vol plot

######################################################################
###################            vol_plot          #####################
######################################################################


#install.packages("ggplot2")
#install.packages("ggrepel")
library(dplyr)
library(ggplot2)
library(ggrepel)







logFCfilter=1                                                    #Fold Change调整
adj.P.Val.Filter=0.05                                            #FDR调整
inputFile="all.txt"                                              #修改处；输入文件名称，具有Fold Change和adj.p.val的文件
rt = read.table(inputFile, header=T, sep="\t", check.names=F)







Sig=ifelse((rt$adj.P.Val<adj.P.Val.Filter) & (abs(rt$logFC)>logFCfilter), ifelse(rt$logFC>logFCfilter,"Up","Down"), "Not")
rt = mutate(rt, Sig=Sig)
rt = rt[!is.na(rt$adj.P.Val),]
 



p = ggplot(rt, aes(logFC, -log10(adj.P.Val)))+
    geom_point(aes(col=Sig))+
    scale_color_manual(values=c("green", "black","red"))+
    labs(title = " ")+
    theme(plot.title = element_text(size = 16, hjust = 0.5, face = "bold"))




p1=p+geom_label_repel(data=filter(rt, ((rt$adj.P.Val<adj.P.Val.Filter) & (abs(rt$logFC)>logFCfilter))),
                    box.padding=0.1, point.padding=0.1, min.segment.length=0.05,
                    size=1.8, aes(label=id)) + theme_bw()
pdf(file="vol.pdf", width=7, height=6.1)
print(p1)
dev.off()

write.table(rt,file="rt.csv",sep="\t",quote=F,row.names=F)