R — Pathway富集分析气泡图

气泡图（bubble chart）与散点图类似，绘制时将一个变量放在横轴，另一个变量放在纵轴，而第三个变量则用气泡的大小来表示，可用于展示三个变量之间的关系，如生物狗常用的 — Pathway富集分析气泡图。

# 交互式文件夹选择，运行后依次打开文件夹，目的文件的路径被存在file里面
file <- file.choose()
# 读取文件 sep 根据文件格式确定
pathway_data <- read.table(file,header = TRUE, sep = "\t")
library(ggplot2)

# 做主图
bubble <- ggplot(data = pathway_data, aes(x = richFactor, y = Pathway)) + 
  geom_point(aes(size = R0vsR3,color = -1*log10(Qvalue))) +
  scale_color_gradient(low = "green", high = "red")

# 字体修饰
windowsFonts(myFont = windowsFont("Times New Roman"))

# 修改细节 — 图注，点大小，点shape
bubble_style <- bubble + theme_classic()+
  labs(
    title =
      "Pathway Enrichment",
    caption = 
      "Data from http://www.biotrainee.com/thread-927-1-1.html",
    x = "Rich Factor",
    y = "Pathway Name",
    color="-log10(Qvalue)", # 颜色图注名
    size="Gene number")+    # 大小图注名
scale_size(range  =  c(0, 10)) +  #等比修改圆圈大小
  theme(plot.title=element_text(family="myFont",size=12,
                                color="red",face="italic",
                                hjust=0.5,lineheight=0.5),
        plot.subtitle = element_text(hjust = 0.5)) 

Pathway Enrichment.png