Read a directed graph in R

Question

I have trouble reading/creating a directed graph. I followed the steps I have found here. This is my text file graph.txt: ``` 1 2 1 3 2 5 3 4 3 5 4 5 5 6 5 10 6 7 7 8 7 9 7 12 8 9 9 10 9 11 9 12 10 11 11 7 11 12 ``` Now I read this graph.txt: ``` library("igraph") xlist<-read.graph("graph.txt", format="edgelist") ``` And then I plot it: ``` plot(xlist) ``` But it is not the graph I have read into xlist: As you can see there is no edge between 1->2, 1->3, 5->10 and so on. How can I read the directed graph correctly? Having done this, how can I show all shortest paths between two nodes?

Accepted Answer

This seems to work fine for me:

```
 xlist<-read.table("graph.txt")
 xlist <- graph.data.frame(xlist)
 plot(xlist)
```

Note `R` changes nodes and indexes them from zero upwards (not in the most recent `igraph` update as @Sacha Epskamp comments below). Using:

```
plot(xlist, vertex.label= V(xlist)$name)
```

you will see the names that you want. i.e. edges between 1 and 2.

One way to plot shortest paths is use `get.all.shortest.paths` and then use this to subset your graph and overplot it. See my answer to this question for similar example where I plot a spanning tree.

Read a directed graph in R

Solution

Problem