volcano of DEG

最新推荐文章于 2022-07-22 17:18:04 发布

许我少年

最新推荐文章于 2022-07-22 17:18:04 发布

阅读量156

点赞数

分类专栏： R-ggplot2 文章标签： r语言

本文链接：https://blog.csdn.net/weixin_44879403/article/details/125110513

版权

R-ggplot2 专栏收录该内容

21 篇文章 3 订阅

订阅专栏

setwd('D:\\16_huangjian\\02_DEG')

library(ggplot2)
library(readxl)

DEG=read.table('./whole.gene.oreadcount_new.xls.N2_vs_YCD.edgeR.DE_results',sep = '\t',header = 1)
#logFC_cutoff <- with(DEG,mean(abs(log2FoldChange)) + 2*sd(abs(log2FoldChange)) ) 
head(DEG)
logFC_cutoff=1 


DEG$change = as.factor(ifelse(DEG$FDR < 0.05 & abs(DEG$logFC) >=logFC_cutoff, 
                              ifelse(DEG$logFC >=logFC_cutoff ,'Up-regulated','Down-regulated'),'Not significant ') 
) 
this_tile <- paste0('Cutoff for log2FoldChange is ',round(logFC_cutoff,3),
                    '\nCutoff for Padj is 0.05') 

# data<-read.csv('./whole.gene.oreadcount_new.xls.CK_vs_YCD.edgeR.DE_results.sigdiff.xls',sep = '\t')
# head(data)
# table(data$regulated)
head(DEG)
> head(DEG)
                    logFC     logCPM       PValue          FDR         change
WBGene00009213   5.354328  0.3463606 1.552651e-19 8.165860e-15   Up-regulated
WBsf220289     -10.439054 -2.1951413 2.515035e-17 3.306830e-13 Down-regulated
WBGene00015019 -10.439054 -2.1951413 2.515035e-17 3.306830e-13 Down-regulated
B0205.4:wp150  -10.439054 -2.1951413 2.515035e-17 3.306830e-13 Down-regulated
WBGene00009316  -6.541225 -2.0569668 8.820392e-16 9.277818e-12 Down-regulated
TCONS_00007308   9.887423 -2.7029521 1.251839e-14 1.097299e-10   Up-regulated
table(DEG$change)
ggplot(data=DEG,  
       aes(x=DEG$logFC, y=-log10(FDR),  
           color=change)) + 
  geom_point(alpha=0.6, size=2) + 
  theme_set(theme_set(theme_bw(base_size=20)))+ 
  xlab("log2(YCD/N2)") + ylab("-log10(FDR)") + 
  # ggtitle( this_tile ) +
  theme(plot.title = element_text(size=15,hjust = 0.5))+ 
  scale_colour_manual(values = c('#20B2AA','gray','#FF9900')) +
  # geom_hline(aes(yintercept=-0.5),colour="#808080",linetype="dashed")+
  geom_vline(aes(xintercept=1),colour="#808080",linetype="dashed")+
  geom_vline(aes(xintercept=-1),colour="#808080",linetype="dashed")+
  # geom_vline(aes(xintercept=1),colour="#808080",linetype="dashed")+
  annotate('text', label = (nrow(DEG[DEG$change =='Up-regulated',])), 5,8,size=5.5,fontface  = 'bold',colour = "black") +
  annotate('text', label = (nrow(DEG[DEG$change =='Down-regulated',])), -5, 8,size=5.5,fontface  = 'bold',colour = "black")+
  theme_classic()+
  xlim(-9,9)+ylim(0,14)+
  geom_hline(aes(yintercept=-log10(0.05)),colour='#030303',linetype='dashed')+
  guides(colour = guide_legend(title = 'YCD vs N2',override.aes = list(size=3, stroke=1.5)))+
  theme(strip.text.x = element_text( colour = 'black',size = 13),#size=8,angle=75
        strip.text.y = element_text( colour = 'black',size = 13),
        strip.background = element_rect(colour="white", fill="grey"),
        axis.title = element_text(face = "bold",
                                  size = "16",color = "black"),
        axis.text.x = element_text(face = "bold",color = "black",
                                   size = 14,  hjust = 0.5, vjust = 0.5),
        axis.text.y = element_text(face = "bold",size = 14,color = "black"),
        legend.text = element_text(size = 12,face = "bold"),
        legend.title = element_text(size = 12,
                                    face = "bold"),
        legend.position =c(0.25,0.9),
        # legend.key.size = 
        panel.grid.major.y = element_blank(),
        panel.grid.minor.y = element_blank(),
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.line = element_line(size=1, colour = "black"),     #####################     坐标轴边框加粗（只能加粗左下轴）
        axis.ticks = element_line(size = 1),
        # panel.border = element_rect(colour = "black", fill=NA, size=1),
        # axis.line = element_line(size=2, colour = "black"),
        plot.title = element_text(lineheight=.8, face="bold", hjust=0.5, size =16))