creating igraph with isolated nodes

Question

I have a similiar problem to this one: Reading adjacency lists with isolated nodes using igraph

I want to plot nodes where some have no relationships. But for some reason the solution mentioned in the thread above is not working

my data

data <- data.frame(ID = c(143918,176206,210749,219170,247818,314764,321459,335945,339637,700689,712607,712946,735907,735907,735907,735907,735907,735907,735908,735908,735908,735908,735908,735908,735910,735911,735912,735913,746929,746929,747540,755003,767168,775558,776656,794173,794175,807493), relation = c(111098,210749,176206,NA,NA,NA,NA,NA,NA,807493,NA,NA,735908,735910,735911,735912,735913,767168,735907,735910,735911,735912,735913,767168,NA,NA,NA,NA,NA,100723,NA,NA,NA,776656,775558,NA,NA,700689))

This should result in a plot that also shows isolated nodes:

v<-unique(data[,1])
e <- na.omit(data)

g<-graph.data.frame(e, vertices = v, directed = T)
plot(g)

For some reason I get the error: "Some vertex names in edge list are not listed in vertex data frame".

I hope someone can tell me what I am doing wrong and how to fix this. Thanks

EDIT: paqmo answers my question, thank you!

However my task requires a different approach. IDs that are in relations, but are missing in the first row, are people in a different location. Those should be omitted, while maintaining every isolated person from the first row. My solution for this uses data.table for now:

v <- unique(c(data[,1]))
v <- as.data.frame(v)
e <- data
setDT(v);setDT(e)
setkey(v)
setkey(e, relation)
e <- e[v]
e <- na.omit(e)
g<-graph.data.frame(e, vertices = v, directed = T)
plot(g)

any advice for a better/more efficient solution would be welcome.

Answer 1

It looks like you are trying to provide vertex name twice, ie once for the first column in e and then again as an argument, vertices = v .

Perhaps what you're really looking for is just

g <- graph.data.frame(e, directed = T)
plot(g)

Answer 2

You need to define your vertex list based on both columns of your object data . Some vertices are in column 1, some in column 2. You are missing those in column 2.

You can check this with %in% :

> c(e[,1], e[,2]) %in% v
 [1]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
[19]  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
[37] FALSE  TRUE  TRUE  TRUE

As you can see, there are 2 elements of e that are not in v . Thus you get the error message that says as much.

Create the vertex list v by taking the unique values of both columns in data , less the NAs.

data <- data.frame(ID = c(143918,176206,210749,219170,
                          247818,314764,321459,335945,
                          339637,700689,712607,712946,
                          735907,735907,735907,735907,
                          735907,735907,735908,735908,
                          735908,735908,735908,735908,
                          735910,735911,735912,735913,
                          746929,746929,747540,755003,
                          767168,775558,776656,794173,
                          794175,807493), 
                   relation = c(111098,210749,176206,
                                NA,NA,NA,NA,NA,NA,807493,
                                NA,NA,735908,735910,735911,
                                735912,735913,767168,735907,
                                735910,735911,735912,735913,
                                767168,NA,NA,NA,NA,NA,100723,
                                NA,NA,NA,776656,775558,NA,NA,700689))

v <- unique(c(data[,1], data[,2])) #Define v from both columns in data
v <- na.omit(v)
e <- na.omit(data)

g<-graph.data.frame(e, vertices = v, directed = T)
plot(g)