profile_mock_cluster2

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P.copri abundance per cluster

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clusters=read.table("microbiome_clustering/plots/MockData_species_PAM.txt",sep = "\t",header = T,stringsAsFactors = F)
clusters$sampleID=rownames(clusters)

> clusters #输出
          Cluster  sampleID
Sample1         1   Sample1
Sample2         1   Sample2

cluster_plot=merge(clusters,dag3_species[,"Prevotella_copri",drop=F],by.x="sampleID",by.y = "row.names",all=F)

#变为三列
> cluster_plot
      sampleID Cluster Prevotella_copri
1      Sample1       1         0.071806
2     Sample10       1         0.071623

cluster_plot=merge(clusters,dag3_species[,"Prevotella_copri",drop=F],by.x="sampleID",by.y = "row.names",all=F)
cluster_plot$Cluster=factor(cluster_plot$Cluster,levels = c("2","1"))
cluster_plot[cluster_plot==0]=NA
cluster_plot=na.omit(cluster_plot)
cluster_plot$Prevotella_copri=-log2(cluster_plot$Prevotella_copri)
cluster_plot[is.na(cluster_plot)]=0
g <- ggplot(cluster_plot, aes(x=Cluster, y=Prevotella_copri,fill=Cluster)) + 
  geom_violin()+
  geom_boxplot(width=0.1, fill="white")+scale_fill_npg()+theme_classic()+ylab("Prevotella Copri, Norm. Rel. Abundance (-log2)")
print(g)