个性化调整GSEAplot--第二篇

#获得gsea对象
gsea_obj%>%gseaplot2(.,pathway,subplots = 1) ->a

#个性化调整
a%>%.$data%>%
  mutate(gene=mapIds(org.Mm.eg.db,names(fig4_sub[[4]]@geneList),"SYMBOL","ENTREZID"))%>% #filter(position==1)
  mutate(label=ifelse(gene%in%c("Fos","Akt1","Mapk3","Ctss","Ctsd"),gene,""))%>%{
  ggplot(.)+
  geom_line(data = .,aes(x=x,y=runningScore))+
  geom_point(data = subset(.,position==1),aes(x=x,y=runningScore),color=rgb(253,174,97,max=255))+
  geom_text_repel(data = subset(.,position==1),aes(x=x,y=runningScore,label=label),color="#F39B7F",max.overlaps = 30)+
  geom_rect(data = subset(.,position==1),
            aes(xmin=x-0.001,
                xmax=x+0.001,
                ymin=min(runningScore)-0.25,
                ymax=min(runningScore)-0.125,
                color=x),
            show.legend = F)+
  geom_rect(data = .,
            aes(xmin=x-0.001,
                xmax=x+0.001,
                ymin=min(runningScore)-0.375,
                ymax=min(runningScore)-0.25,
                color=x
                ),
            show.legend = F)+
    geom_hline(data = .,aes(yintercept = min(runningScore)-0.12),size=0.5)+
    geom_hline(yintercept = 0,lty=2,color="grey",size=1)+
    geom_vline(xintercept = median(.$x),lty=2,color="grey",size=0.5)+
    geom_segment(data = .,aes(x=max(x)*(1/4),
                              xend=max(x)*(1/4)-max(.$x)*(1/16),
                              y=max(runningScore)+0.1,
                              yend=max(runningScore)+0.1), 
                 size = 2,,color=rgb(116,173,209,max=255),
                 arrow = arrow(length = unit(0.5, "cm")))+
    geom_segment(data = .,aes(x=max(x)*(3/4),
                              xend=max(x)*(3/4)+max(.$x)*(1/16),
                              y=max(runningScore)+0.1,
                              yend=max(runningScore)+0.1),
                 size = 2,,color=rgb(253,174,97,max=255),
                 arrow = arrow(length = unit(0.5, "cm")))+
    annotate("text",x=max(.$x)*(3/8),y=max(.$runningScore)+0.1,label="group1",hjust=0,vjust=-0,size=5,color=rgb(116,173,209,max=255))+
    annotate("text",x=max(.$x)*(5/8),y=max(.$runningScore)+0.1,label="group2",hjust=1,vjust=-0,size=5,color=rgb(253,174,97,max=255))+
    annotate("text",x=max(.$x)*(3/4),y=0+0.05,label="runningScore=0")+
    annotate("text",x=max(.$x)*(1/4),y=min(.$runningScore)+0.05,label="P.value=0.05\nP.adj=0.05\nES=0.5")+
    scale_color_gradient2(low = rgb(116,173,209,max=255),
                          midpoint = median(.$x),
                          mid = "white",
                          high = rgb(253,174,97,max=255))+
    scale_x_continuous(limits = c(1,length(.$x)),expand = c(0,0))+
    scale_y_continuous(expand = c(0,0),limits = c(min(.$runningScore)-0.375,max(.$runningScore)+0.15),breaks = seq(round(min(.$runningScore),2),round(max(.$runningScore),2),0.2))+
    labs(x="",title = pathway)+theme_prism()+theme(plot.margin = unit(rep(0.5,4),"cm"),
                                   #axis.text.x = element_blank(),
                                   #axis.ticks.x = element_blank()
                                   panel.border = element_rect(size = 1,fill=NA),
                                   axis.line = element_blank()
                                   )
}

最后的图大概长这样子：

image.png