绘制GO富集图

阅读数: 次 2020-08-11

写在文章之前，这篇文章主要是为了补充clusterprofiler的后续GO作图部分
因为人总是喜欢让自己的图更加炫酷一些不是吗？

数据准备

这一部分的数据可以从利用clusterprofiler包对非模式物种进行GO和KEGG富集分析种获得
我仅仅只在这里列一下数据格式的表头

Ontology    Term    ID    GeneRatio    BgRatio    pvalue    p.adjust    qvalue    geneID    Count
BP    nuclear-transcribed mRNA poly(A) tail shortening    GO:0000289    17/6733    20/14959    0.0002758    0.011340555    0.010334966    Contig10.gene343.t1/Contig16.gene1167.t1/Contig10.gene2133.t1/Contig16.gene1070.t1/Contig2.gene664.t1/Contig10.gene188.t1/Contig28.gene267.t1/Contig12.gene941.t1/Contig45.gene1.t1/Contig45.gene2.t1/Contig45.gene3.t1/Contig47.gene54.t1/Contig47.gene55.t1/Contig47.gene56.t1/Contig47.gene58.t1/Contig26.gene152.t1/Contig30.gene73.t1    17
BP    defense response to insect    GO:0002213    17/6733    22/14959    0.002136591    0.04971361    0.04530541    Contig13.gene696.t1/Contig3.gene159.t1/Contig3.gene163.t1/Contig1.gene1661.t1/Contig2.gene1433.t1/Contig8.gene611.t1/Contig8.gene612.t1/Contig7.gene282.t1/Contig8.gene731.t1/Contig10.gene343.t1/Contig16.gene1167.t1/Contig12.gene941.t1/Contig45.gene2.t1/Contig45.gene3.t1/Contig47.gene54.t1/Contig47.gene55.t1/Contig3.gene169.t1    17

开始画图

真的很简单，几行代码就搞定啦
不信你看，我给你变个魔术


library(ggplot2)
df<-read.table(file="input.txt",header=T,sep="\t")
x<-(-log10(df$pvalue))
y<-factor(df$Term,levels = rev(df$Term))
pcolor<- -log10(df$qvalue)
p<- ggplot(df,aes(x,y))+geom_point(aes(size=Count,color=pcolor,shape=Ontology))+scale_color_gradient(low = "yellow", high = "blue")+scale_size_continuous(range=c(4,8))
p1<- p+theme_bw()+theme(
  #去网格去背景色
  axis.line = element_line(colour = "black"), axis.text = element_text(color = "black",size = 14),
  #刻度字体大小
  legend.text = element_text(size = 14),legend.title=element_text(size=14),
  axis.title.x = element_text(size = 14))
p2<-p1+ labs(color=expression(-Log(qvalue)),
               size="Gene_Number",
               x="-LogP",
               y="",title=""
               )
p2

根据个人需要修改x轴想要表示的东西，以及各气泡的颜色。

bye~ good nights！！！！

希望彼此都有一个好梦