Input: How should I format my data ?
The netcarto function can read network in either adjacency matrix or adjacency list format.
Matrix format
square symmetric matrix. In this format, the weight \(w\) of an between If you choose the matrix format, your network must consist in a vertices \(i\) and \(j\) is given by the corresponding value in the matrix web[i,j]. Auto-loop (i.e. diagonal terms are authorised). You may name the rows and/or columns, those names will be used in the function output. Example:
Example 1: Triplet
input = matrix(0,3,3)
input[1,2] = 1
input[2,3] = 1
input[3,1] = 1
input[2,1] = 1
input[3,2] = 1
input[1,3] = 1
rownames(input) = c("A","B","C")
colnames(input) = rownames(input)
print(input)## A B C
## A 0 1 1
## B 1 0 1
## C 1 1 0Note that igraph package can be used to manipulate and plot graphs:
# import from rnetcarto matrix format to igraph:
G = igraph::graph.adjacency(input,weighted=TRUE,mode="undirected")
# Export to a matrix compatible with netcarto:
input = igraph::get.adjacency(G,sparse=FALSE)
Example 2: Two triplets
input = matrix(0,7,7)
input[1,2] = 10
input[2,3] = 10
input[3,1] = 10
input[4,5] = 10
input[5,6] = 10
input[6,4] = 10
rownames(input) = c("A","B","C","D","E","F","G")
colnames(input) = rownames(input)Note that:
- Empty colums and lines are removed (Here
G). - If the matrix is not symmetric, symmetry will be enforced by taking
web = web+t(web)-diag(web)
So the previous matrix is equivalent to:
## A B C D E F
## A 0 10 10 0 0 0
## B 10 0 10 0 0 0
## C 10 10 0 0 0 0
## D 0 0 0 0 10 10
## E 0 0 0 10 0 10
## F 0 0 0 10 10 0
Example 3: Bipartite triplets
Note that the matrix may not be square and symmetric if and only if you are considering a bipartite network (using the bipartite flag).
input = matrix(0,6,2)
input[1,1] = 1
input[2,1] = 1
input[3,1] = 1
input[4,2] = 1
input[5,2] = 1
input[6,2] = 1
rownames(input) = c("A","B","C","D","E","F")
colnames(input) = c("Team 1", "Team 2")
print(input)## Team 1 Team 2
## A 1 0
## B 1 0
## C 1 0
## D 0 1
## E 0 1
## F 0 1List format
If you choose the list format, your network must be formatted as a R-list. The first element must be a vector giving the label. The third element is a vector of the edge weights. The weights are optional and are all set to one if the list contains only the first two elements.
Example 1: Unweighted network:
nd1 = c("A","B","C","D","E","F","C")
nd2 = c("B","C","A","E","F","D","D")
web = list(nd1,nd2,weights)
print(list(nd1,nd2))## [[1]]
## [1] "A" "B" "C" "D" "E" "F" "C"
##
## [[2]]
## [1] "B" "C" "A" "E" "F" "D" "D"Example 2: Weighted network
nd1 = c("A","B","C","D","E","F","C","A")
nd2 = c("B","C","A","E","F","D","D","D")
weights = c(10,10,10,10,10,10,10,10,1)
web = list(nd1,nd2,weights)
print(web)## [[1]]
## [1] "A" "B" "C" "D" "E" "F" "C" "A"
##
## [[2]]
## [1] "B" "C" "A" "E" "F" "D" "D" "D"
##
## [[3]]
## [1] 10 10 10 10 10 10 10 10 1Example 3: Bipartite network
nd1 = c("A","B","C","D","E","F","C","A")
nd2 = c("Team1","Team2","Team1","Team1","Team2","Team1","Team1","Team2")
bipartite = list(nd1,nd2)
print(bipartite)## [[1]]
## [1] "A" "B" "C" "D" "E" "F" "C" "A"
##
## [[2]]
## [1] "Team1" "Team2" "Team1" "Team1" "Team2" "Team1" "Team1" "Team2"