igraph 解析具有不同节点大小 r 的重叠节点答案

【问题标题】：igraph resolve overlapping nodes with varying node size rigraph 解析具有不同节点大小 r 的重叠节点
【发布时间】：2019-05-21 01:31:15
【问题描述】：

我正在使用 R 中的 igraph 创建一个由大约 600 个节点包围的单个“中心”节点的网络可视化。

节点重叠，然后我可以使用this question 的答案（使用 qgraph）来解决。

然而，这个解决方案似乎只适用于大小都相同的节点。在我的网络中，节点大小是可变的。有没有办法通过在确定节点之间的距离时考虑节点大小来避免重叠？

示例代码如下：

# create network
net <- graph_from_data_frame(d=links, vertices=nodes, directed=T)

# set colors
colrs <- c("#8DD3C7", "#FFFFB3")
V(net)$color <- colrs[V(net)$type]
# no labels
V(net)$label <- NA

# create a network graph with non-overlapping nodes:
# using https://stackoverflow.com/questions/39290909/igraph-resolving-tight-overlapping-nodes
e <- get.edgelist(net,names = F) 
l <- qgraph.layout.fruchtermanreingold(e,vcount=vcount(net))
plot(net,layout=l,vertex.size=4,edge.arrow.mode=0,vertex.label=NA)

这是结果：

但是现在当我改变节点大小时：

# setting node size based on data
V(net)$size <- V(net)$nodesize; 
# plot result 
plot(net,layout=l,edge.arrow.mode=0,vertex.label=NA)

...节点重叠：

感谢您的帮助！

* 编辑 - 添加示例数据集：前 50 个节点 *

节点数据：

dput(head(nodes,50))

structure(list(id = c("s01", "s02", "s03", "s04", "s05", "s06", "s07", "s08", 
"s09", "s10", "s11", "s12", "s13", "s14", "s15", "s16", "s17", "s18", "s19", 
"s20", "s21", "s22", "s23", "s24", "s25", "s26", "s27", "s28", "s29", "s30", 
"s31", "s32", "s33", "s34", "s35", "s36", "s37", "s38", "s39", "s40", "s41", 
"s42", "s43", "s44", "s45", "s46", "s47", "s48", "s49", "s50"), nodesize = 
c(50, 2.025, 2.025, 3.5, 1, 0.725, 2.875, 1.6, 0.175, 2.175, 0, 0.675, 0.5, 
15.7, 1.4, 0.4, 1.375, 0.425, 0.55, 7, 10.375, 1.125, 0.325, 0.925, 3.6, 0.525, 
0.9, 0.1, 0.5, 2.3, 1.825, 1.95, 0.325, 0.9, 3, 0.475, 0.1, 2.975, 6.1, 9.225,
 0.65, 3.05, 2.925, 6.35, 0.7, 0.2, 0.6, 1.7, 1.675, 1.425), type = c(1L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L)), row.names = c(NA, 50L), class = 
"data.frame")

链接数据：

dput(head(links,49))

structure(list(from = c("s01", "s01", "s01", "s01", "s01", "s01",
"s01", "s01", "s01", "s01", "s01", "s01", "s01", "s01", "s01", 
"s01", "s01", "s01", "s01", "s01", "s01", "s01", "s01", "s01", 
"s01", "s01", "s01", "s01", "s01", "s01", "s01", "s01", "s01", 
"s01", "s01", "s01", "s01", "s01", "s01", "s01", "s01", "s01", 
"s01", "s01", "s01", "s01", "s01", "s01", "s01"), to = c("s02", 
"s03", "s04", "s05", "s06", "s07", "s08", "s09", "s10", "s11", 
"s12", "s13", "s14", "s15", "s16", "s17", "s18", "s19", "s20", 
"s21", "s22", "s23", "s24", "s25", "s26", "s27", "s28", "s29", 
"s30", "s31", "s32", "s33", "s34", "s35", "s36", "s37", "s38", 
"s39", "s40", "s41", "s42", "s43", "s44", "s45", "s46", "s47", 
"s48", "s49", "s50")), row.names = c(NA, 49L), class = "data.frame")

【问题讨论】：

您能否添加一些数据以使您的示例可重现？
我使用的数据在GitHub上：github.com/sara-maria/networkvisdata/tree/master
对您的数据（或您的部分数据）使用 dput，以便我们轻松使用它。
感谢 dput() 信息：我相应地添加了示例数据，希望它有效！

标签： r igraph r-qgraph

【解决方案1】：

鉴于您的图表是“星形”图表，我认为您不太可能找到另一种布局算法。大多数会将连接最多的节点推到中心。

有一个新包graphlayouts 具有layout_with_stress 产生大致相同的结果。一种可能有效的方法是调整节点大小的比例。一个简单的方法是调整节点大小的比例，使它们不重叠。 ggraph 库对此有所帮助。

library(tidyverse)
library(igraph)
library(ggraph)
library(tidygraph)
library(graphlayouts)
library(scales)


g <- make_star(600) 

par(mar = rep(0,4))

V(g)$size <- sample(1:10, vcount(g), T)

plot(g, 
     vertex.label = NA, 
     layout = l)

(no_scale_g <- g %>% 
  as_tbl_graph() %>% 
  activate(nodes) %>% 
  mutate(size = sample(1:10, vcount(g), replace = T)) %>% 
  ggraph(., layout = 'stress')+
  geom_edge_fan(aes(alpha = ..index..), 
                show.legend = F, 
                check_overlap = T)+
  geom_node_point(aes(size = size, 
                      color = size))+
  coord_equal())

(scale_g <- no_scale_g+
  scale_size(range = c(1, 3)))

您可以调整缩放参数以确保没有重叠。这并不完美，但对于静态图，这让你非常接近。

【讨论】：

【解决方案2】：

这似乎与following post 相关，其中提到了 qgraph 包的布局功能，该功能具有 repulse.rad 的参数。要使用它，您首先需要通过

将 igraph-network 对象 g 转换为边缘列表

## Transform to edgelist with names = FALSE, otherwise it crashed for me
e <- get.edgelist(g, names = FALSE)

layout <- qgraph.layout.fruchtermanreingold(e, vcount = vcount(g),
  area = 6*(vcount(g)^2), repulse.rad = vcount(g)^3)

## Plot via igraph
plot.igraph(network, vertex.label = NA, layout = fixedLayout)

## Or plot via ggraph
ggraph(network, layout = fixedLayout) +
    geom_edge_link(color = "lightgrey", width = 0.3) +
    geom_node_point(size = 3) +
    theme_void()

您可以调整area 和repulse.rad 参数，让您满意。

我认为修改布局应该是真正保证没有重叠的最佳方式，同时我必须承认有一些重叠的“烟花”风格也很不错！

【讨论】：