如何在 igraph 中连接图形的组件
How to connect components of a graph in igraph
我有一个包含 weighted undirected graph 的边列表的数据集。我的数据集包含 multiple components.
现在，我正在尝试连接图表的组件。我的图表包含 4 components。实际上，我想连接它们any edge of 1 component with any edge of another component and would like to give any weight of this edge。
graph1 <- graph_from_data_frame(g, directed = FALSE)
E(graph1)$weight <- is.numeric(g$new_ssp)
plot(graph1, vertex.label = V(graph1)$name)
is_weighted(graph1)
cl <- components(graph1)
此外，我可以找到 membership of the graph
connected_components <- lapply(seq_along(cl$csize)[cl$csize > 1], function(x)
V(graph1)$name[cl$membership %in% x])
现在，你能告诉我如何连接所有组件吗？可能吗？
可重现数据：
g <- structure(list(query = structure(c(1L, 1L, 1L, 2L, 2L, 3L, 4L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L), .Label = c("ID_00104",
"ID_00136", "ID_00169", "ID_00178", "ID_00180"), class = "factor"),
target = structure(c(16L, 19L, 20L, 1L, 9L, 9L, 6L, 11L,
13L, 15L, 4L, 8L, 10L, 14L, 2L, 3L, 5L, 7L, 12L, 17L, 18L
), .Label = c("ID_00169", "ID_00288", "ID_00324", "ID_00394",
"ID_00663", "ID_00790", "ID_00846", "ID_00860", "ID_00910", "ID_00959",
"ID_01013", "ID_01047", "ID_01130", "ID_01222", "ID_01260", "ID_06663",
"ID_06781", "ID_06786", "ID_06791", "ID_09099"), class = "factor"),
new_ssp = c(0.654172560113154, 0.919096895578551, 0.925821596244131,
0.860406091370558, 0.746376811594203, 0.767195767195767,
0.830379746835443, 0.661577608142494, 0.707520891364902,
0.908193484698914, 0.657118786857624, 0.687664041994751,
0.68586387434555, 0.874513618677043, 0.836646499567848, 0.618361836183618,
0.684163701067616, 0.914728682170543, 0.876297577854671,
0.732707087959009, 0.773116438356164)), row.names = c(NA,
-21L), class = "data.frame")
试试下面的代码
graph2 <- with(
stack(membership(cl)),
add.edges(
graph1,
c(combn(sapply(split(ind, values), sample, size = 1), 2)),
weight = runif(choose(cl$no, 2))
)
)
其中所有组件之间的完整连接如下所示
您可以检查 graph2
的边的权重
> E(graph2)
+ 27/27 edges from 31a7614 (vertex names):
[1] ID_00104--ID_06663 ID_00104--ID_06791 ID_00104--ID_09099 ID_00136--ID_00169
[5] ID_00136--ID_00910 ID_00169--ID_00910 ID_00178--ID_00790 ID_00180--ID_01013
[9] ID_00180--ID_01130 ID_00180--ID_01260 ID_00180--ID_00394 ID_00180--ID_00860
[13] ID_00180--ID_00959 ID_00180--ID_01222 ID_00180--ID_00288 ID_00180--ID_00324
[17] ID_00180--ID_00663 ID_00180--ID_00846 ID_00180--ID_01047 ID_00180--ID_06781
[21] ID_00180--ID_06786 ID_00136--ID_06663 ID_00178--ID_06663 ID_06663--ID_01013
[25] ID_00136--ID_00178 ID_00136--ID_01013 ID_00178--ID_01013
> E(graph2)$weight
[1] 0.6541726 0.9190969 0.9258216 0.8604061 0.7463768 0.7671958 0.8303797
[8] 0.6615776 0.7075209 0.9081935 0.6571188 0.6876640 0.6858639 0.8745136
[15] 0.8366465 0.6183618 0.6841637 0.9147287 0.8762976 0.7327071 0.7731164
[22] 0.3098355 0.5842953 0.7397926 0.7337629 0.7643245 0.8331742
如果要查看边列表，可以使用as_data_frame，例如
> as_data_frame(graph2)
from to new_ssp weight
1 ID_00104 ID_06663 0.6541726 0.6541726
2 ID_00104 ID_06791 0.9190969 0.9190969
3 ID_00104 ID_09099 0.9258216 0.9258216
4 ID_00136 ID_00169 0.8604061 0.8604061
5 ID_00136 ID_00910 0.7463768 0.7463768
6 ID_00169 ID_00910 0.7671958 0.7671958
7 ID_00178 ID_00790 0.8303797 0.8303797
8 ID_00180 ID_01013 0.6615776 0.6615776
9 ID_00180 ID_01130 0.7075209 0.7075209
10 ID_00180 ID_01260 0.9081935 0.9081935
11 ID_00180 ID_00394 0.6571188 0.6571188
12 ID_00180 ID_00860 0.6876640 0.6876640
13 ID_00180 ID_00959 0.6858639 0.6858639
14 ID_00180 ID_01222 0.8745136 0.8745136
15 ID_00180 ID_00288 0.8366465 0.8366465
16 ID_00180 ID_00324 0.6183618 0.6183618
17 ID_00180 ID_00663 0.6841637 0.6841637
18 ID_00180 ID_00846 0.9147287 0.9147287
19 ID_00180 ID_01047 0.8762976 0.8762976
20 ID_00180 ID_06781 0.7327071 0.7327071
21 ID_00180 ID_06786 0.7731164 0.7731164
22 ID_06791 ID_00910 NA 0.5680686
23 ID_00178 ID_06791 NA 0.6278790
24 ID_06791 ID_00288 NA 0.8059711
25 ID_00178 ID_00910 NA 0.2578959
26 ID_00910 ID_00288 NA 0.6189977
27 ID_00178 ID_00288 NA 0.6594792
我有一个包含 weighted undirected graph 的边列表的数据集。我的数据集包含 multiple components.
现在，我正在尝试连接图表的组件。我的图表包含 4 components。实际上，我想连接它们any edge of 1 component with any edge of another component and would like to give any weight of this edge。
graph1 <- graph_from_data_frame(g, directed = FALSE)
E(graph1)$weight <- is.numeric(g$new_ssp)
plot(graph1, vertex.label = V(graph1)$name)
is_weighted(graph1)
cl <- components(graph1)
此外，我可以找到 membership of the graph
connected_components <- lapply(seq_along(cl$csize)[cl$csize > 1], function(x)
V(graph1)$name[cl$membership %in% x])
现在，你能告诉我如何连接所有组件吗？可能吗？
可重现数据：
g <- structure(list(query = structure(c(1L, 1L, 1L, 2L, 2L, 3L, 4L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L), .Label = c("ID_00104",
"ID_00136", "ID_00169", "ID_00178", "ID_00180"), class = "factor"),
target = structure(c(16L, 19L, 20L, 1L, 9L, 9L, 6L, 11L,
13L, 15L, 4L, 8L, 10L, 14L, 2L, 3L, 5L, 7L, 12L, 17L, 18L
), .Label = c("ID_00169", "ID_00288", "ID_00324", "ID_00394",
"ID_00663", "ID_00790", "ID_00846", "ID_00860", "ID_00910", "ID_00959",
"ID_01013", "ID_01047", "ID_01130", "ID_01222", "ID_01260", "ID_06663",
"ID_06781", "ID_06786", "ID_06791", "ID_09099"), class = "factor"),
new_ssp = c(0.654172560113154, 0.919096895578551, 0.925821596244131,
0.860406091370558, 0.746376811594203, 0.767195767195767,
0.830379746835443, 0.661577608142494, 0.707520891364902,
0.908193484698914, 0.657118786857624, 0.687664041994751,
0.68586387434555, 0.874513618677043, 0.836646499567848, 0.618361836183618,
0.684163701067616, 0.914728682170543, 0.876297577854671,
0.732707087959009, 0.773116438356164)), row.names = c(NA,
-21L), class = "data.frame")
试试下面的代码
graph2 <- with(
stack(membership(cl)),
add.edges(
graph1,
c(combn(sapply(split(ind, values), sample, size = 1), 2)),
weight = runif(choose(cl$no, 2))
)
)
其中所有组件之间的完整连接如下所示
您可以检查 graph2
> E(graph2)
+ 27/27 edges from 31a7614 (vertex names):
[1] ID_00104--ID_06663 ID_00104--ID_06791 ID_00104--ID_09099 ID_00136--ID_00169
[5] ID_00136--ID_00910 ID_00169--ID_00910 ID_00178--ID_00790 ID_00180--ID_01013
[9] ID_00180--ID_01130 ID_00180--ID_01260 ID_00180--ID_00394 ID_00180--ID_00860
[13] ID_00180--ID_00959 ID_00180--ID_01222 ID_00180--ID_00288 ID_00180--ID_00324
[17] ID_00180--ID_00663 ID_00180--ID_00846 ID_00180--ID_01047 ID_00180--ID_06781
[21] ID_00180--ID_06786 ID_00136--ID_06663 ID_00178--ID_06663 ID_06663--ID_01013
[25] ID_00136--ID_00178 ID_00136--ID_01013 ID_00178--ID_01013
> E(graph2)$weight
[1] 0.6541726 0.9190969 0.9258216 0.8604061 0.7463768 0.7671958 0.8303797
[8] 0.6615776 0.7075209 0.9081935 0.6571188 0.6876640 0.6858639 0.8745136
[15] 0.8366465 0.6183618 0.6841637 0.9147287 0.8762976 0.7327071 0.7731164
[22] 0.3098355 0.5842953 0.7397926 0.7337629 0.7643245 0.8331742
如果要查看边列表，可以使用as_data_frame，例如
> as_data_frame(graph2)
from to new_ssp weight
1 ID_00104 ID_06663 0.6541726 0.6541726
2 ID_00104 ID_06791 0.9190969 0.9190969
3 ID_00104 ID_09099 0.9258216 0.9258216
4 ID_00136 ID_00169 0.8604061 0.8604061
5 ID_00136 ID_00910 0.7463768 0.7463768
6 ID_00169 ID_00910 0.7671958 0.7671958
7 ID_00178 ID_00790 0.8303797 0.8303797
8 ID_00180 ID_01013 0.6615776 0.6615776
9 ID_00180 ID_01130 0.7075209 0.7075209
10 ID_00180 ID_01260 0.9081935 0.9081935
11 ID_00180 ID_00394 0.6571188 0.6571188
12 ID_00180 ID_00860 0.6876640 0.6876640
13 ID_00180 ID_00959 0.6858639 0.6858639
14 ID_00180 ID_01222 0.8745136 0.8745136
15 ID_00180 ID_00288 0.8366465 0.8366465
16 ID_00180 ID_00324 0.6183618 0.6183618
17 ID_00180 ID_00663 0.6841637 0.6841637
18 ID_00180 ID_00846 0.9147287 0.9147287
19 ID_00180 ID_01047 0.8762976 0.8762976
20 ID_00180 ID_06781 0.7327071 0.7327071
21 ID_00180 ID_06786 0.7731164 0.7731164
22 ID_06791 ID_00910 NA 0.5680686
23 ID_00178 ID_06791 NA 0.6278790
24 ID_06791 ID_00288 NA 0.8059711
25 ID_00178 ID_00910 NA 0.2578959
26 ID_00910 ID_00288 NA 0.6189977
27 ID_00178 ID_00288 NA 0.6594792