节点属性csv图

Question

I have a large number of adjacency matrices, in csv format exported from excel. I also have a large number of csv. files with vertex attribute data. I have linked them in SNA but igraph goes further functionally, so I am looking to move to it, but I am failing to be able to build the graph+attribute files.

I am looking to set up some code that will be a workhorse for doing a range of plots. Although there seem many ways to link these two data sets it seemed this was the simplest: To make the adjacency matrix in the csv a data frame (cut down for missing vertex data) I use:

m <- read.table(header=TRUE, check.names=FALSE, textConnection("
      2 3 4 5 6 7 
    2 0 1 1 0 1 0 
    3 1 0 0 0 1 0 
    4 0 0 0 0 0 0 
    5 1 0 1 0 0 1 
    6 0 0 0 0 0 0 
    7 1 1 0 1 0 0 
"))

In the case of having both vertex and row names in the original file, the imported attributes file has both vertex names and 'row.names' which correspond to the node names. Hex.ed[1,1] gives the value of the attribute for the first node in the m network, ie node 2:

Hex.ed <- read.table(header=TRUE, textConnection("
        HH    Emo  Extra   Aggr Consci    OTE
  2 3.3750 3.0000 3.0000 3.0000 3.0625 3.4375
  3 3.5625 2.9375 3.0625 3.0000 3.3125 3.6250
  4 3.2500 2.8750 3.7500 3.2500 3.8750 3.5000
  5 3.6875 3.1250 3.3750 3.5625 3.6250 3.3125
  6 3.3125 3.0000 3.3125 3.8750 3.2500 3.6875
  7 3.8125 3.2500 3.5625 2.8750 3.6875 3.4375
"))

g <- graph.data.frame(m, directed=TRUE, vertices=Hex.ed)

However, I get the error: Error in graph.data.frame(m, directed = TRUE, vertices = Hex.ed) : Duplicate vertex names

Answer 1

I get a different error message:

Error in graph.data.frame(m, directed = TRUE, vertices = Hex.ed) : 
  Some vertex names in edge list are not listed in vertex data frame

but this is because you were not running the example in the question, but used your complete data set, possibly.

Anyway, graph.data.frame does not use adjacency matrices. From the docs at http://igraph.sourceforge.net/doc/R/graph.data.frame.html :

... the first two columns of d are used as a symbolic edge list and additional columns as edge attributes. The names of the attributes are taken from the names of the columns.

If you cared about reading the manual you would have seen an example at the bottom.

If you have an adjacency matrix, then you can use graph.adjacency to create the graph, and then add the vertex attribute one by one:

g <- graph.adjacency(as.matrix(m))
for (i in seq_len(ncol(Hex.ed))) {
  g <- set.vertex.attribute(g, colnames(Hex.ed)[i], value=Hex.ed[,i])
}
g
# IGRAPH DN-- 6 11 -- 
# + attr: name (v/c), HH (v/n), Emo (v/n), Extra (v/n), Aggr (v/n),
#   Consci (v/n), OTE (v/n)