library(ggplot2)

plot1<-ggplot(mtcars,aes(x=factor(cyl),fill=factor(gear)))+

  geom_bar(width = 0.5)+

  labs(title = "Here is title", subtitle = "Here is subtitle", caption = "R2-12", x = "cyl")

plot1

#creat a new theme

theme_zz <- theme_classic() +

    theme(panel.background=element_rect(fill='white'),#背景白色

          panel.grid = element_blank(),#消除网格

          legend.position = "",#消除坐标

          axis.line = element_line(color = "black"),#axis

          plot.caption = element_text(face = "bold.italic"))#change the font

#use the theme_zz

plot1+theme_zz

第一种做法，参考发布任务

library(latex2exp)

myvolcano<-read.table("nature23643-s4.csv",header = T,sep = ",")

fix(myvolcano)#fix gene.ID

attach(myvolcano)

myvolcano$significant<-ifelse(abs(log2(FC))<1,"not","yes")

myvolcano$lables<-ifelse(abs(log2(FC))<1,NA,as.character(gene.ID))

mysig<-subset(myvolcano,significant=="yes")

mysig

ydrop = -0.6

textdrop=0.3

#volcano

p1<-ggplot(data = myvolcano,aes(x=log2(FC),y=-log2(q_value),size=significant))+

  geom_point(color="grey",alpha=0.4)+

  xlim(c(-3,3))+ylim(c(-1,16))+

  scale_size_manual(values = c(2,0))+

  geom_vline(xintercept = c(0),lty=4,col="black",lwd=0.5)+

  geom_hline(yintercept = -log2(1/32),lty=4,col="red",lwd=0.5)+

  #overlap

  geom_point(data = mysig,aes(x=log2(FC),y=-log2(q_value),color=lables),size=4)+

  geom_text(aes(label=lables),size=3,hjust=0,vjust=-1,col="black",fontface="italic")+

  annotate("segment", x = 1,xend = 2.5,y = ydrop,yend  = ydrop,color = "black",

           size = 1,arrow = arrow(angle = 18,ends = "last",type = "closed")) +

  annotate("segment",x = -1,xend = -2.5,y = ydrop,yend  = ydrop,color = "black",

           size = 1,arrow = arrow(angle = 18,ends = "last",type = "closed")) +

  annotate("text",x = 1.7,y = textdrop,label = "Upregulated",size = 4.5) +

  annotate("text",x = -1.7,y = textdrop,label = "Downregulated",size = 4.5)

p1+theme_zz+ggtitle("R2-12")

第二种参考R2-21想法

volcano_zz<-read.table("nature23643-s4.csv",header = T,sep = ",")

View(volcano_zz)

fix(volcano_zz)#fix gene.ID

volcano_zz$th<-as.factor(ifelse(-log2(volcano_zz$q_value)>4.33&

                                  abs(log2(volcano_zz$FC))>1,"yes","not"))

yes<-subset(volcano_zz,th=="yes")

not<-subset(volcano_zz,th=="not")

np<-ggplot(not,aes(x=log2(FC),y=-log2(q_value)))+

  geom_point(color="grey")+

  geom_point(data=yes,aes(x=log2(FC),y=-log2(q_value),color=gene.ID,size=3))+

  geom_text(data=yes,aes(label=gene.ID),size=3,hjust=0,vjust=-1,col="black",fontface="italic")+

  xlim(-2.5,2.5)+

  ylim(-1,14)+

  annotate("segment",x=-1,xend = -2.5,y=-0.7,yend = -0.7,color="black",size=1,

           arrow=arrow(angle = 20,ends = "last",type = "closed"))+

  annotate("segment",x=1,xend = 2.5,y=-0.7,yend = -0.7,color="black",size=1,

           arrow=arrow(angle = 20,ends = "last",type = "closed"))+

  annotate("text",x=-1.5,y=0,label="Downregulated")+

  annotate("text",x=1.5,y=0,label="Upregulated")+

  geom_vline(xintercept = 0,lty=4,col="black",lwd=0.5)+

  geom_hline(yintercept = -log2(0.05),lty=4,col="black",lwd=0.5)

np+theme_zz+ggtitle("R2-12_volcano")