> library(ggplot2)

> a<-ggplot(mtcars,aes(factor(cyl)))+geom_bar(aes(fill=factor(gear)),width = 0.6)+labs(title="R2-07",x="cyl")+scale_fill_discrete(name="gear")

> mytheme<-theme_classic()+theme(panel.grid.major = element_blank(),panel.grid.minor = element_blank(),legend.position = "none",plot.caption = element_text(face = "bold.italic"))

> a

> a+mytheme

> 

library(ggplot2)

> library(latex2exp)

> a<-read.csv("R2.csv")

> mytheme=theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"),legend.position = "none")

> a$id=a$Gene.ID

> a$q_value=-log2(a$q_value)

> a$FC=log2(a$FC)

> a$threshold=as.factor(ifelse(a$q_value>5,ifelse(abs(plotdata$FC)>1,"yes","not"),"not"))

> yes=subset(a,a$threshold == "yes")

> not=subset(a,a$threshold == "not")

> p = ggplot()+geom_point(data=not,aes(x=FC,y=q_value),color="grey")+geom_point(data=yes,aes(x=FC , y = q_value,color=id),size=2)+xlim(-3,3)+geom_text(data=yes,aes(x=FC,y=q_value,label=yes$id),size = 3, hjust=0,vjust=-1)+geom_vline(xintercept =0,lty=4,col="black")+labs(x = expression(paste(log[2],"(fold change)")),y = expression(paste(-log[2],"(Q value)")))+annotate("segment", x = 1 , xend = 2.5, y= -0.5, yend=-0.5, color = "black", size = 0.5,arrow = arrow(angle = 18,ends = "last",type = "closed"))+annotate("segment", x = -1 , xend = -2.5,  y= -0.5, yend=-0.5, color = "black",size = 0.5,arrow = arrow(angle = 18,ends = "last",type = "closed")) +annotate("text",x = 1.7,y=0.5,label = "Upregulated",size = 4.5) +annotate("text",x = -1.7,y=0.5, label = "Downregulated",size = 4.5)

> p+mytheme+ggtitle("R2-07")

>