从 tidygraph 包获取边缘数据

Question

应该很简单，但是我却被这个操作卡住了。我有兴趣提取块边缘数据：23,502 x 3。并指示节点的名称。简而言之，我需要通过名称知道每对节点的权重。

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代码：

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# A tbl_graph: 11539 nodes and 23502 edges\n#\n# An undirected simple graph with 2493 components\n#\n# Node Data: 11,539 x 3 (active)\n  name            neighbors groups\n  <chr>               <dbl>  <int>\n1 CHANSATITPORN N         1   1540\n2 POBKEEREE V             1   1540\n3 SAINIS G                4    361\n4 HARITOS G               4    361\n5 KRIEMADIS T             4    361\n6 PAPASOLOMOU I           3    361\n# \xe2\x80\xa6 with 11,533 more rows\n#\n# Edge Data: 23,502 x 3\n   from    to weight\n  <int> <int>  <dbl>\n1     1     2      1\n2     3     4      2\n3     3     5      2\n# \xe2\x80\xa6 with 23,499 more rows\n

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Answer 1

data.frame()您可以仅使用边缘来提取边缘信息。您可以将我命名的示例 tidygraph 对象替换tg为您的 tidygraph 对象名称，下面的代码应该适合您。

library(igraph)
library(tidygraph)
library(tibble)

# https://tidygraph.data-imaginist.com/reference/tbl_graph.html
rstat_nodes <- data.frame(name = c("Hadley", "David", "Romain", "Julia"))
rstat_edges <- data.frame(from = c(1, 1, 1, 2, 3, 3, 4, 4, 4),
                          to = c(2, 3, 4, 1, 1, 2, 1, 2, 3),
                          weight = c(1:9))
tg <- tbl_graph(nodes = rstat_nodes, edges = rstat_edges)
tg
#> # A tbl_graph: 4 nodes and 9 edges
#> #
#> # A directed simple graph with 1 component
#> #
#> # Node Data: 4 x 1 (active)
#>   name  
#>   <fct> 
#> 1 Hadley
#> 2 David 
#> 3 Romain
#> 4 Julia 
#> #
#> # Edge Data: 9 x 3
#>    from    to weight
#>   <int> <int>  <int>
#> 1     1     2      1
#> 2     1     3      2
#> 3     1     4      3
#> # ... with 6 more rows


# Get edge information ----
edge_list <-
  tg %>%
  activate(edges) %>%
  data.frame()
edge_list
#>   from to weight
#> 1    1  2      1
#> 2    1  3      2
#> 3    1  4      3
#> 4    2  1      4
#> 5    3  1      5
#> 6    3  2      6
#> 7    4  1      7
#> 8    4  2      8
#> 9    4  3      9

但如果您还想要其中的名称，这里有一些代码可以简单地提取节点信息并将数据连接在一起。

# Separate out edges and node data frames
tg_nodes <-
  tg %>%
  activate(nodes) %>%
  data.frame() %>%
  rownames_to_column("rowid") %>%
  mutate(rowid = as.integer(rowid))
tg_edges <-
  tg %>%
  activate(edges) %>%
  data.frame()

named_edge_list <-
  tg_edges %>%
  # Rename from nodes
  left_join(tg_nodes, by = c("from" = "rowid")) %>%
  select(-from) %>%  # Remove unneeded column
  rename(from = name) %>%  # Rename column with names now
  
  # Rename to nodes
  left_join(tg_nodes, by = c("to" = "rowid")) %>%
  select(-to) %>%  # Remove unneeded column
  rename(to = name) %>%  # Rename column with names now

  # Cleaning up
  select(from, to, weight)


named_edge_list
#>     from     to weight
#> 1 Hadley  David      1
#> 2 Hadley Romain      2
#> 3 Hadley  Julia      3
#> 4  David Hadley      4
#> 5 Romain Hadley      5
#> 6 Romain  David      6
#> 7  Julia Hadley      7
#> 8  Julia  David      8
#> 9  Julia Romain      9

^{由reprex 包(v0.3.0)于 2020-09-21 创建}

Answer 2

提取边缘，然后与节点连接以获得接受的答案中的名称，这很直观，但需要很多步骤。

使用（第二个答案）的方法igraph::get.edgelist会丢失存储在边缘中的附加信息（在问题中：权重）。

这是一个应该有效的解决方案。

your_tbl_graph %>% 
  activate(edges) %>% 
  mutate(to_name = .N()$name[to], 
         from_name = .N()$name[from]) %>% 
  as_tibble() %>% 
  select(from = from_name, to = to_name, weight)