如何使用预定义布局保存 igraph object 的边列表？

Question

I have read the R igraph - save layout? , but in my case it is requared to save positions of begin's and end's edges into a file with the edge list together.

I have a tree igraph object and predefined mylayout layout on the plane.

tree <- make_tree(5, 2, mode = "undirected")
mylayout <- matrix(c(1, 2, 0, 3, 2, 
                     1, 2, 0, 2, 3), ncol=2)

I have add a new attribute name

tree <- make_tree(5, 2, mode = "undirected") %>% 
            set_vertex_attr("name", value = seq(1:vcount(tree)))

and I get the edge list of graph via the get.edgelist() function, and I am going to use name attribute:

   df1 <- data.frame(V1 = get.edgelist(tree)[,1], 
                  V2 = get.edgelist(tree)[,2], 
#           V1_x = mylayout[as.integer(names(V(tree))), 1],
#           V1_y = mylayout[as.integer(names(V(tree))), 2],
#           V2_x = mylayout[, 1],
#           V2_y = mylayout[, 2],
            stringsAsFactors = FALSE)

Question. How to match the nodes positions with the begin's and end's positions of edges?

Answer 1

You can try this

get.data.frame(tree) %>%
  cbind(
    split(
      data.frame(mylayout)[match(unlist(.), 1:nrow(mylayout)), ],
      c(col(.))
    )
  )

which gives

  from to 1.X1 1.X2 2.X1 2.X2
1    1  2    1    1    2    2
2    1  3    1    1    0    0
3    2  4    2    2    3    2
4    2  5    2    2    2    3

Answer 2

I don't know if there's an existing way to do this, but it's not too much work to write a helper function to do this

join_layout <- function(g, layout) {
  edges <- as_edgelist(g)
  idx1 <- match(edges[,1], V(g)$name)
  idx2 <- match(edges[,2], V(g)$name)
  result <- cbind(data.frame(edges),
        layout[idx1, ],
        layout[idx2, ]
  )
  names(result) <- c("V1", "V2", "V1_x", "V1_y", "V2_x","V2_y")
  result
}

Basically we use match() to match up the vertex names to rows in the layout matrix. You call it by passing in the igraph object and your layout

join_layout(tree, mylayout)
#   V1 V2 V1_x V1_y V2_x V2_y
# 1  1  2    1    1    2    2
# 2  1  3    1    1    0    0
# 3  2  4    2    2    3    2
# 4  2  5    2    2    2    3