将关系数据转换为R中的分层列表

Question

这是我的第一个问题；所以，请温柔一点。

我有一些数据格式为：

library('networkD3')
    Relationships<- data.frame(Parent=c("earth","earth","forest","forest","ocean","ocean","ocean","ocean"),
                  Child=c("ocean","forest","tree","sasquatch","fish","seaweed","mantis shrimp","sea monster"))
> Relationships
  Parent         Child
1  earth         ocean
2  earth        forest
3 forest          tree
4 forest     sasquatch
5  ocean          fish
6  ocean       seaweed
7  ocean mantis shrimp
8  ocean   sea monster

本质上这是一个可用于制作网络地图的边列表：

net <- graph_from_data_frame(d = Relationships,
                             directed = T)
plot(net)

我想将其转换为可以在下面的diagonalNetwork 函数中使用的形式。

Hierarchical_list <- list(name = "earth",
                 children = list(list(name = "ocean",
                                      children = list(list(name = "mantis shrimp"),
                                                      list(name = "fish"),
                                                      list(name = "sea monster"),
                                                      list(name = "seaweed")
                                                      )),
                                 list(name = "forest",
                                      children = list(list(name = "sasquatch"),
                                                      list(name = "tree")
                                                      ))
                 ))
diagonalNetwork(Hierarchical_list)

像这样：

当我尝试使用此循环生成列表时：

    List_attempt <- list()

levels<- levels(factor(Relationships$Parent))

for(n in 1:length(levels)){
  Children <- subset(Relationships, Relationships$Parent == levels[n], select = Child)
  for(c in 1:length(Children)){
    sublist <- as.list(Children)
    List_attempt <- list(List_attempt, name = levels[n],children = sublist)
  }
}

diagonalNetwork(List_attempt)

我收到此错误：

Error in FUN(X[[i]], ...) : 
  'options' must be a fully named list, or have no names (NULL)

1) 有没有更好的方法来为diagonalNetwork 创建列表？

2) 做不到这一点；如何修改循环以退出正确结构的列表？

3) 我应该使用其他完整的功能/包吗？

感谢您提供的任何帮助，我已经用头撞墙有一段时间了。我们也欢迎就 SO 问题提出更好的方法提供反馈。

澄清：

在这里可以找到类似的问题，Convert a data frame to a treeNetwork compatible list。然而，它依赖于一个数据结构，其中根始终位于第一列，其子节点位于后续列中，而不是 igraph 中常用的这个问题中的边列表。

Answer 1

您可以使用 data.tree 包，它可以在开箱即用的情况下与分层数据进行许多转换：

library('networkD3')
Relationships<- data.frame(Parent=c("earth","earth","forest","forest","ocean","ocean","ocean","ocean"),
                           Child=c("ocean","forest","tree","sasquatch","fish","seaweed","mantis shrimp","sea monster"))

library('data.tree')
tree <- FromDataFrameNetwork(Relationships)
tree
lol <- ToListExplicit(tree, unname = TRUE)
diagonalNetwork(lol)

Answer 2

感谢@Symbolix 指出错误

受到@MrFlick 评论的启发，建议从根开始并让子级递归地创建列表元素 :) ... 当然可以进一步改进，以提高对意外数据输入的鲁棒性

library(igraph)
library('networkD3')
Relationships<- data.frame(Parent=c("earth","earth","forest","forest","ocean","ocean","ocean","ocean"),
    Child=c("ocean","forest","tree","sasquatch","fish","seaweed","mantis shrimp","sea monster"))
net <- graph_from_data_frame(d=Relationships, directed=T)
plot(net)

#net and Relationships as declared in question
#get root
root <- setdiff(Relationships$Parent, Relationships$Child)

#traverse next layer and then recurve
as.list.igraph <- function(thisNode) {
    nm <- vertex_attr(net, "name", thisNode)
    childNodes <- V(net)[which(shortest.paths(net, thisNode, mode="out") == 1)]
    if (length(childNodes)==0) return(list(name=nm))
    list(name=nm, children=unname(lapply(childNodes, as.list.igraph)))
}

#plot D3 network
diagonalNetwork(as.list.igraph(V(net)[root]))

顺便说一句，如果我没记错的话，igraph 中还有一个 layout.reingold.tilford 选项