使用 ggnetwork 绘制边缘线宽与其权重成比例的网络

Question

我有 graph 个顶点和边，我想使用 fruchtermanreingold 布局绘制它们。

这是 graph 边矩阵：

edge.mat <- matrix(as.numeric(strsplit("3651,0,0,1,0,0,0,0,2,0,11,2,0,0,0,300,0,1,0,0,66,0,78,9,0,0,0,0,0,0,11690,0,1,0,0,0,0,0,0,0,0,493,1,1,0,4288,5,0,0,36,0,9,7,3,0,6,1,0,1,7,490,0,0,0,6,0,0,628,6,12,0,0,0,0,0,641,0,0,4,0,0,0,0,0,0,66,0,0,0,0,3165,0,281,0,0,0,0,0,0,0,0,45,1,0,0,35248,0,1698,2,0,1,0,2,99,0,0,6,29,286,0,31987,0,1,10,0,8,0,16,0,21,1,0,0,1718,0,51234,0,0,17,3,12,0,0,7,0,0,0,1,0,2,16736,0,0,0,3,0,0,4,630,0,0,0,9,0,0,29495,53,6,0,0,0,0,5,0,0,0,0,3,0,19,186,0,0,0,482,8,12,0,1,0,7,1,0,6,0,26338",split=",")[[1]]),nrow=14,dimnames=list(LETTERS[1:14],LETTERS[1:14]))

然后我创建 igraph 对象，使用：

gr <- igraph::graph_from_adjacency_matrix(edge.mat,mode="undirected",weighted=T,diag=F)

然后我按照 R 的 ggnetwork 的示例将 gr 转换为 data.frame:

set.seed(1)
gr.df <- ggnetwork::ggnetwork(gr,layout="fruchtermanreingold",weights="weight",niter=50000, arrow.gap=0)

然后我使用 ggplot2 和 ggnetwork:

绘制它

ggplot2::ggplot(gr.df,ggplot2::aes(x=x,y=y,xend=xend,yend=yend))+
  ggnetwork::geom_edges(color="gray")+
  ggnetwork::geom_nodes(color="black")+
  ggnetwork::geom_nodelabel_repel(aes(label=vertex.names,color=vertex.names),fontface="bold",box.padding=unit(1,"lines"))+
  ggplot2::theme_minimal()+ggplot2::theme(axis.text=ggplot2::element_blank(),axis.title=ggplot2::element_blank(),legend.position="none")

给出：

我的问题是如何让图中边缘线的宽度与 gr (igraph::E(gr)$weight) 中的边缘权重成正比？

正在查看gr.df：

> head(gr.df)
          x         y  na.x vertex.names      xend      yend na.y weight
1 0.3637960 0.8873783 FALSE            A 0.3637960 0.8873783   NA     NA
2 0.7480217 0.4129375 FALSE            B 0.7480217 0.4129375   NA     NA
3 0.1306538 0.0000000 FALSE            C 0.1306538 0.0000000   NA     NA
4 0.4828271 0.6498561 FALSE            D 0.4828271 0.6498561   NA     NA
5 0.2243358 0.4484766 FALSE            E 0.2243358 0.4484766   NA     NA
6 1.0000000 0.6396669 FALSE            F 1.0000000 0.6396669   NA     NA

我看到边缘没有从 gr 转移到 gr.df。

Answer 1

您可以在 geom_edges 调用中指定 size 美学。例如。 aes(size=weight)

ggplot2::ggplot(gr.df,ggplot2::aes(x=x,y=y,xend=xend,yend=yend))+
  ggnetwork::geom_edges(color="gray",size=aes(size=weight))+
  ggnetwork::geom_nodes(color="black")+
  ggnetwork::geom_nodelabel_repel(aes(label=vertex.names,color=vertex.names),fontface="bold",box.padding=unit(1,"lines"))+
  ggplot2::theme_minimal()+ggplot2::theme(axis.text=ggplot2::element_blank(),axis.title=ggplot2::element_blank(),legend.position="none")

请注意，创建的数据框确实包含顶点、边和相关权重。首先列出顶点，然后列出边。在这种情况下，如果您查看整个数据框（或仅查看 tail），您会看到边有权重值。

使用 ggnetwork 绘制边缘线宽与其权重成比例的网络

Plotting a network with edge line widths proportional to their weights using ggnetwork

r

ggplot2

igraph

ggnetwork