GSEA可视化

library(clusterProfiler)
library(enrichplot)
library(org.Hs.eg.db)
library(patchwork)
library(ggpubr)


data(geneList,package = "DOSE")


ego3 <- gseGO(geneList     = geneList,
             OrgDb        = org.Hs.eg.db,
             ont          = "CC",
             nPerm        = 1000,
             minGSSize    = 100,
             maxGSSize    = 500,
             pvalueCutoff = 0.05,
             verbose      = FALSE)
gseaplot2(ego3,ego3@result$ID[1:5])

library(ggplot2)
library(RColorBrewer)
# 定义足够多的颜色，可以自己改
cb_palette <- c("#ed1299", "#09f9f5", "#246b93", "#cc8e12", "#d561dd", "#c93f00", "#ddd53e",
                "#4aef7b", "#e86502", "#9ed84e", "#39ba30", "#6ad157", "#8249aa", "#99db27", "#e07233", "#ff523f",
                "#ce2523", "#f7aa5d", "#cebb10", "#03827f", "#931635", "#373bbf", "#a1ce4c", "#ef3bb6", "#d66551",
                "#1a918f", "#ff66fc", "#2927c4", "#7149af" ,"#57e559" ,"#8e3af4" ,"#f9a270" ,"#22547f", "#db5e92",
                "#edd05e", "#6f25e8", "#0dbc21", "#280f7a", "#6373ed", "#5b910f" ,"#7b34c1" ,"#0cf29a" ,"#d80fc1",
                "#dd27ce", "#07a301", "#167275", "#391c82", "#2baeb5","#925bea", "#63ff4f")

mygseaplot= function(obj,id=1:5,col=cb_palette,heights = c(5,5,0.5)){
  obj%>%gseaplot2(.,obj@result$ID[id],subplots = 2)->mid_plot
  obj%>%gseaplot2(.,obj@result$ID[id],subplots = 1)->up_plot
  data<-mid_plot$data
p=list()
  for (i in id) {
    data2<-filter(data,Description %in% obj@result$Description[i])
    data2$ymin<-0
    data2$ymax<-as.numeric(data2$position)
p[[i]]= ggplot(data2, aes_(x = ~x)) + 
      geom_linerange(aes_(ymin = ~ymin, 
                          ymax = ~ymax 
                          ),
                     color = col[i]) + 
      xlab(NULL) + ylab(NULL) + 
      theme_void()+
      theme(legend.position = "none",
            plot.margin = margin(t = -0.1, b = 0, unit = "cm"), 
            axis.ticks = element_blank(),
            axis.text = element_blank(), 
            axis.line.x = element_blank()) + 
      scale_x_continuous(expand = c(0, 0)) + 
      scale_y_continuous(expand = c(0, 0)) +
      ggtitle(paste0(ego3@result$Description[i]))+
      theme(plot.title = element_text(size=20))
  }
  
bottom=ggplot(data, aes_(x = ~x)) +
    theme_classic()+
    xlab(NULL) + ylab(NULL) + 
    scale_x_continuous(expand = c(0,0)) + 
    scale_y_continuous(limits = c(0, 0.01))+
    theme(axis.ticks.y = element_blank(),
          axis.text.y = element_blank(), 
          axis.line.y = element_blank(),
          plot.margin = margin(t = -0.1, b = 0, unit = "cm"))
mid=do.call(ggarrange,c(p,ncol=1))
xx=(up_plot+theme_classic()+
      theme(plot.margin = margin(t = -0.1, b = 0, unit = "cm"), 
            axis.ticks.x = element_blank(),
            axis.text.x = element_blank(), 
            axis.line.x = element_blank(),
            panel.border = element_rect(fill=NA,color="black", 
                                size=1))
    )+
    mid+bottom+plot_layout(ncol = 1,heights = heights)
return(xx)
}