问用OTUs确定不同分类水平的堆叠条形图

EN

plot<-transform_sample_counts(phyloseq.object, function(x) 100 * x/sum(x))
glom <- tax_glom(plot, taxrank = 'class')
glom # should list taxa as phyla
data_glom<- psmelt(glom) # create dataframe from phyloseq object

data_glom$class <- as.character(data_glom$class) #convert to character

#simple way to rename phyla with < 5% abundance
data_glom$class[data_glom$Abundance < 0.05] <- "< 5% abundance"

#Count phyla to set color palette
Count = length(unique(data_glom$class)); Count
unique(data_glom$class) #add into line below
data_glom$class <- factor(data_glom$class, levels = c("class", "class", "class",  "class", "< 5% abundance")) 

spatial_plot <- ggplot(data_glom, aes(x=Sample, y=Abundance, fill=class)) + facet_grid(~variable, scales = "free")

spatial_plot + geom_bar(aes(), stat="identity", position="stack") + labs (title = "title, x="label", y= "Relative Abundance (%)", ) + scale_fill_manual(values =c("color","color","color","color","etc.")+ theme (legend.position="bottom", plot.title = element_text(hjust=0.5, size=15),axis.text = element_text(size = 15),axis.title = element_text(size = 15), legend.text=element_text(size=12),legend.title = element_text(size=15)) + guides(fill=guide_legend(nrow=4))