- Data format
gene_id Sham-1 Sham-2 Sham-3 Sham-4 Sham-5 Rep-1h-1 Rep-1h-2 Rep-1h-3 Rep-1h-4 Rep-1h-5 Rep-3h-1 Rep-3h-2 Rep-3h-3 Rep-3h-4 Rep-3h-5 Rep-6h-1 Rep-6h-2 Rep-6h-3 Rep-6h-4 Rep-6h-5 Rep-12h-1 Rep-12h-2 Rep-12h-3 Rep-12h-4 Rep-12h-5 Rep-24h-1 Rep-24h-2 Rep-24h-3 Rep-24h-4 Rep-24h-5
Traf1 0.204531 0.358811 0.24649 0.270231 0.169885 0.588808 0.526418 0.87557 0.403861 1.846186 1.890555 1.041459 0.881003 1.036722 1.016675 2.09069 3.09231 1.180259 2.610673 0.888904 2.936677 1.829962 1.857749 2.93743 2.424644 1.3602 2.654057 2.121849 2.309851 2.052516- code show as below:
a=read.table(file="Traf1.fpkm.lst")
c=t.data.frame(a)
gene_id=c(c[,1])
gene=as.vector(gene_id)
id=gene[2:length(gene)]
va=as.vector(c[,2])[2:length(as.vector(c[,2]))]
fpkm=round(as.numeric(va),3)
dd=data.frame(n,fpkm)
ggplot(dd,aes(x=n,y=fpkm))+
geom_bar(stat = "identity",fill ="#09BFFE",colour="grey")+
xlab("Samples")+ylab("FPKM of Traf1 in different sample")+
theme_classic()+
theme(axis.text.y=element_blank(),axis.text.x=element_text(size=8,color="black",angle = 30,face="bold",hjust = 1))+
geom_text(aes(label=dd$fpkm), position=position_stack(vjust=1.05),angle=30)+
scale_y_continuous(breaks = seq(0,3.5,0.5),limits = c(0,3.5),labels = seq(0,3.5,0.5))
Fimo use of Traf1 gene motif of looking
- Download motif database
wget http://meme-suite.org/meme-software/Databases/motifs/motif_databases.12.18.tgz
tar zxvf motif_databases.12.18.tgzcode show as below
ln -s /media/sda/user/chengxu/project/cardiac-IR/lncRNA_sequencing/expression_data/mRNA_symbol_FPKM_matrix.txt ./
les mRNA_symbol_FPKM_matrix.txt|perl -F"\t" -lane 'print join("\t",@F[0..5])."\t".join("\t",@F[43..67])' |head -1 >Traf1.fpkm.lst
les mRNA_symbol_FPKM_matrix.txt|perl -F"\t" -lane 'print join("\t",@F[0..5])."\t".join("\t",@F[43..67])' |grep Traf1 >>Traf1.fpkm.lst
grep Traf1 /media/sda/database/Ensembl/release-89/mus_musculus/gtf/gene.bed.txt |perl -lane '$s=$F[5]-1;$e=$F[6]-1;print qq{$F[3]\t$s\t$e\t$F[7]}' >Traf1.bed
bedtools getfasta -fi /media/sda/database/Ensembl/release-89/mus_musculus/fasta/mm10.fasta -bed Traf1.bed -fo Traf1.gene.fasta
fimo -oc Traf1 JASPAR2018_CORE_vertebrates_non-redundant.meme Traf1.gene.fasta- Note that the count from the start position 0 when the document bed, while gtf document annotation, such as starting a count, so gtf converted into a bed position to reduce a time base
****** - Data Format
aaa sss fpkm
Sham Sham-1 0.204531
Sham Sham-2 0.358811
Sham Sham-3 0.24649
Sham Sham-4 0.270231
Sham Sham-5 0.169885
Rep-1h Rep-1h-1 0.588808
Rep-1h Rep-1h-2 0.526418
Rep-1h Rep-1h-3 0.87557
Rep-1h Rep-1h-4 0.403861
Rep-1h Rep-1h-5 1.846186
Rep-3h Rep-3h-1 1.890555
Rep-3h Rep-3h-2 1.041459
Rep-3h Rep-3h-3 0.881003
Rep-3h Rep-3h-4 1.036722
Rep-3h Rep-3h-5 1.016675
Rep-6h Rep-6h-1 2.09069
Rep-6h Rep-6h-2 3.09231
Rep-6h Rep-6h-3 1.180259
Rep-6h Rep-6h-4 2.610673
Rep-6h Rep-6h-5 0.888904
Rep-12h Rep-12h-1 2.936677
Rep-12h Rep-12h-2 1.829962
Rep-12h Rep-12h-3 1.857749
Rep-12h Rep-12h-4 2.93743
Rep-12h Rep-12h-5 2.424644
Rep-24h Rep-24h-1 1.3602
Rep-24h Rep-24h-2 2.654057
Rep-24h Rep-24h-3 2.121849
Rep-24h Rep-24h-4 2.309851
Rep-24h Rep-24h-5 2.052516- Paint Code
dd=read.table(file = "Traf1.changeformat",header = T)
#修改箱线图的顺序
dd$aaa=factor(dd$aaa,levels=c("Sham","Rep-3h","Rep-6h","Rep-12h","Rep-24h"))
ggplot(dd, aes(x=aaa, y=fpkm, fill=aaa)) +
geom_boxplot() +
scale_fill_manual(values=c("#E41A1C","#377EB8","#4DAF4A","#984EA3","#FF7F00","#FFFF33"), name="Var2") +
labs(x="", y="FPKM of Traf1") + #去掉x轴的Var2
guides(fill = guide_legend(title="Group", keywidth=2, keyheight=2)) +
theme_bw() +
theme(panel.grid = element_blank()) +
theme(axis.title.y = element_text(size=18)) +
theme(axis.text.y = element_text(size=16, hjust=1)) +
theme(axis.text.x = element_text(colour="grey20", size=96/len, angle=30, hjust=1)) +
theme(legend.title = element_text(size=15)) +
theme(legend.text = element_text(size=15))