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，请温柔点。

我有一些数据的形式是：

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)

我收到这个错误：

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

1) 是否有更好的方法为 diagonalNetwork 创建列表？

2) 失败；我如何修改我的循环以踢出正确结构的列表？

3) 我应该使用其他 function/package 吗？

感谢您能提供的任何帮助，我已经在这堵墙上撞了一段时间了。也欢迎就更好的方式提出有关 SO 的问题的反馈。

澄清：

在这里发现了一个类似的问题，。但是，它依赖于一种数据结构，其中根始终在第一列中，其子项在后续列中，而不是像这个问题中那样的边列表，这在 igraph 中很常用。

Answer 1

感谢@Symbolix 指出错误

受@MrFlick 评论的启发，建议从根开始并获得child 以递归地创建列表元素:) ...肯定可以进一步改进以增强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

Answer 2

您可以使用 data.tree 程序包，它可以开箱即用地进行分层数据之间的许多转换：

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)

将关系数据转换为 R 中的分层列表

Turning relationship data into hierarchical list in R

r

hierarchical-data

networkd3