富集散点气泡图R代码

上图：

image.png

R Code：

getwd()
library(ggplot2)
Data <- read.table("data.txt",header = T,sep = "\t")
attach(Data)

p <- ggplot(Data, aes(x = Impact,y = pathway)) + 
  geom_point(aes(size=Hits,color=FDR)) + 
  scale_colour_gradient(low="red",high="green") + 
  theme_bw()
p <- p + labs(size="Compound number",x="Impact",y="Pathway Name",title="Pathway Compound")

数据示例：

pathway	Hits	FDR	Impact
Flavonoid biosynthesis	11	5.48E-15	0.27408
Flavone and flavonol biosynthesis	3	0.0084671	0.4375
Biosynthesis of secondary metabolites	10	0.024065	0.01117
Anthocyanin biosynthesis	2	0.4043	0.02703
Isoflavonoid biosynthesis	2	0.45137	0.02463
Valine, leucine and isoleucine biosynthesis	1	1	0
Valine, leucine and isoleucine degradation	1	1	0
Aminobenzoate degradation	1	1	0.00683
2-Oxocarboxylic acid metabolism	1	1	0
Biosynthesis of amino acids	1	1	0
Metabolic pathways	8	1	0.00209
Microbial metabolism in diverse environments	1	1	0.0018