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将多个节点向量合并为边列表并将其转换为邻接矩阵

adjacency-list adjacency-matrix igraph r

Chris T. · 技术社区 · 7 年前

我想映射一些关系圈(由一系列关系组成) id

circle_1 = c(1, 3, 5)
circle_2 = c(17, 22, 35, 49)
circle_3 = c(2, 9)
circle_4 = c(12, 28, 33)
circle_5 = c(1, 3, 8, 16, 40)

d_mat = matrix(ncol = 2)

for (i in 1:5) {
#extract id from list
dat = get(paste("circle", i, sep="_"))
#convert to edgelist, each pair is unique
dat_t = t(combn(dat, 2))
#rbind edge list together
edge_list <- rbind(d_mat, dat_t)
}

然而,输出 edge_list circle_5

此外,假设这五个圆是从一组50人中画出来的,我如何将这些边列表的值映射到50×50邻接矩阵的相应单元格(我想 make_graph 和 as_adjacency_matrix 作用于 igraph 应该做的把戏,但我现在不知道怎么做)

circle_1 ,这意味着1和3在这个50人的网络中链接了两次。如何聚合此计数频率并将邻接矩阵转换为加权矩阵?

2 回复 | 直到 7 年前

gfgm 7 年前

您可以在开始时通过组合边列表来完成,然后直接创建矩阵。

circle_1 = c(1, 3, 5)
circle_2 = c(17, 22, 35, 49)
circle_3 = c(2, 9)
circle_4 = c(12, 28, 33)
circle_5 = c(1, 3, 8, 16, 40)

# lets put all the circles in a list for convenience
circles <- list(circle_1, circle_2, circle_3,
                circle_4, circle_5)

# we will lapply along the list, get the complete set of 
# edges with combn, and then rbind all the resulting
# structures together
edge_list <- do.call(rbind, lapply(circles, function(circ){t(combn(circ, 2))}))

# we convert to a data.frame and set the factor levels
# such that R knows these are nodes from a set of 50 nodes
edge_list <- data.frame(from = factor(edge_list[,1], levels=1:50),
                        to = factor(edge_list[,2], levels=1:50))
# take a look
head(edge_list)
#>   from to
#> 1    1  3
#> 2    1  5
#> 3    3  5
#> 4   17 22
#> 5   17 35
#> 6   17 49
# we can just use table to make the adjacency matrix. R will create
# a row/column for each level of the factor. We look at the first
# 6x6 entries
table(edge_list)[1:6,1:6] # luckily entry (1,3) = 2 as we hoped
#>     to
#> from 1 2 3 4 5 6
#>    1 0 0 2 0 1 0
#>    2 0 0 0 0 0 0
#>    3 0 0 0 0 1 0
#>    4 0 0 0 0 0 0
#>    5 0 0 0 0 0 0
#>    6 0 0 0 0 0 0

这个邻接矩阵是上三角形的。如果希望邻接矩阵像反射无向图一样对称,可以使用 adj.mat[lower.tri(adj.mat)] <- adj.mat[upper.tri(adj.mat)] .

# to convert to purely binary
adj.mat <- table(edge_list)
adj.mat.bin <- ifelse(adj.mat>1, 1, adj.mat)
adj.mat.bin[1:6,1:6]
#>     to
#> from 1 2 3 4 5 6
#>    1 0 0 1 0 1 0
#>    2 0 0 0 0 0 0
#>    3 0 0 0 0 1 0
#>    4 0 0 0 0 0 0
#>    5 0 0 0 0 0 0
#>    6 0 0 0 0 0 0

^{于2018年11月16日由

reprex package

(v0.2.1)}

Henrik plannapus 7 年前

我从@gfgm借用顶点列表(“圆”)并使用 igraph 功能。

使用鼠标在顶点列表上循环 lapply make_full_graph n 等于向量的长度。设置顶点的名称( V(g)$name ). 转换为“边缘列表”( as_edgelist ). rbind

library(igraph)
m <- do.call(rbind, lapply(circles, function(vert){
  g <- make_full_graph(n = length(vert))
  V(g)$name <- vert
  as_edgelist(g)
}))

设置 factor “从”和“到”顶点的级别,并使用 table (类似于@gfgm)

tt <- table(factor(m[ , 1], levels = 1:50),
            factor(m[ , 2], levels = 1:50)) 

t[1:8, 1:16]
#   1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
# 1 0 0 2 0 1 0 0 1 0  0  0  0  0  0  0  1
# 2 0 0 0 0 0 0 0 0 1  0  0  0  0  0  0  0
# 3 0 0 0 0 1 0 0 1 0  0  0  0  0  0  0  1
# 4 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0
# 5 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0
# 6 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0
# 7 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0
# 8 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  1