GO_KEGG_bubble.R

#!/usr/bin/env Rscript
############################
# Usage : ./GO_KEGG_bubble.R <KEGG.txt> 
############################ 
# arguments in command line
options<-commandArgs(trailingOnly = T)
library(ggplot2)
library(stringr)
plot_heigh<-2.5
plot_width<-4.6

my_data<-read.table(file=options[1],header=T,sep="\t")
if(length(my_data[,1]) >= 10) {my_data<-my_data[1:10,]} else {
my_data<-my_data}
my_data$Term<-str_split_fixed(my_data$Term,":",2)[,2]

png_name<-unlist(strsplit(options[1],'.',fixed=T))[1]
png(file=paste(png_name,'png',sep='.'),height = plot_heigh, width = plot_width, res=600, units = "in", family="Arial")

ggplot(my_data,aes(x=-1*log10(PValue),y=Term)) + 
	geom_point(aes(size=Count,color=Fold.Enrichment))+
	scale_colour_gradient(low="steelblue",high="red")+
	labs(
		color=expression(Fold.Enrichment),
		size="Gene number",
		x="-logP-value",
		# y="Pathway name",
		title="KEGG Pathways")+
	theme_bw()+
	theme(
		axis.text.y = element_text(size=rel(1.0),color='black'),
		axis.text.x = element_text(size=rel(1.0)),
		axis.title.x = element_text(size=rel(0.9)),
		axis.title.y = element_blank(),
		legend.key.size = unit(0.1,"inches"),
		legend.text = element_text(size=7),
		legend.title = element_text(size=8),
		legend.background = element_rect(fill="transparent"),
		plot.title = element_text(hjust = 0.5,size=12)
	)
	
dev.off()