How to omit taxa with unassigned or unwanted taxonomy in heatmap (or in figures generally)

[timz0605]

Hello David!

I am trying to make some heatmaps with the microViz package, and I am running into some difficulties with selecting taxa with assigned taxonomy. I am working with a metabarcoding project, so many of the taxa do not have taxonomy assigned even to the order or phylum level. However, when I am trying to make figures, those information will all be included. I was wondering if there is an (possibly elegant) way to select or filter taxa with taxonomy assigned to a specific level?

Below is the code I used first to fix the tax_table. merged_ps is simply a phyloseq object I created for other analyses. After this steps, many of the unassigned taxa will simply have a "taxonomy" of the sequence name for all taxonomic level. For example, "zotu.12" for everything between phylum and species.

ps_microviz <- merged_ps %>% 
  tax_fix() %>% 
  phyloseq_validate()

Below is the code I used to make the heatmap. I was thinking about adding some filtering or selecting codes after tax_agg, but was not having much luck.

taxa_heatmap <- ps_microviz %>%
  tax_agg("order") %>% 
  tax_transform(trans = "hellinger", rank = "order") %>%
  tax_filter(min_prevalence = 0.1, use_counts = TRUE) %>%
  comp_heatmap(
    colors = heat_palette(palette = "Rocket", rev = TRUE), grid_col = NA,
    sample_side = "top", name = "Abd.",
    tax_anno = taxAnnotation(
      Prev. = anno_tax_prev(bar_width = 0.3, size = grid::unit(1, "cm"))),
    sample_anno = sampleAnnotation(
      Location = anno_sample("locality"),
      col = list(Location = cols), border = FALSE))
taxa_heatmap

Thank you!