如題澎迎，這個標(biāo)題有點(diǎn)長，首先我們需要展示的圖是bipartite plot灵份，中文有叫二分圖哮洽、連線圖的，總之就是展示兩組之間網(wǎng)絡(luò)關(guān)系氛什》肆梗可以應(yīng)用的地方有很多，不只是我們介紹的互作關(guān)系贸铜、或者ligands-target蒿秦。起源是一篇《nature communications》文章的圖棍鳖，它展示的是ligand于targets渡处。原文提供了代碼祟辟，可以學(xué)習(xí)川尖！

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（reference：Gliovascular transcriptional perturbations in Alzheimer’s disease reveal molecular mechanisms of blood brain barrier dysfunction）
ggraph叮喳，首先相比于igraph馍悟，在很多設(shè)置上因?yàn)榕cggplot互通锣咒，所以會簡單很多，沒有那么復(fù)雜趣兄，可操作性更強(qiáng)艇潭。layout可以自己設(shè)定蹋凝，也可以參照上面的鳍寂！

node_info <- rbind(data.frame(node = rownames(active_ligand_target_links), group="target"),
                   data.frame(node = colnames(active_ligand_target_links), group="ligands"))


no <- c(rep("no", 20), sample(c('up','down'), size = nrow(node_info)-20, replace = TRUE))
node_info$reg <- sample(no, size =nrow(node_info), replace = TRUE)


#構(gòu)建ggraph作圖數(shù)據(jù)
df_graph <- as_tbl_graph(as.matrix(active_ligand_target_links)) %>% 
  mutate(group=node_info$group, #添加分組信息
         reg  = node_info$reg)



#plot
# sugiyama
ggraph(df_graph, layout = 'igraph', algorithm='bipartite') +
  geom_edge_link(aes(colour=weight), edge_width =1)+
  scale_edge_color_gradientn(colours = c("grey80","grey50","grey30","black"))+
  geom_node_point(aes(fill=reg, filter= group =='ligands'), 
                  size=2,shape=21) +
  geom_node_point(aes(fill=reg, filter= group =='target'), 
                  size=2,shape=23)+
  scale_fill_manual(values = c("#E4502E","#69B7CE","black"),
                    breaks = c("up",'down',"no"),
                    labels = c("up",'down',"no"))+
  geom_node_text(aes(filter= group =='ligands',
                     label = name),
                  fontface = "italic",
                 hjust=1.1)+
  geom_node_text(aes(filter= group =='target',
                     label = name),
                 fontface = "italic",
                 hjust=-0.1)+
  coord_flip()+
  theme_minimal() +
  scale_y_discrete(expand = c(0.2,0.2))+
  ggraph::th_no_axes()




#調(diào)整layout

LO1 <- layout_as_bipartite(df_graph, maxiter=0);
re_pos <- c(seq(from = 0.5, by = 1, length.out = length(LO1[which(LO1[,2]==1)])),
            seq(from = 0.5, by = 1.1, length.out = length(LO1[which(LO1[,2]==0)])))

LO1[,1] <- re_pos



ggraph(df_graph, layout = LO1) +
  geom_edge_link(aes(colour=weight), edge_width =1)+ #連線
  scale_edge_color_gradientn(colours = c(alpha("grey90",0.5),
                                         alpha("grey60",0.5),
                                         alpha("grey30",0.5),"black"))+#連線顏色
  geom_node_point(aes(fill=reg, filter= group =='ligands'), 
                  size=2,shape=21) +#節(jié)點(diǎn)設(shè)置
  geom_node_point(aes(fill=reg, filter= group =='target'), 
                  size=2,shape=23)+
  scale_fill_manual(values = c("#E4502E","#69B7CE","black"),
                    breaks = c("up",'down',"no"),
                    labels = c("up",'down',"no"))+
  geom_node_text(aes(filter= group =='ligands',
                     label = name),
                 fontface = "italic",
                 hjust=1.1)+ #文字標(biāo)注
  geom_node_text(aes(filter= group =='target',
                     label = name),
                 fontface = "italic",
                 hjust=-0.1)+
  coord_flip()+
  theme_minimal() +
  scale_y_discrete(expand = c(0.2,0.2))+
  ggraph::th_no_axes()

image.png