提取有关图形中特定节点的邻域/子图

Question

我在麻烦某些idy中相对简单的Tidygraph操作时遇到麻烦。

我特别想分析不同顺序的特定社区。我认为我需要为此使用Morphs，但我只是没有使它起作用。

library(tidygraph)
library(ggraph)

net <- tibble::tibble(A = letters[1:6],
               B = rep(c("x", "y"), each = 3)) %>% 
  tidygraph::as_tbl_graph()

例如，假设我具有以下网络结构：

我想分析关于x的邻域。

net %>% 
  ggraph(layout = "nicely") +
    geom_edge_link() +
    geom_node_point(size = 10, fill = "white", shape = 21) +
    geom_node_text(aes(label = name)) +
    theme_graph()

iGraph实现的工作方式如下：

提取节点x的邻域。

v <- net %>% 
  tidygraph::as.igraph() %>% 
  igraph::neighborhood(nodes = "x", order = 1)

通过取消列出igraph.vs对象来构建子图

igraph::induced_subgraph(net, vids = unlist(v)) %>% 
  tidygraph::as_tbl_graph() %>% 
  ggraph(layout = "nicely") +
    geom_edge_link() +
    geom_node_point(size = 10, fill = "white", shape = 21) +
    geom_node_text(aes(label = name)) +
    theme_graph()

我如何使用tidygraph？

以下实现返回相同的错误：

net %>% 
  tidygraph::morph(to_local_neighborhood, node = "x", order = 1, mode = "all")

net %>% 
  to_local_neighborhood(node = "x", order = 1, mode = "all")

Error in if (is.numeric(v) && any(v < 0)) { : missing value where TRUE/FALSE needed

Answer 1

如果您不太熟悉tidygraph API，则使用一些基本的R函数比使用GitHub-linked solution多一些回旋，但是我们可以使用@camille's insight获得节点的索引，以要求使用node参数为数字。

library(tidygraph)
#> Attaching package: 'tidygraph'
#> The following object is masked from 'package:stats':
#> 
#>     filter
library(ggraph)
#> Loading required package: ggplot2

# Example
net <- tibble::tibble(A = letters[1:6],
                      B = rep(c("x", "y"), each = 3)) %>% 
  tidygraph::as_tbl_graph()

# Get row name index as integer because tidygraph requirement
node_tbl <- data.frame(activate(net, nodes))  # Make sure focus on nodes
node_idx <- rownames(node_tbl)[node_tbl$name == "x"]
node_idx <- as.integer(node_idx)  # tidygraph needs it as number, not string

net %>%
  tidygraph::convert(to_local_neighborhood,
                     node = node_idx,
                     order = 1,
                     mode = "all") %>%
  ggraph(layout = "nicely") +
  geom_edge_link() +
  geom_node_point(size = 10, fill = "white", shape = 21) +
  geom_node_text(aes(label = name)) +
  theme_graph()

^{由reprex package（v0.3.0）于2020-07-03创建}

这是GitHub链接的解决方案，通过在转换中使用.N()来引用which(.N()$name == "x")中的节点表，从而更多地利用了tidygraph的API。

library(tidygraph)
#> Attaching package: 'tidygraph'
#> The following object is masked from 'package:stats':
#> 
#>     filter
library(ggraph)
#> Loading required package: ggplot2

# Example
net <- tibble::tibble(A = letters[1:6],
                      B = rep(c("x", "y"), each = 3)) %>% 
  tidygraph::as_tbl_graph()

net %>%
  tidygraph::convert(to_local_neighborhood,
                     node = which(.N()$name == "x"),
                     order = 1,
                     mode = "all") %>%
  ggraph(layout = "nicely") +
  geom_edge_link() +
  geom_node_point(size = 10, fill = "white", shape = 21) +
  geom_node_text(aes(label = name)) +
  theme_graph()

^{由reprex package（v0.3.0）于2020-07-03创建}