library("ggplot2")

library("latex2exp")

mytheme <- theme_classic() +

  theme(panel.grid.major = element_blank(),

        panel.grid.minor = element_blank(),   

        legend.position = "none",            

        plot.caption = element_text(face = "bold.italic") )

myvolcano <- read.csv(file.choose())       

head(myvolcano)

myvolcano$significant <- ifelse(abs(log2(myvolcano$FC)) > 1 & myvolcano$q_value < 0.05,"yes","no" )

myvolcano$mylabels <- ifelse(abs(log2(myvolcano$FC)) > 1 & myvolcano$q_value < 0.05,

                             as.character(myvolcano$Gene.ID),NA)

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

mysig

ydrop = -0.6

textdrop = 0.3

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

  geom_point(col = "grey70",alpha = 1) +  

  xlim(-2.5,2.7) +

  ylim(-0.8,15) +

  scale_size_manual(values = c(2,0)) +   

  geom_point(data = mysig,aes(x = log2(FC),y = -log2(q_value),color=锘縂ene.ID),

             size = 4,

             position = position_jitter(height = 0.1,width = 0)) + 

  geom_text(aes(label = mylabels),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)  +

  labs(title = "CMTM6 sgRNA2 vs Control",

       caption = "R2-09") +   

  labs(x = expression(log[2])) +         

  labs(x = expression(paste(log[2],"(fold change)")),

       y = expression(paste(-log[2],"(Q value)")))

myplot + 

  theme(plot.title = element_text(hjust = mean(range(log2(myvolcano$FC)))+ 0.1)) +

  geom_vline(xintercept = 0,linetype = 2 ,size= rel(0.8)) +  # adding a line

  mytheme