I have a really basic phyloseq question which I annoyingly am unable to resolve.
I have a phyloseq object (OTU table, taxonomy, and sample data) with 4 sample variables like this

• Sample Data: [16 samples by 4 sample variables]
• Plain text

  Copy to clipboard

  Open code in new window

  EnlighterJS 3 Syntax Highlighter

  <code> type Plot host_species block

  </code>

  <code> type Plot host_species block </code>

               type Plot  host_species block
  

I have done a transformation of sample counts, agglomeration and a psmelt:

#Genus1pct root
ps.rel3 = transform_sample_counts(ps.root, function(x) x/sum(x)*100)
# agglomerate taxa
glom3 <- tax_glom(ps.rel3, taxrank = 'Genus1pct', NArm = FALSE)
ps.melt3 <- psmelt(glom3)

in order to do a stacked barchart of my 16 samples here, divided by the three host species (Dryas, Salix, and Kobresia):

#level_order <- factor(species, c(')))
ggplot(ps.melt3, aes(x = Sample, y = Abundance, fill = Genus1pct)) + 
  geom_bar(stat = "identity", aes(fill=Genus1pct)) + 
  labs(x="", y="%",title = "Roots") +
  facet_wrap(~sample_species, scales= "free_x", nrow=1) +
  theme_bw() + 
  theme(legend.position = "right", 
        strip.background = element_blank(), 
        axis.text.x.bottom = element_blank(),
        axis.ticks.x.bottom = element_blank())

However, I would like to do a stacked barchart with relative abundances by my three host species now.

How do I do this? I am basically looking for something like a transform_sample_counts-function just for sample variables. (This must, of course, be able to account

This is a (hapless) ggplot just plotting the host_species as x, without having done the transformation:

There are 5,6 and 5 samples on each of the three host species, and obviously I would like this plot here with even heights summing to a 100%.