Hua's Cabin

做好当下，不犹未来

网络图: 如何对网络图进行分组展示

Posted on In , Valine:
Symbols count in article: 4k Reading time ≈ 4 mins.

导入网络数据

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data(karate)
karate
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## IGRAPH 4b458a1 UNW- 34 78 -- Zachary's karate club network
## + attr: name (g/c), Citation (g/c), Author (g/c), Faction (v/n), name (v/c), label (v/c), color (v/n),
## | weight (e/n)
## + edges from 4b458a1 (vertex names):
##  [1] Mr Hi  --Actor 2  Mr Hi  --Actor 3  Mr Hi  --Actor 4  Mr Hi  --Actor 5  Mr Hi  --Actor 6  Mr Hi  --Actor 7 
##  [7] Mr Hi  --Actor 8  Mr Hi  --Actor 9  Mr Hi  --Actor 11 Mr Hi  --Actor 12 Mr Hi  --Actor 13 Mr Hi  --Actor 14
## [13] Mr Hi  --Actor 18 Mr Hi  --Actor 20 Mr Hi  --Actor 22 Mr Hi  --Actor 32 Actor 2--Actor 3  Actor 2--Actor 4 
## [19] Actor 2--Actor 8  Actor 2--Actor 14 Actor 2--Actor 18 Actor 2--Actor 20 Actor 2--Actor 22 Actor 2--Actor 31
## [25] Actor 3--Actor 4  Actor 3--Actor 8  Actor 3--Actor 9  Actor 3--Actor 10 Actor 3--Actor 14 Actor 3--Actor 28
## [31] Actor 3--Actor 29 Actor 3--Actor 33 Actor 4--Actor 8  Actor 4--Actor 13 Actor 4--Actor 14 Actor 5--Actor 7 
## [37] Actor 5--Actor 11 Actor 6--Actor 7  Actor 6--Actor 11 Actor 6--Actor 17 Actor 7--Actor 17 Actor 9--Actor 31
## + ... omitted several edges

可视化网络数据

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set.seed(123)
karateLayout <- layout_with_fr(karate)

# par是调节基础画图细节的函数
par(mar = c(0,0,2,0))
plot(karate, 
     vertex.size = 10, 
     vertex.color = "steelblue4", 
     edge.width = 1, 
     vertex.label = NA, 
     edge.color = "darkgrey", 
     layout = karateLayout,
     main = "Zachary's karate club network" )

以群落为模块，设置组间距离，展示网络图

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# 提取模块分组信息
Communitykarate <- cluster_louvain(karate)
prettyColors <- c("turquoise4", "azure4", "olivedrab","deeppink4")
# 设置模块颜色
communityColors <- prettyColors[membership(Communitykarate)]

# 重新设置组间的weight
edge.weights <- function(community, network, weight.within = 100, weight.between = 1) {
  bridges <- crossing(communities = community, graph = network)
  weights <- ifelse(test = bridges, yes = weight.between, no = weight.within)
  return(weights) 
}
E(karate)$weight <- edge.weights(Communitykarate, karate)
karateLayoutA <- layout_with_fr(karate, karateLayout)

set.seed(123)
plot(x = Communitykarate, 
     y = karate, 
     edge.width = 1, 
     vertex.size = 10, 
     mark.groups = NULL, 
     layout = karateLayoutA, 
     vertex.label = NA, 
     col = communityColors, 
     c("darkgrey","tomato2")[crossing(Communitykarate, karate) + 1],
     main = "Communities in Zachary's karate club network (grouped)")

修改组间距离大小

注：不知道怎么以监督方式设置分组展示，只能根据网络属性—模块设置分组，不知道大家有没有什么好的办法

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E(karate)$weight <- edge.weights(Communitykarate, karate, weight.within = 1000)
karateLayoutB <- layout_with_fr(karate, karateLayout)
plot(x = Communitykarate, 
     y = karate, 
     edge.width = 1, 
     vertex.size = 10,
     mark.groups = NULL, 
     layout = karateLayoutB, 
     vertex.label = NA, 
     col = communityColors, 
     c("darkgrey","tomato2")[crossing(Communitykarate, karate) + 1],
     main = "Communities in Zachary's karate club network (grouped)")

以按照分组顺序在circle形状上展示数据

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karate_groups <- cluster_optimal(karate) # cluster_fast_greedy(karate)
coords <- layout_in_circle(karate, order =
          order(membership(karate_groups)))
V(karate)$label <- sub("Actor ", "", V(karate)$name)
V(karate)$label.color <- membership(karate_groups)
V(karate)$shape <- "none"
plot(karate, layout = coords)

R information

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sessionInfo()
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## R version 4.0.2 (2020-06-22)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19042)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
## [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
## [5] LC_TIME=English_United States.1252    
## system code page: 936
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] igraphdata_1.0.1 igraph_1.2.5    
## 
## loaded via a namespace (and not attached):
##  [1] rstudioapi_0.11  knitr_1.30       magrittr_1.5     tidyselect_1.1.0 R6_2.5.0         rlang_0.4.7     
##  [7] highr_0.8        stringr_1.4.0    dplyr_1.0.2      tools_4.0.2      xfun_0.19        htmltools_0.5.0 
## [13] ellipsis_0.3.1   yaml_2.2.1       digest_0.6.25    tibble_3.0.3     lifecycle_0.2.0  crayon_1.3.4    
## [19] purrr_0.3.4      vctrs_0.3.4      glue_1.4.2       evaluate_0.14    rmarkdown_2.5    stringi_1.5.3   
## [25] compiler_4.0.2   pillar_1.4.6     generics_0.1.0   jsonlite_1.7.1   pkgconfig_2.0.3

参考

  1. 如何在igraph中进行分组展示

参考文章如引起任何侵权问题，可以与我联系，谢谢。


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