for easier later browsing

library("igraph")
#> 
#> Attaching package: 'igraph'
#> The following objects are masked from 'package:stats':
#> 
#>     decompose, spectrum
#> The following object is masked from 'package:base':
#> 
#>     union
edges <- data.frame(V1 = c(100,101), V2 = c(101,102))
edges <- as.matrix(edges)
edges
#>       V1  V2
#> [1,] 100 101
#> [2,] 101 102
plot(igraph::graph_from_edgelist(edges))

^{Created on 2024-12-13 with reprex v2.1.1}

[maelle]

library("igraph")
#> 
#> Attaching package: 'igraph'
#> The following objects are masked from 'package:stats':
#> 
#>     decompose, spectrum
#> The following object is masked from 'package:base':
#> 
#>     union
edges <- data.frame(V1 = c(100,101), V2 = c(101,102))
edges <- as.matrix(edges)
edges
#>       V1  V2
#> [1,] 100 101
#> [2,] 101 102

g <- igraph::graph_from_edgelist(edges)
E(g)
#> + 2/2 edges from d019165:
#> [1] 100->101 101->102
V(g)
#> + 102/102 vertices, from d019165:
#>   [1]   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18
#>  [19]  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36
#>  [37]  37  38  39  40  41  42  43  44  45  46  47  48  49  50  51  52  53  54
#>  [55]  55  56  57  58  59  60  61  62  63  64  65  66  67  68  69  70  71  72
#>  [73]  73  74  75  76  77  78  79  80  81  82  83  84  85  86  87  88  89  90
#>  [91]  91  92  93  94  95  96  97  98  99 100 101 102

^{Created on 2024-12-13 with reprex v2.1.1}

[maelle]

The docs say

If it is a numeric matrix then its elements are interpreted as vertex ids

But maybe we should make this point more prominent in the docs. @TheLaughingDuck where and how would you expect this info? Happy to then update the docs.