从igraph all_simple_paths检索路径名列表

Question

我有一个有向循环矩阵，需要提取i和j之间的所有简单路径。

以下是我的前任。 矩阵：

>M2<-matrix(c(1,1,0,0,0,1,1,1,1,0,0,1,1,1,0,0,1,0,1,1,0,0,0,1,1), 5, byrow=T)
>colnames(M2)<-c("A", "B", "C", "D", "E")
>row.names(M2)=colnames(M2)
>M2
  A B C D E
A 1 1 0 0 0
B 1 1 1 1 0
C 0 1 1 1 0
D 0 1 0 1 1
E 0 0 0 1 1

我使用igraph使用graph_from_adjency_matrix函数将矩阵转换为图形对象。

>graph<-graph_from_adjacency_matrix(M2, mode=c("directed"), weighted=NULL, diag=F, add.colnames=NULL, add.rownames=NA)
>graph
IGRAPH DN-- 5 9 -- 
+ attr: name (v/c)
+ edges (vertex names):
[1] A->B B->A B->C B->D C->B C->D D->B D->E E->D

然后从那里使用all_simple_paths函数获取i和j之间的所有简单路径。 从这里开始我的问题。

1）我可以指定j（ to具有to=V(graph) ）为所有可能的最终顶点。 但是我无法指定from参数来计算寻找所有顶点的路径可能的起点。 我必须一次指定每个变量。 有什么办法吗？

2） all_simple_path函数运行良好，并为我提供了i和j之间的所有简单路径，例如，对于以A开头并以任何可能的j结尾的简单路径：

>Simple_path_list<-all_simple_paths(graph, from ="A", to=V(graph), mode = c("out"))
>Simple_path_list
[[1]]
+ 2/5 vertices, named:
[1] A B

[[2]]
+ 3/5 vertices, named:
[1] A B C

[[3]]
+ 4/5 vertices, named:
[1] A B C D

[[4]]
+ 5/5 vertices, named:
[1] A B C D E

[[5]]
+ 3/5 vertices, named:
[1] A B D

[[6]]
+ 4/5 vertices, named:
[1] A B D E

我的问题是，我需要收集所有这些路径并放在列表中，例如：

Paths
A B
A B C
A B C D
A B C D E 
A B D
A B D E

我试图创建一个列表并使用普通list<-Simple_path_list[1]左右来调用路径名，但是我总是与路径一起检索有关所涉及的顶点数的信息（例如+ 4/5 vertices, named ）。 关于如何仅检索路径名而不检索其他信息的任何想法？

Answer 1

该lapply的功能all_simple_paths做一个列表的列表（即路径每个顶点的名单列表）。 使用unlist(..., recursive = F)将列表的列表简化为列表，然后使用names或igraph的as_ids单独提取顶点ID。

library(igraph)
M2<-matrix(c(1,1,0,0,0,1,1,1,1,0,0,1,1,1,0,0,1,0,1,1,0,0,0,1,1), 5, byrow=T)
colnames(M2)<-c("A", "B", "C", "D", "E")
row.names(M2)=colnames(M2)
M2
graph<-graph_from_adjacency_matrix(M2, mode=c("directed"), weighted=NULL, diag=F, add.colnames=NULL, add.rownames=NA)
l <- unlist(lapply(V(graph) , function(x) all_simple_paths(graph, from=x)), recursive = F)
paths <- lapply(1:length(l), function(x) as_ids(l[[x]]))

这将产生：

> paths
[[1]]
[1] "A" "B"

[[2]]
[1] "A" "B" "C"

[[3]]
[1] "A" "B" "C" "D"

[[4]]
[1] "A" "B" "C" "D" "E"

[[5]]
[1] "A" "B" "D"

[[6]]
[1] "A" "B" "D" "E"

[[7]]
[1] "B" "A"

[[8]]
[1] "B" "C"

[[9]]
[1] "B" "C" "D"

[[10]]
[1] "B" "C" "D" "E"

[[11]]
[1] "B" "D"

[[12]]
[1] "B" "D" "E"

[[13]]
[1] "C" "B"

[[14]]
[1] "C" "B" "A"

[[15]]
[1] "C" "B" "D"

[[16]]
[1] "C" "B" "D" "E"

[[17]]
[1] "C" "D"

[[18]]
[1] "C" "D" "B"

[[19]]
[1] "C" "D" "B" "A"

[[20]]
[1] "C" "D" "E"

[[21]]
[1] "D" "B"

[[22]]
[1] "D" "B" "A"

[[23]]
[1] "D" "B" "C"

[[24]]
[1] "D" "E"

[[25]]
[1] "E" "D"

[[26]]
[1] "E" "D" "B"

[[27]]
[1] "E" "D" "B" "A"

[[28]]
[1] "E" "D" "B" "C"

加成

对于all_shortest_paths ，必须对每个节点的路径列表进行子集化，以排除测地线信息。

l <- lapply(V(graph), function(x) all_shortest_paths(graph, from = x))
l <- lapply(l, function(x) x[[-2]])
l <- unlist(l, recursive = F)
paths <- lapply(1:length(l), function(x) as_ids(l[[x]]))