个人网站 审批深圳aso优化

如题，这个标题有点长，首先我们需要展示的图是bipartite plot，中文有叫二分图、连线图的，总之就是展示两组之间网络关系。可以应用的地方有很多，不只是我们介绍的互作关系、或者ligands-target。起源是一篇《nature communications》文章的图，它展示的是ligand于targets。原文提供了代码，可以学习！

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（reference：Gliovascular transcriptional perturbations in Alzheimer’s disease reveal molecular mechanisms of blood brain barrier dysfunction）
ggraph，首先相比于igraph，在很多设置上因为与ggplot互通，所以会简单很多，没有那么复杂，可操作性更强。layout可以自己设定，也可以参照上面的！

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$reg <- sample(no, size =nrow(node_info), replace = TRUE)#构建ggraph作图数据
df_graph <- as_tbl_graph(as.matrix(active_ligand_target_links)) %>% mutate(group=node_info$group, #添加分组信息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()#调整layoutLO1 <- 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_posggraph(df_graph, layout = LO1) +geom_edge_link(aes(colour=weight), edge_width =1)+ #连线scale_edge_color_gradientn(colours = c(alpha("grey90",0.5),alpha("grey60",0.5),alpha("grey30",0.5),"black"))+#连线颜色geom_node_point(aes(fill=reg, filter= group =='ligands'), size=2,shape=21) +#节点设置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)+ #文字标注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()