原文链接

1.安装包

install.packages("graphlayouts")
install.packages(igraph)   
install.packages(ggraph)   

2.应力优化：联通网络

library(igraph)   
library(ggraph)   
library(graphlayouts)

set.seed(666)
pa <- sample_pa(1000,1,1,directed = F)

ggraph(pa,layout = "nicely")+
  geom_edge_link(width=0.2,colour="grey")+
  geom_node_point(col="black",size=0.3)+
  theme_graph()

image.png

改变网络排布方式

ggraph(pa,layout="stress")+
  geom_edge_link(width=0.2,colour="grey")+
  geom_node_point(col="black",size=0.3)+
  theme_graph()

image.png

3.应力优化：非联通网络

set.seed(666)
g <- disjoint_union(
  sample_pa(10,directed = F),
  sample_pa(20,directed = F),
  sample_pa(30,directed = F),
  sample_pa(40,directed = F),
  sample_pa(50,directed = F),
  sample_pa(60,directed = F),
  sample_pa(80,directed = F)
)

ggraph(g,layout = "nicely") +
  geom_edge_link() +
  geom_node_point() +
  theme_graph()

image.png

ggraph(g, layout = "stress",bbox = 40) +
  geom_edge_link() +
  geom_node_point() +
  theme_graph()

image.png

4.骨干网络布局

set.seed(665)
#create network with a group structure
g <- sample_islands(9,40,0.4,15)
g <- simplify(g)
V(g)$grp <- as.character(rep(1:9,each=40))

ggraph(g,layout = "stress")+
  geom_edge_link(colour=rgb(0,0,0,0.5),width=0.1)+
  geom_node_point(aes(col=grp))+
  scale_color_brewer(palette = "Set1")+
  theme_graph()+
  theme(legend.position = "none")

image.png

bb <- layout_as_backbone(g,keep=0.4)
E(g)$col <- F
E(g)$col[bb$backbone] <- T

ggraph(g,layout="manual",x=bb$xy[,1],y=bb$xy[,2])+
  geom_edge_link(aes(col=col),width=0.1)+
  geom_node_point(aes(col=grp))+
  scale_color_brewer(palette = "Set1")+
  scale_edge_color_manual(values=c(rgb(0,0,0,0.3),rgb(0,0,0,1)))+
  theme_graph()+
  theme(legend.position = "none")

image.png

5.焦点节点径向布局

install.packages("igraphdata")
devtools::install_github("thomasp85/patchwork")
library(igraphdata)
library(patchwork)
data("karate")

p1 <- ggraph(karate,layout = "focus",focus = 1) +
  draw_circle(use = "focus",max.circle = 3)+
  geom_edge_link(edge_color="black",edge_width=0.3)+
  geom_node_point(aes(fill=as.factor(Faction)),size=2,shape=21)+
  scale_fill_manual(values=c("#8B2323", "#EEAD0E"))+
  theme_graph()+
  theme(legend.position = "none")+
  coord_fixed()+
  labs(title= "Focus on Mr. Hi")

p2 <- ggraph(karate,layout = "focus",focus = 34) +
  draw_circle(use = "focus",max.circle = 4)+
  geom_edge_link(edge_color="black",edge_width=0.3)+
  geom_node_point(aes(fill=as.factor(Faction)),size=2,shape=21)+
  scale_fill_manual(values=c("#8B2323", "#EEAD0E"))+
  theme_graph()+
  theme(legend.position = "none")+
  coord_fixed()+
  labs(title= "Focus on John A.")

p1+p2

image.png

5.径向中心布局

library(igraphdata)
library(patchwork)
data("karate")

bc <- betweenness(karate)
p1 <- ggraph(karate,layout = "centrality", centrality = bc, tseq = seq(0,1,0.15)) +
  draw_circle(use = "cent") +
  annotate_circle(bc,format="",pos="bottom") +
  geom_edge_link(edge_color="black",edge_width=0.3)+
  geom_node_point(aes(fill=as.factor(Faction)),size=2,shape=21)+
  scale_fill_manual(values=c("#8B2323", "#EEAD0E"))+
  theme_graph()+
  theme(legend.position = "none")+
  coord_fixed()+
  labs(title="betweenness centrality")


cc <- closeness(karate)
p2 <- ggraph(karate,layout = "centrality", centrality = cc, tseq = seq(0,1,0.2)) +
  draw_circle(use = "cent") +
  annotate_circle(cc,format="scientific",pos="bottom") +
  geom_edge_link(edge_color="black",edge_width=0.3)+
  geom_node_point(aes(fill=as.factor(Faction)),size=2,shape=21)+
  scale_fill_manual(values=c("#8B2323", "#EEAD0E"))+
  theme_graph()+
  theme(legend.position = "none")+
  coord_fixed()+
  labs(title="closeness centrality")

p1+p2

image.png

6.大网络

用layout_with_sparse_stress()画很多节点的网络

image.png

18k节点和61k边的网络

image.png

12k节点和68k边的网络

7.动态布局

library(patchwork)
#gList is a list of longitudinal networks.

xy <- layout_as_dynamic(gList,alpha = 0.2)
pList <- vector("list",length(gList))

for(i in 1:length(gList)){
  pList[[i]] <- ggraph(gList[[i]],layout="manual",x=xy[[i]][,1],y=xy[[i]][,2])+
    geom_edge_link0(edge_width=0.6,edge_colour="grey66")+
    geom_node_point(shape=21,aes(fill=smoking),size=3)+
    geom_node_text(aes(label=1:50),repel = T)+
    scale_fill_manual(values=c("forestgreen","grey25","firebrick"),guide=ifelse(i!=2,FALSE,"legend"))+
    theme_graph()+
    theme(legend.position="bottom")+
    labs(title=paste0("Wave ",i))
}
Reduce("+",pList)+
  plot_annotation(title="Friendship network",theme = theme(title = element_text(family="Arial Narrow",face = "bold",size=16)))

image.png

8.布局操控

用layout_mirror()和 layout_rotate()操控已有的布局

image.png