#install.packages("ggplot2")

library(plyr)
library(ggplot2)
library(grid)
library(gridExtra)

setwd("D:\\biowolf\\metabolism\\24.multipleGSEA")          #设置工作目录
files=grep(".xls",dir(),value=T)                                         #获取目录下的所有xls文件
data = lapply(files,read.delim)                                          #读取每个文件
names(data) = files

dataSet = ldply(data, data.frame)
dataSet$pathway = gsub(".xls","",dataSet$.id)                            #将文件后缀删掉

gseaCol=c("#58CDD9","#7A142C","#5D90BA","#431A3D","#91612D","#6E568C","#E0367A","#D8D155","#64495D","#7CC767","#223D6C","#D20A13","#FFD121","#088247","#11AA4D")
pGsea=ggplot(dataSet,aes(x=RANK.IN.GENE.LIST,y=RUNNING.ES,fill=pathway,group=pathway))+
  geom_point(shape=21) + scale_fill_manual(values = gseaCol[1:nrow(dataSet)]) + 
  labs(x = "", y = "Enrichment Score", title = "") + scale_x_continuous(expand = c(0, 0)) + 
  scale_y_continuous(expand = c(0, 0),limits =c(min(dataSet$RUNNING.ES-0.02), max(dataSet$RUNNING.ES+0.02))) +   
  theme_bw() + theme(panel.grid =element_blank()) + theme(panel.border = element_blank()) + 
  theme(axis.line = element_line(colour = "black")) + theme(axis.line.x = element_blank(),axis.ticks.x = element_blank(),axis.text.x = element_blank()) + 
  geom_hline(yintercept = 0) + guides(fill=guide_legend(title = NULL)) + 
  theme(legend.background = element_blank()) + theme(legend.key = element_blank())
pGene=ggplot(dataSet,aes(RANK.IN.GENE.LIST,pathway,colour=pathway))+geom_tile()+
  scale_color_manual(values = gseaCol[1:nrow(dataSet)]) + 
  labs(x = "High risk<----------->Low risk", y = "", title = "") + 
  scale_x_discrete(expand = c(0, 0)) + scale_y_discrete(expand = c(0, 0)) +  
  theme_bw() + theme(panel.grid = element_blank()) + theme(panel.border = element_blank()) + theme(axis.line = element_line(colour = "black"))+
  theme(axis.line.y = element_blank(),axis.ticks.y = element_blank(),axis.text.y = element_blank())+ guides(color=FALSE)

gGsea = ggplot_gtable(ggplot_build(pGsea))
gGene = ggplot_gtable(ggplot_build(pGene))
maxWidth = grid::unit.pmax(gGsea$widths, gGene$widths)
gGsea$widths = as.list(maxWidth)
gGene$widths = as.list(maxWidth)
dev.off()

#将图形可视化，保存在"multipleGSEA.pdf"
pdf('multipleGSEA.pdf',      #输出图片的文件
     width=9,                #设置输出图片高度
     height=5)               #设置输出图片高度
par(mar=c(5,5,2,5))
grid.arrange(arrangeGrob(gGsea,gGene,nrow=2,heights=c(.8,.3)))
dev.off()