背景：網(wǎng)絡圖是由點和邊構成的圖結構更振，常用來可視化基因調控網(wǎng)絡等酥筝。本地圖形化界面的網(wǎng)絡圖軟件有Gephi和Cytoscape，這里使用R中的包繪制網(wǎng)絡圖，以便可視化加入到流程中。

• 數(shù)據(jù)預處理
  可視化的網(wǎng)絡圖通常需要兩個文件碑韵，邊edges文件和點nodes文件，其中邊文件通常包含（源節(jié)點，目標節(jié)點窝稿，邊權重）的信息，點文件則包括所有的節(jié)點的唯一值即可凿掂。

#'數(shù)據(jù)預處理伴榔，構建edges和nodes表格
p_load("navdata","tidyverse", "igraph", "tidygraph", "ggraph")
data("phone.call")
head(phone.call, 3)
sources <- phone.call %>% distinct(source) %>% rename(label = source)
destinations <- phone.call %>% distinct(destination) %>% rename(label = destination)
nodes <- full_join(sources, destinations, by = "label")
nodes <- nodes %>% mutate(id = 1:nrow(nodes)) %>% select(id, everything()) #' 添加id
head(nodes)
phone.call <- phone.call %>% rename(weight = n.call) #' 列重命名
edges <- phone.call %>% left_join(nodes, by = c("source" = "label")) %>% rename(from = id) #'構建邊列表
edges <- edges %>% left_join(nodes, by = c("destination" = "label")) %>% rename(to = id)
edges <- select(edges, from, to, weight)
head(edges)

• 方法一 使用igraph

#'方法一 使用igraph
library(igraph)
net.igraph <- graph_from_data_frame(d = edges, vertices = nodes,directed = TRUE)
set.seed(123)
png("fig1_my_test.png")
plot(net.igraph, edge.arrow.size = 0.2,layout = layout_with_graphopt)
dev.off()

結果like this:

igraph.png

• 方法二 使用tidygraph和ggraph

library(tidygraph)
library(ggraph)
net.tidy <- tbl_graph(nodes = nodes, edges = edges, directed = TRUE)
pp<-ggraph(net.tidy, layout = "graphopt") +
  geom_node_point(col = 'gold',size = 2) + #'點信息
  geom_edge_link(aes(width = weight), alpha = 0.8) +  #'邊信息
  scale_edge_width(range = c(0.2, 2)) + #'控制粗細
  geom_node_text(aes(label = label), repel = TRUE) + #'增加節(jié)點的標簽，reple避免節(jié)點重疊
  labs(edge_width = "phone.call") + #'圖例標簽
  theme_graph()
ggsave("fig2_test.png",pp)

結果like this:

ggraph.png

如果想畫成圓形：

pp<-ggraph(net.tidy, layout = "linear",circular=TRUE) +
  geom_node_point(col = 'gold',size = 2) + #'點信息
  geom_edge_link(aes(width = weight), alpha = 0.8) +  #'邊信息
  scale_edge_width(range = c(0.2, 2)) + #'控制粗細
  geom_node_text(aes(label = label), repel = TRUE) + #'增加節(jié)點的標簽缠劝，reple避免節(jié)點重疊
  labs(edge_width = "phone.call") + #'圖例標簽
  theme_graph()
ggsave("fig3_test.png",pp)

ggraph.png

總結：根據(jù)自己的習慣惨恭，封裝成函數(shù)很好用秉馏。