r中有向无向图的加权边列表_R_Igraph

r中有向无向图的加权边列表

r中有向无向图的加权边列表,r,igraph,R,Igraph,我有以下加权边缘列表el structure(list(from = c(1001L, 1001L, 1002L, 1002L, 1003L, 1003L ), to = c(1002L, 1003L, 1001L, 1003L, 1001L, 1002L), weight = c(2L, 0L, 1L, 0L, 0L, 0L)), .Names = c("from", "to", "weight"), class = "data.frame", row.names = c(NA, -6L)

我有以下加权边缘列表

el

structure(list(from = c(1001L, 1001L, 1002L, 1002L, 1003L, 1003L
), to = c(1002L, 1003L, 1001L, 1003L, 1001L, 1002L), weight = c(2L, 
0L, 1L, 0L, 0L, 0L)), .Names = c("from", "to", "weight"), class = "data.frame", row.names = c(NA, 
-6L))

我想创建一些可视化：（1）一个有向图，其中权重用于加厚两个给定节点之间的线，（2）一个无向图，将所有交互（

weight

s）相加并生成相同的图，以及在不使用权重的情况下重新创建（1）和（2）的图

对于（1）我使用

我认为发生的事情是，

weight=0

没有做我认为应该做的事情（表示没有链接）

我也不确定为什么节点不在页面上展开[

，请考虑下面的选项。

################################################################### FIRST OPTION

el <- data.frame(from = c(1001L, 1001L, 1002L, 1002L, 1003L, 1003L),
                 to = c(1002L, 1003L, 1001L, 1003L, 1001L, 1002L),
                 weight = c(2L, 0L, 1L, 0L, 0L, 0L))
el
# This design of edgelist implies that there are links between (i) 1003 and 1001
# and between (ii) 1003 and 1002 but the weight of those links is 0
library(igraph)
directed_graph_wgt <- graph.data.frame(el, directed = TRUE)
# the adjacency matrix of your network looks like this
adj.mat <- as_adjacency_matrix(directed_graph_wgt, type = "both", names = TRUE,
                               sparse = FALSE)
adj.mat # as you can see, the adjacency_matrix shows links between 
# (i) 1003 and 1001 and and between (ii) 1003 and 1002

                                ### IMPORTANT ### 
# When you move from an adjacency matrix to a graph, you might consider
# that a "weight" of 0 in the matrix leads to no interaction (edge) between nodes. 
# But be careful,  the adjacency matrix is actually a relationnal matrix
# (or connection matrix), not just a weights matrix. It actually provides the 
# number of edges between nodes from the graph.
# Therefore, when you are designing your graph.data.frame, your must include 
# ONLY connected nodes

# Something like this should be relevent here
nodes <-  c(1001L, 1002L, 1003L) # create a vector of nodes 
nodes # we have three nodes
el <- data.frame(from = c(1001L, 1002L),
                 to = c(1002L, 1001L),
                 weight = c(2L, 1L)) # use ONLY connected nodes
el # structrure of links
# Now, you can include all the nodes in the network with the "vertices" argument

# (1) directed graph
directed_graph_wgt <- graph.data.frame(el, directed = TRUE,
                                       vertices = nodes)
# the right adjacency matrix of your network looks like this
adj.mat <- as_adjacency_matrix(directed_graph_wgt, type = "both", names = TRUE,
                               sparse = FALSE)
adj.mat # as you can see, the adjacency matrix shows all the nodes 
# and here is the plot
plot(directed_graph_wgt, layout = layout.fruchterman.reingold,
     edge.width = E(directed_graph_wgt)$weight/2)

# (2) undirected graph
undirected_graph_wgt <- as.undirected(directed_graph_wgt, mode = "collapse",
                                      edge.attr.comb = "sum")
plot(undirected_graph_wgt)


### KEYPOINT
# When you are designing your own edgelist, setting a weight as 0 means that 
# the weight of the considered link is 0, not that the link doesn't exist. 
# However, a 0 in the adjacency matrix leads to no interaction (edge)
# between nodes.

# It looks like you are confusing "weights" and "number of interactions". Even 
# though both can be used interchangeably, you must be careful when using them
# in igraph functions


################################################################## SECOND OPTION

# To use the weights in "el" as indicator of relations, you need to consider
# the assumption that weight == 0 means no link.
# You can use the delete_edges() function

el <- data.frame(from = c(1001L, 1001L, 1002L, 1002L, 1003L, 1003L),
                 to = c(1002L, 1003L, 1001L, 1003L, 1001L, 1002L),
                 weight = c(2L, 0L, 1L, 0L, 0L, 0L))
el #t this is your initial edgelist

# (1) directed graph
directed_graph_wgt <- graph.data.frame(el, directed = TRUE)
directed_graph_wgt
# use delete_edges() to consider ONLY weight != 0 (no link)
# We will remove link with weight == 0 (i.e no link)
directed_graph_wgt2 <- delete_edges(directed_graph_wgt,
                                    which(E(directed_graph_wgt)$weight == 0))
plot(directed_graph_wgt2, layout = layout.fruchterman.reingold,
     edge.width = E(directed_graph_wgt)$weight/2)

# (2) undirected graph
undirected_graph_wgt <- as.undirected(directed_graph_wgt, mode = "collapse",
                                      edge.attr.comb = "sum")
undirected_graph_wgt2 <- delete_edges(undirected_graph_wgt,
                                      which(E(undirected_graph_wgt)$weight == 0))
plot(undirected_graph_wgt2)

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如果我有一个非常大的数据库（N=500万），那么选项一的自动化程度会降低，对吗？我可能遗漏了什么。另外，在我的图中，我希望显示隔离，这就是为什么我使用

weight==0

。选项2似乎删除了隔离，这个假设是否错误？是的，对于如此大的数据库，第二个选项更合适。此选项（以及选项1）不会删除孤立节点；它删除权重=0的链接。在本例中，您可以看到节点

即使没有链接也仍然存在于网络中。我收到了一个代码错误：

directed\u graph\u wgt2它是delete\u edges
而不是delete.edges`对于我来说，至少使用igraph
还有as.undirected（directed\u graph\u wgt，mode=“collapse”，edge.attr.comb=“sum”）当我有一个日期变量时，行错误被清除。当然，最初的版本忽略了这一点，但是如果程序能够忽略这个变量或者至少将它指向weight列，我将不胜感激
 undirected_graph_wgt <- as.undirected(directed_graph, mode = "collapse", edge.attr.comb = "sum")
plot(undirected_graph_wgt)

################################################################### FIRST OPTION

el <- data.frame(from = c(1001L, 1001L, 1002L, 1002L, 1003L, 1003L),
                 to = c(1002L, 1003L, 1001L, 1003L, 1001L, 1002L),
                 weight = c(2L, 0L, 1L, 0L, 0L, 0L))
el
# This design of edgelist implies that there are links between (i) 1003 and 1001
# and between (ii) 1003 and 1002 but the weight of those links is 0
library(igraph)
directed_graph_wgt <- graph.data.frame(el, directed = TRUE)
# the adjacency matrix of your network looks like this
adj.mat <- as_adjacency_matrix(directed_graph_wgt, type = "both", names = TRUE,
                               sparse = FALSE)
adj.mat # as you can see, the adjacency_matrix shows links between 
# (i) 1003 and 1001 and and between (ii) 1003 and 1002

                                ### IMPORTANT ### 
# When you move from an adjacency matrix to a graph, you might consider
# that a "weight" of 0 in the matrix leads to no interaction (edge) between nodes. 
# But be careful,  the adjacency matrix is actually a relationnal matrix
# (or connection matrix), not just a weights matrix. It actually provides the 
# number of edges between nodes from the graph.
# Therefore, when you are designing your graph.data.frame, your must include 
# ONLY connected nodes

# Something like this should be relevent here
nodes <-  c(1001L, 1002L, 1003L) # create a vector of nodes 
nodes # we have three nodes
el <- data.frame(from = c(1001L, 1002L),
                 to = c(1002L, 1001L),
                 weight = c(2L, 1L)) # use ONLY connected nodes
el # structrure of links
# Now, you can include all the nodes in the network with the "vertices" argument

# (1) directed graph
directed_graph_wgt <- graph.data.frame(el, directed = TRUE,
                                       vertices = nodes)
# the right adjacency matrix of your network looks like this
adj.mat <- as_adjacency_matrix(directed_graph_wgt, type = "both", names = TRUE,
                               sparse = FALSE)
adj.mat # as you can see, the adjacency matrix shows all the nodes 
# and here is the plot
plot(directed_graph_wgt, layout = layout.fruchterman.reingold,
     edge.width = E(directed_graph_wgt)$weight/2)

# (2) undirected graph
undirected_graph_wgt <- as.undirected(directed_graph_wgt, mode = "collapse",
                                      edge.attr.comb = "sum")
plot(undirected_graph_wgt)


### KEYPOINT
# When you are designing your own edgelist, setting a weight as 0 means that 
# the weight of the considered link is 0, not that the link doesn't exist. 
# However, a 0 in the adjacency matrix leads to no interaction (edge)
# between nodes.

# It looks like you are confusing "weights" and "number of interactions". Even 
# though both can be used interchangeably, you must be careful when using them
# in igraph functions


################################################################## SECOND OPTION

# To use the weights in "el" as indicator of relations, you need to consider
# the assumption that weight == 0 means no link.
# You can use the delete_edges() function

el <- data.frame(from = c(1001L, 1001L, 1002L, 1002L, 1003L, 1003L),
                 to = c(1002L, 1003L, 1001L, 1003L, 1001L, 1002L),
                 weight = c(2L, 0L, 1L, 0L, 0L, 0L))
el #t this is your initial edgelist

# (1) directed graph
directed_graph_wgt <- graph.data.frame(el, directed = TRUE)
directed_graph_wgt
# use delete_edges() to consider ONLY weight != 0 (no link)
# We will remove link with weight == 0 (i.e no link)
directed_graph_wgt2 <- delete_edges(directed_graph_wgt,
                                    which(E(directed_graph_wgt)$weight == 0))
plot(directed_graph_wgt2, layout = layout.fruchterman.reingold,
     edge.width = E(directed_graph_wgt)$weight/2)

# (2) undirected graph
undirected_graph_wgt <- as.undirected(directed_graph_wgt, mode = "collapse",
                                      edge.attr.comb = "sum")
undirected_graph_wgt2 <- delete_edges(undirected_graph_wgt,
                                      which(E(undirected_graph_wgt)$weight == 0))
plot(undirected_graph_wgt2)