[R] Import graph object

[Marc Schwartz]

On Jul 14, 2010, at 3:19 PM, Michael Haenlein wrote:

> Dear all,
> 
> I have a txt file of the following format that describes the relationships
> between a network of a certain number of nodes.
> 
> {4, 2, 3}
> {3, 4, 1}
> {4, 2, 1}
> {2, 1, 3}
> {2, 3}
> {}
> {2, 5, 1}
> {3, 5, 4}
> {3, 4}
> {2, 5, 3}
> 
> For example the first line {4, 2, 3} implies that there is a connection
> between Node 1 and Node 4, a connection between Node 1 and Node 2 and a
> connection between Node 1 and Node 3. The second line {3, 4, 1} implies that
> there is a connection between Node 2 and Node 3 as well as Node 4 and Node
> 1. Note that some of the nodes can be isolated (i.e., not have any
> connections to any other node) which is then indicated by {}. Also note that
> the elements in each row are not necessarily ordered (i.e., {4, 2, 3}
> instead of {2, 3, 4}). I would like to (a) read the txt file into R and (b)
> convert it to an adjacency matrix. For example the adjacency matrix
> corresponding to the aforementioned example is as follows:
> 
> 0 1 1 1 0 0 0 0 0 0
> 1 0 1 1 0 0 0 0 0 0
> 1 1 0 1 0 0 0 0 0 0
> 1 1 1 0 0 0 0 0 0 0
> 0 1 1 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0
> 1 1 0 0 1 0 0 0 0 0
> 0 0 1 1 1 0 0 0 0 0
> 0 0 1 1 0 0 0 0 0 0
> 0 1 1 0 1 0 0 0 0 0
> 
> Is there any convenient way of doing this?
> 
> Thanks,
> 
> Michael


Read the file in with readLines():

# I am on OSX, so copied from the clipboard

Lines <- readLines(pipe("pbpaste"))

> Lines
 [1] "{4, 2, 3}" "{3, 4, 1}" "{4, 2, 1}" "{2, 1, 3}" "{2, 3}"   
 [6] "{}"        "{2, 5, 1}" "{3, 5, 4}" "{3, 4}"    "{2, 5, 3}"


# parse the numbers from Lines

L.split <- strsplit(Lines, split = "[{},]")

> L.split
[[1]]
[1] ""   "4"  " 2" " 3"

[[2]]
[1] ""   "3"  " 4" " 1"

[[3]]
[1] ""   "4"  " 2" " 1"

[[4]]
[1] ""   "2"  " 1" " 3"

[[5]]
[1] ""   "2"  " 3"

[[6]]
[1] "" ""

[[7]]
[1] ""   "2"  " 5" " 1"

[[8]]
[1] ""   "3"  " 5" " 4"

[[9]]
[1] ""   "3"  " 4"

[[10]]
[1] ""   "2"  " 5" " 3"


# Create an initial square matrix of 0's

mat <- matrix(0, length(Lines), length(Lines))

> mat
      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
 [1,]    0    0    0    0    0    0    0    0    0     0
 [2,]    0    0    0    0    0    0    0    0    0     0
 [3,]    0    0    0    0    0    0    0    0    0     0
 [4,]    0    0    0    0    0    0    0    0    0     0
 [5,]    0    0    0    0    0    0    0    0    0     0
 [6,]    0    0    0    0    0    0    0    0    0     0
 [7,]    0    0    0    0    0    0    0    0    0     0
 [8,]    0    0    0    0    0    0    0    0    0     0
 [9,]    0    0    0    0    0    0    0    0    0     0
[10,]    0    0    0    0    0    0    0    0    0     0



# Set the positions in each row to 1

for (i in seq(along = L.split)) mat[i, as.numeric(L.split[[i]])] <- 1

> mat
      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
 [1,]    0    1    1    1    0    0    0    0    0     0
 [2,]    1    0    1    1    0    0    0    0    0     0
 [3,]    1    1    0    1    0    0    0    0    0     0
 [4,]    1    1    1    0    0    0    0    0    0     0
 [5,]    0    1    1    0    0    0    0    0    0     0
 [6,]    0    0    0    0    0    0    0    0    0     0
 [7,]    1    1    0    0    1    0    0    0    0     0
 [8,]    0    0    1    1    1    0    0    0    0     0
 [9,]    0    0    1    1    0    0    0    0    0     0
[10,]    0    1    1    0    1    0    0    0    0     0


HTH,

Marc Schwartz