igraph：从布局中删除顶点

Question

我想以 4 个步骤（即不同的时间点）创建图表的可视化。我的顶点（节点）的位置应该始终保持不变（使用完整图表的位置）。我想要的只是从 R igraph 图中删除一些顶点。似乎是一个问题是顶点名称发生了变化。

# Erdos
par(mfrow=c(1,3))
g <- erdos.renyi.game(20, 1/20)
locs <- layout.fruchterman.reingold(g)
V(g)$name <- V(g)
# In the original file, vector names look like this (not "1,2,3,4...):
V(g)$name <- as.vector(c(8,9,3,5,13,6,7,1,2,18,11,12,16,14,15,4,17,10,20,19))
V(g)$name

plot(g, 
     layout=locs, 
     main="Original")

# Remove a few vertices
removals1 <- c("12","2","9","11","4")
g2 <- delete.vertices(g,removals1)
plot(g2, 
     layout=locs[-as.numeric(removals1),], 
     main="Removals")

# Remove some more
removals2 <- c("15","14","7","8","5","19","10")
g3 <- delete.vertices(g2,removals2)
plot(g3, 
     layout=locs[-as.numeric(c(removals1,removals2)),], 
     main="More Removals")

我真的很高兴在这里找到解决方案。也许，还有比上述更优雅的解决方案。谢谢！

Answer 1

与其使用以某种方式移动顶点的删除（我什至无法完全覆盖图形，标签无法承受），不如使用induced_subgraph。我不知道为什么会这样，但它似乎有效。

# Erdos
g <- erdos.renyi.game(20, 1/20)
locs <- layout.fruchterman.reingold(g)
V(g)$name <- V(g)
# In the original file, vector names look like this (not "1,2,3,4...):
V(g)$name <- as.vector(c(8,9,3,5,13,6,7,1,2,18,11,12,16,14,15,4,17,10,20,19))
V(g)$name

par(mfrow=c(1,3))
plot(g, 
     layout=locs, 
     main="Original")

# Remove a few vertices
removals1 <- c("12","2","9","11","4")
g2 <- induced_subgraph(g, V(g)[-as.numeric(removals1)])
plot(g2, 
     layout=locs[-as.numeric(removals1),], 
     main="Removals")

# Remove some more
removals2 <- c("15","14","7","8","5","19","10")
g3 <- induced_subgraph(g, V(g)[-as.numeric(c(removals1, removals2))])
plot(g3, 
     layout=locs[-as.numeric(c(removals1,removals2)),], 
     main="More Removals")

Answer 2

@emiliman5 的回答很到位；但是，我想展示一个稍微不同的解决方案以及原版的问题。

locs[-as.numeric(removals1),] 行没有删除 顶点 c("12","2","9","11","4")，而是 行 c("12","2","9","11","4")。

比较：

> head(cbind(as_ids(V(g)),locs))
     [,1] [,2]               [,3]              
[1,] "8"  "42.1520624498397" "29.0822309512088"
[2,] "9"  "42.9864581422991" "28.6882159221222"
[3,] "3"  "42.9653898313169" "30.9232356041607"
[4,] "5"  "46.6704380162041" "29.7404624492056"
[5,] "13" "47.4190242396939" "28.5469829852443"
[6,] "6"  "46.6173689817953" "25.6916967155951"

收件人：

> head(cbind(as_ids(V(g2)),locs[-as.numeric(removals1),]))
     [,1] [,2]               [,3]              
[1,] "8"  "42.1520624498397" "29.0822309512088"
[2,] "3"  "42.9653898313169" "30.9232356041607"
[3,] "5"  "47.4190242396939" "28.5469829852443"
[4,] "13" "46.6173689817953" "25.6916967155951"
[5,] "6"  "44.3293887668239" "30.6957434444784"
[6,] "7"  "47.4947062707832" "27.0391131188028"

请注意，节点 5 的坐标不同。检查子集后 x 坐标和 y 坐标是否匹配：

> r1 <- cbind(as_ids(V(g)),locs)
> r2 <-cbind(as_ids(V(g2)),locs[-as.numeric(removals1),])
> r1[match(r2[,1],r1[,1]),2] == r2[,2]
 [1]  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE
> r1[match(r2[,1],r1[,1]),3] == r2[,3]
 [1]  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE

作为induced_subgraph 解决方案的替代方案，通过顶点ID 的索引对locs 矩阵进行子集化：

plot(g2, 
     layout=(locs[-which(as_ids(V(g)) %in% removals1),]), 
     main="Removals")

which(as_ids(V(g)) %in% removals1)这一行获取指定顶点的行索引：

> which(as_ids(V(g)) %in% removals1)
[1]  2  9 11 12 16

顶点“9”在第 2 行，顶点“2”在第 9 行，以此类推

第三张图：

removals2 <- c("15","14","7","8","5","19","10")
g3 <- delete.vertices(g2,removals2)
plot(g3, 
     layout=locs[-locs[-which(as_ids(V(g)) %in% c(removals1, removals2)),], 
     main="More Removals")