R画柱形图和箱线图-白红宇

R画柱形图和箱线图

阅读量：5287 次

发布时间：2019-06-14

本文共 3687 字，大约阅读时间需要 12 分钟。

数据格式如下

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-5Traf1 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

代码如下：

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))

使用fimo对Traf1基因进行motif的寻找

下载motif数据库

wget http://meme-suite.org/meme-software/Databases/motifs/motif_databases.12.18.tgztar zxvf motif_databases.12.18.tgz

代码如下

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.lstles 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.lstgrep 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.bedbedtools getfasta -fi /media/sda/database/Ensembl/release-89/mus_musculus/fasta/mm10.fasta -bed Traf1.bed -fo Traf1.gene.fastafimo -oc Traf1 JASPAR2018_CORE_vertebrates_non-redundant.meme Traf1.gene.fasta

需要注意的是bed文件时从0开始算位置的，而gtf等注释文件时从1开始算的，所以gtf转换成bed的时候要减少一个碱基的位置
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数据格式

aaa sss fpkmSham Sham-1 0.204531Sham Sham-2 0.358811Sham Sham-3 0.24649Sham Sham-4 0.270231Sham Sham-5 0.169885Rep-1h Rep-1h-1 0.588808Rep-1h Rep-1h-2 0.526418Rep-1h Rep-1h-3 0.87557Rep-1h Rep-1h-4 0.403861Rep-1h Rep-1h-5 1.846186Rep-3h Rep-3h-1 1.890555Rep-3h Rep-3h-2 1.041459Rep-3h Rep-3h-3 0.881003Rep-3h Rep-3h-4 1.036722Rep-3h Rep-3h-5 1.016675Rep-6h Rep-6h-1 2.09069Rep-6h Rep-6h-2 3.09231Rep-6h Rep-6h-3 1.180259Rep-6h Rep-6h-4 2.610673Rep-6h Rep-6h-5 0.888904Rep-12h Rep-12h-1 2.936677Rep-12h Rep-12h-2 1.829962Rep-12h Rep-12h-3 1.857749Rep-12h Rep-12h-4 2.93743Rep-12h Rep-12h-5 2.424644Rep-24h Rep-24h-1 1.3602Rep-24h Rep-24h-2 2.654057Rep-24h Rep-24h-3 2.121849Rep-24h Rep-24h-4 2.309851Rep-24h Rep-24h-5 2.052516

画图代码

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Var2guides(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))