跟着Microbiome学画图物种组成图

应用案例

Fig.4PhylumdistributionoftheOTUs.Relativesequenceabundanceofbacterialphylaassociatedwiththerhizospheresoilandtheroot,stemandleafendosphere.ProteobacteriaOTUhasbeenreplacedby5OTUsatthesubclasslevel(alpha,beta,delta,epsilon,gamma).（Beckerseta.,,Microbiome)

分析代码

######物种组成图

otu-read.csv("D://PJJ/test_otu.csv",row.names=1)#(测试数据可后台获取)

design-read.csv("D://PJJ/test_design.csv")

library(car)

library(ggplot2)

library(reshape2)

otu-otu[1:,]

#主要phylum统计

data-aggregate(otu[,1:32],by=list(otu$Tax),FUN=sum)

rownames(data)-data[,1]

mean-data[,-1]

#排序

mean-mean[order(rowSums(mean),decreasing=T),]

aa-cbind(t(mean),design)

##不同处理丰度统计

data-aggregate(aa[,1:6],by=list(aa$Treatment),FUN=mean)

rownames(data)-data[,1]

#去掉名字列

pp-t(data[,2:7])

pp-cbind(rownames(pp),pp)

#构建数据框

df=melt(pp,id.vars="V1",value.name="Relativeabundance",variable.name="sps")####把宽数据变为长数据

head(df)

#去掉多余因子

df-df[7:30,]

#转化为数值型

df$`Relativeabundance`-as.numeric(as.character(df$`Relativeabundance`))

##出图

ggplot(data=df,aes(x=df$Var2,y=df$`Relativeabundance`,fill=df$Var1))+

geom_bar(position="fill",stat="identity",width=0.7)+##设置为相对比例%,真实数据需根据数据调整

ylab("Relativeabundance")+#y轴设置

scale_fill_manual(values=c("#BC8F8F","#B","#AFF","#F","#B4EEB4","#CD69C9"))+

scale_y_reverse(expand=c(0,0),labels=c("1","0.75","0.50","0.25","0"))+##x轴单位设置，如非%，需根据数据调整

scale_x_discrete(name=Treatment)+

guides(fill=guide_legend(title="Phylum",color="black",reverse=TRUE))+theme_classic()#设置主题

分析结果

参考文献

Beckers,B.,OpDeBeeck,M.,Weyens,N.,Boerjan,W.,Vangronsveld,J.,.Structuralvariabilityandnichedifferentiationintherhizosphereandendospherebacterialmicrobiomeoffield-grownpoplartrees.Microbiome5.

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