GO功能注释条目图

> go <- read.csv("go.csv",header = T)    #Go 条目一般只选择最显著的前10个或20个Term来绘图#
> head(go)
            Ontology
1 Biological process
2 Biological process
3 Biological process
4 Biological process
5 Biological process
6 Biological process
                                                                  Term      GO_ID
1                                                  signal transduction GO:0007165
2 positive regulation of transcription from RNA polymerase II promoter GO:0045944
3 negative regulation of transcription from RNA polymerase II promoter GO:0000122
4                                                        cell adhesion GO:0007155
5                            positive regulation of cell proliferation GO:0008284
6                  positive regulation of transcription, DNA-templated GO:0045893
  Input_number Percentage
1           72   8.062710
2           66   7.390817
3           64   7.166853
4           46   5.151176
5           41   4.591265
6           40   4.47928

> library(ggplot2)
> go_sort <- go[order(go$Ontology,-go$Percentage),]#根据go$Percentage和go$Percentage排序

> m <- go_sort[go_sort$Ontology=="Molecular function",][1:10,]
> head(m)
             Ontology
31 Molecular function
32 Molecular function
33 Molecular function
34 Molecular function
35 Molecular function
36 Molecular function
                                                           Term      GO_ID
31                                              protein binding GO:0005515
32                            protein homodimerization activity GO:0042803
33 transcription factor activity, sequence-specific DNA binding GO:0003700
34                                          calcium ion binding GO:0005509
35                                    identical protein binding GO:0042802
36                                sequence-specific DNA binding GO:0043565
   Input_number Percentage
31          455  50.951848
32           60   6.718925
33           59   6.606943
34           58   6.494961
35           49   5.487122
36           41   4.591265
> c <- go_sort[go_sort$Ontology=="Cellular component",][1:10,]
> b <- go_sort[go_sort$Ontology=="Biological process",][1:10,]
> slimgo <- rbind(b,c,m)  #把b,c,m合并到了一起#

> slimgo$Term = factor(slimgo$Term,levels = slimgo$Term) # 将term列转换为因子#
> class(slimgo$Term)
[1] "factor"
> colnames(slimgo)  #ggplot2用到好多列名，先输出来#
[1] "Ontology"     "Term"         "GO_ID"        "Input_number" "Percentage"  
 
> pp <- ggplot(data = slimgo,mapping = aes(x=Term,y=Percentage,fill=Ontology))
#fill=Ontology，意为Ontology为填充色#
> pp

 > pp+geom_bar(stat = "identity")

> pp+geom_bar(stat = "identity")+coord_flip()  #Term太多了，反转一下x，y轴#

#term是从小到大排列，习惯从大到小排列#
> pp+geom_bar(stat = "identity")+coord_flip()+scale_x_discrete(limits=rev(levels(slimgo$Term)))

> pp+geom_bar(stat = "identity")+coord_flip()+scale_x_discrete(limits=rev(levels(slimgo$Term)))+guides(fill=FALSE)
#去掉了图列#

> pp+geom_bar(stat = "identity")+coord_flip()+scale_x_discrete(limits=rev(levels(slimgo$Term)))+guides(fill=FALSE)+theme_bw()
#切换成黑白背景的主题#

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《R语言与生物信息绘图》课程笔记