二分 igraph 中的节点顺序

Question

我有以下邻接矩阵 "dat":

dat <- read.table(text = '     TZ1   TZ2   TZ3   TZ4
  RSP1 0.456 0.232 0.234 0.000
  RSN1 0.248 0.613 0.754 0.413
  RSP2 0.206 0.000 0.493 0.000
  RSN2 0.000 0.000 0.000 0.000
  RSP3 0.000 0.000 0.218 0.000
  RSN3 0.000 0.000 0.000 0.000
  RSP4 0.000 0.000 0.000 0.851
  RSN4 0.000 0.000 0.000 0.000' ) %>%
    as.matrix()

并使用下面的代码生成二分法

g<-graph_from_incidence_matrix(dat, directed = TRUE, mode = "out", multiple = FALSE, weighted = T, add.names = NULL)
V(g)$color <- ifelse(V(g)$type, "lightblue", "salmon")
V(g)$shape <- ifelse(V(g)$type, "square","circle")
V(g)$frame.color <-  "gray" 
V(g)$size <- 18
E(g)$color <- "blue"
plot.igraph(g, edge.width=E(g)$weight*5, layout=layout.bipartite,edge.arrow.size=0.5,
 vertex.label.cex = 0.8, vertex.label.color = "black", vertex.shape=V(g)$shape, vertex.size=degree(g)*5)

但是节点的顺序不是按照下面的顺序

RSP1    RSN1    RSP2    RSN2    RSP3    RSN3    RSP4    RSN4

和

TZ1   TZ2   TZ3   TZ4

我们如何制作具有上述节点排序的图形？

Answer 1

因此 igraph、layout.bipartite 中的许多布局功能都包括在内，重点是最小化边缘交叉：

The layout is created by first placing the vertices in two rows, according to their types. Then the positions within the rows are optimized to minimize edge crossings,

如果你想控制节点位置，那么你将不得不通过使用 x 和 y[=28= 制作矩阵来制作自定义布局] 在列和行中的位置与 V(g) 的顺序相同。 purrr 可以帮到你：

Rs <- V(g)$name[grepl('^R', V(g)$name)] %>% purrr::imap(function(x, i){ c(i, 2) }) %>% do.call(rbind, .) Ts <- V(g)$name[grepl('^T', V(g)$name)] %>% purrr::map2(3:6, function(x, i){ c(i, 1) }) %>% do.call(rbind, .) l <- rbind(Rs, Ts)

这会给你一个矩阵：

[,1] [,2] [1,] 1 2 [2,] 2 2 [3,] 3 2 [4,] 4 2 [5,] 5 2 [6,] 6 2 [7,] 7 2 [8,] 8 2 [9,] 3 1 [10,] 4 1 [11,] 5 1 [12,] 6 1

二分 igraph 中的节点顺序

Node order in bipartite igraph

r

igraph

bipartite