How to Build a Graph from a Data Frame Using the Igraph Package

How do you build a graph from a data frame using the igraph package?

igraph is very flexible and I'm sure there are a number ways to accomplish this. I found the tutorials provided on the website to be very helpful.

Here's one simple way to create a network plot from a data.frame:

library(igraph)

df <- data.frame(
  A = c("Berlin", "Amsterdam", "New York") , 
  B = c("Munich", "Utrecht", "Chicago"))

df.g <- graph.data.frame(d = df, directed = FALSE)

plot(df.g, vertex.label = V(df.g)$name)

Note: For current versions of igraph (as of Version 1.2.1), the graph.data.frame() function is changed to graph_from_data_frame(), which is the only function out of these two to appear in the documentation. The graph.data.frame() function will still work, though.

How to make a network plot using a from-to-dataframe ?

You can plot this using the igraph package like so:

library(igraph)
graph <- graph_from_edgelist(data)
plot(graph)

R, Igraph: convert edges to tibble or data frame

You have extracted edge identifiers from the graph-object. Now you need to understand how the graphs and edges are represented. So use the plot and str commands to examine the details of the g and dd objects:

> g <- make_ring(10)
> plot(g)
> dd <- E(g)[from(1:4)]
> dd
+ 5/10 edges from 96250aa:
[1] 1-- 2 2-- 3 3-- 4 4-- 5 1--10
> str(dd)
 'igraph.es' int [1:5] 1 2 3 4 10   # so it's really just a numeric vector
 - attr(*, "env")=<weakref> 
 - attr(*, "graph")= chr "96250aab-d2ab-43aa-882d-6ef695323b0a"
> help(pack=igraph)
> as_edgelist(g)
      [,1] [,2]     # whereas the original graph (list) converts to two columns
 [1,]    1    2
 [2,]    2    3
 [3,]    3    4
 [4,]    4    5
 [5,]    5    6
 [6,]    6    7
 [7,]    7    8
 [8,]    8    9
 [9,]    9   10
[10,]    1   10
> as_edgelist(dd)
Error in as_edgelist(dd) : Not a graph object

After looking at the results I opened the igraph help index and noted a function named as_ids that was described as: "Convert a vertex or edge sequence to an ordinary vector"

> as_ids(dd)
[1]  1  2  3  4 10
> str(g)
List of 10
 $ :List of 1
  ..$ : 'igraph.vs' int [1:2] 2 10
  .. ..- attr(*, "env")=<weakref> 
  .. ..- attr(*, "graph")= chr "96250aab-d2ab-43aa-882d-6ef695323b0a"
 $ :List of 1
  ..$ : 'igraph.vs' int [1:2] 1 3
  .. ..- attr(*, "env")=<weakref> 
  .. ..- attr(*, "graph")= chr "96250aab-d2ab-43aa-882d-6ef695323b0a"
 $ :List of 1
  ..$ : 'igraph.vs' int [1:2] 2 4
  .. ..- attr(*, "env")=<weakref> 
  .. ..- attr(*, "graph")= chr "96250aab-d2ab-43aa-882d-6ef695323b0a"
 $ :List of 1
  ..$ : 'igraph.vs' int [1:2] 3 5
  .. ..- attr(*, "env")=<weakref> 
  .. ..- attr(*, "graph")= chr "96250aab-d2ab-43aa-882d-6ef695323b0a"
 $ :List of 1
  ..$ : 'igraph.vs' int [1:2] 4 6
  .. ..- attr(*, "env")=<weakref> 
  .. ..- attr(*, "graph")= chr "96250aab-d2ab-43aa-882d-6ef695323b0a"
 $ :List of 1
  ..$ : 'igraph.vs' int [1:2] 5 7
  .. ..- attr(*, "env")=<weakref> 
  .. ..- attr(*, "graph")= chr "96250aab-d2ab-43aa-882d-6ef695323b0a"
 $ :List of 1
  ..$ : 'igraph.vs' int [1:2] 6 8
  .. ..- attr(*, "env")=<weakref> 
  .. ..- attr(*, "graph")= chr "96250aab-d2ab-43aa-882d-6ef695323b0a"
 $ :List of 1
  ..$ : 'igraph.vs' int [1:2] 7 9
  .. ..- attr(*, "env")=<weakref> 
  .. ..- attr(*, "graph")= chr "96250aab-d2ab-43aa-882d-6ef695323b0a"
 $ :List of 1
  ..$ : 'igraph.vs' int [1:2] 8 10
  .. ..- attr(*, "env")=<weakref> 
  .. ..- attr(*, "graph")= chr "96250aab-d2ab-43aa-882d-6ef695323b0a"
 $ :List of 1
  ..$ : 'igraph.vs' int [1:2] 1 9
  .. ..- attr(*, "env")=<weakref> 
  .. ..- attr(*, "graph")= chr "96250aab-d2ab-43aa-882d-6ef695323b0a"
 - attr(*, "class")= chr "igraph"

So if you wanted a data.frame to hold the edge identifiers, you could get a dataframe with a single column, by just doing:

 dd_df <- data.frame( ids <- as_ids(dd) )

But if you wanted a two column result that use as_data_frame method for graph object and then select the first 4 rows of the graph:

> as_data_frame(g)[1:4, ]
  from to
1    1  2
2    2  3
3    3  4
4    4  5

Create bipartite graph in R?

If the graph is created straight from the data.frame it will not be a bipartite graph.

library(igraph)

g <- graph_from_data_frame(df)
is.bipartite(g)
#[1] FALSE

But it will be a bipartite graph if created from the incidence matrix.

tdf <- table(df)
g <- graph.incidence(tdf, weighted = TRUE)
is.bipartite(g)
#[1] TRUE

Now plot it.

colrs <- c("green", "cyan")[V(g)$type + 1L]
plot(g, vertex.color = colrs, layout = layout_as_bipartite)

Add new edges to a igraph using dataframe in R

igraph has a union() method that combines graphs:

library(igraph)

df<-data.frame(from=c(1,2,3), to=c(1,2,3), time=c(1,2,3))
g<-graph_from_data_frame(df,directed=TRUE,vertices=NULL)

df1<-data.frame(from=c(1,2,3), to=c(2,3,1), time=c(4,5,6))
g2 <- graph_from_data_frame(df1, directed = TRUE) 

g3 <- union(g, g2)

plot(g3)

^{Created on 2020-04-15 by the reprex package (v0.3.0)}

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