ggplot2画KEGG富集柱形图

barplot.enrichResult {enrichplot}  R Documentation
barplot
Description
barplot of enrichResult

Usage
## S3 method for class 'enrichResult'
barplot(
  height,
  x = "Count",
  color = "p.adjust",
  showCategory = 8,
  font.size = 12,
  title = "",
  ...
)

#加载ggplot2包
library(ggplot2)
#一键清除
rm(list=ls())
#读取功能富集结
kegg <- read.csv("KEGG-enrich.csv",stringsAsFactors=F)
#对富集结果按照p.adjust进行从小到大排序，保证最显著的通路在前
kegg <- kegg[order(kegg$p.adjust),]

#这里画图只展示top10的通路
kegg <- kegg[1:10,]

#提取每条通路里面差异表达的基因数
top10 <- data.frame(kegg$Description,kegg$Count ,kegg$p.adjust)
colnames(top10) <- c("Description","count","padj")

#fill=padj fill颜色填充，使用连续值padj
p <- ggplot(data=top10,aes(x=Description,y=count,fill=padj))

#coord_flip()颠倒坐标轴
p1 <- p + geom_bar(stat="identity") + coord_flip()
p2 <- p1 + theme(panel.background=element_rect(fill='transparent',color='gray'),
                 axis.text.y=element_text(color="black",size=12))


#ylim(0,30) 更改横坐标的范围这里坐标轴颠倒了，虽然看起来是x轴，但其实是y轴
p3 <- p2 + ylim(0,30) + scale_fill_gradient(low="red",high="blue")

p4 <- p3 + scale_x_discrete(limits=rev(top10[,1])) +labs(x="",y="",title="KEGG")

#输出为png格式的图片
png("KEGG_bar_plot.png",width=680,height=480)
print(p4)
dev.off()

#输出为pdf的文件
pdf("KEGG_bar_plot.pdf",width=9)
print(p4)
dev.off()