igraph 不适用于 edge.width 负相关系数

Question

简单地说，我想在去除不重要的值后，根据相关强度绘制边缘。我可以对 edge.betweeness 的正相关对执行此操作，但不幸的是不能对负相关对执行此操作：

data <- matrix(rnorm(100),10,10)    
colnames(data) <- LETTERS[1:10]

library(Hmisc)
cor1 <- rcorr(data)
diag(cor1$r) <- 0

library(igraph)

#####Example 1:
graph <- graph.adjacency(cor1$r, weighted=TRUE, mode="lower")
graph <- delete.edges(graph, E(graph)[ weight < 0.3 & weight > -0.3])
#####trying to pass edge weights to edge.width
plot.igraph(graph, vertex.size=20, edge.width=E(graph)$weight)
###edge.width=E(graph)$weight is ignored

#####Example 2:
graph <- graph.adjacency(cor1$r, weighted=TRUE, mode="lower")
graph <- delete.edges(graph, E(graph)[ weight < 0.3]) #omitting the 2nd condition
E(graph)$weight <- edge.betweenness(graph) #apparently required
plot.igraph(graph, vertex.size=20, edge.width=E(graph)$weight)
####this does work, but only for positive correlation coefficients 

#####Example 3:
graph <- graph.adjacency(cor1$r, weighted=TRUE, mode="lower")
graph <- delete.edges(graph, E(graph)[ weight < 0.3 & weight > -0.3])
E(graph)$weight <- edge.betweenness(graph)
#####gives error: Error in .Call("R_igraph_edge_betweenness", graph, directed, weights,  : 
#################At centrality.c:2046 : Weight vector must be non-negative, Invalid value

那么，我如何将负相关值传递给 edge.width？

Answer 1

您可以使用彩色边来表示负相关和正相关，并使用 edge.width 来表示相关的大小。在下面的示例中，我进行了以下更改：

将图形对象的名称更改为g1，因为graph是 igraph 包中的一个函数。
为简洁起见，使用边删除条件的绝对值。
将 edge.width 参数更改为 abs(E(g1)$weight)*8。这绝对值确保权重始终为正。乘以8只会使边宽变大。
添加了 edge.color 参数来为蓝色的顶点着色正相关，红色表示负相关。

#####Example 3:
g1 <- graph.adjacency(cor1$r, weighted=TRUE, mode="lower")
g1 <- delete.edges(g1, E(g1)[ abs(weight) < 0.3 ])
plot.igraph(g1, vertex.size=20, edge.width=abs(E(g1)$weight)*8, 
        edge.color=ifelse(cor1$r > 0, "blue","red"))

igraph 不适用于 edge.width 负相关系数

igraph does not apply edge.width for negative correlation coefficients

r

igraph